anfo-0.98/0000777000371600007640000000000011447127355007423 500000000000000anfo-0.98/example/0000777000371600007640000000000011447127354011055 500000000000000anfo-0.98/example/ancient.cfg0000644000371600007640000000341711447113506013072 00000000000000policy { use_compact_index { name: "hg18" wordsize: 12 cutoff: 500 stride: 4 allow_near_perfect: 1 } use_compact_index { name: "pt2" wordsize: 12 cutoff: 500 stride: 4 allow_near_perfect: 1 } use_compact_index { name: "hcscca" wordsize: 12 cutoff: 125 stride: 4 allow_near_perfect: 1 } use_compact_index { name: "hg19_hap" cutoff: 5 } maxlength: 54 name_pattern: "M_*" } policy { use_compact_index { name: "hg18" wordsize: 12 cutoff: 500 stride: 4 allow_near_perfect: 0 } use_compact_index { name: "pt2" wordsize: 12 cutoff: 500 stride: 4 allow_near_perfect: 0 } use_compact_index { name: "hcscca" wordsize: 12 cutoff: 125 stride: 4 allow_near_perfect: 0 } use_compact_index { name: "hg19_hap" cutoff: 5 } minlength: 55 name_pattern: "M_*" } policy { repeat_threshold: 1000 } policy { maxlength: 26 min_seed_len: 12 } policy { minlength: 27 maxlength: 31 min_seed_len: 16 } policy { minlength: 32 maxlength: 36 min_seed_len: 20 } policy { minlength: 37 maxlength: 41 min_seed_len: 24 } policy { minlength: 42 maxlength: 54 min_seed_len: 28 } policy { minlength: 55 maxlength: 71 min_seed_len: 20 } policy { minlength: 72 maxlength: 90 min_seed_len: 24 } policy { minlength: 91 maxlength: 107 min_seed_len: 28 } policy { minlength: 108 min_seed_len: 32 } aligner { rate_of_transversions: 0.001 rate_of_transitions: 0.003 gap_open_rate: 0.0001 gap_extension_rate: 0.003 rate_of_ds_deamination: 0.01 rate_of_ss_deamination: 0.9 mean_overhang_length: 0.5 max_penalty_per_nuc: 8 max_mapq: 60 } anfo-0.98/example/default.cfg0000644000371600007640000000401011447113506013063 00000000000000policy { use_compact_index { name: "chr21" wordsize: 12 stride: 4 allow_near_perfect: 2 } use_compact_index { name: "hg18" wordsize: 12 stride: 4 allow_near_perfect: 2 } use_compact_index { name: "pt2" wordsize: 12 stride: 4 allow_near_perfect: 2 } use_compact_index { name: "hcscca" wordsize: 12 stride: 4 allow_near_perfect: 2 } maxlength: 58 repeat_threshold: 1000 } policy { use_compact_index { name: "chr21" wordsize: 12 stride: 4 allow_near_perfect: 1 } use_compact_index { name: "hg18" cutoff: 500 stride: 4 allow_near_perfect: 1 } use_compact_index { name: "pt2" cutoff: 500 stride: 4 allow_near_perfect: 1 } use_compact_index { name: "hcscca" cutoff: 125 stride: 4 allow_near_perfect: 1 } minlength: 59 repeat_threshold: 1000 } policy { maxlength: 118 max_mismatches_in_seed: 2 } policy { minlength: 119 max_mismatches_in_seed: 1 } policy { minlength: 23 maxlength: 34 min_seed_len: 12 } policy { minlength: 35 maxlength: 42 min_seed_len: 16 } policy { minlength: 43 maxlength: 58 min_seed_len: 20 } policy { minlength: 59 maxlength: 70 min_seed_len: 24 } policy { minlength: 71 maxlength: 86 min_seed_len: 28 } policy { minlength: 87 maxlength: 102 min_seed_len: 32 } policy { minlength: 103 maxlength: 118 min_seed_len: 36 } policy { minlength: 119 maxlength: 138 min_seed_len: 28 } policy { minlength: 139 maxlength: 162 min_seed_len: 32 } policy { minlength: 163 min_seed_len: 36 } aligner { rate_of_transversions: 0.001 rate_of_transitions: 0.003 gap_open_rate: 0.0001 gap_extension_rate: 0.003 max_penalty_per_nuc: 8 max_mapq: 60 } anfo-0.98/example/split-anfo.scm0000644000371600007640000000101111447113105013527 00000000000000(require 'anfo) (set-verbosity 'info) (define (seq a b) (if (eq? a b) '() (cons a (seq (+ a 1) b)))) (define genome "hg18") (define input-file "Vi-hg18.anfo") (define output-file "Vi-hg18-chr") (define sequences (map (lambda (c) (string-append "chr" c)) (append (map number->string (seq 1 22)) '("X" "Y" "M")))) (define (output s) (chain (require-hit genomes: genome sequences: s) (write-native (string-append output-file s ".anfo")))) (anfo-run input-file (apply tee (map output sequences))) anfo-0.98/example/threebam.scm0000644000371600007640000000106711447113105013255 00000000000000(load 'anfo.scm) (set-verbosity 'info) (anfo-run (chain (concat "foo.anfo" "bar.anfo") (filter-score slope: 7.5 intercept: 20)) (chain (only-genomes "hg18") require-hit (write-sam "| samtools view -bt /mnt/454/SolexaMPI/PhaseIV/hg18.map -o hg18.bam -")) (chain (only-genomes "pt2") require-hit (write-sam "| samtools view -bt /mnt/454/SolexaMPI/PhaseIV/pt2.map -o pt2.bam -")) (chain (only-genomes "hcscca") require-hit (write-sam "| samtools view -bt /mnt/454/SolexaMPI/PhaseIV/hcscca.map -o hcscca.bam -"))) anfo-0.98/m4/0000777000371600007640000000000011447127354007742 500000000000000anfo-0.98/m4/libtool.m40000644000371600007640000077426611447114167011610 00000000000000# libtool.m4 - Configure libtool for the host system. -*-Autoconf-*- # # Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005, # 2006, 2007, 2008 Free Software Foundation, Inc. # Written by Gordon Matzigkeit, 1996 # # This file is free software; the Free Software Foundation gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. m4_define([_LT_COPYING], [dnl # Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005, # 2006, 2007, 2008 Free Software Foundation, Inc. # Written by Gordon Matzigkeit, 1996 # # This file is part of GNU Libtool. # # GNU Libtool is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License as # published by the Free Software Foundation; either version 2 of # the License, or (at your option) any later version. # # As a special exception to the GNU General Public License, # if you distribute this file as part of a program or library that # is built using GNU Libtool, you may include this file under the # same distribution terms that you use for the rest of that program. # # GNU Libtool is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with GNU Libtool; see the file COPYING. If not, a copy # can be downloaded from http://www.gnu.org/licenses/gpl.html, or # obtained by writing to the Free Software Foundation, Inc., # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. ]) # serial 56 LT_INIT # LT_PREREQ(VERSION) # ------------------ # Complain and exit if this libtool version is less that VERSION. m4_defun([LT_PREREQ], [m4_if(m4_version_compare(m4_defn([LT_PACKAGE_VERSION]), [$1]), -1, [m4_default([$3], [m4_fatal([Libtool version $1 or higher is required], 63)])], [$2])]) # _LT_CHECK_BUILDDIR # ------------------ # Complain if the absolute build directory name contains unusual characters m4_defun([_LT_CHECK_BUILDDIR], [case `pwd` in *\ * | *\ *) AC_MSG_WARN([Libtool does not cope well with whitespace in `pwd`]) ;; esac ]) # LT_INIT([OPTIONS]) # ------------------ AC_DEFUN([LT_INIT], [AC_PREREQ([2.58])dnl We use AC_INCLUDES_DEFAULT AC_BEFORE([$0], [LT_LANG])dnl AC_BEFORE([$0], [LT_OUTPUT])dnl AC_BEFORE([$0], [LTDL_INIT])dnl m4_require([_LT_CHECK_BUILDDIR])dnl dnl Autoconf doesn't catch unexpanded LT_ macros by default: m4_pattern_forbid([^_?LT_[A-Z_]+$])dnl m4_pattern_allow([^(_LT_EOF|LT_DLGLOBAL|LT_DLLAZY_OR_NOW|LT_MULTI_MODULE)$])dnl dnl aclocal doesn't pull ltoptions.m4, ltsugar.m4, or ltversion.m4 dnl unless we require an AC_DEFUNed macro: AC_REQUIRE([LTOPTIONS_VERSION])dnl AC_REQUIRE([LTSUGAR_VERSION])dnl AC_REQUIRE([LTVERSION_VERSION])dnl AC_REQUIRE([LTOBSOLETE_VERSION])dnl m4_require([_LT_PROG_LTMAIN])dnl dnl Parse OPTIONS _LT_SET_OPTIONS([$0], [$1]) # This can be used to rebuild libtool when needed LIBTOOL_DEPS="$ltmain" # Always use our own libtool. LIBTOOL='$(SHELL) $(top_builddir)/libtool' AC_SUBST(LIBTOOL)dnl _LT_SETUP # Only expand once: m4_define([LT_INIT]) ])# LT_INIT # Old names: AU_ALIAS([AC_PROG_LIBTOOL], [LT_INIT]) AU_ALIAS([AM_PROG_LIBTOOL], [LT_INIT]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AC_PROG_LIBTOOL], []) dnl AC_DEFUN([AM_PROG_LIBTOOL], []) # _LT_CC_BASENAME(CC) # ------------------- # Calculate cc_basename. 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then lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \[$]2)); skip = 1; } { if (!skip) print \[$]0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '` sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra" fi # We used to test for /lib/ld.so.1 and disable shared libraries on # powerpc, because MkLinux only supported shared libraries with the # GNU dynamic linker. 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newsos6) version_type=linux library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes ;; *nto* | *qnx*) version_type=qnx need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no hardcode_into_libs=yes dynamic_linker='ldqnx.so' ;; openbsd*) version_type=sunos sys_lib_dlsearch_path_spec="/usr/lib" need_lib_prefix=no # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs. case $host_os in openbsd3.3 | openbsd3.3.*) need_version=yes ;; *) need_version=no ;; esac library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir' shlibpath_var=LD_LIBRARY_PATH if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then case $host_os in openbsd2.[[89]] | openbsd2.[[89]].*) shlibpath_overrides_runpath=no ;; *) shlibpath_overrides_runpath=yes ;; esac else shlibpath_overrides_runpath=yes fi ;; os2*) libname_spec='$name' shrext_cmds=".dll" need_lib_prefix=no library_names_spec='$libname${shared_ext} $libname.a' dynamic_linker='OS/2 ld.exe' shlibpath_var=LIBPATH ;; osf3* | osf4* | osf5*) version_type=osf need_lib_prefix=no need_version=no soname_spec='${libname}${release}${shared_ext}$major' library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' shlibpath_var=LD_LIBRARY_PATH sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib" sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec" ;; rdos*) dynamic_linker=no ;; solaris*) version_type=linux need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes hardcode_into_libs=yes # ldd complains unless libraries are executable postinstall_cmds='chmod +x $lib' ;; sunos4*) version_type=sunos library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes if test "$with_gnu_ld" = yes; then need_lib_prefix=no fi need_version=yes ;; sysv4 | sysv4.3*) version_type=linux library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH case $host_vendor in sni) shlibpath_overrides_runpath=no need_lib_prefix=no runpath_var=LD_RUN_PATH ;; siemens) need_lib_prefix=no ;; motorola) need_lib_prefix=no need_version=no shlibpath_overrides_runpath=no sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib' ;; esac ;; sysv4*MP*) if test -d /usr/nec ;then version_type=linux library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}' soname_spec='$libname${shared_ext}.$major' shlibpath_var=LD_LIBRARY_PATH fi ;; sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*) version_type=freebsd-elf need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes hardcode_into_libs=yes if test "$with_gnu_ld" = yes; then sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib' else sys_lib_search_path_spec='/usr/ccs/lib /usr/lib' case $host_os in sco3.2v5*) sys_lib_search_path_spec="$sys_lib_search_path_spec /lib" ;; esac fi sys_lib_dlsearch_path_spec='/usr/lib' ;; tpf*) # TPF is a cross-target only. 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sni) lt_cv_file_magic_cmd='/bin/file' lt_cv_deplibs_check_method="file_magic ELF [[0-9]][[0-9]]*-bit [[LM]]SB dynamic lib" lt_cv_file_magic_test_file=/lib/libc.so ;; siemens) lt_cv_deplibs_check_method=pass_all ;; pc) lt_cv_deplibs_check_method=pass_all ;; esac ;; tpf*) lt_cv_deplibs_check_method=pass_all ;; esac ]) file_magic_cmd=$lt_cv_file_magic_cmd deplibs_check_method=$lt_cv_deplibs_check_method test -z "$deplibs_check_method" && deplibs_check_method=unknown _LT_DECL([], [deplibs_check_method], [1], [Method to check whether dependent libraries are shared objects]) _LT_DECL([], [file_magic_cmd], [1], [Command to use when deplibs_check_method == "file_magic"]) ])# _LT_CHECK_MAGIC_METHOD # LT_PATH_NM # ---------- # find the pathname to a BSD- or MS-compatible name lister AC_DEFUN([LT_PATH_NM], [AC_REQUIRE([AC_PROG_CC])dnl AC_CACHE_CHECK([for BSD- or MS-compatible name lister (nm)], lt_cv_path_NM, [if test -n "$NM"; then # Let the user override the test. lt_cv_path_NM="$NM" else lt_nm_to_check="${ac_tool_prefix}nm" if test -n "$ac_tool_prefix" && test "$build" = "$host"; then lt_nm_to_check="$lt_nm_to_check nm" fi for lt_tmp_nm in $lt_nm_to_check; do lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR for ac_dir in $PATH /usr/ccs/bin/elf /usr/ccs/bin /usr/ucb /bin; do IFS="$lt_save_ifs" test -z "$ac_dir" && ac_dir=. tmp_nm="$ac_dir/$lt_tmp_nm" if test -f "$tmp_nm" || test -f "$tmp_nm$ac_exeext" ; then # Check to see if the nm accepts a BSD-compat flag. # Adding the `sed 1q' prevents false positives on HP-UX, which says: # nm: unknown option "B" ignored # Tru64's nm complains that /dev/null is an invalid object file case `"$tmp_nm" -B /dev/null 2>&1 | sed '1q'` in */dev/null* | *'Invalid file or object type'*) lt_cv_path_NM="$tmp_nm -B" break ;; *) case `"$tmp_nm" -p /dev/null 2>&1 | sed '1q'` in */dev/null*) lt_cv_path_NM="$tmp_nm -p" break ;; *) lt_cv_path_NM=${lt_cv_path_NM="$tmp_nm"} # keep the first match, but continue # so that we can try to find one that supports BSD flags ;; esac ;; esac fi done IFS="$lt_save_ifs" done : ${lt_cv_path_NM=no} fi]) if test "$lt_cv_path_NM" != "no"; then NM="$lt_cv_path_NM" else # Didn't find any BSD compatible name lister, look for dumpbin. AC_CHECK_TOOLS(DUMPBIN, ["dumpbin -symbols" "link -dump -symbols"], :) AC_SUBST([DUMPBIN]) if test "$DUMPBIN" != ":"; then NM="$DUMPBIN" fi fi test -z "$NM" && NM=nm AC_SUBST([NM]) _LT_DECL([], [NM], [1], [A BSD- or MS-compatible name lister])dnl AC_CACHE_CHECK([the name lister ($NM) interface], [lt_cv_nm_interface], [lt_cv_nm_interface="BSD nm" echo "int some_variable = 0;" > conftest.$ac_ext (eval echo "\"\$as_me:__oline__: $ac_compile\"" >&AS_MESSAGE_LOG_FD) (eval "$ac_compile" 2>conftest.err) cat conftest.err >&AS_MESSAGE_LOG_FD (eval echo "\"\$as_me:__oline__: $NM \\\"conftest.$ac_objext\\\"\"" >&AS_MESSAGE_LOG_FD) (eval "$NM \"conftest.$ac_objext\"" 2>conftest.err > conftest.out) cat conftest.err >&AS_MESSAGE_LOG_FD (eval echo "\"\$as_me:__oline__: output\"" >&AS_MESSAGE_LOG_FD) cat conftest.out >&AS_MESSAGE_LOG_FD if $GREP 'External.*some_variable' conftest.out > /dev/null; then lt_cv_nm_interface="MS dumpbin" fi rm -f conftest*]) ])# LT_PATH_NM # Old names: AU_ALIAS([AM_PROG_NM], [LT_PATH_NM]) AU_ALIAS([AC_PROG_NM], [LT_PATH_NM]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AM_PROG_NM], []) dnl AC_DEFUN([AC_PROG_NM], []) # LT_LIB_M # -------- # check for math library AC_DEFUN([LT_LIB_M], [AC_REQUIRE([AC_CANONICAL_HOST])dnl LIBM= case $host in *-*-beos* | *-*-cygwin* | *-*-pw32* | *-*-darwin*) # These system don't have libm, or don't need it ;; *-ncr-sysv4.3*) AC_CHECK_LIB(mw, _mwvalidcheckl, LIBM="-lmw") AC_CHECK_LIB(m, cos, LIBM="$LIBM -lm") ;; *) AC_CHECK_LIB(m, cos, LIBM="-lm") ;; esac AC_SUBST([LIBM]) ])# LT_LIB_M # Old name: AU_ALIAS([AC_CHECK_LIBM], [LT_LIB_M]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AC_CHECK_LIBM], []) # _LT_COMPILER_NO_RTTI([TAGNAME]) # ------------------------------- m4_defun([_LT_COMPILER_NO_RTTI], [m4_require([_LT_TAG_COMPILER])dnl _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)= if test "$GCC" = yes; then _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=' -fno-builtin' _LT_COMPILER_OPTION([if $compiler supports -fno-rtti -fno-exceptions], lt_cv_prog_compiler_rtti_exceptions, [-fno-rtti -fno-exceptions], [], [_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)="$_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1) -fno-rtti -fno-exceptions"]) fi _LT_TAGDECL([no_builtin_flag], [lt_prog_compiler_no_builtin_flag], [1], [Compiler flag to turn off builtin functions]) ])# _LT_COMPILER_NO_RTTI # _LT_CMD_GLOBAL_SYMBOLS # ---------------------- m4_defun([_LT_CMD_GLOBAL_SYMBOLS], [AC_REQUIRE([AC_CANONICAL_HOST])dnl AC_REQUIRE([AC_PROG_CC])dnl AC_REQUIRE([LT_PATH_NM])dnl AC_REQUIRE([LT_PATH_LD])dnl m4_require([_LT_DECL_SED])dnl m4_require([_LT_DECL_EGREP])dnl m4_require([_LT_TAG_COMPILER])dnl # Check for command to grab the raw symbol name followed by C symbol from nm. AC_MSG_CHECKING([command to parse $NM output from $compiler object]) AC_CACHE_VAL([lt_cv_sys_global_symbol_pipe], [ # These are sane defaults that work on at least a few old systems. # [They come from Ultrix. What could be older than Ultrix?!! ;)] # Character class describing NM global symbol codes. symcode='[[BCDEGRST]]' # Regexp to match symbols that can be accessed directly from C. sympat='\([[_A-Za-z]][[_A-Za-z0-9]]*\)' # Define system-specific variables. case $host_os in aix*) symcode='[[BCDT]]' ;; cygwin* | mingw* | pw32* | cegcc*) symcode='[[ABCDGISTW]]' ;; hpux*) if test "$host_cpu" = ia64; then symcode='[[ABCDEGRST]]' fi ;; irix* | nonstopux*) symcode='[[BCDEGRST]]' ;; osf*) symcode='[[BCDEGQRST]]' ;; solaris*) symcode='[[BDRT]]' ;; sco3.2v5*) symcode='[[DT]]' ;; sysv4.2uw2*) symcode='[[DT]]' ;; sysv5* | sco5v6* | unixware* | OpenUNIX*) symcode='[[ABDT]]' ;; sysv4) symcode='[[DFNSTU]]' ;; esac # If we're using GNU nm, then use its standard symbol codes. case `$NM -V 2>&1` in *GNU* | *'with BFD'*) symcode='[[ABCDGIRSTW]]' ;; esac # Transform an extracted symbol line into a proper C declaration. # Some systems (esp. on ia64) link data and code symbols differently, # so use this general approach. lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'" # Transform an extracted symbol line into symbol name and symbol address lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([[^ ]]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([[^ ]]*\) \([[^ ]]*\)$/ {\"\2\", (void *) \&\2},/p'" lt_cv_sys_global_symbol_to_c_name_address_lib_prefix="sed -n -e 's/^: \([[^ ]]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([[^ ]]*\) \(lib[[^ ]]*\)$/ {\"\2\", (void *) \&\2},/p' -e 's/^$symcode* \([[^ ]]*\) \([[^ ]]*\)$/ {\"lib\2\", (void *) \&\2},/p'" # Handle CRLF in mingw tool chain opt_cr= case $build_os in mingw*) opt_cr=`$ECHO 'x\{0,1\}' | tr x '\015'` # option cr in regexp ;; esac # Try without a prefix underscore, then with it. for ac_symprfx in "" "_"; do # Transform symcode, sympat, and symprfx into a raw symbol and a C symbol. symxfrm="\\1 $ac_symprfx\\2 \\2" # Write the raw and C identifiers. if test "$lt_cv_nm_interface" = "MS dumpbin"; then # Fake it for dumpbin and say T for any non-static function # and D for any global variable. # Also find C++ and __fastcall symbols from MSVC++, # which start with @ or ?. lt_cv_sys_global_symbol_pipe="$AWK ['"\ " {last_section=section; section=\$ 3};"\ " /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\ " \$ 0!~/External *\|/{next};"\ " / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\ " {if(hide[section]) next};"\ " {f=0}; \$ 0~/\(\).*\|/{f=1}; {printf f ? \"T \" : \"D \"};"\ " {split(\$ 0, a, /\||\r/); split(a[2], s)};"\ " s[1]~/^[@?]/{print s[1], s[1]; next};"\ " s[1]~prfx {split(s[1],t,\"@\"); print t[1], substr(t[1],length(prfx))}"\ " ' prfx=^$ac_symprfx]" else lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[[ ]]\($symcode$symcode*\)[[ ]][[ ]]*$ac_symprfx$sympat$opt_cr$/$symxfrm/p'" fi # Check to see that the pipe works correctly. pipe_works=no rm -f conftest* cat > conftest.$ac_ext <<_LT_EOF #ifdef __cplusplus extern "C" { #endif char nm_test_var; void nm_test_func(void); void nm_test_func(void){} #ifdef __cplusplus } #endif int main(){nm_test_var='a';nm_test_func();return(0);} _LT_EOF if AC_TRY_EVAL(ac_compile); then # Now try to grab the symbols. nlist=conftest.nm if AC_TRY_EVAL(NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist) && test -s "$nlist"; then # Try sorting and uniquifying the output. if sort "$nlist" | uniq > "$nlist"T; then mv -f "$nlist"T "$nlist" else rm -f "$nlist"T fi # Make sure that we snagged all the symbols we need. if $GREP ' nm_test_var$' "$nlist" >/dev/null; then if $GREP ' nm_test_func$' "$nlist" >/dev/null; then cat <<_LT_EOF > conftest.$ac_ext #ifdef __cplusplus extern "C" { #endif _LT_EOF # Now generate the symbol file. eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | $GREP -v main >> conftest.$ac_ext' cat <<_LT_EOF >> conftest.$ac_ext /* The mapping between symbol names and symbols. */ const struct { const char *name; void *address; } lt__PROGRAM__LTX_preloaded_symbols[[]] = { { "@PROGRAM@", (void *) 0 }, _LT_EOF $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (void *) \&\2},/" < "$nlist" | $GREP -v main >> conftest.$ac_ext cat <<\_LT_EOF >> conftest.$ac_ext {0, (void *) 0} }; /* This works around a problem in FreeBSD linker */ #ifdef FREEBSD_WORKAROUND static const void *lt_preloaded_setup() { return lt__PROGRAM__LTX_preloaded_symbols; } #endif #ifdef __cplusplus } #endif _LT_EOF # Now try linking the two files. mv conftest.$ac_objext conftstm.$ac_objext lt_save_LIBS="$LIBS" lt_save_CFLAGS="$CFLAGS" LIBS="conftstm.$ac_objext" CFLAGS="$CFLAGS$_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)" if AC_TRY_EVAL(ac_link) && test -s conftest${ac_exeext}; then pipe_works=yes fi LIBS="$lt_save_LIBS" CFLAGS="$lt_save_CFLAGS" else echo "cannot find nm_test_func in $nlist" >&AS_MESSAGE_LOG_FD fi else echo "cannot find nm_test_var in $nlist" >&AS_MESSAGE_LOG_FD fi else echo "cannot run $lt_cv_sys_global_symbol_pipe" >&AS_MESSAGE_LOG_FD fi else echo "$progname: failed program was:" >&AS_MESSAGE_LOG_FD cat conftest.$ac_ext >&5 fi rm -rf conftest* conftst* # Do not use the global_symbol_pipe unless it works. if test "$pipe_works" = yes; then break else lt_cv_sys_global_symbol_pipe= fi done ]) if test -z "$lt_cv_sys_global_symbol_pipe"; then lt_cv_sys_global_symbol_to_cdecl= fi if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then AC_MSG_RESULT(failed) else AC_MSG_RESULT(ok) fi _LT_DECL([global_symbol_pipe], [lt_cv_sys_global_symbol_pipe], [1], [Take the output of nm and produce a listing of raw symbols and C names]) _LT_DECL([global_symbol_to_cdecl], [lt_cv_sys_global_symbol_to_cdecl], [1], [Transform the output of nm in a proper C declaration]) _LT_DECL([global_symbol_to_c_name_address], [lt_cv_sys_global_symbol_to_c_name_address], [1], [Transform the output of nm in a C name address pair]) _LT_DECL([global_symbol_to_c_name_address_lib_prefix], [lt_cv_sys_global_symbol_to_c_name_address_lib_prefix], [1], [Transform the output of nm in a C name address pair when lib prefix is needed]) ]) # _LT_CMD_GLOBAL_SYMBOLS # _LT_COMPILER_PIC([TAGNAME]) # --------------------------- m4_defun([_LT_COMPILER_PIC], [m4_require([_LT_TAG_COMPILER])dnl _LT_TAGVAR(lt_prog_compiler_wl, $1)= _LT_TAGVAR(lt_prog_compiler_pic, $1)= _LT_TAGVAR(lt_prog_compiler_static, $1)= AC_MSG_CHECKING([for $compiler option to produce PIC]) m4_if([$1], [CXX], [ # C++ specific cases for pic, static, wl, etc. if test "$GXX" = yes; then _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' case $host_os in aix*) # All AIX code is PIC. if test "$host_cpu" = ia64; then # AIX 5 now supports IA64 processor _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' fi ;; amigaos*) case $host_cpu in powerpc) # see comment about AmigaOS4 .so support _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; m68k) # FIXME: we need at least 68020 code to build shared libraries, but # adding the `-m68020' flag to GCC prevents building anything better, # like `-m68040'. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-m68020 -resident32 -malways-restore-a4' ;; esac ;; beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*) # PIC is the default for these OSes. ;; mingw* | cygwin* | os2* | pw32* | cegcc*) # This hack is so that the source file can tell whether it is being # built for inclusion in a dll (and should export symbols for example). # Although the cygwin gcc ignores -fPIC, still need this for old-style # (--disable-auto-import) libraries m4_if([$1], [GCJ], [], [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT']) ;; darwin* | rhapsody*) # PIC is the default on this platform # Common symbols not allowed in MH_DYLIB files _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fno-common' ;; *djgpp*) # DJGPP does not support shared libraries at all _LT_TAGVAR(lt_prog_compiler_pic, $1)= ;; interix[[3-9]]*) # Interix 3.x gcc -fpic/-fPIC options generate broken code. # Instead, we relocate shared libraries at runtime. ;; sysv4*MP*) if test -d /usr/nec; then _LT_TAGVAR(lt_prog_compiler_pic, $1)=-Kconform_pic fi ;; hpux*) # PIC is the default for 64-bit PA HP-UX, but not for 32-bit # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag # sets the default TLS model and affects inlining. case $host_cpu in hppa*64*) ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; esac ;; *qnx* | *nto*) # QNX uses GNU C++, but need to define -shared option too, otherwise # it will coredump. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared' ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; esac else case $host_os in aix[[4-9]]*) # All AIX code is PIC. if test "$host_cpu" = ia64; then # AIX 5 now supports IA64 processor _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' else _LT_TAGVAR(lt_prog_compiler_static, $1)='-bnso -bI:/lib/syscalls.exp' fi ;; chorus*) case $cc_basename in cxch68*) # Green Hills C++ Compiler # _LT_TAGVAR(lt_prog_compiler_static, $1)="--no_auto_instantiation -u __main -u __premain -u _abort -r $COOL_DIR/lib/libOrb.a $MVME_DIR/lib/CC/libC.a $MVME_DIR/lib/classix/libcx.s.a" ;; esac ;; dgux*) case $cc_basename in ec++*) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' ;; ghcx*) # Green Hills C++ Compiler _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' ;; *) ;; esac ;; freebsd* | dragonfly*) # FreeBSD uses GNU C++ ;; hpux9* | hpux10* | hpux11*) case $cc_basename in CC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive' if test "$host_cpu" != ia64; then _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z' fi ;; aCC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive' case $host_cpu in hppa*64*|ia64*) # +Z the default ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z' ;; esac ;; *) ;; esac ;; interix*) # This is c89, which is MS Visual C++ (no shared libs) # Anyone wants to do a port? ;; irix5* | irix6* | nonstopux*) case $cc_basename in CC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' # CC pic flag -KPIC is the default. ;; *) ;; esac ;; linux* | k*bsd*-gnu) case $cc_basename in KCC*) # KAI C++ Compiler _LT_TAGVAR(lt_prog_compiler_wl, $1)='--backend -Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; ecpc* ) # old Intel C++ for x86_64 which still supported -KPIC. _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' ;; icpc* ) # Intel C++, used to be incompatible with GCC. # ICC 10 doesn't accept -KPIC any more. _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' ;; pgCC* | pgcpp*) # Portland Group C++ compiler _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fpic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; cxx*) # Compaq C++ # Make sure the PIC flag is empty. It appears that all Alpha # Linux and Compaq Tru64 Unix objects are PIC. _LT_TAGVAR(lt_prog_compiler_pic, $1)= _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' ;; xlc* | xlC*) # IBM XL 8.0 on PPC _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-qpic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-qstaticlink' ;; *) case `$CC -V 2>&1 | sed 5q` in *Sun\ C*) # Sun C++ 5.9 _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ' ;; esac ;; esac ;; lynxos*) ;; m88k*) ;; mvs*) case $cc_basename in cxx*) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-W c,exportall' ;; *) ;; esac ;; netbsd* | netbsdelf*-gnu) ;; *qnx* | *nto*) # QNX uses GNU C++, but need to define -shared option too, otherwise # it will coredump. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared' ;; osf3* | osf4* | osf5*) case $cc_basename in KCC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='--backend -Wl,' ;; RCC*) # Rational C++ 2.4.1 _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' ;; cxx*) # Digital/Compaq C++ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' # Make sure the PIC flag is empty. It appears that all Alpha # Linux and Compaq Tru64 Unix objects are PIC. _LT_TAGVAR(lt_prog_compiler_pic, $1)= _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' ;; *) ;; esac ;; psos*) ;; solaris*) case $cc_basename in CC*) # Sun C++ 4.2, 5.x and Centerline C++ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ' ;; gcx*) # Green Hills C++ Compiler _LT_TAGVAR(lt_prog_compiler_pic, $1)='-PIC' ;; *) ;; esac ;; sunos4*) case $cc_basename in CC*) # Sun C++ 4.x _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; lcc*) # Lucid _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' ;; *) ;; esac ;; sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*) case $cc_basename in CC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; esac ;; tandem*) case $cc_basename in NCC*) # NonStop-UX NCC 3.20 _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' ;; *) ;; esac ;; vxworks*) ;; *) _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no ;; esac fi ], [ if test "$GCC" = yes; then _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' case $host_os in aix*) # All AIX code is PIC. if test "$host_cpu" = ia64; then # AIX 5 now supports IA64 processor _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' fi ;; amigaos*) case $host_cpu in powerpc) # see comment about AmigaOS4 .so support _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; m68k) # FIXME: we need at least 68020 code to build shared libraries, but # adding the `-m68020' flag to GCC prevents building anything better, # like `-m68040'. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-m68020 -resident32 -malways-restore-a4' ;; esac ;; beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*) # PIC is the default for these OSes. ;; mingw* | cygwin* | pw32* | os2* | cegcc*) # This hack is so that the source file can tell whether it is being # built for inclusion in a dll (and should export symbols for example). # Although the cygwin gcc ignores -fPIC, still need this for old-style # (--disable-auto-import) libraries m4_if([$1], [GCJ], [], [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT']) ;; darwin* | rhapsody*) # PIC is the default on this platform # Common symbols not allowed in MH_DYLIB files _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fno-common' ;; hpux*) # PIC is the default for 64-bit PA HP-UX, but not for 32-bit # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag # sets the default TLS model and affects inlining. case $host_cpu in hppa*64*) # +Z the default ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; esac ;; interix[[3-9]]*) # Interix 3.x gcc -fpic/-fPIC options generate broken code. # Instead, we relocate shared libraries at runtime. ;; msdosdjgpp*) # Just because we use GCC doesn't mean we suddenly get shared libraries # on systems that don't support them. _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no enable_shared=no ;; *nto* | *qnx*) # QNX uses GNU C++, but need to define -shared option too, otherwise # it will coredump. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared' ;; sysv4*MP*) if test -d /usr/nec; then _LT_TAGVAR(lt_prog_compiler_pic, $1)=-Kconform_pic fi ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; esac else # PORTME Check for flag to pass linker flags through the system compiler. case $host_os in aix*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' if test "$host_cpu" = ia64; then # AIX 5 now supports IA64 processor _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' else _LT_TAGVAR(lt_prog_compiler_static, $1)='-bnso -bI:/lib/syscalls.exp' fi ;; mingw* | cygwin* | pw32* | os2* | cegcc*) # This hack is so that the source file can tell whether it is being # built for inclusion in a dll (and should export symbols for example). m4_if([$1], [GCJ], [], [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT']) ;; hpux9* | hpux10* | hpux11*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but # not for PA HP-UX. case $host_cpu in hppa*64*|ia64*) # +Z the default ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z' ;; esac # Is there a better lt_prog_compiler_static that works with the bundled CC? _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive' ;; irix5* | irix6* | nonstopux*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' # PIC (with -KPIC) is the default. _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' ;; linux* | k*bsd*-gnu) case $cc_basename in # old Intel for x86_64 which still supported -KPIC. ecc*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' ;; 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netbsd* | netbsdelf*-gnu) if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out else _LT_TAGVAR(archive_cmds, $1)='$LD -shared -o $lib $libobjs $deplibs $linker_flags' # ELF fi _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir' _LT_TAGVAR(hardcode_direct, $1)=yes _LT_TAGVAR(hardcode_shlibpath_var, $1)=no ;; newsos6) _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' _LT_TAGVAR(hardcode_direct, $1)=yes _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir' _LT_TAGVAR(hardcode_libdir_separator, $1)=: _LT_TAGVAR(hardcode_shlibpath_var, $1)=no ;; *nto* | *qnx*) ;; openbsd*) if test -f /usr/libexec/ld.so; then _LT_TAGVAR(hardcode_direct, $1)=yes _LT_TAGVAR(hardcode_shlibpath_var, $1)=no _LT_TAGVAR(hardcode_direct_absolute, $1)=yes if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols' _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir' _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E' else case $host_os in openbsd[[01]].* | openbsd2.[[0-7]] | openbsd2.[[0-7]].*) _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir' ;; *) _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir' ;; esac fi else _LT_TAGVAR(ld_shlibs, $1)=no fi ;; os2*) _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir' _LT_TAGVAR(hardcode_minus_L, $1)=yes _LT_TAGVAR(allow_undefined_flag, $1)=unsupported _LT_TAGVAR(archive_cmds, $1)='$ECHO "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$ECHO "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~$ECHO DATA >> $output_objdir/$libname.def~$ECHO " SINGLE NONSHARED" >> $output_objdir/$libname.def~$ECHO EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def' _LT_TAGVAR(old_archive_from_new_cmds, $1)='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def' ;; 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do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; printf "%s\\n" "-hidden">> $lib.exp~ $CC -shared${allow_undefined_flag} ${wl}-input ${wl}$lib.exp $compiler_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib~$RM $lib.exp' # Both c and cxx compiler support -rpath directly _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-rpath $libdir' fi _LT_TAGVAR(archive_cmds_need_lc, $1)='no' _LT_TAGVAR(hardcode_libdir_separator, $1)=: ;; solaris*) _LT_TAGVAR(no_undefined_flag, $1)=' -z defs' if test "$GCC" = yes; then wlarc='${wl}' _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-z ${wl}text ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ $CC -shared ${wl}-z ${wl}text ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp' else case `$CC -V 2>&1` in *"Compilers 5.0"*) wlarc='' _LT_TAGVAR(archive_cmds, $1)='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags' _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; 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AC_MSG_CHECKING([whether -lc should be explicitly linked in]) $RM conftest* echo "$lt_simple_compile_test_code" > conftest.$ac_ext if AC_TRY_EVAL(ac_compile) 2>conftest.err; then soname=conftest lib=conftest libobjs=conftest.$ac_objext deplibs= wl=$_LT_TAGVAR(lt_prog_compiler_wl, $1) pic_flag=$_LT_TAGVAR(lt_prog_compiler_pic, $1) compiler_flags=-v linker_flags=-v verstring= output_objdir=. libname=conftest lt_save_allow_undefined_flag=$_LT_TAGVAR(allow_undefined_flag, $1) _LT_TAGVAR(allow_undefined_flag, $1)= if AC_TRY_EVAL(_LT_TAGVAR(archive_cmds, $1) 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1) then _LT_TAGVAR(archive_cmds_need_lc, $1)=no else _LT_TAGVAR(archive_cmds_need_lc, $1)=yes fi _LT_TAGVAR(allow_undefined_flag, $1)=$lt_save_allow_undefined_flag else cat conftest.err 1>&5 fi $RM conftest* AC_MSG_RESULT([$_LT_TAGVAR(archive_cmds_need_lc, $1)]) ;; esac fi ;; esac _LT_TAGDECL([build_libtool_need_lc], [archive_cmds_need_lc], [0], [Whether or not to add -lc for building shared libraries]) _LT_TAGDECL([allow_libtool_libs_with_static_runtimes], [enable_shared_with_static_runtimes], [0], [Whether or not to disallow shared libs when runtime libs are static]) _LT_TAGDECL([], [export_dynamic_flag_spec], [1], [Compiler flag to allow reflexive dlopens]) _LT_TAGDECL([], [whole_archive_flag_spec], [1], [Compiler flag to generate shared objects directly from archives]) _LT_TAGDECL([], [compiler_needs_object], [1], [Whether the compiler copes with passing no objects directly]) _LT_TAGDECL([], [old_archive_from_new_cmds], [2], [Create an old-style archive from a shared archive]) _LT_TAGDECL([], [old_archive_from_expsyms_cmds], [2], [Create a temporary old-style archive to link instead of a shared archive]) _LT_TAGDECL([], [archive_cmds], [2], [Commands used to build a shared archive]) _LT_TAGDECL([], [archive_expsym_cmds], [2]) _LT_TAGDECL([], [module_cmds], [2], [Commands used to build a loadable module if different from building a shared archive.]) _LT_TAGDECL([], [module_expsym_cmds], [2]) _LT_TAGDECL([], [with_gnu_ld], [1], [Whether we are building with GNU ld or not]) _LT_TAGDECL([], [allow_undefined_flag], [1], [Flag that allows shared libraries with undefined symbols to be built]) _LT_TAGDECL([], [no_undefined_flag], [1], [Flag that enforces no undefined symbols]) _LT_TAGDECL([], [hardcode_libdir_flag_spec], [1], [Flag to hardcode $libdir into a binary during linking. 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Vaughan, 2004 # # This file is free software; the Free Software Foundation gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # serial 6 ltoptions.m4 # This is to help aclocal find these macros, as it can't see m4_define. AC_DEFUN([LTOPTIONS_VERSION], [m4_if([1])]) # _LT_MANGLE_OPTION(MACRO-NAME, OPTION-NAME) # ------------------------------------------ m4_define([_LT_MANGLE_OPTION], [[_LT_OPTION_]m4_bpatsubst($1__$2, [[^a-zA-Z0-9_]], [_])]) # _LT_SET_OPTION(MACRO-NAME, OPTION-NAME) # --------------------------------------- # Set option OPTION-NAME for macro MACRO-NAME, and if there is a # matching handler defined, dispatch to it. 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Vaughan, 2004 # # This file is free software; the Free Software Foundation gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # serial 6 ltsugar.m4 # This is to help aclocal find these macros, as it can't see m4_define. AC_DEFUN([LTSUGAR_VERSION], [m4_if([0.1])]) # lt_join(SEP, ARG1, [ARG2...]) # ----------------------------- # Produce ARG1SEPARG2...SEPARGn, omitting [] arguments and their # associated separator. # Needed until we can rely on m4_join from Autoconf 2.62, since all earlier # versions in m4sugar had bugs. m4_define([lt_join], [m4_if([$#], [1], [], [$#], [2], [[$2]], [m4_if([$2], [], [], [[$2]_])$0([$1], m4_shift(m4_shift($@)))])]) m4_define([_lt_join], [m4_if([$#$2], [2], [], [m4_if([$2], [], [], [[$1$2]])$0([$1], m4_shift(m4_shift($@)))])]) # lt_car(LIST) # lt_cdr(LIST) # ------------ # Manipulate m4 lists. # These macros are necessary as long as will still need to support # Autoconf-2.59 which quotes differently. m4_define([lt_car], [[$1]]) m4_define([lt_cdr], [m4_if([$#], 0, [m4_fatal([$0: cannot be called without arguments])], [$#], 1, [], [m4_dquote(m4_shift($@))])]) m4_define([lt_unquote], $1) # lt_append(MACRO-NAME, STRING, [SEPARATOR]) # ------------------------------------------ # Redefine MACRO-NAME to hold its former content plus `SEPARATOR'`STRING'. # Note that neither SEPARATOR nor STRING are expanded; they are appended # to MACRO-NAME as is (leaving the expansion for when MACRO-NAME is invoked). # No SEPARATOR is output if MACRO-NAME was previously undefined (different # than defined and empty). # # This macro is needed until we can rely on Autoconf 2.62, since earlier # versions of m4sugar mistakenly expanded SEPARATOR but not STRING. m4_define([lt_append], [m4_define([$1], m4_ifdef([$1], [m4_defn([$1])[$3]])[$2])]) # lt_combine(SEP, PREFIX-LIST, INFIX, SUFFIX1, [SUFFIX2...]) # ---------------------------------------------------------- # Produce a SEP delimited list of all paired combinations of elements of # PREFIX-LIST with SUFFIX1 through SUFFIXn. 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See the GNU # General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. # # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that program. # PKG_PROG_PKG_CONFIG([MIN-VERSION]) # ---------------------------------- AC_DEFUN([PKG_PROG_PKG_CONFIG], [m4_pattern_forbid([^_?PKG_[A-Z_]+$]) m4_pattern_allow([^PKG_CONFIG(_PATH)?$]) AC_ARG_VAR([PKG_CONFIG], [path to pkg-config utility])dnl if test "x$ac_cv_env_PKG_CONFIG_set" != "xset"; then AC_PATH_TOOL([PKG_CONFIG], [pkg-config]) fi if test -n "$PKG_CONFIG"; then _pkg_min_version=m4_default([$1], [0.9.0]) AC_MSG_CHECKING([pkg-config is at least version $_pkg_min_version]) if $PKG_CONFIG --atleast-pkgconfig-version $_pkg_min_version; then AC_MSG_RESULT([yes]) else AC_MSG_RESULT([no]) PKG_CONFIG="" fi fi[]dnl ])# PKG_PROG_PKG_CONFIG # PKG_CHECK_EXISTS(MODULES, [ACTION-IF-FOUND], [ACTION-IF-NOT-FOUND]) # # Check to see whether a particular set of modules exists. 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Can be found at http://doxygen.org - zlib from zlib.net - libbz2 from bzip2.org - Elk from http://sam.zoy.org/elk/ If you have those, call './configure', 'make', then 'make doc' to create the documentation, then 'make install'. How to use it? To test, you need a genome, an index, and some input in FastA or FastQ format: - Locate a genome in FASTA format (or any other format that has a converter; .2bit is fine, my own .dna isn't). Run fa2dna on it (--help tells you how); you can pipe the input if you want. - On your new .dna file, run file-info. It should spit out the meta data for that genome. If not, you're hosed... - Build an index for the .dna file using dnaindex (--help tells you how, the defaults are probably fine) - You can run file-info on that, too. It will tell you the word size you just set. If not, you're hosed again... - Write a sensible anfo.cfg using the examples in example/ and config.proto as guideline. - You can run index-test or anfo now. Index-test just does lookups in the index, and optionally (on simulated data) checks if a seed in the correct region was found. - anfo can be run on any FASTA/FASTQ file now. - anfo-tool can operate on the output files (but it's cumbersome to use) - the Elk binding can do what anfo and anfo-tool do, is much more flexible, but undocumented. What's stable and what isn't? Pretty much stabilized are... - Genome handling and creation (files sequence.h, sequence.cc, index.h, index.cc, fa2dna.cc) I store genomes with four bits per nucleotide, which sounded like a fscking brilliant idea, since it's only half as wasteful as the text form and still allows ambiguity codes. The headaches came with the implementation of the auxilliary DnaP class... Anyway, the nucleotides A,C,T,G map to bits 0,1,2,3. That order (you did notice T coming before G, didn't you?) also sounded like a fscking brilliant idea, but in realilty it doesn't matter and I keep mixing it up. Chromosomes are split into contigs at long stretches of Ns, contigs are separated by single gaps and the first and last ones terminate in a gap at either side. This means you can start anywhere and safely run forward or backward until you hit a gap. - Index handling and creation (files index.h, index.cc, dnaindex.cc) The index is quite simple: oligos are mapped to integer offsets, a first level array contains a pointer to a second array for each of the possible oligos, and the second level array contains one long list of positions where these oligos were found. Only the forward strand is indexed, but lookup is of course done for both strands. (This primitive thing seems such a waste when the much better FM-index family is just out of reach... to bad, for now.) - Handling of reads (files sequence.h and sequence.cc) Just a simple structure for sequences with quality scores and a FastA/FastQ/FourQ reader. There's no support for mate pairs, I haven't even decided what to do about them. - File formats (genome, index, config file, output) Genome and index files are documented somewhere in the code. Metadata, config, complex output, etc. is encapsulated in protobuf messages. That way I don't need to mess with parsers and pretty printers and the messages are extensible. The two .proto files are more or less finalized, but it's easy to change them without breaking stuff, which also means you should think before changing them. - The aligner (align.h, align.cc) Completely rewritten now, it is much faster than the previous version and practically finished. The general structure and the specific alignment mechanisms are somewhat separated from each other, making extensions like a special 454 aligner possible at least in principle. Copyright Anfo is (C) 2009 by Udo Stenzel ANFO is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . anfo-0.98/configure.ac0000644000371600007640000000426711447120161011622 00000000000000# -*- Autoconf -*- # Process this file with autoconf to produce a configure script. AC_PREREQ(2.60) AC_INIT([anfo], [0.98], [udo_stenzel@eva.mpg.de]) AM_INIT_AUTOMAKE([-Wall -Werror foreign]) AC_CONFIG_SRCDIR([src/util.cc]) AC_CONFIG_HEADER([config.h]) AC_CONFIG_MACRO_DIR([m4]) # Checks for programs. 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" >&6; } if test "${ac_cv_path_FGREP+set}" = set; then $as_echo_n "(cached) " >&6 else if echo 'ab*c' | $GREP -F 'ab*c' >/dev/null 2>&1 then ac_cv_path_FGREP="$GREP -F" else if test -z "$FGREP"; then ac_path_FGREP_found=false # Loop through the user's path and test for each of PROGNAME-LIST as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_prog in fgrep; do for ac_exec_ext in '' $ac_executable_extensions; do ac_path_FGREP="$as_dir/$ac_prog$ac_exec_ext" { test -f "$ac_path_FGREP" && $as_test_x "$ac_path_FGREP"; } || continue # Check for GNU ac_path_FGREP and select it if it is found. # Check for GNU $ac_path_FGREP case `"$ac_path_FGREP" --version 2>&1` in *GNU*) ac_cv_path_FGREP="$ac_path_FGREP" ac_path_FGREP_found=:;; *) ac_count=0 $as_echo_n 0123456789 >"conftest.in" while : do cat "conftest.in" "conftest.in" >"conftest.tmp" mv "conftest.tmp" "conftest.in" cp "conftest.in" "conftest.nl" $as_echo 'FGREP' >> "conftest.nl" "$ac_path_FGREP" FGREP < "conftest.nl" >"conftest.out" 2>/dev/null || break diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break ac_count=`expr $ac_count + 1` if test $ac_count -gt ${ac_path_FGREP_max-0}; then # Best one so far, save it but keep looking for a better one ac_cv_path_FGREP="$ac_path_FGREP" ac_path_FGREP_max=$ac_count fi # 10*(2^10) chars as input seems more than enough test $ac_count -gt 10 && break done rm -f conftest.in conftest.tmp conftest.nl conftest.out;; esac $ac_path_FGREP_found && break 3 done done done IFS=$as_save_IFS if test -z "$ac_cv_path_FGREP"; then { { $as_echo "$as_me:$LINENO: error: no acceptable fgrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&5 $as_echo "$as_me: error: no acceptable fgrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&2;} { (exit 1); exit 1; }; } fi else ac_cv_path_FGREP=$FGREP fi fi fi { $as_echo "$as_me:$LINENO: result: $ac_cv_path_FGREP" >&5 $as_echo "$ac_cv_path_FGREP" >&6; } FGREP="$ac_cv_path_FGREP" test -z "$GREP" && GREP=grep # Check whether --with-gnu-ld was given. if test "${with_gnu_ld+set}" = set; then withval=$with_gnu_ld; test "$withval" = no || with_gnu_ld=yes else with_gnu_ld=no fi ac_prog=ld if test "$GCC" = yes; then # Check if gcc -print-prog-name=ld gives a path. { $as_echo "$as_me:$LINENO: checking for ld used by $CC" >&5 $as_echo_n "checking for ld used by $CC... 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" >&6; } if test "${lt_cv_prog_gnu_ld+set}" = set; then $as_echo_n "(cached) " >&6 else # I'd rather use --version here, but apparently some GNU lds only accept -v. case `$LD -v 2>&1 &5 $as_echo "$lt_cv_prog_gnu_ld" >&6; } with_gnu_ld=$lt_cv_prog_gnu_ld { $as_echo "$as_me:$LINENO: checking for BSD- or MS-compatible name lister (nm)" >&5 $as_echo_n "checking for BSD- or MS-compatible name lister (nm)... 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" >&6; } if test "${lt_cv_nm_interface+set}" = set; then $as_echo_n "(cached) " >&6 else lt_cv_nm_interface="BSD nm" echo "int some_variable = 0;" > conftest.$ac_ext (eval echo "\"\$as_me:4351: $ac_compile\"" >&5) (eval "$ac_compile" 2>conftest.err) cat conftest.err >&5 (eval echo "\"\$as_me:4354: $NM \\\"conftest.$ac_objext\\\"\"" >&5) (eval "$NM \"conftest.$ac_objext\"" 2>conftest.err > conftest.out) cat conftest.err >&5 (eval echo "\"\$as_me:4357: output\"" >&5) cat conftest.out >&5 if $GREP 'External.*some_variable' conftest.out > /dev/null; then lt_cv_nm_interface="MS dumpbin" fi rm -f conftest* fi { $as_echo "$as_me:$LINENO: result: $lt_cv_nm_interface" >&5 $as_echo "$lt_cv_nm_interface" >&6; } { $as_echo "$as_me:$LINENO: checking whether ln -s works" >&5 $as_echo_n "checking whether ln -s works... 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Even if it were fixed, the result of this # check would be larger than it should be. lt_cv_sys_max_cmd_len=12288; # 12K is about right ;; gnu*) # Under GNU Hurd, this test is not required because there is # no limit to the length of command line arguments. # Libtool will interpret -1 as no limit whatsoever lt_cv_sys_max_cmd_len=-1; ;; cygwin* | mingw* | cegcc*) # On Win9x/ME, this test blows up -- it succeeds, but takes # about 5 minutes as the teststring grows exponentially. # Worse, since 9x/ME are not pre-emptively multitasking, # you end up with a "frozen" computer, even though with patience # the test eventually succeeds (with a max line length of 256k). # Instead, let's just punt: use the minimum linelength reported by # all of the supported platforms: 8192 (on NT/2K/XP). lt_cv_sys_max_cmd_len=8192; ;; amigaos*) # On AmigaOS with pdksh, this test takes hours, literally. # So we just punt and use a minimum line length of 8192. lt_cv_sys_max_cmd_len=8192; ;; netbsd* | freebsd* | openbsd* | darwin* | dragonfly*) # This has been around since 386BSD, at least. Likely further. if test -x /sbin/sysctl; then lt_cv_sys_max_cmd_len=`/sbin/sysctl -n kern.argmax` elif test -x /usr/sbin/sysctl; then lt_cv_sys_max_cmd_len=`/usr/sbin/sysctl -n kern.argmax` else lt_cv_sys_max_cmd_len=65536 # usable default for all BSDs fi # And add a safety zone lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4` lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3` ;; interix*) # We know the value 262144 and hardcode it with a safety zone (like BSD) lt_cv_sys_max_cmd_len=196608 ;; osf*) # Dr. Hans Ekkehard Plesser reports seeing a kernel panic running configure # due to this test when exec_disable_arg_limit is 1 on Tru64. It is not # nice to cause kernel panics so lets avoid the loop below. # First set a reasonable default. lt_cv_sys_max_cmd_len=16384 # if test -x /sbin/sysconfig; then case `/sbin/sysconfig -q proc exec_disable_arg_limit` in *1*) lt_cv_sys_max_cmd_len=-1 ;; esac fi ;; sco3.2v5*) lt_cv_sys_max_cmd_len=102400 ;; sysv5* | sco5v6* | sysv4.2uw2*) kargmax=`grep ARG_MAX /etc/conf/cf.d/stune 2>/dev/null` if test -n "$kargmax"; then lt_cv_sys_max_cmd_len=`echo $kargmax | sed 's/.*[ ]//'` else lt_cv_sys_max_cmd_len=32768 fi ;; *) lt_cv_sys_max_cmd_len=`(getconf ARG_MAX) 2> /dev/null` if test -n "$lt_cv_sys_max_cmd_len"; then lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4` lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3` else # Make teststring a little bigger before we do anything with it. # a 1K string should be a reasonable start. for i in 1 2 3 4 5 6 7 8 ; do teststring=$teststring$teststring done SHELL=${SHELL-${CONFIG_SHELL-/bin/sh}} # If test is not a shell built-in, we'll probably end up computing a # maximum length that is only half of the actual maximum length, but # we can't tell. while { test "X"`$SHELL $0 --fallback-echo "X$teststring$teststring" 2>/dev/null` \ = "XX$teststring$teststring"; } >/dev/null 2>&1 && test $i != 17 # 1/2 MB should be enough do i=`expr $i + 1` teststring=$teststring$teststring done # Only check the string length outside the loop. lt_cv_sys_max_cmd_len=`expr "X$teststring" : ".*" 2>&1` teststring= # Add a significant safety factor because C++ compilers can tack on # massive amounts of additional arguments before passing them to the # linker. It appears as though 1/2 is a usable value. lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 2` fi ;; esac fi if test -n $lt_cv_sys_max_cmd_len ; then { $as_echo "$as_me:$LINENO: result: $lt_cv_sys_max_cmd_len" >&5 $as_echo "$lt_cv_sys_max_cmd_len" >&6; } else { $as_echo "$as_me:$LINENO: result: none" >&5 $as_echo "none" >&6; } fi max_cmd_len=$lt_cv_sys_max_cmd_len : ${CP="cp -f"} : ${MV="mv -f"} : ${RM="rm -f"} { $as_echo "$as_me:$LINENO: checking whether the shell understands some XSI constructs" >&5 $as_echo_n "checking whether the shell understands some XSI constructs... " >&6; } # Try some XSI features xsi_shell=no ( _lt_dummy="a/b/c" test "${_lt_dummy##*/},${_lt_dummy%/*},"${_lt_dummy%"$_lt_dummy"}, \ = c,a/b,, \ && eval 'test $(( 1 + 1 )) -eq 2 \ && test "${#_lt_dummy}" -eq 5' ) >/dev/null 2>&1 \ && xsi_shell=yes { $as_echo "$as_me:$LINENO: result: $xsi_shell" >&5 $as_echo "$xsi_shell" >&6; } { $as_echo "$as_me:$LINENO: checking whether the shell understands \"+=\"" >&5 $as_echo_n "checking whether the shell understands \"+=\"... " >&6; } lt_shell_append=no ( foo=bar; set foo baz; eval "$1+=\$2" && test "$foo" = barbaz ) \ >/dev/null 2>&1 \ && lt_shell_append=yes { $as_echo "$as_me:$LINENO: result: $lt_shell_append" >&5 $as_echo "$lt_shell_append" >&6; } if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then lt_unset=unset else lt_unset=false fi # test EBCDIC or ASCII case `echo X|tr X '\101'` in A) # ASCII based system # \n is not interpreted correctly by Solaris 8 /usr/ucb/tr lt_SP2NL='tr \040 \012' lt_NL2SP='tr \015\012 \040\040' ;; *) # EBCDIC based system lt_SP2NL='tr \100 \n' lt_NL2SP='tr \r\n \100\100' ;; esac { $as_echo "$as_me:$LINENO: checking for $LD option to reload object files" >&5 $as_echo_n "checking for $LD option to reload object files... " >&6; } if test "${lt_cv_ld_reload_flag+set}" = set; then $as_echo_n "(cached) " >&6 else lt_cv_ld_reload_flag='-r' fi { $as_echo "$as_me:$LINENO: result: $lt_cv_ld_reload_flag" >&5 $as_echo "$lt_cv_ld_reload_flag" >&6; } reload_flag=$lt_cv_ld_reload_flag case $reload_flag in "" | " "*) ;; *) reload_flag=" $reload_flag" ;; esac reload_cmds='$LD$reload_flag -o $output$reload_objs' case $host_os in darwin*) if test "$GCC" = yes; then reload_cmds='$LTCC $LTCFLAGS -nostdlib ${wl}-r -o $output$reload_objs' else reload_cmds='$LD$reload_flag -o $output$reload_objs' fi ;; esac if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}objdump", so it can be a program name with args. set dummy ${ac_tool_prefix}objdump; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_OBJDUMP+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$OBJDUMP"; then ac_cv_prog_OBJDUMP="$OBJDUMP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_OBJDUMP="${ac_tool_prefix}objdump" $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi OBJDUMP=$ac_cv_prog_OBJDUMP if test -n "$OBJDUMP"; then { $as_echo "$as_me:$LINENO: result: $OBJDUMP" >&5 $as_echo "$OBJDUMP" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_OBJDUMP"; then ac_ct_OBJDUMP=$OBJDUMP # Extract the first word of "objdump", so it can be a program name with args. set dummy objdump; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_OBJDUMP+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_OBJDUMP"; then ac_cv_prog_ac_ct_OBJDUMP="$ac_ct_OBJDUMP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_OBJDUMP="objdump" $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_OBJDUMP=$ac_cv_prog_ac_ct_OBJDUMP if test -n "$ac_ct_OBJDUMP"; then { $as_echo "$as_me:$LINENO: result: $ac_ct_OBJDUMP" >&5 $as_echo "$ac_ct_OBJDUMP" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_OBJDUMP" = x; then OBJDUMP="false" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac OBJDUMP=$ac_ct_OBJDUMP fi else OBJDUMP="$ac_cv_prog_OBJDUMP" fi test -z "$OBJDUMP" && OBJDUMP=objdump { $as_echo "$as_me:$LINENO: checking how to recognize dependent libraries" >&5 $as_echo_n "checking how to recognize dependent libraries... " >&6; } if test "${lt_cv_deplibs_check_method+set}" = set; then $as_echo_n "(cached) " >&6 else lt_cv_file_magic_cmd='$MAGIC_CMD' lt_cv_file_magic_test_file= lt_cv_deplibs_check_method='unknown' # Need to set the preceding variable on all platforms that support # interlibrary dependencies. # 'none' -- dependencies not supported. # `unknown' -- same as none, but documents that we really don't know. # 'pass_all' -- all dependencies passed with no checks. # 'test_compile' -- check by making test program. # 'file_magic [[regex]]' -- check by looking for files in library path # which responds to the $file_magic_cmd with a given extended regex. # If you have `file' or equivalent on your system and you're not sure # whether `pass_all' will *always* work, you probably want this one. case $host_os in aix[4-9]*) lt_cv_deplibs_check_method=pass_all ;; beos*) lt_cv_deplibs_check_method=pass_all ;; bsdi[45]*) lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (shared object|dynamic lib)' lt_cv_file_magic_cmd='/usr/bin/file -L' lt_cv_file_magic_test_file=/shlib/libc.so ;; cygwin*) # func_win32_libid is a shell function defined in ltmain.sh lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL' lt_cv_file_magic_cmd='func_win32_libid' ;; mingw* | pw32*) # Base MSYS/MinGW do not provide the 'file' command needed by # func_win32_libid shell function, so use a weaker test based on 'objdump', # unless we find 'file', for example because we are cross-compiling. if ( file / ) >/dev/null 2>&1; then lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL' lt_cv_file_magic_cmd='func_win32_libid' else lt_cv_deplibs_check_method='file_magic file format pei*-i386(.*architecture: i386)?' lt_cv_file_magic_cmd='$OBJDUMP -f' fi ;; cegcc) # use the weaker test based on 'objdump'. See mingw*. lt_cv_deplibs_check_method='file_magic file format pe-arm-.*little(.*architecture: arm)?' lt_cv_file_magic_cmd='$OBJDUMP -f' ;; darwin* | rhapsody*) lt_cv_deplibs_check_method=pass_all ;; freebsd* | dragonfly*) if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then case $host_cpu in i*86 ) # Not sure whether the presence of OpenBSD here was a mistake. # Let's accept both of them until this is cleared up. lt_cv_deplibs_check_method='file_magic (FreeBSD|OpenBSD|DragonFly)/i[3-9]86 (compact )?demand paged shared library' lt_cv_file_magic_cmd=/usr/bin/file lt_cv_file_magic_test_file=`echo /usr/lib/libc.so.*` ;; esac else lt_cv_deplibs_check_method=pass_all fi ;; gnu*) lt_cv_deplibs_check_method=pass_all ;; hpux10.20* | hpux11*) lt_cv_file_magic_cmd=/usr/bin/file case $host_cpu in ia64*) lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - IA64' lt_cv_file_magic_test_file=/usr/lib/hpux32/libc.so ;; hppa*64*) lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - PA-RISC [0-9].[0-9]' lt_cv_file_magic_test_file=/usr/lib/pa20_64/libc.sl ;; *) lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|PA-RISC[0-9].[0-9]) shared library' lt_cv_file_magic_test_file=/usr/lib/libc.sl ;; esac ;; interix[3-9]*) # PIC code is broken on Interix 3.x, that's why |\.a not |_pic\.a here lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|\.a)$' ;; irix5* | irix6* | nonstopux*) case $LD in *-32|*"-32 ") libmagic=32-bit;; *-n32|*"-n32 ") libmagic=N32;; *-64|*"-64 ") libmagic=64-bit;; *) libmagic=never-match;; esac lt_cv_deplibs_check_method=pass_all ;; # This must be Linux ELF. linux* | k*bsd*-gnu) lt_cv_deplibs_check_method=pass_all ;; netbsd* | netbsdelf*-gnu) if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$' else lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|_pic\.a)$' fi ;; newos6*) lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (executable|dynamic lib)' lt_cv_file_magic_cmd=/usr/bin/file lt_cv_file_magic_test_file=/usr/lib/libnls.so ;; *nto* | *qnx*) lt_cv_deplibs_check_method=pass_all ;; openbsd*) if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|\.so|_pic\.a)$' else lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$' fi ;; osf3* | osf4* | osf5*) lt_cv_deplibs_check_method=pass_all ;; rdos*) lt_cv_deplibs_check_method=pass_all ;; solaris*) lt_cv_deplibs_check_method=pass_all ;; sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*) lt_cv_deplibs_check_method=pass_all ;; sysv4 | sysv4.3*) case $host_vendor in motorola) lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (shared object|dynamic lib) M[0-9][0-9]* Version [0-9]' lt_cv_file_magic_test_file=`echo /usr/lib/libc.so*` ;; ncr) lt_cv_deplibs_check_method=pass_all ;; sequent) lt_cv_file_magic_cmd='/bin/file' lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [LM]SB (shared object|dynamic lib )' ;; sni) lt_cv_file_magic_cmd='/bin/file' lt_cv_deplibs_check_method="file_magic ELF [0-9][0-9]*-bit [LM]SB dynamic lib" lt_cv_file_magic_test_file=/lib/libc.so ;; siemens) lt_cv_deplibs_check_method=pass_all ;; pc) lt_cv_deplibs_check_method=pass_all ;; esac ;; tpf*) lt_cv_deplibs_check_method=pass_all ;; esac fi { $as_echo "$as_me:$LINENO: result: $lt_cv_deplibs_check_method" >&5 $as_echo "$lt_cv_deplibs_check_method" >&6; } file_magic_cmd=$lt_cv_file_magic_cmd deplibs_check_method=$lt_cv_deplibs_check_method test -z "$deplibs_check_method" && deplibs_check_method=unknown if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}ar", so it can be a program name with args. set dummy ${ac_tool_prefix}ar; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_AR+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$AR"; then ac_cv_prog_AR="$AR" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_AR="${ac_tool_prefix}ar" $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi AR=$ac_cv_prog_AR if test -n "$AR"; then { $as_echo "$as_me:$LINENO: result: $AR" >&5 $as_echo "$AR" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_AR"; then ac_ct_AR=$AR # Extract the first word of "ar", so it can be a program name with args. set dummy ar; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_AR+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_AR"; then ac_cv_prog_ac_ct_AR="$ac_ct_AR" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_AR="ar" $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_AR=$ac_cv_prog_ac_ct_AR if test -n "$ac_ct_AR"; then { $as_echo "$as_me:$LINENO: result: $ac_ct_AR" >&5 $as_echo "$ac_ct_AR" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_AR" = x; then AR="false" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac AR=$ac_ct_AR fi else AR="$ac_cv_prog_AR" fi test -z "$AR" && AR=ar test -z "$AR_FLAGS" && AR_FLAGS=cru if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args. set dummy ${ac_tool_prefix}strip; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_STRIP+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$STRIP"; then ac_cv_prog_STRIP="$STRIP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_STRIP="${ac_tool_prefix}strip" $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi STRIP=$ac_cv_prog_STRIP if test -n "$STRIP"; then { $as_echo "$as_me:$LINENO: result: $STRIP" >&5 $as_echo "$STRIP" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_STRIP"; then ac_ct_STRIP=$STRIP # Extract the first word of "strip", so it can be a program name with args. set dummy strip; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_STRIP"; then ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_STRIP="strip" $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP if test -n "$ac_ct_STRIP"; then { $as_echo "$as_me:$LINENO: result: $ac_ct_STRIP" >&5 $as_echo "$ac_ct_STRIP" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_STRIP" = x; then STRIP=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac STRIP=$ac_ct_STRIP fi else STRIP="$ac_cv_prog_STRIP" fi test -z "$STRIP" && STRIP=: if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args. set dummy ${ac_tool_prefix}ranlib; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_RANLIB+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$RANLIB"; then ac_cv_prog_RANLIB="$RANLIB" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib" $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi RANLIB=$ac_cv_prog_RANLIB if test -n "$RANLIB"; then { $as_echo "$as_me:$LINENO: result: $RANLIB" >&5 $as_echo "$RANLIB" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_RANLIB"; then ac_ct_RANLIB=$RANLIB # Extract the first word of "ranlib", so it can be a program name with args. set dummy ranlib; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_RANLIB+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_RANLIB"; then ac_cv_prog_ac_ct_RANLIB="$ac_ct_RANLIB" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_RANLIB="ranlib" $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_RANLIB=$ac_cv_prog_ac_ct_RANLIB if test -n "$ac_ct_RANLIB"; then { $as_echo "$as_me:$LINENO: result: $ac_ct_RANLIB" >&5 $as_echo "$ac_ct_RANLIB" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_RANLIB" = x; then RANLIB=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac RANLIB=$ac_ct_RANLIB fi else RANLIB="$ac_cv_prog_RANLIB" fi test -z "$RANLIB" && RANLIB=: # Determine commands to create old-style static archives. old_archive_cmds='$AR $AR_FLAGS $oldlib$oldobjs' old_postinstall_cmds='chmod 644 $oldlib' old_postuninstall_cmds= if test -n "$RANLIB"; then case $host_os in openbsd*) old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$oldlib" ;; *) old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$oldlib" ;; esac old_archive_cmds="$old_archive_cmds~\$RANLIB \$oldlib" fi # If no C compiler was specified, use CC. LTCC=${LTCC-"$CC"} # If no C compiler flags were specified, use CFLAGS. LTCFLAGS=${LTCFLAGS-"$CFLAGS"} # Allow CC to be a program name with arguments. compiler=$CC # Check for command to grab the raw symbol name followed by C symbol from nm. { $as_echo "$as_me:$LINENO: checking command to parse $NM output from $compiler object" >&5 $as_echo_n "checking command to parse $NM output from $compiler object... " >&6; } if test "${lt_cv_sys_global_symbol_pipe+set}" = set; then $as_echo_n "(cached) " >&6 else # These are sane defaults that work on at least a few old systems. # [They come from Ultrix. What could be older than Ultrix?!! ;)] # Character class describing NM global symbol codes. symcode='[BCDEGRST]' # Regexp to match symbols that can be accessed directly from C. sympat='\([_A-Za-z][_A-Za-z0-9]*\)' # Define system-specific variables. case $host_os in aix*) symcode='[BCDT]' ;; cygwin* | mingw* | pw32* | cegcc*) symcode='[ABCDGISTW]' ;; hpux*) if test "$host_cpu" = ia64; then symcode='[ABCDEGRST]' fi ;; irix* | nonstopux*) symcode='[BCDEGRST]' ;; osf*) symcode='[BCDEGQRST]' ;; solaris*) symcode='[BDRT]' ;; sco3.2v5*) symcode='[DT]' ;; sysv4.2uw2*) symcode='[DT]' ;; sysv5* | sco5v6* | unixware* | OpenUNIX*) symcode='[ABDT]' ;; sysv4) symcode='[DFNSTU]' ;; esac # If we're using GNU nm, then use its standard symbol codes. case `$NM -V 2>&1` in *GNU* | *'with BFD'*) symcode='[ABCDGIRSTW]' ;; esac # Transform an extracted symbol line into a proper C declaration. # Some systems (esp. on ia64) link data and code symbols differently, # so use this general approach. lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'" # Transform an extracted symbol line into symbol name and symbol address lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([^ ]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"\2\", (void *) \&\2},/p'" lt_cv_sys_global_symbol_to_c_name_address_lib_prefix="sed -n -e 's/^: \([^ ]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([^ ]*\) \(lib[^ ]*\)$/ {\"\2\", (void *) \&\2},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"lib\2\", (void *) \&\2},/p'" # Handle CRLF in mingw tool chain opt_cr= case $build_os in mingw*) opt_cr=`$ECHO 'x\{0,1\}' | tr x '\015'` # option cr in regexp ;; esac # Try without a prefix underscore, then with it. for ac_symprfx in "" "_"; do # Transform symcode, sympat, and symprfx into a raw symbol and a C symbol. symxfrm="\\1 $ac_symprfx\\2 \\2" # Write the raw and C identifiers. if test "$lt_cv_nm_interface" = "MS dumpbin"; then # Fake it for dumpbin and say T for any non-static function # and D for any global variable. # Also find C++ and __fastcall symbols from MSVC++, # which start with @ or ?. lt_cv_sys_global_symbol_pipe="$AWK '"\ " {last_section=section; section=\$ 3};"\ " /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\ " \$ 0!~/External *\|/{next};"\ " / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\ " {if(hide[section]) next};"\ " {f=0}; \$ 0~/\(\).*\|/{f=1}; {printf f ? \"T \" : \"D \"};"\ " {split(\$ 0, a, /\||\r/); split(a[2], s)};"\ " s[1]~/^[@?]/{print s[1], s[1]; next};"\ " s[1]~prfx {split(s[1],t,\"@\"); print t[1], substr(t[1],length(prfx))}"\ " ' prfx=^$ac_symprfx" else lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[ ]\($symcode$symcode*\)[ ][ ]*$ac_symprfx$sympat$opt_cr$/$symxfrm/p'" fi # Check to see that the pipe works correctly. pipe_works=no rm -f conftest* cat > conftest.$ac_ext <<_LT_EOF #ifdef __cplusplus extern "C" { #endif char nm_test_var; void nm_test_func(void); void nm_test_func(void){} #ifdef __cplusplus } #endif int main(){nm_test_var='a';nm_test_func();return(0);} _LT_EOF if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; then # Now try to grab the symbols. nlist=conftest.nm if { (eval echo "$as_me:$LINENO: \"$NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist\"") >&5 (eval $NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist) 2>&5 ac_status=$? $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && test -s "$nlist"; then # Try sorting and uniquifying the output. if sort "$nlist" | uniq > "$nlist"T; then mv -f "$nlist"T "$nlist" else rm -f "$nlist"T fi # Make sure that we snagged all the symbols we need. if $GREP ' nm_test_var$' "$nlist" >/dev/null; then if $GREP ' nm_test_func$' "$nlist" >/dev/null; then cat <<_LT_EOF > conftest.$ac_ext #ifdef __cplusplus extern "C" { #endif _LT_EOF # Now generate the symbol file. eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | $GREP -v main >> conftest.$ac_ext' cat <<_LT_EOF >> conftest.$ac_ext /* The mapping between symbol names and symbols. */ const struct { const char *name; void *address; } lt__PROGRAM__LTX_preloaded_symbols[] = { { "@PROGRAM@", (void *) 0 }, _LT_EOF $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (void *) \&\2},/" < "$nlist" | $GREP -v main >> conftest.$ac_ext cat <<\_LT_EOF >> conftest.$ac_ext {0, (void *) 0} }; /* This works around a problem in FreeBSD linker */ #ifdef FREEBSD_WORKAROUND static const void *lt_preloaded_setup() { return lt__PROGRAM__LTX_preloaded_symbols; } #endif #ifdef __cplusplus } #endif _LT_EOF # Now try linking the two files. mv conftest.$ac_objext conftstm.$ac_objext lt_save_LIBS="$LIBS" lt_save_CFLAGS="$CFLAGS" LIBS="conftstm.$ac_objext" CFLAGS="$CFLAGS$lt_prog_compiler_no_builtin_flag" if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>&5 ac_status=$? $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && test -s conftest${ac_exeext}; then pipe_works=yes fi LIBS="$lt_save_LIBS" CFLAGS="$lt_save_CFLAGS" else echo "cannot find nm_test_func in $nlist" >&5 fi else echo "cannot find nm_test_var in $nlist" >&5 fi else echo "cannot run $lt_cv_sys_global_symbol_pipe" >&5 fi else echo "$progname: failed program was:" >&5 cat conftest.$ac_ext >&5 fi rm -rf conftest* conftst* # Do not use the global_symbol_pipe unless it works. if test "$pipe_works" = yes; then break else lt_cv_sys_global_symbol_pipe= fi done fi if test -z "$lt_cv_sys_global_symbol_pipe"; then lt_cv_sys_global_symbol_to_cdecl= fi if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then { $as_echo "$as_me:$LINENO: result: failed" >&5 $as_echo "failed" >&6; } else { $as_echo "$as_me:$LINENO: result: ok" >&5 $as_echo "ok" >&6; } fi # Check whether --enable-libtool-lock was given. if test "${enable_libtool_lock+set}" = set; then enableval=$enable_libtool_lock; fi test "x$enable_libtool_lock" != xno && enable_libtool_lock=yes # Some flags need to be propagated to the compiler or linker for good # libtool support. case $host in ia64-*-hpux*) # Find out which ABI we are using. echo 'int i;' > conftest.$ac_ext if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; then case `/usr/bin/file conftest.$ac_objext` in *ELF-32*) HPUX_IA64_MODE="32" ;; *ELF-64*) HPUX_IA64_MODE="64" ;; esac fi rm -rf conftest* ;; *-*-irix6*) # Find out which ABI we are using. echo '#line 5563 "configure"' > conftest.$ac_ext if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; then if test "$lt_cv_prog_gnu_ld" = yes; then case `/usr/bin/file conftest.$ac_objext` in *32-bit*) LD="${LD-ld} -melf32bsmip" ;; *N32*) LD="${LD-ld} -melf32bmipn32" ;; *64-bit*) LD="${LD-ld} -melf64bmip" ;; esac else case `/usr/bin/file conftest.$ac_objext` in *32-bit*) LD="${LD-ld} -32" ;; *N32*) LD="${LD-ld} -n32" ;; *64-bit*) LD="${LD-ld} -64" ;; esac fi fi rm -rf conftest* ;; x86_64-*kfreebsd*-gnu|x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*| \ s390*-*linux*|s390*-*tpf*|sparc*-*linux*) # Find out which ABI we are using. echo 'int i;' > conftest.$ac_ext if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; then case `/usr/bin/file conftest.o` in *32-bit*) case $host in x86_64-*kfreebsd*-gnu) LD="${LD-ld} -m elf_i386_fbsd" ;; x86_64-*linux*) LD="${LD-ld} -m elf_i386" ;; ppc64-*linux*|powerpc64-*linux*) LD="${LD-ld} -m elf32ppclinux" ;; s390x-*linux*) LD="${LD-ld} -m elf_s390" ;; sparc64-*linux*) LD="${LD-ld} -m elf32_sparc" ;; esac ;; *64-bit*) case $host in x86_64-*kfreebsd*-gnu) LD="${LD-ld} -m elf_x86_64_fbsd" ;; x86_64-*linux*) LD="${LD-ld} -m elf_x86_64" ;; ppc*-*linux*|powerpc*-*linux*) LD="${LD-ld} -m elf64ppc" ;; s390*-*linux*|s390*-*tpf*) LD="${LD-ld} -m elf64_s390" ;; sparc*-*linux*) LD="${LD-ld} -m elf64_sparc" ;; esac ;; esac fi rm -rf conftest* ;; *-*-sco3.2v5*) # On SCO OpenServer 5, we need -belf to get full-featured binaries. SAVE_CFLAGS="$CFLAGS" CFLAGS="$CFLAGS -belf" { $as_echo "$as_me:$LINENO: checking whether the C compiler needs -belf" >&5 $as_echo_n "checking whether the C compiler needs -belf... " >&6; } if test "${lt_cv_cc_needs_belf+set}" = set; then $as_echo_n "(cached) " >&6 else ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int main () { ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (ac_try="$ac_link" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" $as_echo "$ac_try_echo") >&5 (eval "$ac_link") 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { test -z "$ac_c_werror_flag" || test ! -s conftest.err } && test -s conftest$ac_exeext && { test "$cross_compiling" = yes || $as_test_x conftest$ac_exeext }; then lt_cv_cc_needs_belf=yes else $as_echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 lt_cv_cc_needs_belf=no fi rm -rf conftest.dSYM rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ conftest$ac_exeext conftest.$ac_ext ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu fi { $as_echo "$as_me:$LINENO: result: $lt_cv_cc_needs_belf" >&5 $as_echo "$lt_cv_cc_needs_belf" >&6; } if test x"$lt_cv_cc_needs_belf" != x"yes"; then # this is probably gcc 2.8.0, egcs 1.0 or newer; no need for -belf CFLAGS="$SAVE_CFLAGS" fi ;; sparc*-*solaris*) # Find out which ABI we are using. echo 'int i;' > conftest.$ac_ext if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; then case `/usr/bin/file conftest.o` in *64-bit*) case $lt_cv_prog_gnu_ld in yes*) LD="${LD-ld} -m elf64_sparc" ;; *) if ${LD-ld} -64 -r -o conftest2.o conftest.o >/dev/null 2>&1; then LD="${LD-ld} -64" fi ;; esac ;; esac fi rm -rf conftest* ;; esac need_locks="$enable_libtool_lock" case $host_os in rhapsody* | darwin*) if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}dsymutil", so it can be a program name with args. set dummy ${ac_tool_prefix}dsymutil; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_DSYMUTIL+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$DSYMUTIL"; then ac_cv_prog_DSYMUTIL="$DSYMUTIL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_DSYMUTIL="${ac_tool_prefix}dsymutil" $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi DSYMUTIL=$ac_cv_prog_DSYMUTIL if test -n "$DSYMUTIL"; then { $as_echo "$as_me:$LINENO: result: $DSYMUTIL" >&5 $as_echo "$DSYMUTIL" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_DSYMUTIL"; then ac_ct_DSYMUTIL=$DSYMUTIL # Extract the first word of "dsymutil", so it can be a program name with args. set dummy dsymutil; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_DSYMUTIL+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_DSYMUTIL"; then ac_cv_prog_ac_ct_DSYMUTIL="$ac_ct_DSYMUTIL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_DSYMUTIL="dsymutil" $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_DSYMUTIL=$ac_cv_prog_ac_ct_DSYMUTIL if test -n "$ac_ct_DSYMUTIL"; then { $as_echo "$as_me:$LINENO: result: $ac_ct_DSYMUTIL" >&5 $as_echo "$ac_ct_DSYMUTIL" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_DSYMUTIL" = x; then DSYMUTIL=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac DSYMUTIL=$ac_ct_DSYMUTIL fi else DSYMUTIL="$ac_cv_prog_DSYMUTIL" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}nmedit", so it can be a program name with args. set dummy ${ac_tool_prefix}nmedit; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_NMEDIT+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$NMEDIT"; then ac_cv_prog_NMEDIT="$NMEDIT" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_NMEDIT="${ac_tool_prefix}nmedit" $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi NMEDIT=$ac_cv_prog_NMEDIT if test -n "$NMEDIT"; then { $as_echo "$as_me:$LINENO: result: $NMEDIT" >&5 $as_echo "$NMEDIT" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_NMEDIT"; then ac_ct_NMEDIT=$NMEDIT # Extract the first word of "nmedit", so it can be a program name with args. set dummy nmedit; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_NMEDIT+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_NMEDIT"; then ac_cv_prog_ac_ct_NMEDIT="$ac_ct_NMEDIT" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_NMEDIT="nmedit" $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_NMEDIT=$ac_cv_prog_ac_ct_NMEDIT if test -n "$ac_ct_NMEDIT"; then { $as_echo "$as_me:$LINENO: result: $ac_ct_NMEDIT" >&5 $as_echo "$ac_ct_NMEDIT" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_NMEDIT" = x; then NMEDIT=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac NMEDIT=$ac_ct_NMEDIT fi else NMEDIT="$ac_cv_prog_NMEDIT" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}lipo", so it can be a program name with args. set dummy ${ac_tool_prefix}lipo; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_LIPO+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$LIPO"; then ac_cv_prog_LIPO="$LIPO" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_LIPO="${ac_tool_prefix}lipo" $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi LIPO=$ac_cv_prog_LIPO if test -n "$LIPO"; then { $as_echo "$as_me:$LINENO: result: $LIPO" >&5 $as_echo "$LIPO" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_LIPO"; then ac_ct_LIPO=$LIPO # Extract the first word of "lipo", so it can be a program name with args. set dummy lipo; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_LIPO+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_LIPO"; then ac_cv_prog_ac_ct_LIPO="$ac_ct_LIPO" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_LIPO="lipo" $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_LIPO=$ac_cv_prog_ac_ct_LIPO if test -n "$ac_ct_LIPO"; then { $as_echo "$as_me:$LINENO: result: $ac_ct_LIPO" >&5 $as_echo "$ac_ct_LIPO" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_LIPO" = x; then LIPO=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac LIPO=$ac_ct_LIPO fi else LIPO="$ac_cv_prog_LIPO" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}otool", so it can be a program name with args. set dummy ${ac_tool_prefix}otool; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_OTOOL+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$OTOOL"; then ac_cv_prog_OTOOL="$OTOOL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_OTOOL="${ac_tool_prefix}otool" $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi OTOOL=$ac_cv_prog_OTOOL if test -n "$OTOOL"; then { $as_echo "$as_me:$LINENO: result: $OTOOL" >&5 $as_echo "$OTOOL" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_OTOOL"; then ac_ct_OTOOL=$OTOOL # Extract the first word of "otool", so it can be a program name with args. set dummy otool; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_OTOOL+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_OTOOL"; then ac_cv_prog_ac_ct_OTOOL="$ac_ct_OTOOL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_OTOOL="otool" $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_OTOOL=$ac_cv_prog_ac_ct_OTOOL if test -n "$ac_ct_OTOOL"; then { $as_echo "$as_me:$LINENO: result: $ac_ct_OTOOL" >&5 $as_echo "$ac_ct_OTOOL" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_OTOOL" = x; then OTOOL=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac OTOOL=$ac_ct_OTOOL fi else OTOOL="$ac_cv_prog_OTOOL" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}otool64", so it can be a program name with args. set dummy ${ac_tool_prefix}otool64; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_OTOOL64+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$OTOOL64"; then ac_cv_prog_OTOOL64="$OTOOL64" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_OTOOL64="${ac_tool_prefix}otool64" $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi OTOOL64=$ac_cv_prog_OTOOL64 if test -n "$OTOOL64"; then { $as_echo "$as_me:$LINENO: result: $OTOOL64" >&5 $as_echo "$OTOOL64" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_OTOOL64"; then ac_ct_OTOOL64=$OTOOL64 # Extract the first word of "otool64", so it can be a program name with args. set dummy otool64; ac_word=$2 { $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_OTOOL64+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_OTOOL64"; then ac_cv_prog_ac_ct_OTOOL64="$ac_ct_OTOOL64" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_OTOOL64="otool64" $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_OTOOL64=$ac_cv_prog_ac_ct_OTOOL64 if test -n "$ac_ct_OTOOL64"; then { $as_echo "$as_me:$LINENO: result: $ac_ct_OTOOL64" >&5 $as_echo "$ac_ct_OTOOL64" >&6; } else { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_OTOOL64" = x; then OTOOL64=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac OTOOL64=$ac_ct_OTOOL64 fi else OTOOL64="$ac_cv_prog_OTOOL64" fi { $as_echo "$as_me:$LINENO: checking for -single_module linker flag" >&5 $as_echo_n "checking for -single_module linker flag... " >&6; } if test "${lt_cv_apple_cc_single_mod+set}" = set; then $as_echo_n "(cached) " >&6 else lt_cv_apple_cc_single_mod=no if test -z "${LT_MULTI_MODULE}"; then # By default we will add the -single_module flag. You can override # by either setting the environment variable LT_MULTI_MODULE # non-empty at configure time, or by adding -multi_module to the # link flags. rm -rf libconftest.dylib* echo "int foo(void){return 1;}" > conftest.c echo "$LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \ -dynamiclib -Wl,-single_module conftest.c" >&5 $LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \ -dynamiclib -Wl,-single_module conftest.c 2>conftest.err _lt_result=$? if test -f libconftest.dylib && test ! -s conftest.err && test $_lt_result = 0; then lt_cv_apple_cc_single_mod=yes else cat conftest.err >&5 fi rm -rf libconftest.dylib* rm -f conftest.* fi fi { $as_echo "$as_me:$LINENO: result: $lt_cv_apple_cc_single_mod" >&5 $as_echo "$lt_cv_apple_cc_single_mod" >&6; } { $as_echo "$as_me:$LINENO: checking for -exported_symbols_list linker flag" >&5 $as_echo_n "checking for -exported_symbols_list linker flag... " >&6; } if test "${lt_cv_ld_exported_symbols_list+set}" = set; then $as_echo_n "(cached) " >&6 else lt_cv_ld_exported_symbols_list=no save_LDFLAGS=$LDFLAGS echo "_main" > conftest.sym LDFLAGS="$LDFLAGS -Wl,-exported_symbols_list,conftest.sym" cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int main () { ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (ac_try="$ac_link" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" $as_echo "$ac_try_echo") >&5 (eval "$ac_link") 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { test -z "$ac_c_werror_flag" || test ! -s conftest.err } && test -s conftest$ac_exeext && { test "$cross_compiling" = yes || $as_test_x conftest$ac_exeext }; then lt_cv_ld_exported_symbols_list=yes else $as_echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 lt_cv_ld_exported_symbols_list=no fi rm -rf conftest.dSYM rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ conftest$ac_exeext conftest.$ac_ext LDFLAGS="$save_LDFLAGS" fi { $as_echo "$as_me:$LINENO: result: $lt_cv_ld_exported_symbols_list" >&5 $as_echo "$lt_cv_ld_exported_symbols_list" >&6; } case $host_os in rhapsody* | darwin1.[012]) _lt_dar_allow_undefined='${wl}-undefined ${wl}suppress' ;; darwin1.*) _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;; darwin*) # darwin 5.x on # if running on 10.5 or later, the deployment target defaults # to the OS version, if on x86, and 10.4, the deployment # target defaults to 10.4. Don't you love it? case ${MACOSX_DEPLOYMENT_TARGET-10.0},$host in 10.0,*86*-darwin8*|10.0,*-darwin[91]*) _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;; 10.[012]*) _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;; 10.*) _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;; esac ;; esac if test "$lt_cv_apple_cc_single_mod" = "yes"; then _lt_dar_single_mod='$single_module' fi if test "$lt_cv_ld_exported_symbols_list" = "yes"; then _lt_dar_export_syms=' ${wl}-exported_symbols_list,$output_objdir/${libname}-symbols.expsym' else _lt_dar_export_syms='~$NMEDIT -s $output_objdir/${libname}-symbols.expsym ${lib}' fi if test "$DSYMUTIL" != ":"; then _lt_dsymutil='~$DSYMUTIL $lib || :' else _lt_dsymutil= fi ;; esac ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu { $as_echo "$as_me:$LINENO: checking how to run the C preprocessor" >&5 $as_echo_n "checking how to run the C preprocessor... " >&6; } # On Suns, sometimes $CPP names a directory. if test -n "$CPP" && test -d "$CPP"; then CPP= fi if test -z "$CPP"; then if test "${ac_cv_prog_CPP+set}" = set; then $as_echo_n "(cached) " >&6 else # Double quotes because CPP needs to be expanded for CPP in "$CC -E" "$CC -E -traditional-cpp" "/lib/cpp" do ac_preproc_ok=false for ac_c_preproc_warn_flag in '' yes do # Use a header file that comes with gcc, so configuring glibc # with a fresh cross-compiler works. # Prefer to if __STDC__ is defined, since # exists even on freestanding compilers. # On the NeXT, cc -E runs the code through the compiler's parser, # not just through cpp. "Syntax error" is here to catch this case. cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #ifdef __STDC__ # include #else # include #endif Syntax error _ACEOF if { (ac_try="$ac_cpp conftest.$ac_ext" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" $as_echo "$ac_try_echo") >&5 (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } >/dev/null && { test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || test ! -s conftest.err }; then : else $as_echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 # Broken: fails on valid input. continue fi rm -f conftest.err conftest.$ac_ext # OK, works on sane cases. 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" >&6; } if test "${lt_cv_prog_compiler_rtti_exceptions+set}" = set; then $as_echo_n "(cached) " >&6 else lt_cv_prog_compiler_rtti_exceptions=no ac_outfile=conftest.$ac_objext echo "$lt_simple_compile_test_code" > conftest.$ac_ext lt_compiler_flag="-fno-rtti -fno-exceptions" # Insert the option either (1) after the last *FLAGS variable, or # (2) before a word containing "conftest.", or (3) at the end. # Note that $ac_compile itself does not contain backslashes and begins # with a dollar sign (not a hyphen), so the echo should work correctly. # The option is referenced via a variable to avoid confusing sed. lt_compile=`echo "$ac_compile" | $SED \ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \ -e 's:$: $lt_compiler_flag:'` (eval echo "\"\$as_me:7420: $lt_compile\"" >&5) (eval "$lt_compile" 2>conftest.err) ac_status=$? cat conftest.err >&5 echo "$as_me:7424: \$? = $ac_status" >&5 if (exit $ac_status) && test -s "$ac_outfile"; then # The compiler can only warn and ignore the option if not recognized # So say no if there are warnings other than the usual output. $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2 if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then lt_cv_prog_compiler_rtti_exceptions=yes fi fi $RM conftest* fi { $as_echo "$as_me:$LINENO: result: $lt_cv_prog_compiler_rtti_exceptions" >&5 $as_echo "$lt_cv_prog_compiler_rtti_exceptions" >&6; } if test x"$lt_cv_prog_compiler_rtti_exceptions" = xyes; then lt_prog_compiler_no_builtin_flag="$lt_prog_compiler_no_builtin_flag -fno-rtti -fno-exceptions" else : fi fi lt_prog_compiler_wl= lt_prog_compiler_pic= lt_prog_compiler_static= { $as_echo "$as_me:$LINENO: checking for $compiler option to produce PIC" >&5 $as_echo_n "checking for $compiler option to produce PIC... " >&6; } if test "$GCC" = yes; then lt_prog_compiler_wl='-Wl,' lt_prog_compiler_static='-static' case $host_os in aix*) # All AIX code is PIC. if test "$host_cpu" = ia64; then # AIX 5 now supports IA64 processor lt_prog_compiler_static='-Bstatic' fi ;; amigaos*) case $host_cpu in powerpc) # see comment about AmigaOS4 .so support lt_prog_compiler_pic='-fPIC' ;; m68k) # FIXME: we need at least 68020 code to build shared libraries, but # adding the `-m68020' flag to GCC prevents building anything better, # like `-m68040'. lt_prog_compiler_pic='-m68020 -resident32 -malways-restore-a4' ;; esac ;; beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*) # PIC is the default for these OSes. ;; mingw* | cygwin* | pw32* | os2* | cegcc*) # This hack is so that the source file can tell whether it is being # built for inclusion in a dll (and should export symbols for example). # Although the cygwin gcc ignores -fPIC, still need this for old-style # (--disable-auto-import) libraries lt_prog_compiler_pic='-DDLL_EXPORT' ;; darwin* | rhapsody*) # PIC is the default on this platform # Common symbols not allowed in MH_DYLIB files lt_prog_compiler_pic='-fno-common' ;; hpux*) # PIC is the default for 64-bit PA HP-UX, but not for 32-bit # PA HP-UX. 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If you *** really care for shared libraries, you may want to modify your PATH *** so that a non-GNU linker is found, and then restart. _LT_EOF fi ;; amigaos*) case $host_cpu in powerpc) # see comment about AmigaOS4 .so support archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' archive_expsym_cmds='' ;; m68k) archive_cmds='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)' hardcode_libdir_flag_spec='-L$libdir' hardcode_minus_L=yes ;; esac ;; beos*) if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then allow_undefined_flag=unsupported # Joseph Beckenbach says some releases of gcc # support --undefined. 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FIXME archive_cmds='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' else ld_shlibs=no fi ;; cygwin* | mingw* | pw32* | cegcc*) # _LT_TAGVAR(hardcode_libdir_flag_spec, ) is actually meaningless, # as there is no search path for DLLs. hardcode_libdir_flag_spec='-L$libdir' allow_undefined_flag=unsupported always_export_symbols=no enable_shared_with_static_runtimes=yes export_symbols_cmds='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[BCDGRS][ ]/s/.*[ ]\([^ ]*\)/\1 DATA/'\'' | $SED -e '\''/^[AITW][ ]/s/.*[ ]//'\'' | sort | uniq > $export_symbols' if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib' # If the export-symbols file already is a .def file (1st line # is EXPORTS), use it as is; otherwise, prepend... archive_expsym_cmds='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then cp $export_symbols $output_objdir/$soname.def; else echo EXPORTS > $output_objdir/$soname.def; cat $export_symbols >> $output_objdir/$soname.def; fi~ $CC -shared $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib' else ld_shlibs=no fi ;; interix[3-9]*) hardcode_direct=no hardcode_shlibpath_var=no hardcode_libdir_flag_spec='${wl}-rpath,$libdir' export_dynamic_flag_spec='${wl}-E' # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc. # Instead, shared libraries are loaded at an image base (0x10000000 by # default) and relocated if they conflict, which is a slow very memory # consuming and fragmenting process. To avoid this, we pick a random, # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link # time. Moving up from 0x10000000 also allows more sbrk(2) space. archive_cmds='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib' archive_expsym_cmds='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib' ;; gnu* | linux* | tpf* | k*bsd*-gnu) tmp_diet=no if test "$host_os" = linux-dietlibc; then case $cc_basename in diet\ *) tmp_diet=yes;; # linux-dietlibc with static linking (!diet-dyn) esac fi if $LD --help 2>&1 | $EGREP ': supported targets:.* elf' > /dev/null \ && test "$tmp_diet" = no then tmp_addflag= tmp_sharedflag='-shared' case $cc_basename,$host_cpu in pgcc*) # Portland Group C compiler whole_archive_flag_spec='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive' tmp_addflag=' $pic_flag' ;; pgf77* | pgf90* | pgf95*) # Portland Group f77 and f90 compilers whole_archive_flag_spec='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive' tmp_addflag=' $pic_flag -Mnomain' ;; ecc*,ia64* | icc*,ia64*) # Intel C compiler on ia64 tmp_addflag=' -i_dynamic' ;; efc*,ia64* | ifort*,ia64*) # Intel Fortran compiler on ia64 tmp_addflag=' -i_dynamic -nofor_main' ;; ifc* | ifort*) # Intel Fortran compiler tmp_addflag=' -nofor_main' ;; lf95*) # Lahey Fortran 8.1 whole_archive_flag_spec= tmp_sharedflag='--shared' ;; xl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below) tmp_sharedflag='-qmkshrobj' tmp_addflag= ;; esac case `$CC -V 2>&1 | sed 5q` in *Sun\ C*) # Sun C 5.9 whole_archive_flag_spec='${wl}--whole-archive`new_convenience=; for conv in $convenience\"\"; do test -z \"$conv\" || new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive' compiler_needs_object=yes tmp_sharedflag='-G' ;; *Sun\ F*) # Sun Fortran 8.3 tmp_sharedflag='-G' ;; esac archive_cmds='$CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' if test "x$supports_anon_versioning" = xyes; then archive_expsym_cmds='echo "{ global:" > $output_objdir/$libname.ver~ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~ echo "local: *; };" >> $output_objdir/$libname.ver~ $CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib' fi case $cc_basename in xlf*) # IBM XL Fortran 10.1 on PPC cannot create shared libs itself whole_archive_flag_spec='--whole-archive$convenience --no-whole-archive' hardcode_libdir_flag_spec= hardcode_libdir_flag_spec_ld='-rpath $libdir' archive_cmds='$LD -shared $libobjs $deplibs $compiler_flags -soname $soname -o $lib' if test "x$supports_anon_versioning" = xyes; then archive_expsym_cmds='echo "{ global:" > $output_objdir/$libname.ver~ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~ echo "local: *; };" >> $output_objdir/$libname.ver~ $LD -shared $libobjs $deplibs $compiler_flags -soname $soname -version-script $output_objdir/$libname.ver -o $lib' fi ;; esac else ld_shlibs=no fi ;; netbsd* | netbsdelf*-gnu) if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then archive_cmds='$LD -Bshareable $libobjs $deplibs $linker_flags -o $lib' wlarc= else archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' fi ;; solaris*) if $LD -v 2>&1 | $GREP 'BFD 2\.8' > /dev/null; then ld_shlibs=no cat <<_LT_EOF 1>&2 *** Warning: The releases 2.8.* of the GNU linker cannot reliably *** create shared libraries on Solaris systems. Therefore, libtool *** is disabling shared libraries support. We urge you to upgrade GNU *** binutils to release 2.9.1 or newer. Another option is to modify *** your PATH or compiler configuration so that the native linker is *** used, and then restart. _LT_EOF elif $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' else ld_shlibs=no fi ;; sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX*) case `$LD -v 2>&1` in *\ [01].* | *\ 2.[0-9].* | *\ 2.1[0-5].*) ld_shlibs=no cat <<_LT_EOF 1>&2 *** Warning: Releases of the GNU linker prior to 2.16.91.0.3 can not *** reliably create shared libraries on SCO systems. Therefore, libtool *** is disabling shared libraries support. We urge you to upgrade GNU *** binutils to release 2.16.91.0.3 or newer. Another option is to modify *** your PATH or compiler configuration so that the native linker is *** used, and then restart. _LT_EOF ;; *) # For security reasons, it is highly recommended that you always # use absolute paths for naming shared libraries, and exclude the # DT_RUNPATH tag from executables and libraries. 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If -brtl is somewhere in LDFLAGS, we # need to do runtime linking. case $host_os in aix4.[23]|aix4.[23].*|aix[5-9]*) for ld_flag in $LDFLAGS; do if (test $ld_flag = "-brtl" || test $ld_flag = "-Wl,-brtl"); then aix_use_runtimelinking=yes break fi done ;; esac exp_sym_flag='-bexport' no_entry_flag='-bnoentry' fi # When large executables or shared objects are built, AIX ld can # have problems creating the table of contents. If linking a library # or program results in "error TOC overflow" add -mminimal-toc to # CXXFLAGS/CFLAGS for g++/gcc. 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The following line is correct: shared_flag='-G' else if test "$aix_use_runtimelinking" = yes; then shared_flag='${wl}-G' else shared_flag='${wl}-bM:SRE' fi fi fi export_dynamic_flag_spec='${wl}-bexpall' # It seems that -bexpall does not export symbols beginning with # underscore (_), so it is better to generate a list of symbols to export. always_export_symbols=yes if test "$aix_use_runtimelinking" = yes; then # Warning - without using the other runtime loading flags (-brtl), # -berok will link without error, but may produce a broken library. allow_undefined_flag='-berok' # Determine the default libpath from the value encoded in an # empty executable. cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int main () { ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (ac_try="$ac_link" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" $as_echo "$ac_try_echo") >&5 (eval "$ac_link") 2>conftest.er1 ac_status=$? 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Future versions do this automatically, but an explicit c++rt0.o # does not break anything, and helps significantly (at the cost of a little # extra space). freebsd2.2*) archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags /usr/lib/c++rt0.o' hardcode_libdir_flag_spec='-R$libdir' hardcode_direct=yes hardcode_shlibpath_var=no ;; # Unfortunately, older versions of FreeBSD 2 do not have this feature. freebsd2*) archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' hardcode_direct=yes hardcode_minus_L=yes hardcode_shlibpath_var=no ;; # FreeBSD 3 and greater uses gcc -shared to do shared libraries. freebsd* | dragonfly*) archive_cmds='$CC -shared -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec='-R$libdir' hardcode_direct=yes hardcode_shlibpath_var=no ;; hpux9*) if test "$GCC" = yes; then archive_cmds='$RM $output_objdir/$soname~$CC -shared -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $libobjs $deplibs $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' else archive_cmds='$RM $output_objdir/$soname~$LD -b +b $install_libdir -o $output_objdir/$soname $libobjs $deplibs $linker_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' fi hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' hardcode_libdir_separator=: hardcode_direct=yes # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L=yes export_dynamic_flag_spec='${wl}-E' ;; hpux10*) if test "$GCC" = yes -a "$with_gnu_ld" = no; then archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' else archive_cmds='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags' fi if test "$with_gnu_ld" = no; then hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' hardcode_libdir_flag_spec_ld='+b $libdir' hardcode_libdir_separator=: hardcode_direct=yes hardcode_direct_absolute=yes export_dynamic_flag_spec='${wl}-E' # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L=yes fi ;; hpux11*) if test "$GCC" = yes -a "$with_gnu_ld" = no; then case $host_cpu in hppa*64*) archive_cmds='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' ;; ia64*) archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' ;; *) archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' ;; esac else case $host_cpu in hppa*64*) archive_cmds='$CC -b ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' ;; ia64*) archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' ;; *) archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' ;; esac fi if test "$with_gnu_ld" = no; then hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' hardcode_libdir_separator=: case $host_cpu in hppa*64*|ia64*) hardcode_direct=no hardcode_shlibpath_var=no ;; *) hardcode_direct=yes hardcode_direct_absolute=yes export_dynamic_flag_spec='${wl}-E' # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L=yes ;; esac fi ;; irix5* | irix6* | nonstopux*) if test "$GCC" = yes; then archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' # Try to use the -exported_symbol ld option, if it does not # work, assume that -exports_file does not work either and # implicitly export all symbols. save_LDFLAGS="$LDFLAGS" LDFLAGS="$LDFLAGS -shared ${wl}-exported_symbol ${wl}foo ${wl}-update_registry ${wl}/dev/null" cat >conftest.$ac_ext <<_ACEOF int foo(void) {} _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (ac_try="$ac_link" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" $as_echo "$ac_try_echo") >&5 (eval "$ac_link") 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { test -z "$ac_c_werror_flag" || test ! -s conftest.err } && test -s conftest$ac_exeext && { test "$cross_compiling" = yes || $as_test_x conftest$ac_exeext }; then archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations ${wl}-exports_file ${wl}$export_symbols -o $lib' else $as_echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 fi rm -rf conftest.dSYM rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ conftest$ac_exeext conftest.$ac_ext LDFLAGS="$save_LDFLAGS" else archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib' archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -exports_file $export_symbols -o $lib' fi archive_cmds_need_lc='no' hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator=: inherit_rpath=yes link_all_deplibs=yes ;; netbsd* | netbsdelf*-gnu) if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out else archive_cmds='$LD -shared -o $lib $libobjs $deplibs $linker_flags' # ELF fi hardcode_libdir_flag_spec='-R$libdir' hardcode_direct=yes hardcode_shlibpath_var=no ;; newsos6) archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_direct=yes hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator=: hardcode_shlibpath_var=no ;; *nto* | *qnx*) ;; openbsd*) if test -f /usr/libexec/ld.so; then hardcode_direct=yes hardcode_shlibpath_var=no hardcode_direct_absolute=yes if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols' hardcode_libdir_flag_spec='${wl}-rpath,$libdir' export_dynamic_flag_spec='${wl}-E' else case $host_os in openbsd[01].* | openbsd2.[0-7] | openbsd2.[0-7].*) archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' hardcode_libdir_flag_spec='-R$libdir' ;; *) archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec='${wl}-rpath,$libdir' ;; esac fi else ld_shlibs=no fi ;; os2*) hardcode_libdir_flag_spec='-L$libdir' hardcode_minus_L=yes allow_undefined_flag=unsupported archive_cmds='$ECHO "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$ECHO "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~$ECHO DATA >> $output_objdir/$libname.def~$ECHO " SINGLE NONSHARED" >> $output_objdir/$libname.def~$ECHO EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def' old_archive_from_new_cmds='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def' ;; osf3*) if test "$GCC" = yes; then allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*' archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' else allow_undefined_flag=' -expect_unresolved \*' archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib' fi archive_cmds_need_lc='no' hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator=: ;; 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solaris*) no_undefined_flag=' -z defs' if test "$GCC" = yes; then wlarc='${wl}' archive_cmds='$CC -shared ${wl}-z ${wl}text ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ $CC -shared ${wl}-z ${wl}text ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp' else case `$CC -V 2>&1` in *"Compilers 5.0"*) wlarc='' archive_cmds='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags' archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ $LD -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $linker_flags~$RM $lib.exp' ;; *) wlarc='${wl}' archive_cmds='$CC -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ $CC -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp' ;; esac fi hardcode_libdir_flag_spec='-R$libdir' hardcode_shlibpath_var=no case $host_os in solaris2.[0-5] | solaris2.[0-5].*) ;; *) # The compiler driver will combine and reorder linker options, # but understands `-z linker_flag'. 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" >&6; } if test "${ac_cv_header_stdbool_h+set}" = set; then $as_echo_n "(cached) " >&6 else cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include #ifndef bool "error: bool is not defined" #endif #ifndef false "error: false is not defined" #endif #if false "error: false is not 0" #endif #ifndef true "error: true is not defined" #endif #if true != 1 "error: true is not 1" #endif #ifndef __bool_true_false_are_defined "error: __bool_true_false_are_defined is not defined" #endif struct s { _Bool s: 1; _Bool t; } s; char a[true == 1 ? 1 : -1]; char b[false == 0 ? 1 : -1]; char c[__bool_true_false_are_defined == 1 ? 1 : -1]; char d[(bool) 0.5 == true ? 1 : -1]; bool e = &s; char f[(_Bool) 0.0 == false ? 1 : -1]; char g[true]; char h[sizeof (_Bool)]; char i[sizeof s.t]; enum { j = false, k = true, l = false * true, m = true * 256 }; /* The following fails for HP aC++/ANSI C B3910B A.05.55 [Dec 04 2003]. */ _Bool n[m]; char o[sizeof n == m * sizeof n[0] ? 1 : -1]; char p[-1 - (_Bool) 0 < 0 && -1 - (bool) 0 < 0 ? 1 : -1]; # if defined __xlc__ || defined __GNUC__ /* Catch a bug in IBM AIX xlc compiler version 6.0.0.0 reported by James Lemley on 2005-10-05; see http://lists.gnu.org/archive/html/bug-coreutils/2005-10/msg00086.html This test is not quite right, since xlc is allowed to reject this program, as the initializer for xlcbug is not one of the forms that C requires support for. However, doing the test right would require a runtime test, and that would make cross-compilation harder. Let us hope that IBM fixes the xlc bug, and also adds support for this kind of constant expression. In the meantime, this test will reject xlc, which is OK, since our stdbool.h substitute should suffice. We also test this with GCC, where it should work, to detect more quickly whether someone messes up the test in the future. */ char digs[] = "0123456789"; int xlcbug = 1 / (&(digs + 5)[-2 + (bool) 1] == &digs[4] ? 1 : -1); # endif /* Catch a bug in an HP-UX C compiler. 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We can't simply define LARGE_OFF_T to be 9223372036854775807, since some C++ compilers masquerading as C compilers incorrectly reject 9223372036854775807. */ #define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62)) int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721 && LARGE_OFF_T % 2147483647 == 1) ? 1 : -1]; int main () { ; return 0; } _ACEOF rm -f conftest.$ac_objext if { (ac_try="$ac_compile" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" $as_echo "$ac_try_echo") >&5 (eval "$ac_compile") 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { test -z "$ac_cxx_werror_flag" || test ! -s conftest.err } && test -s conftest.$ac_objext; then break else $as_echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 fi rm -f core conftest.err conftest.$ac_objext CC="$CC -n32" rm -f conftest.$ac_objext if { (ac_try="$ac_compile" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" $as_echo "$ac_try_echo") >&5 (eval "$ac_compile") 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { test -z "$ac_cxx_werror_flag" || test ! -s conftest.err } && test -s conftest.$ac_objext; then ac_cv_sys_largefile_CC=' -n32'; break else $as_echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 fi rm -f core conftest.err conftest.$ac_objext break done CC=$ac_save_CC rm -f conftest.$ac_ext fi fi { $as_echo "$as_me:$LINENO: result: $ac_cv_sys_largefile_CC" >&5 $as_echo "$ac_cv_sys_largefile_CC" >&6; } if test "$ac_cv_sys_largefile_CC" != no; then CC=$CC$ac_cv_sys_largefile_CC fi { $as_echo "$as_me:$LINENO: checking for _FILE_OFFSET_BITS value needed for large files" >&5 $as_echo_n "checking for _FILE_OFFSET_BITS value needed for large files... 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We can't simply define LARGE_OFF_T to be 9223372036854775807, since some C++ compilers masquerading as C compilers incorrectly reject 9223372036854775807. */ #define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62)) int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721 && LARGE_OFF_T % 2147483647 == 1) ? 1 : -1]; int main () { ; return 0; } _ACEOF rm -f conftest.$ac_objext if { (ac_try="$ac_compile" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" $as_echo "$ac_try_echo") >&5 (eval "$ac_compile") 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { test -z "$ac_cxx_werror_flag" || test ! -s conftest.err } && test -s conftest.$ac_objext; then ac_cv_sys_file_offset_bits=no; break else $as_echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 fi rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #define _FILE_OFFSET_BITS 64 #include /* Check that off_t can represent 2**63 - 1 correctly. 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We can't simply define LARGE_OFF_T to be 9223372036854775807, since some C++ compilers masquerading as C compilers incorrectly reject 9223372036854775807. */ #define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62)) int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721 && LARGE_OFF_T % 2147483647 == 1) ? 1 : -1]; int main () { ; return 0; } _ACEOF rm -f conftest.$ac_objext if { (ac_try="$ac_compile" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" $as_echo "$ac_try_echo") >&5 (eval "$ac_compile") 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { test -z "$ac_cxx_werror_flag" || test ! -s conftest.err } && test -s conftest.$ac_objext; then ac_cv_sys_large_files=no; break else $as_echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 fi rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #define _LARGE_FILES 1 #include /* Check that off_t can represent 2**63 - 1 correctly. 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You may not convey a covered work if you are a party to an arrangement with a third party that is in the business of distributing software, under which you make payment to the third party based on the extent of your activity of conveying the work, and under which the third party grants, to any of the parties who would receive the covered work from you, a discriminatory patent license (a) in connection with copies of the covered work conveyed by you (or copies made from those copies), or (b) primarily for and in connection with specific products or compilations that contain the covered work, unless you entered into that arrangement, or that patent license was granted, prior to 28 March 2007. Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law. 12. No Surrender of Others' Freedom. If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program. 13. Use with the GNU Affero General Public License. Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. The terms of this License will continue to apply to the part which is the covered work, but the special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such. 14. Revised Versions of this License. The Free Software Foundation may publish revised and/or new versions of the GNU General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the GNU General Public License "or any later version" applies to it, you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation. 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IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. 17. Interpretation of Sections 15 and 16. If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee. END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Also add information on how to contact you by electronic and paper mail. If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode: Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, your program's commands might be different; for a GUI interface, you would use an "about box". You should also get your employer (if you work as a programmer) or school, if any, to sign a "copyright disclaimer" for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see . The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read . anfo-0.98/TODO0000644000371600007640000000015211447113711010014 00000000000000- Stream processing has an unclear interface. - SAM output does not generate MD field and context (XU,XD) anfo-0.98/config.guess0000755000371600007640000012753411447114172011664 00000000000000#! /bin/sh # Attempt to guess a canonical system name. # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, # 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 # Free Software Foundation, Inc. timestamp='2008-01-23' # This file is free software; you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU # General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA # 02110-1301, USA. # # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that program. # Originally written by Per Bothner . # Please send patches to . Submit a context # diff and a properly formatted ChangeLog entry. # # This script attempts to guess a canonical system name similar to # config.sub. If it succeeds, it prints the system name on stdout, and # exits with 0. Otherwise, it exits with 1. # # The plan is that this can be called by configure scripts if you # don't specify an explicit build system type. me=`echo "$0" | sed -e 's,.*/,,'` usage="\ Usage: $0 [OPTION] Output the configuration name of the system \`$me' is run on. Operation modes: -h, --help print this help, then exit -t, --time-stamp print date of last modification, then exit -v, --version print version number, then exit Report bugs and patches to ." version="\ GNU config.guess ($timestamp) Originally written by Per Bothner. Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." help=" Try \`$me --help' for more information." # Parse command line while test $# -gt 0 ; do case $1 in --time-stamp | --time* | -t ) echo "$timestamp" ; exit ;; --version | -v ) echo "$version" ; exit ;; --help | --h* | -h ) echo "$usage"; exit ;; -- ) # Stop option processing shift; break ;; - ) # Use stdin as input. break ;; -* ) echo "$me: invalid option $1$help" >&2 exit 1 ;; * ) break ;; esac done if test $# != 0; then echo "$me: too many arguments$help" >&2 exit 1 fi trap 'exit 1' 1 2 15 # CC_FOR_BUILD -- compiler used by this script. Note that the use of a # compiler to aid in system detection is discouraged as it requires # temporary files to be created and, as you can see below, it is a # headache to deal with in a portable fashion. # Historically, `CC_FOR_BUILD' used to be named `HOST_CC'. We still # use `HOST_CC' if defined, but it is deprecated. # Portable tmp directory creation inspired by the Autoconf team. set_cc_for_build=' trap "exitcode=\$?; (rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null) && exit \$exitcode" 0 ; trap "rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null; exit 1" 1 2 13 15 ; : ${TMPDIR=/tmp} ; { tmp=`(umask 077 && mktemp -d "$TMPDIR/cgXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" ; } || { test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir $tmp) ; } || { tmp=$TMPDIR/cg-$$ && (umask 077 && mkdir $tmp) && echo "Warning: creating insecure temp directory" >&2 ; } || { echo "$me: cannot create a temporary directory in $TMPDIR" >&2 ; exit 1 ; } ; dummy=$tmp/dummy ; tmpfiles="$dummy.c $dummy.o $dummy.rel $dummy" ; case $CC_FOR_BUILD,$HOST_CC,$CC in ,,) echo "int x;" > $dummy.c ; for c in cc gcc c89 c99 ; do if ($c -c -o $dummy.o $dummy.c) >/dev/null 2>&1 ; then CC_FOR_BUILD="$c"; break ; fi ; done ; if test x"$CC_FOR_BUILD" = x ; then CC_FOR_BUILD=no_compiler_found ; fi ;; ,,*) CC_FOR_BUILD=$CC ;; ,*,*) CC_FOR_BUILD=$HOST_CC ;; esac ; set_cc_for_build= ;' # This is needed to find uname on a Pyramid OSx when run in the BSD universe. # (ghazi@noc.rutgers.edu 1994-08-24) if (test -f /.attbin/uname) >/dev/null 2>&1 ; then PATH=$PATH:/.attbin ; export PATH fi UNAME_MACHINE=`(uname -m) 2>/dev/null` || UNAME_MACHINE=unknown UNAME_RELEASE=`(uname -r) 2>/dev/null` || UNAME_RELEASE=unknown UNAME_SYSTEM=`(uname -s) 2>/dev/null` || UNAME_SYSTEM=unknown UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown # Note: order is significant - the case branches are not exclusive. case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in *:NetBSD:*:*) # NetBSD (nbsd) targets should (where applicable) match one or # more of the tupples: *-*-netbsdelf*, *-*-netbsdaout*, # *-*-netbsdecoff* and *-*-netbsd*. For targets that recently # switched to ELF, *-*-netbsd* would select the old # object file format. This provides both forward # compatibility and a consistent mechanism for selecting the # object file format. # # Note: NetBSD doesn't particularly care about the vendor # portion of the name. We always set it to "unknown". sysctl="sysctl -n hw.machine_arch" UNAME_MACHINE_ARCH=`(/sbin/$sysctl 2>/dev/null || \ /usr/sbin/$sysctl 2>/dev/null || echo unknown)` case "${UNAME_MACHINE_ARCH}" in armeb) machine=armeb-unknown ;; arm*) machine=arm-unknown ;; sh3el) machine=shl-unknown ;; sh3eb) machine=sh-unknown ;; sh5el) machine=sh5le-unknown ;; *) machine=${UNAME_MACHINE_ARCH}-unknown ;; esac # The Operating System including object format, if it has switched # to ELF recently, or will in the future. case "${UNAME_MACHINE_ARCH}" in arm*|i386|m68k|ns32k|sh3*|sparc|vax) eval $set_cc_for_build if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \ | grep __ELF__ >/dev/null then # Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout). # Return netbsd for either. FIX? os=netbsd else os=netbsdelf fi ;; *) os=netbsd ;; esac # The OS release # Debian GNU/NetBSD machines have a different userland, and # thus, need a distinct triplet. However, they do not need # kernel version information, so it can be replaced with a # suitable tag, in the style of linux-gnu. case "${UNAME_VERSION}" in Debian*) release='-gnu' ;; *) release=`echo ${UNAME_RELEASE}|sed -e 's/[-_].*/\./'` ;; esac # Since CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM: # contains redundant information, the shorter form: # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used. echo "${machine}-${os}${release}" exit ;; *:OpenBSD:*:*) UNAME_MACHINE_ARCH=`arch | sed 's/OpenBSD.//'` echo ${UNAME_MACHINE_ARCH}-unknown-openbsd${UNAME_RELEASE} exit ;; *:ekkoBSD:*:*) echo ${UNAME_MACHINE}-unknown-ekkobsd${UNAME_RELEASE} exit ;; *:SolidBSD:*:*) echo ${UNAME_MACHINE}-unknown-solidbsd${UNAME_RELEASE} exit ;; macppc:MirBSD:*:*) echo powerpc-unknown-mirbsd${UNAME_RELEASE} exit ;; *:MirBSD:*:*) echo ${UNAME_MACHINE}-unknown-mirbsd${UNAME_RELEASE} exit ;; alpha:OSF1:*:*) case $UNAME_RELEASE in *4.0) UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'` ;; *5.*) UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'` ;; esac # According to Compaq, /usr/sbin/psrinfo has been available on # OSF/1 and Tru64 systems produced since 1995. I hope that # covers most systems running today. This code pipes the CPU # types through head -n 1, so we only detect the type of CPU 0. ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1` case "$ALPHA_CPU_TYPE" in "EV4 (21064)") UNAME_MACHINE="alpha" ;; "EV4.5 (21064)") UNAME_MACHINE="alpha" ;; "LCA4 (21066/21068)") UNAME_MACHINE="alpha" ;; "EV5 (21164)") UNAME_MACHINE="alphaev5" ;; "EV5.6 (21164A)") UNAME_MACHINE="alphaev56" ;; "EV5.6 (21164PC)") UNAME_MACHINE="alphapca56" ;; "EV5.7 (21164PC)") UNAME_MACHINE="alphapca57" ;; "EV6 (21264)") UNAME_MACHINE="alphaev6" ;; "EV6.7 (21264A)") UNAME_MACHINE="alphaev67" ;; "EV6.8CB (21264C)") UNAME_MACHINE="alphaev68" ;; "EV6.8AL (21264B)") UNAME_MACHINE="alphaev68" ;; "EV6.8CX (21264D)") UNAME_MACHINE="alphaev68" ;; "EV6.9A (21264/EV69A)") UNAME_MACHINE="alphaev69" ;; "EV7 (21364)") UNAME_MACHINE="alphaev7" ;; "EV7.9 (21364A)") UNAME_MACHINE="alphaev79" ;; esac # A Pn.n version is a patched version. # A Vn.n version is a released version. # A Tn.n version is a released field test version. # A Xn.n version is an unreleased experimental baselevel. # 1.2 uses "1.2" for uname -r. echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[PVTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'` exit ;; Alpha\ *:Windows_NT*:*) # How do we know it's Interix rather than the generic POSIX subsystem? # Should we change UNAME_MACHINE based on the output of uname instead # of the specific Alpha model? echo alpha-pc-interix exit ;; 21064:Windows_NT:50:3) echo alpha-dec-winnt3.5 exit ;; Amiga*:UNIX_System_V:4.0:*) echo m68k-unknown-sysv4 exit ;; *:[Aa]miga[Oo][Ss]:*:*) echo ${UNAME_MACHINE}-unknown-amigaos exit ;; *:[Mm]orph[Oo][Ss]:*:*) echo ${UNAME_MACHINE}-unknown-morphos exit ;; *:OS/390:*:*) echo i370-ibm-openedition exit ;; *:z/VM:*:*) echo s390-ibm-zvmoe exit ;; *:OS400:*:*) echo powerpc-ibm-os400 exit ;; arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*) echo arm-acorn-riscix${UNAME_RELEASE} exit ;; arm:riscos:*:*|arm:RISCOS:*:*) echo arm-unknown-riscos exit ;; SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*) echo hppa1.1-hitachi-hiuxmpp exit ;; Pyramid*:OSx*:*:* | MIS*:OSx*:*:* | MIS*:SMP_DC-OSx*:*:*) # akee@wpdis03.wpafb.af.mil (Earle F. Ake) contributed MIS and NILE. if test "`(/bin/universe) 2>/dev/null`" = att ; then echo pyramid-pyramid-sysv3 else echo pyramid-pyramid-bsd fi exit ;; NILE*:*:*:dcosx) echo pyramid-pyramid-svr4 exit ;; DRS?6000:unix:4.0:6*) echo sparc-icl-nx6 exit ;; DRS?6000:UNIX_SV:4.2*:7* | DRS?6000:isis:4.2*:7*) case `/usr/bin/uname -p` in sparc) echo sparc-icl-nx7; exit ;; esac ;; sun4H:SunOS:5.*:*) echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*) echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*) echo i386-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4*:SunOS:6*:*) # According to config.sub, this is the proper way to canonicalize # SunOS6. Hard to guess exactly what SunOS6 will be like, but # it's likely to be more like Solaris than SunOS4. echo sparc-sun-solaris3`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4*:SunOS:*:*) case "`/usr/bin/arch -k`" in Series*|S4*) UNAME_RELEASE=`uname -v` ;; esac # Japanese Language versions have a version number like `4.1.3-JL'. echo sparc-sun-sunos`echo ${UNAME_RELEASE}|sed -e 's/-/_/'` exit ;; sun3*:SunOS:*:*) echo m68k-sun-sunos${UNAME_RELEASE} exit ;; sun*:*:4.2BSD:*) UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null` test "x${UNAME_RELEASE}" = "x" && UNAME_RELEASE=3 case "`/bin/arch`" in sun3) echo m68k-sun-sunos${UNAME_RELEASE} ;; sun4) echo sparc-sun-sunos${UNAME_RELEASE} ;; esac exit ;; aushp:SunOS:*:*) echo sparc-auspex-sunos${UNAME_RELEASE} exit ;; # The situation for MiNT is a little confusing. The machine name # can be virtually everything (everything which is not # "atarist" or "atariste" at least should have a processor # > m68000). The system name ranges from "MiNT" over "FreeMiNT" # to the lowercase version "mint" (or "freemint"). Finally # the system name "TOS" denotes a system which is actually not # MiNT. But MiNT is downward compatible to TOS, so this should # be no problem. atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit ;; atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit ;; *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit ;; milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*) echo m68k-milan-mint${UNAME_RELEASE} exit ;; hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*) echo m68k-hades-mint${UNAME_RELEASE} exit ;; *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*) echo m68k-unknown-mint${UNAME_RELEASE} exit ;; m68k:machten:*:*) echo m68k-apple-machten${UNAME_RELEASE} exit ;; powerpc:machten:*:*) echo powerpc-apple-machten${UNAME_RELEASE} exit ;; RISC*:Mach:*:*) echo mips-dec-mach_bsd4.3 exit ;; RISC*:ULTRIX:*:*) echo mips-dec-ultrix${UNAME_RELEASE} exit ;; VAX*:ULTRIX*:*:*) echo vax-dec-ultrix${UNAME_RELEASE} exit ;; 2020:CLIX:*:* | 2430:CLIX:*:*) echo clipper-intergraph-clix${UNAME_RELEASE} exit ;; mips:*:*:UMIPS | mips:*:*:RISCos) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #ifdef __cplusplus #include /* for printf() prototype */ int main (int argc, char *argv[]) { #else int main (argc, argv) int argc; char *argv[]; { #endif #if defined (host_mips) && defined (MIPSEB) #if defined (SYSTYPE_SYSV) printf ("mips-mips-riscos%ssysv\n", argv[1]); exit (0); #endif #if defined (SYSTYPE_SVR4) printf ("mips-mips-riscos%ssvr4\n", argv[1]); exit (0); #endif #if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD) printf ("mips-mips-riscos%sbsd\n", argv[1]); exit (0); #endif #endif exit (-1); } EOF $CC_FOR_BUILD -o $dummy $dummy.c && dummyarg=`echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` && SYSTEM_NAME=`$dummy $dummyarg` && { echo "$SYSTEM_NAME"; exit; } echo mips-mips-riscos${UNAME_RELEASE} exit ;; Motorola:PowerMAX_OS:*:*) echo powerpc-motorola-powermax exit ;; Motorola:*:4.3:PL8-*) echo powerpc-harris-powermax exit ;; Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*) echo powerpc-harris-powermax exit ;; Night_Hawk:Power_UNIX:*:*) echo powerpc-harris-powerunix exit ;; m88k:CX/UX:7*:*) echo m88k-harris-cxux7 exit ;; m88k:*:4*:R4*) echo m88k-motorola-sysv4 exit ;; m88k:*:3*:R3*) echo m88k-motorola-sysv3 exit ;; AViiON:dgux:*:*) # DG/UX returns AViiON for all architectures UNAME_PROCESSOR=`/usr/bin/uname -p` if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ] then if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \ [ ${TARGET_BINARY_INTERFACE}x = x ] then echo m88k-dg-dgux${UNAME_RELEASE} else echo m88k-dg-dguxbcs${UNAME_RELEASE} fi else echo i586-dg-dgux${UNAME_RELEASE} fi exit ;; M88*:DolphinOS:*:*) # DolphinOS (SVR3) echo m88k-dolphin-sysv3 exit ;; M88*:*:R3*:*) # Delta 88k system running SVR3 echo m88k-motorola-sysv3 exit ;; XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3) echo m88k-tektronix-sysv3 exit ;; Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD) echo m68k-tektronix-bsd exit ;; *:IRIX*:*:*) echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'` exit ;; ????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX. echo romp-ibm-aix # uname -m gives an 8 hex-code CPU id exit ;; # Note that: echo "'`uname -s`'" gives 'AIX ' i*86:AIX:*:*) echo i386-ibm-aix exit ;; ia64:AIX:*:*) if [ -x /usr/bin/oslevel ] ; then IBM_REV=`/usr/bin/oslevel` else IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} fi echo ${UNAME_MACHINE}-ibm-aix${IBM_REV} exit ;; *:AIX:2:3) if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #include main() { if (!__power_pc()) exit(1); puts("powerpc-ibm-aix3.2.5"); exit(0); } EOF if $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` then echo "$SYSTEM_NAME" else echo rs6000-ibm-aix3.2.5 fi elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then echo rs6000-ibm-aix3.2.4 else echo rs6000-ibm-aix3.2 fi exit ;; *:AIX:*:[456]) IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'` if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then IBM_ARCH=rs6000 else IBM_ARCH=powerpc fi if [ -x /usr/bin/oslevel ] ; then IBM_REV=`/usr/bin/oslevel` else IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} fi echo ${IBM_ARCH}-ibm-aix${IBM_REV} exit ;; *:AIX:*:*) echo rs6000-ibm-aix exit ;; ibmrt:4.4BSD:*|romp-ibm:BSD:*) echo romp-ibm-bsd4.4 exit ;; ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and echo romp-ibm-bsd${UNAME_RELEASE} # 4.3 with uname added to exit ;; # report: romp-ibm BSD 4.3 *:BOSX:*:*) echo rs6000-bull-bosx exit ;; DPX/2?00:B.O.S.:*:*) echo m68k-bull-sysv3 exit ;; 9000/[34]??:4.3bsd:1.*:*) echo m68k-hp-bsd exit ;; hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*) echo m68k-hp-bsd4.4 exit ;; 9000/[34678]??:HP-UX:*:*) HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` case "${UNAME_MACHINE}" in 9000/31? ) HP_ARCH=m68000 ;; 9000/[34]?? ) HP_ARCH=m68k ;; 9000/[678][0-9][0-9]) if [ -x /usr/bin/getconf ]; then sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null` sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null` case "${sc_cpu_version}" in 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1 532) # CPU_PA_RISC2_0 case "${sc_kernel_bits}" in 32) HP_ARCH="hppa2.0n" ;; 64) HP_ARCH="hppa2.0w" ;; '') HP_ARCH="hppa2.0" ;; # HP-UX 10.20 esac ;; esac fi if [ "${HP_ARCH}" = "" ]; then eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #define _HPUX_SOURCE #include #include int main () { #if defined(_SC_KERNEL_BITS) long bits = sysconf(_SC_KERNEL_BITS); #endif long cpu = sysconf (_SC_CPU_VERSION); switch (cpu) { case CPU_PA_RISC1_0: puts ("hppa1.0"); break; case CPU_PA_RISC1_1: puts ("hppa1.1"); break; case CPU_PA_RISC2_0: #if defined(_SC_KERNEL_BITS) switch (bits) { case 64: puts ("hppa2.0w"); break; case 32: puts ("hppa2.0n"); break; default: puts ("hppa2.0"); break; } break; #else /* !defined(_SC_KERNEL_BITS) */ puts ("hppa2.0"); break; #endif default: puts ("hppa1.0"); break; } exit (0); } EOF (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy` test -z "$HP_ARCH" && HP_ARCH=hppa fi ;; esac if [ ${HP_ARCH} = "hppa2.0w" ] then eval $set_cc_for_build # hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating # 32-bit code. hppa64-hp-hpux* has the same kernel and a compiler # generating 64-bit code. GNU and HP use different nomenclature: # # $ CC_FOR_BUILD=cc ./config.guess # => hppa2.0w-hp-hpux11.23 # $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess # => hppa64-hp-hpux11.23 if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | grep __LP64__ >/dev/null then HP_ARCH="hppa2.0w" else HP_ARCH="hppa64" fi fi echo ${HP_ARCH}-hp-hpux${HPUX_REV} exit ;; ia64:HP-UX:*:*) HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` echo ia64-hp-hpux${HPUX_REV} exit ;; 3050*:HI-UX:*:*) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #include int main () { long cpu = sysconf (_SC_CPU_VERSION); /* The order matters, because CPU_IS_HP_MC68K erroneously returns true for CPU_PA_RISC1_0. CPU_IS_PA_RISC returns correct results, however. */ if (CPU_IS_PA_RISC (cpu)) { switch (cpu) { case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break; case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break; case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break; default: puts ("hppa-hitachi-hiuxwe2"); break; } } else if (CPU_IS_HP_MC68K (cpu)) puts ("m68k-hitachi-hiuxwe2"); else puts ("unknown-hitachi-hiuxwe2"); exit (0); } EOF $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` && { echo "$SYSTEM_NAME"; exit; } echo unknown-hitachi-hiuxwe2 exit ;; 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:* ) echo hppa1.1-hp-bsd exit ;; 9000/8??:4.3bsd:*:*) echo hppa1.0-hp-bsd exit ;; *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*) echo hppa1.0-hp-mpeix exit ;; hp7??:OSF1:*:* | hp8?[79]:OSF1:*:* ) echo hppa1.1-hp-osf exit ;; hp8??:OSF1:*:*) echo hppa1.0-hp-osf exit ;; i*86:OSF1:*:*) if [ -x /usr/sbin/sysversion ] ; then echo ${UNAME_MACHINE}-unknown-osf1mk else echo ${UNAME_MACHINE}-unknown-osf1 fi exit ;; parisc*:Lites*:*:*) echo hppa1.1-hp-lites exit ;; C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*) echo c1-convex-bsd exit ;; C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*) if getsysinfo -f scalar_acc then echo c32-convex-bsd else echo c2-convex-bsd fi exit ;; C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*) echo c34-convex-bsd exit ;; C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*) echo c38-convex-bsd exit ;; C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*) echo c4-convex-bsd exit ;; CRAY*Y-MP:*:*:*) echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; CRAY*[A-Z]90:*:*:*) echo ${UNAME_MACHINE}-cray-unicos${UNAME_RELEASE} \ | sed -e 's/CRAY.*\([A-Z]90\)/\1/' \ -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \ -e 's/\.[^.]*$/.X/' exit ;; CRAY*TS:*:*:*) echo t90-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; CRAY*T3E:*:*:*) echo alphaev5-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; CRAY*SV1:*:*:*) echo sv1-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; *:UNICOS/mp:*:*) echo craynv-cray-unicosmp${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*) FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'` FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'` echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" exit ;; 5000:UNIX_System_V:4.*:*) FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'` echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" exit ;; i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*) echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE} exit ;; sparc*:BSD/OS:*:*) echo sparc-unknown-bsdi${UNAME_RELEASE} exit ;; *:BSD/OS:*:*) echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE} exit ;; *:FreeBSD:*:*) case ${UNAME_MACHINE} in pc98) echo i386-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; amd64) echo x86_64-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; *) echo ${UNAME_MACHINE}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; esac exit ;; i*:CYGWIN*:*) echo ${UNAME_MACHINE}-pc-cygwin exit ;; *:MINGW*:*) echo ${UNAME_MACHINE}-pc-mingw32 exit ;; i*:windows32*:*) # uname -m includes "-pc" on this system. echo ${UNAME_MACHINE}-mingw32 exit ;; i*:PW*:*) echo ${UNAME_MACHINE}-pc-pw32 exit ;; *:Interix*:[3456]*) case ${UNAME_MACHINE} in x86) echo i586-pc-interix${UNAME_RELEASE} exit ;; EM64T | authenticamd) echo x86_64-unknown-interix${UNAME_RELEASE} exit ;; IA64) echo ia64-unknown-interix${UNAME_RELEASE} exit ;; esac ;; [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*) echo i${UNAME_MACHINE}-pc-mks exit ;; i*:Windows_NT*:* | Pentium*:Windows_NT*:*) # How do we know it's Interix rather than the generic POSIX subsystem? # It also conflicts with pre-2.0 versions of AT&T UWIN. Should we # UNAME_MACHINE based on the output of uname instead of i386? echo i586-pc-interix exit ;; i*:UWIN*:*) echo ${UNAME_MACHINE}-pc-uwin exit ;; amd64:CYGWIN*:*:* | x86_64:CYGWIN*:*:*) echo x86_64-unknown-cygwin exit ;; p*:CYGWIN*:*) echo powerpcle-unknown-cygwin exit ;; prep*:SunOS:5.*:*) echo powerpcle-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; *:GNU:*:*) # the GNU system echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'` exit ;; *:GNU/*:*:*) # other systems with GNU libc and userland echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-gnu exit ;; i*86:Minix:*:*) echo ${UNAME_MACHINE}-pc-minix exit ;; arm*:Linux:*:*) eval $set_cc_for_build if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \ | grep -q __ARM_EABI__ then echo ${UNAME_MACHINE}-unknown-linux-gnu else echo ${UNAME_MACHINE}-unknown-linux-gnueabi fi exit ;; avr32*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; cris:Linux:*:*) echo cris-axis-linux-gnu exit ;; crisv32:Linux:*:*) echo crisv32-axis-linux-gnu exit ;; frv:Linux:*:*) echo frv-unknown-linux-gnu exit ;; ia64:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; m32r*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; m68*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; mips:Linux:*:*) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #undef CPU #undef mips #undef mipsel #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) CPU=mipsel #else #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) CPU=mips #else CPU= #endif #endif EOF eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n ' /^CPU/{ s: ::g p }'`" test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; } ;; mips64:Linux:*:*) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #undef CPU #undef mips64 #undef mips64el #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) CPU=mips64el #else #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) CPU=mips64 #else CPU= #endif #endif EOF eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n ' /^CPU/{ s: ::g p }'`" test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; } ;; or32:Linux:*:*) echo or32-unknown-linux-gnu exit ;; ppc:Linux:*:*) echo powerpc-unknown-linux-gnu exit ;; ppc64:Linux:*:*) echo powerpc64-unknown-linux-gnu exit ;; alpha:Linux:*:*) case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in EV5) UNAME_MACHINE=alphaev5 ;; EV56) UNAME_MACHINE=alphaev56 ;; PCA56) UNAME_MACHINE=alphapca56 ;; PCA57) UNAME_MACHINE=alphapca56 ;; EV6) UNAME_MACHINE=alphaev6 ;; EV67) UNAME_MACHINE=alphaev67 ;; EV68*) UNAME_MACHINE=alphaev68 ;; esac objdump --private-headers /bin/sh | grep ld.so.1 >/dev/null if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC} exit ;; parisc:Linux:*:* | hppa:Linux:*:*) # Look for CPU level case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in PA7*) echo hppa1.1-unknown-linux-gnu ;; PA8*) echo hppa2.0-unknown-linux-gnu ;; *) echo hppa-unknown-linux-gnu ;; esac exit ;; parisc64:Linux:*:* | hppa64:Linux:*:*) echo hppa64-unknown-linux-gnu exit ;; s390:Linux:*:* | s390x:Linux:*:*) echo ${UNAME_MACHINE}-ibm-linux exit ;; 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i*86:OS/2:*:*) # If we were able to find `uname', then EMX Unix compatibility # is probably installed. echo ${UNAME_MACHINE}-pc-os2-emx exit ;; i*86:XTS-300:*:STOP) echo ${UNAME_MACHINE}-unknown-stop exit ;; i*86:atheos:*:*) echo ${UNAME_MACHINE}-unknown-atheos exit ;; i*86:syllable:*:*) echo ${UNAME_MACHINE}-pc-syllable exit ;; i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.0*:*) echo i386-unknown-lynxos${UNAME_RELEASE} exit ;; i*86:*DOS:*:*) echo ${UNAME_MACHINE}-pc-msdosdjgpp exit ;; i*86:*:4.*:* | i*86:SYSTEM_V:4.*:*) UNAME_REL=`echo ${UNAME_RELEASE} | sed 's/\/MP$//'` if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then echo ${UNAME_MACHINE}-univel-sysv${UNAME_REL} else echo ${UNAME_MACHINE}-pc-sysv${UNAME_REL} fi exit ;; i*86:*:5:[678]*) # UnixWare 7.x, OpenUNIX and OpenServer 6. case `/bin/uname -X | grep "^Machine"` in *486*) UNAME_MACHINE=i486 ;; *Pentium) UNAME_MACHINE=i586 ;; *Pent*|*Celeron) UNAME_MACHINE=i686 ;; esac echo ${UNAME_MACHINE}-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION} exit ;; 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TSUNAMI:LynxOS:2.*:*) echo sparc-unknown-lynxos${UNAME_RELEASE} exit ;; rs6000:LynxOS:2.*:*) echo rs6000-unknown-lynxos${UNAME_RELEASE} exit ;; PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.0*:*) echo powerpc-unknown-lynxos${UNAME_RELEASE} exit ;; SM[BE]S:UNIX_SV:*:*) echo mips-dde-sysv${UNAME_RELEASE} exit ;; RM*:ReliantUNIX-*:*:*) echo mips-sni-sysv4 exit ;; RM*:SINIX-*:*:*) echo mips-sni-sysv4 exit ;; *:SINIX-*:*:*) if uname -p 2>/dev/null >/dev/null ; then UNAME_MACHINE=`(uname -p) 2>/dev/null` echo ${UNAME_MACHINE}-sni-sysv4 else echo ns32k-sni-sysv fi exit ;; PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort # says echo i586-unisys-sysv4 exit ;; *:UNIX_System_V:4*:FTX*) # From Gerald Hewes . # How about differentiating between stratus architectures? -djm echo hppa1.1-stratus-sysv4 exit ;; *:*:*:FTX*) # From seanf@swdc.stratus.com. echo i860-stratus-sysv4 exit ;; i*86:VOS:*:*) # From Paul.Green@stratus.com. echo ${UNAME_MACHINE}-stratus-vos exit ;; *:VOS:*:*) # From Paul.Green@stratus.com. echo hppa1.1-stratus-vos exit ;; mc68*:A/UX:*:*) echo m68k-apple-aux${UNAME_RELEASE} exit ;; news*:NEWS-OS:6*:*) echo mips-sony-newsos6 exit ;; R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*) if [ -d /usr/nec ]; then echo mips-nec-sysv${UNAME_RELEASE} else echo mips-unknown-sysv${UNAME_RELEASE} fi exit ;; BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only. echo powerpc-be-beos exit ;; BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only. echo powerpc-apple-beos exit ;; BePC:BeOS:*:*) # BeOS running on Intel PC compatible. echo i586-pc-beos exit ;; SX-4:SUPER-UX:*:*) echo sx4-nec-superux${UNAME_RELEASE} exit ;; SX-5:SUPER-UX:*:*) echo sx5-nec-superux${UNAME_RELEASE} exit ;; SX-6:SUPER-UX:*:*) echo sx6-nec-superux${UNAME_RELEASE} exit ;; SX-7:SUPER-UX:*:*) echo sx7-nec-superux${UNAME_RELEASE} exit ;; SX-8:SUPER-UX:*:*) echo sx8-nec-superux${UNAME_RELEASE} exit ;; SX-8R:SUPER-UX:*:*) echo sx8r-nec-superux${UNAME_RELEASE} exit ;; 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then UNAME_MACHINE=i386 else UNAME_MACHINE="$cputype" fi echo ${UNAME_MACHINE}-unknown-plan9 exit ;; *:TOPS-10:*:*) echo pdp10-unknown-tops10 exit ;; *:TENEX:*:*) echo pdp10-unknown-tenex exit ;; KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*) echo pdp10-dec-tops20 exit ;; XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*) echo pdp10-xkl-tops20 exit ;; *:TOPS-20:*:*) echo pdp10-unknown-tops20 exit ;; *:ITS:*:*) echo pdp10-unknown-its exit ;; SEI:*:*:SEIUX) echo mips-sei-seiux${UNAME_RELEASE} exit ;; *:DragonFly:*:*) echo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` exit ;; *:*VMS:*:*) UNAME_MACHINE=`(uname -p) 2>/dev/null` case "${UNAME_MACHINE}" in A*) echo alpha-dec-vms ; exit ;; I*) echo ia64-dec-vms ; exit ;; V*) echo vax-dec-vms ; exit ;; esac ;; *:XENIX:*:SysV) echo i386-pc-xenix exit ;; i*86:skyos:*:*) echo ${UNAME_MACHINE}-pc-skyos`echo ${UNAME_RELEASE}` | sed -e 's/ .*$//' exit ;; i*86:rdos:*:*) echo ${UNAME_MACHINE}-pc-rdos exit ;; esac #echo '(No uname command or uname output not recognized.)' 1>&2 #echo "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" 1>&2 eval $set_cc_for_build cat >$dummy.c < # include #endif main () { #if defined (sony) #if defined (MIPSEB) /* BFD wants "bsd" instead of "newsos". 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It does not imply ALL GNU software can. # # This file is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA # 02110-1301, USA. # # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that program. # Please send patches to . Submit a context # diff and a properly formatted ChangeLog entry. # # Configuration subroutine to validate and canonicalize a configuration type. # Supply the specified configuration type as an argument. # If it is invalid, we print an error message on stderr and exit with code 1. # Otherwise, we print the canonical config type on stdout and succeed. # This file is supposed to be the same for all GNU packages # and recognize all the CPU types, system types and aliases # that are meaningful with *any* GNU software. # Each package is responsible for reporting which valid configurations # it does not support. The user should be able to distinguish # a failure to support a valid configuration from a meaningless # configuration. # The goal of this file is to map all the various variations of a given # machine specification into a single specification in the form: # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM # or in some cases, the newer four-part form: # CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM # It is wrong to echo any other type of specification. me=`echo "$0" | sed -e 's,.*/,,'` usage="\ Usage: $0 [OPTION] CPU-MFR-OPSYS $0 [OPTION] ALIAS Canonicalize a configuration name. Operation modes: -h, --help print this help, then exit -t, --time-stamp print date of last modification, then exit -v, --version print version number, then exit Report bugs and patches to ." version="\ GNU config.sub ($timestamp) Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. 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There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." help=" Try \`$me --help' for more information." # Parse command line while test $# -gt 0 ; do case $1 in --time-stamp | --time* | -t ) echo "$timestamp" ; exit ;; --version | -v ) echo "$version" ; exit ;; --help | --h* | -h ) echo "$usage"; exit ;; -- ) # Stop option processing shift; break ;; - ) # Use stdin as input. break ;; -* ) echo "$me: invalid option $1$help" exit 1 ;; *local*) # First pass through any local machine types. echo $1 exit ;; * ) break ;; esac done case $# in 0) echo "$me: missing argument$help" >&2 exit 1;; 1) ;; *) echo "$me: too many arguments$help" >&2 exit 1;; esac # Separate what the user gave into CPU-COMPANY and OS or KERNEL-OS (if any). # Here we must recognize all the valid KERNEL-OS combinations. maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'` case $maybe_os in nto-qnx* | linux-gnu* | linux-dietlibc | linux-newlib* | linux-uclibc* | \ uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* | \ storm-chaos* | os2-emx* | rtmk-nova*) os=-$maybe_os basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'` ;; *) basic_machine=`echo $1 | sed 's/-[^-]*$//'` if [ $basic_machine != $1 ] then os=`echo $1 | sed 's/.*-/-/'` else os=; fi ;; esac ### Let's recognize common machines as not being operating systems so ### that things like config.sub decstation-3100 work. We also ### recognize some manufacturers as not being operating systems, so we ### can provide default operating systems below. case $os in -sun*os*) # Prevent following clause from handling this invalid input. ;; -dec* | -mips* | -sequent* | -encore* | -pc532* | -sgi* | -sony* | \ -att* | -7300* | -3300* | -delta* | -motorola* | -sun[234]* | \ -unicom* | -ibm* | -next | -hp | -isi* | -apollo | -altos* | \ -convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\ -c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \ -harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \ -apple | -axis | -knuth | -cray) os= basic_machine=$1 ;; -sim | -cisco | -oki | -wec | -winbond) os= basic_machine=$1 ;; -scout) ;; -wrs) os=-vxworks basic_machine=$1 ;; -chorusos*) os=-chorusos basic_machine=$1 ;; -chorusrdb) os=-chorusrdb basic_machine=$1 ;; -hiux*) os=-hiuxwe2 ;; -sco6) os=-sco5v6 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco5) os=-sco3.2v5 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco4) os=-sco3.2v4 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco3.2.[4-9]*) os=`echo $os | sed -e 's/sco3.2./sco3.2v/'` basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco3.2v[4-9]*) # Don't forget version if it is 3.2v4 or newer. basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco5v6*) # Don't forget version if it is 3.2v4 or newer. basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco*) os=-sco3.2v2 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -udk*) basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -isc) os=-isc2.2 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -clix*) basic_machine=clipper-intergraph ;; -isc*) basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -lynx*) os=-lynxos ;; -ptx*) basic_machine=`echo $1 | sed -e 's/86-.*/86-sequent/'` ;; -windowsnt*) os=`echo $os | sed -e 's/windowsnt/winnt/'` ;; -psos*) os=-psos ;; -mint | -mint[0-9]*) basic_machine=m68k-atari os=-mint ;; esac # Decode aliases for certain CPU-COMPANY combinations. case $basic_machine in # Recognize the basic CPU types without company name. # Some are omitted here because they have special meanings below. 1750a | 580 \ | a29k \ | alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \ | alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \ | am33_2.0 \ | arc | arm | arm[bl]e | arme[lb] | armv[2345] | armv[345][lb] | avr | avr32 \ | bfin \ | c4x | clipper \ | d10v | d30v | dlx | dsp16xx \ | fido | fr30 | frv \ | h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \ | i370 | i860 | i960 | ia64 \ | ip2k | iq2000 \ | m32c | m32r | m32rle | m68000 | m68k | m88k \ | maxq | mb | microblaze | mcore | mep \ | mips | mipsbe | mipseb | mipsel | mipsle \ | mips16 \ | mips64 | mips64el \ | mips64vr | mips64vrel \ | mips64orion | mips64orionel \ | mips64vr4100 | mips64vr4100el \ | mips64vr4300 | mips64vr4300el \ | mips64vr5000 | mips64vr5000el \ | mips64vr5900 | mips64vr5900el \ | mipsisa32 | mipsisa32el \ | mipsisa32r2 | mipsisa32r2el \ | mipsisa64 | mipsisa64el \ | mipsisa64r2 | mipsisa64r2el \ | mipsisa64sb1 | mipsisa64sb1el \ | mipsisa64sr71k | mipsisa64sr71kel \ | mipstx39 | mipstx39el \ | mn10200 | mn10300 \ | mt \ | msp430 \ | nios | nios2 \ | ns16k | ns32k \ | or32 \ | pdp10 | pdp11 | pj | pjl \ | powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \ | pyramid \ | score \ | sh | sh[1234] | sh[24]a | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \ | sh64 | sh64le \ | sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \ | sparcv8 | sparcv9 | sparcv9b | sparcv9v \ | spu | strongarm \ | tahoe | thumb | tic4x | tic80 | tron \ | v850 | v850e \ | we32k \ | x86 | xc16x | xscale | xscalee[bl] | xstormy16 | xtensa \ | z8k) basic_machine=$basic_machine-unknown ;; m6811 | m68hc11 | m6812 | m68hc12) # Motorola 68HC11/12. basic_machine=$basic_machine-unknown os=-none ;; m88110 | m680[12346]0 | m683?2 | m68360 | m5200 | v70 | w65 | z8k) ;; ms1) basic_machine=mt-unknown ;; # We use `pc' rather than `unknown' # because (1) that's what they normally are, and # (2) the word "unknown" tends to confuse beginning users. i*86 | x86_64) basic_machine=$basic_machine-pc ;; # Object if more than one company name word. *-*-*) echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2 exit 1 ;; # Recognize the basic CPU types with company name. 580-* \ | a29k-* \ | alpha-* | alphaev[4-8]-* | alphaev56-* | alphaev6[78]-* \ | alpha64-* | alpha64ev[4-8]-* | alpha64ev56-* | alpha64ev6[78]-* \ | alphapca5[67]-* | alpha64pca5[67]-* | arc-* \ | arm-* | armbe-* | armle-* | armeb-* | armv*-* \ | avr-* | avr32-* \ | bfin-* | bs2000-* \ | c[123]* | c30-* | [cjt]90-* | c4x-* | c54x-* | c55x-* | c6x-* \ | clipper-* | craynv-* | cydra-* \ | d10v-* | d30v-* | dlx-* \ | elxsi-* \ | f30[01]-* | f700-* | fido-* | fr30-* | frv-* | fx80-* \ | h8300-* | h8500-* \ | hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \ | i*86-* | i860-* | i960-* | ia64-* \ | ip2k-* | iq2000-* \ | m32c-* | m32r-* | m32rle-* \ | m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \ | m88110-* | m88k-* | maxq-* | mcore-* \ | mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \ | mips16-* \ | mips64-* | mips64el-* \ | mips64vr-* | mips64vrel-* \ | mips64orion-* | mips64orionel-* \ | mips64vr4100-* | mips64vr4100el-* \ | mips64vr4300-* | mips64vr4300el-* \ | mips64vr5000-* | mips64vr5000el-* \ | mips64vr5900-* | mips64vr5900el-* \ | mipsisa32-* | mipsisa32el-* \ | mipsisa32r2-* | mipsisa32r2el-* \ | mipsisa64-* | mipsisa64el-* \ | mipsisa64r2-* | mipsisa64r2el-* \ | mipsisa64sb1-* | mipsisa64sb1el-* \ | mipsisa64sr71k-* | mipsisa64sr71kel-* \ | mipstx39-* | mipstx39el-* \ | mmix-* \ | mt-* \ | msp430-* \ | nios-* | nios2-* \ | none-* | np1-* | ns16k-* | ns32k-* \ | orion-* \ | pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \ | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \ | pyramid-* \ | romp-* | rs6000-* \ | sh-* | sh[1234]-* | sh[24]a-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \ | shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \ | sparc-* | sparc64-* | sparc64b-* | sparc64v-* | sparc86x-* | sparclet-* \ | sparclite-* \ | sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | strongarm-* | sv1-* | sx?-* \ | tahoe-* | thumb-* \ | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \ | tron-* \ | v850-* | v850e-* | vax-* \ | we32k-* \ | x86-* | x86_64-* | xc16x-* | xps100-* | xscale-* | xscalee[bl]-* \ | xstormy16-* | xtensa*-* \ | ymp-* \ | z8k-*) ;; # Recognize the basic CPU types without company name, with glob match. xtensa*) basic_machine=$basic_machine-unknown ;; # Recognize the various machine names and aliases which stand # for a CPU type and a company and sometimes even an OS. 386bsd) basic_machine=i386-unknown os=-bsd ;; 3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc) basic_machine=m68000-att ;; 3b*) basic_machine=we32k-att ;; a29khif) basic_machine=a29k-amd os=-udi ;; abacus) basic_machine=abacus-unknown ;; adobe68k) basic_machine=m68010-adobe os=-scout ;; alliant | fx80) basic_machine=fx80-alliant ;; altos | altos3068) basic_machine=m68k-altos ;; am29k) basic_machine=a29k-none os=-bsd ;; amd64) basic_machine=x86_64-pc ;; amd64-*) basic_machine=x86_64-`echo $basic_machine | sed 's/^[^-]*-//'` ;; amdahl) basic_machine=580-amdahl os=-sysv ;; amiga | amiga-*) basic_machine=m68k-unknown ;; amigaos | amigados) basic_machine=m68k-unknown os=-amigaos ;; amigaunix | amix) basic_machine=m68k-unknown os=-sysv4 ;; apollo68) basic_machine=m68k-apollo os=-sysv ;; apollo68bsd) basic_machine=m68k-apollo os=-bsd ;; aux) basic_machine=m68k-apple os=-aux ;; balance) basic_machine=ns32k-sequent os=-dynix ;; blackfin) basic_machine=bfin-unknown os=-linux ;; blackfin-*) basic_machine=bfin-`echo $basic_machine | sed 's/^[^-]*-//'` os=-linux ;; c90) basic_machine=c90-cray os=-unicos ;; convex-c1) basic_machine=c1-convex os=-bsd ;; convex-c2) basic_machine=c2-convex os=-bsd ;; convex-c32) basic_machine=c32-convex os=-bsd ;; convex-c34) basic_machine=c34-convex os=-bsd ;; convex-c38) basic_machine=c38-convex os=-bsd ;; cray | j90) basic_machine=j90-cray os=-unicos ;; craynv) basic_machine=craynv-cray os=-unicosmp ;; cr16) basic_machine=cr16-unknown os=-elf ;; crds | unos) basic_machine=m68k-crds ;; crisv32 | crisv32-* | etraxfs*) basic_machine=crisv32-axis ;; cris | cris-* | etrax*) basic_machine=cris-axis ;; crx) basic_machine=crx-unknown os=-elf ;; da30 | da30-*) basic_machine=m68k-da30 ;; decstation | decstation-3100 | pmax | pmax-* | pmin | dec3100 | decstatn) basic_machine=mips-dec ;; decsystem10* | dec10*) basic_machine=pdp10-dec os=-tops10 ;; decsystem20* | dec20*) basic_machine=pdp10-dec os=-tops20 ;; delta | 3300 | motorola-3300 | motorola-delta \ | 3300-motorola | delta-motorola) basic_machine=m68k-motorola ;; delta88) basic_machine=m88k-motorola os=-sysv3 ;; djgpp) basic_machine=i586-pc os=-msdosdjgpp ;; dpx20 | dpx20-*) basic_machine=rs6000-bull os=-bosx ;; dpx2* | dpx2*-bull) basic_machine=m68k-bull os=-sysv3 ;; ebmon29k) basic_machine=a29k-amd os=-ebmon ;; elxsi) basic_machine=elxsi-elxsi os=-bsd ;; encore | umax | mmax) basic_machine=ns32k-encore ;; es1800 | OSE68k | ose68k | ose | OSE) basic_machine=m68k-ericsson os=-ose ;; fx2800) basic_machine=i860-alliant ;; genix) basic_machine=ns32k-ns ;; gmicro) basic_machine=tron-gmicro os=-sysv ;; go32) basic_machine=i386-pc os=-go32 ;; h3050r* | hiux*) basic_machine=hppa1.1-hitachi os=-hiuxwe2 ;; h8300hms) basic_machine=h8300-hitachi os=-hms ;; h8300xray) basic_machine=h8300-hitachi os=-xray ;; h8500hms) basic_machine=h8500-hitachi os=-hms ;; harris) basic_machine=m88k-harris os=-sysv3 ;; hp300-*) basic_machine=m68k-hp ;; hp300bsd) basic_machine=m68k-hp os=-bsd ;; hp300hpux) basic_machine=m68k-hp os=-hpux ;; hp3k9[0-9][0-9] | hp9[0-9][0-9]) basic_machine=hppa1.0-hp ;; hp9k2[0-9][0-9] | hp9k31[0-9]) basic_machine=m68000-hp ;; hp9k3[2-9][0-9]) basic_machine=m68k-hp ;; hp9k6[0-9][0-9] | hp6[0-9][0-9]) basic_machine=hppa1.0-hp ;; hp9k7[0-79][0-9] | hp7[0-79][0-9]) basic_machine=hppa1.1-hp ;; hp9k78[0-9] | hp78[0-9]) # FIXME: really hppa2.0-hp basic_machine=hppa1.1-hp ;; hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893) # FIXME: really hppa2.0-hp basic_machine=hppa1.1-hp ;; hp9k8[0-9][13679] | hp8[0-9][13679]) basic_machine=hppa1.1-hp ;; hp9k8[0-9][0-9] | hp8[0-9][0-9]) basic_machine=hppa1.0-hp ;; hppa-next) os=-nextstep3 ;; hppaosf) basic_machine=hppa1.1-hp os=-osf ;; hppro) basic_machine=hppa1.1-hp os=-proelf ;; i370-ibm* | ibm*) basic_machine=i370-ibm ;; # I'm not sure what "Sysv32" means. Should this be sysv3.2? i*86v32) basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` os=-sysv32 ;; i*86v4*) basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` os=-sysv4 ;; i*86v) basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` os=-sysv ;; i*86sol2) basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` os=-solaris2 ;; i386mach) basic_machine=i386-mach os=-mach ;; i386-vsta | vsta) basic_machine=i386-unknown os=-vsta ;; iris | iris4d) basic_machine=mips-sgi case $os in -irix*) ;; *) os=-irix4 ;; esac ;; isi68 | isi) basic_machine=m68k-isi os=-sysv ;; m68knommu) basic_machine=m68k-unknown os=-linux ;; m68knommu-*) basic_machine=m68k-`echo $basic_machine | sed 's/^[^-]*-//'` os=-linux ;; m88k-omron*) basic_machine=m88k-omron ;; magnum | m3230) basic_machine=mips-mips os=-sysv ;; merlin) basic_machine=ns32k-utek os=-sysv ;; mingw32) basic_machine=i386-pc os=-mingw32 ;; mingw32ce) basic_machine=arm-unknown os=-mingw32ce ;; miniframe) basic_machine=m68000-convergent ;; *mint | -mint[0-9]* | *MiNT | *MiNT[0-9]*) basic_machine=m68k-atari os=-mint ;; mips3*-*) basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'` ;; mips3*) basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`-unknown ;; monitor) basic_machine=m68k-rom68k os=-coff ;; morphos) basic_machine=powerpc-unknown os=-morphos ;; msdos) basic_machine=i386-pc os=-msdos ;; ms1-*) basic_machine=`echo $basic_machine | sed -e 's/ms1-/mt-/'` ;; mvs) basic_machine=i370-ibm os=-mvs ;; ncr3000) basic_machine=i486-ncr os=-sysv4 ;; netbsd386) basic_machine=i386-unknown os=-netbsd ;; netwinder) basic_machine=armv4l-rebel os=-linux ;; news | news700 | news800 | news900) basic_machine=m68k-sony os=-newsos ;; news1000) basic_machine=m68030-sony os=-newsos ;; news-3600 | risc-news) basic_machine=mips-sony os=-newsos ;; necv70) basic_machine=v70-nec os=-sysv ;; next | m*-next ) basic_machine=m68k-next case $os in -nextstep* ) ;; -ns2*) os=-nextstep2 ;; *) os=-nextstep3 ;; esac ;; nh3000) basic_machine=m68k-harris os=-cxux ;; nh[45]000) basic_machine=m88k-harris os=-cxux ;; nindy960) basic_machine=i960-intel os=-nindy ;; mon960) basic_machine=i960-intel os=-mon960 ;; nonstopux) basic_machine=mips-compaq os=-nonstopux ;; np1) basic_machine=np1-gould ;; nsr-tandem) basic_machine=nsr-tandem ;; op50n-* | op60c-*) basic_machine=hppa1.1-oki os=-proelf ;; openrisc | openrisc-*) basic_machine=or32-unknown ;; os400) basic_machine=powerpc-ibm os=-os400 ;; OSE68000 | ose68000) basic_machine=m68000-ericsson os=-ose ;; os68k) basic_machine=m68k-none os=-os68k ;; pa-hitachi) basic_machine=hppa1.1-hitachi os=-hiuxwe2 ;; paragon) basic_machine=i860-intel os=-osf ;; parisc) basic_machine=hppa-unknown os=-linux ;; parisc-*) basic_machine=hppa-`echo $basic_machine | sed 's/^[^-]*-//'` os=-linux ;; pbd) basic_machine=sparc-tti ;; pbb) basic_machine=m68k-tti ;; pc532 | pc532-*) basic_machine=ns32k-pc532 ;; pc98) basic_machine=i386-pc ;; pc98-*) basic_machine=i386-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pentium | p5 | k5 | k6 | nexgen | viac3) basic_machine=i586-pc ;; pentiumpro | p6 | 6x86 | athlon | athlon_*) basic_machine=i686-pc ;; pentiumii | pentium2 | pentiumiii | pentium3) basic_machine=i686-pc ;; pentium4) basic_machine=i786-pc ;; pentium-* | p5-* | k5-* | k6-* | nexgen-* | viac3-*) basic_machine=i586-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pentiumpro-* | p6-* | 6x86-* | athlon-*) basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pentiumii-* | pentium2-* | pentiumiii-* | pentium3-*) basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pentium4-*) basic_machine=i786-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pn) basic_machine=pn-gould ;; power) basic_machine=power-ibm ;; ppc) basic_machine=powerpc-unknown ;; ppc-*) basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'` ;; ppcle | powerpclittle | ppc-le | powerpc-little) basic_machine=powerpcle-unknown ;; ppcle-* | powerpclittle-*) basic_machine=powerpcle-`echo $basic_machine | sed 's/^[^-]*-//'` ;; ppc64) basic_machine=powerpc64-unknown ;; ppc64-*) basic_machine=powerpc64-`echo $basic_machine | sed 's/^[^-]*-//'` ;; ppc64le | powerpc64little | ppc64-le | powerpc64-little) basic_machine=powerpc64le-unknown ;; ppc64le-* | powerpc64little-*) basic_machine=powerpc64le-`echo $basic_machine | sed 's/^[^-]*-//'` ;; ps2) basic_machine=i386-ibm ;; pw32) basic_machine=i586-unknown os=-pw32 ;; rdos) basic_machine=i386-pc os=-rdos ;; rom68k) basic_machine=m68k-rom68k os=-coff ;; rm[46]00) basic_machine=mips-siemens ;; rtpc | rtpc-*) basic_machine=romp-ibm ;; s390 | s390-*) basic_machine=s390-ibm ;; s390x | s390x-*) basic_machine=s390x-ibm ;; sa29200) basic_machine=a29k-amd os=-udi ;; sb1) basic_machine=mipsisa64sb1-unknown ;; sb1el) basic_machine=mipsisa64sb1el-unknown ;; sde) basic_machine=mipsisa32-sde os=-elf ;; sei) basic_machine=mips-sei os=-seiux ;; sequent) basic_machine=i386-sequent ;; sh) basic_machine=sh-hitachi os=-hms ;; sh5el) basic_machine=sh5le-unknown ;; sh64) basic_machine=sh64-unknown ;; sparclite-wrs | simso-wrs) basic_machine=sparclite-wrs os=-vxworks ;; sps7) basic_machine=m68k-bull os=-sysv2 ;; spur) basic_machine=spur-unknown ;; st2000) basic_machine=m68k-tandem ;; stratus) basic_machine=i860-stratus os=-sysv4 ;; sun2) basic_machine=m68000-sun ;; sun2os3) basic_machine=m68000-sun os=-sunos3 ;; sun2os4) basic_machine=m68000-sun os=-sunos4 ;; sun3os3) basic_machine=m68k-sun os=-sunos3 ;; sun3os4) basic_machine=m68k-sun os=-sunos4 ;; sun4os3) basic_machine=sparc-sun os=-sunos3 ;; sun4os4) basic_machine=sparc-sun os=-sunos4 ;; sun4sol2) basic_machine=sparc-sun os=-solaris2 ;; sun3 | sun3-*) basic_machine=m68k-sun ;; sun4) basic_machine=sparc-sun ;; sun386 | sun386i | roadrunner) basic_machine=i386-sun ;; sv1) basic_machine=sv1-cray os=-unicos ;; symmetry) basic_machine=i386-sequent os=-dynix ;; t3e) basic_machine=alphaev5-cray os=-unicos ;; t90) basic_machine=t90-cray os=-unicos ;; tic54x | c54x*) basic_machine=tic54x-unknown os=-coff ;; tic55x | c55x*) basic_machine=tic55x-unknown os=-coff ;; tic6x | c6x*) basic_machine=tic6x-unknown os=-coff ;; tile*) basic_machine=tile-unknown os=-linux-gnu ;; tx39) basic_machine=mipstx39-unknown ;; tx39el) basic_machine=mipstx39el-unknown ;; toad1) basic_machine=pdp10-xkl os=-tops20 ;; tower | tower-32) basic_machine=m68k-ncr ;; tpf) basic_machine=s390x-ibm os=-tpf ;; udi29k) basic_machine=a29k-amd os=-udi ;; ultra3) basic_machine=a29k-nyu os=-sym1 ;; v810 | necv810) basic_machine=v810-nec os=-none ;; vaxv) basic_machine=vax-dec os=-sysv ;; vms) basic_machine=vax-dec os=-vms ;; vpp*|vx|vx-*) basic_machine=f301-fujitsu ;; vxworks960) basic_machine=i960-wrs os=-vxworks ;; vxworks68) basic_machine=m68k-wrs os=-vxworks ;; vxworks29k) basic_machine=a29k-wrs os=-vxworks ;; w65*) basic_machine=w65-wdc os=-none ;; w89k-*) basic_machine=hppa1.1-winbond os=-proelf ;; xbox) basic_machine=i686-pc os=-mingw32 ;; xps | xps100) basic_machine=xps100-honeywell ;; ymp) basic_machine=ymp-cray os=-unicos ;; z8k-*-coff) basic_machine=z8k-unknown os=-sim ;; none) basic_machine=none-none os=-none ;; # Here we handle the default manufacturer of certain CPU types. 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See the # GNU General Public License for more details. # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA # 02110-1301, USA. # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that program. # Originally written by Alexandre Oliva . case $1 in '') echo "$0: No command. Try \`$0 --help' for more information." 1>&2 exit 1; ;; -h | --h*) cat <<\EOF Usage: depcomp [--help] [--version] PROGRAM [ARGS] Run PROGRAMS ARGS to compile a file, generating dependencies as side-effects. Environment variables: depmode Dependency tracking mode. source Source file read by `PROGRAMS ARGS'. object Object file output by `PROGRAMS ARGS'. DEPDIR directory where to store dependencies. depfile Dependency file to output. tmpdepfile Temporary file to use when outputing dependencies. libtool Whether libtool is used (yes/no). Report bugs to . EOF exit $? ;; -v | --v*) echo "depcomp $scriptversion" exit $? ;; esac if test -z "$depmode" || test -z "$source" || test -z "$object"; then echo "depcomp: Variables source, object and depmode must be set" 1>&2 exit 1 fi # Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po. depfile=${depfile-`echo "$object" | sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`} tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`} rm -f "$tmpdepfile" # Some modes work just like other modes, but use different flags. We # parameterize here, but still list the modes in the big case below, # to make depend.m4 easier to write. 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However on # icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c # ICC 7.0 will fill foo.d with something like # foo.o: sub/foo.c # foo.o: sub/foo.h # which is wrong. We want: # sub/foo.o: sub/foo.c # sub/foo.o: sub/foo.h # sub/foo.c: # sub/foo.h: # ICC 7.1 will output # foo.o: sub/foo.c sub/foo.h # and will wrap long lines using \ : # foo.o: sub/foo.c ... \ # sub/foo.h ... \ # ... "$@" -MD -MF "$tmpdepfile" stat=$? if test $stat -eq 0; then : else rm -f "$tmpdepfile" exit $stat fi rm -f "$depfile" # Each line is of the form `foo.o: dependent.h', # or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'. # Do two passes, one to just change these to # `$object: dependent.h' and one to simply `dependent.h:'. sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile" # Some versions of the HPUX 10.20 sed can't process this invocation # correctly. Breaking it into two sed invocations is a workaround. sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" | sed -e 's/$/ :/' >> "$depfile" rm -f "$tmpdepfile" ;; hp2) # The "hp" stanza above does not work with aCC (C++) and HP's ia64 # compilers, which have integrated preprocessors. 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If an odd number of `\' preceded a '$' # in input to double_quote_subst, that '$' was protected from expansion. # Since each input `\' is now two `\'s, look for any number of runs of # four `\'s followed by two `\'s and then a '$'. `\' that '$'. bs='\\' bs2='\\\\' bs4='\\\\\\\\' dollar='\$' sed_double_backslash="\ s/$bs4/&\\ /g s/^$bs2$dollar/$bs&/ s/\\([^$bs]\\)$bs2$dollar/\\1$bs2$bs$dollar/g s/\n//g" # Standard options: opt_dry_run=false opt_help=false opt_quiet=false opt_verbose=false opt_warning=: # func_echo arg... # Echo program name prefixed message, along with the current mode # name if it has been set yet. func_echo () { $ECHO "$progname${mode+: }$mode: $*" } # func_verbose arg... # Echo program name prefixed message in verbose mode only. func_verbose () { $opt_verbose && func_echo ${1+"$@"} # A bug in bash halts the script if the last line of a function # fails when set -e is in force, so we need another command to # work around that: : } # func_error arg... # Echo program name prefixed message to standard error. func_error () { $ECHO "$progname${mode+: }$mode: "${1+"$@"} 1>&2 } # func_warning arg... # Echo program name prefixed warning message to standard error. func_warning () { $opt_warning && $ECHO "$progname${mode+: }$mode: warning: "${1+"$@"} 1>&2 # bash bug again: : } # func_fatal_error arg... # Echo program name prefixed message to standard error, and exit. func_fatal_error () { func_error ${1+"$@"} exit $EXIT_FAILURE } # func_fatal_help arg... # Echo program name prefixed message to standard error, followed by # a help hint, and exit. func_fatal_help () { func_error ${1+"$@"} func_fatal_error "$help" } help="Try \`$progname --help' for more information." ## default # func_grep expression filename # Check whether EXPRESSION matches any line of FILENAME, without output. func_grep () { $GREP "$1" "$2" >/dev/null 2>&1 } # func_mkdir_p directory-path # Make sure the entire path to DIRECTORY-PATH is available. func_mkdir_p () { my_directory_path="$1" my_dir_list= if test -n "$my_directory_path" && test "$opt_dry_run" != ":"; then # Protect directory names starting with `-' case $my_directory_path in -*) my_directory_path="./$my_directory_path" ;; esac # While some portion of DIR does not yet exist... while test ! -d "$my_directory_path"; do # ...make a list in topmost first order. Use a colon delimited # list incase some portion of path contains whitespace. my_dir_list="$my_directory_path:$my_dir_list" # If the last portion added has no slash in it, the list is done case $my_directory_path in */*) ;; *) break ;; esac # ...otherwise throw away the child directory and loop my_directory_path=`$ECHO "X$my_directory_path" | $Xsed -e "$dirname"` done my_dir_list=`$ECHO "X$my_dir_list" | $Xsed -e 's,:*$,,'` save_mkdir_p_IFS="$IFS"; IFS=':' for my_dir in $my_dir_list; do IFS="$save_mkdir_p_IFS" # mkdir can fail with a `File exist' error if two processes # try to create one of the directories concurrently. Don't # stop in that case! $MKDIR "$my_dir" 2>/dev/null || : done IFS="$save_mkdir_p_IFS" # Bail out if we (or some other process) failed to create a directory. test -d "$my_directory_path" || \ func_fatal_error "Failed to create \`$1'" fi } # func_mktempdir [string] # Make a temporary directory that won't clash with other running # libtool processes, and avoids race conditions if possible. If # given, STRING is the basename for that directory. func_mktempdir () { my_template="${TMPDIR-/tmp}/${1-$progname}" if test "$opt_dry_run" = ":"; then # Return a directory name, but don't create it in dry-run mode my_tmpdir="${my_template}-$$" else # If mktemp works, use that first and foremost my_tmpdir=`mktemp -d "${my_template}-XXXXXXXX" 2>/dev/null` if test ! -d "$my_tmpdir"; then # Failing that, at least try and use $RANDOM to avoid a race my_tmpdir="${my_template}-${RANDOM-0}$$" save_mktempdir_umask=`umask` umask 0077 $MKDIR "$my_tmpdir" umask $save_mktempdir_umask fi # If we're not in dry-run mode, bomb out on failure test -d "$my_tmpdir" || \ func_fatal_error "cannot create temporary directory \`$my_tmpdir'" fi $ECHO "X$my_tmpdir" | $Xsed } # func_quote_for_eval arg # Aesthetically quote ARG to be evaled later. # This function returns two values: FUNC_QUOTE_FOR_EVAL_RESULT # is double-quoted, suitable for a subsequent eval, whereas # FUNC_QUOTE_FOR_EVAL_UNQUOTED_RESULT has merely all characters # which are still active within double quotes backslashified. func_quote_for_eval () { case $1 in *[\\\`\"\$]*) func_quote_for_eval_unquoted_result=`$ECHO "X$1" | $Xsed -e "$sed_quote_subst"` ;; *) func_quote_for_eval_unquoted_result="$1" ;; esac case $func_quote_for_eval_unquoted_result in # Double-quote args containing shell metacharacters to delay # word splitting, command substitution and and variable # expansion for a subsequent eval. # Many Bourne shells cannot handle close brackets correctly # in scan sets, so we specify it separately. *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \ ]*|*]*|"") func_quote_for_eval_result="\"$func_quote_for_eval_unquoted_result\"" ;; *) func_quote_for_eval_result="$func_quote_for_eval_unquoted_result" esac } # func_quote_for_expand arg # Aesthetically quote ARG to be evaled later; same as above, # but do not quote variable references. func_quote_for_expand () { case $1 in *[\\\`\"]*) my_arg=`$ECHO "X$1" | $Xsed \ -e "$double_quote_subst" -e "$sed_double_backslash"` ;; *) my_arg="$1" ;; esac case $my_arg in # Double-quote args containing shell metacharacters to delay # word splitting and command substitution for a subsequent eval. # Many Bourne shells cannot handle close brackets correctly # in scan sets, so we specify it separately. *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \ ]*|*]*|"") my_arg="\"$my_arg\"" ;; esac func_quote_for_expand_result="$my_arg" } # func_show_eval cmd [fail_exp] # Unless opt_silent is true, then output CMD. Then, if opt_dryrun is # not true, evaluate CMD. If the evaluation of CMD fails, and FAIL_EXP # is given, then evaluate it. func_show_eval () { my_cmd="$1" my_fail_exp="${2-:}" ${opt_silent-false} || { func_quote_for_expand "$my_cmd" eval "func_echo $func_quote_for_expand_result" } if ${opt_dry_run-false}; then :; else eval "$my_cmd" my_status=$? if test "$my_status" -eq 0; then :; else eval "(exit $my_status); $my_fail_exp" fi fi } # func_show_eval_locale cmd [fail_exp] # Unless opt_silent is true, then output CMD. Then, if opt_dryrun is # not true, evaluate CMD. If the evaluation of CMD fails, and FAIL_EXP # is given, then evaluate it. Use the saved locale for evaluation. func_show_eval_locale () { my_cmd="$1" my_fail_exp="${2-:}" ${opt_silent-false} || { func_quote_for_expand "$my_cmd" eval "func_echo $func_quote_for_expand_result" } if ${opt_dry_run-false}; then :; else eval "$lt_user_locale $my_cmd" my_status=$? eval "$lt_safe_locale" if test "$my_status" -eq 0; then :; else eval "(exit $my_status); $my_fail_exp" fi fi } # func_version # Echo version message to standard output and exit. func_version () { $SED -n '/^# '$PROGRAM' (GNU /,/# warranty; / { s/^# // s/^# *$// s/\((C)\)[ 0-9,-]*\( [1-9][0-9]*\)/\1\2/ p }' < "$progpath" exit $? } # func_usage # Echo short help message to standard output and exit. func_usage () { $SED -n '/^# Usage:/,/# -h/ { s/^# // s/^# *$// s/\$progname/'$progname'/ p }' < "$progpath" $ECHO $ECHO "run \`$progname --help | more' for full usage" exit $? } # func_help # Echo long help message to standard output and exit. func_help () { $SED -n '/^# Usage:/,/# Report bugs to/ { s/^# // s/^# *$// s*\$progname*'$progname'* s*\$host*'"$host"'* s*\$SHELL*'"$SHELL"'* s*\$LTCC*'"$LTCC"'* s*\$LTCFLAGS*'"$LTCFLAGS"'* s*\$LD*'"$LD"'* s/\$with_gnu_ld/'"$with_gnu_ld"'/ s/\$automake_version/'"`(automake --version) 2>/dev/null |$SED 1q`"'/ s/\$autoconf_version/'"`(autoconf --version) 2>/dev/null |$SED 1q`"'/ p }' < "$progpath" exit $? } # func_missing_arg argname # Echo program name prefixed message to standard error and set global # exit_cmd. func_missing_arg () { func_error "missing argument for $1" exit_cmd=exit } exit_cmd=: # Check that we have a working $ECHO. if test "X$1" = X--no-reexec; then # Discard the --no-reexec flag, and continue. shift elif test "X$1" = X--fallback-echo; then # Avoid inline document here, it may be left over : elif test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t'; then # Yippee, $ECHO works! : else # Restart under the correct shell, and then maybe $ECHO will work. exec $SHELL "$progpath" --no-reexec ${1+"$@"} fi if test "X$1" = X--fallback-echo; then # used as fallback echo shift cat </dev/null 2>&1; then taglist="$taglist $tagname" # Evaluate the configuration. Be careful to quote the path # and the sed script, to avoid splitting on whitespace, but # also don't use non-portable quotes within backquotes within # quotes we have to do it in 2 steps: extractedcf=`$SED -n -e "$sed_extractcf" < "$progpath"` eval "$extractedcf" else func_error "ignoring unknown tag $tagname" fi ;; esac } # Parse options once, thoroughly. This comes as soon as possible in # the script to make things like `libtool --version' happen quickly. { # Shorthand for --mode=foo, only valid as the first argument case $1 in clean|clea|cle|cl) shift; set dummy --mode clean ${1+"$@"}; shift ;; compile|compil|compi|comp|com|co|c) shift; set dummy --mode compile ${1+"$@"}; shift ;; execute|execut|execu|exec|exe|ex|e) shift; set dummy --mode execute ${1+"$@"}; shift ;; finish|finis|fini|fin|fi|f) shift; set dummy --mode finish ${1+"$@"}; shift ;; install|instal|insta|inst|ins|in|i) shift; set dummy --mode install ${1+"$@"}; shift ;; link|lin|li|l) shift; set dummy --mode link ${1+"$@"}; shift ;; uninstall|uninstal|uninsta|uninst|unins|unin|uni|un|u) shift; set dummy --mode uninstall ${1+"$@"}; shift ;; esac # Parse non-mode specific arguments: while test "$#" -gt 0; do opt="$1" shift case $opt in --config) func_config ;; --debug) preserve_args="$preserve_args $opt" func_echo "enabling shell trace mode" opt_debug='set -x' $opt_debug ;; -dlopen) test "$#" -eq 0 && func_missing_arg "$opt" && break execute_dlfiles="$execute_dlfiles $1" shift ;; --dry-run | -n) opt_dry_run=: ;; --features) func_features ;; --finish) mode="finish" ;; --mode) test "$#" -eq 0 && func_missing_arg "$opt" && break case $1 in # Valid mode arguments: clean) ;; compile) ;; execute) ;; finish) ;; install) ;; link) ;; relink) ;; uninstall) ;; # Catch anything else as an error *) func_error "invalid argument for $opt" exit_cmd=exit break ;; esac mode="$1" shift ;; --preserve-dup-deps) opt_duplicate_deps=: ;; --quiet|--silent) preserve_args="$preserve_args $opt" opt_silent=: ;; --verbose| -v) preserve_args="$preserve_args $opt" opt_silent=false ;; --tag) test "$#" -eq 0 && func_missing_arg "$opt" && break preserve_args="$preserve_args $opt $1" func_enable_tag "$1" # tagname is set here shift ;; # Separate optargs to long options: -dlopen=*|--mode=*|--tag=*) func_opt_split "$opt" set dummy "$func_opt_split_opt" "$func_opt_split_arg" ${1+"$@"} shift ;; -\?|-h) func_usage ;; --help) opt_help=: ;; --version) func_version ;; -*) func_fatal_help "unrecognized option \`$opt'" ;; *) nonopt="$opt" break ;; esac done case $host in *cygwin* | *mingw* | *pw32* | *cegcc*) # don't eliminate duplications in $postdeps and $predeps opt_duplicate_compiler_generated_deps=: ;; *) opt_duplicate_compiler_generated_deps=$opt_duplicate_deps ;; esac # Having warned about all mis-specified options, bail out if # anything was wrong. $exit_cmd $EXIT_FAILURE } # func_check_version_match # Ensure that we are using m4 macros, and libtool script from the same # release of libtool. func_check_version_match () { if test "$package_revision" != "$macro_revision"; then if test "$VERSION" != "$macro_version"; then if test -z "$macro_version"; then cat >&2 <<_LT_EOF $progname: Version mismatch error. This is $PACKAGE $VERSION, but the $progname: definition of this LT_INIT comes from an older release. $progname: You should recreate aclocal.m4 with macros from $PACKAGE $VERSION $progname: and run autoconf again. _LT_EOF else cat >&2 <<_LT_EOF $progname: Version mismatch error. This is $PACKAGE $VERSION, but the $progname: definition of this LT_INIT comes from $PACKAGE $macro_version. $progname: You should recreate aclocal.m4 with macros from $PACKAGE $VERSION $progname: and run autoconf again. _LT_EOF fi else cat >&2 <<_LT_EOF $progname: Version mismatch error. This is $PACKAGE $VERSION, revision $package_revision, $progname: but the definition of this LT_INIT comes from revision $macro_revision. $progname: You should recreate aclocal.m4 with macros from revision $package_revision $progname: of $PACKAGE $VERSION and run autoconf again. _LT_EOF fi exit $EXIT_MISMATCH fi } ## ----------- ## ## Main. ## ## ----------- ## $opt_help || { # Sanity checks first: func_check_version_match if test "$build_libtool_libs" != yes && test "$build_old_libs" != yes; then func_fatal_configuration "not configured to build any kind of library" fi test -z "$mode" && func_fatal_error "error: you must specify a MODE." # Darwin sucks eval std_shrext=\"$shrext_cmds\" # Only execute mode is allowed to have -dlopen flags. if test -n "$execute_dlfiles" && test "$mode" != execute; then func_error "unrecognized option \`-dlopen'" $ECHO "$help" 1>&2 exit $EXIT_FAILURE fi # Change the help message to a mode-specific one. generic_help="$help" help="Try \`$progname --help --mode=$mode' for more information." } # func_lalib_p file # True iff FILE is a libtool `.la' library or `.lo' object file. # This function is only a basic sanity check; it will hardly flush out # determined imposters. func_lalib_p () { test -f "$1" && $SED -e 4q "$1" 2>/dev/null \ | $GREP "^# Generated by .*$PACKAGE" > /dev/null 2>&1 } # func_lalib_unsafe_p file # True iff FILE is a libtool `.la' library or `.lo' object file. # This function implements the same check as func_lalib_p without # resorting to external programs. To this end, it redirects stdin and # closes it afterwards, without saving the original file descriptor. # As a safety measure, use it only where a negative result would be # fatal anyway. Works if `file' does not exist. func_lalib_unsafe_p () { lalib_p=no if test -f "$1" && test -r "$1" && exec 5<&0 <"$1"; then for lalib_p_l in 1 2 3 4 do read lalib_p_line case "$lalib_p_line" in \#\ Generated\ by\ *$PACKAGE* ) lalib_p=yes; break;; esac done exec 0<&5 5<&- fi test "$lalib_p" = yes } # func_ltwrapper_script_p file # True iff FILE is a libtool wrapper script # This function is only a basic sanity check; it will hardly flush out # determined imposters. func_ltwrapper_script_p () { func_lalib_p "$1" } # func_ltwrapper_executable_p file # True iff FILE is a libtool wrapper executable # This function is only a basic sanity check; it will hardly flush out # determined imposters. func_ltwrapper_executable_p () { func_ltwrapper_exec_suffix= case $1 in *.exe) ;; *) func_ltwrapper_exec_suffix=.exe ;; esac $GREP "$magic_exe" "$1$func_ltwrapper_exec_suffix" >/dev/null 2>&1 } # func_ltwrapper_scriptname file # Assumes file is an ltwrapper_executable # uses $file to determine the appropriate filename for a # temporary ltwrapper_script. func_ltwrapper_scriptname () { func_ltwrapper_scriptname_result="" if func_ltwrapper_executable_p "$1"; then func_dirname_and_basename "$1" "" "." func_stripname '' '.exe' "$func_basename_result" func_ltwrapper_scriptname_result="$func_dirname_result/$objdir/${func_stripname_result}_ltshwrapper" fi } # func_ltwrapper_p file # True iff FILE is a libtool wrapper script or wrapper executable # This function is only a basic sanity check; it will hardly flush out # determined imposters. func_ltwrapper_p () { func_ltwrapper_script_p "$1" || func_ltwrapper_executable_p "$1" } # func_execute_cmds commands fail_cmd # Execute tilde-delimited COMMANDS. # If FAIL_CMD is given, eval that upon failure. # FAIL_CMD may read-access the current command in variable CMD! func_execute_cmds () { $opt_debug save_ifs=$IFS; IFS='~' for cmd in $1; do IFS=$save_ifs eval cmd=\"$cmd\" func_show_eval "$cmd" "${2-:}" done IFS=$save_ifs } # func_source file # Source FILE, adding directory component if necessary. # Note that it is not necessary on cygwin/mingw to append a dot to # FILE even if both FILE and FILE.exe exist: automatic-append-.exe # behavior happens only for exec(3), not for open(2)! Also, sourcing # `FILE.' does not work on cygwin managed mounts. func_source () { $opt_debug case $1 in */* | *\\*) . "$1" ;; *) . "./$1" ;; esac } # func_infer_tag arg # Infer tagged configuration to use if any are available and # if one wasn't chosen via the "--tag" command line option. # Only attempt this if the compiler in the base compile # command doesn't match the default compiler. # arg is usually of the form 'gcc ...' func_infer_tag () { $opt_debug if test -n "$available_tags" && test -z "$tagname"; then CC_quoted= for arg in $CC; do func_quote_for_eval "$arg" CC_quoted="$CC_quoted $func_quote_for_eval_result" done case $@ in # Blanks in the command may have been stripped by the calling shell, # but not from the CC environment variable when configure was run. " $CC "* | "$CC "* | " `$ECHO $CC` "* | "`$ECHO $CC` "* | " $CC_quoted"* | "$CC_quoted "* | " `$ECHO $CC_quoted` "* | "`$ECHO $CC_quoted` "*) ;; # Blanks at the start of $base_compile will cause this to fail # if we don't check for them as well. *) for z in $available_tags; do if $GREP "^# ### BEGIN LIBTOOL TAG CONFIG: $z$" < "$progpath" > /dev/null; then # Evaluate the configuration. eval "`${SED} -n -e '/^# ### BEGIN LIBTOOL TAG CONFIG: '$z'$/,/^# ### END LIBTOOL TAG CONFIG: '$z'$/p' < $progpath`" CC_quoted= for arg in $CC; do # Double-quote args containing other shell metacharacters. func_quote_for_eval "$arg" CC_quoted="$CC_quoted $func_quote_for_eval_result" done case "$@ " in " $CC "* | "$CC "* | " `$ECHO $CC` "* | "`$ECHO $CC` "* | " $CC_quoted"* | "$CC_quoted "* | " `$ECHO $CC_quoted` "* | "`$ECHO $CC_quoted` "*) # The compiler in the base compile command matches # the one in the tagged configuration. # Assume this is the tagged configuration we want. tagname=$z break ;; esac fi done # If $tagname still isn't set, then no tagged configuration # was found and let the user know that the "--tag" command # line option must be used. if test -z "$tagname"; then func_echo "unable to infer tagged configuration" func_fatal_error "specify a tag with \`--tag'" # else # func_verbose "using $tagname tagged configuration" fi ;; esac fi } # func_write_libtool_object output_name pic_name nonpic_name # Create a libtool object file (analogous to a ".la" file), # but don't create it if we're doing a dry run. func_write_libtool_object () { write_libobj=${1} if test "$build_libtool_libs" = yes; then write_lobj=\'${2}\' else write_lobj=none fi if test "$build_old_libs" = yes; then write_oldobj=\'${3}\' else write_oldobj=none fi $opt_dry_run || { cat >${write_libobj}T <?"'"'"' &()|`$[]' \ && func_warning "libobj name \`$libobj' may not contain shell special characters." func_dirname_and_basename "$obj" "/" "" objname="$func_basename_result" xdir="$func_dirname_result" lobj=${xdir}$objdir/$objname test -z "$base_compile" && \ func_fatal_help "you must specify a compilation command" # Delete any leftover library objects. if test "$build_old_libs" = yes; then removelist="$obj $lobj $libobj ${libobj}T" else removelist="$lobj $libobj ${libobj}T" fi # On Cygwin there's no "real" PIC flag so we must build both object types case $host_os in cygwin* | mingw* | pw32* | os2* | cegcc*) pic_mode=default ;; esac if test "$pic_mode" = no && test "$deplibs_check_method" != pass_all; then # non-PIC code in shared libraries is not supported pic_mode=default fi # Calculate the filename of the output object if compiler does # not support -o with -c if test "$compiler_c_o" = no; then output_obj=`$ECHO "X$srcfile" | $Xsed -e 's%^.*/%%' -e 's%\.[^.]*$%%'`.${objext} lockfile="$output_obj.lock" else output_obj= need_locks=no lockfile= fi # Lock this critical section if it is needed # We use this script file to make the link, it avoids creating a new file if test "$need_locks" = yes; then until $opt_dry_run || ln "$progpath" "$lockfile" 2>/dev/null; do func_echo "Waiting for $lockfile to be removed" sleep 2 done elif test "$need_locks" = warn; then if test -f "$lockfile"; then $ECHO "\ *** ERROR, $lockfile exists and contains: `cat $lockfile 2>/dev/null` This indicates that another process is trying to use the same temporary object file, and libtool could not work around it because your compiler does not support \`-c' and \`-o' together. If you repeat this compilation, it may succeed, by chance, but you had better avoid parallel builds (make -j) in this platform, or get a better compiler." $opt_dry_run || $RM $removelist exit $EXIT_FAILURE fi removelist="$removelist $output_obj" $ECHO "$srcfile" > "$lockfile" fi $opt_dry_run || $RM $removelist removelist="$removelist $lockfile" trap '$opt_dry_run || $RM $removelist; exit $EXIT_FAILURE' 1 2 15 if test -n "$fix_srcfile_path"; then eval srcfile=\"$fix_srcfile_path\" fi func_quote_for_eval "$srcfile" qsrcfile=$func_quote_for_eval_result # Only build a PIC object if we are building libtool libraries. if test "$build_libtool_libs" = yes; then # Without this assignment, base_compile gets emptied. fbsd_hideous_sh_bug=$base_compile if test "$pic_mode" != no; then command="$base_compile $qsrcfile $pic_flag" else # Don't build PIC code command="$base_compile $qsrcfile" fi func_mkdir_p "$xdir$objdir" if test -z "$output_obj"; then # Place PIC objects in $objdir command="$command -o $lobj" fi func_show_eval_locale "$command" \ 'test -n "$output_obj" && $RM $removelist; exit $EXIT_FAILURE' if test "$need_locks" = warn && test "X`cat $lockfile 2>/dev/null`" != "X$srcfile"; then $ECHO "\ *** ERROR, $lockfile contains: `cat $lockfile 2>/dev/null` but it should contain: $srcfile This indicates that another process is trying to use the same temporary object file, and libtool could not work around it because your compiler does not support \`-c' and \`-o' together. If you repeat this compilation, it may succeed, by chance, but you had better avoid parallel builds (make -j) in this platform, or get a better compiler." $opt_dry_run || $RM $removelist exit $EXIT_FAILURE fi # Just move the object if needed, then go on to compile the next one if test -n "$output_obj" && test "X$output_obj" != "X$lobj"; then func_show_eval '$MV "$output_obj" "$lobj"' \ 'error=$?; $opt_dry_run || $RM $removelist; exit $error' fi # Allow error messages only from the first compilation. if test "$suppress_opt" = yes; then suppress_output=' >/dev/null 2>&1' fi fi # Only build a position-dependent object if we build old libraries. if test "$build_old_libs" = yes; then if test "$pic_mode" != yes; then # Don't build PIC code command="$base_compile $qsrcfile$pie_flag" else command="$base_compile $qsrcfile $pic_flag" fi if test "$compiler_c_o" = yes; then command="$command -o $obj" fi # Suppress compiler output if we already did a PIC compilation. command="$command$suppress_output" func_show_eval_locale "$command" \ '$opt_dry_run || $RM $removelist; exit $EXIT_FAILURE' if test "$need_locks" = warn && test "X`cat $lockfile 2>/dev/null`" != "X$srcfile"; then $ECHO "\ *** ERROR, $lockfile contains: `cat $lockfile 2>/dev/null` but it should contain: $srcfile This indicates that another process is trying to use the same temporary object file, and libtool could not work around it because your compiler does not support \`-c' and \`-o' together. If you repeat this compilation, it may succeed, by chance, but you had better avoid parallel builds (make -j) in this platform, or get a better compiler." $opt_dry_run || $RM $removelist exit $EXIT_FAILURE fi # Just move the object if needed if test -n "$output_obj" && test "X$output_obj" != "X$obj"; then func_show_eval '$MV "$output_obj" "$obj"' \ 'error=$?; $opt_dry_run || $RM $removelist; exit $error' fi fi $opt_dry_run || { func_write_libtool_object "$libobj" "$objdir/$objname" "$objname" # Unlock the critical section if it was locked if test "$need_locks" != no; then removelist=$lockfile $RM "$lockfile" fi } exit $EXIT_SUCCESS } $opt_help || { test "$mode" = compile && func_mode_compile ${1+"$@"} } func_mode_help () { # We need to display help for each of the modes. case $mode in "") # Generic help is extracted from the usage comments # at the start of this file. func_help ;; clean) $ECHO \ "Usage: $progname [OPTION]... --mode=clean RM [RM-OPTION]... FILE... Remove files from the build directory. RM is the name of the program to use to delete files associated with each FILE (typically \`/bin/rm'). RM-OPTIONS are options (such as \`-f') to be passed to RM. If FILE is a libtool library, object or program, all the files associated with it are deleted. Otherwise, only FILE itself is deleted using RM." ;; compile) $ECHO \ "Usage: $progname [OPTION]... --mode=compile COMPILE-COMMAND... SOURCEFILE Compile a source file into a libtool library object. This mode accepts the following additional options: -o OUTPUT-FILE set the output file name to OUTPUT-FILE -no-suppress do not suppress compiler output for multiple passes -prefer-pic try to building PIC objects only -prefer-non-pic try to building non-PIC objects only -shared do not build a \`.o' file suitable for static linking -static only build a \`.o' file suitable for static linking COMPILE-COMMAND is a command to be used in creating a \`standard' object file from the given SOURCEFILE. The output file name is determined by removing the directory component from SOURCEFILE, then substituting the C source code suffix \`.c' with the library object suffix, \`.lo'." ;; execute) $ECHO \ "Usage: $progname [OPTION]... --mode=execute COMMAND [ARGS]... Automatically set library path, then run a program. This mode accepts the following additional options: -dlopen FILE add the directory containing FILE to the library path This mode sets the library path environment variable according to \`-dlopen' flags. If any of the ARGS are libtool executable wrappers, then they are translated into their corresponding uninstalled binary, and any of their required library directories are added to the library path. Then, COMMAND is executed, with ARGS as arguments." ;; finish) $ECHO \ "Usage: $progname [OPTION]... --mode=finish [LIBDIR]... Complete the installation of libtool libraries. Each LIBDIR is a directory that contains libtool libraries. The commands that this mode executes may require superuser privileges. Use the \`--dry-run' option if you just want to see what would be executed." ;; install) $ECHO \ "Usage: $progname [OPTION]... --mode=install INSTALL-COMMAND... Install executables or libraries. INSTALL-COMMAND is the installation command. The first component should be either the \`install' or \`cp' program. The following components of INSTALL-COMMAND are treated specially: -inst-prefix PREFIX-DIR Use PREFIX-DIR as a staging area for installation The rest of the components are interpreted as arguments to that command (only BSD-compatible install options are recognized)." ;; link) $ECHO \ "Usage: $progname [OPTION]... --mode=link LINK-COMMAND... Link object files or libraries together to form another library, or to create an executable program. LINK-COMMAND is a command using the C compiler that you would use to create a program from several object files. The following components of LINK-COMMAND are treated specially: -all-static do not do any dynamic linking at all -avoid-version do not add a version suffix if possible -dlopen FILE \`-dlpreopen' FILE if it cannot be dlopened at runtime -dlpreopen FILE link in FILE and add its symbols to lt_preloaded_symbols -export-dynamic allow symbols from OUTPUT-FILE to be resolved with dlsym(3) -export-symbols SYMFILE try to export only the symbols listed in SYMFILE -export-symbols-regex REGEX try to export only the symbols matching REGEX -LLIBDIR search LIBDIR for required installed libraries -lNAME OUTPUT-FILE requires the installed library libNAME -module build a library that can dlopened -no-fast-install disable the fast-install mode -no-install link a not-installable executable -no-undefined declare that a library does not refer to external symbols -o OUTPUT-FILE create OUTPUT-FILE from the specified objects -objectlist FILE Use a list of object files found in FILE to specify objects -precious-files-regex REGEX don't remove output files matching REGEX -release RELEASE specify package release information -rpath LIBDIR the created library will eventually be installed in LIBDIR -R[ ]LIBDIR add LIBDIR to the runtime path of programs and libraries -shared only do dynamic linking of libtool libraries -shrext SUFFIX override the standard shared library file extension -static do not do any dynamic linking of uninstalled libtool libraries -static-libtool-libs do not do any dynamic linking of libtool libraries -version-info CURRENT[:REVISION[:AGE]] specify library version info [each variable defaults to 0] -weak LIBNAME declare that the target provides the LIBNAME interface All other options (arguments beginning with \`-') are ignored. Every other argument is treated as a filename. Files ending in \`.la' are treated as uninstalled libtool libraries, other files are standard or library object files. If the OUTPUT-FILE ends in \`.la', then a libtool library is created, only library objects (\`.lo' files) may be specified, and \`-rpath' is required, except when creating a convenience library. If OUTPUT-FILE ends in \`.a' or \`.lib', then a standard library is created using \`ar' and \`ranlib', or on Windows using \`lib'. If OUTPUT-FILE ends in \`.lo' or \`.${objext}', then a reloadable object file is created, otherwise an executable program is created." ;; uninstall) $ECHO \ "Usage: $progname [OPTION]... --mode=uninstall RM [RM-OPTION]... FILE... Remove libraries from an installation directory. RM is the name of the program to use to delete files associated with each FILE (typically \`/bin/rm'). RM-OPTIONS are options (such as \`-f') to be passed to RM. If FILE is a libtool library, all the files associated with it are deleted. Otherwise, only FILE itself is deleted using RM." ;; *) func_fatal_help "invalid operation mode \`$mode'" ;; esac $ECHO $ECHO "Try \`$progname --help' for more information about other modes." exit $? } # Now that we've collected a possible --mode arg, show help if necessary $opt_help && func_mode_help # func_mode_execute arg... func_mode_execute () { $opt_debug # The first argument is the command name. cmd="$nonopt" test -z "$cmd" && \ func_fatal_help "you must specify a COMMAND" # Handle -dlopen flags immediately. for file in $execute_dlfiles; do test -f "$file" \ || func_fatal_help "\`$file' is not a file" dir= case $file in *.la) # Check to see that this really is a libtool archive. func_lalib_unsafe_p "$file" \ || func_fatal_help "\`$lib' is not a valid libtool archive" # Read the libtool library. dlname= library_names= func_source "$file" # Skip this library if it cannot be dlopened. if test -z "$dlname"; then # Warn if it was a shared library. test -n "$library_names" && \ func_warning "\`$file' was not linked with \`-export-dynamic'" continue fi func_dirname "$file" "" "." dir="$func_dirname_result" if test -f "$dir/$objdir/$dlname"; then dir="$dir/$objdir" else if test ! -f "$dir/$dlname"; then func_fatal_error "cannot find \`$dlname' in \`$dir' or \`$dir/$objdir'" fi fi ;; *.lo) # Just add the directory containing the .lo file. func_dirname "$file" "" "." dir="$func_dirname_result" ;; *) func_warning "\`-dlopen' is ignored for non-libtool libraries and objects" continue ;; esac # Get the absolute pathname. absdir=`cd "$dir" && pwd` test -n "$absdir" && dir="$absdir" # Now add the directory to shlibpath_var. if eval "test -z \"\$$shlibpath_var\""; then eval "$shlibpath_var=\"\$dir\"" else eval "$shlibpath_var=\"\$dir:\$$shlibpath_var\"" fi done # This variable tells wrapper scripts just to set shlibpath_var # rather than running their programs. libtool_execute_magic="$magic" # Check if any of the arguments is a wrapper script. args= for file do case $file in -*) ;; *) # Do a test to see if this is really a libtool program. if func_ltwrapper_script_p "$file"; then func_source "$file" # Transform arg to wrapped name. file="$progdir/$program" elif func_ltwrapper_executable_p "$file"; then func_ltwrapper_scriptname "$file" func_source "$func_ltwrapper_scriptname_result" # Transform arg to wrapped name. file="$progdir/$program" fi ;; esac # Quote arguments (to preserve shell metacharacters). func_quote_for_eval "$file" args="$args $func_quote_for_eval_result" done if test "X$opt_dry_run" = Xfalse; then if test -n "$shlibpath_var"; then # Export the shlibpath_var. eval "export $shlibpath_var" fi # Restore saved environment variables for lt_var in LANG LANGUAGE LC_ALL LC_CTYPE LC_COLLATE LC_MESSAGES do eval "if test \"\${save_$lt_var+set}\" = set; then $lt_var=\$save_$lt_var; export $lt_var else $lt_unset $lt_var fi" done # Now prepare to actually exec the command. exec_cmd="\$cmd$args" else # Display what would be done. if test -n "$shlibpath_var"; then eval "\$ECHO \"\$shlibpath_var=\$$shlibpath_var\"" $ECHO "export $shlibpath_var" fi $ECHO "$cmd$args" exit $EXIT_SUCCESS fi } test "$mode" = execute && func_mode_execute ${1+"$@"} # func_mode_finish arg... func_mode_finish () { $opt_debug libdirs="$nonopt" admincmds= if test -n "$finish_cmds$finish_eval" && test -n "$libdirs"; then for dir do libdirs="$libdirs $dir" done for libdir in $libdirs; do if test -n "$finish_cmds"; then # Do each command in the finish commands. func_execute_cmds "$finish_cmds" 'admincmds="$admincmds '"$cmd"'"' fi if test -n "$finish_eval"; then # Do the single finish_eval. eval cmds=\"$finish_eval\" $opt_dry_run || eval "$cmds" || admincmds="$admincmds $cmds" fi done fi # Exit here if they wanted silent mode. $opt_silent && exit $EXIT_SUCCESS $ECHO "X----------------------------------------------------------------------" | $Xsed $ECHO "Libraries have been installed in:" for libdir in $libdirs; do $ECHO " $libdir" done $ECHO $ECHO "If you ever happen to want to link against installed libraries" $ECHO "in a given directory, LIBDIR, you must either use libtool, and" $ECHO "specify the full pathname of the library, or use the \`-LLIBDIR'" $ECHO "flag during linking and do at least one of the following:" if test -n "$shlibpath_var"; then $ECHO " - add LIBDIR to the \`$shlibpath_var' environment variable" $ECHO " during execution" fi if test -n "$runpath_var"; then $ECHO " - add LIBDIR to the \`$runpath_var' environment variable" $ECHO " during linking" fi if test -n "$hardcode_libdir_flag_spec"; then libdir=LIBDIR eval flag=\"$hardcode_libdir_flag_spec\" $ECHO " - use the \`$flag' linker flag" fi if test -n "$admincmds"; then $ECHO " - have your system administrator run these commands:$admincmds" fi if test -f /etc/ld.so.conf; then $ECHO " - have your system administrator add LIBDIR to \`/etc/ld.so.conf'" fi $ECHO $ECHO "See any operating system documentation about shared libraries for" case $host in solaris2.[6789]|solaris2.1[0-9]) $ECHO "more information, such as the ld(1), crle(1) and ld.so(8) manual" $ECHO "pages." ;; *) $ECHO "more information, such as the ld(1) and ld.so(8) manual pages." ;; esac $ECHO "X----------------------------------------------------------------------" | $Xsed exit $EXIT_SUCCESS } test "$mode" = finish && func_mode_finish ${1+"$@"} # func_mode_install arg... func_mode_install () { $opt_debug # There may be an optional sh(1) argument at the beginning of # install_prog (especially on Windows NT). if test "$nonopt" = "$SHELL" || test "$nonopt" = /bin/sh || # Allow the use of GNU shtool's install command. $ECHO "X$nonopt" | $GREP shtool >/dev/null; then # Aesthetically quote it. func_quote_for_eval "$nonopt" install_prog="$func_quote_for_eval_result " arg=$1 shift else install_prog= arg=$nonopt fi # The real first argument should be the name of the installation program. # Aesthetically quote it. func_quote_for_eval "$arg" install_prog="$install_prog$func_quote_for_eval_result" # We need to accept at least all the BSD install flags. dest= files= opts= prev= install_type= isdir=no stripme= for arg do if test -n "$dest"; then files="$files $dest" dest=$arg continue fi case $arg in -d) isdir=yes ;; -f) case " $install_prog " in *[\\\ /]cp\ *) ;; *) prev=$arg ;; esac ;; -g | -m | -o) prev=$arg ;; -s) stripme=" -s" continue ;; -*) ;; *) # If the previous option needed an argument, then skip it. if test -n "$prev"; then prev= else dest=$arg continue fi ;; esac # Aesthetically quote the argument. func_quote_for_eval "$arg" install_prog="$install_prog $func_quote_for_eval_result" done test -z "$install_prog" && \ func_fatal_help "you must specify an install program" test -n "$prev" && \ func_fatal_help "the \`$prev' option requires an argument" if test -z "$files"; then if test -z "$dest"; then func_fatal_help "no file or destination specified" else func_fatal_help "you must specify a destination" fi fi # Strip any trailing slash from the destination. func_stripname '' '/' "$dest" dest=$func_stripname_result # Check to see that the destination is a directory. test -d "$dest" && isdir=yes if test "$isdir" = yes; then destdir="$dest" destname= else func_dirname_and_basename "$dest" "" "." destdir="$func_dirname_result" destname="$func_basename_result" # Not a directory, so check to see that there is only one file specified. set dummy $files; shift test "$#" -gt 1 && \ func_fatal_help "\`$dest' is not a directory" fi case $destdir in [\\/]* | [A-Za-z]:[\\/]*) ;; *) for file in $files; do case $file in *.lo) ;; *) func_fatal_help "\`$destdir' must be an absolute directory name" ;; esac done ;; esac # This variable tells wrapper scripts just to set variables rather # than running their programs. libtool_install_magic="$magic" staticlibs= future_libdirs= current_libdirs= for file in $files; do # Do each installation. case $file in *.$libext) # Do the static libraries later. staticlibs="$staticlibs $file" ;; *.la) # Check to see that this really is a libtool archive. func_lalib_unsafe_p "$file" \ || func_fatal_help "\`$file' is not a valid libtool archive" library_names= old_library= relink_command= func_source "$file" # Add the libdir to current_libdirs if it is the destination. if test "X$destdir" = "X$libdir"; then case "$current_libdirs " in *" $libdir "*) ;; *) current_libdirs="$current_libdirs $libdir" ;; esac else # Note the libdir as a future libdir. case "$future_libdirs " in *" $libdir "*) ;; *) future_libdirs="$future_libdirs $libdir" ;; esac fi func_dirname "$file" "/" "" dir="$func_dirname_result" dir="$dir$objdir" if test -n "$relink_command"; then # Determine the prefix the user has applied to our future dir. inst_prefix_dir=`$ECHO "X$destdir" | $Xsed -e "s%$libdir\$%%"` # Don't allow the user to place us outside of our expected # location b/c this prevents finding dependent libraries that # are installed to the same prefix. # At present, this check doesn't affect windows .dll's that # are installed into $libdir/../bin (currently, that works fine) # but it's something to keep an eye on. test "$inst_prefix_dir" = "$destdir" && \ func_fatal_error "error: cannot install \`$file' to a directory not ending in $libdir" if test -n "$inst_prefix_dir"; then # Stick the inst_prefix_dir data into the link command. relink_command=`$ECHO "X$relink_command" | $Xsed -e "s%@inst_prefix_dir@%-inst-prefix-dir $inst_prefix_dir%"` else relink_command=`$ECHO "X$relink_command" | $Xsed -e "s%@inst_prefix_dir@%%"` fi func_warning "relinking \`$file'" func_show_eval "$relink_command" \ 'func_fatal_error "error: relink \`$file'\'' with the above command before installing it"' fi # See the names of the shared library. set dummy $library_names; shift if test -n "$1"; then realname="$1" shift srcname="$realname" test -n "$relink_command" && srcname="$realname"T # Install the shared library and build the symlinks. func_show_eval "$install_prog $dir/$srcname $destdir/$realname" \ 'exit $?' tstripme="$stripme" case $host_os in cygwin* | mingw* | pw32* | cegcc*) case $realname in *.dll.a) tstripme="" ;; esac ;; esac if test -n "$tstripme" && test -n "$striplib"; then func_show_eval "$striplib $destdir/$realname" 'exit $?' fi if test "$#" -gt 0; then # Delete the old symlinks, and create new ones. # Try `ln -sf' first, because the `ln' binary might depend on # the symlink we replace! Solaris /bin/ln does not understand -f, # so we also need to try rm && ln -s. for linkname do test "$linkname" != "$realname" \ && func_show_eval "(cd $destdir && { $LN_S -f $realname $linkname || { $RM $linkname && $LN_S $realname $linkname; }; })" done fi # Do each command in the postinstall commands. lib="$destdir/$realname" func_execute_cmds "$postinstall_cmds" 'exit $?' fi # Install the pseudo-library for information purposes. func_basename "$file" name="$func_basename_result" instname="$dir/$name"i func_show_eval "$install_prog $instname $destdir/$name" 'exit $?' # Maybe install the static library, too. test -n "$old_library" && staticlibs="$staticlibs $dir/$old_library" ;; *.lo) # Install (i.e. copy) a libtool object. # Figure out destination file name, if it wasn't already specified. if test -n "$destname"; then destfile="$destdir/$destname" else func_basename "$file" destfile="$func_basename_result" destfile="$destdir/$destfile" fi # Deduce the name of the destination old-style object file. case $destfile in *.lo) func_lo2o "$destfile" staticdest=$func_lo2o_result ;; *.$objext) staticdest="$destfile" destfile= ;; *) func_fatal_help "cannot copy a libtool object to \`$destfile'" ;; esac # Install the libtool object if requested. test -n "$destfile" && \ func_show_eval "$install_prog $file $destfile" 'exit $?' # Install the old object if enabled. if test "$build_old_libs" = yes; then # Deduce the name of the old-style object file. func_lo2o "$file" staticobj=$func_lo2o_result func_show_eval "$install_prog \$staticobj \$staticdest" 'exit $?' fi exit $EXIT_SUCCESS ;; *) # Figure out destination file name, if it wasn't already specified. if test -n "$destname"; then destfile="$destdir/$destname" else func_basename "$file" destfile="$func_basename_result" destfile="$destdir/$destfile" fi # If the file is missing, and there is a .exe on the end, strip it # because it is most likely a libtool script we actually want to # install stripped_ext="" case $file in *.exe) if test ! -f "$file"; then func_stripname '' '.exe' "$file" file=$func_stripname_result stripped_ext=".exe" fi ;; esac # Do a test to see if this is really a libtool program. case $host in *cygwin* | *mingw*) if func_ltwrapper_executable_p "$file"; then func_ltwrapper_scriptname "$file" wrapper=$func_ltwrapper_scriptname_result else func_stripname '' '.exe' "$file" wrapper=$func_stripname_result fi ;; *) wrapper=$file ;; esac if func_ltwrapper_script_p "$wrapper"; then notinst_deplibs= relink_command= func_source "$wrapper" # Check the variables that should have been set. test -z "$generated_by_libtool_version" && \ func_fatal_error "invalid libtool wrapper script \`$wrapper'" finalize=yes for lib in $notinst_deplibs; do # Check to see that each library is installed. libdir= if test -f "$lib"; then func_source "$lib" fi libfile="$libdir/"`$ECHO "X$lib" | $Xsed -e 's%^.*/%%g'` ### testsuite: skip nested quoting test if test -n "$libdir" && test ! -f "$libfile"; then func_warning "\`$lib' has not been installed in \`$libdir'" finalize=no fi done relink_command= func_source "$wrapper" outputname= if test "$fast_install" = no && test -n "$relink_command"; then $opt_dry_run || { if test "$finalize" = yes; then tmpdir=`func_mktempdir` func_basename "$file$stripped_ext" file="$func_basename_result" outputname="$tmpdir/$file" # Replace the output file specification. relink_command=`$ECHO "X$relink_command" | $Xsed -e 's%@OUTPUT@%'"$outputname"'%g'` $opt_silent || { func_quote_for_expand "$relink_command" eval "func_echo $func_quote_for_expand_result" } if eval "$relink_command"; then : else func_error "error: relink \`$file' with the above command before installing it" $opt_dry_run || ${RM}r "$tmpdir" continue fi file="$outputname" else func_warning "cannot relink \`$file'" fi } else # Install the binary that we compiled earlier. file=`$ECHO "X$file$stripped_ext" | $Xsed -e "s%\([^/]*\)$%$objdir/\1%"` fi fi # remove .exe since cygwin /usr/bin/install will append another # one anyway case $install_prog,$host in */usr/bin/install*,*cygwin*) case $file:$destfile in *.exe:*.exe) # this is ok ;; *.exe:*) destfile=$destfile.exe ;; *:*.exe) func_stripname '' '.exe' "$destfile" destfile=$func_stripname_result ;; esac ;; esac func_show_eval "$install_prog\$stripme \$file \$destfile" 'exit $?' $opt_dry_run || if test -n "$outputname"; then ${RM}r "$tmpdir" fi ;; esac done for file in $staticlibs; do func_basename "$file" name="$func_basename_result" # Set up the ranlib parameters. oldlib="$destdir/$name" func_show_eval "$install_prog \$file \$oldlib" 'exit $?' if test -n "$stripme" && test -n "$old_striplib"; then func_show_eval "$old_striplib $oldlib" 'exit $?' fi # Do each command in the postinstall commands. func_execute_cmds "$old_postinstall_cmds" 'exit $?' done test -n "$future_libdirs" && \ func_warning "remember to run \`$progname --finish$future_libdirs'" if test -n "$current_libdirs"; then # Maybe just do a dry run. $opt_dry_run && current_libdirs=" -n$current_libdirs" exec_cmd='$SHELL $progpath $preserve_args --finish$current_libdirs' else exit $EXIT_SUCCESS fi } test "$mode" = install && func_mode_install ${1+"$@"} # func_generate_dlsyms outputname originator pic_p # Extract symbols from dlprefiles and create ${outputname}S.o with # a dlpreopen symbol table. func_generate_dlsyms () { $opt_debug my_outputname="$1" my_originator="$2" my_pic_p="${3-no}" my_prefix=`$ECHO "$my_originator" | sed 's%[^a-zA-Z0-9]%_%g'` my_dlsyms= if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then if test -n "$NM" && test -n "$global_symbol_pipe"; then my_dlsyms="${my_outputname}S.c" else func_error "not configured to extract global symbols from dlpreopened files" fi fi if test -n "$my_dlsyms"; then case $my_dlsyms in "") ;; *.c) # Discover the nlist of each of the dlfiles. nlist="$output_objdir/${my_outputname}.nm" func_show_eval "$RM $nlist ${nlist}S ${nlist}T" # Parse the name list into a source file. func_verbose "creating $output_objdir/$my_dlsyms" $opt_dry_run || $ECHO > "$output_objdir/$my_dlsyms" "\ /* $my_dlsyms - symbol resolution table for \`$my_outputname' dlsym emulation. */ /* Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION */ #ifdef __cplusplus extern \"C\" { #endif /* External symbol declarations for the compiler. */\ " if test "$dlself" = yes; then func_verbose "generating symbol list for \`$output'" $opt_dry_run || echo ': @PROGRAM@ ' > "$nlist" # Add our own program objects to the symbol list. progfiles=`$ECHO "X$objs$old_deplibs" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP` for progfile in $progfiles; do func_verbose "extracting global C symbols from \`$progfile'" $opt_dry_run || eval "$NM $progfile | $global_symbol_pipe >> '$nlist'" done if test -n "$exclude_expsyms"; then $opt_dry_run || { eval '$EGREP -v " ($exclude_expsyms)$" "$nlist" > "$nlist"T' eval '$MV "$nlist"T "$nlist"' } fi if test -n "$export_symbols_regex"; then $opt_dry_run || { eval '$EGREP -e "$export_symbols_regex" "$nlist" > "$nlist"T' eval '$MV "$nlist"T "$nlist"' } fi # Prepare the list of exported symbols if test -z "$export_symbols"; then export_symbols="$output_objdir/$outputname.exp" $opt_dry_run || { $RM $export_symbols eval "${SED} -n -e '/^: @PROGRAM@ $/d' -e 's/^.* \(.*\)$/\1/p' "'< "$nlist" > "$export_symbols"' case $host in *cygwin* | *mingw* | *cegcc* ) eval "echo EXPORTS "'> "$output_objdir/$outputname.def"' eval 'cat "$export_symbols" >> "$output_objdir/$outputname.def"' ;; esac } else $opt_dry_run || { eval "${SED} -e 's/\([].[*^$]\)/\\\\\1/g' -e 's/^/ /' -e 's/$/$/'"' < "$export_symbols" > "$output_objdir/$outputname.exp"' eval '$GREP -f "$output_objdir/$outputname.exp" < "$nlist" > "$nlist"T' eval '$MV "$nlist"T "$nlist"' case $host in *cygwin | *mingw* | *cegcc* ) eval "echo EXPORTS "'> "$output_objdir/$outputname.def"' eval 'cat "$nlist" >> "$output_objdir/$outputname.def"' ;; esac } fi fi for dlprefile in $dlprefiles; do func_verbose "extracting global C symbols from \`$dlprefile'" func_basename "$dlprefile" name="$func_basename_result" $opt_dry_run || { eval '$ECHO ": $name " >> "$nlist"' eval "$NM $dlprefile 2>/dev/null | $global_symbol_pipe >> '$nlist'" } done $opt_dry_run || { # Make sure we have at least an empty file. test -f "$nlist" || : > "$nlist" if test -n "$exclude_expsyms"; then $EGREP -v " ($exclude_expsyms)$" "$nlist" > "$nlist"T $MV "$nlist"T "$nlist" fi # Try sorting and uniquifying the output. if $GREP -v "^: " < "$nlist" | if sort -k 3 /dev/null 2>&1; then sort -k 3 else sort +2 fi | uniq > "$nlist"S; then : else $GREP -v "^: " < "$nlist" > "$nlist"S fi if test -f "$nlist"S; then eval "$global_symbol_to_cdecl"' < "$nlist"S >> "$output_objdir/$my_dlsyms"' else $ECHO '/* NONE */' >> "$output_objdir/$my_dlsyms" fi $ECHO >> "$output_objdir/$my_dlsyms" "\ /* The mapping between symbol names and symbols. */ typedef struct { const char *name; void *address; } lt_dlsymlist; " case $host in *cygwin* | *mingw* | *cegcc* ) $ECHO >> "$output_objdir/$my_dlsyms" "\ /* DATA imports from DLLs on WIN32 con't be const, because runtime relocations are performed -- see ld's documentation on pseudo-relocs. */" lt_dlsym_const= ;; *osf5*) echo >> "$output_objdir/$my_dlsyms" "\ /* This system does not cope well with relocations in const data */" lt_dlsym_const= ;; *) lt_dlsym_const=const ;; esac $ECHO >> "$output_objdir/$my_dlsyms" "\ extern $lt_dlsym_const lt_dlsymlist lt_${my_prefix}_LTX_preloaded_symbols[]; $lt_dlsym_const lt_dlsymlist lt_${my_prefix}_LTX_preloaded_symbols[] = {\ { \"$my_originator\", (void *) 0 }," case $need_lib_prefix in no) eval "$global_symbol_to_c_name_address" < "$nlist" >> "$output_objdir/$my_dlsyms" ;; *) eval "$global_symbol_to_c_name_address_lib_prefix" < "$nlist" >> "$output_objdir/$my_dlsyms" ;; esac $ECHO >> "$output_objdir/$my_dlsyms" "\ {0, (void *) 0} }; /* This works around a problem in FreeBSD linker */ #ifdef FREEBSD_WORKAROUND static const void *lt_preloaded_setup() { return lt_${my_prefix}_LTX_preloaded_symbols; } #endif #ifdef __cplusplus } #endif\ " } # !$opt_dry_run pic_flag_for_symtable= case "$compile_command " in *" -static "*) ;; *) case $host in # compiling the symbol table file with pic_flag works around # a FreeBSD bug that causes programs to crash when -lm is # linked before any other PIC object. But we must not use # pic_flag when linking with -static. The problem exists in # FreeBSD 2.2.6 and is fixed in FreeBSD 3.1. *-*-freebsd2*|*-*-freebsd3.0*|*-*-freebsdelf3.0*) pic_flag_for_symtable=" $pic_flag -DFREEBSD_WORKAROUND" ;; *-*-hpux*) pic_flag_for_symtable=" $pic_flag" ;; *) if test "X$my_pic_p" != Xno; then pic_flag_for_symtable=" $pic_flag" fi ;; esac ;; esac symtab_cflags= for arg in $LTCFLAGS; do case $arg in -pie | -fpie | -fPIE) ;; *) symtab_cflags="$symtab_cflags $arg" ;; esac done # Now compile the dynamic symbol file. func_show_eval '(cd $output_objdir && $LTCC$symtab_cflags -c$no_builtin_flag$pic_flag_for_symtable "$my_dlsyms")' 'exit $?' # Clean up the generated files. func_show_eval '$RM "$output_objdir/$my_dlsyms" "$nlist" "${nlist}S" "${nlist}T"' # Transform the symbol file into the correct name. symfileobj="$output_objdir/${my_outputname}S.$objext" case $host in *cygwin* | *mingw* | *cegcc* ) if test -f "$output_objdir/$my_outputname.def"; then compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"` finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"` else compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"` finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"` fi ;; *) compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"` finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"` ;; esac ;; *) func_fatal_error "unknown suffix for \`$my_dlsyms'" ;; esac else # We keep going just in case the user didn't refer to # lt_preloaded_symbols. The linker will fail if global_symbol_pipe # really was required. # Nullify the symbol file. compile_command=`$ECHO "X$compile_command" | $Xsed -e "s% @SYMFILE@%%"` finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s% @SYMFILE@%%"` fi } # func_win32_libid arg # return the library type of file 'arg' # # Need a lot of goo to handle *both* DLLs and import libs # Has to be a shell function in order to 'eat' the argument # that is supplied when $file_magic_command is called. func_win32_libid () { $opt_debug win32_libid_type="unknown" win32_fileres=`file -L $1 2>/dev/null` case $win32_fileres in *ar\ archive\ import\ library*) # definitely import win32_libid_type="x86 archive import" ;; *ar\ archive*) # could be an import, or static if eval $OBJDUMP -f $1 | $SED -e '10q' 2>/dev/null | $EGREP 'file format pe-i386(.*architecture: i386)?' >/dev/null ; then win32_nmres=`eval $NM -f posix -A $1 | $SED -n -e ' 1,100{ / I /{ s,.*,import, p q } }'` case $win32_nmres in import*) win32_libid_type="x86 archive import";; *) win32_libid_type="x86 archive static";; esac fi ;; *DLL*) win32_libid_type="x86 DLL" ;; *executable*) # but shell scripts are "executable" too... case $win32_fileres in *MS\ Windows\ PE\ Intel*) win32_libid_type="x86 DLL" ;; esac ;; esac $ECHO "$win32_libid_type" } # func_extract_an_archive dir oldlib func_extract_an_archive () { $opt_debug f_ex_an_ar_dir="$1"; shift f_ex_an_ar_oldlib="$1" func_show_eval "(cd \$f_ex_an_ar_dir && $AR x \"\$f_ex_an_ar_oldlib\")" 'exit $?' if ($AR t "$f_ex_an_ar_oldlib" | sort | sort -uc >/dev/null 2>&1); then : else func_fatal_error "object name conflicts in archive: $f_ex_an_ar_dir/$f_ex_an_ar_oldlib" fi } # func_extract_archives gentop oldlib ... func_extract_archives () { $opt_debug my_gentop="$1"; shift my_oldlibs=${1+"$@"} my_oldobjs="" my_xlib="" my_xabs="" my_xdir="" for my_xlib in $my_oldlibs; do # Extract the objects. case $my_xlib in [\\/]* | [A-Za-z]:[\\/]*) my_xabs="$my_xlib" ;; *) my_xabs=`pwd`"/$my_xlib" ;; esac func_basename "$my_xlib" my_xlib="$func_basename_result" my_xlib_u=$my_xlib while :; do case " $extracted_archives " in *" $my_xlib_u "*) func_arith $extracted_serial + 1 extracted_serial=$func_arith_result my_xlib_u=lt$extracted_serial-$my_xlib ;; *) break ;; esac done extracted_archives="$extracted_archives $my_xlib_u" my_xdir="$my_gentop/$my_xlib_u" func_mkdir_p "$my_xdir" case $host in *-darwin*) func_verbose "Extracting $my_xabs" # Do not bother doing anything if just a dry run $opt_dry_run || { darwin_orig_dir=`pwd` cd $my_xdir || exit $? darwin_archive=$my_xabs darwin_curdir=`pwd` darwin_base_archive=`basename "$darwin_archive"` darwin_arches=`$LIPO -info "$darwin_archive" 2>/dev/null | $GREP Architectures 2>/dev/null || true` if test -n "$darwin_arches"; then darwin_arches=`$ECHO "$darwin_arches" | $SED -e 's/.*are://'` darwin_arch= func_verbose "$darwin_base_archive has multiple architectures $darwin_arches" for darwin_arch in $darwin_arches ; do func_mkdir_p "unfat-$$/${darwin_base_archive}-${darwin_arch}" $LIPO -thin $darwin_arch -output "unfat-$$/${darwin_base_archive}-${darwin_arch}/${darwin_base_archive}" "${darwin_archive}" cd "unfat-$$/${darwin_base_archive}-${darwin_arch}" func_extract_an_archive "`pwd`" "${darwin_base_archive}" cd "$darwin_curdir" $RM "unfat-$$/${darwin_base_archive}-${darwin_arch}/${darwin_base_archive}" done # $darwin_arches ## Okay now we've a bunch of thin objects, gotta fatten them up :) darwin_filelist=`find unfat-$$ -type f -name \*.o -print -o -name \*.lo -print | $SED -e "$basename" | sort -u` darwin_file= darwin_files= for darwin_file in $darwin_filelist; do darwin_files=`find unfat-$$ -name $darwin_file -print | $NL2SP` $LIPO -create -output "$darwin_file" $darwin_files done # $darwin_filelist $RM -rf unfat-$$ cd "$darwin_orig_dir" else cd $darwin_orig_dir func_extract_an_archive "$my_xdir" "$my_xabs" fi # $darwin_arches } # !$opt_dry_run ;; *) func_extract_an_archive "$my_xdir" "$my_xabs" ;; esac my_oldobjs="$my_oldobjs "`find $my_xdir -name \*.$objext -print -o -name \*.lo -print | $NL2SP` done func_extract_archives_result="$my_oldobjs" } # func_emit_wrapper_part1 [arg=no] # # Emit the first part of a libtool wrapper script on stdout. # For more information, see the description associated with # func_emit_wrapper(), below. func_emit_wrapper_part1 () { func_emit_wrapper_part1_arg1=no if test -n "$1" ; then func_emit_wrapper_part1_arg1=$1 fi $ECHO "\ #! $SHELL # $output - temporary wrapper script for $objdir/$outputname # Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION # # The $output program cannot be directly executed until all the libtool # libraries that it depends on are installed. # # This wrapper script should never be moved out of the build directory. # If it is, it will not operate correctly. # Sed substitution that helps us do robust quoting. It backslashifies # metacharacters that are still active within double-quoted strings. Xsed='${SED} -e 1s/^X//' sed_quote_subst='$sed_quote_subst' # Be Bourne compatible if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then emulate sh NULLCMD=: # Zsh 3.x and 4.x performs word splitting on \${1+\"\$@\"}, which # is contrary to our usage. Disable this feature. alias -g '\${1+\"\$@\"}'='\"\$@\"' setopt NO_GLOB_SUBST else case \`(set -o) 2>/dev/null\` in *posix*) set -o posix;; esac fi BIN_SH=xpg4; export BIN_SH # for Tru64 DUALCASE=1; export DUALCASE # for MKS sh # The HP-UX ksh and POSIX shell print the target directory to stdout # if CDPATH is set. (unset CDPATH) >/dev/null 2>&1 && unset CDPATH relink_command=\"$relink_command\" # This environment variable determines our operation mode. if test \"\$libtool_install_magic\" = \"$magic\"; then # install mode needs the following variables: generated_by_libtool_version='$macro_version' notinst_deplibs='$notinst_deplibs' else # When we are sourced in execute mode, \$file and \$ECHO are already set. if test \"\$libtool_execute_magic\" != \"$magic\"; then ECHO=\"$qecho\" file=\"\$0\" # Make sure echo works. if test \"X\$1\" = X--no-reexec; then # Discard the --no-reexec flag, and continue. shift elif test \"X\`{ \$ECHO '\t'; } 2>/dev/null\`\" = 'X\t'; then # Yippee, \$ECHO works! : else # Restart under the correct shell, and then maybe \$ECHO will work. exec $SHELL \"\$0\" --no-reexec \${1+\"\$@\"} fi fi\ " $ECHO "\ # Find the directory that this script lives in. thisdir=\`\$ECHO \"X\$file\" | \$Xsed -e 's%/[^/]*$%%'\` test \"x\$thisdir\" = \"x\$file\" && thisdir=. # Follow symbolic links until we get to the real thisdir. file=\`ls -ld \"\$file\" | ${SED} -n 's/.*-> //p'\` while test -n \"\$file\"; do destdir=\`\$ECHO \"X\$file\" | \$Xsed -e 's%/[^/]*\$%%'\` # If there was a directory component, then change thisdir. if test \"x\$destdir\" != \"x\$file\"; then case \"\$destdir\" in [\\\\/]* | [A-Za-z]:[\\\\/]*) thisdir=\"\$destdir\" ;; *) thisdir=\"\$thisdir/\$destdir\" ;; esac fi file=\`\$ECHO \"X\$file\" | \$Xsed -e 's%^.*/%%'\` file=\`ls -ld \"\$thisdir/\$file\" | ${SED} -n 's/.*-> //p'\` done " } # end: func_emit_wrapper_part1 # func_emit_wrapper_part2 [arg=no] # # Emit the second part of a libtool wrapper script on stdout. # For more information, see the description associated with # func_emit_wrapper(), below. func_emit_wrapper_part2 () { func_emit_wrapper_part2_arg1=no if test -n "$1" ; then func_emit_wrapper_part2_arg1=$1 fi $ECHO "\ # Usually 'no', except on cygwin/mingw when embedded into # the cwrapper. WRAPPER_SCRIPT_BELONGS_IN_OBJDIR=$func_emit_wrapper_part2_arg1 if test \"\$WRAPPER_SCRIPT_BELONGS_IN_OBJDIR\" = \"yes\"; then # special case for '.' if test \"\$thisdir\" = \".\"; then thisdir=\`pwd\` fi # remove .libs from thisdir case \"\$thisdir\" in *[\\\\/]$objdir ) thisdir=\`\$ECHO \"X\$thisdir\" | \$Xsed -e 's%[\\\\/][^\\\\/]*$%%'\` ;; $objdir ) thisdir=. ;; esac fi # Try to get the absolute directory name. absdir=\`cd \"\$thisdir\" && pwd\` test -n \"\$absdir\" && thisdir=\"\$absdir\" " if test "$fast_install" = yes; then $ECHO "\ program=lt-'$outputname'$exeext progdir=\"\$thisdir/$objdir\" if test ! -f \"\$progdir/\$program\" || { file=\`ls -1dt \"\$progdir/\$program\" \"\$progdir/../\$program\" 2>/dev/null | ${SED} 1q\`; \\ test \"X\$file\" != \"X\$progdir/\$program\"; }; then file=\"\$\$-\$program\" if test ! -d \"\$progdir\"; then $MKDIR \"\$progdir\" else $RM \"\$progdir/\$file\" fi" $ECHO "\ # relink executable if necessary if test -n \"\$relink_command\"; then if relink_command_output=\`eval \$relink_command 2>&1\`; then : else $ECHO \"\$relink_command_output\" >&2 $RM \"\$progdir/\$file\" exit 1 fi fi $MV \"\$progdir/\$file\" \"\$progdir/\$program\" 2>/dev/null || { $RM \"\$progdir/\$program\"; $MV \"\$progdir/\$file\" \"\$progdir/\$program\"; } $RM \"\$progdir/\$file\" fi" else $ECHO "\ program='$outputname' progdir=\"\$thisdir/$objdir\" " fi $ECHO "\ if test -f \"\$progdir/\$program\"; then" # Export our shlibpath_var if we have one. if test "$shlibpath_overrides_runpath" = yes && test -n "$shlibpath_var" && test -n "$temp_rpath"; then $ECHO "\ # Add our own library path to $shlibpath_var $shlibpath_var=\"$temp_rpath\$$shlibpath_var\" # Some systems cannot cope with colon-terminated $shlibpath_var # The second colon is a workaround for a bug in BeOS R4 sed $shlibpath_var=\`\$ECHO \"X\$$shlibpath_var\" | \$Xsed -e 's/::*\$//'\` export $shlibpath_var " fi # fixup the dll searchpath if we need to. if test -n "$dllsearchpath"; then $ECHO "\ # Add the dll search path components to the executable PATH PATH=$dllsearchpath:\$PATH " fi $ECHO "\ if test \"\$libtool_execute_magic\" != \"$magic\"; then # Run the actual program with our arguments. " case $host in # Backslashes separate directories on plain windows *-*-mingw | *-*-os2* | *-cegcc*) $ECHO "\ exec \"\$progdir\\\\\$program\" \${1+\"\$@\"} " ;; *) $ECHO "\ exec \"\$progdir/\$program\" \${1+\"\$@\"} " ;; esac $ECHO "\ \$ECHO \"\$0: cannot exec \$program \$*\" 1>&2 exit 1 fi else # The program doesn't exist. \$ECHO \"\$0: error: \\\`\$progdir/\$program' does not exist\" 1>&2 \$ECHO \"This script is just a wrapper for \$program.\" 1>&2 $ECHO \"See the $PACKAGE documentation for more information.\" 1>&2 exit 1 fi fi\ " } # end: func_emit_wrapper_part2 # func_emit_wrapper [arg=no] # # Emit a libtool wrapper script on stdout. # Don't directly open a file because we may want to # incorporate the script contents within a cygwin/mingw # wrapper executable. Must ONLY be called from within # func_mode_link because it depends on a number of variables # set therein. # # ARG is the value that the WRAPPER_SCRIPT_BELONGS_IN_OBJDIR # variable will take. If 'yes', then the emitted script # will assume that the directory in which it is stored is # the $objdir directory. This is a cygwin/mingw-specific # behavior. func_emit_wrapper () { func_emit_wrapper_arg1=no if test -n "$1" ; then func_emit_wrapper_arg1=$1 fi # split this up so that func_emit_cwrapperexe_src # can call each part independently. func_emit_wrapper_part1 "${func_emit_wrapper_arg1}" func_emit_wrapper_part2 "${func_emit_wrapper_arg1}" } # func_to_host_path arg # # Convert paths to host format when used with build tools. # Intended for use with "native" mingw (where libtool itself # is running under the msys shell), or in the following cross- # build environments: # $build $host # mingw (msys) mingw [e.g. native] # cygwin mingw # *nix + wine mingw # where wine is equipped with the `winepath' executable. # In the native mingw case, the (msys) shell automatically # converts paths for any non-msys applications it launches, # but that facility isn't available from inside the cwrapper. # Similar accommodations are necessary for $host mingw and # $build cygwin. Calling this function does no harm for other # $host/$build combinations not listed above. # # ARG is the path (on $build) that should be converted to # the proper representation for $host. The result is stored # in $func_to_host_path_result. func_to_host_path () { func_to_host_path_result="$1" if test -n "$1" ; then case $host in *mingw* ) lt_sed_naive_backslashify='s|\\\\*|\\|g;s|/|\\|g;s|\\|\\\\|g' case $build in *mingw* ) # actually, msys # awkward: cmd appends spaces to result lt_sed_strip_trailing_spaces="s/[ ]*\$//" func_to_host_path_tmp1=`( cmd //c echo "$1" |\ $SED -e "$lt_sed_strip_trailing_spaces" ) 2>/dev/null || echo ""` func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\ $SED -e "$lt_sed_naive_backslashify"` ;; *cygwin* ) func_to_host_path_tmp1=`cygpath -w "$1"` func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\ $SED -e "$lt_sed_naive_backslashify"` ;; * ) # Unfortunately, winepath does not exit with a non-zero # error code, so we are forced to check the contents of # stdout. On the other hand, if the command is not # found, the shell will set an exit code of 127 and print # *an error message* to stdout. So we must check for both # error code of zero AND non-empty stdout, which explains # the odd construction: func_to_host_path_tmp1=`winepath -w "$1" 2>/dev/null` if test "$?" -eq 0 && test -n "${func_to_host_path_tmp1}"; then func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\ $SED -e "$lt_sed_naive_backslashify"` else # Allow warning below. func_to_host_path_result="" fi ;; esac if test -z "$func_to_host_path_result" ; then func_error "Could not determine host path corresponding to" func_error " '$1'" func_error "Continuing, but uninstalled executables may not work." # Fallback: func_to_host_path_result="$1" fi ;; esac fi } # end: func_to_host_path # func_to_host_pathlist arg # # Convert pathlists to host format when used with build tools. # See func_to_host_path(), above. This function supports the # following $build/$host combinations (but does no harm for # combinations not listed here): # $build $host # mingw (msys) mingw [e.g. native] # cygwin mingw # *nix + wine mingw # # Path separators are also converted from $build format to # $host format. If ARG begins or ends with a path separator # character, it is preserved (but converted to $host format) # on output. # # ARG is a pathlist (on $build) that should be converted to # the proper representation on $host. The result is stored # in $func_to_host_pathlist_result. func_to_host_pathlist () { func_to_host_pathlist_result="$1" if test -n "$1" ; then case $host in *mingw* ) lt_sed_naive_backslashify='s|\\\\*|\\|g;s|/|\\|g;s|\\|\\\\|g' # Remove leading and trailing path separator characters from # ARG. msys behavior is inconsistent here, cygpath turns them # into '.;' and ';.', and winepath ignores them completely. func_to_host_pathlist_tmp2="$1" # Once set for this call, this variable should not be # reassigned. It is used in tha fallback case. func_to_host_pathlist_tmp1=`echo "$func_to_host_pathlist_tmp2" |\ $SED -e 's|^:*||' -e 's|:*$||'` case $build in *mingw* ) # Actually, msys. # Awkward: cmd appends spaces to result. lt_sed_strip_trailing_spaces="s/[ ]*\$//" func_to_host_pathlist_tmp2=`( cmd //c echo "$func_to_host_pathlist_tmp1" |\ $SED -e "$lt_sed_strip_trailing_spaces" ) 2>/dev/null || echo ""` func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp2" |\ $SED -e "$lt_sed_naive_backslashify"` ;; *cygwin* ) func_to_host_pathlist_tmp2=`cygpath -w -p "$func_to_host_pathlist_tmp1"` func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp2" |\ $SED -e "$lt_sed_naive_backslashify"` ;; * ) # unfortunately, winepath doesn't convert pathlists func_to_host_pathlist_result="" func_to_host_pathlist_oldIFS=$IFS IFS=: for func_to_host_pathlist_f in $func_to_host_pathlist_tmp1 ; do IFS=$func_to_host_pathlist_oldIFS if test -n "$func_to_host_pathlist_f" ; then func_to_host_path "$func_to_host_pathlist_f" if test -n "$func_to_host_path_result" ; then if test -z "$func_to_host_pathlist_result" ; then func_to_host_pathlist_result="$func_to_host_path_result" else func_to_host_pathlist_result="$func_to_host_pathlist_result;$func_to_host_path_result" fi fi fi IFS=: done IFS=$func_to_host_pathlist_oldIFS ;; esac if test -z "$func_to_host_pathlist_result" ; then func_error "Could not determine the host path(s) corresponding to" func_error " '$1'" func_error "Continuing, but uninstalled executables may not work." # Fallback. This may break if $1 contains DOS-style drive # specifications. The fix is not to complicate the expression # below, but for the user to provide a working wine installation # with winepath so that path translation in the cross-to-mingw # case works properly. lt_replace_pathsep_nix_to_dos="s|:|;|g" func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp1" |\ $SED -e "$lt_replace_pathsep_nix_to_dos"` fi # Now, add the leading and trailing path separators back case "$1" in :* ) func_to_host_pathlist_result=";$func_to_host_pathlist_result" ;; esac case "$1" in *: ) func_to_host_pathlist_result="$func_to_host_pathlist_result;" ;; esac ;; esac fi } # end: func_to_host_pathlist # func_emit_cwrapperexe_src # emit the source code for a wrapper executable on stdout # Must ONLY be called from within func_mode_link because # it depends on a number of variable set therein. func_emit_cwrapperexe_src () { cat < #include #ifdef _MSC_VER # include # include # include # define setmode _setmode #else # include # include # ifdef __CYGWIN__ # include # define HAVE_SETENV # ifdef __STRICT_ANSI__ char *realpath (const char *, char *); int putenv (char *); int setenv (const char *, const char *, int); # endif # endif #endif #include #include #include #include #include #include #include #include #if defined(PATH_MAX) # define LT_PATHMAX PATH_MAX #elif defined(MAXPATHLEN) # define LT_PATHMAX MAXPATHLEN #else # define LT_PATHMAX 1024 #endif #ifndef S_IXOTH # define S_IXOTH 0 #endif #ifndef S_IXGRP # define S_IXGRP 0 #endif #ifdef _MSC_VER # define S_IXUSR _S_IEXEC # define stat _stat # ifndef _INTPTR_T_DEFINED # define intptr_t int # endif #endif #ifndef DIR_SEPARATOR # define DIR_SEPARATOR '/' # define PATH_SEPARATOR ':' #endif #if defined (_WIN32) || defined (__MSDOS__) || defined (__DJGPP__) || \ defined (__OS2__) # define HAVE_DOS_BASED_FILE_SYSTEM # define FOPEN_WB "wb" # ifndef DIR_SEPARATOR_2 # define DIR_SEPARATOR_2 '\\' # endif # ifndef PATH_SEPARATOR_2 # define PATH_SEPARATOR_2 ';' # endif #endif #ifndef DIR_SEPARATOR_2 # define IS_DIR_SEPARATOR(ch) ((ch) == DIR_SEPARATOR) #else /* DIR_SEPARATOR_2 */ # define IS_DIR_SEPARATOR(ch) \ (((ch) == DIR_SEPARATOR) || ((ch) == DIR_SEPARATOR_2)) #endif /* DIR_SEPARATOR_2 */ #ifndef PATH_SEPARATOR_2 # define IS_PATH_SEPARATOR(ch) ((ch) == PATH_SEPARATOR) #else /* PATH_SEPARATOR_2 */ # define IS_PATH_SEPARATOR(ch) ((ch) == PATH_SEPARATOR_2) #endif /* PATH_SEPARATOR_2 */ #ifdef __CYGWIN__ # define FOPEN_WB "wb" #endif #ifndef FOPEN_WB # define FOPEN_WB "w" #endif #ifndef _O_BINARY # define _O_BINARY 0 #endif #define XMALLOC(type, num) ((type *) xmalloc ((num) * sizeof(type))) #define XFREE(stale) do { \ if (stale) { free ((void *) stale); stale = 0; } \ } while (0) #undef LTWRAPPER_DEBUGPRINTF #if defined DEBUGWRAPPER # define LTWRAPPER_DEBUGPRINTF(args) ltwrapper_debugprintf args static void ltwrapper_debugprintf (const char *fmt, ...) { va_list args; va_start (args, fmt); (void) vfprintf (stderr, fmt, args); va_end (args); } #else # define LTWRAPPER_DEBUGPRINTF(args) #endif const char *program_name = NULL; void *xmalloc (size_t num); char *xstrdup (const char *string); const char *base_name (const char *name); char *find_executable (const char *wrapper); char *chase_symlinks (const char *pathspec); int make_executable (const char *path); int check_executable (const char *path); char *strendzap (char *str, const char *pat); void lt_fatal (const char *message, ...); void lt_setenv (const char *name, const char *value); char *lt_extend_str (const char *orig_value, const char *add, int to_end); void lt_opt_process_env_set (const char *arg); void lt_opt_process_env_prepend (const char *arg); void lt_opt_process_env_append (const char *arg); int lt_split_name_value (const char *arg, char** name, char** value); void lt_update_exe_path (const char *name, const char *value); void lt_update_lib_path (const char *name, const char *value); static const char *script_text_part1 = EOF func_emit_wrapper_part1 yes | $SED -e 's/\([\\"]\)/\\\1/g' \ -e 's/^/ "/' -e 's/$/\\n"/' echo ";" cat <"))); for (i = 0; i < newargc; i++) { LTWRAPPER_DEBUGPRINTF (("(main) newargz[%d] : %s\n", i, (newargz[i] ? newargz[i] : ""))); } EOF case $host_os in mingw*) cat <<"EOF" /* execv doesn't actually work on mingw as expected on unix */ rval = _spawnv (_P_WAIT, lt_argv_zero, (const char * const *) newargz); if (rval == -1) { /* failed to start process */ LTWRAPPER_DEBUGPRINTF (("(main) failed to launch target \"%s\": errno = %d\n", lt_argv_zero, errno)); return 127; } return rval; EOF ;; *) cat <<"EOF" execv (lt_argv_zero, newargz); return rval; /* =127, but avoids unused variable warning */ EOF ;; esac cat <<"EOF" } void * xmalloc (size_t num) { void *p = (void *) malloc (num); if (!p) lt_fatal ("Memory exhausted"); return p; } char * xstrdup (const char *string) { return string ? strcpy ((char *) xmalloc (strlen (string) + 1), string) : NULL; } const char * base_name (const char *name) { const char *base; #if defined (HAVE_DOS_BASED_FILE_SYSTEM) /* Skip over the disk name in MSDOS pathnames. */ if (isalpha ((unsigned char) name[0]) && name[1] == ':') name += 2; #endif for (base = name; *name; name++) if (IS_DIR_SEPARATOR (*name)) base = name + 1; return base; } int check_executable (const char *path) { struct stat st; LTWRAPPER_DEBUGPRINTF (("(check_executable) : %s\n", path ? (*path ? path : "EMPTY!") : "NULL!")); if ((!path) || (!*path)) return 0; if ((stat (path, &st) >= 0) && (st.st_mode & (S_IXUSR | S_IXGRP | S_IXOTH))) return 1; else return 0; } int make_executable (const char *path) { int rval = 0; struct stat st; LTWRAPPER_DEBUGPRINTF (("(make_executable) : %s\n", path ? (*path ? path : "EMPTY!") : "NULL!")); if ((!path) || (!*path)) return 0; if (stat (path, &st) >= 0) { rval = chmod (path, st.st_mode | S_IXOTH | S_IXGRP | S_IXUSR); } return rval; } /* Searches for the full path of the wrapper. Returns newly allocated full path name if found, NULL otherwise Does not chase symlinks, even on platforms that support them. */ char * find_executable (const char *wrapper) { int has_slash = 0; const char *p; const char *p_next; /* static buffer for getcwd */ char tmp[LT_PATHMAX + 1]; int tmp_len; char *concat_name; LTWRAPPER_DEBUGPRINTF (("(find_executable) : %s\n", wrapper ? (*wrapper ? wrapper : "EMPTY!") : "NULL!")); if ((wrapper == NULL) || (*wrapper == '\0')) return NULL; /* Absolute path? */ #if defined (HAVE_DOS_BASED_FILE_SYSTEM) if (isalpha ((unsigned char) wrapper[0]) && wrapper[1] == ':') { concat_name = xstrdup (wrapper); if (check_executable (concat_name)) return concat_name; XFREE (concat_name); } else { #endif if (IS_DIR_SEPARATOR (wrapper[0])) { concat_name = xstrdup (wrapper); if (check_executable (concat_name)) return concat_name; XFREE (concat_name); } #if defined (HAVE_DOS_BASED_FILE_SYSTEM) } #endif for (p = wrapper; *p; p++) if (*p == '/') { has_slash = 1; break; } if (!has_slash) { /* no slashes; search PATH */ const char *path = getenv ("PATH"); if (path != NULL) { for (p = path; *p; p = p_next) { const char *q; size_t p_len; for (q = p; *q; q++) if (IS_PATH_SEPARATOR (*q)) break; p_len = q - p; p_next = (*q == '\0' ? q : q + 1); if (p_len == 0) { /* empty path: current directory */ if (getcwd (tmp, LT_PATHMAX) == NULL) lt_fatal ("getcwd failed"); tmp_len = strlen (tmp); concat_name = XMALLOC (char, tmp_len + 1 + strlen (wrapper) + 1); memcpy (concat_name, tmp, tmp_len); concat_name[tmp_len] = '/'; strcpy (concat_name + tmp_len + 1, wrapper); } else { concat_name = XMALLOC (char, p_len + 1 + strlen (wrapper) + 1); memcpy (concat_name, p, p_len); concat_name[p_len] = '/'; strcpy (concat_name + p_len + 1, wrapper); } if (check_executable (concat_name)) return concat_name; XFREE (concat_name); } } /* not found in PATH; assume curdir */ } /* Relative path | not found in path: prepend cwd */ if (getcwd (tmp, LT_PATHMAX) == NULL) lt_fatal ("getcwd failed"); tmp_len = strlen (tmp); concat_name = XMALLOC (char, tmp_len + 1 + strlen (wrapper) + 1); memcpy (concat_name, tmp, tmp_len); concat_name[tmp_len] = '/'; strcpy (concat_name + tmp_len + 1, wrapper); if (check_executable (concat_name)) return concat_name; XFREE (concat_name); return NULL; } char * chase_symlinks (const char *pathspec) { #ifndef S_ISLNK return xstrdup (pathspec); #else char buf[LT_PATHMAX]; struct stat s; char *tmp_pathspec = xstrdup (pathspec); char *p; int has_symlinks = 0; while (strlen (tmp_pathspec) && !has_symlinks) { LTWRAPPER_DEBUGPRINTF (("checking path component for symlinks: %s\n", tmp_pathspec)); if (lstat (tmp_pathspec, &s) == 0) { if (S_ISLNK (s.st_mode) != 0) { has_symlinks = 1; break; } /* search backwards for last DIR_SEPARATOR */ p = tmp_pathspec + strlen (tmp_pathspec) - 1; while ((p > tmp_pathspec) && (!IS_DIR_SEPARATOR (*p))) p--; if ((p == tmp_pathspec) && (!IS_DIR_SEPARATOR (*p))) { /* no more DIR_SEPARATORS left */ break; } *p = '\0'; } else { char *errstr = strerror (errno); lt_fatal ("Error accessing file %s (%s)", tmp_pathspec, errstr); } } XFREE (tmp_pathspec); if (!has_symlinks) { return xstrdup (pathspec); } tmp_pathspec = realpath (pathspec, buf); if (tmp_pathspec == 0) { lt_fatal ("Could not follow symlinks for %s", pathspec); } return xstrdup (tmp_pathspec); #endif } char * strendzap (char *str, const char *pat) { size_t len, patlen; assert (str != NULL); assert (pat != NULL); len = strlen (str); patlen = strlen (pat); if (patlen <= len) { str += len - patlen; if (strcmp (str, pat) == 0) *str = '\0'; } return str; } static void lt_error_core (int exit_status, const char *mode, const char *message, va_list ap) { fprintf (stderr, "%s: %s: ", program_name, mode); vfprintf (stderr, message, ap); fprintf (stderr, ".\n"); if (exit_status >= 0) exit (exit_status); } void lt_fatal (const char *message, ...) { va_list ap; va_start (ap, message); lt_error_core (EXIT_FAILURE, "FATAL", message, ap); va_end (ap); } void lt_setenv (const char *name, const char *value) { LTWRAPPER_DEBUGPRINTF (("(lt_setenv) setting '%s' to '%s'\n", (name ? name : ""), (value ? value : ""))); { #ifdef HAVE_SETENV /* always make a copy, for consistency with !HAVE_SETENV */ char *str = xstrdup (value); setenv (name, str, 1); #else int len = strlen (name) + 1 + strlen (value) + 1; char *str = XMALLOC (char, len); sprintf (str, "%s=%s", name, value); if (putenv (str) != EXIT_SUCCESS) { XFREE (str); } #endif } } char * lt_extend_str (const char *orig_value, const char *add, int to_end) { char *new_value; if (orig_value && *orig_value) { int orig_value_len = strlen (orig_value); int add_len = strlen (add); new_value = XMALLOC (char, add_len + orig_value_len + 1); if (to_end) { strcpy (new_value, orig_value); strcpy (new_value + orig_value_len, add); } else { strcpy (new_value, add); strcpy (new_value + add_len, orig_value); } } else { new_value = xstrdup (add); } return new_value; } int lt_split_name_value (const char *arg, char** name, char** value) { const char *p; int len; if (!arg || !*arg) return 1; p = strchr (arg, (int)'='); if (!p) return 1; *value = xstrdup (++p); len = strlen (arg) - strlen (*value); *name = XMALLOC (char, len); strncpy (*name, arg, len-1); (*name)[len - 1] = '\0'; return 0; } void lt_opt_process_env_set (const char *arg) { char *name = NULL; char *value = NULL; if (lt_split_name_value (arg, &name, &value) != 0) { XFREE (name); XFREE (value); lt_fatal ("bad argument for %s: '%s'", env_set_opt, arg); } lt_setenv (name, value); XFREE (name); XFREE (value); } void lt_opt_process_env_prepend (const char *arg) { char *name = NULL; char *value = NULL; char *new_value = NULL; if (lt_split_name_value (arg, &name, &value) != 0) { XFREE (name); XFREE (value); lt_fatal ("bad argument for %s: '%s'", env_prepend_opt, arg); } new_value = lt_extend_str (getenv (name), value, 0); lt_setenv (name, new_value); XFREE (new_value); XFREE (name); XFREE (value); } void lt_opt_process_env_append (const char *arg) { char *name = NULL; char *value = NULL; char *new_value = NULL; if (lt_split_name_value (arg, &name, &value) != 0) { XFREE (name); XFREE (value); lt_fatal ("bad argument for %s: '%s'", env_append_opt, arg); } new_value = lt_extend_str (getenv (name), value, 1); lt_setenv (name, new_value); XFREE (new_value); XFREE (name); XFREE (value); } void lt_update_exe_path (const char *name, const char *value) { LTWRAPPER_DEBUGPRINTF (("(lt_update_exe_path) modifying '%s' by prepending '%s'\n", (name ? name : ""), (value ? value : ""))); if (name && *name && value && *value) { char *new_value = lt_extend_str (getenv (name), value, 0); /* some systems can't cope with a ':'-terminated path #' */ int len = strlen (new_value); while (((len = strlen (new_value)) > 0) && IS_PATH_SEPARATOR (new_value[len-1])) { new_value[len-1] = '\0'; } lt_setenv (name, new_value); XFREE (new_value); } } void lt_update_lib_path (const char *name, const char *value) { LTWRAPPER_DEBUGPRINTF (("(lt_update_lib_path) modifying '%s' by prepending '%s'\n", (name ? name : ""), (value ? value : ""))); if (name && *name && value && *value) { char *new_value = lt_extend_str (getenv (name), value, 0); lt_setenv (name, new_value); XFREE (new_value); } } EOF } # end: func_emit_cwrapperexe_src # func_mode_link arg... func_mode_link () { $opt_debug case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*) # It is impossible to link a dll without this setting, and # we shouldn't force the makefile maintainer to figure out # which system we are compiling for in order to pass an extra # flag for every libtool invocation. # allow_undefined=no # FIXME: Unfortunately, there are problems with the above when trying # to make a dll which has undefined symbols, in which case not # even a static library is built. For now, we need to specify # -no-undefined on the libtool link line when we can be certain # that all symbols are satisfied, otherwise we get a static library. allow_undefined=yes ;; *) allow_undefined=yes ;; esac libtool_args=$nonopt base_compile="$nonopt $@" compile_command=$nonopt finalize_command=$nonopt compile_rpath= finalize_rpath= compile_shlibpath= finalize_shlibpath= convenience= old_convenience= deplibs= old_deplibs= compiler_flags= linker_flags= dllsearchpath= lib_search_path=`pwd` inst_prefix_dir= new_inherited_linker_flags= avoid_version=no dlfiles= dlprefiles= dlself=no export_dynamic=no export_symbols= export_symbols_regex= generated= libobjs= ltlibs= module=no no_install=no objs= non_pic_objects= precious_files_regex= prefer_static_libs=no preload=no prev= prevarg= release= rpath= xrpath= perm_rpath= temp_rpath= thread_safe=no vinfo= vinfo_number=no weak_libs= single_module="${wl}-single_module" func_infer_tag $base_compile # We need to know -static, to get the right output filenames. for arg do case $arg in -shared) test "$build_libtool_libs" != yes && \ func_fatal_configuration "can not build a shared library" build_old_libs=no break ;; -all-static | -static | -static-libtool-libs) case $arg in -all-static) if test "$build_libtool_libs" = yes && test -z "$link_static_flag"; then func_warning "complete static linking is impossible in this configuration" fi if test -n "$link_static_flag"; then dlopen_self=$dlopen_self_static fi prefer_static_libs=yes ;; -static) if test -z "$pic_flag" && test -n "$link_static_flag"; then dlopen_self=$dlopen_self_static fi prefer_static_libs=built ;; -static-libtool-libs) if test -z "$pic_flag" && test -n "$link_static_flag"; then dlopen_self=$dlopen_self_static fi prefer_static_libs=yes ;; esac build_libtool_libs=no build_old_libs=yes break ;; esac done # See if our shared archives depend on static archives. test -n "$old_archive_from_new_cmds" && build_old_libs=yes # Go through the arguments, transforming them on the way. while test "$#" -gt 0; do arg="$1" shift func_quote_for_eval "$arg" qarg=$func_quote_for_eval_unquoted_result func_append libtool_args " $func_quote_for_eval_result" # If the previous option needs an argument, assign it. if test -n "$prev"; then case $prev in output) func_append compile_command " @OUTPUT@" func_append finalize_command " @OUTPUT@" ;; esac case $prev in dlfiles|dlprefiles) if test "$preload" = no; then # Add the symbol object into the linking commands. func_append compile_command " @SYMFILE@" func_append finalize_command " @SYMFILE@" preload=yes fi case $arg in *.la | *.lo) ;; # We handle these cases below. force) if test "$dlself" = no; then dlself=needless export_dynamic=yes fi prev= continue ;; self) if test "$prev" = dlprefiles; then dlself=yes elif test "$prev" = dlfiles && test "$dlopen_self" != yes; then dlself=yes else dlself=needless export_dynamic=yes fi prev= continue ;; *) if test "$prev" = dlfiles; then dlfiles="$dlfiles $arg" else dlprefiles="$dlprefiles $arg" fi prev= continue ;; esac ;; expsyms) export_symbols="$arg" test -f "$arg" \ || func_fatal_error "symbol file \`$arg' does not exist" prev= continue ;; expsyms_regex) export_symbols_regex="$arg" prev= continue ;; framework) case $host in *-*-darwin*) case "$deplibs " in *" $qarg.ltframework "*) ;; *) deplibs="$deplibs $qarg.ltframework" # this is fixed later ;; esac ;; esac prev= continue ;; inst_prefix) inst_prefix_dir="$arg" prev= continue ;; objectlist) if test -f "$arg"; then save_arg=$arg moreargs= for fil in `cat "$save_arg"` do # moreargs="$moreargs $fil" arg=$fil # A libtool-controlled object. # Check to see that this really is a libtool object. if func_lalib_unsafe_p "$arg"; then pic_object= non_pic_object= # Read the .lo file func_source "$arg" if test -z "$pic_object" || test -z "$non_pic_object" || test "$pic_object" = none && test "$non_pic_object" = none; then func_fatal_error "cannot find name of object for \`$arg'" fi # Extract subdirectory from the argument. func_dirname "$arg" "/" "" xdir="$func_dirname_result" if test "$pic_object" != none; then # Prepend the subdirectory the object is found in. pic_object="$xdir$pic_object" if test "$prev" = dlfiles; then if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then dlfiles="$dlfiles $pic_object" prev= continue else # If libtool objects are unsupported, then we need to preload. prev=dlprefiles fi fi # CHECK ME: I think I busted this. -Ossama if test "$prev" = dlprefiles; then # Preload the old-style object. dlprefiles="$dlprefiles $pic_object" prev= fi # A PIC object. func_append libobjs " $pic_object" arg="$pic_object" fi # Non-PIC object. if test "$non_pic_object" != none; then # Prepend the subdirectory the object is found in. non_pic_object="$xdir$non_pic_object" # A standard non-PIC object func_append non_pic_objects " $non_pic_object" if test -z "$pic_object" || test "$pic_object" = none ; then arg="$non_pic_object" fi else # If the PIC object exists, use it instead. # $xdir was prepended to $pic_object above. non_pic_object="$pic_object" func_append non_pic_objects " $non_pic_object" fi else # Only an error if not doing a dry-run. if $opt_dry_run; then # Extract subdirectory from the argument. func_dirname "$arg" "/" "" xdir="$func_dirname_result" func_lo2o "$arg" pic_object=$xdir$objdir/$func_lo2o_result non_pic_object=$xdir$func_lo2o_result func_append libobjs " $pic_object" func_append non_pic_objects " $non_pic_object" else func_fatal_error "\`$arg' is not a valid libtool object" fi fi done else func_fatal_error "link input file \`$arg' does not exist" fi arg=$save_arg prev= continue ;; precious_regex) precious_files_regex="$arg" prev= continue ;; release) release="-$arg" prev= continue ;; rpath | xrpath) # We need an absolute path. case $arg in [\\/]* | [A-Za-z]:[\\/]*) ;; *) func_fatal_error "only absolute run-paths are allowed" ;; esac if test "$prev" = rpath; then case "$rpath " in *" $arg "*) ;; *) rpath="$rpath $arg" ;; esac else case "$xrpath " in *" $arg "*) ;; *) xrpath="$xrpath $arg" ;; esac fi prev= continue ;; shrext) shrext_cmds="$arg" prev= continue ;; weak) weak_libs="$weak_libs $arg" prev= continue ;; xcclinker) linker_flags="$linker_flags $qarg" compiler_flags="$compiler_flags $qarg" prev= func_append compile_command " $qarg" func_append finalize_command " $qarg" continue ;; xcompiler) compiler_flags="$compiler_flags $qarg" prev= func_append compile_command " $qarg" func_append finalize_command " $qarg" continue ;; xlinker) linker_flags="$linker_flags $qarg" compiler_flags="$compiler_flags $wl$qarg" prev= func_append compile_command " $wl$qarg" func_append finalize_command " $wl$qarg" continue ;; *) eval "$prev=\"\$arg\"" prev= continue ;; esac fi # test -n "$prev" prevarg="$arg" case $arg in -all-static) if test -n "$link_static_flag"; then # See comment for -static flag below, for more details. func_append compile_command " $link_static_flag" func_append finalize_command " $link_static_flag" fi continue ;; -allow-undefined) # FIXME: remove this flag sometime in the future. func_fatal_error "\`-allow-undefined' must not be used because it is the default" ;; -avoid-version) avoid_version=yes continue ;; -dlopen) prev=dlfiles continue ;; -dlpreopen) prev=dlprefiles continue ;; -export-dynamic) export_dynamic=yes continue ;; -export-symbols | -export-symbols-regex) if test -n "$export_symbols" || test -n "$export_symbols_regex"; then func_fatal_error "more than one -exported-symbols argument is not allowed" fi if test "X$arg" = "X-export-symbols"; then prev=expsyms else prev=expsyms_regex fi continue ;; -framework) prev=framework continue ;; -inst-prefix-dir) prev=inst_prefix continue ;; 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esac elif test "X$arg" = "X-lc_r"; then case $host in *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*) # Do not include libc_r directly, use -pthread flag. continue ;; esac fi deplibs="$deplibs $arg" continue ;; -module) module=yes continue ;; # Tru64 UNIX uses -model [arg] to determine the layout of C++ # classes, name mangling, and exception handling. # Darwin uses the -arch flag to determine output architecture. -model|-arch|-isysroot) compiler_flags="$compiler_flags $arg" func_append compile_command " $arg" func_append finalize_command " $arg" prev=xcompiler continue ;; -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe|-threads) compiler_flags="$compiler_flags $arg" func_append compile_command " $arg" func_append finalize_command " $arg" case "$new_inherited_linker_flags " in *" $arg "*) ;; * ) new_inherited_linker_flags="$new_inherited_linker_flags $arg" ;; esac continue ;; -multi_module) single_module="${wl}-multi_module" continue ;; -no-fast-install) fast_install=no continue ;; -no-install) case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-darwin* | *-cegcc*) # The PATH hackery in wrapper scripts is required on Windows # and Darwin in order for the loader to find any dlls it needs. func_warning "\`-no-install' is ignored for $host" func_warning "assuming \`-no-fast-install' instead" fast_install=no ;; *) no_install=yes ;; esac continue ;; -no-undefined) allow_undefined=no continue ;; -objectlist) prev=objectlist continue ;; -o) prev=output ;; -precious-files-regex) prev=precious_regex continue ;; -release) prev=release continue ;; -rpath) prev=rpath continue ;; -R) prev=xrpath continue ;; -R*) func_stripname '-R' '' "$arg" dir=$func_stripname_result # We need an absolute path. case $dir in [\\/]* | [A-Za-z]:[\\/]*) ;; *) func_fatal_error "only absolute run-paths are allowed" ;; esac case "$xrpath " in *" $dir "*) ;; *) xrpath="$xrpath $dir" ;; esac continue ;; -shared) # The effects of -shared are defined in a previous loop. continue ;; -shrext) prev=shrext continue ;; -static | -static-libtool-libs) # The effects of -static are defined in a previous loop. # We used to do the same as -all-static on platforms that # didn't have a PIC flag, but the assumption that the effects # would be equivalent was wrong. It would break on at least # Digital Unix and AIX. continue ;; -thread-safe) thread_safe=yes continue ;; -version-info) prev=vinfo continue ;; -version-number) prev=vinfo vinfo_number=yes continue ;; -weak) prev=weak continue ;; -Wc,*) func_stripname '-Wc,' '' "$arg" args=$func_stripname_result arg= save_ifs="$IFS"; IFS=',' for flag in $args; do IFS="$save_ifs" func_quote_for_eval "$flag" arg="$arg $wl$func_quote_for_eval_result" compiler_flags="$compiler_flags $func_quote_for_eval_result" done IFS="$save_ifs" func_stripname ' ' '' "$arg" arg=$func_stripname_result ;; -Wl,*) func_stripname '-Wl,' '' "$arg" args=$func_stripname_result arg= save_ifs="$IFS"; IFS=',' for flag in $args; do IFS="$save_ifs" func_quote_for_eval "$flag" arg="$arg $wl$func_quote_for_eval_result" compiler_flags="$compiler_flags $wl$func_quote_for_eval_result" linker_flags="$linker_flags $func_quote_for_eval_result" done IFS="$save_ifs" func_stripname ' ' '' "$arg" arg=$func_stripname_result ;; -Xcompiler) prev=xcompiler continue ;; -Xlinker) prev=xlinker continue ;; -XCClinker) prev=xcclinker continue ;; # -msg_* for osf cc -msg_*) func_quote_for_eval "$arg" arg="$func_quote_for_eval_result" ;; # -64, -mips[0-9] enable 64-bit mode on the SGI compiler # -r[0-9][0-9]* specifies the processor on the SGI compiler # -xarch=*, -xtarget=* enable 64-bit mode on the Sun compiler # +DA*, +DD* enable 64-bit mode on the HP compiler # -q* pass through compiler args for the IBM compiler # -m*, -t[45]*, -txscale* pass through architecture-specific # compiler args for GCC # -F/path gives path to uninstalled frameworks, gcc on darwin # -p, -pg, --coverage, -fprofile-* pass through profiling flag for GCC # @file GCC response files -64|-mips[0-9]|-r[0-9][0-9]*|-xarch=*|-xtarget=*|+DA*|+DD*|-q*|-m*| \ -t[45]*|-txscale*|-p|-pg|--coverage|-fprofile-*|-F*|@*) func_quote_for_eval "$arg" arg="$func_quote_for_eval_result" func_append compile_command " $arg" func_append finalize_command " $arg" compiler_flags="$compiler_flags $arg" continue ;; # Some other compiler flag. -* | +*) func_quote_for_eval "$arg" arg="$func_quote_for_eval_result" ;; *.$objext) # A standard object. objs="$objs $arg" ;; *.lo) # A libtool-controlled object. # Check to see that this really is a libtool object. if func_lalib_unsafe_p "$arg"; then pic_object= non_pic_object= # Read the .lo file func_source "$arg" if test -z "$pic_object" || test -z "$non_pic_object" || test "$pic_object" = none && test "$non_pic_object" = none; then func_fatal_error "cannot find name of object for \`$arg'" fi # Extract subdirectory from the argument. func_dirname "$arg" "/" "" xdir="$func_dirname_result" if test "$pic_object" != none; then # Prepend the subdirectory the object is found in. pic_object="$xdir$pic_object" if test "$prev" = dlfiles; then if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then dlfiles="$dlfiles $pic_object" prev= continue else # If libtool objects are unsupported, then we need to preload. prev=dlprefiles fi fi # CHECK ME: I think I busted this. -Ossama if test "$prev" = dlprefiles; then # Preload the old-style object. dlprefiles="$dlprefiles $pic_object" prev= fi # A PIC object. func_append libobjs " $pic_object" arg="$pic_object" fi # Non-PIC object. if test "$non_pic_object" != none; then # Prepend the subdirectory the object is found in. non_pic_object="$xdir$non_pic_object" # A standard non-PIC object func_append non_pic_objects " $non_pic_object" if test -z "$pic_object" || test "$pic_object" = none ; then arg="$non_pic_object" fi else # If the PIC object exists, use it instead. # $xdir was prepended to $pic_object above. non_pic_object="$pic_object" func_append non_pic_objects " $non_pic_object" fi else # Only an error if not doing a dry-run. if $opt_dry_run; then # Extract subdirectory from the argument. func_dirname "$arg" "/" "" xdir="$func_dirname_result" func_lo2o "$arg" pic_object=$xdir$objdir/$func_lo2o_result non_pic_object=$xdir$func_lo2o_result func_append libobjs " $pic_object" func_append non_pic_objects " $non_pic_object" else func_fatal_error "\`$arg' is not a valid libtool object" fi fi ;; *.$libext) # An archive. deplibs="$deplibs $arg" old_deplibs="$old_deplibs $arg" continue ;; *.la) # A libtool-controlled library. if test "$prev" = dlfiles; then # This library was specified with -dlopen. dlfiles="$dlfiles $arg" prev= elif test "$prev" = dlprefiles; then # The library was specified with -dlpreopen. dlprefiles="$dlprefiles $arg" prev= else deplibs="$deplibs $arg" fi continue ;; # Some other compiler argument. *) # Unknown arguments in both finalize_command and compile_command need # to be aesthetically quoted because they are evaled later. func_quote_for_eval "$arg" arg="$func_quote_for_eval_result" ;; esac # arg # Now actually substitute the argument into the commands. if test -n "$arg"; then func_append compile_command " $arg" func_append finalize_command " $arg" fi done # argument parsing loop test -n "$prev" && \ func_fatal_help "the \`$prevarg' option requires an argument" if test "$export_dynamic" = yes && test -n "$export_dynamic_flag_spec"; then eval arg=\"$export_dynamic_flag_spec\" func_append compile_command " $arg" func_append finalize_command " $arg" fi oldlibs= # calculate the name of the file, without its directory func_basename "$output" outputname="$func_basename_result" libobjs_save="$libobjs" if test -n "$shlibpath_var"; then # get the directories listed in $shlibpath_var eval shlib_search_path=\`\$ECHO \"X\${$shlibpath_var}\" \| \$Xsed -e \'s/:/ /g\'\` else shlib_search_path= fi eval sys_lib_search_path=\"$sys_lib_search_path_spec\" eval sys_lib_dlsearch_path=\"$sys_lib_dlsearch_path_spec\" func_dirname "$output" "/" "" output_objdir="$func_dirname_result$objdir" # Create the object directory. func_mkdir_p "$output_objdir" # Determine the type of output case $output in "") func_fatal_help "you must specify an output file" ;; *.$libext) linkmode=oldlib ;; *.lo | *.$objext) linkmode=obj ;; *.la) linkmode=lib ;; *) linkmode=prog ;; # Anything else should be a program. esac specialdeplibs= libs= # Find all interdependent deplibs by searching for libraries # that are linked more than once (e.g. -la -lb -la) for deplib in $deplibs; do if $opt_duplicate_deps ; then case "$libs " in *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;; esac fi libs="$libs $deplib" done if test "$linkmode" = lib; then libs="$predeps $libs $compiler_lib_search_path $postdeps" # Compute libraries that are listed more than once in $predeps # $postdeps and mark them as special (i.e., whose duplicates are # not to be eliminated). pre_post_deps= if $opt_duplicate_compiler_generated_deps; then for pre_post_dep in $predeps $postdeps; do case "$pre_post_deps " in *" $pre_post_dep "*) specialdeplibs="$specialdeplibs $pre_post_deps" ;; esac pre_post_deps="$pre_post_deps $pre_post_dep" done fi pre_post_deps= fi deplibs= newdependency_libs= newlib_search_path= need_relink=no # whether we're linking any uninstalled libtool libraries notinst_deplibs= # not-installed libtool libraries notinst_path= # paths that contain not-installed libtool libraries case $linkmode in lib) passes="conv dlpreopen link" for file in $dlfiles $dlprefiles; do case $file in *.la) ;; *) func_fatal_help "libraries can \`-dlopen' only libtool libraries: $file" ;; esac done ;; prog) compile_deplibs= finalize_deplibs= alldeplibs=no newdlfiles= newdlprefiles= passes="conv scan dlopen dlpreopen link" ;; *) passes="conv" ;; esac for pass in $passes; do # The preopen pass in lib mode reverses $deplibs; put it back here # so that -L comes before libs that need it for instance... if test "$linkmode,$pass" = "lib,link"; then ## FIXME: Find the place where the list is rebuilt in the wrong ## order, and fix it there properly tmp_deplibs= for deplib in $deplibs; do tmp_deplibs="$deplib $tmp_deplibs" done deplibs="$tmp_deplibs" fi if test "$linkmode,$pass" = "lib,link" || test "$linkmode,$pass" = "prog,scan"; then libs="$deplibs" deplibs= fi if test "$linkmode" = prog; then case $pass in dlopen) libs="$dlfiles" ;; dlpreopen) libs="$dlprefiles" ;; link) libs="$deplibs %DEPLIBS%" test "X$link_all_deplibs" != Xno && libs="$libs $dependency_libs" ;; esac fi if test "$linkmode,$pass" = "lib,dlpreopen"; then # Collect and forward deplibs of preopened libtool libs for lib in $dlprefiles; do # Ignore non-libtool-libs dependency_libs= case $lib in *.la) func_source "$lib" ;; esac # Collect preopened libtool deplibs, except any this library # has declared as weak libs for deplib in $dependency_libs; do deplib_base=`$ECHO "X$deplib" | $Xsed -e "$basename"` case " $weak_libs " in *" $deplib_base "*) ;; *) deplibs="$deplibs $deplib" ;; esac done done libs="$dlprefiles" fi if test "$pass" = dlopen; then # Collect dlpreopened libraries save_deplibs="$deplibs" deplibs= fi for deplib in $libs; do lib= found=no case $deplib in -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe|-threads) if test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else compiler_flags="$compiler_flags $deplib" if test "$linkmode" = lib ; then case "$new_inherited_linker_flags " in *" $deplib "*) ;; * ) new_inherited_linker_flags="$new_inherited_linker_flags $deplib" ;; esac fi fi continue ;; -l*) if test "$linkmode" != lib && test "$linkmode" != prog; then func_warning "\`-l' is ignored for archives/objects" continue fi func_stripname '-l' '' "$deplib" name=$func_stripname_result if test "$linkmode" = lib; then searchdirs="$newlib_search_path $lib_search_path $compiler_lib_search_dirs $sys_lib_search_path $shlib_search_path" else searchdirs="$newlib_search_path $lib_search_path $sys_lib_search_path $shlib_search_path" fi for searchdir in $searchdirs; do for search_ext in .la $std_shrext .so .a; do # Search the libtool library lib="$searchdir/lib${name}${search_ext}" if test -f "$lib"; then if test "$search_ext" = ".la"; then found=yes else found=no fi break 2 fi done done if test "$found" != yes; then # deplib doesn't seem to be a libtool library if test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else deplibs="$deplib $deplibs" test "$linkmode" = lib && newdependency_libs="$deplib $newdependency_libs" fi continue else # deplib is a libtool library # If $allow_libtool_libs_with_static_runtimes && $deplib is a stdlib, # We need to do some special things here, and not later. if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then case " $predeps $postdeps " in *" $deplib "*) if func_lalib_p "$lib"; then library_names= old_library= func_source "$lib" for l in $old_library $library_names; do ll="$l" done if test "X$ll" = "X$old_library" ; then # only static version available found=no func_dirname "$lib" "" "." ladir="$func_dirname_result" lib=$ladir/$old_library if test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else deplibs="$deplib $deplibs" test "$linkmode" = lib && newdependency_libs="$deplib $newdependency_libs" fi continue fi fi ;; *) ;; esac fi fi ;; # -l *.ltframework) if test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else deplibs="$deplib $deplibs" if test "$linkmode" = lib ; then case "$new_inherited_linker_flags " in *" $deplib "*) ;; * ) new_inherited_linker_flags="$new_inherited_linker_flags $deplib" ;; esac fi fi continue ;; -L*) case $linkmode in lib) deplibs="$deplib $deplibs" test "$pass" = conv && continue newdependency_libs="$deplib $newdependency_libs" func_stripname '-L' '' "$deplib" newlib_search_path="$newlib_search_path $func_stripname_result" ;; prog) if test "$pass" = conv; then deplibs="$deplib $deplibs" continue fi if test "$pass" = scan; then deplibs="$deplib $deplibs" else compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" fi func_stripname '-L' '' "$deplib" newlib_search_path="$newlib_search_path $func_stripname_result" ;; *) func_warning "\`-L' is ignored for archives/objects" ;; esac # linkmode continue ;; # -L -R*) if test "$pass" = link; then func_stripname '-R' '' "$deplib" dir=$func_stripname_result # Make sure the xrpath contains only unique directories. case "$xrpath " in *" $dir "*) ;; *) xrpath="$xrpath $dir" ;; esac fi deplibs="$deplib $deplibs" continue ;; *.la) lib="$deplib" ;; *.$libext) if test "$pass" = conv; then deplibs="$deplib $deplibs" continue fi case $linkmode in lib) # Linking convenience modules into shared libraries is allowed, # but linking other static libraries is non-portable. case " $dlpreconveniencelibs " in *" $deplib "*) ;; *) valid_a_lib=no case $deplibs_check_method in match_pattern*) set dummy $deplibs_check_method; shift match_pattern_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"` if eval "\$ECHO \"X$deplib\"" 2>/dev/null | $Xsed -e 10q \ | $EGREP "$match_pattern_regex" > /dev/null; then valid_a_lib=yes fi ;; pass_all) valid_a_lib=yes ;; esac if test "$valid_a_lib" != yes; then $ECHO $ECHO "*** Warning: Trying to link with static lib archive $deplib." $ECHO "*** I have the capability to make that library automatically link in when" $ECHO "*** you link to this library. But I can only do this if you have a" $ECHO "*** shared version of the library, which you do not appear to have" $ECHO "*** because the file extensions .$libext of this argument makes me believe" $ECHO "*** that it is just a static archive that I should not use here." else $ECHO $ECHO "*** Warning: Linking the shared library $output against the" $ECHO "*** static library $deplib is not portable!" deplibs="$deplib $deplibs" fi ;; esac continue ;; prog) if test "$pass" != link; then deplibs="$deplib $deplibs" else compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" fi continue ;; esac # linkmode ;; # *.$libext *.lo | *.$objext) if test "$pass" = conv; then deplibs="$deplib $deplibs" elif test "$linkmode" = prog; then if test "$pass" = dlpreopen || test "$dlopen_support" != yes || test "$build_libtool_libs" = no; then # If there is no dlopen support or we're linking statically, # we need to preload. newdlprefiles="$newdlprefiles $deplib" compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else newdlfiles="$newdlfiles $deplib" fi fi continue ;; %DEPLIBS%) alldeplibs=yes continue ;; esac # case $deplib if test "$found" = yes || test -f "$lib"; then : else func_fatal_error "cannot find the library \`$lib' or unhandled argument \`$deplib'" fi # Check to see that this really is a libtool archive. func_lalib_unsafe_p "$lib" \ || func_fatal_error "\`$lib' is not a valid libtool archive" func_dirname "$lib" "" "." ladir="$func_dirname_result" dlname= dlopen= dlpreopen= libdir= library_names= old_library= inherited_linker_flags= # If the library was installed with an old release of libtool, # it will not redefine variables installed, or shouldnotlink installed=yes shouldnotlink=no avoidtemprpath= # Read the .la file func_source "$lib" # Convert "-framework foo" to "foo.ltframework" if test -n "$inherited_linker_flags"; then tmp_inherited_linker_flags=`$ECHO "X$inherited_linker_flags" | $Xsed -e 's/-framework \([^ $]*\)/\1.ltframework/g'` for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do case " $new_inherited_linker_flags " in *" $tmp_inherited_linker_flag "*) ;; *) new_inherited_linker_flags="$new_inherited_linker_flags $tmp_inherited_linker_flag";; esac done fi dependency_libs=`$ECHO "X $dependency_libs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` if test "$linkmode,$pass" = "lib,link" || test "$linkmode,$pass" = "prog,scan" || { test "$linkmode" != prog && test "$linkmode" != lib; }; then test -n "$dlopen" && dlfiles="$dlfiles $dlopen" test -n "$dlpreopen" && dlprefiles="$dlprefiles $dlpreopen" fi if test "$pass" = conv; then # Only check for convenience libraries deplibs="$lib $deplibs" if test -z "$libdir"; then if test -z "$old_library"; then func_fatal_error "cannot find name of link library for \`$lib'" fi # It is a libtool convenience library, so add in its objects. convenience="$convenience $ladir/$objdir/$old_library" old_convenience="$old_convenience $ladir/$objdir/$old_library" elif test "$linkmode" != prog && test "$linkmode" != lib; then func_fatal_error "\`$lib' is not a convenience library" fi tmp_libs= for deplib in $dependency_libs; do deplibs="$deplib $deplibs" if $opt_duplicate_deps ; then case "$tmp_libs " in *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;; esac fi tmp_libs="$tmp_libs $deplib" done continue fi # $pass = conv # Get the name of the library we link against. linklib= for l in $old_library $library_names; do linklib="$l" done if test -z "$linklib"; then func_fatal_error "cannot find name of link library for \`$lib'" fi # This library was specified with -dlopen. if test "$pass" = dlopen; then if test -z "$libdir"; then func_fatal_error "cannot -dlopen a convenience library: \`$lib'" fi if test -z "$dlname" || test "$dlopen_support" != yes || test "$build_libtool_libs" = no; then # If there is no dlname, no dlopen support or we're linking # statically, we need to preload. We also need to preload any # dependent libraries so libltdl's deplib preloader doesn't # bomb out in the load deplibs phase. dlprefiles="$dlprefiles $lib $dependency_libs" else newdlfiles="$newdlfiles $lib" fi continue fi # $pass = dlopen # We need an absolute path. case $ladir in [\\/]* | [A-Za-z]:[\\/]*) abs_ladir="$ladir" ;; *) abs_ladir=`cd "$ladir" && pwd` if test -z "$abs_ladir"; then func_warning "cannot determine absolute directory name of \`$ladir'" func_warning "passing it literally to the linker, although it might fail" abs_ladir="$ladir" fi ;; esac func_basename "$lib" laname="$func_basename_result" # Find the relevant object directory and library name. if test "X$installed" = Xyes; then if test ! -f "$libdir/$linklib" && test -f "$abs_ladir/$linklib"; then func_warning "library \`$lib' was moved." dir="$ladir" absdir="$abs_ladir" libdir="$abs_ladir" else dir="$libdir" absdir="$libdir" fi test "X$hardcode_automatic" = Xyes && avoidtemprpath=yes else if test ! -f "$ladir/$objdir/$linklib" && test -f "$abs_ladir/$linklib"; then dir="$ladir" absdir="$abs_ladir" # Remove this search path later notinst_path="$notinst_path $abs_ladir" else dir="$ladir/$objdir" absdir="$abs_ladir/$objdir" # Remove this search path later notinst_path="$notinst_path $abs_ladir" fi fi # $installed = yes func_stripname 'lib' '.la' "$laname" name=$func_stripname_result # This library was specified with -dlpreopen. if test "$pass" = dlpreopen; then if test -z "$libdir" && test "$linkmode" = prog; then func_fatal_error "only libraries may -dlpreopen a convenience library: \`$lib'" fi # Prefer using a static library (so that no silly _DYNAMIC symbols # are required to link). if test -n "$old_library"; then newdlprefiles="$newdlprefiles $dir/$old_library" # Keep a list of preopened convenience libraries to check # that they are being used correctly in the link pass. test -z "$libdir" && \ dlpreconveniencelibs="$dlpreconveniencelibs $dir/$old_library" # Otherwise, use the dlname, so that lt_dlopen finds it. elif test -n "$dlname"; then newdlprefiles="$newdlprefiles $dir/$dlname" else newdlprefiles="$newdlprefiles $dir/$linklib" fi fi # $pass = dlpreopen if test -z "$libdir"; then # Link the convenience library if test "$linkmode" = lib; then deplibs="$dir/$old_library $deplibs" elif test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$dir/$old_library $compile_deplibs" finalize_deplibs="$dir/$old_library $finalize_deplibs" else deplibs="$lib $deplibs" # used for prog,scan pass fi continue fi if test "$linkmode" = prog && test "$pass" != link; then newlib_search_path="$newlib_search_path $ladir" deplibs="$lib $deplibs" linkalldeplibs=no if test "$link_all_deplibs" != no || test -z "$library_names" || test "$build_libtool_libs" = no; then linkalldeplibs=yes fi tmp_libs= for deplib in $dependency_libs; do case $deplib in -L*) func_stripname '-L' '' "$deplib" newlib_search_path="$newlib_search_path $func_stripname_result" ;; esac # Need to link against all dependency_libs? if test "$linkalldeplibs" = yes; then deplibs="$deplib $deplibs" else # Need to hardcode shared library paths # or/and link against static libraries newdependency_libs="$deplib $newdependency_libs" fi if $opt_duplicate_deps ; then case "$tmp_libs " in *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;; esac fi tmp_libs="$tmp_libs $deplib" done # for deplib continue fi # $linkmode = prog... if test "$linkmode,$pass" = "prog,link"; then if test -n "$library_names" && { { test "$prefer_static_libs" = no || test "$prefer_static_libs,$installed" = "built,yes"; } || test -z "$old_library"; }; then # We need to hardcode the library path if test -n "$shlibpath_var" && test -z "$avoidtemprpath" ; then # Make sure the rpath contains only unique directories. case "$temp_rpath:" in *"$absdir:"*) ;; *) temp_rpath="$temp_rpath$absdir:" ;; esac fi # Hardcode the library path. # Skip directories that are in the system default run-time # search path. case " $sys_lib_dlsearch_path " in *" $absdir "*) ;; *) case "$compile_rpath " in *" $absdir "*) ;; *) compile_rpath="$compile_rpath $absdir" esac ;; esac case " $sys_lib_dlsearch_path " in *" $libdir "*) ;; *) case "$finalize_rpath " in *" $libdir "*) ;; *) finalize_rpath="$finalize_rpath $libdir" esac ;; esac fi # $linkmode,$pass = prog,link... if test "$alldeplibs" = yes && { test "$deplibs_check_method" = pass_all || { test "$build_libtool_libs" = yes && test -n "$library_names"; }; }; then # We only need to search for static libraries continue fi fi link_static=no # Whether the deplib will be linked statically use_static_libs=$prefer_static_libs if test "$use_static_libs" = built && test "$installed" = yes; then use_static_libs=no fi if test -n "$library_names" && { test "$use_static_libs" = no || test -z "$old_library"; }; then case $host in *cygwin* | *mingw* | *cegcc*) # No point in relinking DLLs because paths are not encoded notinst_deplibs="$notinst_deplibs $lib" need_relink=no ;; *) if test "$installed" = no; then notinst_deplibs="$notinst_deplibs $lib" need_relink=yes fi ;; esac # This is a shared library # Warn about portability, can't link against -module's on some # systems (darwin). Don't bleat about dlopened modules though! dlopenmodule="" for dlpremoduletest in $dlprefiles; do if test "X$dlpremoduletest" = "X$lib"; then dlopenmodule="$dlpremoduletest" break fi done if test -z "$dlopenmodule" && test "$shouldnotlink" = yes && test "$pass" = link; then $ECHO if test "$linkmode" = prog; then $ECHO "*** Warning: Linking the executable $output against the loadable module" else $ECHO "*** Warning: Linking the shared library $output against the loadable module" fi $ECHO "*** $linklib is not portable!" fi if test "$linkmode" = lib && test "$hardcode_into_libs" = yes; then # Hardcode the library path. # Skip directories that are in the system default run-time # search path. case " $sys_lib_dlsearch_path " in *" $absdir "*) ;; *) case "$compile_rpath " in *" $absdir "*) ;; *) compile_rpath="$compile_rpath $absdir" esac ;; esac case " $sys_lib_dlsearch_path " in *" $libdir "*) ;; *) case "$finalize_rpath " in *" $libdir "*) ;; *) finalize_rpath="$finalize_rpath $libdir" esac ;; esac fi if test -n "$old_archive_from_expsyms_cmds"; then # figure out the soname set dummy $library_names shift realname="$1" shift libname=`eval "\\$ECHO \"$libname_spec\""` # use dlname if we got it. it's perfectly good, no? if test -n "$dlname"; then soname="$dlname" elif test -n "$soname_spec"; then # bleh windows case $host in *cygwin* | mingw* | *cegcc*) func_arith $current - $age major=$func_arith_result versuffix="-$major" ;; esac eval soname=\"$soname_spec\" else soname="$realname" fi # Make a new name for the extract_expsyms_cmds to use soroot="$soname" func_basename "$soroot" soname="$func_basename_result" func_stripname 'lib' '.dll' "$soname" newlib=libimp-$func_stripname_result.a # If the library has no export list, then create one now if test -f "$output_objdir/$soname-def"; then : else func_verbose "extracting exported symbol list from \`$soname'" func_execute_cmds "$extract_expsyms_cmds" 'exit $?' fi # Create $newlib if test -f "$output_objdir/$newlib"; then :; else func_verbose "generating import library for \`$soname'" func_execute_cmds "$old_archive_from_expsyms_cmds" 'exit $?' fi # make sure the library variables are pointing to the new library dir=$output_objdir linklib=$newlib fi # test -n "$old_archive_from_expsyms_cmds" if test "$linkmode" = prog || test "$mode" != relink; then add_shlibpath= add_dir= add= lib_linked=yes case $hardcode_action in immediate | unsupported) if test "$hardcode_direct" = no; then add="$dir/$linklib" case $host in *-*-sco3.2v5.0.[024]*) add_dir="-L$dir" ;; *-*-sysv4*uw2*) add_dir="-L$dir" ;; *-*-sysv5OpenUNIX* | *-*-sysv5UnixWare7.[01].[10]* | \ *-*-unixware7*) add_dir="-L$dir" ;; *-*-darwin* ) # if the lib is a (non-dlopened) module then we can not # link against it, someone is ignoring the earlier warnings if /usr/bin/file -L $add 2> /dev/null | $GREP ": [^:]* bundle" >/dev/null ; then if test "X$dlopenmodule" != "X$lib"; then $ECHO "*** Warning: lib $linklib is a module, not a shared library" if test -z "$old_library" ; then $ECHO $ECHO "*** And there doesn't seem to be a static archive available" $ECHO "*** The link will probably fail, sorry" else add="$dir/$old_library" fi elif test -n "$old_library"; then add="$dir/$old_library" fi fi esac elif test "$hardcode_minus_L" = no; then case $host in *-*-sunos*) add_shlibpath="$dir" ;; esac add_dir="-L$dir" add="-l$name" elif test "$hardcode_shlibpath_var" = no; then add_shlibpath="$dir" add="-l$name" else lib_linked=no fi ;; relink) if test "$hardcode_direct" = yes && test "$hardcode_direct_absolute" = no; then add="$dir/$linklib" elif test "$hardcode_minus_L" = yes; then add_dir="-L$dir" # Try looking first in the location we're being installed to. if test -n "$inst_prefix_dir"; then case $libdir in [\\/]*) add_dir="$add_dir -L$inst_prefix_dir$libdir" ;; esac fi add="-l$name" elif test "$hardcode_shlibpath_var" = yes; then add_shlibpath="$dir" add="-l$name" else lib_linked=no fi ;; *) lib_linked=no ;; esac if test "$lib_linked" != yes; then func_fatal_configuration "unsupported hardcode properties" fi if test -n "$add_shlibpath"; then case :$compile_shlibpath: in *":$add_shlibpath:"*) ;; *) compile_shlibpath="$compile_shlibpath$add_shlibpath:" ;; esac fi if test "$linkmode" = prog; then test -n "$add_dir" && compile_deplibs="$add_dir $compile_deplibs" test -n "$add" && compile_deplibs="$add $compile_deplibs" else test -n "$add_dir" && deplibs="$add_dir $deplibs" test -n "$add" && deplibs="$add $deplibs" if test "$hardcode_direct" != yes && test "$hardcode_minus_L" != yes && test "$hardcode_shlibpath_var" = yes; then case :$finalize_shlibpath: in *":$libdir:"*) ;; *) finalize_shlibpath="$finalize_shlibpath$libdir:" ;; esac fi fi fi if test "$linkmode" = prog || test "$mode" = relink; then add_shlibpath= add_dir= add= # Finalize command for both is simple: just hardcode it. if test "$hardcode_direct" = yes && test "$hardcode_direct_absolute" = no; then add="$libdir/$linklib" elif test "$hardcode_minus_L" = yes; then add_dir="-L$libdir" add="-l$name" elif test "$hardcode_shlibpath_var" = yes; then case :$finalize_shlibpath: in *":$libdir:"*) ;; *) finalize_shlibpath="$finalize_shlibpath$libdir:" ;; esac add="-l$name" elif test "$hardcode_automatic" = yes; then if test -n "$inst_prefix_dir" && test -f "$inst_prefix_dir$libdir/$linklib" ; then add="$inst_prefix_dir$libdir/$linklib" else add="$libdir/$linklib" fi else # We cannot seem to hardcode it, guess we'll fake it. add_dir="-L$libdir" # Try looking first in the location we're being installed to. if test -n "$inst_prefix_dir"; then case $libdir in [\\/]*) add_dir="$add_dir -L$inst_prefix_dir$libdir" ;; esac fi add="-l$name" fi if test "$linkmode" = prog; then test -n "$add_dir" && finalize_deplibs="$add_dir $finalize_deplibs" test -n "$add" && finalize_deplibs="$add $finalize_deplibs" else test -n "$add_dir" && deplibs="$add_dir $deplibs" test -n "$add" && deplibs="$add $deplibs" fi fi elif test "$linkmode" = prog; then # Here we assume that one of hardcode_direct or hardcode_minus_L # is not unsupported. This is valid on all known static and # shared platforms. if test "$hardcode_direct" != unsupported; then test -n "$old_library" && linklib="$old_library" compile_deplibs="$dir/$linklib $compile_deplibs" finalize_deplibs="$dir/$linklib $finalize_deplibs" else compile_deplibs="-l$name -L$dir $compile_deplibs" finalize_deplibs="-l$name -L$dir $finalize_deplibs" fi elif test "$build_libtool_libs" = yes; then # Not a shared library if test "$deplibs_check_method" != pass_all; then # We're trying link a shared library against a static one # but the system doesn't support it. # Just print a warning and add the library to dependency_libs so # that the program can be linked against the static library. $ECHO $ECHO "*** Warning: This system can not link to static lib archive $lib." $ECHO "*** I have the capability to make that library automatically link in when" $ECHO "*** you link to this library. But I can only do this if you have a" $ECHO "*** shared version of the library, which you do not appear to have." if test "$module" = yes; then $ECHO "*** But as you try to build a module library, libtool will still create " $ECHO "*** a static module, that should work as long as the dlopening application" $ECHO "*** is linked with the -dlopen flag to resolve symbols at runtime." if test -z "$global_symbol_pipe"; then $ECHO $ECHO "*** However, this would only work if libtool was able to extract symbol" $ECHO "*** lists from a program, using \`nm' or equivalent, but libtool could" $ECHO "*** not find such a program. So, this module is probably useless." $ECHO "*** \`nm' from GNU binutils and a full rebuild may help." fi if test "$build_old_libs" = no; then build_libtool_libs=module build_old_libs=yes else build_libtool_libs=no fi fi else deplibs="$dir/$old_library $deplibs" link_static=yes fi fi # link shared/static library? if test "$linkmode" = lib; then if test -n "$dependency_libs" && { test "$hardcode_into_libs" != yes || test "$build_old_libs" = yes || test "$link_static" = yes; }; then # Extract -R from dependency_libs temp_deplibs= for libdir in $dependency_libs; do case $libdir in -R*) func_stripname '-R' '' "$libdir" temp_xrpath=$func_stripname_result case " $xrpath " in *" $temp_xrpath "*) ;; *) xrpath="$xrpath $temp_xrpath";; esac;; *) temp_deplibs="$temp_deplibs $libdir";; esac done dependency_libs="$temp_deplibs" fi newlib_search_path="$newlib_search_path $absdir" # Link against this library test "$link_static" = no && newdependency_libs="$abs_ladir/$laname $newdependency_libs" # ... and its dependency_libs tmp_libs= for deplib in $dependency_libs; do newdependency_libs="$deplib $newdependency_libs" if $opt_duplicate_deps ; then case "$tmp_libs " in *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;; esac fi tmp_libs="$tmp_libs $deplib" done if test "$link_all_deplibs" != no; then # Add the search paths of all dependency libraries for deplib in $dependency_libs; do case $deplib in -L*) path="$deplib" ;; *.la) func_dirname "$deplib" "" "." dir="$func_dirname_result" # We need an absolute path. case $dir in [\\/]* | [A-Za-z]:[\\/]*) absdir="$dir" ;; *) absdir=`cd "$dir" && pwd` if test -z "$absdir"; then func_warning "cannot determine absolute directory name of \`$dir'" absdir="$dir" fi ;; esac if $GREP "^installed=no" $deplib > /dev/null; then case $host in *-*-darwin*) depdepl= eval deplibrary_names=`${SED} -n -e 's/^library_names=\(.*\)$/\1/p' $deplib` if test -n "$deplibrary_names" ; then for tmp in $deplibrary_names ; do depdepl=$tmp done if test -f "$absdir/$objdir/$depdepl" ; then depdepl="$absdir/$objdir/$depdepl" darwin_install_name=`${OTOOL} -L $depdepl | awk '{if (NR == 2) {print $1;exit}}'` if test -z "$darwin_install_name"; then darwin_install_name=`${OTOOL64} -L $depdepl | awk '{if (NR == 2) {print $1;exit}}'` fi compiler_flags="$compiler_flags ${wl}-dylib_file ${wl}${darwin_install_name}:${depdepl}" linker_flags="$linker_flags -dylib_file ${darwin_install_name}:${depdepl}" path= fi fi ;; *) path="-L$absdir/$objdir" ;; esac else eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $deplib` test -z "$libdir" && \ func_fatal_error "\`$deplib' is not a valid libtool archive" test "$absdir" != "$libdir" && \ func_warning "\`$deplib' seems to be moved" path="-L$absdir" fi ;; esac case " $deplibs " in *" $path "*) ;; *) deplibs="$path $deplibs" ;; esac done fi # link_all_deplibs != no fi # linkmode = lib done # for deplib in $libs if test "$pass" = link; then if test "$linkmode" = "prog"; then compile_deplibs="$new_inherited_linker_flags $compile_deplibs" finalize_deplibs="$new_inherited_linker_flags $finalize_deplibs" else compiler_flags="$compiler_flags "`$ECHO "X $new_inherited_linker_flags" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` fi fi dependency_libs="$newdependency_libs" if test "$pass" = dlpreopen; then # Link the dlpreopened libraries before other libraries for deplib in $save_deplibs; do deplibs="$deplib $deplibs" done fi if test "$pass" != dlopen; then if test "$pass" != conv; then # Make sure lib_search_path contains only unique directories. lib_search_path= for dir in $newlib_search_path; do case "$lib_search_path " in *" $dir "*) ;; *) lib_search_path="$lib_search_path $dir" ;; esac done newlib_search_path= fi if test "$linkmode,$pass" != "prog,link"; then vars="deplibs" else vars="compile_deplibs finalize_deplibs" fi for var in $vars dependency_libs; do # Add libraries to $var in reverse order eval tmp_libs=\"\$$var\" new_libs= for deplib in $tmp_libs; do # FIXME: Pedantically, this is the right thing to do, so # that some nasty dependency loop isn't accidentally # broken: #new_libs="$deplib $new_libs" # Pragmatically, this seems to cause very few problems in # practice: case $deplib in -L*) new_libs="$deplib $new_libs" ;; -R*) ;; *) # And here is the reason: when a library appears more # than once as an explicit dependence of a library, or # is implicitly linked in more than once by the # compiler, it is considered special, and multiple # occurrences thereof are not removed. Compare this # with having the same library being listed as a # dependency of multiple other libraries: in this case, # we know (pedantically, we assume) the library does not # need to be listed more than once, so we keep only the # last copy. This is not always right, but it is rare # enough that we require users that really mean to play # such unportable linking tricks to link the library # using -Wl,-lname, so that libtool does not consider it # for duplicate removal. case " $specialdeplibs " in *" $deplib "*) new_libs="$deplib $new_libs" ;; *) case " $new_libs " in *" $deplib "*) ;; *) new_libs="$deplib $new_libs" ;; esac ;; esac ;; esac done tmp_libs= for deplib in $new_libs; do case $deplib in -L*) case " $tmp_libs " in *" $deplib "*) ;; *) tmp_libs="$tmp_libs $deplib" ;; esac ;; *) tmp_libs="$tmp_libs $deplib" ;; esac done eval $var=\"$tmp_libs\" done # for var fi # Last step: remove runtime libs from dependency_libs # (they stay in deplibs) tmp_libs= for i in $dependency_libs ; do case " $predeps $postdeps $compiler_lib_search_path " in *" $i "*) i="" ;; esac if test -n "$i" ; then tmp_libs="$tmp_libs $i" fi done dependency_libs=$tmp_libs done # for pass if test "$linkmode" = prog; then dlfiles="$newdlfiles" fi if test "$linkmode" = prog || test "$linkmode" = lib; then dlprefiles="$newdlprefiles" fi case $linkmode in oldlib) if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then func_warning "\`-dlopen' is ignored for archives" fi case " $deplibs" in *\ -l* | *\ -L*) func_warning "\`-l' and \`-L' are ignored for archives" ;; esac test -n "$rpath" && \ func_warning "\`-rpath' is ignored for archives" test -n "$xrpath" && \ func_warning "\`-R' is ignored for archives" test -n "$vinfo" && \ func_warning "\`-version-info/-version-number' is ignored for archives" test -n "$release" && \ func_warning "\`-release' is ignored for archives" test -n "$export_symbols$export_symbols_regex" && \ func_warning "\`-export-symbols' is ignored for archives" # Now set the variables for building old libraries. build_libtool_libs=no oldlibs="$output" objs="$objs$old_deplibs" ;; lib) # Make sure we only generate libraries of the form `libNAME.la'. case $outputname in lib*) func_stripname 'lib' '.la' "$outputname" name=$func_stripname_result eval shared_ext=\"$shrext_cmds\" eval libname=\"$libname_spec\" ;; *) test "$module" = no && \ func_fatal_help "libtool library \`$output' must begin with \`lib'" if test "$need_lib_prefix" != no; then # Add the "lib" prefix for modules if required func_stripname '' '.la' "$outputname" name=$func_stripname_result eval shared_ext=\"$shrext_cmds\" eval libname=\"$libname_spec\" else func_stripname '' '.la' "$outputname" libname=$func_stripname_result fi ;; esac if test -n "$objs"; then if test "$deplibs_check_method" != pass_all; then func_fatal_error "cannot build libtool library \`$output' from non-libtool objects on this host:$objs" else $ECHO $ECHO "*** Warning: Linking the shared library $output against the non-libtool" $ECHO "*** objects $objs is not portable!" libobjs="$libobjs $objs" fi fi test "$dlself" != no && \ func_warning "\`-dlopen self' is ignored for libtool libraries" set dummy $rpath shift test "$#" -gt 1 && \ func_warning "ignoring multiple \`-rpath's for a libtool library" install_libdir="$1" oldlibs= if test -z "$rpath"; then if test "$build_libtool_libs" = yes; then # Building a libtool convenience library. # Some compilers have problems with a `.al' extension so # convenience libraries should have the same extension an # archive normally would. oldlibs="$output_objdir/$libname.$libext $oldlibs" build_libtool_libs=convenience build_old_libs=yes fi test -n "$vinfo" && \ func_warning "\`-version-info/-version-number' is ignored for convenience libraries" test -n "$release" && \ func_warning "\`-release' is ignored for convenience libraries" else # Parse the version information argument. save_ifs="$IFS"; IFS=':' set dummy $vinfo 0 0 0 shift IFS="$save_ifs" test -n "$7" && \ func_fatal_help "too many parameters to \`-version-info'" # convert absolute version numbers to libtool ages # this retains compatibility with .la files and attempts # to make the code below a bit more comprehensible case $vinfo_number in yes) number_major="$1" number_minor="$2" number_revision="$3" # # There are really only two kinds -- those that # use the current revision as the major version # and those that subtract age and use age as # a minor version. But, then there is irix # which has an extra 1 added just for fun # case $version_type in darwin|linux|osf|windows|none) func_arith $number_major + $number_minor current=$func_arith_result age="$number_minor" revision="$number_revision" ;; freebsd-aout|freebsd-elf|sunos) current="$number_major" revision="$number_minor" age="0" ;; irix|nonstopux) func_arith $number_major + $number_minor current=$func_arith_result age="$number_minor" revision="$number_minor" lt_irix_increment=no ;; *) func_fatal_configuration "$modename: unknown library version type \`$version_type'" ;; esac ;; no) current="$1" revision="$2" age="$3" ;; esac # Check that each of the things are valid numbers. case $current in 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;; *) func_error "CURRENT \`$current' must be a nonnegative integer" func_fatal_error "\`$vinfo' is not valid version information" ;; esac case $revision in 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;; *) func_error "REVISION \`$revision' must be a nonnegative integer" func_fatal_error "\`$vinfo' is not valid version information" ;; esac case $age in 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;; *) func_error "AGE \`$age' must be a nonnegative integer" func_fatal_error "\`$vinfo' is not valid version information" ;; esac if test "$age" -gt "$current"; then func_error "AGE \`$age' is greater than the current interface number \`$current'" func_fatal_error "\`$vinfo' is not valid version information" fi # Calculate the version variables. major= versuffix= verstring= case $version_type in none) ;; darwin) # Like Linux, but with the current version available in # verstring for coding it into the library header func_arith $current - $age major=.$func_arith_result versuffix="$major.$age.$revision" # Darwin ld doesn't like 0 for these options... func_arith $current + 1 minor_current=$func_arith_result xlcverstring="${wl}-compatibility_version ${wl}$minor_current ${wl}-current_version ${wl}$minor_current.$revision" verstring="-compatibility_version $minor_current -current_version $minor_current.$revision" ;; freebsd-aout) major=".$current" versuffix=".$current.$revision"; ;; freebsd-elf) major=".$current" versuffix=".$current" ;; irix | nonstopux) if test "X$lt_irix_increment" = "Xno"; then func_arith $current - $age else func_arith $current - $age + 1 fi major=$func_arith_result case $version_type in nonstopux) verstring_prefix=nonstopux ;; *) verstring_prefix=sgi ;; esac verstring="$verstring_prefix$major.$revision" # Add in all the interfaces that we are compatible with. loop=$revision while test "$loop" -ne 0; do func_arith $revision - $loop iface=$func_arith_result func_arith $loop - 1 loop=$func_arith_result verstring="$verstring_prefix$major.$iface:$verstring" done # Before this point, $major must not contain `.'. major=.$major versuffix="$major.$revision" ;; linux) func_arith $current - $age major=.$func_arith_result versuffix="$major.$age.$revision" ;; osf) func_arith $current - $age major=.$func_arith_result versuffix=".$current.$age.$revision" verstring="$current.$age.$revision" # Add in all the interfaces that we are compatible with. loop=$age while test "$loop" -ne 0; do func_arith $current - $loop iface=$func_arith_result func_arith $loop - 1 loop=$func_arith_result verstring="$verstring:${iface}.0" done # Make executables depend on our current version. verstring="$verstring:${current}.0" ;; qnx) major=".$current" versuffix=".$current" ;; sunos) major=".$current" versuffix=".$current.$revision" ;; windows) # Use '-' rather than '.', since we only want one # extension on DOS 8.3 filesystems. func_arith $current - $age major=$func_arith_result versuffix="-$major" ;; *) func_fatal_configuration "unknown library version type \`$version_type'" ;; esac # Clear the version info if we defaulted, and they specified a release. if test -z "$vinfo" && test -n "$release"; then major= case $version_type in darwin) # we can't check for "0.0" in archive_cmds due to quoting # problems, so we reset it completely verstring= ;; *) verstring="0.0" ;; esac if test "$need_version" = no; then versuffix= else versuffix=".0.0" fi fi # Remove version info from name if versioning should be avoided if test "$avoid_version" = yes && test "$need_version" = no; then major= versuffix= verstring="" fi # Check to see if the archive will have undefined symbols. if test "$allow_undefined" = yes; then if test "$allow_undefined_flag" = unsupported; then func_warning "undefined symbols not allowed in $host shared libraries" build_libtool_libs=no build_old_libs=yes fi else # Don't allow undefined symbols. allow_undefined_flag="$no_undefined_flag" fi fi func_generate_dlsyms "$libname" "$libname" "yes" libobjs="$libobjs $symfileobj" test "X$libobjs" = "X " && libobjs= if test "$mode" != relink; then # Remove our outputs, but don't remove object files since they # may have been created when compiling PIC objects. removelist= tempremovelist=`$ECHO "$output_objdir/*"` for p in $tempremovelist; do case $p in *.$objext | *.gcno) ;; $output_objdir/$outputname | $output_objdir/$libname.* | $output_objdir/${libname}${release}.*) if test "X$precious_files_regex" != "X"; then if $ECHO "$p" | $EGREP -e "$precious_files_regex" >/dev/null 2>&1 then continue fi fi removelist="$removelist $p" ;; *) ;; esac done test -n "$removelist" && \ func_show_eval "${RM}r \$removelist" fi # Now set the variables for building old libraries. if test "$build_old_libs" = yes && test "$build_libtool_libs" != convenience ; then oldlibs="$oldlibs $output_objdir/$libname.$libext" # Transform .lo files to .o files. oldobjs="$objs "`$ECHO "X$libobjs" | $SP2NL | $Xsed -e '/\.'${libext}'$/d' -e "$lo2o" | $NL2SP` fi # Eliminate all temporary directories. #for path in $notinst_path; do # lib_search_path=`$ECHO "X$lib_search_path " | $Xsed -e "s% $path % %g"` # deplibs=`$ECHO "X$deplibs " | $Xsed -e "s% -L$path % %g"` # dependency_libs=`$ECHO "X$dependency_libs " | $Xsed -e "s% -L$path % %g"` #done if test -n "$xrpath"; then # If the user specified any rpath flags, then add them. temp_xrpath= for libdir in $xrpath; do temp_xrpath="$temp_xrpath -R$libdir" case "$finalize_rpath " in *" $libdir "*) ;; *) finalize_rpath="$finalize_rpath $libdir" ;; esac done if test "$hardcode_into_libs" != yes || test "$build_old_libs" = yes; then dependency_libs="$temp_xrpath $dependency_libs" fi fi # Make sure dlfiles contains only unique files that won't be dlpreopened old_dlfiles="$dlfiles" dlfiles= for lib in $old_dlfiles; do case " $dlprefiles $dlfiles " in *" $lib "*) ;; *) dlfiles="$dlfiles $lib" ;; esac done # Make sure dlprefiles contains only unique files old_dlprefiles="$dlprefiles" dlprefiles= for lib in $old_dlprefiles; do case "$dlprefiles " in *" $lib "*) ;; *) dlprefiles="$dlprefiles $lib" ;; esac done if test "$build_libtool_libs" = yes; then if test -n "$rpath"; then case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-beos* | *-cegcc*) # these systems don't actually have a c library (as such)! ;; *-*-rhapsody* | *-*-darwin1.[012]) # Rhapsody C library is in the System framework deplibs="$deplibs System.ltframework" ;; *-*-netbsd*) # Don't link with libc until the a.out ld.so is fixed. ;; *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*) # Do not include libc due to us having libc/libc_r. ;; *-*-sco3.2v5* | *-*-sco5v6*) # Causes problems with __ctype ;; *-*-sysv4.2uw2* | *-*-sysv5* | *-*-unixware* | *-*-OpenUNIX*) # Compiler inserts libc in the correct place for threads to work ;; *) # Add libc to deplibs on all other systems if necessary. if test "$build_libtool_need_lc" = "yes"; then deplibs="$deplibs -lc" fi ;; esac fi # Transform deplibs into only deplibs that can be linked in shared. name_save=$name libname_save=$libname release_save=$release versuffix_save=$versuffix major_save=$major # I'm not sure if I'm treating the release correctly. I think # release should show up in the -l (ie -lgmp5) so we don't want to # add it in twice. Is that correct? release="" versuffix="" major="" newdeplibs= droppeddeps=no case $deplibs_check_method in pass_all) # Don't check for shared/static. Everything works. # This might be a little naive. We might want to check # whether the library exists or not. But this is on # osf3 & osf4 and I'm not really sure... Just # implementing what was already the behavior. newdeplibs=$deplibs ;; test_compile) # This code stresses the "libraries are programs" paradigm to its # limits. Maybe even breaks it. We compile a program, linking it # against the deplibs as a proxy for the library. Then we can check # whether they linked in statically or dynamically with ldd. $opt_dry_run || $RM conftest.c cat > conftest.c </dev/null` for potent_lib in $potential_libs; do # Follow soft links. if ls -lLd "$potent_lib" 2>/dev/null | $GREP " -> " >/dev/null; then continue fi # The statement above tries to avoid entering an # endless loop below, in case of cyclic links. # We might still enter an endless loop, since a link # loop can be closed while we follow links, # but so what? potlib="$potent_lib" while test -h "$potlib" 2>/dev/null; do potliblink=`ls -ld $potlib | ${SED} 's/.* -> //'` case $potliblink in [\\/]* | [A-Za-z]:[\\/]*) potlib="$potliblink";; *) potlib=`$ECHO "X$potlib" | $Xsed -e 's,[^/]*$,,'`"$potliblink";; esac done if eval $file_magic_cmd \"\$potlib\" 2>/dev/null | $SED -e 10q | $EGREP "$file_magic_regex" > /dev/null; then newdeplibs="$newdeplibs $a_deplib" a_deplib="" break 2 fi done done fi if test -n "$a_deplib" ; then droppeddeps=yes $ECHO $ECHO "*** Warning: linker path does not have real file for library $a_deplib." $ECHO "*** I have the capability to make that library automatically link in when" $ECHO "*** you link to this library. But I can only do this if you have a" $ECHO "*** shared version of the library, which you do not appear to have" $ECHO "*** because I did check the linker path looking for a file starting" if test -z "$potlib" ; then $ECHO "*** with $libname but no candidates were found. (...for file magic test)" else $ECHO "*** with $libname and none of the candidates passed a file format test" $ECHO "*** using a file magic. Last file checked: $potlib" fi fi ;; *) # Add a -L argument. newdeplibs="$newdeplibs $a_deplib" ;; esac done # Gone through all deplibs. ;; match_pattern*) set dummy $deplibs_check_method; shift match_pattern_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"` for a_deplib in $deplibs; do case $a_deplib in -l*) func_stripname -l '' "$a_deplib" name=$func_stripname_result if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then case " $predeps $postdeps " in *" $a_deplib "*) newdeplibs="$newdeplibs $a_deplib" a_deplib="" ;; esac fi if test -n "$a_deplib" ; then libname=`eval "\\$ECHO \"$libname_spec\""` for i in $lib_search_path $sys_lib_search_path $shlib_search_path; do potential_libs=`ls $i/$libname[.-]* 2>/dev/null` for potent_lib in $potential_libs; do potlib="$potent_lib" # see symlink-check above in file_magic test if eval "\$ECHO \"X$potent_lib\"" 2>/dev/null | $Xsed -e 10q | \ $EGREP "$match_pattern_regex" > /dev/null; then newdeplibs="$newdeplibs $a_deplib" a_deplib="" break 2 fi done done fi if test -n "$a_deplib" ; then droppeddeps=yes $ECHO $ECHO "*** Warning: linker path does not have real file for library $a_deplib." $ECHO "*** I have the capability to make that library automatically link in when" $ECHO "*** you link to this library. But I can only do this if you have a" $ECHO "*** shared version of the library, which you do not appear to have" $ECHO "*** because I did check the linker path looking for a file starting" if test -z "$potlib" ; then $ECHO "*** with $libname but no candidates were found. (...for regex pattern test)" else $ECHO "*** with $libname and none of the candidates passed a file format test" $ECHO "*** using a regex pattern. Last file checked: $potlib" fi fi ;; *) # Add a -L argument. newdeplibs="$newdeplibs $a_deplib" ;; esac done # Gone through all deplibs. ;; none | unknown | *) newdeplibs="" tmp_deplibs=`$ECHO "X $deplibs" | $Xsed \ -e 's/ -lc$//' -e 's/ -[LR][^ ]*//g'` if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then for i in $predeps $postdeps ; do # can't use Xsed below, because $i might contain '/' tmp_deplibs=`$ECHO "X $tmp_deplibs" | $Xsed -e "s,$i,,"` done fi if $ECHO "X $tmp_deplibs" | $Xsed -e 's/[ ]//g' | $GREP . >/dev/null; then $ECHO if test "X$deplibs_check_method" = "Xnone"; then $ECHO "*** Warning: inter-library dependencies are not supported in this platform." else $ECHO "*** Warning: inter-library dependencies are not known to be supported." fi $ECHO "*** All declared inter-library dependencies are being dropped." droppeddeps=yes fi ;; esac versuffix=$versuffix_save major=$major_save release=$release_save libname=$libname_save name=$name_save case $host in *-*-rhapsody* | *-*-darwin1.[012]) # On Rhapsody replace the C library with the System framework newdeplibs=`$ECHO "X $newdeplibs" | $Xsed -e 's/ -lc / System.ltframework /'` ;; esac if test "$droppeddeps" = yes; then if test "$module" = yes; then $ECHO $ECHO "*** Warning: libtool could not satisfy all declared inter-library" $ECHO "*** dependencies of module $libname. Therefore, libtool will create" $ECHO "*** a static module, that should work as long as the dlopening" $ECHO "*** application is linked with the -dlopen flag." if test -z "$global_symbol_pipe"; then $ECHO $ECHO "*** However, this would only work if libtool was able to extract symbol" $ECHO "*** lists from a program, using \`nm' or equivalent, but libtool could" $ECHO "*** not find such a program. So, this module is probably useless." $ECHO "*** \`nm' from GNU binutils and a full rebuild may help." fi if test "$build_old_libs" = no; then oldlibs="$output_objdir/$libname.$libext" build_libtool_libs=module build_old_libs=yes else build_libtool_libs=no fi else $ECHO "*** The inter-library dependencies that have been dropped here will be" $ECHO "*** automatically added whenever a program is linked with this library" $ECHO "*** or is declared to -dlopen it." if test "$allow_undefined" = no; then $ECHO $ECHO "*** Since this library must not contain undefined symbols," $ECHO "*** because either the platform does not support them or" $ECHO "*** it was explicitly requested with -no-undefined," $ECHO "*** libtool will only create a static version of it." if test "$build_old_libs" = no; then oldlibs="$output_objdir/$libname.$libext" build_libtool_libs=module build_old_libs=yes else build_libtool_libs=no fi fi fi fi # Done checking deplibs! deplibs=$newdeplibs fi # Time to change all our "foo.ltframework" stuff back to "-framework foo" case $host in *-*-darwin*) newdeplibs=`$ECHO "X $newdeplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` new_inherited_linker_flags=`$ECHO "X $new_inherited_linker_flags" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` deplibs=`$ECHO "X $deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` ;; esac # move library search paths that coincide with paths to not yet # installed libraries to the beginning of the library search list new_libs= for path in $notinst_path; do case " $new_libs " in *" -L$path/$objdir "*) ;; *) case " $deplibs " in *" -L$path/$objdir "*) new_libs="$new_libs -L$path/$objdir" ;; esac ;; esac done for deplib in $deplibs; do case $deplib in -L*) case " $new_libs " in *" $deplib "*) ;; *) new_libs="$new_libs $deplib" ;; esac ;; *) new_libs="$new_libs $deplib" ;; esac done deplibs="$new_libs" # All the library-specific variables (install_libdir is set above). library_names= old_library= dlname= # Test again, we may have decided not to build it any more if test "$build_libtool_libs" = yes; then if test "$hardcode_into_libs" = yes; then # Hardcode the library paths hardcode_libdirs= dep_rpath= rpath="$finalize_rpath" test "$mode" != relink && rpath="$compile_rpath$rpath" for libdir in $rpath; do if test -n "$hardcode_libdir_flag_spec"; then if test -n "$hardcode_libdir_separator"; then if test -z "$hardcode_libdirs"; then hardcode_libdirs="$libdir" else # Just accumulate the unique libdirs. case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*) ;; *) hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir" ;; esac fi else eval flag=\"$hardcode_libdir_flag_spec\" dep_rpath="$dep_rpath $flag" fi elif test -n "$runpath_var"; then case "$perm_rpath " in *" $libdir "*) ;; *) perm_rpath="$perm_rpath $libdir" ;; esac fi done # Substitute the hardcoded libdirs into the rpath. if test -n "$hardcode_libdir_separator" && test -n "$hardcode_libdirs"; then libdir="$hardcode_libdirs" if test -n "$hardcode_libdir_flag_spec_ld"; then eval dep_rpath=\"$hardcode_libdir_flag_spec_ld\" else eval dep_rpath=\"$hardcode_libdir_flag_spec\" fi fi if test -n "$runpath_var" && test -n "$perm_rpath"; then # We should set the runpath_var. rpath= for dir in $perm_rpath; do rpath="$rpath$dir:" done eval "$runpath_var='$rpath\$$runpath_var'; export $runpath_var" fi test -n "$dep_rpath" && deplibs="$dep_rpath $deplibs" fi shlibpath="$finalize_shlibpath" test "$mode" != relink && shlibpath="$compile_shlibpath$shlibpath" if test -n "$shlibpath"; then eval "$shlibpath_var='$shlibpath\$$shlibpath_var'; export $shlibpath_var" fi # Get the real and link names of the library. eval shared_ext=\"$shrext_cmds\" eval library_names=\"$library_names_spec\" set dummy $library_names shift realname="$1" shift if test -n "$soname_spec"; then eval soname=\"$soname_spec\" else soname="$realname" fi if test -z "$dlname"; then dlname=$soname fi lib="$output_objdir/$realname" linknames= for link do linknames="$linknames $link" done # Use standard objects if they are pic test -z "$pic_flag" && libobjs=`$ECHO "X$libobjs" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP` test "X$libobjs" = "X " && libobjs= delfiles= if test -n "$export_symbols" && test -n "$include_expsyms"; then $opt_dry_run || cp "$export_symbols" "$output_objdir/$libname.uexp" export_symbols="$output_objdir/$libname.uexp" delfiles="$delfiles $export_symbols" fi orig_export_symbols= case $host_os in cygwin* | mingw* | cegcc*) if test -n "$export_symbols" && test -z "$export_symbols_regex"; then # exporting using user supplied symfile if test "x`$SED 1q $export_symbols`" != xEXPORTS; then # and it's NOT already a .def file. Must figure out # which of the given symbols are data symbols and tag # them as such. So, trigger use of export_symbols_cmds. # export_symbols gets reassigned inside the "prepare # the list of exported symbols" if statement, so the # include_expsyms logic still works. orig_export_symbols="$export_symbols" export_symbols= always_export_symbols=yes fi fi ;; esac # Prepare the list of exported symbols if test -z "$export_symbols"; then if test "$always_export_symbols" = yes || test -n "$export_symbols_regex"; then func_verbose "generating symbol list for \`$libname.la'" export_symbols="$output_objdir/$libname.exp" $opt_dry_run || $RM $export_symbols cmds=$export_symbols_cmds save_ifs="$IFS"; IFS='~' for cmd in $cmds; do IFS="$save_ifs" eval cmd=\"$cmd\" func_len " $cmd" len=$func_len_result if test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then func_show_eval "$cmd" 'exit $?' skipped_export=false else # The command line is too long to execute in one step. func_verbose "using reloadable object file for export list..." skipped_export=: # Break out early, otherwise skipped_export may be # set to false by a later but shorter cmd. break fi done IFS="$save_ifs" if test -n "$export_symbols_regex" && test "X$skipped_export" != "X:"; then func_show_eval '$EGREP -e "$export_symbols_regex" "$export_symbols" > "${export_symbols}T"' func_show_eval '$MV "${export_symbols}T" "$export_symbols"' fi fi fi if test -n "$export_symbols" && test -n "$include_expsyms"; then tmp_export_symbols="$export_symbols" test -n "$orig_export_symbols" && tmp_export_symbols="$orig_export_symbols" $opt_dry_run || eval '$ECHO "X$include_expsyms" | $Xsed | $SP2NL >> "$tmp_export_symbols"' fi if test "X$skipped_export" != "X:" && test -n "$orig_export_symbols"; then # The given exports_symbols file has to be filtered, so filter it. func_verbose "filter symbol list for \`$libname.la' to tag DATA exports" # FIXME: $output_objdir/$libname.filter potentially contains lots of # 's' commands which not all seds can handle. GNU sed should be fine # though. Also, the filter scales superlinearly with the number of # global variables. join(1) would be nice here, but unfortunately # isn't a blessed tool. $opt_dry_run || $SED -e '/[ ,]DATA/!d;s,\(.*\)\([ \,].*\),s|^\1$|\1\2|,' < $export_symbols > $output_objdir/$libname.filter delfiles="$delfiles $export_symbols $output_objdir/$libname.filter" export_symbols=$output_objdir/$libname.def $opt_dry_run || $SED -f $output_objdir/$libname.filter < $orig_export_symbols > $export_symbols fi tmp_deplibs= for test_deplib in $deplibs; do case " $convenience " in *" $test_deplib "*) ;; *) tmp_deplibs="$tmp_deplibs $test_deplib" ;; esac done deplibs="$tmp_deplibs" if test -n "$convenience"; then if test -n "$whole_archive_flag_spec" && test "$compiler_needs_object" = yes && test -z "$libobjs"; then # extract the archives, so we have objects to list. # TODO: could optimize this to just extract one archive. whole_archive_flag_spec= fi if test -n "$whole_archive_flag_spec"; then save_libobjs=$libobjs eval libobjs=\"\$libobjs $whole_archive_flag_spec\" test "X$libobjs" = "X " && libobjs= else gentop="$output_objdir/${outputname}x" generated="$generated $gentop" func_extract_archives $gentop $convenience libobjs="$libobjs $func_extract_archives_result" test "X$libobjs" = "X " && libobjs= fi fi if test "$thread_safe" = yes && test -n "$thread_safe_flag_spec"; then eval flag=\"$thread_safe_flag_spec\" linker_flags="$linker_flags $flag" fi # Make a backup of the uninstalled library when relinking if test "$mode" = relink; then $opt_dry_run || eval '(cd $output_objdir && $RM ${realname}U && $MV $realname ${realname}U)' || exit $? fi # Do each of the archive commands. if test "$module" = yes && test -n "$module_cmds" ; then if test -n "$export_symbols" && test -n "$module_expsym_cmds"; then eval test_cmds=\"$module_expsym_cmds\" cmds=$module_expsym_cmds else eval test_cmds=\"$module_cmds\" cmds=$module_cmds fi else if test -n "$export_symbols" && test -n "$archive_expsym_cmds"; then eval test_cmds=\"$archive_expsym_cmds\" cmds=$archive_expsym_cmds else eval test_cmds=\"$archive_cmds\" cmds=$archive_cmds fi fi if test "X$skipped_export" != "X:" && func_len " $test_cmds" && len=$func_len_result && test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then : else # The command line is too long to link in one step, link piecewise # or, if using GNU ld and skipped_export is not :, use a linker # script. # Save the value of $output and $libobjs because we want to # use them later. If we have whole_archive_flag_spec, we # want to use save_libobjs as it was before # whole_archive_flag_spec was expanded, because we can't # assume the linker understands whole_archive_flag_spec. # This may have to be revisited, in case too many # convenience libraries get linked in and end up exceeding # the spec. if test -z "$convenience" || test -z "$whole_archive_flag_spec"; then save_libobjs=$libobjs fi save_output=$output output_la=`$ECHO "X$output" | $Xsed -e "$basename"` # Clear the reloadable object creation command queue and # initialize k to one. test_cmds= concat_cmds= objlist= last_robj= k=1 if test -n "$save_libobjs" && test "X$skipped_export" != "X:" && test "$with_gnu_ld" = yes; then output=${output_objdir}/${output_la}.lnkscript func_verbose "creating GNU ld script: $output" $ECHO 'INPUT (' > $output for obj in $save_libobjs do $ECHO "$obj" >> $output done $ECHO ')' >> $output delfiles="$delfiles $output" elif test -n "$save_libobjs" && test "X$skipped_export" != "X:" && test "X$file_list_spec" != X; then output=${output_objdir}/${output_la}.lnk func_verbose "creating linker input file list: $output" : > $output set x $save_libobjs shift firstobj= if test "$compiler_needs_object" = yes; then firstobj="$1 " shift fi for obj do $ECHO "$obj" >> $output done delfiles="$delfiles $output" output=$firstobj\"$file_list_spec$output\" else if test -n "$save_libobjs"; then func_verbose "creating reloadable object files..." output=$output_objdir/$output_la-${k}.$objext eval test_cmds=\"$reload_cmds\" func_len " $test_cmds" len0=$func_len_result len=$len0 # Loop over the list of objects to be linked. for obj in $save_libobjs do func_len " $obj" func_arith $len + $func_len_result len=$func_arith_result if test "X$objlist" = X || test "$len" -lt "$max_cmd_len"; then func_append objlist " $obj" else # The command $test_cmds is almost too long, add a # command to the queue. if test "$k" -eq 1 ; then # The first file doesn't have a previous command to add. eval concat_cmds=\"$reload_cmds $objlist $last_robj\" else # All subsequent reloadable object files will link in # the last one created. eval concat_cmds=\"\$concat_cmds~$reload_cmds $objlist $last_robj~\$RM $last_robj\" fi last_robj=$output_objdir/$output_la-${k}.$objext func_arith $k + 1 k=$func_arith_result output=$output_objdir/$output_la-${k}.$objext objlist=$obj func_len " $last_robj" func_arith $len0 + $func_len_result len=$func_arith_result fi done # Handle the remaining objects by creating one last # reloadable object file. All subsequent reloadable object # files will link in the last one created. test -z "$concat_cmds" || concat_cmds=$concat_cmds~ eval concat_cmds=\"\${concat_cmds}$reload_cmds $objlist $last_robj\" if test -n "$last_robj"; then eval concat_cmds=\"\${concat_cmds}~\$RM $last_robj\" fi delfiles="$delfiles $output" else output= fi if ${skipped_export-false}; then func_verbose "generating symbol list for \`$libname.la'" export_symbols="$output_objdir/$libname.exp" $opt_dry_run || $RM $export_symbols libobjs=$output # Append the command to create the export file. test -z "$concat_cmds" || concat_cmds=$concat_cmds~ eval concat_cmds=\"\$concat_cmds$export_symbols_cmds\" if test -n "$last_robj"; then eval concat_cmds=\"\$concat_cmds~\$RM $last_robj\" fi fi test -n "$save_libobjs" && func_verbose "creating a temporary reloadable object file: $output" # Loop through the commands generated above and execute them. save_ifs="$IFS"; IFS='~' for cmd in $concat_cmds; do IFS="$save_ifs" $opt_silent || { func_quote_for_expand "$cmd" eval "func_echo $func_quote_for_expand_result" } $opt_dry_run || eval "$cmd" || { lt_exit=$? # Restore the uninstalled library and exit if test "$mode" = relink; then ( cd "$output_objdir" && \ $RM "${realname}T" && \ $MV "${realname}U" "$realname" ) fi exit $lt_exit } done IFS="$save_ifs" if test -n "$export_symbols_regex" && ${skipped_export-false}; then func_show_eval '$EGREP -e "$export_symbols_regex" "$export_symbols" > "${export_symbols}T"' func_show_eval '$MV "${export_symbols}T" "$export_symbols"' fi fi if ${skipped_export-false}; then if test -n "$export_symbols" && test -n "$include_expsyms"; then tmp_export_symbols="$export_symbols" test -n "$orig_export_symbols" && tmp_export_symbols="$orig_export_symbols" $opt_dry_run || eval '$ECHO "X$include_expsyms" | $Xsed | $SP2NL >> "$tmp_export_symbols"' fi if test -n "$orig_export_symbols"; then # The given exports_symbols file has to be filtered, so filter it. func_verbose "filter symbol list for \`$libname.la' to tag DATA exports" # FIXME: $output_objdir/$libname.filter potentially contains lots of # 's' commands which not all seds can handle. GNU sed should be fine # though. Also, the filter scales superlinearly with the number of # global variables. join(1) would be nice here, but unfortunately # isn't a blessed tool. $opt_dry_run || $SED -e '/[ ,]DATA/!d;s,\(.*\)\([ \,].*\),s|^\1$|\1\2|,' < $export_symbols > $output_objdir/$libname.filter delfiles="$delfiles $export_symbols $output_objdir/$libname.filter" export_symbols=$output_objdir/$libname.def $opt_dry_run || $SED -f $output_objdir/$libname.filter < $orig_export_symbols > $export_symbols fi fi libobjs=$output # Restore the value of output. output=$save_output if test -n "$convenience" && test -n "$whole_archive_flag_spec"; then eval libobjs=\"\$libobjs $whole_archive_flag_spec\" test "X$libobjs" = "X " && libobjs= fi # Expand the library linking commands again to reset the # value of $libobjs for piecewise linking. # Do each of the archive commands. if test "$module" = yes && test -n "$module_cmds" ; then if test -n "$export_symbols" && test -n "$module_expsym_cmds"; then cmds=$module_expsym_cmds else cmds=$module_cmds fi else if test -n "$export_symbols" && test -n "$archive_expsym_cmds"; then cmds=$archive_expsym_cmds else cmds=$archive_cmds fi fi fi if test -n "$delfiles"; then # Append the command to remove temporary files to $cmds. eval cmds=\"\$cmds~\$RM $delfiles\" fi # Add any objects from preloaded convenience libraries if test -n "$dlprefiles"; then gentop="$output_objdir/${outputname}x" generated="$generated $gentop" func_extract_archives $gentop $dlprefiles libobjs="$libobjs $func_extract_archives_result" test "X$libobjs" = "X " && libobjs= fi save_ifs="$IFS"; IFS='~' for cmd in $cmds; do IFS="$save_ifs" eval cmd=\"$cmd\" $opt_silent || { func_quote_for_expand "$cmd" eval "func_echo $func_quote_for_expand_result" } $opt_dry_run || eval "$cmd" || { lt_exit=$? # Restore the uninstalled library and exit if test "$mode" = relink; then ( cd "$output_objdir" && \ $RM "${realname}T" && \ $MV "${realname}U" "$realname" ) fi exit $lt_exit } done IFS="$save_ifs" # Restore the uninstalled library and exit if test "$mode" = relink; then $opt_dry_run || eval '(cd $output_objdir && $RM ${realname}T && $MV $realname ${realname}T && $MV ${realname}U $realname)' || exit $? if test -n "$convenience"; then if test -z "$whole_archive_flag_spec"; then func_show_eval '${RM}r "$gentop"' fi fi exit $EXIT_SUCCESS fi # Create links to the real library. for linkname in $linknames; do if test "$realname" != "$linkname"; then func_show_eval '(cd "$output_objdir" && $RM "$linkname" && $LN_S "$realname" "$linkname")' 'exit $?' fi done # If -module or -export-dynamic was specified, set the dlname. if test "$module" = yes || test "$export_dynamic" = yes; then # On all known operating systems, these are identical. dlname="$soname" fi fi ;; obj) if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then func_warning "\`-dlopen' is ignored for objects" fi case " $deplibs" in *\ -l* | *\ -L*) func_warning "\`-l' and \`-L' are ignored for objects" ;; esac test -n "$rpath" && \ func_warning "\`-rpath' is ignored for objects" test -n "$xrpath" && \ func_warning "\`-R' is ignored for objects" test -n "$vinfo" && \ func_warning "\`-version-info' is ignored for objects" test -n "$release" && \ func_warning "\`-release' is ignored for objects" case $output in *.lo) test -n "$objs$old_deplibs" && \ func_fatal_error "cannot build library object \`$output' from non-libtool objects" libobj=$output func_lo2o "$libobj" obj=$func_lo2o_result ;; *) libobj= obj="$output" ;; esac # Delete the old objects. $opt_dry_run || $RM $obj $libobj # Objects from convenience libraries. This assumes # single-version convenience libraries. Whenever we create # different ones for PIC/non-PIC, this we'll have to duplicate # the extraction. reload_conv_objs= gentop= # reload_cmds runs $LD directly, so let us get rid of # -Wl from whole_archive_flag_spec and hope we can get by with # turning comma into space.. wl= if test -n "$convenience"; then if test -n "$whole_archive_flag_spec"; then eval tmp_whole_archive_flags=\"$whole_archive_flag_spec\" reload_conv_objs=$reload_objs\ `$ECHO "X$tmp_whole_archive_flags" | $Xsed -e 's|,| |g'` else gentop="$output_objdir/${obj}x" generated="$generated $gentop" func_extract_archives $gentop $convenience reload_conv_objs="$reload_objs $func_extract_archives_result" fi fi # Create the old-style object. reload_objs="$objs$old_deplibs "`$ECHO "X$libobjs" | $SP2NL | $Xsed -e '/\.'${libext}$'/d' -e '/\.lib$/d' -e "$lo2o" | $NL2SP`" $reload_conv_objs" ### testsuite: skip nested quoting test output="$obj" func_execute_cmds "$reload_cmds" 'exit $?' # Exit if we aren't doing a library object file. if test -z "$libobj"; then if test -n "$gentop"; then func_show_eval '${RM}r "$gentop"' fi exit $EXIT_SUCCESS fi if test "$build_libtool_libs" != yes; then if test -n "$gentop"; then func_show_eval '${RM}r "$gentop"' fi # Create an invalid libtool object if no PIC, so that we don't # accidentally link it into a program. # $show "echo timestamp > $libobj" # $opt_dry_run || eval "echo timestamp > $libobj" || exit $? exit $EXIT_SUCCESS fi if test -n "$pic_flag" || test "$pic_mode" != default; then # Only do commands if we really have different PIC objects. reload_objs="$libobjs $reload_conv_objs" output="$libobj" func_execute_cmds "$reload_cmds" 'exit $?' fi if test -n "$gentop"; then func_show_eval '${RM}r "$gentop"' fi exit $EXIT_SUCCESS ;; prog) case $host in *cygwin*) func_stripname '' '.exe' "$output" output=$func_stripname_result.exe;; esac test -n "$vinfo" && \ func_warning "\`-version-info' is ignored for programs" test -n "$release" && \ func_warning "\`-release' is ignored for programs" test "$preload" = yes \ && test "$dlopen_support" = unknown \ && test "$dlopen_self" = unknown \ && test "$dlopen_self_static" = unknown && \ func_warning "\`LT_INIT([dlopen])' not used. Assuming no dlopen support." case $host in *-*-rhapsody* | *-*-darwin1.[012]) # On Rhapsody replace the C library is the System framework compile_deplibs=`$ECHO "X $compile_deplibs" | $Xsed -e 's/ -lc / System.ltframework /'` finalize_deplibs=`$ECHO "X $finalize_deplibs" | $Xsed -e 's/ -lc / System.ltframework /'` ;; esac case $host in *-*-darwin*) # Don't allow lazy linking, it breaks C++ global constructors # But is supposedly fixed on 10.4 or later (yay!). if test "$tagname" = CXX ; then case ${MACOSX_DEPLOYMENT_TARGET-10.0} in 10.[0123]) compile_command="$compile_command ${wl}-bind_at_load" finalize_command="$finalize_command ${wl}-bind_at_load" ;; esac fi # Time to change all our "foo.ltframework" stuff back to "-framework foo" compile_deplibs=`$ECHO "X $compile_deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` finalize_deplibs=`$ECHO "X $finalize_deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` ;; esac # move library search paths that coincide with paths to not yet # installed libraries to the beginning of the library search list new_libs= for path in $notinst_path; do case " $new_libs " in *" -L$path/$objdir "*) ;; *) case " $compile_deplibs " in *" -L$path/$objdir "*) new_libs="$new_libs -L$path/$objdir" ;; esac ;; esac done for deplib in $compile_deplibs; do case $deplib in -L*) case " $new_libs " in *" $deplib "*) ;; *) new_libs="$new_libs $deplib" ;; esac ;; *) new_libs="$new_libs $deplib" ;; esac done compile_deplibs="$new_libs" compile_command="$compile_command $compile_deplibs" finalize_command="$finalize_command $finalize_deplibs" if test -n "$rpath$xrpath"; then # If the user specified any rpath flags, then add them. for libdir in $rpath $xrpath; do # This is the magic to use -rpath. case "$finalize_rpath " in *" $libdir "*) ;; *) finalize_rpath="$finalize_rpath $libdir" ;; esac done fi # Now hardcode the library paths rpath= hardcode_libdirs= for libdir in $compile_rpath $finalize_rpath; do if test -n "$hardcode_libdir_flag_spec"; then if test -n "$hardcode_libdir_separator"; then if test -z "$hardcode_libdirs"; then hardcode_libdirs="$libdir" else # Just accumulate the unique libdirs. case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*) ;; *) hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir" ;; esac fi else eval flag=\"$hardcode_libdir_flag_spec\" rpath="$rpath $flag" fi elif test -n "$runpath_var"; then case "$perm_rpath " in *" $libdir "*) ;; *) perm_rpath="$perm_rpath $libdir" ;; esac fi case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*) testbindir=`${ECHO} "$libdir" | ${SED} -e 's*/lib$*/bin*'` case :$dllsearchpath: in *":$libdir:"*) ;; ::) dllsearchpath=$libdir;; *) dllsearchpath="$dllsearchpath:$libdir";; esac case :$dllsearchpath: in *":$testbindir:"*) ;; ::) dllsearchpath=$testbindir;; *) dllsearchpath="$dllsearchpath:$testbindir";; esac ;; esac done # Substitute the hardcoded libdirs into the rpath. if test -n "$hardcode_libdir_separator" && test -n "$hardcode_libdirs"; then libdir="$hardcode_libdirs" eval rpath=\" $hardcode_libdir_flag_spec\" fi compile_rpath="$rpath" rpath= hardcode_libdirs= for libdir in $finalize_rpath; do if test -n "$hardcode_libdir_flag_spec"; then if test -n "$hardcode_libdir_separator"; then if test -z "$hardcode_libdirs"; then hardcode_libdirs="$libdir" else # Just accumulate the unique libdirs. case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*) ;; *) hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir" ;; esac fi else eval flag=\"$hardcode_libdir_flag_spec\" rpath="$rpath $flag" fi elif test -n "$runpath_var"; then case "$finalize_perm_rpath " in *" $libdir "*) ;; *) finalize_perm_rpath="$finalize_perm_rpath $libdir" ;; esac fi done # Substitute the hardcoded libdirs into the rpath. if test -n "$hardcode_libdir_separator" && test -n "$hardcode_libdirs"; then libdir="$hardcode_libdirs" eval rpath=\" $hardcode_libdir_flag_spec\" fi finalize_rpath="$rpath" if test -n "$libobjs" && test "$build_old_libs" = yes; then # Transform all the library objects into standard objects. compile_command=`$ECHO "X$compile_command" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP` finalize_command=`$ECHO "X$finalize_command" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP` fi func_generate_dlsyms "$outputname" "@PROGRAM@" "no" # template prelinking step if test -n "$prelink_cmds"; then func_execute_cmds "$prelink_cmds" 'exit $?' fi wrappers_required=yes case $host in *cygwin* | *mingw* ) if test "$build_libtool_libs" != yes; then wrappers_required=no fi ;; *cegcc) # Disable wrappers for cegcc, we are cross compiling anyway. wrappers_required=no ;; *) if test "$need_relink" = no || test "$build_libtool_libs" != yes; then wrappers_required=no fi ;; esac if test "$wrappers_required" = no; then # Replace the output file specification. compile_command=`$ECHO "X$compile_command" | $Xsed -e 's%@OUTPUT@%'"$output"'%g'` link_command="$compile_command$compile_rpath" # We have no uninstalled library dependencies, so finalize right now. exit_status=0 func_show_eval "$link_command" 'exit_status=$?' # Delete the generated files. if test -f "$output_objdir/${outputname}S.${objext}"; then func_show_eval '$RM "$output_objdir/${outputname}S.${objext}"' fi exit $exit_status fi if test -n "$compile_shlibpath$finalize_shlibpath"; then compile_command="$shlibpath_var=\"$compile_shlibpath$finalize_shlibpath\$$shlibpath_var\" $compile_command" fi if test -n "$finalize_shlibpath"; then finalize_command="$shlibpath_var=\"$finalize_shlibpath\$$shlibpath_var\" $finalize_command" fi compile_var= finalize_var= if test -n "$runpath_var"; then if test -n "$perm_rpath"; then # We should set the runpath_var. rpath= for dir in $perm_rpath; do rpath="$rpath$dir:" done compile_var="$runpath_var=\"$rpath\$$runpath_var\" " fi if test -n "$finalize_perm_rpath"; then # We should set the runpath_var. rpath= for dir in $finalize_perm_rpath; do rpath="$rpath$dir:" done finalize_var="$runpath_var=\"$rpath\$$runpath_var\" " fi fi if test "$no_install" = yes; then # We don't need to create a wrapper script. link_command="$compile_var$compile_command$compile_rpath" # Replace the output file specification. link_command=`$ECHO "X$link_command" | $Xsed -e 's%@OUTPUT@%'"$output"'%g'` # Delete the old output file. $opt_dry_run || $RM $output # Link the executable and exit func_show_eval "$link_command" 'exit $?' exit $EXIT_SUCCESS fi if test "$hardcode_action" = relink; then # Fast installation is not supported link_command="$compile_var$compile_command$compile_rpath" relink_command="$finalize_var$finalize_command$finalize_rpath" func_warning "this platform does not like uninstalled shared libraries" func_warning "\`$output' will be relinked during installation" else if test "$fast_install" != no; then link_command="$finalize_var$compile_command$finalize_rpath" if test "$fast_install" = yes; then relink_command=`$ECHO "X$compile_var$compile_command$compile_rpath" | $Xsed -e 's%@OUTPUT@%\$progdir/\$file%g'` else # fast_install is set to needless relink_command= fi else link_command="$compile_var$compile_command$compile_rpath" relink_command="$finalize_var$finalize_command$finalize_rpath" fi fi # Replace the output file specification. link_command=`$ECHO "X$link_command" | $Xsed -e 's%@OUTPUT@%'"$output_objdir/$outputname"'%g'` # Delete the old output files. $opt_dry_run || $RM $output $output_objdir/$outputname $output_objdir/lt-$outputname func_show_eval "$link_command" 'exit $?' # Now create the wrapper script. func_verbose "creating $output" # Quote the relink command for shipping. if test -n "$relink_command"; then # Preserve any variables that may affect compiler behavior for var in $variables_saved_for_relink; do if eval test -z \"\${$var+set}\"; then relink_command="{ test -z \"\${$var+set}\" || $lt_unset $var || { $var=; export $var; }; }; $relink_command" elif eval var_value=\$$var; test -z "$var_value"; then relink_command="$var=; export $var; $relink_command" else func_quote_for_eval "$var_value" relink_command="$var=$func_quote_for_eval_result; export $var; $relink_command" fi done relink_command="(cd `pwd`; $relink_command)" relink_command=`$ECHO "X$relink_command" | $Xsed -e "$sed_quote_subst"` fi # Quote $ECHO for shipping. if test "X$ECHO" = "X$SHELL $progpath --fallback-echo"; then case $progpath in [\\/]* | [A-Za-z]:[\\/]*) qecho="$SHELL $progpath --fallback-echo";; *) qecho="$SHELL `pwd`/$progpath --fallback-echo";; esac qecho=`$ECHO "X$qecho" | $Xsed -e "$sed_quote_subst"` else qecho=`$ECHO "X$ECHO" | $Xsed -e "$sed_quote_subst"` fi # Only actually do things if not in dry run mode. $opt_dry_run || { # win32 will think the script is a binary if it has # a .exe suffix, so we strip it off here. case $output in *.exe) func_stripname '' '.exe' "$output" output=$func_stripname_result ;; esac # test for cygwin because mv fails w/o .exe extensions case $host in *cygwin*) exeext=.exe func_stripname '' '.exe' "$outputname" outputname=$func_stripname_result ;; 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fi ;; esac done func_show_eval "ln $obj $gentop/$newobj || cp $obj $gentop/$newobj" oldobjs="$oldobjs $gentop/$newobj" ;; *) oldobjs="$oldobjs $obj" ;; esac done fi eval cmds=\"$old_archive_cmds\" func_len " $cmds" len=$func_len_result if test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then cmds=$old_archive_cmds else # the command line is too long to link in one step, link in parts func_verbose "using piecewise archive linking..." save_RANLIB=$RANLIB RANLIB=: objlist= concat_cmds= save_oldobjs=$oldobjs oldobjs= # Is there a better way of finding the last object in the list? for obj in $save_oldobjs do last_oldobj=$obj done eval test_cmds=\"$old_archive_cmds\" func_len " $test_cmds" len0=$func_len_result len=$len0 for obj in $save_oldobjs do func_len " $obj" func_arith $len + $func_len_result len=$func_arith_result func_append objlist " $obj" if test "$len" -lt "$max_cmd_len"; then : else # the above command should be used before it gets too long oldobjs=$objlist if test "$obj" = "$last_oldobj" ; then RANLIB=$save_RANLIB fi test -z "$concat_cmds" || concat_cmds=$concat_cmds~ eval concat_cmds=\"\${concat_cmds}$old_archive_cmds\" objlist= len=$len0 fi done RANLIB=$save_RANLIB oldobjs=$objlist if test "X$oldobjs" = "X" ; then eval cmds=\"\$concat_cmds\" else eval cmds=\"\$concat_cmds~\$old_archive_cmds\" fi fi fi func_execute_cmds "$cmds" 'exit $?' done test -n "$generated" && \ func_show_eval "${RM}r$generated" # Now create the libtool archive. case $output in *.la) old_library= test "$build_old_libs" = yes && old_library="$libname.$libext" func_verbose "creating $output" # Preserve any variables that may affect compiler behavior for var in $variables_saved_for_relink; do if eval test -z \"\${$var+set}\"; then relink_command="{ test -z \"\${$var+set}\" || $lt_unset $var || { $var=; export $var; }; }; $relink_command" elif eval var_value=\$$var; test -z "$var_value"; then relink_command="$var=; export $var; $relink_command" else func_quote_for_eval "$var_value" relink_command="$var=$func_quote_for_eval_result; 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do case $lib in *.la) func_basename "$lib" name="$func_basename_result" eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $lib` test -z "$libdir" && \ func_fatal_error "\`$lib' is not a valid libtool archive" newdlfiles="$newdlfiles $libdir/$name" ;; *) newdlfiles="$newdlfiles $lib" ;; esac done dlfiles="$newdlfiles" newdlprefiles= for lib in $dlprefiles; do case $lib in *.la) # Only pass preopened files to the pseudo-archive (for # eventual linking with the app. that links it) if we # didn't already link the preopened objects directly into # the library: func_basename "$lib" name="$func_basename_result" eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $lib` test -z "$libdir" && \ func_fatal_error "\`$lib' is not a valid libtool archive" newdlprefiles="$newdlprefiles $libdir/$name" ;; esac done dlprefiles="$newdlprefiles" else newdlfiles= for lib in $dlfiles; do case $lib in [\\/]* | [A-Za-z]:[\\/]*) abs="$lib" ;; *) abs=`pwd`"/$lib" ;; esac newdlfiles="$newdlfiles $abs" done dlfiles="$newdlfiles" newdlprefiles= for lib in $dlprefiles; do case $lib in [\\/]* | [A-Za-z]:[\\/]*) abs="$lib" ;; *) abs=`pwd`"/$lib" ;; esac newdlprefiles="$newdlprefiles $abs" done dlprefiles="$newdlprefiles" fi $RM $output # place dlname in correct position for cygwin tdlname=$dlname case $host,$output,$installed,$module,$dlname in *cygwin*,*lai,yes,no,*.dll | *mingw*,*lai,yes,no,*.dll | *cegcc*,*lai,yes,no,*.dll) tdlname=../bin/$dlname ;; esac $ECHO > $output "\ # $outputname - a libtool library file # Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION # # Please DO NOT delete this file! # It is necessary for linking the library. # The name that we can dlopen(3). dlname='$tdlname' # Names of this library. library_names='$library_names' # The name of the static archive. old_library='$old_library' # Linker flags that can not go in dependency_libs. inherited_linker_flags='$new_inherited_linker_flags' # Libraries that this one depends upon. dependency_libs='$dependency_libs' # Names of additional weak libraries provided by this library weak_library_names='$weak_libs' # Version information for $libname. current=$current age=$age revision=$revision # Is this an already installed library? installed=$installed # Should we warn about portability when linking against -modules? shouldnotlink=$module # Files to dlopen/dlpreopen dlopen='$dlfiles' dlpreopen='$dlprefiles' # Directory that this library needs to be installed in: libdir='$install_libdir'" if test "$installed" = no && test "$need_relink" = yes; then $ECHO >> $output "\ relink_command=\"$relink_command\"" fi done } # Do a symbolic link so that the libtool archive can be found in # LD_LIBRARY_PATH before the program is installed. func_show_eval '( cd "$output_objdir" && $RM "$outputname" && $LN_S "../$outputname" "$outputname" )' 'exit $?' ;; esac exit $EXIT_SUCCESS } { test "$mode" = link || test "$mode" = relink; } && func_mode_link ${1+"$@"} # func_mode_uninstall arg... func_mode_uninstall () { $opt_debug RM="$nonopt" files= rmforce= exit_status=0 # This variable tells wrapper scripts just to set variables rather # than running their programs. libtool_install_magic="$magic" for arg do case $arg in -f) RM="$RM $arg"; rmforce=yes ;; -*) RM="$RM $arg" ;; *) files="$files $arg" ;; esac done test -z "$RM" && \ func_fatal_help "you must specify an RM program" rmdirs= origobjdir="$objdir" for file in $files; do func_dirname "$file" "" "." dir="$func_dirname_result" if test "X$dir" = X.; then objdir="$origobjdir" else objdir="$dir/$origobjdir" fi func_basename "$file" name="$func_basename_result" test "$mode" = uninstall && objdir="$dir" # Remember objdir for removal later, being careful to avoid duplicates if test "$mode" = clean; then case " $rmdirs " in *" $objdir "*) ;; *) rmdirs="$rmdirs $objdir" ;; esac fi # Don't error if the file doesn't exist and rm -f was used. if { test -L "$file"; } >/dev/null 2>&1 || { test -h "$file"; } >/dev/null 2>&1 || test -f "$file"; then : elif test -d "$file"; then exit_status=1 continue elif test "$rmforce" = yes; then continue fi rmfiles="$file" case $name in *.la) # Possibly a libtool archive, so verify it. if func_lalib_p "$file"; then func_source $dir/$name # Delete the libtool libraries and symlinks. for n in $library_names; do rmfiles="$rmfiles $objdir/$n" done test -n "$old_library" && rmfiles="$rmfiles $objdir/$old_library" case "$mode" in clean) case " $library_names " in # " " in the beginning catches empty $dlname *" $dlname "*) ;; *) rmfiles="$rmfiles $objdir/$dlname" ;; esac test -n "$libdir" && rmfiles="$rmfiles $objdir/$name $objdir/${name}i" ;; uninstall) if test -n "$library_names"; then # Do each command in the postuninstall commands. func_execute_cmds "$postuninstall_cmds" 'test "$rmforce" = yes || exit_status=1' fi if test -n "$old_library"; then # Do each command in the old_postuninstall commands. func_execute_cmds "$old_postuninstall_cmds" 'test "$rmforce" = yes || exit_status=1' fi # FIXME: should reinstall the best remaining shared library. ;; esac fi ;; *.lo) # Possibly a libtool object, so verify it. if func_lalib_p "$file"; then # Read the .lo file func_source $dir/$name # Add PIC object to the list of files to remove. if test -n "$pic_object" && test "$pic_object" != none; then rmfiles="$rmfiles $dir/$pic_object" fi # Add non-PIC object to the list of files to remove. if test -n "$non_pic_object" && test "$non_pic_object" != none; then rmfiles="$rmfiles $dir/$non_pic_object" fi fi ;; *) if test "$mode" = clean ; then noexename=$name case $file in *.exe) func_stripname '' '.exe' "$file" file=$func_stripname_result func_stripname '' '.exe' "$name" noexename=$func_stripname_result # $file with .exe has already been added to rmfiles, # add $file without .exe rmfiles="$rmfiles $file" ;; esac # Do a test to see if this is a libtool program. if func_ltwrapper_p "$file"; then if func_ltwrapper_executable_p "$file"; then func_ltwrapper_scriptname "$file" relink_command= func_source $func_ltwrapper_scriptname_result rmfiles="$rmfiles $func_ltwrapper_scriptname_result" else relink_command= func_source $dir/$noexename fi # note $name still contains .exe if it was in $file originally # as does the version of $file that was added into $rmfiles rmfiles="$rmfiles $objdir/$name $objdir/${name}S.${objext}" if test "$fast_install" = yes && test -n "$relink_command"; then rmfiles="$rmfiles $objdir/lt-$name" fi if test "X$noexename" != "X$name" ; then rmfiles="$rmfiles $objdir/lt-${noexename}.c" fi fi fi ;; esac func_show_eval "$RM $rmfiles" 'exit_status=1' done objdir="$origobjdir" # Try to remove the ${objdir}s in the directories where we deleted files for dir in $rmdirs; do if test -d "$dir"; then func_show_eval "rmdir $dir >/dev/null 2>&1" fi done exit $exit_status } { test "$mode" = uninstall || test "$mode" = clean; } && func_mode_uninstall ${1+"$@"} test -z "$mode" && { help="$generic_help" func_fatal_help "you must specify a MODE" } test -z "$exec_cmd" && \ func_fatal_help "invalid operation mode \`$mode'" if test -n "$exec_cmd"; then eval exec "$exec_cmd" exit $EXIT_FAILURE fi exit $exit_status # The TAGs below are defined such that we never get into a situation # in which we disable both kinds of libraries. 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You may also peek at any GNU archive site, in case some other package would contain this missing \`$1' program." exit 1 ;; esac exit 0 # Local variables: # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" # time-stamp-end: "$" # End: anfo-0.98/src/0000777000371600007640000000000011447127355010212 500000000000000anfo-0.98/src/config.proto0000644000371600007640000001520011447113464012452 00000000000000// Copyright 2009 Udo Stenzel // This file is part of ANFO // // ANFO is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // Anfo is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with Anfo. If not, see . package config ; message Homolog { optional string genome = 1 ; optional string sequence = 2 ; // start of alignment, negative if RC'd required int32 start = 3 ; // cigar codes to reproduce the alignment repeated uint32 cigar = 4 ; } message Contig { // number of half-bytes to seek into the genome file to get to the // start of the contig required uint32 offset = 1 ; // start of the contig in the original sequence, 0-based required uint32 range_start = 2 ; // one-past-the-end of the contig in original sequence, 0-based required uint32 range_end = 3 ; // aligned homologs, if available // (This is intended for artificial genomes that result from // alignments, here we store information to recreate those // alignments.) repeated Homolog homolog = 4 ; } message Sequence { // sequence name (first word of header in FASTA file) required string name = 1 ; // description of sequence (rest of header in FASTA file) optional string description = 2 ; // contigs (stretches without many Ns) repeated Contig contig = 3 ; // taxonomic id, if known and different from enclosing genome optional uint32 taxid = 6 ; } message Genome { // handle for the genome, used to report matches and to look up genome files optional string name = 1 ; // description of the genome (most likely from command line) optional string description = 3 ; // sequences (typically one per chromosome) repeated Sequence sequence = 4 ; // total length in nucleotides, essentially the file size required uint32 total_size = 5 ; // taxonomic id, if known and applies to whole genome optional uint32 taxid = 6 ; // maximum number of contiguous Ns; more constitute a gap optional uint32 maxn = 7 ; } message CompactIndex { // file name of the indexed genome required string genome_name = 2 ; // length of words (the k in k-mer) required uint32 wordsize = 3 ; // cutoff for overrepresented k-mers, if absent, all k-mers are // indexed optional uint32 cutoff = 4 ; // total number of indexed k-mers (nearly equal to genome size // in the absence of a cutoff) optional uint32 indexsize = 5 ; // stride if not every word is indexed optional uint32 stride = 6 [default=1] ; // list of gap positions in genome repeated uint32 gap = 7 [ packed=true ] ; } message CompactIndexSpec { required string name = 2 ; optional uint32 cutoff = 4 ; optional uint32 wordsize = 3 ; optional uint32 stride = 6 ; // number of mismatches to allow per seed // Only values of 0, 1 or 2 are currently supported, and more // probably doesn't make any sense anyway. optional uint32 allow_near_perfect = 5 [ default = 0 ] ; } // Configuration of mapper/aligner for a subset of sequences. The idea // is to use every policy that matches a given sequence, merging them in // the order they appear in the configuration(s) message Policy { // applies to sequences of this minimum length optional uint32 minlength = 1 ; // applies to sequences of this maximum length optional uint32 maxlength = 2 ; // use these indexes repeated CompactIndexSpec use_compact_index = 3 ; // don't bother aligning if there are too many seeds optional uint32 repeat_threshold = 4 ; // minimum total length of combined seeds to make an alignment optional uint32 min_seed_len = 7 ; // pattern to match names against optional string name_pattern = 9 ; // maximum number of mismatches in a combined seed region optional uint32 max_mismatches_in_seed = 10 [ default = 0 ] ; } message Aligner { // rate of transversions, basically defines the mismatch penalty required float rate_of_transversions = 1 ; // rate of transitions, defaults to tranversion rate optional float rate_of_transitions = 2 ; // probability of a gap appearing, efectively defines the gap-open-penalty // defaults to gap-extension-penalty to yield linear gap costs optional float gap_open_rate = 3 ; // probability of a gap extension required float gap_extension_rate = 4 ; // deamination rate, double stranded optional float rate_of_ds_deamination = 5 [default = 0.0] ; // deamination rate, single stranded optional float rate_of_ss_deamination = 6 [default = 0.0] ; // mean overhang length // at each end of a read we say there's half a chance that it has an // overhang in the right (detectable) direction, and if so, the length is // geometrically distributed with a suitable parameter // if left out, no overhangs are produced optional float mean_overhang_length = 7 ; // distance cutoff scaled by 1000 // (need to add an E-Value cutoff at some point) optional uint32 max_penalty_per_nuc = 8 [ default = 15 ] ; optional uint32 max_mapq = 9 [ default = 254 ] ; } // Configuration messages are both read from a file to configure the program // and written as a kind of header to the output to leave an audit trail. message Config { // rules to select indices repeated Policy policy = 3 ; // aligner configuration // This is in fact required, because practically all tools rely on it // being present anyway. Configuration of different aligners is // currently not supported anyway. optional Aligner aligner = 4 ; // trimming configuration: sequences to look for and kill off // We look for the given sequence, which may overlap the read // sequence or be contained within it. If the overlap is good // enough, it is cut off. We can do this on the 3' end (adapters) // or the 5' end (strange artefacts). Trimming is done before // indexing. repeated string trim_right = 5 ; repeated string trim_left = 6 ; // minimum score needed for something to be trimmed. default should // be fine optional uint32 min_trim_score = 7 [ default = 4 ] ; } // :vim:expandtab:ts=4:sw=4:cindent: anfo-0.98/src/output.proto0000644000371600007640000003432211447113464012553 00000000000000// Copyright 2009 Udo Stenzel // This file is part of ANFO // // ANFO is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // Anfo is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with Anfo. If not, see . package output ; option optimize_for = SPEED ; import "config.proto" ; import "google/protobuf/descriptor.proto" ; extend google.protobuf.FieldOptions { // show method for pretty text output optional string show = 31775 ; } message Header { // program version string optional string version = 1 ; // file format version, in case incompatible changes are introduced optional uint32 file_version = 8 [ default = 1 ] ; // copy of the config block used in the run optional config.Config config = 2 ; // copy of command line repeated string command_line = 5 ; // to ease tracking of problems: grid engine job id and task id, if // available optional uint32 sge_job_id = 6 ; optional uint32 sge_task_id = 7 ; // indicates whether an output file is sorted by read name // (useful to merge files?) optional bool is_sorted_by_name = 15 [default=false] ; // indicates whether an output file is sorted by genome coordinate, // and if so, which genomes were used in what order (that is target // sequence name, then earliest matching position, then alignment // length; needed for consensus calling and merging) repeated string is_sorted_by_coordinate = 13 ; // old way to encode sorting, don't use optional bool was_sorted_by_coordinate = 14 [default=false] ; optional bool is_sorted_by_all_genomes = 12 [default=false] ; } // XXX: a few easily accessible statistics should be included here, // assuming the footer is somehow easily found. Requires a bit more // infrastructure, though. While we're at it, an index would be well // placed here, too. message Footer { optional uint32 exit_code = 1 [default=0] ; } // Result hits... all very ad-hoc and ugly. We need: // - best hit globally // - score of best hit globally with different species // - score of best hit globally with different order // - best hit to some genome (usually, but not always human or // human/chimp hybrid) // - score of second best hit to said genome // - score of best hit to said genome, but different chromosome // - if best is on sex chromosomes, score of best hit on same genome // outside sex chromosomes enum Reason { // ordinary alignment aligned = 0 ; // couldn't align because there was no seed at all no_seeds = 1 ; // decided not to align because there were too many seeds too_many_seeds = 2 ; // all alignments exceeded the e-value or score cutoff bad_alignment = 3 ; // no policy how to align, therefore no alignment no_policy = 4 ; // only repetitive seeds repeats_only = 5 ; } // deprecated, don't use if possible message OldResult { // sequence identifier, can be left out iff it is implicit, e.g. // from being contained in a database where the id is the key optional string seqid = 1 ; // optional description (taken e.g. from FASTA file) optional string description = 13 ; // quality scores (Phred scale, raw, without silly offsets) optional bytes quality = 14 ; // the sequence itself, if so desired (ASCII encoding---do we want // something more compact?) required string sequence = 2 ; // index of first base that's not trimmed from 5' end optional uint32 trim_left = 11 [ default = 0 ] ; // index of first base that is trimmed from 3' end // Note that the part trimmed from the 5' end still counts for this // index. If absent, nothing was trimmed from the 3' end. optional uint32 trim_right = 12 ; // Reason we arrived at this result optional Reason reason = 10 [ default = aligned ] ; // Some statistics about the seeding process optional uint32 num_raw_seeds = 16 ; optional uint32 num_grown_seeds = 17 ; optional uint32 num_clumps = 18 ; optional uint32 num_useless = 22 ; // Some statistics about the alignment process optional uint32 open_nodes_after_alignment = 19 ; optional uint32 closed_nodes_after_alignment = 20 ; optional uint32 tracked_closed_nodes_after_alignment = 21 ; // Best hit globally, if any. Difference in bit score to the next // best one with different species, with different order, iff such // hits exist. optional OldHit best_hit = 3 ; optional sint32 diff_to_next_species = 4 ; optional sint32 diff_to_next_order = 5 ; // Best hit to some selected genome (probably human), if any. // Difference in bit score to next best hit, to next best on // different chromosome, to next on different class of chromosomes, // if they exist. Classes for this purpose are sex chromosomes, // autosomes and organelles. optional OldHit best_to_genome = 6 ; optional sint32 diff_to_next = 7 ; optional sint32 diff_to_next_chromosome = 8 ; optional sint32 diff_to_next_chromosome_class = 9 ; // if this result is the consensus of multiple reads, those reads // can go here repeated Read member = 23 ; } message Read { // sequence identifier required string seqid = 1 ; // optional description (taken e.g. from FASTA/FASTQ file) optional string description = 13 ; // the sequence itself, if so desired (ASCII encoding---do we want // something more compact?) required string sequence = 2 ; // quality scores (Phred scale, raw, without silly offsets) // also: min_lk in the sense of GLF when applicable optional bytes quality = 14 [ (show) = "show_quality" ] ; // likelihoods of consensus sequence // This is intended to resemble the GL format or at least allow // generation of GLF. For each position in the sequence, we store // either 0, 4 or 10 likelihood ratios (for haploid/diploid genomes) // as specified for GLF. Each entry is as long as the sequence, the // order of the entries is [AA,CC,GG,TT,AC,AG,AT,CG,CT,GT]. // Bytes should be sufficient for storage, since we clamp almost // everything at 254 anyway. repeated bytes likelihoods = 15 ; // raw counts of what base was seen in a position // Not needed or useful for GLF, but useful to retain 'just in // case'. Length must equal 4*(length sequence), treated as 2D // array, inner index is [A,C,G,T]. repeated uint32 seen_bases = 16 [ packed=true, (show) = "show_seen_bases" ] ; // total depth at each position // Coverage at each position is the sum of bases A,C,G,T and gaps. // Length is supposed to equal (length sequence). repeated uint32 depth = 17 [ packed=true, (show) = "show_uint32_array" ] ; // number of bases trimmed at 5' (at 3') end if trimming was done optional uint32 trim_left = 11 ; optional uint32 trim_right = 12 ; } // A set of starting points. The understanding is that each one of them // is already long enough, but may still contain too many mismatches tio // be any good. // Invariant: ref_positions, query_positions and seed_sizes have the // same length. message Seeds { // genome we seeded on (typ. hg18, pt2, etc.) required string genome_name = 1 ; // Positions of seed regions on the reference. We always store the // smallest coordinate of the seed region. repeated uint32 ref_positions = 2 [ packed=true, (show) = "show_uint32_array" ] ; // Positions of starting points on the query. We use negative // numbers to indicate seeds on the reverse complemented strand in // the following way: a virtual sequence is constructed from the // reverse-complemented query, a gap and the query. The central gap // has position 0. We always store the smallest // coordinate of the seed region. (The central gap ensures that we // never combine seeds on different strands by mistake.) repeated int32 query_positions = 3 [ packed=true, (show) = "show_int32_array" ] ; // Sizes of seed regions. repeated uint32 seed_sizes = 4 [ packed=true, (show) = "show_uint32_array" ] ; // Maximum number of mismatches in seed region. Passed on from // indexing stage so the aligner doesn't need to parse the // configuration again. required uint32 max_mismatches = 5 ; // Minimum seed length. Passed on from indexing stage so the // aligner doesn't need to parse the configuration again. required uint32 min_seed_length = 6 ; } message Result { // raw sequence or consensus required Read read = 1 ; // if this result is the consensus of multiple reads, those reads // can go here. if there are too many, just their number can be // stored instead. repeated Read members = 2 ; optional uint32 nmembers = 9 [ default = 0 ] ; // alignments, if any repeated Hit hit = 3 [ (show) = "show_hit" ] ; // statistics/debug info, if any repeated AlnStats aln_stats = 4 ; // difference to subsequent hits, if that ever comes to pass... // This is again Phred-scaled, so could be interpreted as some sort // of mapping quality. optional sint32 diff_to_next_species = 5 ; optional sint32 diff_to_next_order = 6 ; // if reads were joined into contigs, their number optional int32 num_reads = 7 ; // seeds to be communicated between indexer and aligner // for internal use only repeated Seeds seeds = 8 ; } // We store multiple best hits, one per genome (where something like the // nr database can also count as a 'genome'). Occasionally, we operate // on the globally 'best' hit, which is simply the best one of the // available ones. message Hit { // globally unique name of the genome (used when sorting hits by // coordinate, can be used to locate the reference sequence if // present; if empty, the sequence name should be globally unique) required string genome_name = 1 ; // name of the subject sequence (== chromosome or similar) required string sequence = 2 ; // minimum position where any nucleotide aligns, zero-based // This is the position of the 5'-most base if on the forward // strand, the position of the 3'-most based if on the reverse strand required uint32 start_pos = 3 ; // length of alignment on reference sequence, negative if on the // reverse strand required sint32 aln_length = 4 ; // Score // This is actually a penalty, and it represents the Phred-scaled // probability of this alignment being right. Signed because we may // want to allow negative scores, too (though only if the scale ever // changes). Optional, because majority sequences won't have a // sensible score. optional sint32 score = 5 ; // E-value (because it's customary to have one) optional float evalue = 6 ; // Alignment as (binary near-equivalent of) a CIGAR line // The low four bits encode the operation as an enum, the rest // encodes the length. This way, no real length restriction exists. // This encoding happens to be the same as that used by BAM, with // two extensions: A match of length 0 encodes for the seed center // and the Mismatch operation is equivalent to the Match operation, // but signifies that the sequences actually differ. enum Operation { Match = 0 ; Insert = 1 ; Delete = 2 ; Skip = 3 ; // unused SoftClip = 4 ; // unused HardClip = 5 ; // unused Pad = 6 ; // unused Mismatch = 15 ; // not yet used } ; repeated uint32 cigar = 7 [ packed = true, (show) = "show_cigar" ] ; // Difference in bit score to next best hit, to next best on // different chromosome, to next on different class of chromosomes, // if they exist. Classes for this purpose are sex chromosomes, // autosomes and organelles. // This is the same as MAPQ in sam/bam, and it is calculated from // all hits that were found besides the best one. The calculation // is more accurate than what maq and bwa do, but still a (pretty // good) approximation. If we're looking at a pseudo-assembly, it // is actually the RMS of the MAPQs of the reads // that were included in it. optional sint32 map_quality = 8 ; // following two aren't actually used yet optional sint32 diff_to_next_chromosome = 9 ; optional sint32 diff_to_next_chromosome_class = 10 ; // Taxids if known: most specific, species and order // An absent taxid means it's not known. optional int32 taxid = 15 ; optional int32 taxid_species = 14 ; optional int32 taxid_order = 13 ; // used only internally when producing textual output optional string aln_ref = 101 [ (show) = "show_noop" ] ; optional string aln_qry = 102 [ (show) = "show_noop" ] ; } // statistics about alignment, collected for debugging purposes message AlnStats { // Reason we arrived at this result optional Reason reason = 1 [ default = aligned ] ; // Some statistics about the seeding process optional uint32 num_raw_seeds = 2 ; optional uint32 num_grown_seeds = 3 ; optional uint32 num_clumps = 4 ; optional uint32 num_useless = 5 ; // Some statistics about the alignment process optional uint32 open_nodes_after_alignment = 6 ; optional uint32 closed_nodes_after_alignment = 7 ; optional uint32 tracked_closed_nodes_after_alignment = 8 ; // some tag to identify this record if there are many optional string tag = 15 ; } // Deprecated, don't touch. message OldHit { required string sequence = 2 ; required uint32 start_pos = 3 ; required sint32 aln_length = 4 ; optional sint32 score = 5 [ default = 0 ] ; optional float evalue = 6 ; required bytes cigar = 7 ; optional string genome_name = 8 ; optional int32 taxid = 16 ; optional int32 taxid_species = 17 ; optional int32 taxid_order = 18 ; optional string ref = 32 ; optional string qry = 33 ; optional string con = 34 ; } // vim:expandtab anfo-0.98/src/srfi-88.scm0000644000371600007640000000504111447112753012026 00000000000000; Everything in here was copied nearly verbatim from ; http://srfi.schemers.org/srfi-88/srfi-88.html, therefore: ; ; Copyright (C) Marc Feeley (2006). All Rights Reserved. ; Permission is hereby granted, free of charge, to any person obtaining ; a copy of this software and associated documentation files (the ; "Software"), to deal in the Software without restriction, including ; without limitation the rights to use, copy, modify, merge, publish, ; distribute, sublicense, and/or sell copies of the Software, and to ; permit persons to whom the Software is furnished to do so, subject to ; the following conditions: ; ; The above copyright notice and this permission notice shall be ; included in all copies or substantial portions of the Software. ; ; THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, ; EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF ; MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. ; IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY ; CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, ; TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE ; SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. (define real-symbol? symbol?) (define real-symbol->string symbol->string) (define real-string->symbol string->symbol) (define looks-like-an-unquoted-keyword? (lambda (s) (let ((n (string-length s))) (and (> n 1) (char=? (string-ref s (- n 1)) #\:))))) (set! symbol? (lambda (obj) (and (real-symbol? obj) (not (looks-like-an-unquoted-keyword? (real-symbol->string obj)))))) (define keyword? (lambda (obj) (and (real-symbol? obj) (looks-like-an-unquoted-keyword? (real-symbol->string obj))))) (set! symbol->string real-symbol->string) (define keyword->string (lambda (k) (let* ((s (real-symbol->string k)) (n (string-length s))) (substring s 0 (- n 1))))) ; remove the colon (set! string->symbol (lambda (s) (if (looks-like-an-unquoted-keyword? s) (error "sorry... the symbol would look like a keyword!") (real-string->symbol s)))) (define string->keyword (lambda (s) (let ((s-colon (string-append s ":"))) (if (looks-like-an-unquoted-keyword? s-colon) (real-string->symbol s-colon) (error "sorry... the keyword would look like a symbol!"))))) (provide 'srfi-88) anfo-0.98/src/srfi-89.scm0000644000371600007640000002755211447112753012042 00000000000000; Everything in here was copied nearly verbatim from ; http://srfi.schemers.org/srfi-89/srfi-89.html, therefore: ; ; Copyright (C) Marc Feeley (2006). All Rights Reserved. ; Permission is hereby granted, free of charge, to any person obtaining ; a copy of this software and associated documentation files (the ; "Software"), to deal in the Software without restriction, including ; without limitation the rights to use, copy, modify, merge, publish, ; distribute, sublicense, and/or sell copies of the Software, and to ; permit persons to whom the Software is furnished to do so, subject to ; the following conditions: ; ; The above copyright notice and this permission notice shall be ; included in all copies or substantial portions of the Software. ; ; THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, ; EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF ; MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. ; IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY ; CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, ; TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE ; SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. (require 'srfi-88) ;------------------------------------------------------------------------------ ; Macro expander for define*. (define-macro (define* pattern . body) (if (pair? pattern) `(define ,(car pattern) (lambda* ,(cdr pattern) ,@body)) `(define ,pattern ,@body))) ; Macro expander for lambda*. (define-macro (lambda* formals . body) ;------------------------------------------------------------------------------ ; Procedures needed at expansion time. (define (parse-formals formals) (define (variable? x) (symbol? x)) (define (required-positional? x) (variable? x)) (define (optional-positional? x) (and (pair? x) (pair? (cdr x)) (null? (cddr x)) (variable? (car x)))) (define (required-named? x) (and (pair? x) (pair? (cdr x)) (null? (cddr x)) (keyword? (car x)) (variable? (cadr x)))) (define (optional-named? x) (and (pair? x) (pair? (cdr x)) (pair? (cddr x)) (null? (cdddr x)) (keyword? (car x)) (variable? (cadr x)))) (define (named? x) (or (required-named? x) (optional-named? x))) (define (duplicates? lst) (cond ((null? lst) #f) ((memq (car lst) (cdr lst)) #t) (else (duplicates? (cdr lst))))) (define (parse-positional-section lst cont) (let loop1 ((lst lst) (rev-reqs '())) (if (and (pair? lst) (required-positional? (car lst))) (loop1 (cdr lst) (cons (car lst) rev-reqs)) (let loop2 ((lst lst) (rev-opts '())) (if (and (pair? lst) (optional-positional? (car lst))) (loop2 (cdr lst) (cons (car lst) rev-opts)) (cont lst (cons (reverse rev-reqs) (reverse rev-opts)))))))) (define (parse-named-section lst cont) (let loop ((lst lst) (rev-named '())) (if (and (pair? lst) (named? (car lst))) (loop (cdr lst) (cons (car lst) rev-named)) (cont lst (reverse rev-named))))) (define (parse-rest lst positional-before-named? positional-reqs/opts named) (if (null? lst) (parse-end positional-before-named? positional-reqs/opts named #f) (if (variable? lst) (parse-end positional-before-named? positional-reqs/opts named lst) (error "syntax error in formal parameter list")))) (define (parse-end positional-before-named? positional-reqs/opts named rest) (let ((positional-reqs (car positional-reqs/opts)) (positional-opts (cdr positional-reqs/opts))) (let ((vars (append positional-reqs (map car positional-opts) (map cadr named) (if rest (list rest) '()))) (keys (map car named))) (cond ((duplicates? vars) (error "duplicate variable in formal parameter list")) ((duplicates? keys) (error "duplicate keyword in formal parameter list")) (else (list positional-before-named? positional-reqs positional-opts named rest)))))) (define (parse lst) (if (and (pair? lst) (named? (car lst))) (parse-named-section lst (lambda (lst named) (parse-positional-section lst (lambda (lst positional-reqs/opts) (parse-rest lst #f positional-reqs/opts named))))) (parse-positional-section lst (lambda (lst positional-reqs/opts) (parse-named-section lst (lambda (lst named) (parse-rest lst #t positional-reqs/opts named))))))) (parse formals)) (define (expand-lambda* formals body) (define (range lo hi) (if (< lo hi) (cons lo (range (+ lo 1) hi)) '())) (define (expand positional-before-named? positional-reqs positional-opts named rest) (if (and (null? positional-opts) (null? named)) ; direct R5RS equivalent `(lambda ,(append positional-reqs (or rest '())) ,@body) (let () (define utility-fns `(,@(if (or positional-before-named? (null? positional-reqs)) `() `(($req (lambda () (if (pair? $args) (let ((arg (car $args))) (set! $args (cdr $args)) arg) (error "too few actual parameters")))))) ,@(if (null? positional-opts) `() `(($opt (lambda (default) (if (pair? $args) (let ((arg (car $args))) (set! $args (cdr $args)) arg) (default)))))))) (define positional-bindings `(,@(if positional-before-named? `() (map (lambda (x) `(,x ($req))) positional-reqs)) ,@(map (lambda (x) `(,(car x) ($opt (lambda () ,(cadr x))))) positional-opts))) (define named-bindings (if (null? named) `() `(($key-values (vector ,@(map (lambda (x) `$undefined) named))) ($args ($process-keys $args ',(make-perfect-hash-table (map (lambda (x i) (cons (car x) i)) named (range 0 (length named)))) $key-values)) ,@(map (lambda (x i) `(,(cadr x) ,(if (null? (cddr x)) `($req-key $key-values ,i) `($opt-key $key-values ,i (lambda () ,(caddr x)))))) named (range 0 (length named)))))) (define rest-binding (if (not rest) `(($args (or (null? $args) (error "too many actual parameters")))) `((,rest $args)))) (let ((bindings (append (if positional-before-named? (append utility-fns positional-bindings named-bindings) (append named-bindings utility-fns positional-bindings)) rest-binding))) `(lambda ,(append (if positional-before-named? positional-reqs '()) '$args) (let* ,bindings ,@body)))))) (apply expand (parse-formals formals))) (define (make-perfect-hash-table alist) ; "alist" is a list of pairs of the form "(keyword . value)" ; The result is a perfect hash-table represented as a vector of ; length 2*N, where N is the hash modulus. If the keyword K is in ; the hash-table it is at index ; ; X = (* 2 ($hash-keyword K N)) ; ; and the associated value is at index X+1. (let loop1 ((n (length alist))) (let ((v (make-vector (* 2 n) #f))) (let loop2 ((lst alist)) (if (pair? lst) (let* ((key-val (car lst)) (key (car key-val))) (let ((x (* 2 ($hash-keyword key n)))) (if (vector-ref v x) (loop1 (+ n 1)) (begin (vector-set! v x key) (vector-set! v (+ x 1) (cdr key-val)) (loop2 (cdr lst)))))) v))))) (define ($hash-keyword key n) (let ((str (keyword->string key))) (let loop ((h 0) (i 0)) (if (< i (string-length str)) (loop (modulo (+ (* h 65536) (char->integer (string-ref str i))) n) (+ i 1)) h)))) (expand-lambda* formals body)) ;------------------------------------------------------------------------------ ; Procedures needed at run time (called by the expanded code): ; Perfect hash-tables with keyword keys. (define ($hash-keyword key n) (let ((str (keyword->string key))) (let loop ((h 0) (i 0)) (if (< i (string-length str)) (loop (modulo (+ (* h 65536) (char->integer (string-ref str i))) n) (+ i 1)) h)))) (define ($perfect-hash-table-lookup table key) (let* ((n (quotient (vector-length table) 2)) (x (* 2 ($hash-keyword key n)))) (and (eq? (vector-ref table x) key) (vector-ref table (+ x 1))))) ; Handling of named parameters. (define $undefined (list 'undefined)) (define ($req-key key-values i) (let ((val (vector-ref key-values i))) (if (eq? val $undefined) (error "a required named parameter was not provided") val))) (define ($opt-key key-values i default) (let ((val (vector-ref key-values i))) (if (eq? val $undefined) (default) val))) (define ($process-keys args key-hash-table key-values) (let loop ((args args)) (if (null? args) args (let ((k (car args))) (if (not (keyword? k)) args (let ((i ($perfect-hash-table-lookup key-hash-table k))) (if (not i) (error "unknown parameter keyword" k) (if (null? (cdr args)) (error "a value was expected after keyword" k) (begin (if (eq? (vector-ref key-values i) $undefined) (vector-set! key-values i (cadr args)) (error "duplicate parameter" k)) (loop (cddr args))))))))))) (provide 'srfi-89) anfo-0.98/src/align.h0000644000371600007640000003403111447113463011365 00000000000000// Copyright 2009 Udo Stenzel // This file is part of ANFO // // ANFO is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // Anfo is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with Anfo. If not, see . #ifndef INCLUDED_ALIGN_H #define INCLUDED_ALIGN_H #include "align_fwd.h" #include "index.h" #include "stream.h" #include #include #include #include template< int N, typename T > class Array { private: T arr_[N] ; public: Array() {} Array( T t ) { for( int i = 0 ; i != N ; ++i ) arr_[i] = t ; } T& operator[] ( int i ) { return arr_[i] ; } const T& operator[] ( int i ) const { return arr_[i] ; } } ; //! \brief an alignment that has been seeded //! When initializing an alignment, the seed region is traversed and //! then extended greedily. We store the final seed region (a pointer //! into the reference, an offset into the query, the seeded length) and //! the score over the seed region. struct SeededAlignment { DnaP reference_ ; Logdom score_ ; int qoffs_ ; int size_ ; SeededAlignment() : qoffs_(0), size_(0) {} SeededAlignment( const adna_parblock& pb, DnaP reference, const QSequence& query, int qoffs, int size ) : reference_( reference ), score_( Logdom::one() ), qoffs_( qoffs ), size_( size ) { // greedy initialization: run over the seed, accumulating a // score. then extend greedily as long as there are // matches, store the resulting score. for( int i = 0 ; i <= size_ ; ++i ) score_ *= pb.subst_penalty( 0, reference_[i], query[qoffs_+i] ) ; for( ; reference_[size_] && query[qoffs_+size_].ambicode && reference_[size_] == query[qoffs_+size_].ambicode ; ++size_ ) score_ *= pb.subst_penalty( 0, reference_[size_], query[qoffs_+size_] ) ; for( ; reference_[-1] && query[qoffs_-1].ambicode && reference_[-1] == query[qoffs_-1].ambicode ; ++size_, --reference_, --qoffs_ ) score_ *= pb.subst_penalty( 0, reference_[-1], query[qoffs_-1] ) ; } } ; struct FullCell { Logdom score ; uint8_t from_state ; uint8_t from_x_offset ; uint8_t from_y_offset ; void clear() { score = Logdom::null() ; } void assign( Logdom z, int os, int xo, int yo ) { if( score < z ) { score = z ; from_state = os ; from_x_offset = xo ; from_y_offset = yo ; } } } ; struct SimpleCell { Logdom score ; void clear() { score = Logdom::null() ; } void assign( Logdom z, int, int, int ) { if( score < z ) score = z ; } } ; //! \brief extension of an alignment through DP //! This starts with two pointers and a cost limit, and it returns the //! penalty that was incurred. The limit can be exceeded while //! producing an alignment (it would be foolish to throw it away), if //! nothing is found, std::numeric_limits::max() is returned. //! //! We align until we hit a zero in either query or reference. Starting //! state is 0, late the state is inly held implicitly. //! //! If only there were real lexical closures... *sigh* template< typename Cell > class ExtendAlignment { private: int width_ ; std::vector< Array< adna_parblock::num_states, Cell > > cells_ ; std::vector< int > mins_, maxs_ ; Logdom limit_, result_ ; int max_s_, max_x_, max_y_, max_tail_ ; void extend(const adna_parblock &pb_,Logdom score,int s,int x,int y,DnaP ref,const QSequence::Base *qry ); public: ExtendAlignment() {} ExtendAlignment( const adna_parblock& pb, DnaP reference, const QSequence::Base *query, Logdom limit ) ; Logdom get_result() const { return result_ ; } int max_x() const { return max_x_ ; } void backtrace( std::vector& ) const ; void swap( ExtendAlignment& rhs ) throw() { std::swap( width_, rhs.width_ ) ; std::swap( cells_, rhs.cells_ ) ; std::swap( mins_, rhs.mins_ ) ; std::swap( maxs_, rhs.maxs_ ) ; std::swap( limit_, rhs.limit_ ) ; std::swap( result_, rhs.result_ ) ; std::swap( max_s_, rhs.max_s_ ) ; std::swap( max_x_, rhs.max_x_ ) ; std::swap( max_y_, rhs.max_y_ ) ; std::swap( max_tail_, rhs.max_tail_ ) ; } } ; template< typename Cell > struct ExtendBothEnds { ExtendAlignment forwards_, backwards_ ; Logdom score_ ; ExtendBothEnds() {} ExtendBothEnds( const adna_parblock& pb, const QSequence& query, const SeededAlignment& seed, Logdom limit ) ; //! \brief backtraces an alignment and return a CIGAR line //! //! Backtracing works by simply walking the chain of ols states and //! x/y offsets stored in the DP matrix. See output.proto for the //! encoding of the produced CIGAR lines. //! //! \param minpos will be filled by position of first aligned //! reference base //! \param maxpos will be filled by position of first non-aligned //! reference base, so that maxpos-minpos gives the //! aligned length //! \return binary CIGAR string //! \internal //! \todo Write mismatches with different code (to allow various //! calculations without the genome being available). std::vector backtrace( const SeededAlignment& seed, DnaP &minpos, DnaP &maxpos ) const ; void swap( ExtendBothEnds& rhs ) throw() { forwards_.swap( rhs.forwards_ ) ; backwards_.swap( rhs.backwards_ ) ; score_.swap( rhs.score_ ) ; } } ; namespace { inline int query_length( const QSequence::Base *query ) { int r = 0 ; while( query->ambicode ) ++query, ++r ; return r ; } } ; // Alignment proper: the intial greedy matching must have been done, // here we extend one side of this into a full alignment, as long as it // doesn't score more than a prescribed limit. template< typename Cell > ExtendAlignment::ExtendAlignment( const adna_parblock& pb, DnaP reference, const QSequence::Base *query, Logdom limit ) : width_( 2*query_length( query )+2 ), cells_( width_*width_ ), mins_( width_ ), maxs_( width_ ), limit_( limit ), result_( Logdom::null() ) { if( limit > Logdom::one() ) return ; mins_[0] = 0 ; maxs_[0] = 1 ; cells_[0][0].assign( Logdom::one(), 0, 0, 0 ) ; for( int s = 1 ; s != adna_parblock::num_states ; ++s ) cells_[ 0 ][ s ].clear() ; for( int y = 0 ; y != width_-1 && mins_[y] != maxs_[y] ; ++y ) { assert( y <= width_ ) ; assert( mins_[y] >= 0 ) ; assert( maxs_[y] <= width_ ) ; assert( mins_[y] <= maxs_[y] ) ; mins_[y+1] = maxs_[y+1] = 0 ; // expand the current row for each state in turn... of course, // each state is a special case. for( int x = mins_[y] ; x != width_-1 && x != maxs_[y] ; ++x ) { for( int s = 0 ; s != adna_parblock::num_states ; ++s ) { assert( width_*y + x < width_ * width_ ) ; assert( width_*y + x < (int)cells_.size() ) ; Logdom score = cells_[ width_*y + x ][ s ].score ; if( score > limit_ ) extend( pb, score, s, x, y, reference+x, query+y ) ; } } } } #define PUT(ns,xo,yo,z) \ if( (z) >= limit_ ) { \ if( mins_[ y+(yo) ] == maxs_[ y+(yo) ] ) \ mins_[ y+(yo) ] = maxs_[ y+(yo) ] = x+(xo) ; \ \ for( ; maxs_[ y+(yo) ] <= x+(xo) ; ++maxs_[ y+(yo) ] ) \ for( int ss = 0 ; ss != adna_parblock::num_states ; ++ss ) \ cells_[ width_*(y+(yo)) + maxs_[ y+(yo) ] ][ ss ].clear() ; \ \ assert( y+(yo) < width_ ) ; \ assert( x+(xo) < width_ ) ; \ assert( width_*(y+(yo)) + x+(xo) < width_ * width_ ) ; \ \ cells_[ width_*(y+(yo)) + x+(xo) ][ ns ].assign( z, s, xo, yo ) ; \ } else {} // what to do? // If in matching state, we know there's no immediate match, so we can... // - mismatch // - detect deamination and change to SS state (while matching) // - open ref gap // - open query gap // // If a gap is open, we can... // - extend it // - close it // // If we hit a gap symbol, we must... // - start over at second half in initial state template< typename Cell > void ExtendAlignment::extend( const adna_parblock &pb_, Logdom score, int s, int x, int y, DnaP ref, const QSequence::Base *qry ) { // Note the penalties: The appropriate substitution penalty is // applied whenever we (mis-)match two codes, the gap open penalties // are applied when opening/extending a gap, the // overhang_enter_penalty is applied when changing to SS mode and // the overhang_ext_penalty is applied whenever moving along the // query while single stranded, even when a gap is open! This gives // correct scores for a geometric distribution of overhang lengths. if( !*ref || !qry->ambicode ) { // We hit a gap in either the reference or the query. Whatever // is left of the query (if any) must be penalized. To do this, // we virtually extend the reference with Ns and align to those. // This is a white lie in that it will overestimate the real // penalty, but that's okay, because such an alignment isn't all // that interesting in reality anyway. Afterwards we're // finished and adjust result and limit accordingly. int yy = 0 ; for( ; qry[ yy ].ambicode ; ++yy ) { score *= pb_.subst_penalty( s, 15, qry[ yy ] ) ; if( s & adna_parblock::mask_ss ) score *= pb_.overhang_ext_penalty ; } if( score > result_ ) { result_ = limit_ = score ; max_s_ = s ; max_x_ = x ; max_y_ = y ; max_tail_ = yy ; } } else if( (s & adna_parblock::mask_gaps) == 0 ) { // no gaps open --> mismatch, open either gap, enter SS PUT( s, 1, 1, score * pb_.subst_penalty( s, *ref, *qry ) * ( s & adna_parblock::mask_ss ? pb_.overhang_ext_penalty : Logdom::one() ) ) ; if( *ref != qry->ambicode ) { // only on a mismatch try anything fancy PUT( s | adna_parblock::mask_gap_qry, 1, 0, score * pb_.gap_open_penalty ) ; PUT( s | adna_parblock::mask_gap_ref, 0, 1, score * pb_.gap_open_penalty ) ; if( pb_.overhang_enter_penalty.is_finite() && (s & adna_parblock::mask_ss) == 0 ) { // To enter single stranded we require that the penalty for // doing so is immediately recovered by the better match. // This is easily the case for the observed deamination // rates in aDNA. Logdom p0 = pb_.subst_penalty( s, *ref, *qry ) ; Logdom p4 = pb_.subst_penalty( s | adna_parblock::mask_ss, *ref, *qry ) * pb_.overhang_enter_penalty * pb_.overhang_ext_penalty ; if( p4 > p0 ) { PUT( s | adna_parblock::mask_ss, 1, 1, score * p4 ) ; } } } } else if( (s & adna_parblock::mask_gaps) == adna_parblock::mask_gap_ref ) { PUT( s, 0, 1, score * pb_.gap_ext_penalty * ( s & adna_parblock::mask_ss ? pb_.overhang_ext_penalty : Logdom::one() ) ) ; PUT( s & ~adna_parblock::mask_gap_ref, 1, 1, score * pb_.subst_penalty( s, *ref, *qry ) * ( s & adna_parblock::mask_ss ? pb_.overhang_ext_penalty : Logdom::one() ) ) ; } else { PUT( s, 1, 0, score * pb_.gap_ext_penalty ) ; PUT( s & ~adna_parblock::mask_gap_qry, 1, 1, score * pb_.subst_penalty( s, *ref, *qry ) * ( s & adna_parblock::mask_ss ? pb_.overhang_ext_penalty : Logdom::one() ) ) ; } } #undef PUT // Extension of both sides. We first run a forward extension at half // the limit. If this succeeds, we do the backwards extension limited // to whatever is left. If forward extension fails, we do backwards // extension to half the limit, then add forward using up what's left. // // Only one alignment is produced, but we make sure it is the cheapest // one. The score may exceed the limit, if we happen to finish right // when stepping over the limit. If really nothing is found, we return // Logdom::null(). template< typename Cell> ExtendBothEnds::ExtendBothEnds( const adna_parblock& pb, const QSequence& query, const SeededAlignment& seed, Logdom limit ) : forwards_( pb, seed.reference_ + seed.size_, query.start() + seed.qoffs_ + seed.size_, ( limit / seed.score_ ).sqrt() ), backwards_( pb, seed.reference_.reverse() + 1, query.start() - seed.qoffs_ + 1, limit / seed.score_ / forwards_.get_result() ), score_( seed.score_ * forwards_.get_result() * backwards_.get_result() ) { if( score_.is_finite() ) return ; ExtendAlignment backwards2( pb, seed.reference_.reverse() + 1, query.start() - seed.qoffs_ + 1, (limit / seed.score_).sqrt() ) ; ExtendAlignment forwards2( pb, seed.reference_ + seed.size_, query.start() + seed.qoffs_ + seed.size_, limit / backwards2.get_result() / seed.score_ ) ; Logdom score2 = forwards2.get_result() * backwards2.get_result() * seed.score_ ; if( score2.is_finite() ) { score_ = score2 ; forwards_.swap( forwards2 ) ; backwards_.swap( backwards2 ) ; } } template<> inline void ExtendAlignment::backtrace( std::vector& out ) const { if( max_tail_ ) streams::push_i( out, max_tail_ ) ; for( size_t x = max_x_, y = max_y_, s = max_s_ ; x || y ; ) { const FullCell& c = cells_[ width_*y + x ][ s ] ; if( !c.from_x_offset && !c.from_y_offset ) throw "stuck in backtracing" ; else if( !c.from_x_offset ) streams::push_i( out, c.from_y_offset ) ; else if( !c.from_y_offset ) streams::push_d( out, c.from_x_offset ) ; else if( c.from_y_offset == c.from_x_offset ) streams::push_m( out, c.from_x_offset ) ; else throw "inconsistency in backtracing" ; x -= c.from_x_offset ; y -= c.from_y_offset ; s = c.from_state ; } } template<> inline std::vector ExtendBothEnds::backtrace( const SeededAlignment& seed, DnaP &minpos, DnaP &maxpos ) const { minpos = seed.reference_ - backwards_.max_x() ; maxpos = seed.reference_ + seed.size_ + forwards_.max_x() ; std::vector trace ; backwards_.backtrace( trace ) ; trace.push_back( 0 ) ; streams::push_m( trace, seed.size_ ) ; trace.push_back( 0 ) ; std::vector rtrace ; forwards_.backtrace( rtrace ) ; std::copy( rtrace.rbegin(), rtrace.rend(), back_inserter( trace ) ) ; return trace ; } #endif anfo-0.98/src/align_fwd.h0000644000371600007640000000504311447113464012227 00000000000000#ifndef INCLUDED_ALIGN_FWD_H #define INCLUDED_ALIGN_FWD_H #include "logdom.h" #include "sequence.h" //! \page adna_alignment Operations on Ancient DNA Alignments //! This type of alignment models aDNA as two additional states, one //! with higher deamination rate, with an asymmetric substitution //! matrix, and with affine gap costs. Additional parameters are all //! static. //! //! \todo We actually don't need the parameter set to be static, and it //! may even pay to have it configurable so differently //! parameterized alignments an be mixed in a single run. //! //! @{ //! \brief substitution matrix //! We prepare a full matrix of 16 ambiguity codes vs. 16 ambiguity //! codes, this avoid the need for expensive additions in the log-domain //! should the need to align ambiguity codes arise. First index is //! "from" (reference code), second index is "to" (query code). typedef Logdom subst_mat[16][16] ; namespace config { class Aligner ; } ; //! \brief parameters for simple_adna //! One such parblock is a static variable for the aligner proper, //! various support tools shunt additional structures around. struct adna_parblock { enum { mask_ss = 1, mask_gap_ref = 2, mask_gap_qry = 4, mask_gaps = mask_gap_ref | mask_gap_ref, num_states = 6 } ; adna_parblock() {} adna_parblock( const config::Aligner& conf ) ; //! \brief DS substitution matrix, forward direction subst_mat ds_mat ; //! \brief SS substitution matrix, forward direction //! Deamination shows up as C->T as it is best understood this way. //! To process reverse-complemented deamination, we have to do //! rev-complemented lookups while actually moving in the forward //! (5'->3') direction. \see simple_adna::subst_penalty() subst_mat ss_mat ; //! \brief Penalty for extending an overhang. //! Having a constant penalty for the overhang length models its //! length distribution as geometric. Logdom overhang_ext_penalty ; //! \brief penalty for entering SS state //! This is essentially the probability of having an overhang at //! all. Logdom overhang_enter_penalty ; //! \brief gap open penalty Logdom gap_open_penalty ; //! \brief gap extension penalty Logdom gap_ext_penalty ; Logdom subst_penalty( int s, Ambicode r, const QSequence::Base &qry ) const { Logdom prob = Logdom::null() ; for( uint8_t p = 0 ; p != 4 ; ++p ) prob += ( s & mask_ss ? ss_mat[r][1<. #ifndef INCLUDED_ANFO_COMMON_H #define INCLUDED_ANFO_COMMON_H // Commonalities between different command line utilities, factored out. #include "align.h" #include "index.h" #include "stream.h" #include "config.pb.h" #include "output.pb.h" #include #include #include //! \brief Configures type of alignment to be done. //! This is a hack and only intended as a stopgap. // typedef flat_alignment alignment_type ; // typedef simple_adna alignment_type ; /* struct reference_overlaps { DnaP x, y ; reference_overlaps( DnaP u, DnaP v ) : x(u), y(v) {} bool operator()( const alignment_type& a ) { return a.reference >= x && a.reference <= y ; } } ; */ namespace streams { //! \brief takes care of stuff needed before aligning //! This is for "housekeeping" that needs to be done before indexing //! and alignment, most notably adapter/artefact trimming. class Housekeeper : public Stream { private: const int minscore_ ; vector< string > trim_left_ ; vector< string > trim_right_ ; public: Housekeeper( const config::Config &config ) : minscore_( config.min_trim_score() ), trim_left_( config.trim_left().begin(), config.trim_left().end() ), trim_right_( config.trim_right().begin(), config.trim_right().end() ) {} Housekeeper( vector left, vector right, int minscore ) : minscore_( minscore_ ), trim_left_( left ), trim_right_( right ) {} virtual void put_result( const Result& ) ; } ; //! \brief configured Indexer //! Knows about one index, will look at each record, check the policy //! and if appropriate, will do an index lookup. Constructed seeds are //! stored and passed on. The policy is taken from a config file and //! stored in the header. class Indexer : public Stream { private: config::Config conf_ ; std::string index_name_ ; const FixedIndex& index_ ; public: Indexer( const config::Config &config, const std::string& index_name ) ; virtual ~Indexer() ; virtual void put_header( const Header& ) ; virtual void put_result( const Result& ) ; } ; //! \brief configured mapper //! Knows about one genome and an aligner configuration. Looks at each //! record, takes the seed collection for its genome and aligns. Seeds //! are removed, the result is added and passed on. class Mapper : public Stream { private: config::Aligner conf_ ; GenomeHolder genome_ ; adna_parblock parblock_ ; public: Mapper( const config::Aligner &config, const std::string& genome_name ) ; virtual void put_header( const Header& ) ; virtual void put_result( const Result& ) ; } ; } ; // namespace streams std::string expand( const std::string&, int ) ; #endif anfo-0.98/src/compress_stream.h0000644000371600007640000002730511447113072013503 00000000000000// Copyright 2009 Udo Stenzel // This file is part of ANFO // // ANFO is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // Anfo is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with Anfo. If not, see . #ifndef INCLUDED_COMPRESS_STREAM_H #define INCLUDED_COMPRESS_STREAM_H #include "util.h" #include #include #include #include #if HAVE_LIBZ && HAVE_ZLIB_H #include //! \brief decompression filter that uses the zlib class InflateStream : public google::protobuf::io::ZeroCopyInputStream { private: std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; z_stream zs_ ; const Bytef *next_undelivered_ ; int64_t total_ ; Bytef obuf_[15500] ; bool next( const void **data, int *size ) { // nothing in output buffer? inflate more while( zs_.next_out == next_undelivered_ ) { zs_.avail_out = sizeof( obuf_ ) ; zs_.next_out = obuf_ ; next_undelivered_ = obuf_ ; // input buffer empty? try and get more if( !zs_.avail_in ) { const void *nin ; int avin ; if( !is_->Next( &nin, &avin ) ) return false ; zs_.next_in = (Bytef*)nin ; zs_.avail_in = avin ; } // inflate some; after that we either have output or // need to get more input (or have an error) int r = inflate( &zs_, Z_NO_FLUSH ) ; // when are we finished? when the input is fully // consumed. In case the gzip stream ends with input // left, we simply re-initialize. // we may still have a block to hand out if( r == Z_STREAM_END ) { r = inflateEnd( &zs_ ) ; if( r == Z_OK ) r = inflateInit2( &zs_, 15+16 ) ; } else if( r != Z_OK ) throw zs_.msg ; } *data = (const void*)next_undelivered_ ; *size = zs_.next_out - next_undelivered_ ; next_undelivered_ = zs_.next_out ; total_ += *size ; return *size ; } void back_up( int count ) { next_undelivered_ -= count ; total_ -= count ; } bool skip( int count ) { while( count ) { const void *p ; int l ; if( !next( &p, &l ) ) return false ; count -= l ; } if( count < 0 ) back_up( -count ) ; return true ; } public: InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) { zs_.avail_in = 0 ; const void* p ; int l ; if( !is_->Next( &p, &l ) ) throw "no data" ; try { if( l < 2 || ((const uint8_t*)p)[0] != 31 || ((const uint8_t*)p)[1] != 139 ) throw "not a gzip file" ; zs_.zalloc = 0 ; zs_.zfree = 0 ; zs_.opaque = 0 ; zs_.next_in = (Bytef*)p ; zs_.avail_in = l ; if( inflateInit2( &zs_, 15+16 ) != Z_OK ) throw zs_.msg ; zs_.next_out = obuf_ ; zs_.avail_out = sizeof( obuf_ ) ; next_undelivered_ = obuf_ ; } catch( ... ) { is_->BackUp( l ) ; throw ; } } virtual ~InflateStream() { inflateEnd( &zs_ ) ; if( zs_.avail_in ) is_->BackUp( zs_.avail_in ) ; } virtual bool Next( const void **data, int *size ) { return next( data, size ) ; } virtual void BackUp( int count ) { back_up( count ) ; } virtual bool Skip( int count ) { return skip( count ) ; } virtual int64_t ByteCount() const { return total_ ; } } ; class DeflateStream : public google::protobuf::io::ZeroCopyOutputStream { private: google::protobuf::io::ZeroCopyOutputStream *os_ ; z_stream zs_ ; Bytef ibuf_[15500] ; int64_t total_ ; bool next( void **data, int *size ) { // anything in input buffer? deflate more while( zs_.avail_in ) { // output buffer full? try and flush it if( !zs_.avail_out ) { void *nout ; int avout ; if( !os_->Next( &nout, &avout ) ) return false ; zs_.next_out = (Bytef*)nout ; zs_.avail_out = avout ; } // deflate some; after that we either have room for input or // need to flush more output (or we have an error) int r = deflate( &zs_, Z_NO_FLUSH ) ; if( r != Z_OK ) throw zs_.msg ; } zs_.next_in = ibuf_ ; zs_.avail_in = sizeof( ibuf_ ) ; *data = (void*)ibuf_ ; *size = zs_.avail_in ; total_ += zs_.avail_in ; return true ; } void back_up( int count ) { zs_.avail_in -= count ; } public: DeflateStream( google::protobuf::io::ZeroCopyOutputStream *os, int lv=Z_DEFAULT_COMPRESSION ) : os_(os), total_(0) { zs_.zalloc = 0 ; zs_.zfree = 0 ; zs_.opaque = 0 ; if( deflateInit2( &zs_, lv, Z_DEFLATED, 15+16, 8, Z_DEFAULT_STRATEGY ) != Z_OK ) throw zs_.msg ; zs_.next_in = 0 ; zs_.avail_in = 0 ; zs_.avail_out = 0 ; } virtual ~DeflateStream() { // compress whatever is left in buffer or internal state for(;;) { if( !zs_.avail_out ) { void *nout ; int avout ; if( !os_->Next( &nout, &avout ) ) break ; zs_.next_out = (Bytef*)nout ; zs_.avail_out = avout ; } int r = deflate( &zs_, Z_FINISH ) ; if( r == Z_STREAM_END ) break ; else if( r != Z_OK ) throw zs_.msg ; } // give back leftover output buffer, free resources if( zs_.avail_out ) os_->BackUp( zs_.avail_out ) ; deflateEnd( &zs_ ) ; delete os_ ; } virtual bool Next( void **data, int *size ) { return next( data, size ) ; } virtual void BackUp( int count ) { back_up( count ) ; } virtual int64_t ByteCount() const { return total_ ; } } ; #endif struct BzipError : public Exception { int e_ ; BzipError( int e ) : e_(e) {} virtual void print_to( std::ostream& s ) const { s << "bzip error " << e_ ; } } ; #if HAVE_LIBBZ2 && HAVE_BZLIB_H #include //! \brief decompression filter that uses the libbz2 class BunzipStream : public google::protobuf::io::ZeroCopyInputStream { private: std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; bz_stream zs_ ; char *next_undelivered_ ; char obuf_[15500] ; bool next( const void **data, int *size ) { // nothing in output buffer? inflate more while( zs_.next_out == next_undelivered_ ) { zs_.avail_out = sizeof( obuf_ ) ; zs_.next_out = obuf_ ; next_undelivered_ = obuf_ ; // input buffer empty? try and get more if( !zs_.avail_in ) { const void *nin ; int avin ; if( !is_->Next( &nin, &avin ) ) return false ; zs_.next_in = (char*)nin ; zs_.avail_in = avin ; } // inflate some; after that we either have output or // need to get more input (or have an error) int r = BZ2_bzDecompress( &zs_ ) ; // when are we finished? when we get BZ_STREAM_END, but // we may still have a block to hand out if( r == BZ_STREAM_END ) break ; else if( r < BZ_OK ) throw BzipError( r ) ; } *data = (const void*)next_undelivered_ ; *size = zs_.next_out - next_undelivered_ ; next_undelivered_ = zs_.next_out ; return *size ; } void back_up( int count ) { next_undelivered_ -= count ; } bool skip( int count ) { while( count ) { const void *p ; int l ; if( !next( &p, &l ) ) return false ; count -= l ; } if( count < 0 ) back_up( -count ) ; return true ; } public: BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) { zs_.avail_in = 0 ; const void* p ; int l ; if( !is_->Next( &p, &l ) ) throw "no data" ; try { const char* q = (const char*)p ; if( l < 3 || q[0] != 'B' || q[1] != 'Z' || q[2] != 'h' ) throw "not a bzip2 file" ; zs_.bzalloc = 0 ; zs_.bzfree = 0 ; zs_.opaque = 0 ; int r = BZ2_bzDecompressInit( &zs_, 0, 0 ) ; if( r < BZ_OK ) throw BzipError( r ) ; zs_.next_in = (char*)p ; zs_.avail_in = l ; zs_.next_out = obuf_ ; zs_.avail_out = sizeof( obuf_ ) ; next_undelivered_ = obuf_ ; } catch( ... ) { is_->BackUp( l ) ; throw ; } } virtual ~BunzipStream() { BZ2_bzDecompressEnd( &zs_ ) ; if( zs_.avail_in ) is_->BackUp( zs_.avail_in ) ; } virtual bool Next( const void **data, int *size ) { return next( data, size ) ; } virtual void BackUp( int count ) { back_up( count ) ; } virtual bool Skip( int count ) { return skip( count ) ; } virtual int64_t ByteCount() const { return (int64_t)zs_.total_out_hi32 << 32 | zs_.total_out_lo32 ; } } ; class BzipStream : public google::protobuf::io::ZeroCopyOutputStream { private: google::protobuf::io::ZeroCopyOutputStream *os_ ; bz_stream zs_ ; char ibuf_[15500] ; bool next( void **data, int *size ) { // anything in input buffer? deflate more while( zs_.avail_in ) { // output buffer full? try and flush it if( !zs_.avail_out ) { void *nout ; int avout ; if( !os_->Next( &nout, &avout ) ) return false ; zs_.next_out = (char*)nout ; zs_.avail_out = avout ; } // deflate some; after that we either have room for input or // need to flush more output (or we have an error) int r = BZ2_bzCompress( &zs_, BZ_RUN ) ; if( r < BZ_OK ) throw BzipError( r ) ; } zs_.next_in = ibuf_ ; zs_.avail_in = sizeof( ibuf_ ) ; *data = (void*)ibuf_ ; *size = zs_.avail_in ; return true ; } void back_up( int count ) { zs_.avail_in -= count ; } public: BzipStream( google::protobuf::io::ZeroCopyOutputStream *os ) : os_(os) { zs_.bzalloc = 0 ; zs_.bzfree = 0 ; zs_.opaque = 0 ; int r = BZ2_bzCompressInit( &zs_, 9, 0, 0 ) ; if( r < BZ_OK ) throw BzipError( r ) ; zs_.next_in = 0 ; zs_.avail_in = 0 ; zs_.avail_out = 0 ; } virtual ~BzipStream() { // compress whatever is left in buffer or internal state for(;;) { if( !zs_.avail_out ) { void *nout ; int avout ; if( !os_->Next( &nout, &avout ) ) break ; zs_.next_out = (char*)nout ; zs_.avail_out = avout ; } int r = BZ2_bzCompress( &zs_, BZ_FINISH ) ; if( r == BZ_STREAM_END ) break ; else if( r < BZ_OK ) throw BzipError( r ) ; } // give back leftover output buffer, free resources if( zs_.avail_out ) os_->BackUp( zs_.avail_out ) ; BZ2_bzCompressEnd( &zs_ ) ; delete os_ ; } virtual bool Next( void **data, int *size ) { return next( data, size ) ; } virtual void BackUp( int count ) { back_up( count ) ; } virtual int64_t ByteCount() const { return ((int64_t)zs_.total_in_hi32 << 32) | zs_.total_in_lo32 ; } } ; #endif inline google::protobuf::io::FileOutputStream *make_output_stream( const char *name ) { std::auto_ptr< google::protobuf::io::FileOutputStream > fos( new google::protobuf::io::FileOutputStream( !name || 0 == strcmp( name, "-" ) ? dup( 1 ) : throw_errno_if_minus1( open( name, O_WRONLY | O_CREAT, 0666 ), "opening", name ) ) ) ; fos->SetCloseOnDelete( true ) ; return fos.release() ; } inline google::protobuf::io::ZeroCopyOutputStream *compress_small( google::protobuf::io::ZeroCopyOutputStream *s ) { #if HAVE_BZLIB_H && HAVE_LIBBZ2 try { return new BzipStream( s ) ; } catch( ... ) {} #endif #if HAVE_LIBZ && HAVE_ZLIB_H try { return new DeflateStream( s, Z_BEST_COMPRESSION ) ; } catch( ... ) {} #endif return s ; } inline google::protobuf::io::ZeroCopyOutputStream *compress_fast( google::protobuf::io::ZeroCopyOutputStream *s ) { #if HAVE_LIBZ && HAVE_ZLIB_H try { return new DeflateStream( s, Z_BEST_SPEED ) ; } catch( ... ) {} #endif return s ; } inline google::protobuf::io::ZeroCopyOutputStream *compress_any( bool expensive, google::protobuf::io::ZeroCopyOutputStream *s ) { return expensive ? compress_small( s ) : compress_fast( s ) ; } #endif anfo-0.98/src/concurrent_stream.h0000644000371600007640000001145211447113465014034 00000000000000/* inspired by c-pthread-queue - c implementation of a bounded buffer queue using posix threads Copyright (C) 2008 Matthew Dickinson This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . */ #ifndef INCLUDED_CONCURRENT_STREAM_H #define INCLUDED_CONCURRENT_STREAM_H #include "stream.h" #include #include #include namespace streams { //! \brief multithreaded adapter for streams //! This is our primitive for multithreading: something that looks like //! an ordinary stream, but in reality drives stream processors in //! separate threads. //! //! \todo we need to know if we need a header. It's awkward otherwise. //! //! Here's how it works: we initialize with a list of streams. They //! should probably all be clones of a single stream processor, //! otherwise weird stuff might happen, but we don't enforce that. //! //! We now check the state of every stream. If at least one needs a //! header, we don't do anything until we get a header. When we get the //! header, it is distributed to every stream, then each stream is //! started in its own thread. If no header is wanted, we start the //! threads immediately. //! //! We maintain two queues of 'Result' records, incoming and outgoing. //! Each thread checks the stream status: if output is available, it is //! put into outgoing, the thread sleeps if there's no room. If input is needed, //! it's taken from incoming, the thread sleeps if nothing's there. If the stream //! ends, a marker is put into outgoing and the thread is terminated. If //! the input ends, the end marker is put back(!), and the footer is //! processed (which means we must first put a footer in, then terminate //! the input queue). //! //! The main thread decides what to do depending on the queues. If //! there's room in incoming and we haven't received a footer, we ask for //! input. Else if output is available, we offer it. Else we wait (on //! the combined condition). If input ends, we store the footer and enter a zero into //! incoming. If output ends often enough (it does so once per thread), //! we wait on all threads, collect the footers, combine them with error //! codes and signal end of stream. // //! \todo We might need a state for "have output *and* need input". //! //! If a result is asked for (from ELK), we collect all of them into a //! list. No interlock is necessary, as long is the result is only //! demanded after processing finishes. class ConcurrentStream : public Stream { private: enum { size_ = 16 } ; vector< pair< StreamHolder, ConcurrentStream* > > streams_ ; Result *incoming_[ size_ ] ; Result *outgoing_[ size_ ] ; pthread_cond_t input_available_ ; pthread_cond_t room_for_output_ ; pthread_cond_t action_needed_ ; int next_in_, next_in_free_ ; // equal iff incoming is empty int next_out_, next_out_free_ ; // equal iff outgoing is empty pthread_mutex_t mutex_ ; unsigned eos_outstanding_ ; bool incoming_empty() const { return next_in_ == next_in_free_ ; } bool outgoing_empty() const { return next_out_ == next_out_free_ ; } bool incoming_full() const { return (next_in_+1) % size_ == next_in_free_ ; } bool outgoing_full() const { return (next_out_+1) % size_ == next_out_free_ ; } bool incoming_terminated() const { return !incoming_empty() && !incoming_[next_in_] ; } void init() ; void dequeue( Stream* ) ; void enqueue( Result* ) ; public: //! \brief starts streams in parallel in the background //! This takes a list of streams (need not be identical, but the //! results will be weird if they aren't) and wires them in //! parallel. Every stream gets its own thread. template< typename Iter > ConcurrentStream( Iter begin, Iter end ) : next_in_(0), next_in_free_(0), next_out_(0), next_out_free_(0), eos_outstanding_(0) { init() ; for( ; begin != end ; ++begin ) streams_.push_back( make_pair( *begin, this ) ) ; } ~ConcurrentStream() ; virtual state get_state() ; virtual void put_header( const Header& h ) ; virtual void put_result( const Result& r ) ; virtual void put_footer( const Footer& f ) ; virtual Header fetch_header() ; virtual Result fetch_result() ; virtual Footer fetch_footer() ; virtual Object get_summary() ; void* run_thread( Stream* ) ; } ; } ; // namespace streams #endif anfo-0.98/src/conffile.h0000644000371600007640000000561711447113104012060 00000000000000// Copyright 2009 Udo Stenzel // This file is part of ANFO // // ANFO is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // Anfo is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with Anfo. If not, see . #ifndef INCLUDED_CONFFILE_H #define INCLUDED_CONFFILE_H #include "config.pb.h" #include #include #include #include /*! \page configuration Configuration Files, Metadata, Output Format * * In order to keep configuration files and somewhat complicated, * persistent data structures in a sensible format and extensible, we * abuse Google's protocol buffers (http://code.google.com/p/protobuf/) * for this. Code to handle protocol buffers can be generated for C++, * Java and Pyhton by the Google toolchain, but also for Haskell * (http://hackage.haskell.org/cgi-bin/hackage-scripts/package/hprotoc) * and possibly for more languages. The definition of the possible * parts of the configuration resides in \c config.proto, we store the * configuration in a single file using the protobuf text format. * Metadata for genomes and indices is also defined there, those files * incorporate their metadata in binary form. If the need arises, we * can easily move to multiple files, binary files, or a combination of * both. Text and binary files are interconvertible using \c protoc. */ //! \brief reads the configuration from a text file. //! A text format configuration file is read and parsed into a config //! object. //! //! \param filename filename of configuration file //! \return parsed configuration inline config::Config parse_text_config( const std::string& filename ) { config::Config c ; std::ifstream config_in( filename.c_str() ) ; google::protobuf::io::IstreamInputStream fis( &config_in ) ; if( !google::protobuf::TextFormat::Parse( &fis, &c ) ) throw "parse error reading " + filename ; return c ; } inline config::Config get_default_config( const char* config_file = 0 ) { if( config_file ) return parse_text_config( config_file ) ; else if( !access( "anfo.cfg", F_OK ) ) return parse_text_config( "anfo.cfg" ) ; else if( !access( ".anfo.cfg", F_OK ) ) return parse_text_config( ".anfo.cfg" ) ; else { std::string f = getenv( "HOME" ) + std::string( "/.anfo.cfg" ) ; if( !access( f.c_str(), F_OK ) ) return parse_text_config( f.c_str() ) ; else throw "no config file found" ; } } #endif anfo-0.98/src/ducttape.h0000644000371600007640000001167311447113463012113 00000000000000// Copyright 2009 Udo Stenzel // This file is part of ANFO // // ANFO is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // Anfo is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with Anfo. If not, see . #ifndef INCLUDED_DUCTTAPE_H #define INCLUDED_DUCTTAPE_H #include "align_fwd.h" #include "stream.h" #include "util.h" #include #include namespace streams { //! \brief calls a genome wide consensus //! Duct-taping something is almost the same as assembling it, it's just //! not as durable, and that's what we do to a genome here. Input is a //! stream ordered by genome coordinate. For every position covered at //! least once, we calculate the likelihood for every possible //! combination of two alleles. In principle, those bases can be //! written out as soon as reads stop covering them, however, since we //! will write contigs, we can only write them when we no longer have //! coverage (or reach the end of a contig in the reference?), as the //! GLZ format wants to know the contig length in advance. //! //! \todo What to do at edges? Sometimes reads will overlap the ends of //! contigs, and in principle, we might want to call a consensus //! there, too. Probably nothing at all... //! \todo What about indels? How to deal with the shifting coordinates //! if our consensus actually contains indels? class DuctTaper : public Stream { private: string name_ ; Chan report_ ; Logdom het_prior_ ; bool have_foot_ ; // tracking of current reference sequence; we need to start a // new contig if one of these changes std::string cur_genome_ ; std::string cur_sequence_ ; // start of current contig on the reference; we're always on the // forward strand uint32_t contig_start_ ; uint32_t contig_end_ ; // Collects number of observed bases or gaps per position in // contig (to allow calling of indels, and because someone might // ask for it) and accumulated likelihoods for each base. // Accumulated quantity is \f$ P(\omega | x) * P(y->x) * P(y) // \f$, for we can easily calculate a probability from that. // Order is A,C,G,T,-. Also tracks whether a column is inserted // relative to the reference. struct Acc { int seen[4] ; // # of times A,C,G,T was seen int gapped ; // # of times a gap was seen int crossed ; // # of times a read overlapped the gap before this col. bool is_ins ; // was this iserted rel. to reference? Logdom lk[10] ; // likelihoods for allele pairs Acc( bool ins = false, int gap = 0 ) : gapped(gap), crossed(0), is_ins(ins) { seen[0] = seen[1] = seen[2] = seen[3] = 0 ; } bool pristine() const { for( int i = 0 ; i != 4 ; ++i ) if( seen[i] ) return false ; return gapped == 0 ; } } ; typedef std::vector< Acc > Accs ; Accs observed_ ; // for silly statistics size_t nreads_, num_ ; // for MAPQ -- GLF wants MAPQ to be the RMS of the MAPQs that // went into a contig. int mapq_accum_ ; // needed for probability calculations adna_parblock adna_ ; void flush_contig() ; public: DuctTaper( const string& name, double hp = 0 ) : name_(name), het_prior_( Logdom::from_float(hp) ) , have_foot_(false), contig_start_(0), contig_end_(0) , nreads_(0), num_(0), mapq_accum_(0), adna_() {} virtual void put_header( const Header& ) ; virtual void put_result( const Result& ) ; virtual void put_footer( const Footer& ) ; virtual Result fetch_result() ; private: void put_result_recent( const Result& ) ; void put_result_ancient( const Result& ) ; } ; class GlzWriter : public Stream { private: DeflateStream gos_ ; Chan chan_ ; public: GlzWriter( const pair< google::protobuf::io::ZeroCopyOutputStream*, string >& p ) : gos_( p.first ) {} virtual void put_result( const Result& ) ; } ; //! \brief writes consensuus in text format //! Format as agreed upon internally: //! > "hg18" chromosome ±start //! ; "pt2" chromosome ±start //! [repeat as necessary?] //! //! <#gaps> <#A> <#C> <#G> <#T> <4 likelihood-ratios> //! [repeat as necessary] //! //! \todo reconstruction of the involved whole genome alignments is not //! yet possible class ThreeAlnWriter : public Stream { private: std::auto_ptr< std::ostream > out_ ; std::string name_ ; Chan chan_ ; public: ThreeAlnWriter( const pair< ostream*, string > &p ) : out_( p.first ), name_( p.second ) {} virtual void put_result( const Result& ) ; } ; } // namespace #endif anfo-0.98/src/index.h0000644000371600007640000004233611447113463011411 00000000000000// Copyright 2009 Udo Stenzel // This file is part of ANFO // // ANFO is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // Anfo is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with Anfo. If not, see . #ifndef INCLUDED_INDEX_H #define INCLUDED_INDEX_H #include "config.pb.h" #include "sequence.h" #include "util.h" #include #include #include #include #include #include #include #include #include #include //! \brief a genome as stored in a DNA file //! This class mmaps a DNA file and wraps it with a sensible interface. class CompactGenome { public: // Why are we using indices here instead of pointers? Because // pointers would be internal and make copying of this object a // lot harder. // key is offset into genome, value is (index of sequence, index // of contig) typedef std::map< uint32_t, std::pair< int, int > > ContigMap ; // value is index of contig typedef std::map< uint32_t, int > PosnMap1 ; // first half of value is index of sequence typedef std::map< std::string, std::pair< int, PosnMap1 > > PosnMap ; static void cleanup( const CompactGenome* ) {} private: DnaP base_ ; size_t file_size_ ; uint32_t length_ ; int fd_ ; ContigMap contig_map_ ; PosnMap posn_map_ ; CompactGenome( const CompactGenome& ) ; // not implemented void operator = ( const CompactGenome& ) ; // not implemented ~CompactGenome() ; // must control life cycle friend class Metagenome ; public: config::Genome g_ ; mutable int refcount_ ; public: //! \brief makes accessible a genome file //! \param name file name of the genome //! \param c program configuration, needed for the search path CompactGenome( const std::string& name ) ; void add_ref() const { ++refcount_ ; } std::string name() const { return g_.name() ; } std::string describe() const { std::string d = g_.name() ; if( g_.has_description() ) d += " (" + g_.description() + ")" ; return d ; } uint32_t total_size() const { return g_.total_size() ; } uint32_t raw_size() const { return length_ ; } DnaP get_base() const { return base_ ; } //! \brief scan over finite words of the dna //! Fixed size words in the genome are iterated. The words may //! well contain ambiguity codes, but are guaranteed not to //! contain gaps. //! //! Words are encoded as four bits per nucleotide, first nucleotide in //! the MSB(!). See ::make_dense_word for why that makes sense. Unused //! MSBs in words passed to mk_word contain junk, do not rely on //! them. //! //! The functor objects in the following will be passed by //! value. Make sure they are tiny and that their function call //! operators can be inlined. //! //! \param w word size, 4*w must not be more than there are bits //! in an unsigned long long. //! \param mk_word functor object called to transform a //! sequence of ambiguity codes into words of //! nucleotides //! \param mk_gap functor that's called at every gap //! \param slice scan this slice of a big genome //! \param slices total number of slices //! \param msg if set, switches on progress reports and is //! included in them template< typename F, typename G > void scan_words( unsigned w, F mk_word, G mk_gap, int slice = 0, int slices = 1, const char* msg = 0 ) const ; const ContigMap &get_contig_map() const { return contig_map_ ; } //! \brief translates a DNA pointer back to sequence coordinates //! If the DNA pointer points into this genome, it is translated //! to the name of the sequence and the offset into it. The //! strand is disregarded, the result is the same regardless of //! the direction the pointer would be moving in. //! \param pos position to be translated //! \param offset is assigned the offset after translation //! \return pointer to sequence that includes the hit, else null const config::Sequence *translate_back( DnaP pos, uint32_t& offset ) const ; //! \brief translates "human" cooordinates into a pointer //! Return 0 if anything goes wrong. DnaP find_pos( const std::string& seq, uint32_t pos ) const ; enum { signature = 0x31414e44u } ; // DNA1 private: //! \brief reports a position while scanning //! \internal static void report( uint32_t, uint32_t, const char* ) ; } ; //! \brief Representation of a list of seeds. //! A seed is described by a size and two coordinates. One is the start //! on the query sequence, the other we choose to be the "diagonal" //! (difference between coordinates), since seeds on the same or close //! diagonal will usually be combined. Offset is negative for rc'ed //! matches, in this case its magnitude is the actual offset from the //! end of the sequence. //! //! Here we actually represent a list of seeds by two pointers into a //! list of reference coordinates. The first entry is chached in the //! data structure itself, so it selves to represent both lists and //! single seeds. //! //! The list of seeds in index files is sorted backwards (more or less //! an artefact of the way indexes are built), so we can merge these //! lists instead of copying and sorting them. struct Matches { const uint32_t *begin, *end ; int32_t offs ; uint16_t wordsize ; uint16_t stride ; int64_t diag ; } ; // Match lists are sorted backwards by reference coordinate (an artefact // of the index construction process) and therefore backwards by // diagonal (ref-coordinate minus offset, by definition); we also choose // to sort backwards on the offset. struct compare_match_lists { bool operator()( const Matches &a, const Matches &b ) { if( b.diag < a.diag ) return true ; if( a.diag < b.diag ) return false ; return b.offs < a.offs ; } } ; struct compare_matches_for_heap { // note the `wrong' order; this is intended for a heap! bool operator()( const Matches &a, const Matches &b ) { return compare_match_lists()( b, a ) ; } } ; //! \brief Collection of short matches. //! We actually collect the ranges of sorted(!) matches in the index //! data structure, then merge-sort them on demand. The calling //! sequence is to first post() ranges of index entries, then //! start_traversal(), then look at the first seed using get(), and //! remove them one by one using take() until the structure becomes //! empty(). class PreSeeds { private: struct equal_match_lists { bool operator()( const Matches &a, const Matches &b ) { return a.begin == b.begin && a.offs == b.offs ; } } ; std::vector< Matches > heap_ ; bool normalize() { while( heap_.back().begin != heap_.back().end && *heap_.back().begin % heap_.back().stride != 0 ) ++heap_.back().begin ; if( heap_.back().begin == heap_.back().end ) { heap_.pop_back() ; return false ; } else { heap_.back().diag = (int64_t)(*heap_.back().begin) - (int64_t)(heap_.back().offs) ; return true ; } } public: PreSeeds() {} void post( const uint32_t *begin, const uint32_t *end, int32_t offs, int wordsize, int stride ) { if( begin != end ) { heap_.push_back( Matches() ) ; heap_.back().begin = begin ; heap_.back().end = end ; heap_.back().offs = offs ; heap_.back().wordsize = wordsize ; heap_.back().stride = stride ; normalize() ; } } bool empty() const { return heap_.empty() ; } const Matches& get() const { return heap_.front() ; } void start_traversal() { std::sort( heap_.begin(), heap_.end(), compare_match_lists() ) ; heap_.erase( std::unique( heap_.begin(), heap_.end(), equal_match_lists() ), heap_.end() ) ; std::make_heap( heap_.begin(), heap_.end(), compare_matches_for_heap() ) ; } void take() { std::pop_heap( heap_.begin(), heap_.end(), compare_matches_for_heap() ) ; ++heap_.back().begin ; assert( heap_.back().begin == heap_.back().end || heap_.back().begin[-1] > heap_.back().begin[0] ) ; if( normalize() ) std::push_heap( heap_.begin(), heap_.end(), compare_matches_for_heap() ) ; } } ; inline std::ostream& operator << ( std::ostream& o, const Matches& s ) { return o << '@' << s.offs << '+' << s.diag << ':' << s.wordsize ; } class FixedIndex { public: struct LookupParams { uint32_t cutoff ; // more common seeds will be ignored uint32_t allow_mismatches ; // number of changed positions per seed word uint32_t wordsize ; // nucleotides per seed word uint32_t stride ; // tiling stepsize } ; enum { signature = 0x33584449u } ; // "IDX3" FixedIndex() : p_(0), base(0), secondary(0), first_level_len(0), length(0), fd_(0), refcount_(0) {} //! \brief loads an index from a file //! \param name filename FixedIndex( const std::string &name ) ; ~FixedIndex() { if( p_ ) munmap( (void*)p_, length ) ; if( fd_ != -1 ) close( fd_ ) ; } unsigned lookupS( const std::string& seq, PreSeeds&, const LookupParams &p, int *num_useless ) const ; unsigned lookup1( Oligo, PreSeeds&, const LookupParams &p, int32_t offs, int *num_useless ) const ; unsigned lookup1m( Oligo, PreSeeds&, const LookupParams &p, int32_t offs, int *num_useless ) const ; unsigned lookup2m( Oligo, PreSeeds&, const LookupParams &p, int32_t offs, int *num_useless ) const ; operator const void * () const { return base ; } const config::CompactIndex& metadata() const { return meta_ ; } void swap( FixedIndex& i ) { std::swap( p_, i.p_ ) ; std::swap( base, i.base ) ; std::swap( secondary, i.secondary ) ; std::swap( first_level_len, i.first_level_len ) ; std::swap( length, i.length ) ; std::swap( fd_, i.fd_ ) ; } private: const void* p_ ; const uint32_t *base, *secondary ; uint32_t first_level_len ; uint64_t length ; int fd_ ; config::CompactIndex meta_ ; unsigned lookup1m( Oligo, PreSeeds&, const LookupParams &p, int32_t offs, int *num_useless, size_t ) const ; public: int refcount_ ; } ; class MetaIndex { private: static std::map< std::string, FixedIndex* > map_ ; public: static const FixedIndex& add_ref( const std::string& name ) { FixedIndex*& ix = map_[ name ] ; if( !ix ) ix = new FixedIndex( name ) ; ++ix->refcount_ ; return *ix ; } static void free_ref( const FixedIndex& ix ) { for( std::map< std::string, FixedIndex* >::iterator i = map_.begin() ; i != map_.end() ; ++i ) if( i->second == &ix && !--i->second->refcount_ ) { delete i->second ; map_.erase( i ) ; return ; } } } ; template< typename F, typename G > void CompactGenome::scan_words( unsigned w, F mk_word, G mk_gap, int slice, int slices, const char* msg ) const { if( (unsigned)std::numeric_limits< Oligo >::digits < 4 * w ) throw "cannot build index: oligo doesn't fit" ; // start here, in case we want slices uint32_t offs = 2 * slice * (int64_t)length_ / slices ; uint32_t eoffs = 2 * (slice+1) * (int64_t)length_ / slices ; Oligo dna = 0 ; // do not start before first contig (that's the header region) assert( g_.sequence_size() && g_.sequence(0).contig_size() ) ; offs = std::max( offs, g_.sequence(0).contig(0).offset()-1 ) ; while( base_[ offs ] != 0 ) ++offs ; // find first gap for( unsigned i = 0 ; i != w ; ++i ) // fill first word { dna <<= 4 ; dna |= base_[ offs ] ; ++offs ; } report(offs,length_,msg) ; // run to end of slice, but stop at gaps only while( offs < eoffs || base_[ offs-1 ] ) { if( (offs & 0xffffff) == 0 ) report(offs,length_,msg) ; dna <<= 4 ; dna |= base_[ offs ] ; ++offs ; if( !base_[offs] ) mk_gap( offs ) ; // throw away words containing gap symbols // (This is necessary since we may want to construct // discontiguous words, but not if a "don't care" position is a // gap.) bool clean = true ; for( unsigned i = 0 ; i != w ; ++i ) clean &= ((dna >> (4*i)) & 0xf) != 0 ; if( clean ) mk_word( w, offs-w, dna ) ; } if( msg ) std::clog << "\r\e[K" << std::flush ; } inline int put_seed( output::Seeds *ss, const Matches& s, int out ) { int i = ss->ref_positions().size() - 1 ; uint32_t oldref = ss->ref_positions().Get( i ) ; int32_t oldqry = ss->query_positions().Get( i ) ; uint32_t oldsiz = ss->seed_sizes().Get( i ) ; // check for overlap (diag within 8, which is arbitrary...) if( (s.offs < 0) == (oldqry < 0) && abs( s.diag - (int64_t)oldref + (int64_t)oldqry ) <= 8 ) { if( s.wordsize > oldsiz ) // new one is bigger, overwrite { ss->mutable_ref_positions()->Set( i, s.diag + s.offs ) ; ss->mutable_query_positions()->Set( i, s.offs ) ; ss->mutable_seed_sizes()->Set( i, s.wordsize ) ; } return out ; } else { ss->mutable_ref_positions()->Add( s.diag + s.offs ) ; ss->mutable_query_positions()->Add( s.offs ) ; ss->mutable_seed_sizes()->Add( s.wordsize ) ; return out+1 ; } } //! \brief Combines short, adjacent seeds into longer ones. //! This is a cheap method to combine seeds: only overlapping and //! adjacent seeds are combined, neighboring diagonals are not //! considered. The code is short and direct, and works well even for //! imperfect seeds. //! //! How to do this? We get seeds ordered first by diagonal (backwards, //! actually), then backwards by offset. Seeds are adjacent iff they //! have the same diagonal index and their offsets differ by no more //! than the seed size. They can be combined on the fly easily. //! //! \note Formerly we tried to somehow deal with neighboring diagonals. //! This has been declared as not worth the hassle, so it was //! dropped. If we get seeds for the same region on neighboring //! diagonals, they are useless repeats anyway and probably //! excluded from the index to begin with. If gaps complicated //! everything, well, tough luck, this only an approximation //! anyway. //! //! \todo Seeds on neighboring diagonals can give rise to effectively //! the same alignment. If that happens, the map quality goes //! down the drain... Need a solution for that. //! //! \param v container of seeds, will be consumed //! \param m minimum length of a good seed //! \param ss output container for seed positions //! \return number of good seeds produced inline int combine_seeds( PreSeeds& v, uint32_t m, output::Seeds *ss ) { int out = 0 ; if( !v.empty() ) { v.start_traversal() ; // combine overlapping and adjacent seeds into larger ones // PreSeeds::const_iterator a = v.begin(), e = v.end() ; Matches s = v.get() ; v.take() ; for( ; !v.empty() ; v.take() ) { const Matches& a = v.get() ; assert( a.diag <= s.diag ) ; if( a.diag == s.diag ) assert( a.offs <= s.offs ) ; if( a.diag == s.diag && a.offs + (int32_t)a.wordsize >= s.offs ) { s.wordsize += s.offs - a.offs ; s.offs = a.offs ; } else { if( s.wordsize >= m ) out = put_seed( ss, s, out ) ; s = a ; } } if( s.wordsize >= m ) out = put_seed( ss, s, out ) ; } return out ; } typedef std::map< std::string, CompactGenome > Genomes ; typedef std::map< std::string, FixedIndex > Indices ; typedef Holder< const CompactGenome > GenomeHolder ; class Metagenome { public: static int nommap ; static void make_room() ; private: // maps file name to genome object typedef std::map< std::string, CompactGenome* > Genomes ; // maps sequence id to genome object typedef std::map< std::string, CompactGenome* > SeqMap1 ; // maps genome id to sequence map typedef std::map< std::string, SeqMap1 > SeqMap ; Genomes genomes ; SeqMap seq_map ; std::list< std::string > path ; static Metagenome the_metagenome ; public: Metagenome( const char* p ) ; ~Metagenome() { for( Genomes::iterator i = genomes.begin() ; i != genomes.end() ; ++i ) delete i->second ; } static void add_path( const std::string& s ) { the_metagenome.path.push_front( s ) ; } //! \brief finds a named sequence //! If a genome is given, only genome files whose name starts with //! the genome name are considered. If genome is empty, all files //! are searched. static GenomeHolder find_sequence( const std::string& genome, const std::string& seq ) ; static GenomeHolder find_genome( const std::string& genome ) ; static glob_t glob_path( const std::string& genome ) ; static bool translate_to_genome_coords( DnaP pos, uint32_t &xpos, const config::Sequence** s_out = 0, const config::Genome** g_out = 0 ) ; //! \brief replacement for mmap() that knows how to free memory //! This is a wrapper wround mmap(). If the system mmap() //! fails, it will try to free up some memory by forgetting //! about an ephemeral genome and then call mmap again. //! Parameters are passed to mmap() unchanged. If //! Metagenome::nommap is set, doesn't mmap() the file //! descriptor, but mmap()s /dev/zero instead and read()s the //! requested region from the file descriptor (intended for file //! systems where mmap() is agonizingly slow, e.g. GCFS). static void *mmap( void *start, size_t length, int *fd, off_t offset ) ; } ; #endif anfo-0.98/src/logdom.h0000644000371600007640000001337111447113464011561 00000000000000// Copyright 2009 Udo Stenzel // This file is part of ANFO // // ANFO is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // Anfo is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with Anfo. If not, see . #ifndef INCLUDED_LOGDOM_H #define INCLUDED_LOGDOM_H #include #include #include //! \brief representation of floating point number in log domain //! This class is supposed to behave like ordinary floating point //! numbers, but the representation is in the log domain, so we don't //! lose precision due to multiplication of many small values. For ease //! of conversion, we'll use the phred scale. That means more work in //! additions, but less on conversion. Assuming \f$ q_2 \geq q_1 \f$ //! the formula for additions is: //! //! \f[ q_s = q_1 - \frac{10}{\ln 10} \ln \left( 1 + \exp \left( \frac{\ln 10}{10} (q_1-q_2) \right) \right) \f] //! //! It turns out that IEEE floating point handles corner cases well: //! from_float(0) gives an internal representation of \f$ -\inf \f$, //! which works fine in calculations, except that adding two such //! numbers gives NaN (so don't do that). class Logdom { private: double v_ ; explicit Logdom( double v ) : v_(v) {} public: //! \brief constructs a value of one(!) //! Why one and not zero? Because we tend to multiply things, //! and one is the neutral element in that case. Logdom() : v_(0) {} void swap( Logdom &rhs ) throw() { std::swap( v_, rhs.v_ ) ; } bool is_finite() const { return isfinite( v_ ) ; } //! \brief calculates log( 1 + exp x ) //! Calculation is done in a way that preserves accuracy, the //! base of the logarithm is chosen to coincide with the Phred //! scale. //! \todo This function need to be accurate only for x < 0; it //! could probably be approximated using a Taylor series. static double ld1pexp10( double x ) { return -10.0 / log(10.0) * log1p( exp( -log(10.0)/10.0*x ) ) ; } //! \brief calculates log( 1 - exp x ) //! \see ld1pexp10() static double ld1mexp10( double x ) { return -10.0 / log(10.0) * log1p( -exp( -log(10.0)/10.0*x ) ) ; } static Logdom null() { return from_float( 0 ) ; } static Logdom one() { return from_float( 1 ) ; } //! \brief converts an ordinary number to log domain static Logdom from_float( double v ) { return Logdom( -10 * log(v) / log(10.0) ) ; } //! \brief converts a Phred-quality score to log domain //! This will normally result in a very small number; the Phred //! score represents the probability of something being wrong. static Logdom from_phred( int p ) { return Logdom( p ) ; } int to_phred() const { return int( v_ + 0.5 ) ; } uint8_t to_phred_byte() const { int p = to_phred() ; return p > 255 ? 255 : p ; } double to_float() const { return exp( -log(10.0) * v_ / 10.0 ) ; } Logdom sqrt() const { return Logdom( v_ / 2 ) ; } // multiplication is addition, division is subtraction Logdom& operator *= ( Logdom b ) { v_ += b.v_ ; return *this ; } Logdom& operator /= ( Logdom b ) { v_ -= b.v_ ; return *this ; } Logdom operator * ( Logdom b ) const { return Logdom( v_ + b.v_ ) ; } Logdom operator / ( Logdom b ) const { return Logdom( v_ - b.v_ ) ; } // addition w/o sacrificing precision is a bit harder Logdom operator + ( Logdom b ) const { if( b == null() ) return *this ; if( *this == null() ) return b ; return Logdom( v_ <= b.v_ ? v_ + ld1pexp10( b.v_ - v_ ) : b.v_ + ld1pexp10( v_ - b.v_ ) ) ; } Logdom operator - ( Logdom b ) const { if( b == null() ) return *this ; return Logdom( v_ <= b.v_ ? v_ + ld1mexp10( b.v_ - v_ ) : b.v_ + ld1mexp10( v_ - b.v_ ) ) ; } Logdom& operator += ( Logdom b ) { if( *this == null() ) { v_ = b.v_ ; } else if( b != null() ) { v_ = v_ <= b.v_ ? v_ + ld1pexp10( b.v_ - v_ ) : b.v_ + ld1pexp10( v_ - b.v_ ) ; } return *this ; } Logdom& operator -= ( Logdom b ) { if( b != null() ) { v_ = v_ <= b.v_ ? v_ + ld1mexp10( b.v_ - v_ ) : b.v_ + ld1mexp10( v_ - b.v_ ) ; } return *this ; } bool operator > ( Logdom b ) const { return b.v_ > v_ ; } bool operator >= ( Logdom b ) const { return b.v_ >= v_ ; } bool operator < ( Logdom b ) const { return b.v_ < v_ ; } bool operator <= ( Logdom b ) const { return b.v_ <= v_ ; } friend inline bool operator == ( Logdom a, Logdom b ) { return a.v_ == b.v_ ; } friend inline bool operator != ( Logdom a, Logdom b ) { return a.v_ != b.v_ ; } } ; inline Logdom operator + ( double a, Logdom b ) { return Logdom::from_float( a ) + b ; } inline Logdom operator + ( Logdom a, double b ) { return a + Logdom::from_float( b ) ; } inline Logdom operator - ( double a, Logdom b ) { return Logdom::from_float( a ) - b ; } inline Logdom operator - ( Logdom a, double b ) { return a - Logdom::from_float( b ) ; } inline Logdom operator * ( double a, Logdom b ) { return Logdom::from_float( a ) * b ; } inline Logdom operator * ( Logdom a, double b ) { return a * Logdom::from_float( b ) ; } inline Logdom operator / ( double a, Logdom b ) { return Logdom::from_float( a ) / b ; } inline Logdom operator / ( Logdom a, double b ) { return a / Logdom::from_float( b ) ; } template A lerp( B p, A a, A b ) { return (1.0-p) * a + p * b ; } #endif anfo-0.98/src/misc_streams.h0000644000371600007640000005301411447113463012766 00000000000000#ifndef INCLUDED_MISC_STREAMS_H #define INCLUDED_MISC_STREAMS_H #include "stream.h" #include #include namespace streams { using namespace std ; inline int eff_length( const Read& r ) { return ( r.has_trim_right() ? r.trim_right() : r.sequence().size() ) - r.trim_left() ; } //! \brief compares hits by smallest genome coordinate //! Comparison is first done lexically on the subject name, then on the //! smallest coordinate that's part of the alignment, then on the //! alignment length. A particular genome can be selected, if this //! isn't done, we sort on the best hit and compare the genome name even //! before the subject name. class by_genome_coordinate { private: const vector gs_ ; bool compare( const Result &a, const Result &b ) { const Hit *u = hit_to( a ), *v = hit_to( b ) ; if( u && !v ) return true ; if( !u ) return false ; if( u->genome_name() < v->genome_name() ) return true ; if( v->genome_name() < u->genome_name() ) return false ; return compare( *u, *v, a.read(), b.read(), false ) ; } bool compare( const Result &a, const Result &b, const string& g ) { const Hit *u = hit_to( a, g ), *v = hit_to( b, g ) ; if( u && !v ) return true ; if( !u ) return false ; return compare( *u, *v, a.read(), b.read(), false ) ; } bool compare( const Hit& u, const Hit& v, const Read& a, const Read& b, bool def ) { if( u.sequence() < v.sequence() ) return true ; if( v.sequence() < u.sequence() ) return false ; if( u.start_pos() < v.start_pos() ) return true ; if( v.start_pos() < u.start_pos() ) return false ; if( u.aln_length() < v.aln_length() ) return true ; if( v.aln_length() < u.aln_length() ) return false ; return def ; } public: by_genome_coordinate( const string &g ) : gs_( &g, &g+1 ) {} by_genome_coordinate( const vector &gs ) : gs_(gs) {} by_genome_coordinate() : gs_() {} bool operator() ( const Result *a, const Result *b ) { if( gs_.empty() ) return compare( *a, *b ) ; for( vector::const_iterator i = gs_.begin(), e = gs_.end() ; i != e ; ++i ) { if( compare( *a, *b, *i ) ) return true ; if( compare( *b, *a, *i ) ) return false ; } return false ; } void tag_header( output::Header& h ) { h.clear_is_sorted_by_name() ; h.clear_is_sorted_by_coordinate() ; if( gs_.empty() ) { h.set_is_sorted_by_all_genomes( true ) ; } else { h.clear_is_sorted_by_all_genomes() ; for( vector::const_iterator i = gs_.begin(), e = gs_.end() ; i != e ; ++i ) h.add_is_sorted_by_coordinate( *i ) ; } } bool is_sorted( const output::Header& h ) { if( gs_.empty() ) return h.is_sorted_by_all_genomes() ; if( (int)gs_.size() != h.is_sorted_by_coordinate_size() ) return false ; return equal( gs_.begin(), gs_.end(), h.is_sorted_by_coordinate().begin() ) ; } bool operator()( const Hit& u, const Hit& v, const Read& a, const Read& b ) { if( u.genome_name() < v.genome_name() ) return true ; if( v.genome_name() < u.genome_name() ) return false ; return compare( u, v, a, b, eff_length( a ) < eff_length( b ) ) ; } } ; struct by_seqid { bool operator() ( const Result *a, const Result *b ) { assert( a && b ) ; return a->read().seqid() < b->read().seqid() ; } void tag_header( output::Header& h ) { h.clear_is_sorted_by_coordinate() ; h.set_is_sorted_by_name( true ) ; } bool is_sorted( const output::Header& h ) { return h.is_sorted_by_name() ; } } ; //! \brief merges sorted streams into a sorted stream //! What to compare on is read from the input streams' header. If they //! are unsorted, we fail. Else we check that they are sorted in the //! same way and merge accordingly. //! //! \note All input streams must necessarily be opened at the same time. //! In principle, we could merge smaller chunks into temporary //! files to avoid hitting the file descriptor limit, but there //! hasn't been a practical need to do that yet. class MergeStream : public StreamBundle { private: deque< Result > rs_ ; enum { unknown, by_name, by_coordinate } mode_ ; vector gs_ ; public: MergeStream() : mode_( unknown ) {} virtual Header fetch_header() ; virtual Result fetch_result() ; //! \todo totally broken, need to think about how to keep the //! necessary information. virtual Object get_summary() const { return False ; } virtual string type_name() const { return "MergeStream" ; } } ; //! \brief merges multiple streams by taking the best hit //! If asked for a result, this class takes results from each of the //! streams in turn, until one sequence has received an entry from each. //! This sequence is then delivered. Everything works fine, as long as //! the sequence names come in in roughly the same order and every name //! is contained in every input. Else it still works, but eats memory. //! This is best used to merge chunks of work done by independent //! processes where the order of records hasn't been disturbed too much //! (multithreading and the implied slight shuffle is fine). class NearSortedJoin : public StreamBundle { private: typedef map< string, pair< size_t, Result > > Buffer ; Buffer buffer_ ; size_t nread_, nwritten_, nstreams_ ; deque< StreamHolder >::iterator cur_input_ ; Chan progress_ ; public: NearSortedJoin() : nread_(0), nwritten_(0), nstreams_(0) {} virtual Header fetch_header() ; virtual Result fetch_result() ; } ; //! \brief presents a container as an input stream //! The container must be of pointers to \c Result, the stream acts as //! input stream. A suitable header and footer are supplied at //! construction time. template< typename I > class ContainerStream : public Stream { private: I cur_, end_ ; unsigned total_, done_ ; Chan chan_ ; public: ContainerStream( const Header &hdr, I begin, I end, const Footer &foot ) : cur_( begin ), end_( end ), total_( std::distance( begin, end ) ), done_(0) { hdr_ = hdr ; foot_ = foot ; state_ = cur_ == end_ ? end_of_stream : have_output ; } virtual Result fetch_result() { if( ++done_ % 1024 == 0 ) { stringstream s ; s << "(mem) " << done_ << "/" << total_ << " (" << (int)(100*done_/total_) << "%)" ; chan_( Console::info, s.str() ) ; } Result r = **cur_ ; ++cur_ ; if( cur_ == end_ ) state_ = end_of_stream ; return r ; } virtual string type_name() const { return "ContainerStream" ; } } ; extern unsigned SortingStream__ninstances ; //! \brief stream filter that sorts its input //! This stream is intended to sort large amounts of data. To do that, //! it performs a quick sort on blocks that fit into memory (the maximum //! size is configured at construction time), writes them out to //! temporary files, then reads them back in and does a merge sort. If //! too many files are open (as counted by \c AnfoReader, again //! configurable at construction time), some temporary files are merge //! sorted into a bigger one. template class SortingStream : public Stream { private: typedef deque< Holder< streams::Stream > > MergeableQueue ; typedef map< unsigned, MergeableQueue > MergeableQueues ; typedef deque< Result* > ScratchSpace ; //! Storage to perform quicksort in. ScratchSpace scratch_space_ ; //! We keep multiple queues of streams ordered and separated by //! the number of times they have been merged. This way we //! don't merge the stuff over and over, and instead tend to do //! a merge that gives the greatest reduction in number of open //! files with least amount of IO. The key is the number of //! times a file has already been merged with others, the value //! is just a set of streams. MergeableQueues mergeable_queues_ ; Holder< Stream > final_stream_ ; uint64_t total_scratch_size_ ; unsigned max_que_size_ ; unsigned num_open_files_ ; unsigned max_arr_size_ ; Comp comp_ ; //! \brief quicksort the scratch area //! \internal void sort_scratch() { if( scratch_space_.size() > 1 ) { std::stringstream s ; s << "SortingStream: qsorting " << scratch_space_.size() << " results" ; console.output( Console::notice, s.str() ) ; sort( scratch_space_.begin(), scratch_space_.end(), comp_ ) ; ScratchSpace::iterator o = scratch_space_.begin() ; for( ScratchSpace::const_iterator i = scratch_space_.begin()+1, e = scratch_space_.end() ;i != e ; ++i ) { if( (*i)->read().seqid() == (*o)->read().seqid() ) merge_sensibly( **o, **i ) ; else *(++o) = *i ; } scratch_space_.erase( ++o, scratch_space_.end() ) ; } } void enqueue_stream( streams::StreamHolder, int = 0 ) ; void flush_scratch() ; virtual ~SortingStream() { for_each( scratch_space_.begin(), scratch_space_.end(), delete_ptr() ) ; --SortingStream__ninstances ; } public: SortingStream( unsigned as = 256, unsigned qs = 256, Comp comp = Comp() ) : final_stream_(), total_scratch_size_(0), max_que_size_(qs), num_open_files_(0), max_arr_size_( as), comp_( comp ) { foot_.set_exit_code( 0 ) ; ++SortingStream__ninstances ; } virtual void put_header( const Header& h ) { Stream::put_header( h ) ; comp_.tag_header( hdr_ ) ; } virtual void put_footer( const Footer& ) ; virtual void put_result( const Result& r ) { scratch_space_.push_back( new Result( r ) ) ; total_scratch_size_ += scratch_space_.back()->SpaceUsed() ; if( (total_scratch_size_ >> 20) >= max_arr_size_ ) flush_scratch() ; } virtual Result fetch_result() { Result r = final_stream_->fetch_result() ; state_ = final_stream_->get_state() ; return r ; } virtual Footer fetch_footer() { merge_sensibly( foot_, final_stream_->fetch_footer() ) ; return foot_ ; } virtual Object get_summary() const { return final_stream_->get_summary() ; } } ; template < typename Comp > void SortingStream::flush_scratch() { sort_scratch() ; string tempname ; int fd = mktempfile( &tempname ) ; { ContainerStream< deque< Result* >::const_iterator > sa( hdr_, scratch_space_.begin(), scratch_space_.end(), foot_ ) ; ChunkedWriter out( fd, 25, tempname.c_str() ) ; console.output( Console::notice, "SortingStream: Writing to tempfile " + tempname ) ; transfer( sa, out ) ; } throw_errno_if_minus1( lseek( fd, 0, SEEK_SET ), "seeking in ", tempname.c_str() ) ; google::protobuf::io::FileInputStream* is = new google::protobuf::io::FileInputStream( fd ) ; is->SetCloseOnDelete( true ) ; enqueue_stream( new UniversalReader( tempname, is ), 1 ) ; for_each( scratch_space_.begin(), scratch_space_.end(), delete_ptr() ) ; scratch_space_.clear() ; total_scratch_size_ = 0 ; } template < typename Comp > void SortingStream::enqueue_stream( streams::StreamHolder s, int level ) { mergeable_queues_[ level ].push_back( s ) ; if( ++num_open_files_ > max_que_size_ ) { // get the biggest bin, we'll merge everything below that unsigned max_bin = 0 ; for( MergeableQueues::const_iterator i = mergeable_queues_.begin() ; i != mergeable_queues_.end() ; ++i ) if( i->second.size() > mergeable_queues_[max_bin].size() ) max_bin = i->first ; unsigned total_inputs = 0 ; for( MergeableQueues::iterator i = mergeable_queues_.begin() ; i->first <= max_bin ; ++i ) total_inputs += i->second.size() ; // we must actually make progress, and more than just a // single stream must be merged to avoid quadratic behaviour // (only important in a weird corner case, in which we simply // use one more file descriptor) if( total_inputs > 2 ) { string fname ; int fd = mktempfile( &fname ) ; std::stringstream s ; s << "SortingStream: Merging bins 0.." << max_bin << " to tempfile " << fname ; console.output( Console::notice, s.str() ) ; { streams::MergeStream ms ; for( MergeableQueues::iterator i = mergeable_queues_.begin() ; i->first <= max_bin ; ++i ) { num_open_files_ -= i->second.size() ; for( size_t j = 0 ; j != i->second.size() ; ++j ) ms.add_stream( i->second[j] ) ; i->second.clear() ; } ChunkedWriter out( fd, 25, fname.c_str() ) ; transfer( ms, out ) ; } throw_errno_if_minus1( lseek( fd, 0, SEEK_SET ), "seeking in ", fname.c_str() ) ; google::protobuf::io::FileInputStream* is = new google::protobuf::io::FileInputStream( fd ) ; is->SetCloseOnDelete( true ) ; enqueue_stream( new UniversalReader( fname, is ), max_bin + 1 ) ; } } } //! \brief ends the input, initiates sorting //! Only when the input ends can we completely sort it, so setting the //! footer switches to output mode. Here we collect the temporary files //! we've written and become a \c MergeStream. template < typename Comp > void SortingStream::put_footer( const Footer& f ) { Stream::put_footer( f ) ; bool need_merge = false ; for( MergeableQueues::const_iterator i = mergeable_queues_.begin() ; !need_merge && i != mergeable_queues_.end() ; ++i ) if( !i->second.empty() ) need_merge = true ; if( need_merge ) { // We have to be careful about buffering; if more than one // SortingStream is active, we could run out of RAM. Therefore, if // we're alone, we sort and add a a stream. Else we flush to // temporary storage. (Also, if the temporay space is empty, we // *always* add the ContainerStream, otherwise we get strange // effects if the output turns out to be empty.) Holder< MergeStream > m( new MergeStream ) ; if( scratch_space_.begin() != scratch_space_.end() && SortingStream__ninstances > 1 ) flush_scratch() ; else { console.output( Console::notice, "SortingStream: final sort" ) ; sort_scratch() ; m->add_stream( new ContainerStream< deque< Result* >::const_iterator >( hdr_, scratch_space_.begin(), scratch_space_.end(), foot_ ) ) ; } // add any streams that have piled up for( MergeableQueues::const_iterator i = mergeable_queues_.begin() ; i != mergeable_queues_.end() ; ++i ) for( MergeableQueue::const_iterator j = i->second.begin() ; j != i->second.end() ; ++j ) m->add_stream( *j ) ; mergeable_queues_.clear() ; if( SortingStream__ninstances == 1 ) { // we're alone. delegate directly to MergeStream console.output( Console::notice, "SortingStream: merging everything to output" ) ; final_stream_ = m ; } else { // not alone. We'll conserve file handles by merging everything // into a temporary file and opening that. string fname ; int fd = mktempfile( &fname ) ; std::stringstream s ; s << "SortingStream: Merging everything to tempfile " << fname ; console.output( Console::notice, s.str() ) ; ChunkedWriter out( fd, 25, fname.c_str() ) ; transfer( *m, out ) ; num_open_files_ = 1 ; throw_errno_if_minus1( lseek( fd, 0, SEEK_SET ), "seeking in ", fname.c_str() ) ; google::protobuf::io::FileInputStream* is = new google::protobuf::io::FileInputStream( fd ) ; is->SetCloseOnDelete( true ) ; final_stream_ = new UniversalReader( fname, is ) ; } } // nothing to merge, just the scratch space else if( scratch_space_.begin() != scratch_space_.end() && SortingStream__ninstances > 1 ) { // not alone. We'll conserve memory by writing to a // temporary file and opening that. flush_scratch() ; console.output( Console::notice, "SortingStream: output comes from single temporary file" ) ; final_stream_ = mergeable_queues_[1].front() ; } else { // alone, we'll use a container stream directly console.output( Console::notice, "SortingStream: final sort" ) ; sort_scratch() ; final_stream_ = new ContainerStream< deque< Result* >::const_iterator >( hdr_, scratch_space_.begin(), scratch_space_.end(), foot_ ) ; console.output( Console::notice, "SortingStream: using scratch space for output" ) ; } final_stream_->fetch_header() ; state_ = final_stream_->get_state() ; } class RepairHeaderStream : public Stream { private: string editor_ ; public: RepairHeaderStream( const string &e ) : editor_( e ) {} virtual void put_header( const Header& ) ; } ; class FanOut : public StreamBundle { public: virtual void put_header( const Header& ) ; virtual void put_result( const Result& ) ; virtual void put_footer( const Footer& ) ; virtual Footer fetch_footer() ; } ; class Compose : public StreamBundle { public: virtual state get_state() ; virtual void put_header( const Header& ) ; virtual void put_result( const Result& r ) { streams_.front()->put_result( r ) ; get_state() ; } virtual void put_footer( const Footer& f ) { streams_.front()->put_footer( f ) ; get_state() ; } virtual Header fetch_header() ; virtual Result fetch_result() { return streams_.back()->fetch_result() ; } virtual Footer fetch_footer() { return streams_.back()->fetch_footer() ; } virtual string type_name() const { return "Compose" ; } } ; class StatStream : public Stream { private: unsigned total_, mapped_, mapped_u_, different_ ; uint64_t bases_, bases_gc_, bases_m_, bases_gc_m_ ; uint64_t bases_squared_, bases_m_squared_ ; public: StatStream() : total_(0), mapped_(0), mapped_u_(0), different_(0) , bases_(0), bases_gc_(0), bases_m_(0), bases_gc_m_(0) , bases_squared_(0), bases_m_squared_(0) {} virtual void put_result( const Result& ) ; virtual Object get_summary() const ; } ; //! \brief calculates divergence //! Divergence is calculated by the Green Triangulation method. Two //! genomes are needed (primary and secondary) and alignments to both of //! them. Differences are counted (all equal, either sequence //! different, all different), then error corrected (math stolen from //! dropin_AHA.pl) and turned into divergence of the last common //! ancestor, expressed as fraction of total divergence between primary //! and secondary genome. class DivergenceStream : public Stream { private: string primary_genome_, secondary_genome_ ; int chop_ ; bool ancient_ ; int64_t b1, b2, b3, b4, b5 ; public: DivergenceStream( const string& primary, const string& secondary, int chop ) : primary_genome_( primary ), secondary_genome_( secondary ), chop_( chop ) , b1(0), b2(0), b3(0), b4(0), b5(0) {} virtual void put_header( const Header& ) ; virtual void put_result( const Result& ) ; virtual Object get_summary() const ; } ; class MismatchStats : public Stream { private: int mat_[4][4] ; public: MismatchStats() { memset( mat_, 0, sizeof( mat_ ) ) ; } virtual void put_result( const Result& ) ; virtual Object get_summary() const ; } ; //! \brief checks for hits to homologous regions //! This filter reads two UCSC Chain files, breaks them down into //! blocks, discards overlapping blocks (so the mapping becomes 1:1), //! then discard blocks from the first chain that wouldn't map back //! according to the second chain. //! //! The filter proper verifies that the alignment to the first genome is //! mostly covered by blocks, then maps them and verifies that they //! cover the alignment to the second genome. A flag is set if either //! alignment is missing or either test fails. //! //! \todo I swear, one of those days I'll implement a symbol table for //! those repeated chromosome names. class AgreesWithChain : public Filter { private: string left_genome_, right_genome_ ; struct Entry ; typedef map< unsigned, Entry > Chains ; // =^= left_start typedef map< string, Chains > Map1 ; // =^= left_chr // Chains have a hierarchical structure: below any chain, there // can be a collection of more. We have one such top-level // collection per chromosome. struct Entry { unsigned left_end ; unsigned right_start ; unsigned right_end : 31 ; unsigned strand : 1 ; string right_chr ; Chains nested ; } ; Map1 map_ ; static Chains::iterator find_any_most_specific_overlap( unsigned start, unsigned end, Chains *chains ) ; public: //! \brief constructs chain filter //! \param p primary genome (e.g. hg18) //! \param s secondary genome (e.g. pt2) //! \param c chain from \c p to \c s (this means \c p is target, //! \c s is query), in the form of //! \param d chain from \c s to \c p AgreesWithChain( const string& l, const string& r, const pair& s ) ; virtual bool xform( Result& ) ; } ; class RegionFilter : public HitFilter { private: typedef std::map< unsigned, unsigned > Regions ; // end(!) & start typedef std::map< std::string, Regions > Regions2 ; // chromosome typedef std::map< std::string, Regions2 > Regions3 ; // filename static Regions3 all_regions ; Regions2 *my_regions ; public: RegionFilter( const pair< istream*, string >& ) ; //! \brief looks for a region overlapping the current alignment //! This will only work correctly for non-overlapping //! annotations. Deal with it. bool inside( const Hit& h ) { unsigned x = h.start_pos() ; const Regions &r = (*my_regions)[ h.sequence() ] ; Regions::const_iterator i = r.lower_bound( x ) ; // we now got the leftmost region whose end is to the right // of our start. if no such thing exists, nothing overlaps. if( i == r.end() ) return false ; // now check if what we got actually overlaps. it does if // it starts before our alignment ends. return i->second <= x + abs(h.aln_length()) && i->first >= x ; } } ; class InsideRegion : public RegionFilter { public: InsideRegion( const pair< istream*, string > &p ) : RegionFilter( p ) {} virtual bool keep( const Hit& h ) { return inside( h ) ; } } ; class OutsideRegion : public RegionFilter { public: OutsideRegion( const pair< istream*, string > &p ) : RegionFilter( p ) {} virtual bool keep( const Hit& h ) { return !inside( h ) ; } } ; class Sanitizer : public Filter { public: virtual void put_header( const Header& ) ; virtual bool xform( Result& ) ; } ; } // namespace #endif anfo-0.98/src/output_streams.h0000644000371600007640000001346611447113463013402 00000000000000// Copyright 2009 Udo Stenzel // This file is part of ANFO // // ANFO is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // Anfo is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with Anfo. If not, see . #ifndef INCLUDED_OUTPUT_STREAMS_H #define INCLUDED_OUTPUT_STREAMS_H #include "index.h" #include "stream.h" #include #include #include #include #include namespace output { class Hit ; } namespace config { class Config ; } namespace streams { using namespace google::protobuf::io ; //! \brief writes in (a modification of) Google's text format //! This is essentially the human readable version of the native format. //! Additionally, alignment strings and a CLUSTAL-style 'conservation' //! line are added, provided they were looked up using the reference //! genome beforehand, and some fields, notably the CIGAR line, are //! printed in a more compact format. class TextWriter : public Stream { private: auto_ptr< std::ostream > out_ ; void print_msg( const google::protobuf::Message& ) ; public: TextWriter( const pair< std::ostream*, string > &p ) : out_( p.first ) {} virtual void put_header( const Header& ) ; virtual void put_result( const Result& ) ; virtual void put_footer( const Footer& ) ; virtual string type_name() const { return "TextWriter" ; } } ; //! \brief writes in SAM format //! Every hit for every sequence is written. A sequence without hits is //! written out anyway. If that's not desired, the input stream must be //! filtered appropriately. //! \todo Writing SAM is probably a bad idea in the long run. Directly //! generating BAM is more sustainable //! \todo Creation of correctly sorted SAM files is next to impossible. //! Maybe creation of BAM files is better anyway. class SamWriter : public Stream { private: enum bad_stuff { goodness = 0, no_hit, multiple_hits, no_seqid, no_seq, bad_cigar, bad_stuff_max } ; static const char *descr[] ; std::auto_ptr< std::ostream > out_ ; string nm_ ; int discarded[bad_stuff_max] ; enum bam_flags { bam_fpaired = 1, // read is paired in sequencing bam_fproper_pair = 2, // read is mapped in proper pair bam_funmap = 4, // query seq. is unmapped bam_fmunmap = 8, // mate is umapped bam_freverse = 16, // strand of query (0 - fwd, 1 - rev) bam_fmreverse = 32, // strand of mate bam_fread1 = 64, // read is 1. in pair bam_fread2 = 128, // read is 2. in pair bam_fsecondary = 256, // alignment is NOT primary bam_fqcfail = 512, // read fails due low quality bam_fdup = 1024 // read is duplicate } ; bad_stuff protoHit_2_bam_Hit( const output::Result& ) ; public: SamWriter( const pair< ostream*, string > &p ) : out_( p.first ), nm_( p.second ) { memset( discarded, 0, sizeof(discarded) ) ; } virtual void put_header( const Header& h ) { Stream::put_header( h ) ; *out_ << "@HD\tVN:1.0" ; if( h.is_sorted_by_name() ) *out_ << "\tSO:queryname" ; *out_ << "\n@PG\tID:ANFO\tVN:" << h.version() << '\n' ; } virtual void put_result( const Result& res ) { if (bad_stuff r = protoHit_2_bam_Hit( res )) discarded[r]++; } virtual void put_footer( const Footer& ) ; } ; //! \brief writes in aligned FASTA-format //! Each alignment appears as a pair of sequences, reference first, //! query last. Score, coordinates and whether an adapter was trimmed //! are encoded in the header. This is considered a legacy format, //! mostly useful to make substitution graphs from. class FastaAlnWriter : public Stream { private: std::auto_ptr< std::ostream > out_ ; public: FastaAlnWriter( const pair< ostream*, string > &p ) : out_( p.first ) {} virtual void put_result( const Result& ) ; } ; //! \brief writes in FASTQ format //! This should simply reproduce the input to ANFO, so I can throw away //! the ugly FASTQ files. Every sequence gets a header, then the //! sequence (50 bases per line), the header is then *not* repeated and //! the quality scores follow in the same layout. class FastqWriter : public Stream { private: std::auto_ptr< std::ostream > out_ ; bool with_qual_ ; public: FastqWriter( const pair< ostream*, string > &p, bool q ) : out_( p.first ), with_qual_(q) {} virtual void put_result( const Result& ) ; } ; class TableWriter : public Stream { private: std::auto_ptr< std::ostream > out_ ; public: TableWriter( const pair< ostream*, string > &p ) : out_( p.first ) {} virtual void put_result( const Result& ) ; } ; class GenTextAlignment : public Filter { private: int context_ ; bool strict_ ; public: GenTextAlignment( int context, bool strict ) : context_( context ), strict_( strict ) {} virtual bool xform( Result& ) ; } ; //! \brief writes out coverage depth in WIG format //! This only works after DuctTaper has been applied, afterwards it //! extracts the depth of coverage (aka number of observations) per //! position. //! Note that the output file will get huge; we're talking about a text //! based format... class WigCoverageWriter : public Stream { private: std::auto_ptr< std::ostream > out_ ; public: WigCoverageWriter( const pair< ostream*, string > &p ) : out_( p.first ) {} virtual void put_result( const Result& ) ; } ; } // namespace #endif anfo-0.98/src/sequence.h0000644000371600007640000003466611447116045012120 00000000000000// Copyright 2009 Udo Stenzel // This file is part of ANFO // // ANFO is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // Anfo is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with Anfo. If not, see . #ifndef INCLUDED_SEQUENCE_H #define INCLUDED_SEQUENCE_H #include #include #include #include #include #include #include #include #include #include "output.pb.h" /*! \defgroup typedefs Useful typedefs * These typedefs are used mostly for their documentation value; C++ * unfortunately won't be able to check their differences * most of the time. * * @{ */ //! \brief Type used to store short DNA sequences. //! //! Oligos are stored with two bits per bases where [0,1,2,3] mean //! [A,C,T,G]. The two LSBs contain the first base, up to 32 bases can //! be stored. typedef uint64_t Oligo ; //! \brief Type used to store a single nucleotide base. //! //! We encode [A,C,T,G] as [0,1,2,3], same as in \c Oligo. typedef uint8_t Nucleotide ; // 0,1,2,3 == A,C,T,G //! \brief Type used to store ambiguity codes. //! //! We encode [A,C,T,G] as [1,2,4,8]. A one shifted by the \c Nucleotide //! code gives the approriate ambiguity code, other codes can be created //! by combining bases with a logical OR. Zero encodes a gap, 15 is an //! N. typedef uint8_t Ambicode ; // 1,2,4,8 == A,C,T,G //! @} //! \brief Decodes a character to a nucleotide. //! //! Takes an arbitrary character and determines the IUPAC ambiguity code //! it stands for. Small and capital letters are understood, everything //! unrecognized becomes a gap. inline Ambicode to_ambicode( char c ) { switch( c ) { case 'a': case 'A': return 1 ; case 'b': case 'B': return 1 ^ 0xf ; case 'c': case 'C': return 2 ; case 'd': case 'D': return 2 ^ 0xf ; case 'g': case 'G': return 8 ; case 'h': case 'H': return 8 ^ 0xf ; case 't': case 'T': return 4 ; case 'u': case 'U': return 4 ; case 'v': case 'V': return 4 ^ 0xf ; case 'n': case 'N': return 15 ; case 'm': case 'M': return 3 ; case 'k': case 'K': return 12 ; case 'w': case 'W': return 5 ; case 's': case 'S': return 10 ; case 'r': case 'R': return 9 ; case 'y': case 'Y': return 6 ; default: return 0 ; } } inline char from_ambicode( Ambicode a ) { return "-ACMTWYHGRSVKDBN"[a] ; } //! \brief Complement an ambiguity code. inline Ambicode complement( Ambicode w ) { return 0xf & (w << 2 | w >> 2) ; } inline char compl_ascii( char x ) { return from_ambicode( complement( to_ambicode( x ) ) ) ; } //! \brief Reverse-complements a pair of ambiguity codes. //! \internal inline uint8_t reverse_complement( uint8_t xy ) { return (xy & 0x03) << 6 | (xy & 0x0c) << 2 | (xy & 0x30) >> 2 | (xy & 0xc0) >> 6 ; } //! \brief Checks whether a character codes for a nucleotide. //! This is euivalent to decoding the character and checking that it //! doesn't encode a gap. inline bool encodes_nuc( char c ) { return to_ambicode(c) != 0 ; } //! Dumb pointer to DNA //! A pointer with sub-byte precision is needed for our mmaped genomes. //! The assumption here is that this fits into 64 bits, which is true on //! any ix86_64 bit that doesn't implement full 64bit addresses, and that //! will be all of them for quite some time to come. It's also true on a //! 32 bit system, obviously. We also steal another bit to encode the //! strand we're pointing to. //! //! To make arithmetic easier, the encoding is as follows: The main //! pointer is converted to an int64_t, it is then shifted left and the //! sub-byte index (just one bit) is shifted in. Then the sign is //! inverted if and only if this is a pointer to the RC strand. This way, //! arithmetic works on both strands the same way. To dereference a //! pointer, the absolute value of the number is taken, interpreted as //! signed 63 bit value, sign extended and reinterpreted as pointer. class DnaP { private: int64_t p_ ; public: //! constructs a DNA pointer //! The pointer is initialized from a pointer to bytes, //! understood to point to the ambiguity code in the 4 LSBs. It //! is then converted to a reverse pointer and finally the offset //! is added, taking directionality into account. //! \param p pointer to ambiguity-encoded DNA //! \param complement set to true to make a pointer to the //! reverse-complemented strand //! \param off offset to add to the final pointer explicit DnaP( const uint8_t *p = 0, bool complement = false, int off = 0 ) { assign( p, complement, off ) ; } void assign( const uint8_t *p = 0, bool complement = false, int off = 0 ) { p_ = (reinterpret_cast(p) << 1) & std::numeric_limits::max() ; if( complement ) p_ = -p_ ; p_ += off ; assert( unsafe_ptr() == p ) ; } Ambicode operator * () const { return (*this)[0] ; } Ambicode operator [] ( int64_t ix ) const { int64_t p = p_ + ix ; int64_t p2 = llabs(p) ; if( (p2 << 1) < 0 ) p2 |= std::numeric_limits::min() ; uint8_t w = *( reinterpret_cast( p2 >> 1 ) ) ; w = 0xf & ( p & 1 ? w >> 4 : w ) ; return p < 0 ? complement(w) : w ; } bool operator! () const { return !p_ ; } operator const void*() const { return (const void*)p_ ; } bool is_reversed() const { return p_ < 0 ; } DnaP abs() const { DnaP q ; q.p_ = llabs(p_) ; return q ; } DnaP reverse() const { DnaP q ; q.p_ = -p_ ; return q ; } DnaP reverse_if( bool p ) const { return p ? reverse() : *this ; } //! \brief returns a pointer to the underlying storage. //! \internal //! If you call this function for anything, you're on your own. const uint8_t *unsafe_ptr() const { int64_t p2 = llabs(p_) ; if( (p2 << 1) < 0 ) p2 |= std::numeric_limits::min() ; return reinterpret_cast( p2 >> 1 ) ; } DnaP &operator ++ () { p_++ ; return *this ; } DnaP &operator -- () { p_-- ; return *this ; } DnaP &operator += ( int64_t o ) { p_ += o ; return *this ; } DnaP &operator += ( uint32_t o ) { p_ += o ; return *this ; } DnaP &operator += ( int32_t o ) { p_ += o ; return *this ; } DnaP &operator -= ( int64_t o ) { p_ -= o ; return *this ; } DnaP &operator -= ( uint32_t o ) { p_ -= o ; return *this ; } DnaP &operator -= ( int32_t o ) { p_ -= o ; return *this ; } unsigned long get() const { return p_ ; } friend inline int64_t operator - ( const DnaP &a, const DnaP &b ) { return a.p_ - b.p_ ; } friend inline bool operator == ( const DnaP &a, const DnaP &b ) { return a.p_ == b.p_ ; } friend inline bool operator != ( const DnaP &a, const DnaP &b ) { return a.p_ != b.p_ ; } friend inline std::ostream& operator << ( std::ostream& s, const DnaP &p ) { return s << std::hex << p.p_ ; } } ; inline DnaP operator + ( const DnaP& a, int64_t o ) { DnaP b = a ; return b += o ; } inline DnaP operator + ( const DnaP& a, int32_t o ) { DnaP b = a ; return b += o ; } inline DnaP operator + ( const DnaP& a, uint32_t o ) { DnaP b = a ; return b += o ; } inline DnaP operator - ( const DnaP& a, int64_t o ) { DnaP b = a ; return b -= o ; } inline DnaP operator - ( const DnaP& a, int32_t o ) { DnaP b = a ; return b -= o ; } inline DnaP operator - ( const DnaP& a, uint32_t o ) { DnaP b = a ; return b -= o ; } class QDnaP { private: const uint16_t *p_ ; public: explicit QDnaP( const uint16_t *p = 0 ) : p_(p) {} QDnaP &operator = ( const QDnaP& p ) { p_ = p.p_ ; return *this ; } Ambicode operator * () const { return *p_ & 0xf ; } uint8_t qual( size_t ix = 0 ) const { return p_[ix] >> 8 ; } Ambicode operator [] ( size_t ix ) const { return p_[ix] & 0xf ; } operator const void*() const { return p_ ; } QDnaP &operator ++ () { p_++ ; return *this ; } QDnaP &operator -- () { p_-- ; return *this ; } QDnaP &operator += ( int64_t o ) { p_ += o ; return *this ; } QDnaP &operator += ( uint32_t o ) { p_ += o ; return *this ; } QDnaP &operator += ( int32_t o ) { p_ += o ; return *this ; } QDnaP &operator -= ( int64_t o ) { p_ -= o ; return *this ; } QDnaP &operator -= ( uint32_t o ) { p_ -= o ; return *this ; } QDnaP &operator -= ( int32_t o ) { p_ -= o ; return *this ; } unsigned long get() const { return (unsigned long)p_ ; } friend inline size_t operator - ( const QDnaP &a, const QDnaP &b ) { return a.p_ - b.p_ ; } friend inline bool operator == ( const QDnaP &a, const QDnaP &b ) { return a.p_ == b.p_ ; } friend inline bool operator != ( const QDnaP &a, const QDnaP &b ) { return a.p_ != b.p_ ; } friend inline std::ostream& operator << ( std::ostream& s, const QDnaP &p ) { return s << std::hex << p.p_ ; } } ; inline QDnaP operator + ( const QDnaP& a, int64_t o ) { QDnaP b = a ; return b += o ; } inline QDnaP operator + ( const QDnaP& a, int32_t o ) { QDnaP b = a ; return b += o ; } inline QDnaP operator + ( const QDnaP& a, uint32_t o ) { QDnaP b = a ; return b += o ; } inline QDnaP operator - ( const QDnaP& a, int64_t o ) { QDnaP b = a ; return b -= o ; } inline QDnaP operator - ( const QDnaP& a, int32_t o ) { QDnaP b = a ; return b -= o ; } inline QDnaP operator - ( const QDnaP& a, uint32_t o ) { QDnaP b = a ; return b -= o ; } //! \brief Wrapper for easier output of gap-terminated sequences. //! \internal struct Sequ { Sequ( const DnaP p, int length = std::numeric_limits::max() ) : p_(p), l_(length) {} DnaP p_ ; int l_ ; } ; inline std::ostream& operator << ( std::ostream& s, const Sequ& d ) { for( DnaP p = d.p_, q = d.p_ + d.l_ ; *p && p != q ; ++p ) s << from_ambicode( *p ) ; return s ; } //! \brief sequence with quality scores //! We store four quality scores for the four possible bases. If the //! sequence was read from a 4Q file (currently not supported, not that //! anyone cares), that's okay. If it came from FASTQ or even FASTA, //! they are just an extrapolation (error probability divided by 3). //! The sequence is duplicated and reverse-complemented, so that //! negative offsets actually yield pointers into the reverse strand. //! Note, the forward strand has offsets [1..len], the reverse strand //! has offsets [-len..-1]. At offset 0, there's a gap. The interval //! [begin,end) also represents the forward strand, without gaps. class QSequence { public: //! \brief An ambiguity code and four qualities together. //! The qualities are undefined if the ambiguity code encodes a //! gap. We keep copies of the quality scores to avoid loss of //! precision when regenerating a FastA file. struct Base { uint8_t ambicode ; uint8_t qscore ; uint8_t qscores[4] ; Base() : ambicode(0), qscore(0) { qscores[0] = qscores[1] = qscores[2] = qscores[3] = 0 ; } Base( uint8_t a, int q_score ) ; } ; private: std::vector< Base > seq_ ; // offset of the central zero int middle_offset() const { return seq_.size()/2 ; } public: typedef std::vector< Base >::const_iterator const_iterator ; typedef std::vector< Base >::const_reverse_iterator const_reverse_iterator ; typedef std::vector< Base >::iterator iterator ; typedef Base const *const_pointer ; typedef Base const &const_reference ; typedef Base pointer ; typedef Base &reference ; typedef Base value_type ; //! \brief creates an empty sequence //! The sequence is terminated correctly by three gaps (one in //! the middle, one at either end) and has no bases. It is //! basically considered invalid and used as a placeholder where //! necessary. QSequence() { seq_.push_back( Base() ) ; seq_.push_back( Base() ) ; seq_.push_back( Base() ) ; } //! \brief creates a quality sequence from a generic Read //! Missing qualities are set to a constant, which is equivalent //! to a Q score of 30 by default. A reverse-complemented //! version is prepended. QSequence( const output::Read& r, int default_q = 30 ) ; void swap( QSequence& rhs ) { std::swap( seq_, rhs.seq_ ) ; } const_pointer start() const { return &seq_[ middle_offset()] ; } unsigned length() const { return seq_.size()/2 -1 ; } const_iterator begin() const { return seq_.begin() + middle_offset() ; } const_iterator end() const { return seq_.end() - 1 ; } reference operator [] ( size_t ix ) { return seq_[middle_offset()+ix] ; } const_reference operator [] ( size_t ix ) const { return seq_[middle_offset()+ix] ; } } ; //! \brief reads a sequence from a FASTA, FASTQ or 4Q file //! To unify all formats (well-defined or not...) this function accepts //! both '@' and '>' as header delimiter. Any lines starting ';' and //! following the header are treated as extended description. Quality //! scores are optional and introduced by '+'; they can be either ASCII //! (U Rockefeller idiocy), or 33-based raw Phred scale values (Sanger //! standard), or 64-based Solexa scale values (Solexa idiocy). The tag //! "SQ " (4Q definition) is ignored in a sequence line. Quality scores //! can also be introduced by '*', in which case the quality line tag is //! read and the remainder is parsed as quality scores in 4Q format. If //! no bases are found, but four Q scores are available, bases are //! "called" internally. //! //! \todo Add sensible error checking (e.g. consistent line lengths, no //! additional junk, no wrong characters). //! //! \param zis stream to read from //! \param r read structure to place the sequence in //! \param solexa_scores //! If set, quality scores are converted from Solexa to Phred //! conventions. //! \param origin //! The origin is subtracted from raw scores in ASCII files. It is //! 33 for original FASTQ files, but 64 for files with Illumina //! brain damage, in which case it may or may not have to be //! combined with setting solexa_scores. //! \return true iff a sequence could be read bool read_fastq( google::protobuf::io::ZeroCopyInputStream *zis, output::Read& r, bool solexa_scores, char origin ) ; //! \brief reads a sequence from a SAM file //! \param zis stream to read from //! \return true iff a sequence could be read bool read_sam( google::protobuf::io::ZeroCopyInputStream *zis, const std::string& genome, output::Result& r ) ; #endif anfo-0.98/src/stream.h0000644000371600007640000007425011447113464011576 00000000000000// Copyright 2009 Udo Stenzel // This file is part of ANFO // // ANFO is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // Anfo is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with Anfo. If not, see . #ifndef INCLUDED_STREAM_H #define INCLUDED_STREAM_H #include "compress_stream.h" #include "logdom.h" #include "output.pb.h" #include "sequence.h" #include "util.h" #include #include #include #include #include #include #include #include #include #include #include #include #include // Including Elk defines some macros that collide with protobuf. We // undefine them (and hope they aren't needed...). #include #undef Print #undef MAX_TYPE namespace streams { using namespace output ; using namespace std ; inline uint32_t mk_msg_tag( uint32_t i ) { return i << 3 | 2 ; } //! \defgroup outputfile Convenience functions to handle output files //! The output file is a series of protocol buffer messages. This makes //! it compact and extensible. Instead of writing a serial file, the //! very same messages could be entered into a Berkeley-DB type //! database. Since conversion to all sorts of text files is a no //! brainer, the binary format is not considered undue hardship on the //! users of scripting languages. //! //! (If you are a user of a glorified logfile munching language and want //! an ASCII-based table, define a sensible layout and ask for it. Or //! write the single function yourself, it isn't that hard.) //! //! The protobuf format itself is not self-delimiting, therefore we //! prepend each message with the number of bytes it occupies, in //! variable protobuf format. The first message in a file //! one is of type output::Header and should contain all sorts of //! meta information, maybe even configuration of the mapper that was //! used to create it (an option would be to include the full set of //! policies). Subsequent messages are of type output::Result. //! //! \note The output file is essentially a single, giant protobuf message. //! However, it is impossible to read it in one go (due to memory //! constraints), but it's also impossible to read it through a single //! CodedInputStream. That's why methods in here tend to construct and //! destruct a fresh CodedInputStream on each invocation. //! //! @{ template< typename Msg > void write_delimited_message( google::protobuf::io::CodedOutputStream& os, int tag, const Msg& m ) { os.WriteTag( mk_msg_tag( tag ) ) ; os.WriteVarint32( m.ByteSize() ) ; if( !m.SerializeToCodedStream( &os ) ) { string s ; google::protobuf::TextFormat::PrintToString( m, &s ) ; cerr << s ; throw "error while serializing: " ; } } template< typename Msg > void write_delimited_message( google::protobuf::io::ZeroCopyOutputStream *os, int tag, const Msg& m ) { google::protobuf::io::CodedOutputStream o( os ) ; write_delimited_message( o, tag, m ) ; } template< typename Msg > bool read_delimited_message( google::protobuf::io::CodedInputStream& is, Msg &m ) { uint32_t size ; std::string code ; if( !is.ReadVarint32( &size ) ) return false ; int lim = is.PushLimit( size ) ; if( !m.ParseFromCodedStream( &is ) ) throw "error while deserializing" ; is.PopLimit( lim ) ; return true ; } void sanitize( Header& ) ; void sanitize( Result& ) ; void merge_sensibly( output::Header& lhs, const output::Header& rhs ) ; void merge_sensibly( output::Footer& lhs, const output::Footer& rhs ) ; void merge_sensibly( output::Result& lhs, const output::Result& rhs ) ; //! \brief returns the hit to some genome //! If an empty genome is asked for, returns the best hit. Behaviour is //! undefined if no suitable hit exists. const output::Hit* hit_to( const output::Result& ) ; const output::Hit* hit_to( const output::Result&, const string& ) ; inline const output::Hit* hit_to( const output::Result& r, const char* g ) { return g ? hit_to( r ) : hit_to( r, string(g) ) ; } template< typename I > const output::Hit* hit_to( const output::Result& r, I begin, I end ) { for( ; begin != end ; ++begin ) if( const output::Hit* h = hit_to( r, *begin ) ) return h ; return 0 ; } //! \brief returns the mutable hit to some genome //! If an empty genome is asked for, returns the best hit. If no //! suitable hit exists, a new one is created. output::Hit* mutable_hit_to( output::Result* ) ; output::Hit* mutable_hit_to( output::Result*, const string& ) ; //! \brief computes (trimmed) query length from CIGAR line template< typename C > unsigned len_from_bin_cigar( const C& cig ) { unsigned l = 0 ; for( typename C::const_iterator i = cig.begin(), e = cig.end() ; i != e ; ++i ) { switch( cigar_op( *i ) ) { case output::Hit::Match: case output::Hit::Mismatch: case output::Hit::Insert: case output::Hit::SoftClip: l += cigar_len( *i ) ; break ; case output::Hit::Delete: case output::Hit::Skip: case output::Hit::HardClip: case output::Hit::Pad: break ; } } return l ; } inline output::Hit::Operation cigar_op( uint32_t c ) { return (output::Hit::Operation)(c & 0xf) ; } inline uint32_t cigar_len( uint32_t c ) { return c >> 4 ; } inline uint32_t mk_cigar( output::Hit::Operation op, uint32_t len ) { return len << 4 | op ; } inline void push_op( std::vector& s, unsigned m, output::Hit::Operation op ) { if( m && !s.empty() && (streams::cigar_op( s.back() ) == op) && streams::cigar_len( s.back() ) ) s.back() = streams::mk_cigar( op, m + streams::cigar_len( s.back() ) ) ; else if( m ) s.push_back( streams::mk_cigar( op, m ) ) ; } inline void push_m( std::vector& s, unsigned m ) { push_op( s, m, output::Hit::Match ) ; } inline void push_M( std::vector& s, unsigned m ) { push_op( s, m, output::Hit::Mismatch ) ; } inline void push_i( std::vector& s, unsigned i ) { push_op( s, i, output::Hit::Insert ) ; } inline void push_d( std::vector& s, unsigned d ) { push_op( s, d, output::Hit::Delete ) ; } inline int effective_length( const Read& rd ) { return (rd.has_trim_right() ? rd.trim_right() : rd.sequence().length()) - rd.trim_left() ; } //! @} //! \brief stream of result messages //! Each stream is a header, followed by many results, followed by a //! single footer. The header will be cached internally, so it can be //! asked for repeatedly. Results are forgotten once read, the footer //! is only available after all results have been read, and then it is //! stored and can be read repeatedly. //! //! This class is both an input stream, an output stream and a stream //! transducer. Concrete implementations decide what sets of methods to //! actually implement. Streams behave as state machine, cycling //! between need_input, have_output and end_of_stream. It's undefined //! behaviour to call methods in states where they don't make sense. class Stream { public: int refcount_ ; enum state { invalid, end_of_stream, need_input, have_output } ; static void cleanup( Stream* p ) { delete p ; } protected: // internal state---not strictly necessary here, but used almost // everywhere and therefore simply convenient Header hdr_ ; Result res_ ; Footer foot_ ; state state_ ; virtual ~Stream() {} // want control over instantiation private: Stream( const Stream& ) ; // must not copy void operator = ( const Stream& ) ; // must not copy public: Stream() : refcount_(0), state_( end_of_stream ) {} //! \brief returns stream state //! The state determines which methods may be called: get_header //! can be called unless the satet is \c invalid, get_result can //! be called in state have_output, put_result only in //! need_input, get_footer only in end_of_stream. put_footer //! can only be called in need_input and it will signal the end //! of the input stream (if there is such a thing). put_header //! can only be called in state invalid, it may change the state //! to either need_input or have_output. Particular streams may //! need special initialization before the state bacomes //! something other than invalid. virtual state get_state() { return state_ ; } //! \brief returns the header //! The header can be requested any time, unless the stream is //! in the invalid state. virtual Header fetch_header() { return hdr_ ; } //! \brief reads the next result //! Every result can only be read once, internal iterator style. //! If the stream state is have_output, this method returns the //! next result. Otherwise the behavior is undefined. virtual Result fetch_result() { state_ = need_input ; return res_ ; } //! \brief returns the footer //! Only after all results have been consumed is the footer //! available. If anything goes wrong internally, the LSB //! should be set in \c exit_code. virtual Footer fetch_footer() { return foot_ ; } //! \brief sets the stream header //! Output streams and stream filters need the header to become //! valid streams. virtual void put_header( const Header& h ) { hdr_ = h ; state_ = need_input ; } //! \brief outputs one result //! This method can only be called in state need_input, and it //! will insert a result record into the stream. Else the //! behaviour is undefined. virtual void put_result( const Result& r ) { res_ = r ; state_ = have_output ; } //! \brief sets the footer //! This method can only be called in state need_input, and it //! signals that no more input is available. A filter will then //! flush internal buffers and signal end_of_stream. virtual void put_footer( const Footer& f ) { foot_ = f ; state_ = end_of_stream ; } //! \brief get the 'summary' of having processed this stream //! This functionality is dependent on Elk being present: since //! the meaning of what the 'summary' is differs from stream to //! stream, the result is simply an Elk object. The default is //! to return the exit code contained in the footer. virtual Object get_summary() const { return False ; } //! \brief some debugging info virtual string type_name() const { return "Stream" ; } protected: // doesn't belong here, but it's convenient void read_next_message( google::protobuf::io::CodedInputStream&, const std::string& ) ; } ; typedef ::Holder StreamHolder ; int transfer( Stream& in, Stream& out ) ; //! \brief base class of streams that read from many streams class StreamBundle : public Stream { protected: std::deque< StreamHolder > streams_ ; typedef std::deque< StreamHolder >::const_iterator citer ; typedef std::deque< StreamHolder >::const_reverse_iterator criter ; public: void add_stream( StreamHolder s ) { streams_.push_back( s ) ; } } ; struct ParseError : public Exception { std::string msg_ ; ParseError( const std::string& m ) : msg_(m) {} virtual void print_to( std::ostream& s ) const { s << "AnfoReader: " << msg_ ; } } ; //! \brief presents ANFO files as series of messages //! This class will read a stream of results formatted as a continuous //! protobuf message. class AnfoReader : public Stream { private: std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; std::string name_ ; public: AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; virtual Result fetch_result() ; //! \internal virtual string type_name() const { return "AnfoReader(" + name_ + ")" ; } } ; // \brief reader for all supported formats // Here we take care not to open files before the header is requested. // This is necessary to allow merging thousands of files without // directly running into a filedescriptor limit. // To this end, the UniversalReader can be initialized with or without a // stream object. If the stream exists, we take care not to read from // it until the header is needed, and the name given serves just for // informational purposes. If no stream exists, we create a // FileInputStream from the name (which must be a filename, obviously) // when the header is requested. At this point we also inspect the // stream to determine its format and create the appropriate filters to // decode it. class UniversalReader : public Stream { private: std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; std::string name_ ; StreamHolder str_ ; bool solexa_scores_ ; int origin_ ; string genome_ ; public: UniversalReader( const std::string& name, google::protobuf::io::ZeroCopyInputStream* is = 0, bool solexa_scores = false, int origin = 33, const string& genome = "" ) ; virtual state get_state() { return str_ ? str_->get_state() : invalid ; } virtual Header fetch_header() ; virtual Result fetch_result() { if( get_state() == have_output ) return str_->fetch_result() ; throw "calling sequence violated" ; } virtual Footer fetch_footer() { return str_->fetch_footer() ; } virtual string type_name() const { return "UniversalReader(" + name_ + ")" ; } } ; //! \brief new blocked native format //! Writes in a format that can be read by stream::ChunkedReader. The //! file is made up of individually compressed blocks so that //! near-random access is possible... in principle. class ChunkedWriter : public Stream { public: // sensible buffer size: big enough to make compression worthwhile, // small enough that BZip won't split it again enum { default_buffer_size = 850000 } ; // supported compression methods enum method { none, fastlz, gzip, bzip } ; private: std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output std::vector< char > buf_ ; // in-memory buffer std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer Chan chan_ ; std::string name_ ; int64_t wrote_ ; uint8_t method_, level_ ; void flush_buffer( unsigned needed = 0 ) ; void init() ; public: static uint8_t method_of( int ) ; static uint8_t level_of( int ) ; ChunkedWriter( const pair< google::protobuf::io::ZeroCopyOutputStream*, string >&, int ) ; ChunkedWriter( int fd, int, const char* = "" ) ; ChunkedWriter( const char* fname, int ) ; virtual ~ChunkedWriter() ; virtual void put_header( const Header& h ) ; virtual void put_result( const Result& r ) ; virtual void put_footer( const Footer& f ) ; virtual string type_name() const { return "ChunkedWriter(" + name_ + ")" ; } } ; class ChunkedReader : public Stream { private: std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; std::vector< char > buf_ ; // in-memory buffer std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer std::string name_ ; bool get_next_chunk() ; public: ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; virtual Result fetch_result() ; //! \internal virtual string type_name() const { return "ChunkedReader(" + name_ + ")" ; } } ; //! \brief filters that drop or modify isolated records //! Think "mapMaybe". //! \todo Maybe some stats could be gathered into some sort of a result. class Filter : public Stream { public: virtual bool xform( Result& ) = 0 ; virtual void put_result( const Result& res ) { res_ = res ; if( xform( res_ ) ) state_ = have_output ; } } ; //! \brief filters that drop some alignments //! Filtering only applies to hits to the specified genome(s), or to all //! hits if no genomes are specified. Other hits pass through. //! \todo Maybe some stats could be gathered into some sort of a result. class HitFilter : public Stream { private: vector gs_ ; public: HitFilter() {} HitFilter( const vector &gs ) : gs_(gs) {} virtual void put_header( const Header& h ) { Stream::put_header( h ) ; hdr_.clear_is_sorted_by_coordinate() ; hdr_.clear_is_sorted_by_all_genomes() ; } virtual bool keep( const Hit& ) = 0 ; virtual void put_result( const Result& res ) ; } ; namespace { template < typename C, typename V > bool contains( const C& c, const V& v ) { return find( c.begin(), c.end(), v ) != c.end() ; } } //! \brief deletes some alignments //! A list of sequences and a list of genomes can be given. An //! alignment is deleted if a) the list of genomes is empty or the hit //! genome is a member of that list and b) the list of sequences is //! empty or the hit sequence is a member of that list. class IgnoreHit : public HitFilter { private: vector< string > ss_ ; public: IgnoreHit( const vector< string > &gs, const vector< string > &ss ) : HitFilter( gs ), ss_( ss ) {} virtual bool keep( const Hit& h ) { return !ss_.empty() && !contains( ss_, h.sequence() ) ; } } ; //! \brief deletes hits to uninteresting genomes //! Hits to the specified genomes pass through, all others are dropped. class OnlyGenome : public Filter { private: vector< string > gs_ ; public: OnlyGenome( const vector< string > &gs ) : Filter(), gs_( gs ) {} virtual bool xform( Result& r ) ; } ; //! \brief stream that filters for a given score //! Alignments that exceed the score are deleted, but the sequences are //! kept. If genomes are given, only alignments to that genome are //! tested and removed, else all are considered individually and //! selectively removed. If no alignments remains, \c reason is set to //! \c bad_alignment. Most interesting downstream operations will //! ignore sequences without alignments. Scores are in Phred scale now, //! experience tells that a typical butoff between good alignments and //! junk is \f$ 7.5 \cdot ( \mbox{length} - 20 ) \f$ class ScoreFilter : public HitFilter { private: double slope_ ; double intercept_ ; public: ScoreFilter( double s, double i, const vector &gs ) : HitFilter(gs), slope_(s), intercept_(i) {} virtual bool keep( const Hit& ) ; } ; class TotalScoreFilter : public Filter { private: double slope_ ; double intercept_ ; vector< string > gs_ ; public: TotalScoreFilter( double s, double i, const vector &gs ) : slope_(s), intercept_(i), gs_(gs) {} virtual bool xform( Result& ) ; } ; //! \brief stream that filters for minimum mapping quality //! All alignments of sequences where the difference to the next hit is //! too low are deleted. Filtering can be restricted to some genomes. //! The sequence itself is always kept. class MapqFilter : public HitFilter { private: int minmapq_ ; ; public: MapqFilter( const vector &gs, int q ) : HitFilter(gs), minmapq_(q) {} virtual bool keep( const Hit& ) ; } ; //! \brief filter for some average quality class QualFilter : public Filter { private: double minqual_ ; ; public: QualFilter( double q ) : minqual_(q) {} virtual bool xform( Result& ) ; } ; //! \brief stream that filters for minimum sequence length //! All alignments of sequences that are too short are deleted, relying //! on down stream filters to completely get rid of the sequences //! themselves. class LengthFilter : public Filter { private: int minlength_, maxlength_ ; public: LengthFilter( int l = 0, int h = std::numeric_limits::max() ) : minlength_(l), maxlength_(h) {} virtual bool xform( Result& ) ; } ; class GcFilter : public Filter { private: int mingc_, maxgc_ ; public: GcFilter( int l = 0, int h = 100 ) : mingc_(l), maxgc_(h) {} virtual bool xform( Result& ) ; } ; //! \brief a stream that removes sequences without a specific hit //! This is intended to shrink a file by removing junk that didn't //! align at all. class RequireHit : public Filter { private: vector< string > gs_, ss_ ; public: RequireHit( const vector &gs, const vector &ss ) : gs_(gs), ss_(ss) {} virtual bool xform( Result& ) ; } ; //! \brief a stream that removes sequences without a specific best hit //! This is intended to shrink a file by removing junk that didn't //! align to the expected genome. class RequireBestHit : public Filter { private: vector< string > gs_, ss_ ; public: RequireBestHit( const vector &gs, const vector &ss ) : gs_(gs), ss_(ss) {} virtual bool xform( Result& ) ; } ; class Subsample : public Filter { private: const float f_ ; public: Subsample( float f ) : f_(f) {} virtual bool xform( Result& ) ; } ; //! \brief filters for minimum multiplicity //! Only results that stem from duplicate removal with a minimum //! multiplicity are retained. Intended for the analysis of libraries //! sequenced with high redundancy to lower sequencing error. class MultiFilter : public Filter { private: unsigned n_ ; public: MultiFilter( unsigned n ) : n_(n) {} virtual bool xform( Result& r ) { return r.members_size() + r.nmembers() >= n_ ; } } ; //! \brief stream that filters out low quality bases //! Bases with insufficient quality are replaced by N symbols. //! (Originally I used gap symbols, which doesn't make sense and //! actually confused the legacy tool downstream. Ns should be fine and //! are actually the correct symbol in a certain sense.) //! This suppresses the counting of low quality bases in whatever //! follows downstream. class QualMasker : public Filter { private: int q_ ; public: QualMasker( int q ) : q_(q) {} virtual bool xform( Result& ) ; } ; /*! \brief stream with PCR duplicates removed A set of duplicates is (more or less by definition) a set of reads that map to the same position. Any set of duplicates is merged (retaining the original reads in an auxilliary structure), and a consensus is called with new quality scores. A quality score (for base A) is defined as \f[ Q := -10 \log_{10} P( \bar{A} | \omega ), \f] that is, a representation of the probability of the base being wrong given some observation \f$ \omega. \f$ It follows that \f[ Q = -10 \log_{10} \frac{ P(\omega|\bar{A}) P(\bar{A}) }{ P(\omega) } = -10 \log_{10} P( \omega | \bar{A} ) \f] by assuming a uniform base composition in the sample (\f$ P(A)=\frac{1}{4} \f$) and after base calling (\f$ P(\omega)=\frac{1}{4} \f$). When combining observations \f$ \omega_1, \ldots, \omega_n \f$ conditional on the same base, they are all independent, hence the probabilities conditioned on the actual base can be multiplied. To get the final quality when calling an A: \f[ P(A|\bigcap_n \omega_n) = \frac{ P(\bigcap_n \omega_n | A) P(A) }{ P(\bigcap_n \omega_n) } = \frac{ P(A) \prod_n P(\omega_n | A) }{ P(\bigcap_n \omega_n) } \f] The unconditional probabilities in the denominator are not independent (for they collectively depend on the true base), we have to replace them by total probabilites: \f[ = \frac{ P(A) \prod_n P(\omega_n | A) }{ \sum_N P(\bigcap_n \omega_n | N) P(N) } \f] Again, assuming a uniform base composition, the priors are all equal and cancel, and now the conditional probabilities are again independent. \f[ = \frac{ \prod_n P(\omega_n | A) }{ \sum_N \prod_n P(\omega_n | N) } \f] Tracking this incrementally is easy, we need to store the four products. Computation needs to be done in the log domain to avoid loss of precision. Likewise, computation of a quality must not involve \f$ P(A|\omega) \f$, since that is too close to one to be representable, so we calculate the quality as \f[ Q := -10 \log_{10} P( \bar{A} | \omega ) = -10 \log_{10} ( P(C | \omega ) + P(G | \omega ) + P(T | \omega ) ) \f] What remains is how to get an estimate of \f$ P(\omega | N) \f$. We easily get \f$ P(\omega | A) \f$ (see above), which will normally be very close to one, and the sum of the other three. To estimate the summands, we set \f[ P(\omega|N) = \frac{P(N|\omega) * P(\omega)}{P(N)} = P(N|\omega) = P(N|\bar{A}) * P(\bar{A}|\omega) \f] and estimate \f$ P(N|\bar{A}) \f$ from misclassfication statistics of the base caller. */ class RmdupStream : public Stream { private: output::Result cur_ ; std::vector< Logdom > quals_[4] ; double slope_ ; double intercept_ ; vector gs_ ; int maxq_ ; bool have_foot_ ; // XXX double err_prob_[4][4] ; // get this from config or // something? bool is_duplicate( const Result& , const Result& ) const ; void add_read( const Result& ) ; void call_consensus() ; bool good_score( const Hit* ) const ; public: //! \brief sets parameters //! \param s Slope of score function, bad alignments are disregarded. //! \param i Intercept of score function. //! \param q (Assumed) quality of the polymerase. RmdupStream( double s, double i, int q ) : slope_(s), intercept_(i), maxq_( std::min(q,127) ), have_foot_(false) {} virtual void put_header( const Header& h ) { if( !h.has_is_sorted_by_all_genomes() && !h.is_sorted_by_coordinate_size() ) throw "RmdupStream: need sorted stream to remove duplicates" ; gs_.assign( h.is_sorted_by_coordinate().begin(), h.is_sorted_by_coordinate().end() ) ; Stream::put_header( h ) ; } virtual void put_result( const Result& ) ; virtual void put_footer( const Footer& ) ; virtual Result fetch_result() ; } ; //! \brief a stream that concatenates its input streams //! The headers and footers are merged sensibly (plain merge with removal of //! redundant information), then the results are simply concatenated. class ConcatStream : public StreamBundle { public: virtual Header fetch_header() ; virtual Result fetch_result() ; } ; class FastqReader : public Stream { private: std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; bool sol_scores_ ; char origin_ ; void read_next_message() { if( read_fastq( is_.get(), *res_.mutable_read(), sol_scores_, origin_ ) ) { state_ = have_output ; sanitize( res_ ) ; } else { state_ = end_of_stream ; is_.reset( 0 ) ; } } public: FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : is_( is ), sol_scores_(solexa_scores), origin_(origin) { read_next_message() ; } virtual Result fetch_result() { Result r ; std::swap( r, res_ ) ; read_next_message() ; return r ; } virtual string type_name() const { return "FastqReader" ; } } ; class SamReader : public Stream { private: std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; string name_, genome_ ; Chan progress_ ; int nmsg_ ; void read_next_message() { if( read_sam( is_.get(), genome_, res_ ) ) { state_ = have_output ; sanitize( res_ ) ; if( (++nmsg_ & 0xffff) == 0 ) { stringstream ss ; ss << name_ << ": " << nmsg_ << " records" ; progress_( Console::info, ss.str() ) ; } } else { state_ = end_of_stream ; is_.reset( 0 ) ; progress_.close() ; foot_.set_exit_code( 0 ) ; } } public: SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : is_( is ), name_( n ), genome_( g ), nmsg_(0) { read_next_message() ; } virtual Header fetch_header() { hdr_.add_is_sorted_by_coordinate( "" ) ; return Stream::fetch_header() ; } virtual Result fetch_result() { Result r ; std::swap( r, res_ ) ; read_next_message() ; return r ; } virtual string type_name() const { return "SamReader" ; } } ; class SffReader : public Stream { private: std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; string name_ ; unsigned remaining_ ; unsigned number_of_flows_ ; const void* buf_ ; int buf_size_ ; uint8_t read_uint8() ; uint16_t read_uint16() ; uint32_t read_uint32() ; void read_string( unsigned, string* ) ; void skip( int ) ; public: SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : is_( is ), name_( name ), buf_(0), buf_size_(0) {} virtual Header fetch_header() ; virtual Result fetch_result() ; virtual string type_name() const { return "SffReader(" + name_ + ")" ; } } ; class BamReader : public Stream { private: std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; string name_ ; string genome_ ; vector< string > refseqs_ ; const void* buf_ ; int buf_size_ ; uint8_t read_uint8() ; uint16_t read_uint16() ; uint32_t read_uint32() ; void read_string( unsigned, string* ) ; public: BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; virtual Result fetch_result() ; virtual string type_name() const { return "BamReader(" + name_ + ")" ; } } ; } // namespace streams class PipeInputStream : public google::protobuf::io::FileInputStream { private: pid_t cpid_ ; public: PipeInputStream( int fd, pid_t cpid ) : google::protobuf::io::FileInputStream( fd ), cpid_( cpid ) {} virtual ~PipeInputStream() { Close() ; throw_errno_if_minus1( waitpid( cpid_, 0, 0 ), "waiting for pipe process" ) ; } } ; std::pair< PipeInputStream*, std::string > make_PipeInputStream( const std::string& ) ; class PipeOutputStream : public google::protobuf::io::FileOutputStream { private: pid_t cpid_ ; public: PipeOutputStream( int fd, pid_t cpid ) : google::protobuf::io::FileOutputStream( fd ), cpid_( cpid ) {} virtual ~PipeOutputStream() { Close() ; throw_errno_if_minus1( waitpid( cpid_, 0, 0 ), "waiting for pipe process" ) ; } } ; std::pair< PipeOutputStream*, std::string > make_PipeOutputStream( const std::string& ) ; //! \brief adapts a ZeroCopyOutputStream into a streambuf class zero_copy_output_buf : public std::streambuf { private: std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; public: zero_copy_output_buf( google::protobuf::io::ZeroCopyOutputStream* os ) : os_(os) {} virtual ~zero_copy_output_buf() ; virtual int sync() ; virtual int_type overflow( int_type ) ; } ; class zero_copy_ostream : public std::ostream { private: zero_copy_output_buf b_ ; public: zero_copy_ostream( google::protobuf::io::ZeroCopyOutputStream* os ) : std::ostream( &b_ ), b_( os ) {} } ; #endif anfo-0.98/src/trim.h0000644000371600007640000001225411447113465011253 00000000000000// Copyright 2009 Udo Stenzel // This file is part of ANFO // // ANFO is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // Anfo is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with Anfo. If not, see . #ifndef INCLUDED_TRIM_H #define INCLUDED_TRIM_H #include #include #include "sequence.h" namespace { template< typename T > T max3( T a, T b, T c ) { return std::max( std::max( a, b ), c ) ; } } inline bool match( char a, char b ) { return to_ambicode(a) & to_ambicode(b) ; } inline bool match( Ambicode a, char b ) { return a & to_ambicode(b) ; } inline bool match( char a, Ambicode b ) { return to_ambicode(a) & b ; } inline bool match( Ambicode a, Ambicode b ) { return a & b ; } inline bool match( const QSequence::Base &a, char b ) { return a.ambicode & to_ambicode(b) ; } inline bool match( char a, const QSequence::Base &b ) { return to_ambicode(a) & b.ambicode ; } /*! \brief aligns two sequences to find an adapter sequence. The alignment algorithm following Eugene W. Myers: "An O(ND) Difference Algorithm and Its Variations", adapted to 'overlap alignment'. We want to align two sequences so they overlap with maximum score. This is not possible with the plain "minimum distance" method, since no overlap always results in the minimum distance of zero. We do need to score the overlapping part, but not the same as an ordinary difference. Now suppose you have an alignment: xxxxxx-- --yyyyzz It scores (k * mat/2 - d * (mat-mis)), where k is |x|+|y| (see the megablast paper by Zhang for an explanation; we stop keeping score once we reach the end of x). Suppose x is longer: xxxxxxx-- ---yyyyzzz This scores ((k+1) * mat/2 - (d+D) * (mat-mis)), and we want to set D such that this is the same as before. This gives: D = 1/2 * mat / (mat-mis) and for typical parameters mat=1 and mis=-3 it equals D=1/8. Therefore, end gaps should score 1/8 (but not for local alignments (not implemented here), where only an X-drop algorithm would be appropriate). To implement this, the following changes to the original algorithm are necessary: - allow a start gap that grows 8x quicker than a normal gap, consider the many more involved diagonals, - once finished, prefer alignments on lower numbered diagonals. This function will try to overlap the left end of sequence A (query sequence) with the right end of sequence B (adapter sequence). (Typical adapter trimming therefore requires the sequences to be passed in in reverse.) It returns the score of the resulting alignment, which will be positive, or -1 if the alignment would be too bad. The number of characters in sequence A that are overlapped is returned in *yout. \param seq_a iterator to beginning of sequence A. \param seq_a_end iterator to end of sequence A. \param seq_b iterator to beginning of sequence B. \param seq_b_end iterator to end of sequence B. \param yout pointer to location where number of trimmed chars is stores. \return alignment score. */ template< typename A, typename B > int overlap_align( A seq_a, A seq_a_end, B seq_b, B seq_b_end, int*yout ) { static const int discount = 8 ; using namespace std ; int len_a = seq_a_end - seq_a ; int len_b = seq_b_end - seq_b ; int maxd = 2 * len_b / discount ; // makes sure that score>=0 int dim = discount*maxd + discount-1 ; vector v_d( dim+maxd+1 ), v_dm1( dim+maxd+1 ) ; // v[d] & v[d-1] for( int d = 0 ; d != maxd ; ++d, swap( v_d, v_dm1 ) ) { // D-paths in order of increasing D int dm = discount*d + discount-1 ; for( int k = -d ; k <= dm ; ++k ) { // diagonals int x = 0 == d ? k : 1 == d && 0 == k ? v_dm1[ k +maxd ]+1 : k == -d ? v_dm1[ k+1 +maxd ] : k > dm-discount+1 ? k : k == -d+1 ? max( v_dm1[ k +maxd ]+1, v_dm1[ k+1 +maxd ] ) : k == dm-discount+1 ? max( v_dm1[ k-1 +maxd ]+1, k ) : k == dm-discount ? max3( v_dm1[ k-1 +maxd ]+1, v_dm1[ k +maxd ]+1, k ) : max3( v_dm1[ k-1 +maxd ]+1, v_dm1[ k +maxd ]+1, v_dm1[ k+1 +maxd ] ) ; int y = x - k ; while( x < len_b && y < len_a && match( seq_b[x], seq_a[y] ) ) ++x, ++y ; v_d[ k +maxd ] = x ; if( x == len_b ) { *yout = y ; return x + y - discount * d ; // computes score. } } } return -1 ; } #endif anfo-0.98/src/util.h0000644000371600007640000002240011447113464011246 00000000000000// Copyright 2009 Udo Stenzel // This file is part of ANFO // // ANFO is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // Anfo is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with Anfo. If not, see . #ifndef INCLUDED_UTIL_H #define INCLUDED_UTIL_H #include #include #include #include #include #include #include #include #include #include #include struct Exception { virtual void print_to( std::ostream& ) const = 0 ; virtual ~Exception() {} } ; inline std::ostream& operator << ( std::ostream& s, const Exception& e ) { e.print_to( s ) ; return s ; } inline void throw_errno( const char* a, const char* b = 0 ) { std::string msg ; msg.append( strerror( errno ) ).append( " while " ).append( a ) ; if( b ) msg.append( " " ).append( b ) ; throw msg ; } template< typename T > T throw_errno_if_minus1( T x, const char* a, const char* b = 0 ) { return throw_errno_if_eq( x, (T)(-1), a, b ) ; } template< typename T > T throw_errno_if_null( T x, const char* a, const char* b = 0 ) { return throw_errno_if_eq( x, (T)0, a, b ) ; } template< typename T > T throw_errno_if_eq( T x, T y, const char* a, const char* b = 0 ) { if( x == y ) throw_errno( a, b ) ; return x ; } template< typename T > T throw_if_negative( T x, const char* a, const char* b = 0 ) { if( x < 0 ) { std::stringstream msg ; msg << x << " while " << a ; if( b ) msg << ' '<< b ; throw msg.str() ; } return x ; } template< typename T > T throw_if_not_null( T x, const char* a, const char* b = 0 ) { if( x != 0 ) { std::stringstream msg ; msg << x << " while " << a ; if( b ) msg << ' '<< b ; throw msg.str() ; } return x ; } inline void throw_strerror_if_not_null( int x, const char* a, const char* b = 0 ) { if( x != 0 ) { std::stringstream msg ; msg << strerror( x ) << " while " << a ; if( b ) msg << ' '<< b ; throw msg.str() ; } } //! \brief near drop-in for write(2) //! Would you believe it, write(2) sometimes decides to write less than //! what was requested. No idea why, but a loop around it solves it. inline void mywrite( int fd, const void* buf, size_t count, const char* msg = 0 ) { while( count > 0 ) { ssize_t w = write( fd, buf, count ) ; if( w == -1 && errno == EINTR ) w = 0 ; throw_errno_if_minus1( w, "writing", msg ) ; count -= w ; buf = (const char*)buf + w ; } } //! \brief near drop-in for read(2) inline void myread( int fd, void* buf, size_t count, const char* msg = 0 ) { while( count > 0 ) { ssize_t w = read( fd, buf, count ) ; if( w == -1 && errno == EINTR ) w = 0 ; throw_errno_if_minus1( w, "reading", msg ) ; count -= w ; buf = (char*)buf + w ; } } namespace { inline int open1( const std::string& s ) { int fd = open( s.c_str(), O_RDONLY ) ; if( errno != ENOENT ) throw_errno_if_minus1( fd, "opening", s.c_str() ) ; return fd ; } inline int open2( const std::string& s, const std::string& ext ) { int fd = open1( s ) ; if( fd == -1 ) fd = open1( s + "." + ext ) ; return fd ; } } ; //! \brief searches a file in the path, opens it for reading //! This is equivalent to calling open( name, O_RDONLY ), but if the //! file is not there, it additionally tried to find it with an //! extension, then a supplied environmenmt variable is followed, then //! an explicit list of paths. //! //! \param name name of the file //! \param ext optional extension (without the dot) //! \param env_var optional name of environment variable in same format //! as PATH //! \return opened file descriptor inline int path_open( const std::string& name, const std::string& ext, const char *env_var ) { int fd = open2( name, ext ) ; if( env_var ) { if( const char *p = getenv(env_var) ) { if( fd == -1 && *p ) { std::string path = p ; size_t end, start = 0 ; for( ; fd == -1 && (end = path.find( ':', start )) != std::string::npos ; start = end+1 ) fd = open2( path.substr( start, end-start ) + "/" + name, ext ) ; if( fd == -1 ) fd = open2( path.substr( start ) + "/" + name, ext ) ; } } } return throw_errno_if_minus1( fd, "opening", name.c_str() ) ; } template< typename T > struct delete_ptr { void operator()( T* p ) const { delete p ; } } ; int wrap_main( int argc, const char * argv[], int(*)(int,const char*[]) ) ; #define WRAPPED_MAIN \ int main_(int,const char*[]) ; \ int main(int argc, const char* argv[]) { return wrap_main( argc, argv, main_ ) ; } \ int main_(int argc, const char* argv[]) /*! \brief tries to set proc title for ps * * This is borderline malpractice: since Linux is missing the * appropriate API, we directly overwrite argv[0]. This \e will trash * argv, so don't try to access that after setting a title, and this \e * may trash other things, should my assumption that argv is terminated * by "\0\0" turn out wrong. * * Ignoring the above, it is quite helpful, though... * \param title new program title to be displayed */ void set_proc_title( const char *title ) ; //! \brief global flag to signal shutdown //! Some long running algoritms will periodically check this variable //! and abort cleanly if it is not null. Use this to cause an early //! shutdown, e.g. on reception of a signal. extern volatile int exit_with ; enum PacketTag { packet_config, packet_read, packet_result, packet_quit } ; //! \brief creates a temporary file //! The name is constructed from a directory taken from the environment //! variables \c ANFO_TEMP, \c TMPDIR, \c TEMP, or \c TMP, whichever //! first one is set, and a unique file name. The file is opened and //! then unlinked, and both the name and the file descriptor are //! returned. Note that the name can only serve informational purposes, //! since it's already gone by the time this function returns. //! \param name contains the file name on return //! \return the file descriptor int mktempfile( std::string* name = 0 ) ; //! \brief here we send progress notification and log information //! Output goes to the controlling terminal (/dev/tty) if possible, //! progress notifications are displayed in the last line and everything //! is updating sensibly. Might grow into a logging system, too. //! //! \todo This isn't thread safe and doesn't work well in a networked //! setting. Should be changed or replaced by something like //! log4cpp. class Console { public: enum Loglevel { debug, info, notice, warning, error, critical } ; Loglevel loglevel ; private: int fd_ ; int next_ ; typedef std::deque< std::pair< int, std::string > > Chans ; Chans chans_ ; public: Console() : loglevel(warning), fd_( open( "/dev/tty", O_WRONLY ) ), next_(0) {} ~Console() { if( fd_ >= 0 ) { if( !chans_.empty() ) { chans_.clear() ; update() ; } close( fd_ ) ; } } int alloc_chan() { return ++next_ ; } void free_chan( int c ) ; void progress( int c, Loglevel l, const std::string& s ) ; void update() ; void output( Loglevel, const std::string& ) ; void set_quiet() { loglevel = error ; } void more_verbose() { loglevel = loglevel > debug ? 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EDIT anfo.scm.in AND RUN MAKE INSTEAD!" > anfo.scm sed -e "s#__LIBDIR__#$(libdir)#g" < $(srcdir)/anfo.scm.in >> anfo.scm config.pb.cc: config.proto $(PROTOC) -I. -I$(dir $(PROTOC))../include --cpp_out=. config.proto output.pb.cc: output.proto $(PROTOC) -I. -I$(dir $(PROTOC))../include --cpp_out=. output.proto config.pb.h: config.pb.cc @: output.pb.h: output.pb.cc @: # Tell versions [3.59,3.63) of GNU make to not export all variables. # Otherwise a system limit (for SysV at least) may be exceeded. .NOEXPORT: anfo-0.98/src/align.cc0000644000371600007640000001453711447113464011535 00000000000000// Copyright 2009 Udo Stenzel // This file is part of ANFO // // ANFO is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // Anfo is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with Anfo. If not, see . #ifdef HAVE_CONFIG_H #include "../config.h" #endif #include "align.h" #include "config.pb.h" #include #include namespace { void print_subst_mat( std::ostream& s, const subst_mat mat ) { s << " r\\q " ; for( Ambicode qry = 1 ; qry != 16 ; ++qry ) { s << std::setw(2) << from_ambicode( qry ) << " " ; } for( Ambicode ref = 1 ; ref != 16 ; ++ref ) { s << "\n " << from_ambicode( ref ) << " " ; for( Ambicode qry = 1 ; qry != 16 ; ++qry ) { s << std::setw(2) << mat[ref][qry].to_phred() << " " ; } } s << '\n' ; } } //! \brief sets up aDNA alignments according to parameter set //! Penalties are logs of probabilities. We calculate a probability in //! a straightforward manner, then take the log, then multiply by (say) //! 10 and round to an integer (effectively shifting the base). //! Afterwards we could shift the score up so the minimum score is zero, //! but it will be zero to within accuracy anyway. Here we //! precalculate the penalties and log-transform them, however, the //! substitution matrices are left in the linear scale, because they //! need to be added later. //! //! For ambiguity codes, we sum over all the possible codes, divide by //! the number of possibilities, and later (when aligning) go to the log //! domain. Note that matches end up costing nothing (almost nothing, //! but accuracy isn't good enough to pick up on that), matching to an N //! *does* cost something, and matching a T to a C is dirt cheap while //! we believe we are in single stranded DNA. //! //! For gaps, we already have probabilities. Taking the log is all it //! takes to make scores from that. //! //! For the overhang, we want something that's easy to parameterize, and //! the single parameter will be the average overhang length. We assume //! there's an even chance that we have a 5' overhang (as opposed to a //! 3' overhang), and if we have a 5' overhang, it's length follows a //! geometric distribution with parameter p. //! //! The mean overhang length ends up being (1-p)/(2p), which is just //! half the mean of the geometric distribution. Solving for p derives //! the parameter from the configuration, but the code operates on \c //! p_comp, which is just 1-p. Entering an overhang involves a penalty //! (since the probability is only one half), but not entering it //! involves the same penalty. The difference in penalties is zero, //! which also means a perfect alignment stays at a zero score. //! //! The penalty for extending an overhang by one nucleotide is just the //! probability of it being longer. //! //! \param conf set of configuration parameters //! \param out if not NULL, receives a protocol of the calculated //! internal parameters adna_parblock::adna_parblock( const config::Aligner& conf ) { gap_ext_penalty = Logdom::from_float( conf.gap_extension_rate() ) ; gap_open_penalty = conf.has_gap_open_rate() ? Logdom::from_float( conf.gap_open_rate() ) : gap_ext_penalty ; if( conf.has_mean_overhang_length() ) { double p_comp = 1 - 1 / (2*conf.mean_overhang_length() + 1) ; overhang_enter_penalty = Logdom::one() ; overhang_ext_penalty = Logdom::from_float( p_comp ) ; } else { overhang_enter_penalty = Logdom::null() ; overhang_ext_penalty = Logdom::one() ; } double tv = conf.rate_of_transversions() ; double ts = conf.has_rate_of_transitions() ? conf.rate_of_transitions() : tv ; double dds = conf.rate_of_ds_deamination() ; double dss = conf.rate_of_ss_deamination() ; double r = 1-ts-tv-tv ; double prim_mat_ds[4][4] = { // to A C T G { r, tv, tv, ts }, // from A { tv, r-dds, ts+dds, tv }, // from C { tv, ts, r, tv }, // from T { ts+dds, tv, tv, r-dds } // from G } ; double prim_mat_ss[4][4] = { // to A C T G { r, tv, tv, ts }, // from A { tv, r-dss, ts+dss, tv }, // from C { tv, ts, r, tv }, // from T { ts+dss, tv, tv, r-dss } // from G } ; // filling the matrices // The entry for any ambiguity code is the sum of the entries in the // prim. matrices over all possible pairs of encoded nucleotides, // divided by the number of pairs, then converted to log domain. // (Yeah, it's inefficient. It also runs only once per invocation, // so sue me.) for( Ambicode ref = 1 ; ref != 16 ; ++ref ) { for( Ambicode qry = 1 ; qry != 16 ; ++qry ) { double p_ds = 0, p_ss = 0 ; int npairs = 0 ; for( int ref_n = 0 ; ref_n != 4 ; ++ref_n ) { for( int qry_n = 0 ; qry_n != 4 ; ++qry_n ) { if( (ref & (1<. #ifdef HAVE_CONFIG_H #include "../config.h" #endif #include "anfo_common.h" #include "stream.h" #include "trim.h" #include "config.pb.h" #include "output.pb.h" //! \todo We want an E-value... //! \todo We want more than just the best match. Think about a sensible //! way to configure this. //! \todo Test this: the canonical test case is homo sapiens, chr 21. using namespace config ; using namespace output ; using namespace std; namespace streams { //! \brief selects a policy appropriate for a given read //! This simply checks whether a read is within a given length bin and //! matches a name pattern, if given. All policies found this way are //! merged. Checking for too many Ns was considered, but isn't actually //! worthwhile since Ns don't contribute to seeds anyway. Policy select_policy( const Config &c, const Read &r ) { Policy p ; for( int i = 0 ; i != c.policy_size() ; ++i ) { const Policy &pi = c.policy(i) ; if( ( !pi.has_minlength() || pi.minlength() <= r.sequence().length() ) && ( !pi.has_maxlength() || pi.maxlength() >= r.sequence().length() ) && ( !pi.has_name_pattern() || 0 == fnmatch( pi.name_pattern().c_str(), r.seqid().c_str(), 0 ) ) ) p.MergeFrom( pi ) ; } return p ; } string effective_sequence( const Read& rd ) { return rd.sequence().substr( rd.trim_left(), rd.has_trim_right() ? rd.trim_right() - rd.trim_left(): std::string::npos ) ; } void trim_cigar_left( google::protobuf::RepeatedField &cig, unsigned len ) { for( int p = 0 ; p != cig.size() ; ++p ) { switch( cigar_op( cig.Get( p ) ) ) { case Hit::Match: case Hit::Mismatch: case Hit::Insert: case Hit::SoftClip: if( cigar_len( cig.Get( p ) ) > len ) { cig.Set( p, mk_cigar( cigar_op( cig.Get( p ) ), cigar_len( cig.Get( p ) ) - len ) ) ; // remove beginning and get out if( !p ) return ; int q = 0 ; while( p != cig.size() ) cig.Set( q++, cig.Get( p++ ) ) ; while( q != cig.size() ) cig.RemoveLast() ; return ; } else len -= cigar_len( cig.Get( p ) ) ; break ; case Hit::Delete: case Hit::Skip: case Hit::Pad: case Hit::HardClip: break ; } } // nothing left if we get here cig.Clear() ; } void trim_cigar_right( google::protobuf::RepeatedField &cig, unsigned len ) { for( int p = cig.size() ; p ; --p ) { switch( cigar_op( cig.Get( p-1 ) ) ) { case Hit::Match: case Hit::Mismatch: case Hit::Insert: case Hit::SoftClip: if( cigar_len( cig.Get( p-1 ) ) > len ) { cig.Set( p-1, mk_cigar( cigar_op( cig.Get( p-1 ) ), cigar_len( cig.Get( p-1 ) ) - len ) ) ; // remove beginning and get out while( p != cig.size() ) cig.RemoveLast() ; return ; } else len -= cigar_len( cig.Get( p-1 ) ) ; break ; case Hit::Delete: case Hit::Skip: case Hit::Pad: case Hit::HardClip: break ; } } // nothing left if we get here cig.Clear() ; } void Housekeeper::put_result( const Result& rs ) { Stream::put_result( rs ) ; // trim adapters, set trim points // How does this work? We create an overlap alignment, then // calculate an alignment score from the number of differences. The // formula equals a match score of 1 and a mismatch score of -3. // Gaps score (mat-mis)/2 to allow for the simple algorithm. If the // score is good enough, we trim. const output::Read &rd = res_.read() ; const string &seq = rd.sequence() ; unsigned r0 = rd.has_trim_right() ? rd.trim_right() : seq.length() ; unsigned l0 = rd.trim_left() ; unsigned r = r0, l = l0 ; // first step: always trim trailing Ns (often caused by 454 // failed quality trimming) while( r && ( seq[r-1] == 'n' || seq[r-1] == 'N') ) --r ; for( size_t i = 0 ; i != trim_right_.size() ; ++i ) { int ymax, score = overlap_align( seq.rbegin() + ( seq.length() - r ), seq.rend(), trim_right_[i].rbegin(), trim_right_[i].rend(), &ymax ) ; if( score >= minscore_ && ymax > 0 ) r -= ymax ; } for( size_t i = 0 ; i != trim_left_.size() ; ++i ) { int ymax, score = overlap_align( seq.begin() + l, seq.end(), trim_left_[i].begin(), trim_left_[i].end(), &ymax ) ; if( score >= minscore_ && ymax > 0 ) l += ymax ; } if( l > l0 ) { for( int i = 0 ; i != res_.hit_size() ; ++i ) trim_cigar_left( *res_.mutable_hit(i)->mutable_cigar(), l-l0 ) ; res_.mutable_read()->set_trim_right( l ) ; } if( r < r0 ) { for( int i = 0 ; i != res_.hit_size() ; ++i ) trim_cigar_right( *res_.mutable_hit(i)->mutable_cigar(), r-r0 ) ; res_.mutable_read()->set_trim_right( r ) ; } } Indexer::Indexer( const config::Config &config, const string& index_name ) : conf_( config ), index_name_( index_name ), index_( MetaIndex::add_ref( index_name ) ) { if( !conf_.policy_size() ) throw "no policies---nothing to do." ; } Indexer::~Indexer() { MetaIndex::free_ref( index_ ) ; } void Indexer::put_header( const Header& h ) { Stream::put_header( h ) ; hdr_.mutable_config()->mutable_policy()->MergeFrom( conf_.policy() ) ; } void Indexer::put_result( const Result& r ) { Stream::put_result( r ) ; Policy p = select_policy( conf_, res_.read() ) ; AlnStats *as = res_.add_aln_stats() ; as->set_tag( index_.metadata().genome_name() ) ; int num_raw = 0, num_clumps = 0, num_useless = 0 ; for( int i = 0 ; i != p.use_compact_index_size() ; ++i ) { const CompactIndexSpec &cis = p.use_compact_index(i) ; if( cis.name() == index_name_ || cis.name() + ".idx" == index_name_ ) { FixedIndex::LookupParams params ; params.cutoff = cis.has_cutoff() ? cis.cutoff() : numeric_limits::max() ; params.allow_mismatches = cis.allow_near_perfect() ; params.wordsize = cis.has_wordsize() ? cis.wordsize() : index_.metadata().wordsize() ; params.stride = cis.has_stride() ? cis.stride() : index_.metadata().stride() ; assert( params.wordsize <= index_.metadata().wordsize() ) ; assert( index_.metadata().stride() % params.stride == 0 ) ; Seeds *ss = 0 ; for( int i = 0 ; !ss && i != res_.seeds_size() ; ++i ) if( res_.seeds(i).genome_name() == index_.metadata().genome_name() ) ss = res_.mutable_seeds(i) ; if( !ss ) { ss = res_.add_seeds() ; ss->set_genome_name( index_.metadata().genome_name() ) ; ss->set_max_mismatches( p.max_mismatches_in_seed() ) ; ss->set_min_seed_length( p.min_seed_len() ) ; } PreSeeds seeds ; num_raw += index_.lookupS( effective_sequence( res_.read() ), seeds, params, &num_useless ) ; num_clumps += combine_seeds( seeds, p.min_seed_len(), ss ) ; if( p.has_repeat_threshold() && (unsigned)ss->ref_positions_size() >= p.repeat_threshold() ) { ss->clear_ref_positions() ; ss->clear_query_positions() ; as->set_reason( output::too_many_seeds ) ; } } } as->set_num_raw_seeds( num_raw ) ; as->set_num_useless( num_useless ) ; as->set_num_clumps( num_clumps ) ; } Mapper::Mapper( const config::Aligner &config, const string& genome_name ) : conf_(config), genome_( Metagenome::find_genome( genome_name ) ) { parblock_ = adna_parblock( conf_ ) ; } void Mapper::put_header( const Header& h ) { Stream::put_header( h ) ; hdr_.mutable_config()->mutable_aligner()->MergeFrom( conf_ ) ; } // Check for a stretch of at least minsize matches with up to mm // mismatches. The pointers should be clean: both point to the start of // a decently matching region of length seedlen. static bool check_seed_quality( DnaP ref, const QSequence::Base *qry, int seedlen, int mm, int minsize ) { int lengths[3] = { 0,0,0 } ; for( ; seedlen ; --seedlen, ++ref, ++qry ) { if( *ref == qry->ambicode ) { ++lengths[0] ; ++lengths[1] ; ++lengths[2] ; } else { lengths[2] = lengths[1] + 1 ; lengths[1] = lengths[0] + 1 ; lengths[0] = 0 ; } if( lengths[mm] == minsize ) return true ; } return false ; } //! \todo Calculate a real E-value, then h->set_evalue() appropriately. //! //! \todo Find second best hit and similar stuff. We want the distance //! to the best hit to another chromosome, maybe also the best hit //! to more genomes. When done, h->set_diff_to_next_species(), //! h->set_diff_to_next_order() //! //! \todo Actually implement search for multiple alignments in its full //! generality... Currently, we search multiple genomes, but //! completely independently of each other. //! //! \note We compute the current score limit (\f$ p_m \f$) from the number of seeds //! remaining (\f$ n \f$), the probability of the current best alignment //! (\f$ p_1 \f$), the total probability of all other known alignments //! (\f$ p_o \f$), and the maximum desired mapping quality (\f$ q \f$). //! We require //! \f[ \frac{np_m + p_o}{p_1 + n_p_m + p_o} < q \f] //! Rearranging and setting \f$ 1-q \approx 1 \f$ gives //! \f[ p_m < (q*p_1 - p_o) / n \f] void Mapper::put_result( const Result& r ) { Stream::put_result( r ) ; AlnStats *as = 0 ; for( int i = 0 ; i != res_.aln_stats_size() ; ++i ) { if( res_.aln_stats(i).tag() == genome_->name() ) as = res_.mutable_aln_stats(i) ; } if( !as ) { as = res_.add_aln_stats() ; as->set_tag( genome_->name() ) ; } Seeds ss ; for( int i = 0 ; i != res_.seeds_size() ; ++i ) { if( res_.seeds(i).genome_name() == genome_->name() ) { ss.Swap( res_.mutable_seeds(i) ) ; if( i != res_.seeds_size()-1 ) res_.mutable_seeds()->SwapElements( i, res_.seeds_size()-1 ) ; if( res_.seeds_size() > 1 ) res_.mutable_seeds()->RemoveLast() ; else res_.clear_seeds() ; break ; } } // is it already clear that we cannot do anything? if( as->has_reason() ) return ; // not seeded means no policy (or logic bug, but let's not go there...) if( ss.genome_name().empty() ) { as->set_reason( output::no_policy ) ; return ; } // invariant violated, we won't deal with that if( ss.ref_positions_size() != ss.query_positions_size() || ss.ref_positions_size() != ss.seed_sizes_size() ) throw "invalid seeds: coordinates must come in triples" ; if( !ss.ref_positions_size() ) { as->set_reason( as->num_useless() ? output::repeats_only : output::no_seeds ) ; return ; } QSequence qs( res_.read() ) ; Logdom max_penalty = Logdom::from_phred( conf_.max_penalty_per_nuc() * qs.length() ) ; // do actual alignments: // 1 initialize each one, make sure the mismatch count is low enough // 2 iterate, increasing the limit if necessary: // 2a evaluate alignments, keep the two best scores and associated seeds // 2b remove seeds that have already produced an alignment // 3 redo winning alignment and backtrace it std::deque< SeededAlignment > seedlist ; for( int i = 0 ; i != ss.ref_positions_size() ; ++i ) { DnaP reference = genome_->get_base() + ss.ref_positions(i) ; int32_t qoffs = ss.query_positions(i) ; uint32_t size = ss.seed_sizes(i) ; if( check_seed_quality( reference, qs.start() + qoffs, size, ss.max_mismatches(), ss.min_seed_length() ) ) seedlist.push_back( SeededAlignment( parblock_, reference, qs, qoffs, size ) ) ; } Logdom best_score = Logdom::null(), other_scores = Logdom::null(), limit = Logdom::from_phred( 60 ) ; SeededAlignment best_seed ; ExtendBothEnds best_ext ; while( !seedlist.empty() ) { std::deque< SeededAlignment >::iterator cur_aln( seedlist.begin() ), end_aln( seedlist.end() ), out_aln( seedlist.begin() ) ; while( cur_aln != end_aln ) { ExtendBothEnds extension( parblock_, qs, *cur_aln, limit ) ; Logdom score = extension.score_ ; // found an alignment? finish with this seed if( score.is_finite() ) { // new best score? if( score > best_score ) { if( best_score.is_finite() ) other_scores += best_score ; best_score = score ; best_seed = *cur_aln ; std::swap( best_ext, extension ) ; } // some inferior hit? else other_scores += score ; // seed is exhausted, compute new limit if( ++cur_aln != end_aln ) limit = max( limit, ( best_score * Logdom::from_phred( conf_.max_mapq() ) - other_scores ) / ( end_aln - cur_aln ) ) ; } else // no alignment: move to next seed { if( out_aln != cur_aln ) *out_aln = *cur_aln ; out_aln++, cur_aln++ ; } } // at least two hits -> we're done (regardless of score, we got // everything we could possibly need) if( other_scores.is_finite() ) break ; // get rid of exhausted seeds seedlist.erase( out_aln, end_aln ) ; // what's the current absolute limit? it's mapq worse than the // first hit we have, or than the max penalty otherwise. Logdom abs_max = ( Logdom::from_phred( conf_.max_mapq() ) * ( best_score.is_finite() ? best_score : max_penalty ) - other_scores ) / seedlist.size() ; // already past the limit? -> we're done if( limit <= abs_max ) break ; // new limit: twice as high, but clamped limit = max( limit*limit, abs_max ) ; } // report best score only if below the actualy max penalty (ensures // that if we report anything, we can also report a sensible mapq) if( !best_score.is_finite() || best_score < max_penalty ) { as->set_reason( output::bad_alignment ) ; return ; } output::Hit *h = res_.add_hit() ; DnaP minpos, maxpos ; std::vector t = best_ext.backtrace( best_seed, minpos, maxpos ) ; int32_t len = best_seed.qoffs_ > 0 ? maxpos - minpos : minpos - maxpos ; assert( maxpos > minpos && !maxpos.is_reversed() && !minpos.is_reversed() ) ; uint32_t start_pos ; const config::Sequence *sequ = genome_->translate_back( minpos, start_pos ) ; if( !sequ ) throw "Not supposed to happen: invalid alignment coordinates" ; if( genome_->g_.has_name() ) h->set_genome_name( genome_->g_.name() ) ; h->set_sequence( sequ->name() ) ; if( sequ->has_taxid() ) h->set_taxid( sequ->taxid() ) ; else if( genome_->g_.has_taxid() ) h->set_taxid( genome_->g_.taxid() ) ; h->set_start_pos( start_pos ) ; h->set_aln_length( len ) ; h->set_score( best_score.to_phred() ) ; std::copy( t.begin(), t.end(), RepeatedFieldBackInserter( h->mutable_cigar() ) ) ; if( other_scores.is_finite() ) h->set_map_quality( (other_scores/(best_score+other_scores)).to_phred() ) ; } } ; // namespace anfo-0.98/src/concurrent_stream.cc0000644000371600007640000001700711447113465014174 00000000000000#include "concurrent_stream.h" #include "util.h" #include namespace { void mutex_init( pthread_mutex_t& m ) { throw_strerror_if_not_null( pthread_mutex_init( &m, 0 ), "pthread_mutex_init" ) ; } void mutex_lock( pthread_mutex_t& m ) { throw_strerror_if_not_null( pthread_mutex_lock( &m ), "pthread_mutex_lock" ) ; } void mutex_unlock( pthread_mutex_t& m ) { throw_strerror_if_not_null( pthread_mutex_unlock( &m ), "pthread_mutex_unlock" ) ; } void cond_init( pthread_cond_t& c ) { throw_strerror_if_not_null( pthread_cond_init( &c, 0 ), "pthread_cond_init" ) ; } void cond_wait( pthread_cond_t& c, pthread_mutex_t& m ) { throw_strerror_if_not_null( pthread_cond_wait( &c, &m ), "pthread_cond_wait" ) ; } void cond_signal( pthread_cond_t& c ) { throw_strerror_if_not_null( pthread_cond_signal( &c ), "pthread_cond_signal" ) ; } } ; namespace streams { void ConcurrentStream::init() { cond_init( input_available_ ) ; cond_init( room_for_output_ ) ; cond_init( action_needed_ ) ; mutex_init( mutex_ ) ; } ConcurrentStream::~ConcurrentStream() { pthread_mutex_destroy( &mutex_ ) ; pthread_cond_destroy( &action_needed_ ) ; pthread_cond_destroy( &room_for_output_ ) ; pthread_cond_destroy( &input_available_ ) ; assert( outgoing_empty() ) ; assert( incoming_terminated() ) ; assert( (next_in_+1) % size_ == next_in_free_ ) ; } //! \brief determines stream state //! State is entirely determined by the queues, so that it can //! change due to background activity. We determine the state of the //! queues, and if neither input is required nor output available, we //! wait. Note that we need to dequeue termination markers from the //! outgoing queue and we need to signal if we did so. //! \todo We may need a way to indicate "both input need and output //! available". Stream::state ConcurrentStream::get_state() { mutex_lock( mutex_ ) ; state s = invalid ; for(;;) { if( !incoming_full() && !incoming_terminated() ) { s = need_input ; break ; } else if( !eos_outstanding_ ) { s = end_of_stream ; break ; } else { while( !outgoing_empty() && !outgoing_[ next_out_ ] ) { --eos_outstanding_ ; ++next_out_ ; next_out_ %= size_ ; cond_signal( room_for_output_ ) ; } if( !eos_outstanding_ ) { s = end_of_stream ; break ; } else if( !outgoing_empty() ) { s = have_output ; break ; } } cond_wait( action_needed_, mutex_ ) ; } mutex_unlock( mutex_ ) ; return s ; } extern "C" void *ConcurrentStream_start_routine( void* param ) { try { pair< StreamHolder, ConcurrentStream* > *p = (pair< StreamHolder, ConcurrentStream* >*) param ; return p->second->run_thread( &*p->first ) ; } catch( const std::string& e ) { perr( e ) ; } catch( const char *e ) { perr( e ) ; } catch( char *e ) { perr( e ) ; } catch( const Exception& e ) { perr( e ) ; } catch( const std::exception& e ) { perr( e.what() ) ; } catch( ... ) { perr( "Oh noes!" ) ; } return 0 ; } //! Putting a header means we put the header to each stream, then //! fire off separate threads for each one. Threads are started in a //! detached state, we get results from the stream objects themselves. void ConcurrentStream::put_header( const Header& h ) { if( !eos_outstanding_ ) { for( size_t i = 0 ; i != streams_.size() ; ++i ) { streams_[i].first->put_header( h ) ; pthread_t tid ; throw_strerror_if_not_null( pthread_create( &tid, 0, &ConcurrentStream_start_routine, &streams_[i] ), "pthread_create" ) ; throw_strerror_if_not_null( pthread_detach( tid ), "pthread_detach" ) ; } eos_outstanding_ = streams_.size() ; } } //! we know we have room for input, so thre's no waiting, we just put it //! in incoming and signal void ConcurrentStream::put_result( const Result& r ) { mutex_lock( mutex_ ) ; assert( !incoming_full() ) ; incoming_[ next_in_free_++ ] = new Result( r ) ; next_in_free_ %= size_ ; cond_signal( input_available_ ) ; mutex_unlock( mutex_ ) ; } //! Putting a footer means we terminate the input queue and store the //! footer for later. Here we don't need to wait for a slot in the //! incoming queue, because that condition must be checked by the caller //! and the queue cannot fill up by itself. void ConcurrentStream::put_footer( const Footer& f ) { mutex_lock( mutex_ ) ; assert( !incoming_full() ) ; foot_ = f ; incoming_[ next_in_free_ ] = 0 ; next_in_free_ = (next_in_free_+1) % size_ ; cond_signal( input_available_ ) ; mutex_unlock( mutex_ ) ; } //! We fetch each header, then merge them. //! \note This assumes that reading the header from any stream is safe //! at any time. While this is unlikely to be a wrong assumption, //! it still feels brittle. Header ConcurrentStream::fetch_header() { Header h ; for( size_t i = 0 ; i != streams_.size() ; ++i ) h.MergeFrom( streams_[i].first->fetch_header() ) ; return h ; } Result ConcurrentStream::fetch_result() { mutex_lock( mutex_ ) ; assert( !outgoing_empty() ) ; auto_ptr< Result > r( outgoing_[ next_out_++ ] ) ; next_out_ %= size_ ; cond_signal( room_for_output_ ) ; mutex_unlock( mutex_ ) ; return *r ; } //! To fetch the footer, output must already have been terminated. That //! means threads aren't running anymore and we can simply get the //! footers and merge them, without regard for concurrent writes. Footer ConcurrentStream::fetch_footer() { int exit_code = 0 ; Footer f ; for( size_t i = 0 ; i != streams_.size() ; ++i ) { Footer f1 = streams_[i].first->fetch_footer() ; exit_code |= f1.exit_code() ; f.MergeFrom( f1 ) ; } f.set_exit_code( exit_code ) ; return f ; } //! \brief dequeues a record from incoming and passes it on //! We dequeue a record, waiting for it if necessary. If we got a //! record, we unlock and pass it on. Else we got a terminator, which //! we leave in, then we copy the footer to change to the end-of-stream //! state. void ConcurrentStream::dequeue( Stream *s ) { mutex_lock( mutex_ ) ; while( incoming_empty() ) cond_wait( input_available_, mutex_ ) ; auto_ptr< Result > r( incoming_[ next_in_ ] ) ; if( r.get() ) { ++next_in_ ; next_in_ %= size_ ; cond_signal( action_needed_ ) ; mutex_unlock( mutex_ ) ; s->put_result( *r ) ; } else { // note ordering: putting the footer can cause output to // appear, which will fiddle with the queue. best not // nest this code inside our critical section. cond_signal( input_available_ ) ; mutex_unlock( mutex_ ) ; s->put_footer( foot_ ) ; } } void ConcurrentStream::enqueue( Result* r ) { mutex_lock( mutex_ ) ; while( outgoing_full() ) cond_wait( room_for_output_, mutex_ ) ; outgoing_[ next_out_free_++ ] = r ; next_out_free_ %= size_ ; cond_signal( action_needed_ ) ; mutex_unlock( mutex_ ) ; } // driven by state of stream. if input is requested, wait for it and // supply it; if eos comes up, fetch the footer, put eos back and supply // the footer. if output is available, wait for space, then deliver it. // if the stream ends, wait for space, deliver eos, and terminate. void* ConcurrentStream::run_thread( Stream* s ) { for(;;) { switch( s->get_state() ) { case invalid: throw "stream in invalid state: not supposed to happen!" ; case need_input: dequeue( s ) ; break ; case have_output: enqueue( new Result( s->fetch_result() ) ) ; break ; case end_of_stream: enqueue( 0 ) ; return 0 ; } } } Object ConcurrentStream::get_summary() { GC_Node ; Object l = Null ; GC_Link( l ) ; for( size_t i = streams_.size() ; i != 0 ; --i ) l = Cons( streams_[i-1].first->get_summary(), l ) ; GC_Unlink ; return l ; } } ; anfo-0.98/src/ducttape.cc0000644000371600007640000005411711447113463012251 00000000000000// Copyright 2009 Udo Stenzel // This file is part of ANFO // // ANFO is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // Anfo is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with Anfo. If not, see . #ifdef HAVE_CONFIG_H #include "../config.h" #endif #include "ducttape.h" #include "index.h" #include #include #include #include #include namespace streams { void DuctTaper::put_header( const Header& h ) { if( !h.has_is_sorted_by_all_genomes() && !h.is_sorted_by_coordinate_size() ) console.output( Console::warning, "[ducttape] input is not sorted, results may be useless" ) ; hdr_ = h ; adna_ = adna_parblock( h.config().aligner() ) ; state_ = need_input ; } //! \brief generates an actual contig from accumulated data //! \internal //! The strategy: If a gap is more likely than a base, we call a //! deletion and do not output anything else. Else we compute //! likelihoods for all possible dialleles. From that we call the most //! likely base. Calling ambiguity codes for heterozygous sites is not //! attempted, as that would be pointless without applying a prior for //! the rate of het sites. Finally we store the new contig as an \c //! output::Result and update internal state. //! //! Storage of likelihoods is done the same way as in GLF: the highest //! likelihood (smallest log-likelihood) becomes the base's quality, //! clipped at 255 if necessary. Likelihoods are stored as differences //! from the (true, unclipped) minimum, the difference being clipped at //! 255. This means the basecall can be reproduced by seeing which //! likelihood value is zero (there should be at least one). //! //! \todo If an indel is seen, there sould be a quality score for it. //! However, there's neither a good way to encode said quality or //! a good way to calculate or even define it... void DuctTaper::flush_contig() { // Assigning in the order A,C,T,G was such a brilliant idea... static int external_to_internal_base[4] = { 0, 1, 3, 2 } ; if( observed_.empty() ) return ; // if the last column was added, but nothing was observed yet, do // not call a base for it if( observed_.back().pristine() ) { observed_.pop_back() ; --contig_end_ ; } res_.Clear() ; res_.set_num_reads( nreads_ ) ; Read &rd = *res_.mutable_read() ; std::stringstream ss1 ; ss1 << name_ << '_' << ++num_ ; rd.set_seqid( ss1.str() ) ; report_( Console::info, ss1.str() ) ; // remove cols where sth. was inserted, but most reads show a gap for( Accs::iterator i = observed_.begin() ; i != observed_.end() ; ) { if( std::accumulate( i->seen, i->seen+4, 0 ) <= i->gapped && i->is_ins ) i = observed_.erase(i) ; else ++i ; } for( int i = 0 ; i != 10 ; ++i ) rd.add_likelihoods() ; std::vector cigar ; for( Accs::iterator i = observed_.begin() ; i != observed_.end() ; ++i ) { int cov = std::accumulate( i->seen, i->seen+4, 0 ) ; if( cov > i->gapped ) { if( i->is_ins ) push_i( cigar, 1 ) ; else push_m( cigar, 1 ) ; for( int j = 0 ; j != 4 ; ++j ) rd.add_seen_bases( i->seen[ external_to_internal_base[j] ] ) ; Logdom lk[10] ; for( int j = 0 ; j != 4 ; ++j ) lk[j] = i->lk[j] * (1-het_prior_) ; for( int j = 4 ; j != 10 ; ++j ) lk[j] = i->lk[j] * het_prior_ ; Logdom lk_tot = std::accumulate( lk, lk+10, Logdom::null() ) ; Logdom *maxlk = std::max_element( lk, lk+10 ) ; rd.add_depth( cov + i->gapped ) ; rd.mutable_sequence()->push_back( "ACGTMRWSYK"[maxlk - lk] ) ; Logdom q = Logdom::null() ; for( Logdom *j = lk ; j != lk+10 ; ++j ) { if( j != maxlk ) q += *j ; rd.mutable_likelihoods(j-lk)->push_back( (*j / *maxlk).to_phred_byte() ) ; } rd.mutable_quality()->push_back( (q / lk_tot).to_phred_byte() ) ; } else push_d( cigar, 1 ) ; } Hit &hit = *res_.add_hit() ; hit.set_genome_name( cur_genome_ ) ; hit.set_sequence( cur_sequence_ ) ; hit.set_start_pos( contig_start_ ) ; hit.set_aln_length( contig_end_ - contig_start_ ) ; hit.set_map_quality( int( 0.5 + std::sqrt( mapq_accum_ / nreads_ ) ) ) ; std::copy( cigar.begin(), cigar.end(), RepeatedFieldBackInserter( hit.mutable_cigar() ) ) ; observed_.clear() ; nreads_ = 0 ; state_ = have_output ; } Result DuctTaper::fetch_result() { state_ = have_foot_ ? end_of_stream : need_input ; return res_ ; } void DuctTaper::put_footer( const Footer& f ) { foot_ = f ; state_ = end_of_stream ; have_foot_ = true ; flush_contig() ; } // A bit annoying: we need to treat RC'd alignments differently. class AlnIter { private: bool fwd_ ; bool has_qual_ ; google::protobuf::RepeatedField::const_iterator cigar_ ; size_t cigar_minor_ ; std::string::const_iterator seq_, qual_ ; void norm_cigar() { if( fwd_ ) while( cigar_len( *cigar_ ) == cigar_minor_ ) { ++cigar_ ; cigar_minor_ = 0 ; } else while( cigar_len( cigar_[-1] ) == cigar_minor_ ) { --cigar_ ; cigar_minor_ = 0 ; } } public: AlnIter( const output::Read& r, const output::Hit& h ) : fwd_( h.aln_length() >= 0 ), has_qual_( r.has_quality() ), cigar_( fwd_ ? h.cigar().begin() : h.cigar().end() ), cigar_minor_( 0 ), seq_( fwd_ ? r.sequence().begin() : r.sequence().end() ) { if( has_qual_ ) qual_ = fwd_ ? r.quality().begin() : r.quality().end() ; norm_cigar() ; } AlnIter( const output::Read& r, const output::Hit& h, int ) : fwd_( h.aln_length() >= 0 ), has_qual_( r.has_quality() ), cigar_( fwd_ ? h.cigar().end() : h.cigar().begin() ), cigar_minor_( 0 ), seq_( fwd_ ? r.sequence().end() : r.sequence().begin() ) { if( has_qual_ ) qual_ = fwd_ ? r.quality().end() : r.quality().begin() ; } bool operator != ( const AlnIter& rhs ) { return seq_ != rhs.seq_ && qual_ != rhs.qual_ && ( cigar_ != rhs.cigar_ || cigar_minor_ != rhs.cigar_minor_ ) ; } AlnIter& operator ++ () { if( cigar_op() != Hit::Delete ) { if( fwd_ ) { ++seq_ ; ++qual_ ; } else { --seq_ ; --qual_ ; } } ++cigar_minor_ ; norm_cigar() ; return *this ; } Hit::Operation cigar_op() const { return streams::cigar_op( fwd_ ? cigar_[0] : cigar_[-1] ) ; } int base() const { return fwd_ ? ( seq_[ 0] == 'A' ? 0 : seq_[ 0] == 'C' ? 1 : seq_[ 0] == 'G' ? 3 : seq_[ 0] == 'T' ? 2 : -1 ) : ( seq_[-1] == 'A' ? 2 : seq_[-1] == 'C' ? 3 : seq_[-1] == 'G' ? 1 : seq_[-1] == 'T' ? 0 : -1 ) ; } Logdom qual() const { return Logdom::from_phred( (uint8_t)( fwd_ ? qual_[0] : qual_[-1] ) ) ; } } ; //! \brief updates likelihood information //! The strategy: Walk along both cigar strings, observed_ and the //! sequence of r. If both cigars do a match, update observed_. If //! both cigars insert, update observed_. If only r inserts, insert in //! observed_ and cigar_. If r deletes, update observed_. That means, //! we can properly call deletions by majority vote, and all inserts are //! forced to overlap and will lead to a majority vote, too (probably //! wreaking havoc in the rare case of apparently polymorphic inserts). //! //! In observed_ we store likelihoods for observations assuming a given //! base. The final base call inverts this by dividing by the total //! likelihood. Incorporation of the BJ model is quite easy: we just //! multiply the likelihood of a C becoming a T onto whatever the //! quality scores yield where appropriate. (That also means we need to //! multiply the probability of a C staying a C onto the appropriate //! likelihoods.) The likelihood depends on how likely we are to be in //! a single stranded region. //! //! The likelihood of the alignment with a given overhang length is //! simply the alignment score, by dividing by the total likelihood, we //! get a likelihood for that overhang length. //! //! Likelihood for having an ss overhang of at least n is just the sum //! of match scores in first n positions; therefore probability is //! L_ss(n) / (L_ss(n)+L_ds(n)) * P_ss(n), the latter being the prior of //! overhang_ext_penalty*n + overhang_enter_penalty. Incremental //! calculation is therfore easy in the forward direction. C->T //! probabilty is then the weighted sum of the two deamination rates, C //! staying C is the converse. // //! Backward direction: same calculation, but we need to initialize //! to the sum of all the match scores, which requires a preliminary //! pass over everything. //! //! \todo map_quality is interpreted as 254 if undefined; we can get a //! better value from the header. void DuctTaper::put_result_ancient( const Result& r ) { const Hit* h = hit_to( r ) ; if( !h ) return ; Logdom rate_ss = Logdom::from_float( hdr_.config().aligner().rate_of_ss_deamination() ), rate_ds = Logdom::from_float( hdr_.config().aligner().rate_of_ds_deamination() ) ; int mapq = h->has_map_quality() ? h->map_quality() : 254 ; mapq_accum_ += mapq*mapq ; if( cur_genome_ != h->genome_name() || cur_sequence_ != h->sequence() || h->start_pos() > contig_end_ ) { flush_contig() ; cur_genome_ = h->genome_name() ; cur_sequence_ = h->sequence() ; contig_start_ = contig_end_ = h->start_pos() ; } ++nreads_ ; if( h->start_pos() < contig_start_ ) throw "ducttaping: input was not sorted" ; Accs::iterator column = observed_.begin() ; for( int offs = h->start_pos() - contig_start_ ; offs ; ++column ) if( !column->is_ins ) --offs ; Logdom lk_ds_5, lk_ss_5 = adna_.overhang_enter_penalty ; Logdom lk_ds_3, lk_ss_3 = adna_.overhang_enter_penalty ; GenomeHolder genome = Metagenome::find_sequence( h->genome_name(), h->sequence() ) ; DnaP ref = genome->find_pos( h->sequence(), h->start_pos() ) ; for( AlnIter aln_i( r.read(), *h ), aln_e( r.read(), *h, 1 ) ; aln_i != aln_e ; ++aln_i ) { if( aln_i.cigar_op() == Hit::Match || aln_i.cigar_op() == Hit::Mismatch ) { lk_ss_3 *= adna_.ss_mat[ 1 << (ref?*ref:0) ][ 1 << aln_i.base() ] ; lk_ds_3 *= adna_.ds_mat[ 1 << (ref?*ref:0) ][ 1 << aln_i.base() ] ; } if( aln_i.cigar_op() != Hit::Insert && aln_i.cigar_op() != Hit::SoftClip && ref ) ++ref ; if( aln_i.cigar_op() != Hit::Delete ) lk_ds_3 *= adna_.overhang_ext_penalty ; } ref = genome->find_pos( h->sequence(), h->start_pos() ) ; for( AlnIter aln_b( r.read(), *h ), aln_i( aln_b ), aln_e( r.read(), *h, 1 ) ; aln_i != aln_e ; ++column ) { if( column == observed_.end() ) { column = observed_.insert( column, Acc() ) ; ++contig_end_ ; } switch( aln_i.cigar_op() ) { case Hit::SoftClip: case Hit::Insert: if( !column->is_ins ) column = observed_.insert( column, Acc(true, column->crossed ) ) ; goto no_match ; case Hit::Match: case Hit::Mismatch: if( column->is_ins ) { ++column->gapped ; break ; } if( ref ) ++ref ; lk_ss_5 *= adna_.ss_mat[ complement(1 << (ref?*ref:0)) ][ complement(1 << aln_i.base()) ] ; lk_ds_5 *= adna_.ds_mat[ complement(1 << (ref?*ref:0)) ][ complement(1 << aln_i.base()) ] ; lk_ss_3 /= adna_.ss_mat[ 1 << (ref?*ref:0) ][ 1 << aln_i.base() ] ; lk_ds_3 /= adna_.ds_mat[ 1 << (ref?*ref:0) ][ 1 << aln_i.base() ] ; no_match: lk_ds_5 *= adna_.overhang_ext_penalty ; lk_ds_3 /= adna_.overhang_ext_penalty ; if( aln_i.base() != -1 ) { ++column->seen[ aln_i.base() ] ; Logdom qual = std::max( aln_i.qual(), Logdom::from_phred( mapq ) ) ; Logdom prob_ss_5 = lk_ss_5 / (lk_ss_5 + lk_ds_5) ; Logdom prob_ss_3 = lk_ss_3 / (lk_ss_3 + lk_ds_3) ; Logdom l_mat = 1 - qual, l_mismat = qual / 3 ; // lk_base[x] is probability of seeing aln_i.base() // given that an x was in the real sequence. It is // the products of the probability of x being // modified to y times the probability of y being // seen as aln_i.base() summed over all possible y. // The former comes directly from blended subst // matrices, the latter is l_mat or l_mismat. // Probabilities for dialleles are simply the // average of probabilities for the constituents. #if 0 // Original code, unrolled and simplified below to // avoid addition of infinite quantities (which // would create NaNs). Logdom lk_base[4] for( int k = 0 ; k != 4 ; ++k ) { lk_base[k] = Logdom::null() ; for( int l = 0 ; l != 4 ; ++l ) { lk_base[k] += ( l == aln_i.base() ? l_mat : l_mismat ) * ( prob_ss_5 > prob_ss_3 ? lerp( prob_ss_5, Logdom::from_float( ss_mat[k][l] ), Logdom::from_float( ds_mat[k][l] ) ) : lerp( prob_ss_3, Logdom::from_float( ss_mat[k^2][l^2] ), Logdom::from_float( ds_mat[k^2][l^2] ) ) ) ; } } #endif Logdom lk_base[4] = { ( 0 == aln_i.base() ? l_mat : l_mismat ), // k == 0 ( 1 == aln_i.base() ? l_mat : l_mismat ) * // k == 1 ( 1 - lerp( prob_ss_5, rate_ss, rate_ds ) ) + // l == 1 ( 2 == aln_i.base() ? l_mat : l_mismat ) * // l == 2 lerp( prob_ss_5, rate_ss, rate_ds ), ( 2 == aln_i.base() ? l_mat : l_mismat ), // k == 2 ( 0 == aln_i.base() ? l_mat : l_mismat ) * // k == 3 lerp( prob_ss_3, rate_ss, rate_ds ) + // l == 0 ( 3 == aln_i.base() ? l_mat : l_mismat ) * // l == 3 ( 1 - lerp( prob_ss_3, rate_ss, rate_ds ) ) } ; // Translation of indices and calculation of het // likelihoods. A bit irregular, so spelled out in // full. column->lk[0] *= lk_base[0] ; // A column->lk[1] *= lk_base[1] ; // C column->lk[2] *= lk_base[3] ; // G(!) column->lk[3] *= lk_base[2] ; // T(!) column->lk[4] *= lerp( 0.5, lk_base[0], lk_base[1] ) ; // AC column->lk[5] *= lerp( 0.5, lk_base[0], lk_base[3] ) ; // AG column->lk[6] *= lerp( 0.5, lk_base[0], lk_base[2] ) ; // AT column->lk[7] *= lerp( 0.5, lk_base[1], lk_base[3] ) ; // CG column->lk[8] *= lerp( 0.5, lk_base[1], lk_base[2] ) ; // CT column->lk[9] *= lerp( 0.5, lk_base[3], lk_base[2] ) ; // GT } ++aln_i ; break ; case Hit::Delete: ++column->gapped ; ++aln_i ; if( ref ) ++ref ; break ; default: // all others are unused throw "unexpected CIGAR operation" ; break ; } if( aln_i != aln_b ) ++column->crossed ; } } void DuctTaper::put_result( const Result& r ) { if( hdr_.config().aligner().has_rate_of_ds_deamination() ) put_result_ancient( r ) ; else put_result_recent( r ) ; } void DuctTaper::put_result_recent( const Result& r ) { const Hit* h = hit_to( r ) ; if( !h ) return ; int mapq = h->has_map_quality() ? h->map_quality() : 254 ; mapq_accum_ += mapq*mapq ; if( cur_genome_ != h->genome_name() || cur_sequence_ != h->sequence() || h->start_pos() > contig_end_ ) { flush_contig() ; cur_genome_ = h->genome_name() ; cur_sequence_ = h->sequence() ; contig_start_ = contig_end_ = h->start_pos() ; } ++nreads_ ; if( h->start_pos() < contig_start_ ) throw "ducttaping: input was not sorted" ; Accs::iterator column = observed_.begin() ; for( int offs = h->start_pos() - contig_start_ ; offs ; ++column ) if( !column->is_ins ) --offs ; for( AlnIter aln_b( r.read(), *h ), aln_i( aln_b ), aln_e( r.read(), *h, 1 ) ; aln_i != aln_e ; ++column ) { if( column == observed_.end() ) { column = observed_.insert( column, Acc() ) ; ++contig_end_ ; } switch( aln_i.cigar_op() ) { case Hit::SoftClip: case Hit::Insert: if( !column->is_ins ) column = observed_.insert( column, Acc(true, column->crossed ) ) ; goto no_match ; case Hit::Match: case Hit::Mismatch: if( column->is_ins ) { ++column->gapped ; break ; } no_match: if( aln_i.base() != -1 ) { ++column->seen[ aln_i.base() ] ; Logdom qual = std::max( aln_i.qual(), Logdom::from_phred( mapq ) ) ; Logdom l_mat = 1 - qual, l_mismat = qual / 3 ; // lk_base[x] is probability of seeing aln_i.base() // given that an x was in the real sequence. It is // the products of the probability of x being // modified to y times the probability of y being // seen as aln_i.base() summed over all possible y. // The former comes directly from blended subst // matrices, the latter is l_mat or l_mismat. // Probabilities for dialleles are simply the // average of probabilities for the constituents. Logdom lk_base[4] = { l_mismat, l_mismat, l_mismat, l_mismat } ; lk_base[ aln_i.base() ] = l_mat ; // Translation of indices and calculation of het // likelihoods. A bit irregular, so spelled out in // full. column->lk[0] *= lk_base[0] ; // A column->lk[1] *= lk_base[1] ; // C column->lk[2] *= lk_base[3] ; // G(!) column->lk[3] *= lk_base[2] ; // T(!) column->lk[4] *= lerp( 0.5, lk_base[0], lk_base[1] ) ; // AC column->lk[5] *= lerp( 0.5, lk_base[0], lk_base[3] ) ; // AG column->lk[6] *= lerp( 0.5, lk_base[0], lk_base[2] ) ; // AT column->lk[7] *= lerp( 0.5, lk_base[1], lk_base[3] ) ; // CG column->lk[8] *= lerp( 0.5, lk_base[1], lk_base[2] ) ; // CT column->lk[9] *= lerp( 0.5, lk_base[3], lk_base[2] ) ; // GT } ++aln_i ; break ; case Hit::Delete: ++column->gapped ; ++aln_i ; break ; default: // all others are unused throw "unexpected CIGAR operation" ; break ; } if( aln_i != aln_b ) ++column->crossed ; } } void GlzWriter::put_result( const Result& rr ) { static uint8_t dna_to_glf_base[] = { 0, 1, 2, 3, 8, 9, 10, 11, 4, 5, 6, 7, 12, 13, 14, 15 } ; const Read& r = rr.read() ; const Hit* h = hit_to( rr ) ; if( r.likelihoods_size() == 10 && h ) { chan_( Console::info, r.seqid() ) ; google::protobuf::io::CodedOutputStream c( &gos_ ) ; // Per chromosome // int chrNameLen ; /* includes terminating 0 */ // char* chrName ; /* chrNamelen chars including 0 */ // int chrLen ; c.WriteLittleEndian32( r.seqid().size()+1 ) ; c.WriteString( r.seqid() ) ; c.WriteTag( 0 ) ; int eff_size = 0 ; for( int i = 0 ; i != h->cigar_size() ; ++i ) { switch( cigar_op( h->cigar(i) ) ) { case Hit::Match: case Hit::Mismatch: eff_size += cigar_len( h->cigar(i) ) ; default: break ; } } c.WriteLittleEndian32( eff_size ) ; GenomeHolder genome = Metagenome::find_sequence( h->genome_name(), h->sequence() ) ; DnaP ref = genome->find_pos( h->sequence(), h->start_pos() ) ; char buf[12] ; int i = 0 ; for( AlnIter beg( r, *h ), end( r, *h, 1 ) ; beg != end ; ++beg ) { switch( beg.cigar_op() ) { case Hit::Match: case Hit::Mismatch: // Per base // unsigned char ref:4, dummy:4 ; /* ref A=1,C=2,G=4,T=8,N=15 etc. */ // unsigned char max_mapQ ; /* maximum mapping quality */ // unsigned char lk[10] ; /* log likelihood ratio, max 255 */ // unsigned min_lk:8, /* minimum lk capped at 255 // depth:24 ; /* and the number of mapped reads */ buf[0] = dna_to_glf_base[ *ref ] ; buf[1] = h->has_map_quality() ? h->map_quality() : 254 ; for( int j = 0 ; j != 10 ; ++j ) buf[2+j] = (uint8_t)(r.likelihoods(j)[i]) ; c.WriteRaw( buf, 12 ) ; c.WriteLittleEndian32( (unsigned(r.depth(i)) << 8) | (uint8_t)r.quality()[i] ) ; // this need to be reversed for GLF v3 // c.WriteLittleEndian32( r.depth(i) | ((unsigned)(uint8_t)r.quality(i) << 24) ) ; ++ref ; ++i ; break ; case Hit::Delete: ++ref ; break ; case Hit::Insert: case Hit::SoftClip: ++i ; break ; default: break ; } } } } // Need to walk along any number of alignments (hg18, pt2, ..., nt), // producing either gaps or bases at each position. If *all* positions // are gapped, the position is skipped. Else produce symbols (gaps or // base, either from genome or from majority sequence), summary // information and likelihoods. // // XXX: for the time being, walks only one alignment void ThreeAlnWriter::put_result( const Result& res ) { const Read& r = res.read() ; const Hit* h = hit_to( res ) ; if( !h ) return ; GenomeHolder genome = Metagenome::find_sequence( h->genome_name(), h->sequence() ) ; DnaP ref = genome->find_pos( h->sequence(), h->start_pos() ) ; std::stringstream ss ; ss << name_ << ": " << h->genome_name() << '/' << h->sequence() << '@' << h->start_pos() ; chan_( Console::info, ss.str() ) ; *out_ << '>' << r.seqid() << ' ' << r.description() << '\n' ; // XXX more header lines like this: // out_ << ';' << h.genome_name() << ' ' << h.sequence() << ' ' // << ( h.aln_length() < 0 ? '-' : '+' ) << h.start_pos() << std::endl ; AlnIter aln( r, *h ), aln_e( r, *h, 1 ) ; int offs = 0 ; for( ; aln != aln_e ; ++aln ) { switch( aln.cigar_op() ) { case Hit::Match: case Hit::Mismatch: case Hit::Delete: *out_ << from_ambicode( *ref ) ; break ; case Hit::Insert: case Hit::SoftClip: *out_ << '-' ; break ; default: break ; } int ngaps = -std::accumulate( r.seen_bases().begin() + 4*offs, r.seen_bases().begin() + 4*offs +4, -r.depth(offs) ) ; switch( aln.cigar_op() ) { case Hit::Match: case Hit::Mismatch: case Hit::Insert: case Hit::SoftClip: *out_ << r.sequence()[offs] << std::setw(4) << (int)(uint8_t)r.quality()[offs] << std::setw(5) << r.depth(offs) << std::setw(5) << ngaps ; *out_ << " " ; for( int i = 0 ; i != 4 ; ++i ) *out_ << std::setw(4) << r.seen_bases( i + 4*offs ) ; *out_ << " " ; for( int i = 0 ; i != 4 ; ++i ) *out_ << std::setw(4) << (int)(uint8_t)r.likelihoods(i)[offs] ; break ; case Hit::Delete: *out_ << '-' ; break ; default: break ; } *out_ << '\n' ; switch( aln.cigar_op() ) { case Hit::Match: case Hit::Mismatch: ++ref ; case Hit::Insert: case Hit::SoftClip: ++offs ; break ; default: ++ref ; break ; } } } } // namespace anfo-0.98/src/index.cc0000644000371600007640000003605511447113463011550 00000000000000// Copyright 2009 Udo Stenzel // This file is part of ANFO // // ANFO is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // Anfo is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with Anfo. If not, see . #ifdef HAVE_CONFIG_H #include "../config.h" #endif #include "index.h" #include "util.h" #include #include #include #include #include #include #include using namespace config ; using namespace std ; static inline void cleanup_genome_name( string& gn ) { size_t gnl = gn.length() ; for( size_t i = 0 ; i != gnl ; ++i ) gn[i] = tolower( gn[i] ) ; if( gnl > 4 && gn.substr( gnl-4 ) == ".dna" ) gn = gn.substr( 0, gnl-4 ) ; } CompactGenome::CompactGenome( const std::string &name ) : base_(), file_size_(0), length_(0), fd_(-1), contig_map_(), posn_map_(), g_(), refcount_(0) { try { fd_ = throw_errno_if_minus1( open( name.c_str(), O_RDONLY ), "opening", name.c_str() ) ; struct stat the_stat ; throw_errno_if_minus1( fstat( fd_, &the_stat ), "statting", name.c_str() ) ; file_size_ = the_stat.st_size ; void *p = Metagenome::mmap( 0, file_size_, &fd_, 0 ) ; throw_errno_if_minus1( p, "mmapping", name.c_str() ) ; base_.assign( (uint8_t*)p ) ; if( ((uint32_t const*)p)[0] != signature ) throw name + string(" does not have 'DNA1' signature") ; uint32_t meta_off = ((uint32_t const*)p)[1] ; uint32_t meta_len = ((uint32_t const*)p)[2] ; if( !g_.ParseFromArray( (const char*)p + meta_off, meta_len ) ) throw "error parsing meta information" ; cleanup_genome_name( *g_.mutable_name() ) ; length_ = meta_off ; for( int i = 0 ; i != g_.sequence_size() ; ++i ) { const Sequence &s = g_.sequence(i) ; posn_map_[ s.name() ].first = i ; PosnMap1& pm = posn_map_[ s.name() ].second ; for( int j = 0 ; j != s.contig_size() ; ++j ) { const Contig &c = s.contig(j) ; contig_map_[ c.offset() ] = std::make_pair( i, j ) ; pm[ c.range_start() ] = j ; } } contig_map_[ g_.total_size() ] = make_pair( -1, -1 ) ; } catch(...) { if( base_ ) munmap( (void*)base_.unsafe_ptr(), file_size_ ) ; if( fd_ != -1 ) close( fd_ ) ; throw ; } } CompactGenome::~CompactGenome() { if( base_ ) munmap( (void*)base_.unsafe_ptr(), file_size_ ) ; if( fd_ != -1 ) close( fd_ ) ; } void CompactGenome::report( uint32_t o, uint32_t l, const char* msg ) { if( msg ) clog << '\r' << msg << ": at offset " << o << " (of " << 2*l << ", " << round((50.0*o)/l) << "%)\e[K" << flush ; } FixedIndex::FixedIndex( const std::string& name ) : base(0), secondary(0), first_level_len(0), length(0), fd_(-1), refcount_(0) { void *p = 0 ; try { fd_ = path_open( name, "idx", "ANFO_PATH" ) ; struct stat the_stat ; throw_errno_if_minus1( fstat( fd_, &the_stat ), "statting", name.c_str() ) ; length = the_stat.st_size ; p = Metagenome::mmap( 0, length, &fd_, 0 ) ; throw_errno_if_minus1( p, "mmapping", name.c_str() ) ; p_ = p ; if( *(const uint32_t*)p != signature ) throw name + " does not have 'IDX3' signature" ; uint32_t meta_len = ((const uint32_t*)p)[1] ; if( !meta_.ParseFromArray( (const char*)p + 8, meta_len ) ) throw "error parsing meta information" ; cleanup_genome_name( *meta_.mutable_genome_name() ) ; first_level_len = (1 << (2 * meta_.wordsize())) + 1 ; base = (const uint32_t*)( (const char*)p + 8 + ((3+meta_len) & ~3) ) ; secondary = base + first_level_len ; } catch(...) { if( p_ ) munmap( (void*)p_, length ) ; if( fd_ != -1 ) close( fd_ ) ; throw ; } } //! \brief directly looks up an oligo //! A single oligo is looked up and results are appended to a vector. //! Seeds that occur too often can be ignored, but for statistical //! purposes, they are always counted in the result. //! //! \note Setting both stride and cutoff will cause unexpected //! interactions, but since it's only intended for debugging, I //! won't fix it. //! //! \param o oligo to be looked up. //! \param v receiver for the resulting seeds //! \param cutoff discard oligos more frequent than this //! \param offs offset value to be placed in the seeds //! \param num_useless filled in with the number of seeds ignored due to //! being too frequent //! \return number of seeds found, including repetitive ones unsigned FixedIndex::lookup1( Oligo o, PreSeeds& v, const FixedIndex::LookupParams& p, int32_t offs, int *num_useless ) const { Oligo o_min = o << ( 2*( metadata().wordsize() - p.wordsize ) ) ; Oligo o_max = ( (o+1) << ( 2*( metadata().wordsize() - p.wordsize ) ) ) ; if( o >= first_level_len ) throw "oligo number out of index' range" ; uint32_t n = base[o_max] - base[o_min] ; if( n < p.cutoff ) v.post( secondary + base[o_min], secondary + base[o_max], offs, p.wordsize, p.stride ) ; else if( num_useless ) *num_useless += n ; return n ; } //! \brief looks up an oligo with up to one mismatch //! The oligo itself will first be looked for, then all its //! one-substituion variants are generated (by successively xor'ing //! every position with 01, 10 and 11) and looked up, too. //! //! \param o oligo to be looked up. //! \param v receiver for the resulting seeds //! \param cutoff discard oligos more frequent than this //! \param offs offset value to be placed in the seeds //! \param num_useless filled in with the number of seeds ignored due to //! being too frequent //! \return number of seeds found, including repetitive ones unsigned FixedIndex::lookup1m( Oligo o, PreSeeds& v, const FixedIndex::LookupParams& p, int32_t offs, int *num_useless ) const { return lookup1m( o, v, p, offs, num_useless, p.wordsize ) ; } unsigned FixedIndex::lookup1m( Oligo o, PreSeeds& v, const FixedIndex::LookupParams& p, int32_t offs, int *num_useless, size_t imax ) const { unsigned total = lookup1( o, v, p, offs, num_useless ) ; Oligo m1 = 1, m2 = 2, m3 = 3 ; for( size_t i = 0 ; i != imax ; ++i ) { total += lookup1( o ^ m1, v, p, offs, num_useless ) ; total += lookup1( o ^ m2, v, p, offs, num_useless ) ; total += lookup1( o ^ m3, v, p, offs, num_useless ) ; m1 <<= 2 ; m2 <<= 2 ; m3 <<= 2 ; } return total ; } unsigned FixedIndex::lookup2m( Oligo o, PreSeeds& v, const FixedIndex::LookupParams& p, int32_t offs, int *num_useless ) const { unsigned total = lookup1m( o, v, p, offs, num_useless ) ; Oligo m1 = 1, m2 = 2, m3 = 3 ; for( size_t i = 0 ; i != p.wordsize ; ++i ) { total += lookup1m( o ^ m1, v, p, offs, num_useless, i ) ; total += lookup1m( o ^ m2, v, p, offs, num_useless, i ) ; total += lookup1m( o ^ m3, v, p, offs, num_useless, i ) ; m1 <<= 2 ; m2 <<= 2 ; m3 <<= 2 ; } return total ; } //! \brief looks up a whole sequence //! The sequence is split into words as appropriate for the index, then //! each one of them is looked up. This method can be implemented for //! any kind of index, whether based on fixed words or not. //! //! \param dna sequence to search //! \param v receiver for resulting seeds //! \param near_perfect set to one to search for seeds with one mismatch //! \param num_useless is filled in with the number of seeds thrown away //! due to being too frequent //! \param cutoff disregard oligos more frequent than this //! \return number of seeds found unsigned FixedIndex::lookupS( const std::string& dna, PreSeeds& v, const FixedIndex::LookupParams &p, int *num_useless ) const { Oligo o_f = 0, o_r = 0 ; Oligo mask = ~( ~0 << (p.wordsize * 2) ) ; int s = 2 * p.wordsize - 2 ; unsigned filled = 0 ; unsigned total = 0 ; for( int32_t offset = 0 ; offset != (int32_t)dna.length() ; ++offset ) { o_f >>= 2 ; o_r = (o_r << 2) & mask ; ++filled ; switch( dna[offset] ) { case 'a': case 'A': o_f |= 0 << s ; o_r |= 2 ; break ; case 'c': case 'C': o_f |= 1 << s ; o_r |= 3 ; break ; case 't': case 'T': o_f |= 2 << s ; o_r |= 0 ; break ; case 'g': case 'G': o_f |= 3 << s ; o_r |= 1 ; break ; default: filled = 0 ; break ; } if( filled >= p.wordsize ) { int32_t off_f = offset - p.wordsize + 2 ; int32_t off_r = - offset - 1 ; if( p.allow_mismatches >= 2 ) total += lookup2m( o_f, v, p, off_f, num_useless ) + lookup2m( o_r, v, p, off_r, num_useless ) ; else if( p.allow_mismatches ) total += lookup1m( o_f, v, p, off_f, num_useless ) + lookup1m( o_r, v, p, off_r, num_useless ) ; else total += lookup1( o_f, v, p, off_f, num_useless ) + lookup1( o_r, v, p, off_r, num_useless ) ; } } return total ; } std::map< std::string, FixedIndex* > MetaIndex::map_ ; const config::Sequence *CompactGenome::translate_back( DnaP pos, uint32_t& offset ) const { ContigMap::const_iterator high = contig_map_.upper_bound( pos.abs() - base_ ) ; if( pos.abs() < base_ ) return 0 ; // before start if( high == contig_map_.end() ) return 0 ; // after end --high ; const config::Sequence &sequ = g_.sequence( high->second.first ) ; const config::Contig &contig = sequ.contig( high->second.second ) ; offset = pos.abs() - base_ - contig.offset() + contig.range_start() ; return &sequ ; } DnaP CompactGenome::find_pos( const std::string& seq, uint32_t pos ) const { PosnMap::const_iterator a = posn_map_.find( seq ) ; if( a != posn_map_.end() && !a->second.second.empty() ) { PosnMap1::const_iterator b = a->second.second.upper_bound( pos ) ; --b ; const config::Contig& c = g_.sequence( a->second.first ).contig( b->second ) ; if( c.range_start() <= pos && c.range_end() >= pos ) return base_ + c.offset() + (pos - c.range_start()) ; } return DnaP(0) ; } Metagenome Metagenome::the_metagenome( getenv("ANFO_PATH") ) ; void Metagenome::make_room() { // make room by forgetting about some genome int nephemeral = 0 ; for( Genomes::iterator gi = the_metagenome.genomes.begin(), ge = the_metagenome.genomes.end() ; gi != ge ; ++gi ) if( gi->second->refcount_ == 0 ) ++nephemeral ; throw_errno_if_null( nephemeral, "mmap()ing" ) ; Genomes::iterator gi = the_metagenome.genomes.begin() ; for( int i = random() % nephemeral ; i || gi->second->refcount_ ; ++gi ) if( gi->second->refcount_ == 0 ) --i ; for( SeqMap::iterator i = the_metagenome.seq_map.begin(), ie = the_metagenome.seq_map.end() ; i != ie ; ++i ) { for( SeqMap1::iterator j = i->second.begin(), je = i->second.end() ; j != je ; ) { SeqMap1::iterator k = j ; ++j ; if( k->second == gi->second ) i->second.erase( k ) ; } } console.output( Console::info, "Metagenome: forgot about " + gi->first ) ; delete gi->second ; the_metagenome.genomes.erase( gi ) ; } Metagenome::Metagenome( const char* p ) { if( p ) { const char* q = p ; while( *p ) { while( *q && *q != ':' ) ++q ; path.push_back( std::string( p, q ) ) ; if( *q ) ++q ; p = q ; } } std::set_new_handler( &Metagenome::make_room ) ; } //! \brief searches genome path for matching files //! This functions looks for exact matches (supporting index files that //! name the genome file) and for files starting with the genome name //! and ending in ".dna" (to support lookup of named genomes). glob_t Metagenome::glob_path( const std::string& genome ) { glob_t the_glob = { 0 } ; int glob_append = 0 ; for( std::list< std::string >::iterator j = the_metagenome.path.begin() ; j != the_metagenome.path.end() ; ++j ) { std::string p = *j + "/" + genome ; if( !genome.empty() ) { glob( p.c_str(), GLOB_NOSORT | glob_append | GLOB_TILDE, 0, &the_glob ) ; glob_append = GLOB_APPEND ; } p += "*.dna" ; glob( p.c_str(), GLOB_NOSORT | glob_append | GLOB_TILDE, 0, &the_glob ) ; } return the_glob ; } GenomeHolder Metagenome::find_sequence( const std::string& genome, const std::string& seq ) { SeqMap1 &m = the_metagenome.seq_map[ genome ] ; // check if we got the sequence somewhere already SeqMap1::iterator i = m.find( seq ) ; if( i == m.end() ) { glob_t the_glob = glob_path( genome ) ; // sequence missing. load genomes until we find the sequence for( size_t j = 0 ; j != the_glob.gl_pathc && i == m.end() ; ++j ) { try { const char *n = the_glob.gl_pathv[j] ; Genomes::iterator gi = the_metagenome.genomes.find( n ) ; if( gi == the_metagenome.genomes.end() ) { console.output( Console::info, "Metagenome: trying file " + std::string(n) ) ; CompactGenome* g = new CompactGenome( n ) ; the_metagenome.genomes[ n ] = g ; console.output( Console::info, "Metagenome: loaded (part of) genome " + g->name() ) ; SeqMap1 &m_ = the_metagenome.seq_map[ g->name() ] ; for( int k = 0 ; k != g->g_.sequence_size() ; ++k ) m_[ g->g_.sequence(k).name() ] = g ; if( g->name() == genome ) i = m.find( seq ) ; } } catch( const std::string& e ) { perr( e ) ; } catch( const char *e ) { perr( e ) ; } catch( char *e ) { perr( e ) ; } catch( const Exception& e ) { perr( e ) ; } catch( const std::exception& e ) { perr( e.what() ) ; } catch( ... ) { perr( "Oh noes!" ) ; } } globfree( &the_glob ) ; } return i == m.end() ? GenomeHolder() : i->second ; } GenomeHolder Metagenome::find_genome( const std::string& genome ) { // would be nicer to check if we already have a suitable genome, but // this is called so rarely, I won't bother glob_t the_glob = glob_path( genome ) ; if( !the_glob.gl_pathc ) throw "no genome file found for " + genome ; const char *n = the_glob.gl_pathv[0] ; Genomes::iterator gi = the_metagenome.genomes.find( n ) ; if( gi == the_metagenome.genomes.end() ) { CompactGenome *g = new CompactGenome( n ) ; the_metagenome.genomes[ n ] = g ; globfree( &the_glob ) ; return g ; } globfree( &the_glob ) ; return gi->second ; } bool Metagenome::translate_to_genome_coords( DnaP pos, uint32_t &xpos, const config::Sequence** s_out, const config::Genome** g_out ) { for( Genomes::const_iterator g = the_metagenome.genomes.begin(), ge = the_metagenome.genomes.end() ; g != ge ; ++g ) { if( const Sequence *sequ = g->second->translate_back( pos, xpos ) ) { if( s_out ) *s_out = sequ ; if( g_out ) *g_out = &g->second->g_ ; return true ; } } return false ; } static int get_zero_device() { static int fdz = throw_errno_if_minus1( open( "/dev/zero", O_RDWR ), "opening", "/dev/zero" ) ; return fdz ; } int Metagenome::nommap = false ; void *Metagenome::mmap( void *start, size_t length, int *fd, off_t offset ) { for(;;) { if( nommap ) { void *p = ::mmap( 0, length, PROT_READ | PROT_WRITE, MAP_PRIVATE, get_zero_device(), 0 ) ; if( p != (void*)(-1) ) { myread( *fd, p, length ) ; close( *fd ) ; *fd = -1 ; return p ; } } else { void *p = ::mmap( start, length, PROT_READ, MAP_PRIVATE | MAP_NORESERVE, *fd, offset ) ; if( p != (void*)(-1) ) return p ; } make_room() ; } } anfo-0.98/src/misc_streams.cc0000644000371600007640000004032111447113506013117 00000000000000#if HAVE_CONFIG_H #include "../config.h" #endif #include "misc_streams.h" #include #include #include #include #include #include namespace streams { using namespace google::protobuf ; using namespace google::protobuf::io ; Header MergeStream::fetch_header() { state_ = end_of_stream ; for( size_t i = 0 ; i != streams_.size() ; ) { Header h = streams_[i]->fetch_header() ; merge_sensibly( hdr_, h ) ; if( h.is_sorted_by_name() ) { if( mode_ == unknown ) mode_ = by_name ; else if( mode_ != by_name ) throw "MergeStream: inconsistent sorting of input (by_name)" ; } else if( h.is_sorted_by_all_genomes() ) { if( mode_ == unknown ) { mode_ = by_coordinate ; gs_.clear() ; } else if( mode_ != by_coordinate || !gs_.empty() ) throw "MergeStream: inconsistent sorting of input (by_all_genomes)" ; } else if( h.is_sorted_by_coordinate_size() ) { if( mode_ == unknown ) { mode_ = by_coordinate ; gs_.assign( h.is_sorted_by_coordinate().begin(), h.is_sorted_by_coordinate().end() ) ; } else if( mode_ != by_coordinate || (int)gs_.size() != h.is_sorted_by_coordinate_size() || !equal( gs_.begin(), gs_.end(), h.is_sorted_by_coordinate().begin() ) ) throw "MergeStream: inconsistent sorting of input (by_genome)" ; } if( streams_[i]->get_state() == have_output ) { rs_.push_back( streams_[i]->fetch_result() ) ; state_ = have_output ; ++i ; } else { merge_sensibly( foot_, streams_[i]->fetch_footer() ) ; streams_.erase( streams_.begin() + i ) ; } } stringstream ss ; ss << "MergeStream: " ; if( mode_ == by_name ) ss << "merge sorting on name" ; else if( mode_ == by_coordinate ) { ss << "merge sorting on coordinates of " ; if( gs_.empty() ) ss << "best hit" ; else { ss << '[' << gs_.front() ; for( size_t i = 1 ; i != gs_.size() ; ++i ) ss << ',' << gs_[i] ; ss << ']' ; } } else ss << "cannot merge" ; console.output( mode_ == unknown ? Console::error : Console::info, ss.str() ) ; return hdr_ ; } //! \todo uses linear search, but a heap would be more appropriate Result MergeStream::fetch_result() { if( state_ != have_output ) throw "logic error: MergeStream::fetch_result called in wrong stream state" ; if( rs_.size() != streams_.size() ) throw "logic error: # of records does not equal # of streams in MergeStream::fetch_result" ; if( !streams_.size() ) throw "logic error: no streams left in MergeStream::fetch_result" ; int min_idx = 0 ; for( size_t i = 1 ; i != rs_.size() ; ++i ) if( ( mode_ == by_coordinate && by_genome_coordinate( gs_ )( &rs_[ i ], &rs_[ min_idx ] ) ) || ( mode_ == by_name && by_seqid()( &rs_[ i ], &rs_[ min_idx ] ) ) ) min_idx = i ; string min_name = rs_[ min_idx ].read().seqid() ; Result res ; for( size_t i = 0 ; i != rs_.size() ; ) { if( rs_[i].read().seqid() == min_name ) { if( res.IsInitialized() ) merge_sensibly( res, rs_[i] ) ; else res = rs_[i] ; Stream &sm = *streams_[i] ; if( sm.get_state() == have_output ) rs_[i++] = sm.fetch_result() ; else { merge_sensibly( foot_, sm.fetch_footer() ) ; streams_.erase( streams_.begin() + i ) ; rs_.erase( rs_.begin() + i ) ; if( rs_.empty() ) state_ = end_of_stream ; } } else ++i ; } return res ; } Header NearSortedJoin::fetch_header() { state_ = end_of_stream ; for( size_t i = 0 ; i != streams_.size() ; ) { merge_sensibly( hdr_, streams_[i]->fetch_header() ) ; ++nstreams_ ; if( streams_[i]->get_state() == have_output ) { state_ = have_output ; ++i ; } else { merge_sensibly( foot_, streams_[i]->fetch_footer() ) ; streams_.erase( streams_.begin() + i ) ; } } cur_input_ = streams_.begin() ; return hdr_ ; } //! Enough information is read until one sequence has been reported on //! by each input stream. Everything else is buffered if necessary. //! This works fine as long as the inputs come in in roughly the same //! order and are complete. Result NearSortedJoin::fetch_result() { while( !streams_.empty() ) { if( cur_input_ == streams_.end() ) cur_input_ = streams_.begin() ; Stream &s = **cur_input_ ; if( s.get_state() != have_output ) throw "logic error: NearSortedJoin::fetch_result wasn't provided with input" ; Result r = s.fetch_result() ; if( s.get_state() == end_of_stream ) { merge_sensibly( foot_, s.fetch_footer() ) ; cur_input_ = streams_.erase( cur_input_ ) ; } else ++cur_input_ ; if( buffer_.size() >= 100000 ) throw "input must be complete and nearly sorted the same way for join to work" ; if( ((nread_ + nwritten_) & 0xFFFF) == 0 ) { stringstream s ; s << "NearSortedJoin: " << nread_ << "in " << nwritten_ << "out " << buffer_.size() << "buf" ; progress_( Console::info, s.str() ) ; } pair< size_t, Result > &p = buffer_[ r.read().seqid() ] ; ++nread_ ; ++p.first ; if( p.second.IsInitialized() ) merge_sensibly( p.second, r ) ; else p.second = r ; if( p.first == nstreams_ ) { ++nwritten_ ; Result r1 ; swap( r1, p.second ) ; buffer_.erase( r.read().seqid() ) ; if( buffer_.empty() && streams_.empty() ) state_ = end_of_stream ; return r1 ; } } Result r1 ; swap( r1, buffer_.begin()->second.second ) ; buffer_.erase( buffer_.begin()->first ) ; if( buffer_.empty() ) state_ = end_of_stream ; return r1 ; } unsigned SortingStream__ninstances = 0 ; void RepairHeaderStream::put_header( const Header& h ) { char tmpname[] = "/tmp/anfo_header_XXXXXX" ; int fd = mkstemp( tmpname ) ; { FileOutputStream fos( fd ) ; TextFormat::Print( h, &fos ) ; } string cmd = (editor_.empty() ? getenv("EDITOR") : editor_) + " " + tmpname ; for(;;) { if( system( cmd.c_str() ) ) break ;; lseek( fd, 0, SEEK_SET ) ; FileInputStream fis( fd ) ; if( TextFormat::Parse( &fis, &hdr_ ) ) break ; } throw_errno_if_minus1( unlink( tmpname ), "unlinking", tmpname ) ; state_ = need_input ; } void FanOut::put_header( const Header& h ) { Stream::put_header( h ) ; for( citer i = streams_.begin() ; i != streams_.end() ; ++i ) (*i)->put_header( h ) ; } void FanOut::put_result( const Result& r ) { for( citer i = streams_.begin() ; i != streams_.end() ; ++i ) if( (*i)->get_state() == need_input ) (*i)->put_result( r ) ; } void FanOut::put_footer( const Footer& f ) { Stream::put_footer( f ) ; for( citer i = streams_.begin() ; i != streams_.end() ; ++i ) (*i)->put_footer( f ) ; } Footer FanOut::fetch_footer() { for( citer i = streams_.begin() ; i != streams_.end() ; ++i ) merge_sensibly( foot_, (*i)->fetch_footer() ) ; return Stream::fetch_footer() ; } void Compose::put_header( const Header& h_ ) { Header h = h_ ; citer i = streams_.begin(), e = streams_.end() ; for( e-- ; i != e ; ++i ) { (*i)->put_header( h ) ; h = (*i)->fetch_header() ; } (*i)->put_header( h ) ; } Header Compose::fetch_header() { citer i = streams_.begin(), e = streams_.end() ; Header h = (*i)->fetch_header() ; for( ++i ; i != e ; ++i ) { (*i)->put_header( h ) ; h = (*i)->fetch_header() ; } return h ; } // note weird calls to base(): makes a weird compiler happy... Stream::state Compose::get_state() { // look at a stream at a time, starting from the end for( criter i = streams_.rbegin() ;; ) { // if we fell of the far end, we need more input if( i.base() == streams_.rend().base() ) { return need_input ; } // else consider the state state s = (*i)->get_state() ; if( s == need_input ) { // input comes from previous stream ++i ; } else if( s == have_output ) { // output's available, either to the outside or to // downstream filters if( i.base() == streams_.rbegin().base() ) { return have_output ; } Result r = (*i)->fetch_result() ; --i ; (*i)->put_result( r ) ; } else if( s == end_of_stream ) { // nothing left, pass the footer to see if some data is // buffered if( i.base() == streams_.rbegin().base() ) { return end_of_stream ; } Footer f = (*i)->fetch_footer() ; --i ; (*i)->put_footer( f ) ; } else { // easy: something's broken return invalid ; } } } void StatStream::put_result( const Result& r ) { unsigned bases = r.read().sequence().size() ; unsigned gc = count( r.read().sequence().begin(), r.read().sequence().end(), 'G' ) + count( r.read().sequence().begin(), r.read().sequence().end(), 'C' ) ; unsigned count = std::max( r.members_size() + r.nmembers(), 1U ) ; total_ += count ; bases_ += bases ; bases_gc_ += gc ; bases_squared_ += bases*bases ; if( const Hit* h = hit_to( r ) ) { mapped_ += count ; bases_m_ += bases ; bases_m_squared_ += bases*bases ; bases_gc_m_ += gc ; if( !h->has_map_quality() || h->map_quality() >= 30 ) { mapped_u_ += count ; ++different_ ; } } } static inline Object Cons2U( uint64_t x, Object l ) { return Cons( Make_Unsigned( x & ~(~0LL << 31) ), Cons( Make_Unsigned( x >> 31 ), l ) ) ; } static inline Object ConsU( unsigned x, Object l ) { return Cons( Make_Unsigned( x ), l ) ; } Object StatStream::get_summary() const { Object r = Null ; r = Cons2U( bases_m_squared_, r ) ; r = Cons2U( bases_m_, r ) ; r = Cons2U( bases_squared_, r ) ; r = Cons2U( bases_, r ) ; r = Cons2U( bases_gc_m_, r ) ; r = Cons2U( bases_gc_, r ) ; r = ConsU( different_, r ) ; r = ConsU( mapped_u_, r ) ; r = ConsU( mapped_, r ) ; r = ConsU( total_, r ) ; return r ; } void MismatchStats::put_result( const Result& r ) { for( int i = 0 ; i != r.hit_size() ; ++i ) { const Hit& h = r.hit(i) ; if( !h.has_aln_ref() || !h.has_aln_qry() ) throw "MismatchStats needs reconstructed alignments" ; for( size_t j = 0 ; j != h.aln_ref().size() && j != h.aln_qry().size() ; ++j ) { char a = h.aln_ref()[j], b = h.aln_qry()[j] ; int u = a == 'A' ? 0 : a == 'C' ? 1 : a == 'G' ? 2 : a == 'T' ? 3 : -1 ; int v = b == 'A' ? 0 : b == 'C' ? 1 : b == 'G' ? 2 : b == 'T' ? 3 : -1 ; if( u >= 0 && v >= 0 ) ++mat_[u][v] ; } } } Object MismatchStats::get_summary() const { GC_Node ; Object r = Make_Vector( 4, False ) ; GC_Link( r ) ; for( int i = 0 ; i != 4 ; ++i ) { Object s = Make_Vector( 4, False ) ; for( int j = 0 ; j != 4 ; ++j ) VECTOR(s)->data[j] = Make_Integer( mat_[i][j] ) ; VECTOR(r)->data[i] = s ; } GC_Unlink ; return r ; } void DivergenceStream::put_header( const Header& h ) { Stream::put_header( h ) ; ancient_ = h.config().has_aligner() && h.config().aligner().has_mean_overhang_length() ; } // Excludes gaps, Ns, and nonsensical symbols inline static bool good( char x ) { return x == 'A' || x == 'C' || x == 'G' || x == 'T' ; } // Excludes transitions that may have been confounded by deamination. // Idea is the same as in contamination checker: "If you see a C you can // trust that you see a C." (Excluding all transitions doesn't change // the results.) inline static bool fine( char x, char y, char z ) { if( x == 'C' && y == 'T' && z == 'T' ) return false ; if( x == 'T' && y == 'T' && z == 'C' ) return false ; if( x == 'G' && y == 'A' && z == 'A' ) return false ; if( x == 'A' && y == 'A' && z == 'G' ) return false ; return true ; } void DivergenceStream::put_result( const Result& r ) { const Hit *pri = hit_to( r, primary_genome_ ) ; const Hit *sec = hit_to( r, secondary_genome_ ) ; if( pri && sec ) { if( !pri->has_aln_ref() || !pri->has_aln_qry() || !sec->has_aln_ref() || !sec->has_aln_qry() ) throw "Divergence: need reconstructed alignments" ; string::const_iterator pri_ref = pri->aln_ref().begin(), pri_qry = pri->aln_qry().begin(), pri_qry_end = pri->aln_qry().end(), sec_ref = sec->aln_ref().begin(), sec_qry = sec->aln_qry().begin(), sec_qry_end = sec->aln_qry().end() ; for( int skip = 0 ; skip != chop_ && pri_qry != pri_qry_end ; ) { if( *pri_qry != '-' ) ++skip ; ++pri_qry, ++pri_ref ; } for( int skip = 0 ; skip != chop_ && pri_qry != pri_qry_end ; ) { --pri_qry_end ; if( *pri_qry_end != '-' ) ++skip ; } for( int skip = 0 ; skip != chop_ && sec_qry != sec_qry_end ; ) { if( *sec_qry != '-' ) ++skip ; ++sec_qry, ++sec_ref ; } for( int skip = 0 ; skip != chop_ && sec_qry != sec_qry_end ; ) { --sec_qry_end ; if( *sec_qry_end != '-' ) ++skip ; } for(;;) { while( pri_qry != pri_qry_end && *pri_qry == '-' ) ++pri_qry, ++pri_ref ; while( sec_qry != sec_qry_end && *sec_qry == '-' ) ++sec_qry, ++sec_ref ; if( pri_qry == pri_qry_end ) break ; if( sec_qry == sec_qry_end ) break ; char p = *pri_ref, s = *sec_ref, q = *pri_qry ; if( q != *sec_qry ) throw "disagreement in alignments (or ugly bug)" ; if( good(p) && good(s) && good(q) && (!ancient_ || fine(p,q,s)) ) { if( q == p && q == s ) ++b1 ; else if( q == p && q != s ) ++b2 ; else if( q != s && p == s ) ++b3 ; else if( q == s && q != p ) ++b4 ; else ++b5 ; } ++pri_ref ; ++pri_qry ; ++sec_ref ; ++sec_qry ; } } } Object DivergenceStream::get_summary() const { Object bb = Make_Vector( 5, False ) ; Object* b = VECTOR(bb)->data ; b[0] = Make_Flonum( b1 ) ; b[1] = Make_Flonum( b2 ) ; b[2] = Make_Flonum( b3 ) ; b[3] = Make_Flonum( b4 ) ; b[4] = Make_Flonum( b5 ) ; return bb ; } RegionFilter::Regions3 RegionFilter::all_regions ; RegionFilter::RegionFilter( const pair< istream*, string >& p ) { auto_ptr< istream > deffile( p.first ) ; const string &fn = p.second ; Regions3::iterator i = all_regions.find( fn ) ; if( i != all_regions.end() ) my_regions = &i->second ; else { my_regions = &all_regions[ fn ] ; console.output( Console::notice, "Loading annotation from " + fn ) ; std::string junk, chrom ; unsigned start, end ; std::getline( *deffile, junk ) ; while( std::getline( *deffile >> junk >> chrom >> start >> end, junk ) ) (*my_regions)[ chrom ][ end ] = start ; } } void Sanitizer::put_header( const Header& h ) { Filter::put_header( h ) ; hdr_.clear_command_line() ; hdr_.clear_sge_job_id() ; hdr_.clear_sge_task_id() ; hdr_.DiscardUnknownFields() ; } bool Sanitizer::xform( Result& r ) { r.clear_aln_stats() ; return true ; } AgreesWithChain::AgreesWithChain( const string& l, const string& r, const pair& p ) : left_genome_( l ), right_genome_( r ), map_() { } AgreesWithChain::Chains::iterator AgreesWithChain::find_any_most_specific_overlap( unsigned start, unsigned end, Chains *chains ) { Chains::iterator best = chains->end() ; for(;;) { // first chain that starts at or to the right of end (this one // doesn't overlap, but the one _before_ it might) Chains::iterator i = chains->lower_bound( end ) ; if( i == chains->begin() ) return best ; Entry* e = &(--i)->second ; // no overlap? return parent. if( start >= e->left_end || i->first >= end ) return best ; // continue with nested chains, making current entry the best best = i ; chains = &e->nested ; } } // Idea is to find the most specific chain that overlaps a read, then // make sure the read is contained in it. bool AgreesWithChain::xform( Result& r ) { const Hit* lh = hit_to( r, left_genome_ ) ; const Hit* rh = hit_to( r, right_genome_ ) ; if( !lh || !rh ) return false ; // find chain hierarchy for correct chromosome Map1::iterator i1 = map_.find( lh->sequence() ) ; if( i1 == map_.end() ) { cerr << "chromosome not found" << endl ; return false ; } // find most specific chain that overlaps left hit Chains::iterator i2 = find_any_most_specific_overlap( lh->start_pos(), lh->start_pos() + abs(lh->aln_length()), &i1->second ) ; if( i2 == i1->second.end() ) return false ; // check if found chain contains both hits if( lh->start_pos() < i2->first || lh->start_pos() + abs( lh->aln_length() ) > i2->second.left_end || rh->start_pos() < i2->second.right_start || rh->start_pos() + abs( rh->aln_length() ) > i2->second.right_end || rh->sequence() != i2->second.right_chr ) return false ; // check strand if( ((rh->aln_length() < 0) != (lh->aln_length() < 0)) != i2->second.strand ) return false ; // Now both hits are covered by a single, most specific chain. // (Note: currently, hitting anywhere in the chain is fine; this // should probably be made somewhat more precise) return true ; } } ; // namespace anfo-0.98/src/output_streams.cc0000644000371600007640000005355311447113465013543 00000000000000// Copyright 2009 Udo Stenzel // This file is part of ANFO // // ANFO is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // Anfo is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with Anfo. If not, see . #ifdef HAVE_CONFIG_H #include "../config.h" #endif #include "output_streams.h" #include "conffile.h" #include "output.pb.h" #include #include #include #include #include #include #include namespace streams { using namespace google::protobuf ; bool GenTextAlignment::xform( Result& res ) { for( int i = 0 ; i != res.hit_size() ; ++i ) { output::Hit& h = *res.mutable_hit(i) ; std::string::const_iterator qry = res.read().sequence().begin() + res.read().trim_left() ; std::string& r = *h.mutable_aln_ref() ; std::string& q = *h.mutable_aln_qry() ; GenomeHolder g = Metagenome::find_sequence( h.genome_name(), h.sequence() ) ; DnaP ref = g ? g->find_pos( h.sequence(), h.start_pos() ) : DnaP() ; if( !ref ) { ostringstream errmsg ; errmsg << "couldn't find reference: " ; if( !h.genome_name().empty() ) errmsg << h.genome_name() << ':' ; errmsg << h.sequence() << '@' << h.start_pos() ; if( strict_ ) throw errmsg.str() ; console.output( Console::warning, errmsg.str() ) ; continue ; } if( h.aln_length() < 0 ) ref = ref.reverse() + h.aln_length() + 1 ; r.clear() ; q.clear() ; if( context_ ) { DnaP ref1 = ref ; for( int i = 0 ; i != context_ ; ++i ) { r = from_ambicode( ref1[-1] ) + r ; if( ref1[-1] ) --ref1 ; } q = std::string( context_, '-' ) ; } for( int i = 0 ; i != h.cigar_size() ; ++i ) { unsigned l = cigar_len( h.cigar(i) ) ; switch( cigar_op( h.cigar(i) ) ) { case output::Hit::Match: case output::Hit::Mismatch: for( size_t j = 0 ; j != l ; ++j, ++ref, ++qry ) { r.push_back( from_ambicode( *ref ) ) ; q.push_back( *qry ) ; } break ; case output::Hit::SoftClip: case output::Hit::Insert: for( size_t j = 0 ; j != l ; ++j, ++qry ) { r.push_back( '-' ) ; q.push_back( *qry ) ; } break ; case output::Hit::Delete: for( size_t j = 0 ; j != l ; ++j, ++ref ) { r.push_back( from_ambicode( *ref ) ) ; q.push_back( '-' ) ; } break ; case output::Hit::Skip: break ; // ??? case output::Hit::HardClip: break ; // ??? case output::Hit::Pad: break ; // ??? } } for( int i = 0 ; i != context_ ; ++i ) { r.push_back( from_ambicode( *ref ) ) ; if( *ref ) ++ref ; } q += std::string( context_, '-' ) ; } return true ; } typedef void (*PrintMethod)( const Message& m, const Reflection*, const FieldDescriptor*, ostream&, int ) ; void generic_show_message( const Message&, std::ostream&, int ) ; void generic_show_known_fields( const Message&, std::ostream&, int ) ; void generic_show_unknown_fields( const UnknownFieldSet&, std::ostream&, int ) ; // hides a field by printing nothing void show_noop( const Message& m, const Reflection*, const FieldDescriptor*, ostream& s, int ) {} // CIGAR line: decode to string, same way SAM would do it void show_cigar( const Message& m, const Reflection* r, const FieldDescriptor* f, ostream& s, int indent ) { s << string( indent, ' ' ) << f->name() << ": " ; for( int i = 0 ; i != r->FieldSize( m, f ) ; ++i ) { uint32_t c = r->GetRepeatedUInt32( m, f, i ) ; if( c == 0 ) s << '/' ; else s << cigar_len(c) << "MIDNSHP........M"[ cigar_op(c) ] ; } s << '\n' ; } // array of ints: formatted into comma-separated line void show_uint32_array( const Message& m, const Reflection* r, const FieldDescriptor* f, ostream& s, int indent ) { s << string( indent, ' ' ) << f->name() << ": " ; if( int l = r->FieldSize( m, f ) ) { s << r->GetRepeatedUInt32( m, f, 0 ) ; for( int i = 1 ; i != l ; ++i ) s << ',' << r->GetRepeatedUInt32( m, f, i ) ; } s << '\n' ; } void show_int32_array( const Message& m, const Reflection* r, const FieldDescriptor* f, ostream& s, int indent ) { s << string( indent, ' ' ) << f->name() << ": " ; if( int l = r->FieldSize( m, f ) ) { s << r->GetRepeatedInt32( m, f, 0 ) ; for( int i = 1 ; i != l ; ++i ) s << ',' << r->GetRepeatedInt32( m, f, i ) ; } s << '\n' ; } // seen bases: same as array of ints, but we have four interleaved // arrays void show_seen_bases( const Message& m, const Reflection* r, const FieldDescriptor* f, ostream& s, int indent ) { for( int i = 0 ; i != 4 ; ++i ) { s << string( indent, ' ' ) << f->name() << '_' << "ACGT"[i] << ": " ; int l = r->FieldSize( m, f ) ; if( i <= l ) { s << r->GetRepeatedUInt32( m, f, i ) ; for( int j = i+4 ; j < l ; j+=4 ) s << ',' << r->GetRepeatedUInt32( m, f, j ) ; } s << '\n' ; } } // Hit: basically a generic message, but we add the textual, // line-wrapped alignment (if present) void show_hit( const Message& m, const Reflection* r, const FieldDescriptor* f, ostream& s, int i ) { for( int j = 0 ; j != r->FieldSize( m, f ) ; ++j ) { const output::Hit& h = static_cast( r->GetRepeatedMessage( m, f, j ) ) ; s << string( i, ' ' ) << f->name() << " {\n" ; generic_show_known_fields( h, s, i+2 ) ; // prints a hit: REF & QRY are hidden anyway; here we add them if( h.has_aln_ref() && h.has_aln_qry() && h.aln_ref().size() == h.aln_qry().size() ) { const std::string& r = h.aln_ref(), q = h.aln_qry() ; for( size_t k = 0 ; k < r.size() ; k += 50 ) { s << '\n' ; s << string( i+2, ' ' ) << "REF: " << r.substr( k, 50 ) << '\n' ; s << string( i+2, ' ' ) << "QRY: " << q.substr( k, 50 ) << '\n' ; s << string( i+2, ' ' ) << "CNS: " ; for( size_t l = k ; l != k+50 && l != r.size() ; ++l ) s << " *"[ r[l] == q[l] ] ; s << '\n' ; } } generic_show_unknown_fields( r->GetUnknownFields(m), s, i+2 ) ; s << string( i, ' ' ) << "}\n" ; } } void generic_show_string( const string& s, std::ostream& o, int off = 0 ) { o << '"' ; for( size_t i = 0 ; i != s.size() ; ++i ) { unsigned c = (unsigned char)s[i] + off ; switch( c ) { case '\r': o << "\\r" ; break ; case '\n': o << "\\n" ; break ; case '"': o << "\\\"" ; break ; case '\\': o << "\\\\" ; break ; case '\t': o << "\\t" ; break ; default: if( c >= ' ' && c <= '~' && c != '"' ) o << (char)c ; else o << '\\' << (char)( '0' + ((c >> 6) & 7) ) << (char)( '0' + ((c >> 3) & 7) ) << (char)( '0' + ((c >> 0) & 7) ) ; } } o << '"' ; } void show_quality( const Message& m, const Reflection* r, const FieldDescriptor* f, ostream& s, int i ) { s << string( i, ' ' ) << f->name() << ": " ; generic_show_string( r->GetString( m, f ), s, 33 ) ; s << '\n' ; } namespace { class Symtab { private: map< string, PrintMethod > m ; public: Symtab() { m[ "show_quality" ] = show_quality ; m[ "show_seen_bases" ] = show_seen_bases ; m[ "show_uint32_array" ] =show_uint32_array ; m[ "show_int32_array" ] = show_int32_array ; m[ "show_hit" ] = show_hit ; m[ "show_cigar" ] = show_cigar ; m[ "show_noop" ] = show_noop ; } PrintMethod find_method( const string& k ) const { map< string, PrintMethod >::const_iterator i = m.find( k ) ; return i == m.end() ? 0 : i->second ; } } ; static Symtab the_symtab ; } ; void universal_print_field( const Message& m, const Reflection* r, const FieldDescriptor* f, ostream& s, int indent ) { if( f->options().HasExtension( output::show ) ) { const std::string& method_name = f->options().GetExtension( output::show ) ; if( PrintMethod p = the_symtab.find_method( method_name ) ) return p( m, r, f, s, indent ) ; std::stringstream ss ; ss << "TextWriter: " << method_name << " declared for " << m.GetDescriptor()->name() << "::" << f->name() << ", but not found." ; console.output( Console::warning, ss.str() ) ; } if( f->label() == FieldDescriptor::LABEL_REPEATED ) { for( int i = 0 ; i != r->FieldSize( m, f ) ; ++i ) { s << string( indent, ' ' ) << f->name() ; if( f->cpp_type() != FieldDescriptor::CPPTYPE_MESSAGE ) s << ':' ; s << ' ' ; switch( f->cpp_type() ) { case FieldDescriptor::CPPTYPE_INT32: s << r->GetRepeatedInt32( m, f, i ) ; break ; case FieldDescriptor::CPPTYPE_INT64: s << r->GetRepeatedInt64( m, f, i ) ; break ; case FieldDescriptor::CPPTYPE_UINT32: s << r->GetRepeatedUInt32( m, f, i ) ; break ; case FieldDescriptor::CPPTYPE_UINT64: s << r->GetRepeatedUInt64( m, f, i ) ; break ; case FieldDescriptor::CPPTYPE_DOUBLE: s << r->GetRepeatedDouble( m, f, i ) ; break ; case FieldDescriptor::CPPTYPE_FLOAT: s << r->GetRepeatedFloat( m, f, i ) ; break ; case FieldDescriptor::CPPTYPE_BOOL: s << ( r->GetRepeatedBool( m, f, i ) ? "true" : "false" ) ; break ; case FieldDescriptor::CPPTYPE_ENUM: s << r->GetRepeatedEnum( m, f, i )->name() ; break ; case FieldDescriptor::CPPTYPE_STRING: generic_show_string( r->GetRepeatedString( m, f, i ), s ) ; break ; case FieldDescriptor::CPPTYPE_MESSAGE: generic_show_message( r->GetRepeatedMessage( m, f, i ), s, indent ) ; break ; default: std::cerr << "don't know how to print cpp_type " << f->cpp_type() << "\n" ; } s << '\n' ; } } else { s << string( indent, ' ' ) << f->name() ; if( f->cpp_type() != FieldDescriptor::CPPTYPE_MESSAGE ) s << ':' ; s << ' ' ; switch( f->cpp_type() ) { case FieldDescriptor::CPPTYPE_INT32: s << r->GetInt32( m, f ) ; break ; case FieldDescriptor::CPPTYPE_INT64: s << r->GetInt64( m, f ) ; break ; case FieldDescriptor::CPPTYPE_UINT32: s << r->GetUInt32( m, f ) ; break ; case FieldDescriptor::CPPTYPE_UINT64: s << r->GetUInt64( m, f ) ; break ; case FieldDescriptor::CPPTYPE_DOUBLE: s << r->GetDouble( m, f ) ; break ; case FieldDescriptor::CPPTYPE_FLOAT: s << r->GetFloat( m, f ) ; break ; case FieldDescriptor::CPPTYPE_BOOL: s << ( r->GetBool( m, f ) ? "true" : "false" ) ; break ; case FieldDescriptor::CPPTYPE_ENUM: s << r->GetEnum( m, f )->name() ; break ; case FieldDescriptor::CPPTYPE_STRING: generic_show_string( r->GetString( m, f ), s ) ; break ; case FieldDescriptor::CPPTYPE_MESSAGE: generic_show_message( r->GetMessage( m, f ), s, indent ) ; break ; default: std::cerr << "don't know how to print cpp_type " << f->cpp_type() << "\n" ; } s << '\n' ; } } void generic_show_known_fields( const Message& m, std::ostream& s, int indent ) { const Reflection* reflection = m.GetReflection() ; std::vector< const FieldDescriptor* > fields; reflection->ListFields( m, &fields ) ; for( size_t i = 0 ; i < fields.size() ; i++ ) { universal_print_field( m, reflection, fields[i], s, indent ) ; } } void generic_show_unknown_fields( const UnknownFieldSet& fields, std::ostream& s, int indent ) { for( int i = 0 ; i != fields.field_count() ; ++i ) { UnknownField f = fields.field( i ) ; s << string( indent, ' ' ) << f.number() ; if( f.type() != UnknownField::TYPE_GROUP ) s << ':' ; s << ' ' ; switch( f.type() ) { case UnknownField::TYPE_VARINT: s << f.varint() ; break ; case UnknownField::TYPE_FIXED32: s << f.fixed32() ; break ; case UnknownField::TYPE_FIXED64: s << f.fixed64() ; break ; case UnknownField::TYPE_LENGTH_DELIMITED: generic_show_string( f.length_delimited(), s ) ; break ; case UnknownField::TYPE_GROUP: s << "{\n" ; generic_show_unknown_fields( f.group(), s, indent+2 ) ; s << string( indent, ' ' ) << "}" ; break ; default: s << "???" ; break ; } s << '\n' ; } } void generic_show_message( const Message& m, std::ostream& s, int indent ) { s << "{\n" ; generic_show_known_fields( m, s, indent+2 ) ; generic_show_unknown_fields( m.GetReflection()->GetUnknownFields(m), s, indent+2 ) ; s << string( indent, ' ' ) << "}" ; } void show_message( const std::string& name, const Message& m, std::ostream& s ) { s << name << ' ' ; generic_show_message( m, s, 0 ) ; s << "\n\n\n" ; } void TextWriter::put_header( const Header& h ) { Stream::put_header( h ) ; show_message( "Header", h, *out_ ) ; } void TextWriter::put_result( const Result& r ) { show_message( "Result", r, *out_ ) ; } void TextWriter::put_footer( const Footer& f ) { Stream::put_footer( f ) ; show_message( "Footer", f, *out_ ) ; } //! \page anfo_to_sam Conversion to SAM //! \c anfo2sam converts a single ANFO file into a single SAM file. If //! the ANFO file is sorted by genome coordinate, the resulting SAM file //! will be sorted, too, and be labelled correctly, so it can directly //! be converted to BAM and be indexed. A few decisions had to be made //! on the interpretation of SAM fields. //! //! About MAPQ: this is supposed to be the "quality of the mapping", //! which should apparently be interpreted as confidence in the aligned //! position. We can infer this from the score of the best and the //! second best alignment: if the difference is D, then the best //! alignment is exp(D/10) times more likely than the second best. The //! SAM documentation hints that this is exactly the quantity they want //! to encode in MAPQ, so all we need to do is rescale it (from natural //! to decadic logarithm). If there is no second hit, we'll assume a //! "perfect" mapping by writing out a 255. //! //! About the hit to convert: ANFO is happy representing more than one //! hit per sequence, but SAM is not (or is it?). We will convert //! either the best hit globallly or the best one to a given genome. //! This is both the most useful alignment and the one best in line with //! the intended use of SAM. //! //! About len: since we're doing semi-global alignments, it is actually //! an error if the sequence length (taking trim points into account) //! and the effective len from the cigar do not match. However, files //! with such errors exist, so we need to filter out those faulty //! alignments. //! //! About the CIGAR line: parts of the samtools suite fail if an //! alignment declares an insertion that overhangs the reference. To //! deal with that, we declare inserts at the ends of alignments as soft //! clips instead. //! //! About the alignment score: This optional field of SAM is filled with //! the raw ANFO alignment score, which is a bit difficult to interpret //! if you're used to other aligners. A lower score means a better //! alignment, and a score of (length-20) * 18 is about the quality that //! would give a zero score in BLAST. Since SAM doesn't specify //! anything about the alignment, we'll leave it that way. //! //! \todo calculate other SAM/BAM flags template std::ostream& decode_binCigar(std::ostream& s, Iter begin, Iter end ) { std::vector< std::pair< unsigned, unsigned > > new_cigar ; unsigned len = 0, op = Hit::Match ; for( Iter cur = begin ; cur != end ; ++cur ) { unsigned o = cigar_op( *cur ), l = cigar_len( *cur ) ; if( o == Hit::Mismatch ) o = Hit::Match ; if( o == op ) len += l ; else { if( len ) new_cigar.push_back( std::make_pair( len, op ) ) ; op = o ; len = l ; } } if( len ) new_cigar.push_back( std::make_pair( len, op ) ) ; if( !new_cigar.empty() ) { if( new_cigar.front().second == Hit::Insert ) new_cigar.front().second = Hit::SoftClip ; if( new_cigar.back().second == Hit::Insert ) new_cigar.back().second = Hit::SoftClip ; } for( size_t i = 0 ; i != new_cigar.size() ; ++i ) s << new_cigar[i].first << "MIDNSHP"[ new_cigar[i].second ] ; return s ; } template std::reverse_iterator mk_rev_iter( Iter i ) { return std::reverse_iterator( i ) ; } inline char qual_to_sam( uint8_t q ) { return 33 + std::min( q, (uint8_t)93 ) ; } SamWriter::bad_stuff SamWriter::protoHit_2_bam_Hit( const output::Result &result ) { if (!result.read().has_seqid()) return no_seqid ; if (!result.read().has_sequence()) return no_seq ; for( int i = 0 ; i != result.hit_size() ; ++i ) { const output::Hit &hit = result.hit(0) ; if( len_from_bin_cigar( hit.cigar() ) != result.read().sequence().length() ) return bad_cigar ; // XXX there's an actual lower limit on map quality; we need to // get it from the configuration somehow int mapq = !hit.has_map_quality() ? 254 : std::min( 254, hit.map_quality() ) ; *out_ << /*QNAME*/ result.read().seqid() << '\t' << /*FLAG */ ( hit.aln_length() < 0 ? bam_freverse : 0 ) << '\t' << /*RNAME*/ hit.sequence() << '\t' << /*POS*/ 1 + hit.start_pos() << '\t' << /*MAPQ*/ mapq << '\t' ; if( hit.aln_length() >= 0 ) { decode_binCigar( *out_, hit.cigar().begin(), hit.cigar().end() ) ; /*CIGAR*/ // We don't have paired end reads (or don't deal with them) *out_ << "\t*\t0\t0\t" // MRNM, MPOS, ISIZE << /*SEQ*/ result.read().sequence() << '\t' ; if( result.read().has_quality() ) /*QUAL*/ for (size_t i = 0 ; i != result.read().quality().size() ; ++i ) *out_ << qual_to_sam( result.read().quality()[i] ) ; else *out_ << '*' ; } else { // need to revcom sequence, reverse qual and cigar decode_binCigar( *out_, mk_rev_iter( hit.cigar().end() ), mk_rev_iter( hit.cigar().begin() ) ) ; /*CIGAR*/ // We don't have paired end reads (or don't deal with them) *out_ << "\t*\t0\t0\t" ; // MRNM, MPOS, ISIZE const std::string& s = result.read().sequence() ; for( size_t i = s.size() ; i != 0 ; --i ) switch( s[i-1] ) { case 'A': case 'a': *out_ << 'T' ; break ; case 'C': case 'c': *out_ << 'G' ; break ; case 'G': case 'g': *out_ << 'C' ; break ; case 'T': case 't': case 'U': case 'u': *out_ << 'A' ; break ; default: *out_ << s[i-1] ; } *out_ << '\t' ; if( result.read().has_quality() ) /*QUAL*/ for (size_t i = result.read().quality().size() ; i != 0 ; --i ) *out_ << qual_to_sam( result.read().quality()[i-1] ) ; else *out_ << '*' ; } /*[TAGS]*/ /* score is actually phred likelihood */ if( hit.has_score() ) *out_ << "\tUQ:i:" << hit.score() ; *out_ << '\n' ; } if( result.hit_size() == 0 ) { // special treatment of unaligned sequence *out_ << /*QNAME*/ result.read().seqid() << '\t' << /*FLAG */ bam_funmap << "\t*\t0\t0\t*\t*\t0\t0\t" // RNAME, POS, MAPQ, CIGAR, MRNM, MPOS, ISIZE << /*SEQ*/ result.read().sequence() << '\t' ; if( result.read().has_quality() ) /*QUAL*/ for (size_t i = 0 ; i != result.read().quality().size() ; ++i ) *out_ << qual_to_sam( result.read().quality()[i] ) ; else *out_ << '*' ; /*[TAGS]*/ *out_ << "\n" ; return no_hit ; } else return goodness ; } const char *SamWriter::descr[] = { "were converted", "had no hit", "had multiple hits", "missed the sequence id" , "missed the sequence", "had a bad CIGAR" } ; void SamWriter::put_footer( const Footer& f ) { Stream::put_footer( f ) ; for( int b = 0 ; b != bad_stuff_max ; ++b ) if (discarded[b]) { std::stringstream s ; s << "SamWriter: " << nm_ << ": " << discarded[b] << " reads " << descr[b] ; console.output( Console::notice, s.str() ) ; } } //! \todo Coordinates in here are quite probably wrong (good thing //! nobody relies on them anyway). void FastaAlnWriter::put_result( const Result& r ) { if( const Hit* h = hit_to( r ) ) { if( h->has_aln_ref() && h->has_aln_qry() ) { *out_ << '>' << h->sequence() << ' ' << h->start_pos() << "-+"[ h->aln_length() > 0 ] << h->start_pos() + abs(h->aln_length()) - 1 << '\n' << h->aln_ref() << '\n' << '>' << r.read().seqid() << ( r.read().has_trim_right() ? " adapter cut off\n" : "\n" ) << h->aln_qry() << std::endl ; } } } void FastqWriter::put_result( const Result& rr ) { const output::Read& r = rr.read() ; if( r.has_quality() ) { *out_ << ( with_qual_ && r.has_quality() ? '@' : '>' ) << r.seqid() ; if( r.has_description() ) *out_ << ' ' << r.description() ; for( size_t i = 0 ; i < r.sequence().size() ; i += 50 ) *out_ << '\n' << r.sequence().substr( i, 50 ) ; *out_ << '\n' ; if( with_qual_ && r.has_quality() ) { *out_ << "+\n" ; const std::string& q = r.quality() ; for( size_t i = 0 ; i < q.size() ; i += 50 ) { for( size_t j = i ; j != i+50 && j != q.size() ; ++j ) *out_ << (char)std::min(126, 33 + (uint8_t)q[j]) ; *out_ << '\n' ; } } } } void TableWriter::put_result( const Result& r ) { if( const Hit *h = hit_to( r ) ) { int e = r.read().has_trim_right() ? r.read().trim_right() : r.read().sequence().size() ; int b = r.read().trim_left() ; int diff = h->has_map_quality() ? h->map_quality() : 9999 ; *out_ << e-b << '\t' << r.hit(0).score() << '\t' << diff << '\n' ; } } void WigCoverageWriter::put_result( const Result& r ) { // depth must be known at all if( !r.read().depth_size() ) return ; // assume one hit, but if there are more, take the best one const Hit* h = hit_to( r ) ; // must be on forward strand (by construction, in fact) if( !h || h->aln_length() <= 0 ) return ; *out_ << "fixedStep\tchrom=" << h->sequence() << "\tstart=" << h->start_pos() << "\tstep=1\n" ; int alnpos = 0 ; int cigar_maj = 0 ; size_t cigar_min = 0 ; while( alnpos != r.read().depth_size() && cigar_maj != h->cigar_size() ) { switch( cigar_op( h->cigar(cigar_maj) ) ) { case Hit::Match: case Hit::Mismatch: case Hit::Delete: *out_ << r.read().depth(alnpos) << '\n' ; ++alnpos ; break ; default: break ; } ++cigar_min ; while( cigar_maj != h->cigar_size() && cigar_min == cigar_len( h->cigar(cigar_maj) ) ) { ++cigar_maj ; cigar_min = 0 ; } } *out_ << '\n' ; } } // namespace anfo-0.98/src/sequence.cc0000644000371600007640000002750211447113463012246 00000000000000// Copyright 2009 Udo Stenzel // This file is part of ANFO // // ANFO is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // Anfo is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with Anfo. If not, see . #ifdef HAVE_CONFIG_H #include "../config.h" #endif #include "sequence.h" #include "logdom.h" #include "stream.h" #include #include #include using namespace std ; namespace { //! \brief test whether a line contains ASCII Q-scores //! \internal //! This is a small DFA that test whether a line contains only small //! ACSII encoded numbers separated by spaces. inline bool all_ascii_qscores( const std::string& s ) { int st = 0 ; for( size_t i = 0 ; i != s.length() ; ++i ) { if( isspace(s[i]) ) st = 0 ; else if( st == 0 && s[i] == '-' ) st = 1 ; else if( st == 0 && isdigit(s[i]) ) st = 2 ; else if( st == 1 && isdigit(s[i]) ) st = 2 ; else if( st == 2 && isdigit(s[i]) ) st = 3 ; else if( st == 3 && isdigit(s[i]) ) st = 4 ; else return false ; } return true ; } inline int sol_to_phred( int sol ) { return sol + (int)( 0.5 + 10 * log1p( pow( 10.0, -sol / 10.0 ) ) / log( 10.0 ) ) ; } int bits_in[] = { 0, 1, 1, 2, 1, 2, 2, 3, 1, 2, 2, 3, 2, 3, 3, 4 } ; class Reader { private: const char *buf_ ; int len_ ; google::protobuf::io::ZeroCopyInputStream *zis_ ; public: Reader( google::protobuf::io::ZeroCopyInputStream *zis ) : zis_(zis) { const void *p ; do { buf_ = zis_->Next( &p, &len_ ) ? (char*)p : 0 ; } while( buf_ && !len_ ) ; } ~Reader() { if( len_ && buf_ ) zis_->BackUp( len_ ) ; } operator const void* () const { return buf_ ; } char peek() const { return buf_ ? *buf_ : 0 ; } char get() { if( !buf_ ) return 0 ; const void *p ; char r = *buf_++ ; --len_ ; while( buf_ && !len_ ) { buf_ = zis_->Next( &p, &len_ ) ? (char*)p : 0 ; } return r ; } } ; inline void getword( Reader& r, std::string& s ) { s.clear() ; while( r && !isspace( r.peek() ) ) s.push_back( r.get() ) ; while( r && isspace( r.peek() && r.peek() != '\n' ) ) r.get() ; } inline void getline( Reader& r, std::string& s ) { s.clear() ; while( r && r.peek() != '\n' ) s.push_back( r.get() ) ; if( r ) r.get() ; } inline bool seq_continues( const Reader &s ) { char c = s.peek() ; return s && c != '@' && c != '>' && c != '+' && c != '*' ; } inline bool descr_follows( const Reader &s ) { return s && s.peek() == ';' ; } inline void skipline ( Reader &r ) { while( r && r.get() != '\n' ) ; } } QSequence::Base::Base( uint8_t a, int q ) : ambicode( a ), qscore( q ) { int bits = bits_in[ a ] ; Logdom prob = Logdom::from_phred( q ) ; for( int i = 0 ; i != 4 ; ++i ) { qscores[i] = a & (1<push_back( '\n' ) ; *r.mutable_description() += line ; } // If at this point we have a valid stream, we definitely have a // sequence. Bail out iff reading of the header failed. if( !s ) return false ; // read sequence while it continues // do not read gaps, ignore junk while( seq_continues(s) ) { string line ; getline( s, line ) ; // If line starts with "SQ ", we ignore it (4Q support). Scan // the rest for nucleotide codes. for( size_t i = line.substr(0,3) == "SQ " ? 3 : 0 ; i != line.size() ; ++i ) { if( encodes_nuc( line[i] ) ) { r.mutable_sequence()->push_back( line[i] ) ; } } } // if quality follows... if( s && s.peek() == '+' ) { // skip delimiter, name, and description no additional // description lines can follow, since ';' is a valid Q-score skipline(s) ; // Workaround for home-made broken FastQ files if( s && s.peek() == '*' ) { skipline(s) ; } // Q-scores must follow unless the sequence was empty or the stream ends else if( s && r.sequence().length() ) { string line ; getline( s, line ) ; // Check one line; if it contains only spaces and numbers in // groups of no more than three with an optional sign, it's // an Alta Cyclic or U Rockefeller file and we decode ASCII // numbers until the next header if( all_ascii_qscores(line) ) { int ix = 1 ; do { stringstream ss( line ) ; for( int q = 0 ; ss >> q ; ++ix ) r.mutable_quality()->push_back( solexa_scores ? sol_to_phred(q) : q ) ; if( !seq_continues(s) ) break ; getline( s, line ) ; } while( s ) ; } // No ASCII coding. Since delimiters aren't very useful // now, we'll take exactly one Q-score for each nucleotide, // ignoring LF and CR. else { size_t total = r.sequence().length(), ix = 0 ; do { for( size_t j = 0 ; ix != total && j != line.size() ; ++j ) { int q = line[j] ; if( q != 13 ) // skip CRs { r.mutable_quality()->push_back( solexa_scores ? sol_to_phred( q-origin ) : q-origin ) ; ++ix ; } } if( ix == total ) break ; getline( s, line ) ; } while( s ) ; // There might be some junk left over; but it will be // eaten away in the next call. } } } // We did get a sequence, no matter the stream state now, so no // failure. return r.IsInitialized() ; } namespace { inline std::string get_column( Reader& r ) { string s ; while( r && r.peek() != '\t' && r.peek() != '\n' ) s.push_back( r.get() ) ; while( r && r.peek() == '\t' ) r.get() ; return s ; } inline int get_int_column( Reader& r ) { int x = 0 ; while( r && isdigit( r.peek() ) ) x = 10*x + (r.get() - '0') ; while( r && r.peek() == '\t' ) r.get() ; return x ; } inline int get_cigar_column( Reader& r, google::protobuf::RepeatedField *cig ) { int len = 0 ; if( r && r.peek() == '*' ) r.get() ; // special code for empty CIGAR else while( r && r.peek() != '\t' && r.peek() != '\n' ) // ordinary CIGAR { int x = 0 ; output::Hit::Operation op ; while( r && isdigit( r.peek() ) ) x = 10*x + (r.get() - '0') ; if( r && isalpha( r.peek() ) ) { switch( r.get() ) { case 'M': op = output::Hit::Match ; len += x ; break ; case 'I': op = output::Hit::Insert ; break ; case 'D': op = output::Hit::Delete ; len += x ; break ; case 'S': op = output::Hit::SoftClip ; break ; case 'H': op = output::Hit::HardClip ; break ; case 'N': op = output::Hit::Skip ; len += x ; break ; case 'P': op = output::Hit::Pad ; break ; } cig->Add( streams::mk_cigar( op, x ) ) ; } } while( r && r.peek() == '\t' ) r.get() ; return len ; } inline bool get_opt_field( Reader& r, char *tag, int &intval, string &stringval ) { for( ;; ) { if( !r || !isalpha( r.peek() ) ) return false ; tag[0] = r.get() ; if( !r || !isalnum( r.peek() ) ) return false ; tag[1] = r.get() ; if( !r || r.get() != ':' || !r || !isalpha( r.peek() ) ) return false ; char key = r.get() ; if( !r || r.get() != ':' || !r ) return false ; switch( key ) { case 'i': intval = get_int_column( r ) ; return true ; case 'Z': stringval = get_column( r ) ; return true ; default: get_column( r ) ; } } } } ; // namespace bool read_sam( google::protobuf::io::ZeroCopyInputStream *zis, const string& genome, output::Result& r ) { for( Reader s( zis ) ; s ; skipline( s ) ) { bool good = true ; r.Clear() ; r.mutable_read()->set_seqid( get_column( s ) ) ; // QNAME int flags = get_int_column( s ) ; // FLAG output::Hit *h = r.add_hit() ; if( !genome.empty() ) h->set_genome_name( genome ) ; h->set_sequence( get_column( s ) ) ; // RNAME h->set_start_pos( get_int_column( s )-1 ) ; // POS int mapq = get_int_column( s ) ; // MAPQ if( mapq < 255 ) h->set_map_quality( mapq ) ; h->set_aln_length(get_cigar_column(s,h->mutable_cigar())) ; // CIGAR string junk = get_column( s ) ; // MRNM (ignored) get_int_column( s ) ; // MPOS (ignored) get_int_column( s ) ; // ISIZE (ignored) string seq = get_column( s ) ; // SEQ for( size_t i = 0 ; i != seq.size() ; ++i ) { char c = toupper( seq[i] ) ; if( c == '.' ) seq[i] = 'N' ; else if( strchr( "ACGTN", c ) ) seq[i] = c ; else { stringstream ss ; ss << "parse error in SAM file: illegal character " << c << " (" << (int)c << ") in SEQ field." ; console.output( Console::warning, ss.str() ) ; good = false ; } } r.mutable_read()->set_sequence( seq ) ; string qual = get_column( s ) ; // QUAL if( qual != "*" ) { for( size_t i = 0 ; i != qual.size() ; ++i ) qual[i] -= 33 ; r.mutable_read()->set_quality( qual ) ; } char tag[2] ; int intval = 0 ; string stringval ; while( get_opt_field( s, tag, intval, stringval ) ) // TAG:VTYPE:VALUE { if( tag[0] == 'U' && tag[1] == 'Q' ) h->set_score( intval ) ; if( tag[0] == 'A' && tag[1] == 'S' ) if( !h->has_score() ) h->set_score( intval ) ; } if( flags & 0x10 ) { h->set_aln_length( -h->aln_length() ) ; std::reverse( h->mutable_cigar()->begin(), h->mutable_cigar()->end() ) ; std::reverse( r.mutable_read()->mutable_sequence()->begin(), r.mutable_read()->mutable_sequence()->end() ) ; std::transform( r.mutable_read()->mutable_sequence()->begin(), r.mutable_read()->mutable_sequence()->end(), r.mutable_read()->mutable_sequence()->begin(), compl_ascii ) ; if( r.read().has_quality() ) std::reverse( r.mutable_read()->mutable_quality()->begin(), r.mutable_read()->mutable_quality()->end() ) ; } if( flags & 0x4 ) r.mutable_hit()->RemoveLast() ; // not actually aligned, get rid of the hit if( good && s && s.get() == '\n' ) return true ; // make sure the line was actually parsed } return false ; // end of stream, we're done } anfo-0.98/src/stream.cc0000644000371600007640000013607011447113464011733 00000000000000// Copyright 2009 Udo Stenzel // This file is part of ANFO // // ANFO is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // Anfo is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with Anfo. If not, see . #ifdef HAVE_CONFIG_H #include "../config.h" #endif #include "compress_stream.h" #include "misc_streams.h" #include "stream.h" #include "util.h" extern "C" { #include "fastlz.h" } #include #include #include #include #include #include #if HAVE_FCNTL_H #include #endif #include namespace std { bool operator < ( const output::Read& p, const output::Read& q ) { return p.SerializeAsString() < q.SerializeAsString() ; } bool operator < ( const config::Policy& p, const config::Policy& q ) { return p.SerializeAsString() < q.SerializeAsString() ; } } ; static inline void lower_string( std::string& s ) { size_t sl = s.size() ; for( size_t j = 0 ; j != sl ; ++j ) s[j] = tolower( s[j] ) ; } static inline std::string basename( const std::string& s ) { std::string::size_type p = s.rfind( '/' ) ; return p != std::string::npos ? s.substr(p+1) : s ; } namespace streams { using namespace google::protobuf::io ; using namespace output ; using namespace std ; int transfer( Stream& in, Stream& out ) { out.put_header( in.fetch_header() ) ; while( in.get_state() == Stream::have_output && out.get_state() == Stream::need_input ) out.put_result( in.fetch_result() ) ; out.put_footer( in.fetch_footer() ) ; return out.fetch_footer().exit_code() ; } int anfo_reader__num_files_ = 0 ; AnfoReader::AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) : is_( is ), name_( name ) { std::string magic ; CodedInputStream cis( is_.get() ) ; if( !cis.ReadString( &magic, 4 ) || magic != "ANFO" ) { throw ParseError( name_ + " is not an ANFO file" ) ; } else { uint32_t tag ; if( cis.ReadVarint32( &tag ) && tag == mk_msg_tag( 1 ) && cis.ReadVarint32( &tag ) ) { int lim = cis.PushLimit( tag ) ; if( hdr_.ParseFromCodedStream( &cis ) ) { sanitize( hdr_ ) ; cis.PopLimit( lim ) ; ++anfo_reader__num_files_ ; read_next_message( cis, name_ ) ; if( state_ == end_of_stream ) is_.reset( 0 ) ; return ; } } throw ParseError( "deserialization error in header of " + name_ ) ; } foot_.set_exit_code(1) ; } Result AnfoReader::fetch_result() { Result r ; swap( r, res_ ) ; CodedInputStream cis( is_.get() ) ; read_next_message( cis, name_ ) ; return r ; } namespace { void upgrade_cigar( google::protobuf::RepeatedField& n, const string& o ) { for( unsigned i = 0 ; i != o.size() ; ++i ) if( (uint8_t)o[i] < 128 ) n.Add( mk_cigar( Hit::Match, (unsigned)(uint8_t)o[i] ) ) ; else if( (uint8_t)o[i] < 192 ) n.Add( mk_cigar( Hit::Insert, (unsigned)(uint8_t)o[i] - 128 ) ) ; else n.Add( mk_cigar( Hit::Delete, (unsigned)(uint8_t)o[i] - 192 ) ) ; } Hit upgrade( const OldHit& o ) { Hit h ; h.set_genome_name( o.has_genome_name() ? o.genome_name() : string() ) ; lower_string( *h.mutable_genome_name() ) ; h.set_sequence( o.sequence() ) ; h.set_start_pos( o.start_pos() ) ; h.set_aln_length( o.aln_length() ) ; h.set_score( (int)( 0.5 + o.score() / log(10.0) ) ) ; if( o.has_evalue() ) h.set_evalue( o.evalue() ) ; if( o.has_taxid() ) h.set_taxid( o.taxid() ) ; if( o.has_taxid_species() ) h.set_taxid_species( o.taxid_species() ) ; if( o.has_taxid_order() ) h.set_taxid_order( o.taxid_order() ) ; upgrade_cigar( *h.mutable_cigar(), o.cigar() ) ; return h ; } Result upgrade( const OldResult& o ) { Result rs ; { Read &r = *rs.mutable_read() ; r.set_seqid( o.has_seqid() ? o.seqid() : string() ) ; if( o.has_description() ) r.set_description( o.description() ) ; r.set_sequence( o.sequence() ) ; if( o.has_quality() ) r.set_quality( o.quality() ) ; if( o.has_trim_left() ) r.set_trim_left( o.trim_left() ) ; if( o.has_trim_right() ) r.set_trim_right( o.trim_right() ) ; } rs.mutable_members()->MergeFrom( o.member() ) ; if( o.has_best_hit() ) *rs.add_hit() = upgrade( o.best_hit() ) ; if( o.has_best_to_genome() ) { Hit &h = *rs.add_hit() ; h = upgrade( o.best_to_genome() ) ; if( o.has_diff_to_next() ) h.set_map_quality( o.diff_to_next() ) ; if( o.has_diff_to_next_chromosome() ) h.set_diff_to_next_chromosome( o.diff_to_next_chromosome() ) ; if( o.has_diff_to_next_chromosome_class() ) h.set_diff_to_next_chromosome_class( o.diff_to_next_chromosome_class() ) ; } { AlnStats &a = *rs.add_aln_stats() ; a.set_reason( o.reason() ) ; if( o.has_num_raw_seeds() ) a.set_num_raw_seeds( o.num_raw_seeds() ) ; if( o.has_num_grown_seeds() ) a.set_num_grown_seeds( o.num_grown_seeds() ) ; if( o.has_num_clumps() ) a.set_num_clumps( o.num_clumps() ) ; if( o.has_num_useless() ) a.set_num_useless( o.num_useless() ) ; if( o.has_open_nodes_after_alignment() ) a.set_open_nodes_after_alignment( o.open_nodes_after_alignment() ) ; if( o.has_closed_nodes_after_alignment() ) a.set_closed_nodes_after_alignment( o.closed_nodes_after_alignment() ) ; if( o.has_tracked_closed_nodes_after_alignment() ) a.set_tracked_closed_nodes_after_alignment( o.tracked_closed_nodes_after_alignment() ) ; } if( o.has_diff_to_next_species() ) rs.set_diff_to_next_species( o.diff_to_next_species() ) ; if( o.has_diff_to_next_order() ) rs.set_diff_to_next_order( o.diff_to_next_order() ) ; return rs ; } } ; void Stream::read_next_message( google::protobuf::io::CodedInputStream& cis, const std::string& name ) { state_ = invalid ; uint32_t tag = 0 ; if( cis.ExpectAtEnd() ) { throw ParseError( name + " ended unexpectedly" ) ; } else if( (tag = cis.ReadTag()) ) { uint32_t size = 0 ; if( cis.ReadVarint32( &size ) ) { int lim = cis.PushLimit( size ) ; OldResult ores ; if( tag == mk_msg_tag( 4 ) && res_.ParseFromCodedStream( &cis ) ) { cis.PopLimit( lim ) ; state_ = have_output ; sanitize( res_ ) ; return ; } if( tag == mk_msg_tag( 2 ) && ores.ParseFromCodedStream( &cis ) ) { cis.PopLimit( lim ) ; state_ = have_output ; res_ = upgrade( ores ) ; sanitize( res_ ) ; return ; } if( tag == mk_msg_tag( 3 ) && foot_.ParseFromCodedStream( &cis ) ) { cis.PopLimit( lim ) ; state_ = end_of_stream ; return ; } throw ParseError( "deserialization error in " + name ) ; } } } inline uint8_t ChunkedWriter::method_of( int l ) { #if HAVE_LIBBZ2 && HAVE_BZLIB_H if( l >= 75 ) return bzip ; #endif #if HAVE_LIBZ && HAVE_ZLIB_H if( l >= 50 ) return gzip ; #endif if( l >= 10 ) return fastlz ; return none ; } inline uint8_t ChunkedWriter::level_of( int l ) { if( l >= 65 ) return 9 ; // thorough gzip or bzip if( l >= 30 ) return 2 ; // thorough fastlz or fast gzip return 1 ; // fast fastlz or none } void ChunkedWriter::init() { buf_.resize( default_buffer_size ) ; aos_.reset( new ArrayOutputStream( &buf_[0], buf_.size() ) ) ; CodedOutputStream o( zos_.get() ) ; o.WriteRaw( "ANF1", 4 ) ; } ChunkedWriter::ChunkedWriter( const pair< ZeroCopyOutputStream*, string >& p, int l ) : zos_( p.first ), name_( p.second ), wrote_(0), method_( method_of(l) ), level_( level_of(l) ) { init() ; } ChunkedWriter::ChunkedWriter( int fd, int l, const char* fname ) : zos_( new FileOutputStream( fd ) ), name_( fname ), wrote_(0), method_( method_of(l) ), level_( level_of(l) ) { init() ; } ChunkedWriter::ChunkedWriter( const char* fname, int l ) : zos_( new FileOutputStream( throw_errno_if_minus1( creat( fname, 0666 ), "opening", fname ) ) ), name_( fname ), wrote_(0), method_( method_of(l) ), level_( level_of(l) ) { init() ; } void ChunkedWriter::flush_buffer( unsigned needed ) { uint32_t uncomp_size = aos_->ByteCount() ; if( needed && buf_.size() - uncomp_size >= needed+8 ) return ; aos_.reset( 0 ) ; CodedOutputStream o( zos_.get() ) ; o.WriteLittleEndian32( uncomp_size ) ; // uncompressed size if( uncomp_size < 16 || method_ == none ) { // very small chunk: confuses compressors, so write uncompressed o.WriteLittleEndian32( uncomp_size ) ; // compressed size & compression method o.WriteRaw( &buf_[0], uncomp_size ) ; } else { vector< char > tmp ; uint32_t comp_size ; uLong comp_size_l ; switch( method_ ) { case fastlz: tmp.resize( uncomp_size * 21 / 20 + 67 ) ; comp_size = fastlz_compress_level( level_, &buf_[0], uncomp_size, &tmp[0] ) ; break ; #if HAVE_LIBZ && HAVE_ZLIB_H case gzip: comp_size_l = compressBound( uncomp_size ) ; tmp.resize( comp_size_l ) ; if( Z_OK != compress2( (Bytef*)&tmp[0], &comp_size_l, (const Bytef*)&buf_[0], uncomp_size, level_ ) ) throw "cannot happen! overflow in compress2" ; comp_size = comp_size_l ; break ; #endif #if HAVE_LIBBZ2 && HAVE_BZLIB_H case bzip: // docu says 5% is overkill. didn't work with 1% reserve, though... comp_size = uncomp_size * 21 / 20 + 601 ; tmp.resize( comp_size ) ; if( BZ_OK != BZ2_bzBuffToBuffCompress( &tmp[0], &comp_size, &buf_[0], uncomp_size, level_, 0, 0 ) ) throw "cannot happen! overflow in BZ2_bzBuffToBuffCompress" ; break ; #endif default: throw "cannot happen! unknown compression method" ; } o.WriteLittleEndian32( (uint32_t)(method_) << 28 | comp_size ) ; // compressed size & compression method o.WriteRaw( &tmp[0], comp_size ) ; } std::vector< char > newbuf ; newbuf.resize( max( (unsigned)default_buffer_size, needed+8 ) ) ; buf_.swap( newbuf ) ; aos_.reset( new ArrayOutputStream( &buf_[0], buf_.size() ) ) ; } void ChunkedWriter::put_header( const Header& h ) { write_delimited_message( aos_.get(), 1, h ) ; Stream::put_header( h ) ; flush_buffer() ; } void ChunkedWriter::put_footer( const Footer& f ) { flush_buffer() ; int64_t footer_start = zos_->ByteCount() ; write_delimited_message( aos_.get(), 3, f ) ; flush_buffer() ; CodedOutputStream cos( zos_.get() ) ; cos.WriteLittleEndian64( footer_start ) ; Stream::put_footer( f ) ; stringstream ss ; ss << name_ << ": footer chunk starts at " << footer_start ; console.output( Console::debug, ss.str() ) ; } void ChunkedWriter::put_result( const Result& r ) { flush_buffer( r.ByteSize() ) ; write_delimited_message( aos_.get(), 4, r ) ; ++wrote_ ; if( wrote_ % 1024 == 0 ) { stringstream s ; s << name_ << ": " << wrote_ << " msgs" ; chan_( Console::info, s.str() ) ; } } ChunkedWriter::~ChunkedWriter() { flush_buffer() ; } bool ChunkedReader::get_next_chunk() { if( ais_.get() && (unsigned)ais_->ByteCount() < buf_.size() ) return true ; ais_.reset( 0 ) ; CodedInputStream cis( is_.get() ) ; if( cis.ExpectAtEnd() ) return false ; uint32_t uncomp_size, comp_size ; if( !cis.ReadLittleEndian32( &uncomp_size ) || !cis.ReadLittleEndian32( &comp_size ) ) throw ParseError( "couldn't read chunk header from " + name_ ) ; int m = comp_size >> 28 ; comp_size &= ~(~0 << 28) ; vector< char > tmp ; buf_.resize( uncomp_size ) ; tmp.resize( comp_size ) ; if( !cis.ReadRaw( &tmp[0], comp_size ) ) throw ParseError( "couldn't read whole chunk from " + name_ ) ; uLongf dlen = uncomp_size ; switch( m ) { case ChunkedWriter::none: if( comp_size != uncomp_size ) throw "size of uncompressed chunk is wrong" ; buf_.swap( tmp ) ; break ; case ChunkedWriter::fastlz: if( (int)uncomp_size != fastlz_decompress( &tmp[0], comp_size, &buf_[0], uncomp_size ) ) throw "FastLZ decompression failed" ; break ; case ChunkedWriter::gzip: #if HAVE_LIBZ && HAVE_ZLIB_H if( Z_OK != uncompress( (Bytef*)&buf_[0], &dlen, (const Bytef*)&tmp[0], comp_size ) || uncomp_size != dlen ) throw "GZip decompression failed" ; #else throw "GZip'ed chunk found, but no zlib support present." ; #endif break ; case ChunkedWriter::bzip: #if HAVE_LIBBZ2 && HAVE_BZLIB_H if( BZ_OK != BZ2_bzBuffToBuffDecompress( &buf_[0], &uncomp_size, &tmp[0], comp_size, 0, 0 ) ) throw "BZip2 decompression failed" ; #else throw "Bzip'ed chunk found, but no libbz2 support present." ; #endif break ; default: throw "unknown compression method" ; } ais_.reset( new ArrayInputStream( &buf_[0], uncomp_size ) ) ; return true ; } ChunkedReader::ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) : is_( is ), name_( name ) { { std::string magic ; CodedInputStream cis( is_.get() ) ; if( !cis.ReadString( &magic, 4 ) || magic != "ANF1" ) throw ParseError( name_ + " is not an ANFO file" ) ; } if( !get_next_chunk() ) throw ParseError( "EOF before header in " + name_ ) ; { CodedInputStream cis( ais_.get() ) ; uint32_t tag ; if( !cis.ReadVarint32( &tag ) || tag != mk_msg_tag( 1 ) || !cis.ReadVarint32( &tag ) ) throw ParseError( "couldn't read message tag in " +name_ ) ; int lim = cis.PushLimit( tag ) ; if( !hdr_.ParseFromCodedStream( &cis ) ) throw ParseError( "deserialization error in header of " + name_ ) ; cis.PopLimit( lim ) ; } sanitize( hdr_ ) ; ++anfo_reader__num_files_ ; if( !get_next_chunk() ) throw ParseError( "EOF before payload in " + name_ ) ; CodedInputStream cis2( ais_.get() ) ; read_next_message( cis2, name_ ) ; } Result ChunkedReader::fetch_result() { Result r ; swap( r, res_ ) ; if( get_next_chunk() ) { CodedInputStream cis( ais_.get() ) ; read_next_message( cis, name_ ) ; if( state_ == end_of_stream ) { // skip backwards link (just because...) is_->Skip( 8 ) ; // delete and close(!) input(-file) is_.reset( 0 ) ; --anfo_reader__num_files_ ; } } else state_ = end_of_stream ; return r ; } template void nub( google::protobuf::RepeatedPtrField& r ) { set s ; size_t b = 0, e = r.size(), o = 0 ; for( ; b != e ; ++b ) { if( s.find( r.Get(b) ) == s.end() ) { s.insert( r.Get(b) ) ; if( b != o ) swap( *r.Mutable(o), *r.Mutable(b) ) ; ++o ; } } for( ; o != b ; ++o ) r.RemoveLast() ; } template void nub( google::protobuf::RepeatedField& r ) { set s ; size_t b = 0, e = r.size(), o = 0 ; for( ; b != e ; ++b ) { if( s.find( r.Get(b) ) == s.end() ) { s.insert( r.Get(b) ) ; if( b != o ) swap( *r.Mutable(o), *r.Mutable(b) ) ; ++o ; } } for( ; o != b ; ++o ) r.RemoveLast() ; } void merge_sensibly( Header& lhs, const Header& rhs ) { if( !lhs.IsInitialized() ) lhs = rhs ; else { bool no_task_id = !lhs.has_sge_task_id() || (rhs.has_sge_task_id() && lhs.sge_task_id() != rhs.sge_task_id()) ; bool no_job_id = !lhs.has_sge_job_id() || (rhs.has_sge_job_id() && lhs.sge_job_id() != rhs.sge_job_id()) ; bool keep_sort = lhs.is_sorted_by_name() == rhs.is_sorted_by_name() && lhs.has_is_sorted_by_all_genomes() == rhs.has_is_sorted_by_all_genomes() && lhs.is_sorted_by_coordinate_size() == rhs.is_sorted_by_coordinate_size() && equal( lhs.is_sorted_by_coordinate().begin(), lhs.is_sorted_by_coordinate().end(), rhs.is_sorted_by_coordinate().begin() ) ; lhs.MergeFrom( rhs ) ; if( no_task_id ) lhs.clear_sge_task_id() ; if( no_job_id ) lhs.clear_sge_job_id() ; if( !keep_sort ) { lhs.clear_is_sorted_by_name() ; lhs.clear_is_sorted_by_coordinate() ; lhs.clear_is_sorted_by_all_genomes() ; } } sanitize( lhs ) ; } void sanitize( Header& hdr ) { nub( *hdr.mutable_command_line() ) ; nub( *hdr.mutable_config()->mutable_policy() ) ; hdr.clear_was_sorted_by_coordinate() ; if( hdr.is_sorted_by_coordinate_size() == 1 && hdr.is_sorted_by_coordinate(0) == "" ) { hdr.clear_is_sorted_by_coordinate() ; hdr.set_is_sorted_by_all_genomes( true ) ; } } //! \brief sanity check, in case we are dealt broken files. //! This only sanitizes dangerous breakage. Right now we fix out of //! range trim points and quality strings of the wrong length. The //! fix is always to discard an optional field. //! //! \todo Check likelihood arrays and discard them in case of length //! mismatch. void sanitize_read( Read& rd ) { unsigned l = rd.sequence().length() ; if( rd.has_quality() && rd.quality().length() != l ) rd.clear_quality() ; if( rd.has_trim_right() && rd.trim_right() > l ) rd.clear_trim_right() ; if( rd.trim_left() > l ) rd.clear_trim_left() ; if( rd.has_description() && rd.description().empty() ) rd.clear_description() ; } void sanitize( Result& r ) { for( int i = 0 ; i != r.hit_size() ; ++i ) lower_string( *r.mutable_hit(i)->mutable_genome_name() ) ; sanitize_read( *r.mutable_read() ) ; for( int i = 0 ; i != r.members_size() ; ++i ) sanitize_read( *r.mutable_members(i) ) ; for( int i = 0 ; i != r.seeds_size() ; ++i ) { string& g = *r.mutable_seeds(i)->mutable_genome_name() ; lower_string( g ) ; if( g.substr( g.size()-4 ) == ".dna" ) g = g.substr( 0, g.size()-4 ) ; } } //! \brief merges two hits by keeping the better one void merge_sensibly( Hit& lhs, const Hit& rhs ) { // take better hit, recalculate diff_to_next{,_chromosome{,_class}} if( lhs.score() <= rhs.score() ) { // left is better // XXX there might be a more accurate way to calculate this if( !lhs.has_map_quality() || lhs.score() + lhs.map_quality() > rhs.score() ) lhs.set_map_quality( rhs.score() - lhs.score() ) ; //! \todo diff to chromosome, chromosome class? dunno... } else { // right is better if( !rhs.has_map_quality() || rhs.score() + rhs.map_quality() > lhs.score() ) { int d = lhs.score() - rhs.score() ; lhs = rhs ; lhs.set_map_quality( d ) ; } else lhs = rhs ; //! \todo diff to chromosome, chromosome class? dunno... } } //! \brief merges two results, keeping the best hit void merge_sensibly( Result& lhs, const Result& rhs ) { // How to merge what... // - read: all equal, no merging needed // - member: concatenate and remove doubles lhs.mutable_members()->MergeFrom( rhs.members() ) ; lhs.set_nmembers( lhs.nmembers() + rhs.nmembers() ) ; nub( *lhs.mutable_members() ) ; if( lhs.members_size() >= 8 ) { lhs.set_nmembers( lhs.nmembers() + lhs.members_size() ) ; lhs.clear_members() ; } // - hits: merge those for the same genome, concatenate the rest for( int j = 0 ; j != rhs.hit_size() ; ) { for( int i = 0 ; i != lhs.hit_size() ; ++i ) { if( rhs.hit(j).genome_name() == lhs.hit(i).genome_name() ) { merge_sensibly( *lhs.mutable_hit(i), rhs.hit(j) ) ; goto next ; } } *lhs.add_hit() = rhs.hit(j) ; next: ++j ; } // - aln_stats: just concat them, this is for debugging only anyway for( int i = 0 ; i != rhs.aln_stats_size() ; ++i ) *lhs.add_aln_stats() = rhs.aln_stats(i) ; // - diff_to_next_species, diff_to_next_order: TODO } //! \brief merges two footers //! Anything unexpected is simply merged, the resulting exit code is the //! logical or of the two inputs. void merge_sensibly( output::Footer& lhs, const output::Footer& rhs ) { int exit_code = lhs.exit_code() | rhs.exit_code() ; lhs.MergeFrom( rhs ) ; lhs.set_exit_code( exit_code ) ; } const output::Hit* hit_to( const output::Result& r ) { if( r.hit_size() ) { const output::Hit *h = &r.hit(0) ; for( int i = 1 ; i != r.hit_size() ; ++i ) if( r.hit(i).score() < h->score() ) h = &r.hit(i) ; return h ; } return 0 ; } const output::Hit* hit_to( const output::Result& r, const string& g ) { for( int i = 0 ; i != r.hit_size() ; ++i ) if( r.hit(i).genome_name() == g ) return &r.hit(i) ; return 0 ; } output::Hit* mutable_hit_to( output::Result* r ) { if( r->hit_size() ) { output::Hit *h = r->mutable_hit(0) ; for( int i = 1 ; i != r->hit_size() ; ++i ) if( r->hit(i).score() < h->score() ) h = r->mutable_hit(i) ; return h ; } return r->add_hit() ; } output::Hit* mutable_hit_to( output::Result* r, const string& g ) { for( int i = 0 ; i != r->hit_size() ; ++i ) if( r->hit(i).genome_name() == g ) return r->mutable_hit(i) ; Hit *h = r->add_hit() ; h->set_genome_name( g ) ; return h ; } void HitFilter::put_result( const Result& res ) { res_ = res ; int ix_in = 0, ix_out = 0 ; while( ix_in != res_.hit_size() ) { // keep hits if we're actually looking for a specific genome and // they hit the wrong one or if they actually fit our predicate if( ( !gs_.empty() && !contains( gs_, res_.hit(ix_in).genome_name() ) ) || keep( res_.hit(ix_in) ) ) { if( ix_in != ix_out ) swap( *res_.mutable_hit(ix_out), *res_.mutable_hit(ix_in) ) ; ++ix_out ; } ++ix_in ; } if( !ix_out ) res_.clear_hit() ; else while( ix_out != res_.hit_size() ) res_.mutable_hit()->RemoveLast() ; state_= have_output ; } bool OnlyGenome::xform( Result& res ) { int ix_in = 0, ix_out = 0 ; while( ix_in != res_.hit_size() ) { // keep hits if we're actually looking for a specific genome and // they hit the wrong one or if they actually fit our predicate if( contains( gs_, res.hit(ix_in).genome_name() ) ) { if( ix_in != ix_out ) swap( *res.mutable_hit(ix_out), *res.mutable_hit(ix_in) ) ; ++ix_out ; } ++ix_in ; } if( !ix_out ) res.clear_hit() ; else while( ix_out != res_.hit_size() ) res.mutable_hit()->RemoveLast() ; return true ; } bool ScoreFilter::keep( const Hit& h ) { return slope_ * ( len_from_bin_cigar( h.cigar() ) - intercept_ ) >= h.score() ; } bool TotalScoreFilter::xform( Result& r ) { int score = 0 ; for( int i = 0 ; i != r.hit_size() ; ++i ) if( contains( gs_, r.hit(i).genome_name() ) ) score += r.hit(i).score() ; return slope_ * ( effective_length( r.read() ) - intercept_ ) >= score ; } bool MapqFilter::keep( const Hit& h ) { return !h.has_map_quality() || h.map_quality() >= minmapq_ ; } bool QualFilter::xform( Result& h ) { const Read& r = h.read() ; return r.has_quality() && accumulate( r.quality().begin(), r.quality().end(), static_cast( 0 ), plus() ) >= r.quality().size() * minqual_ ; } bool LengthFilter::xform( Result& r ) { int len = effective_length( r.read() ) ; if( len < minlength_ || len > maxlength_ ) r.clear_hit() ; return true ; } bool GcFilter::xform( Result& r ) { const Read& rr = r.read() ; int u = rr.trim_left(), v = rr.has_trim_right() ? rr.trim_right() : rr.sequence().size() ; string::const_iterator s = rr.sequence().begin() ; int gc = 100 * (count( s+u, s+v, 'C' ) + count( s+u, s+v, 'G' )) / (v-u) ; return mingc_ <= gc && gc <= maxgc_ ; } namespace { bool good_hit( const Hit& h, const vector& gs, const vector& ss ) { return ( gs.empty() || contains( gs, h.genome_name() ) ) && ( ss.empty() || contains( ss, h.sequence() ) ) ; } } ; bool RequireHit::xform( Result& r ) { for( int i = 0 ; i != r.hit_size() ; ++i ) if( good_hit( r.hit(i), gs_, ss_ ) ) return true ; return false ; } bool RequireBestHit::xform( Result& r ) { const Hit *h = hit_to( r ) ; return h && good_hit( *h, gs_, ss_ ) ; } bool Subsample::xform( Result& ) { return f_ >= drand48() ; } bool RmdupStream::is_duplicate( const Result& lhs, const Result& rhs ) const { const output::Hit *l = hit_to( lhs, gs_.begin(), gs_.end() ), *r = hit_to( rhs, gs_.begin(), gs_.end() ) ; by_genome_coordinate comp ; return l && r && !comp( *l, *r, lhs.read(), rhs.read() ) && !comp( *r, *l, rhs.read(), lhs.read() ) ; } //! \todo How do we deal with ambiguity codes? What's the meaning of //! their quality scores anyway? //! \todo Undefined mapq is interpreted as 254, but there's a better //! value hidden somewhere in the header. void RmdupStream::add_read( const Result& rhs ) { // if the new member is itself a cluster, we add its member reads, // not the single synthetic one if( rhs.nmembers() ) { cur_.set_nmembers( rhs.nmembers() + cur_.nmembers() + cur_.members_size() ) ; cur_.clear_members() ; } else if( rhs.members_size() ) for( int i = 0 ; i != rhs.members_size() ; ++i ) *cur_.add_members() = rhs.members(i) ; else *cur_.add_members() = rhs.read() ; if( cur_.members_size() >= 8 ) { cur_.set_nmembers( cur_.nmembers() + cur_.members_size() ) ; cur_.clear_members() ; } const output::Hit *h = hit_to( rhs, gs_.begin(), gs_.end() ) ; int mapq = h ? h->has_map_quality() ? h->map_quality() : 254 : 0 ; for( size_t i = 0 ; i != rhs.read().sequence().size() ; ++i ) { int base = -1 ; switch( rhs.read().sequence()[i] ) { case 'a': case 'A': base = 0 ; break ; case 'c': case 'C': base = 1 ; break ; case 't': case 'T': case 'u': case 'U': base = 2 ; break ; case 'g': case 'G': base = 3 ; break ; } Logdom qual = Logdom::from_phred( std::min( mapq, rhs.read().has_quality() ? rhs.read().quality()[i] : 30 ) ) ; for( int j = 0 ; j != 4 ; ++j ) // XXX distribute errors sensibly quals_[j].at(i) *= j != base ? qual / 3 : 1 - qual ; } } //! \brief returns the next result //! This also has to change state. If we haven't seen a footer, we //! request more input. Else we're at end of stream. Result RmdupStream::fetch_result() { Result r ; swap( r, res_ ) ; state_ = have_foot_ ? end_of_stream : need_input ; return r ; } namespace { void limit_quality( Read& r, uint8_t maxq ) { if( !r.has_quality() ) return ; for( size_t i = 0 ; i != r.quality().size() ; ++i ) if( r.quality()[i] > maxq ) (*r.mutable_quality())[i] = maxq ; } } ; //! \brief signals end of input stream //! After the footer no more input is possible. We were waiting for //! input, so no output was available. cur_ might contain valid data, //! and if so, we call a consensus and offer it as output. Else we //! signal end of stream. void RmdupStream::put_footer( const Footer& f ) { Stream::put_footer( f ) ; if( cur_.IsInitialized() ) { state_ = have_output ; call_consensus() ; swap( cur_, res_ ) ; } have_foot_ = true ; } inline bool RmdupStream::good_score( const Hit* h ) const { int mscore = int( 0.5 + slope_ * ( len_from_bin_cigar( h->cigar() ) - intercept_ ) ) ; return !h->has_score() || h->score() == 0 || h->score() <= mscore ; } //! \brief receives a result record and merges it if appropriate //! //! There are the following possibilities what to do here: //! - A result with a bad alignment, but correct coordinates is passed //! through (means it is stored in res_ and output becomes available). //! - If cur_ is invalid, the result is stored there and cur_ becomes //! valid. //! - A result with correct coordinates (according to is_duplicate) is //! directly merged into cur_, no output becomes available. //! - Anything else cannot be merged, so a consensus is called, cur_ //! moves to res_, next moves to cur_, and output becomes available. void RmdupStream::put_result( const Result& next ) { const Hit *h = hit_to( next, gs_.begin(), gs_.end() ) ; const Hit *h0 = hit_to( cur_, gs_.begin(), gs_.end() ) ; // first check: is anything buffered? if( !cur_.IsInitialized() ) { // empty buffer. if we now get a good alignment, we store it. // anything else passed through if( h && good_score( h ) ) { cur_ = next ; for( size_t i = 0 ; i != 4 ; ++i ) { quals_[i].clear() ; quals_[i].resize( cur_.read().sequence().size() ) ; } } else { // bad alignment or none at all -- this one passes through // without merging. we clamp qualities, though res_ = next ; Read &r = *res_.mutable_read() ; limit_quality( r, maxq_ ) ; state_ = have_output ; } } // something is stored. If it has a bad alignment, we need to get // rid of it, which makes room to store the next alignment. (Very // annoying, but it's a good thing we never need more than one slot // for buffering...) else if( !h0 || !good_score( h ) ) { swap( res_, cur_ ) ; Read &r = *res_.mutable_read() ; limit_quality( r, maxq_ ) ; state_ = have_output ; cur_ = next ; for( size_t i = 0 ; i != 4 ; ++i ) { quals_[i].clear() ; quals_[i].resize( cur_.read().sequence().size() ) ; } } // we got something stored, and it is known to be eligible for // merging. if we get a matched alignment, we need to check if the // new one is any good... else if( h && is_duplicate( cur_, next ) ) { if( good_score( h ) ) { // a good one, we need to actually merge it. If cur_ is a // plain result, turn it into a degenerate merged one // first... if( cur_.members_size() + cur_.nmembers() == 0 ) { add_read( cur_ ) ; cur_.mutable_read()->set_seqid( "C_" + cur_.read().seqid() ) ; cur_.mutable_read()->clear_description() ; } // Merge the new one. No state change necessary, we continue to // request input. add_read( next ) ; } else { // the new one is crap. Pass it on, keep whatever is in // the accumulator. res_ = next ; Read &r = *res_.mutable_read() ; limit_quality( r, maxq_ ) ; state_ = have_output ; } } else { // we got something that has wrong coordinates or no alignment // at all. Call a consensus for cur_, then move it to res_. // State that output is available, and store new result in cur_. call_consensus() ; swap( res_, cur_ ) ; cur_ = next ; for( size_t i = 0 ; i != 4 ; ++i ) { quals_[i].clear() ; quals_[i].resize( cur_.read().sequence().size() ) ; } state_ = have_output ; } } void RmdupStream::call_consensus() { if( !cur_.members_size() && !cur_.nmembers() ) { limit_quality( *cur_.mutable_read(), maxq_ ) ; return ; } cur_.mutable_read()->clear_sequence() ; cur_.mutable_read()->clear_quality() ; for( size_t i = 0 ; i != quals_[0].size() ; ++i ) { // select base with highest quality size_t m = 0 ; for( size_t j = 1 ; j != 4 ; ++j ) if( quals_[j].at( i ) > quals_[m].at( i ) ) m = j ; // but calculate the error probability from _all_others_ to // retain precision Logdom denom = Logdom::null(), num = Logdom::null() ; for( size_t j = 0 ; j != 4 ; ++j ) { denom += quals_[j].at( i ) ; if( j != m ) num += quals_[j].at( i ) ; } int qscore = (num/denom).to_phred() ; if( qscore > maxq_ ) qscore = maxq_ ; cur_.mutable_read()->mutable_sequence()->push_back( m["ACTG"] ) ; cur_.mutable_read()->mutable_quality()->push_back( qscore ) ; } } //! \todo Tends to return the header from the first input stream, but //! will accumulate further headers (and throw them away). This is //! necessary, because we cannot look ahead to further headers. Clearly //! a better solution would be great, but doesn't readily present //! itself. Could adding arbitrary header information to the footer //! work? Header ConcatStream::fetch_header() { for( state_ = invalid ; state_ == invalid ; ) { if( streams_.empty() ) state_ = end_of_stream ; else { merge_sensibly( hdr_, streams_[0]->fetch_header() ) ; if( streams_[0]->get_state() == have_output ) state_ = have_output ; else { merge_sensibly( foot_, streams_[0]->fetch_footer() ) ; streams_.pop_front() ; } } } return hdr_ ; } Result ConcatStream::fetch_result() { Result r = streams_[0]->fetch_result() ; for( state_ = invalid ; state_ == invalid ; ) { if( streams_.empty() ) state_ = end_of_stream ; else if( streams_[0]->get_state() == have_output ) state_ = have_output ; else { merge_sensibly( foot_, streams_[0]->fetch_footer() ) ; streams_.pop_front() ; if( !streams_.empty() ) merge_sensibly( hdr_, streams_[0]->fetch_header() ) ; } } return r ; } bool QualMasker::xform( Result& r ) { if( r.read().has_quality() ) for( size_t i = 0 ; i != r.read().sequence().size() && i != r.read().quality().size() ; ++i ) if( r.read().quality()[i] < q_ ) (*r.mutable_read()->mutable_sequence())[i] = 'N' ; return true ; } namespace { class StreamWithProgress : public google::protobuf::io::ZeroCopyInputStream { private: std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; std::string name_ ; int64_t total_, read_ ; Chan out_ ; bool check( bool p ) { if( !p ) out_.close() ; else if( is_->ByteCount() >> 16 != read_ >> 16 ) { read_ = is_->ByteCount() ; stringstream s ; s << name_ << ": " << read_ ; if( total_ ) s << '/' << total_ ; s << " Bytes" ; if( total_ ) s << " (" << read_*100/total_ << "%)" ; out_( Console::info, s.str() ) ; } return p ; } public: StreamWithProgress( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, int64_t total ) : is_( is ), name_( basename( name ) ), total_( total ), read_( 0 ) {} virtual bool Next( const void **data, int *size ) { return check( is_->Next( data, size ) ) ; } virtual void BackUp( int count ) { is_->BackUp( count ) ; } virtual bool Skip( int count ) { return check( is_->Skip( count ) ) ; } virtual int64_t ByteCount() const { return is_->ByteCount() ; } } ; bool magic( const void *p, int l, const char* sig ) { for( const char* q = (const char*)p ; *sig ; ++q, --l, ++sig ) if( !l || *q != *sig ) return false ; return true ; } bool is_crap( const void *p, int l ) { return l >= 4 && *((const uint32_t*)p) == 0 ; } bool is_fastq( const void *p, int l ) { const uint8_t* q = (const uint8_t*)p ; return l >= 3 && (*q == '>' || *q == '@') && isprint( q[1] ) && !magic( p, l, "@HD" ) ; } bool is_sam( const void *p, int l ) { const uint8_t* q = (const uint8_t*)p ; if( l < 8 ) return false ; for( int i = 0 ; i != 8 ; ++i ) if( !isprint( q[i] ) ) return false ; return true ; } StreamHolder make_input_stream_( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, bool solexa_scores, char origin, const string& genome ) { // peek into stream, but put it back. then check magic numbers and // create the right stream const void* p ; int l ; if( !is->Next( &p, &l ) ) return new Stream() ; // gives an empty stream is->BackUp( l ) ; if( magic( p, l, "ANFO" ) ) { console.output( Console::debug, name + ": linear ANFO file" ) ; return new AnfoReader( is, name ) ; } if( magic( p, l, "ANF1" ) ) { console.output( Console::debug, name + ": chunked ANFO file" ) ; return new ChunkedReader( is, name ) ; } if( magic( p, l, ".sff" ) ) { console.output( Console::debug, name + ": SFF file" ) ; return new SffReader( is, name ) ; } if( magic( p, l, "BAM\x01" ) ) { console.output( Console::debug, name + ": BAM file" ) ; if( genome.empty() ) console.output( Console::warning, name + ": no genome set for BAM parsing" ) ; return new BamReader( is, name, genome ) ; } if( magic( p, l, "BZh" ) ) { #if HAVE_LIBBZ2 && HAVE_BZLIB_H console.output( Console::debug, name + ": BZip compressed" ) ; std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > bs( new BunzipStream( is ) ) ; return make_input_stream_( bs, name, solexa_scores, origin, genome ) ; #else throw "found BZip'ed file, but have no libbz2 support" ; #endif } if( magic( p, l, "\x1f\x8b" ) ) { #if HAVE_LIBZ && HAVE_ZLIB_H console.output( Console::debug, name + ": GZip compressed" ) ; std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > zs( new InflateStream( is ) ) ; return make_input_stream_( zs, name, solexa_scores, origin, genome ) ; #else throw "found GZip'ed file, but have no zlib support" ; #endif } if( is_crap( p, l ) ) { throw name + ": corrupt file" ; } if( is_fastq( p, l ) ) { console.output( Console::debug, name + ": probably FastA or FastQ" ) ; return new FastqReader( is, solexa_scores, origin ) ; } if( is_sam( p, l ) ) { console.output( Console::notice, name + ": unknown, probably SAM" ) ; if( genome.empty() ) console.output( Console::warning, name + ": no genome set for SAM parsing" ) ; return new SamReader( is, name, genome ) ; } throw name + ": weird unrecognized file" ; } } ; UniversalReader::UniversalReader( const std::string& name, google::protobuf::io::ZeroCopyInputStream* is, bool solexa_scores, int origin, const string& genome ) : is_( is ), name_( name ), str_(), solexa_scores_( solexa_scores ), origin_( origin ), genome_( genome ) { // we cannot open the file just yet, but we can check if it is there if( !is_.get() ) throw_errno_if_minus1( access( name_.c_str(), R_OK ), "accessing ", name_.c_str() ) ; } Header UniversalReader::fetch_header() { if( !str_ ) { if( !is_.get() ) { int fd = throw_errno_if_minus1( open( name_.c_str(), O_RDONLY ), "opening (UniversalReader) ", name_.c_str() ) ; std::auto_ptr< google::protobuf::io::FileInputStream > s( new google::protobuf::io::FileInputStream( fd ) ) ; s->SetCloseOnDelete( true ) ; struct stat st ; if( fstat( fd, &st ) ) is_ = s ; else is_.reset( new StreamWithProgress( std::auto_ptr(s), name_, st.st_size ) ) ; } str_ = make_input_stream_( is_, name_, solexa_scores_, origin_, genome_ ) ; } return str_->fetch_header() ; } uint8_t SffReader::read_uint8() { while( !buf_size_ ) if( !is_->Next( &buf_, &buf_size_ ) ) throw "BamReader: premature end of file in " + name_ ; uint8_t x = *(const char*)buf_ ; buf_ = (const char*)buf_ + 1 ; --buf_size_ ; return x ; } uint16_t SffReader::read_uint16() { return ((uint16_t)read_uint8() << 8) | read_uint8() ; } uint32_t SffReader::read_uint32() { return ((uint32_t)read_uint16() << 16) | read_uint16() ; } void SffReader::read_string( unsigned l, string* s ) { s->clear() ; while( l ) { if( !buf_size_ && !is_->Next( &buf_, &buf_size_ ) ) throw "BamReader: premature end of file in " + name_ ; while( buf_size_ && l ) { s->push_back( *(char*)buf_ ) ; --l ; --buf_size_ ; buf_ = (const char*)buf_ + 1 ; } } } void SffReader::skip( int l ) { while( l ) { if( !buf_size_ && !is_->Next( &buf_, &buf_size_ ) ) throw "BamReader: premature end of file in " + name_ ; unsigned k = min( l, buf_size_ ) ; l -= k ; buf_size_ -= k ; buf_ = (char*)buf_ + k ; } } Header SffReader::fetch_header() { // common header as per section 13.3.8.1 of 454 manual if( read_uint32() != 0x2E736666 || read_uint32() != 1 ) throw "SffReader: " + name_ + " has wrong magic number or version" ; skip( 12 ) ; // index offset and length remaining_ = read_uint32() ; // number of reads unsigned hdr_length = read_uint16() ; // header length read_uint16() ; // length of key (ignored, is trimmed) number_of_flows_ = read_uint16() ; if( read_uint8() != 1 ) throw "SffReader: " + name_ + " has unknown flow format code" ; // rest is ignored, will lump it into the padding skip( hdr_length - 31 ) ; state_ = remaining_ ? have_output : end_of_stream ; hdr_.Clear() ; return hdr_ ; } Result SffReader::fetch_result() { res_.Clear() ; // read header as per section 13.3.8.2 of 454 manual unsigned hdr_length = read_uint16() ; unsigned name_length = read_uint16() ; unsigned num_bases = read_uint32() ; unsigned clip_qual_left = read_uint16() ; unsigned clip_qual_right = read_uint16() ; unsigned clip_adapter_left = read_uint16() ; unsigned clip_adapter_right = read_uint16() ; read_string( name_length, res_.mutable_read()->mutable_seqid() ) ; // read name skip( hdr_length - 16 - name_length ) ; // padding // read data as per section 13.3.8.3 of 454 manual skip( number_of_flows_ * 2 ) ; // flow values skip( num_bases ) ; // flow indexes read_string( num_bases, res_.mutable_read()->mutable_sequence() ) ; // bases read_string( num_bases, res_.mutable_read()->mutable_quality() ) ; // quality skip (7 - ((number_of_flows_ * 2 + num_bases * 3 -1) % 8)) ; // eight_byte_padding if( clip_qual_left || clip_adapter_left ) res_.mutable_read()->set_trim_left( max( clip_qual_left, clip_adapter_left ) -1 ) ; if( clip_qual_right && clip_adapter_right ) res_.mutable_read()->set_trim_right( res_.read().sequence().size() - min( clip_qual_right, clip_adapter_right ) ) ; else if( clip_qual_right ) res_.mutable_read()->set_trim_right( res_.read().sequence().size() - clip_qual_right ) ; else if( clip_adapter_right ) res_.mutable_read()->set_trim_right( res_.read().sequence().size() - clip_adapter_right ) ; if( !--remaining_ ) { state_ = end_of_stream ; is_.reset(0) ; } return res_ ; } uint8_t BamReader::read_uint8() { while( !buf_size_ ) if( !is_->Next( &buf_, &buf_size_ ) ) throw "BamReader: premature end of file in " + name_ ; uint8_t x = *(const char*)buf_ ; buf_ = (const char*)buf_ + 1 ; --buf_size_ ; return x ; } uint16_t BamReader::read_uint16() { return read_uint8() | ((uint16_t)read_uint8() << 8) ; } uint32_t BamReader::read_uint32() { return read_uint16() | ((uint32_t)read_uint16() << 16) ; } void BamReader::read_string( unsigned l, string* s ) { s->clear() ; while( l ) { if( !buf_size_ && !is_->Next( &buf_, &buf_size_ ) ) throw "BamReader: premature end of file in " + name_ ; while( buf_size_ && l ) { s->push_back( *(char*)buf_ ) ; --l ; --buf_size_ ; buf_ = (const char*)buf_ + 1 ; } } } BamReader::BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) : is_( is ), name_( name ), genome_( genome ), buf_(0), buf_size_(0) { if( read_uint32() != 0x014d4142 ) throw "missing BAM magic number" ; string sam_header ; read_string( read_uint32(), &sam_header ) ; unsigned nrefseq = read_uint32() ; refseqs_.resize( nrefseq ) ; for( unsigned i = 0 ; i != nrefseq ; ++i ) { read_string( read_uint32()-1, &refseqs_[i] ) ; read_uint8() ; // NUL terminator read_uint32() ; // chromosome length } while( buf_ && !buf_size_ ) if( !is_->Next( &buf_, &buf_size_ ) ) buf_ = 0 ; state_ = buf_ && buf_size_ ? have_output : end_of_stream ; } Result BamReader::fetch_result() { res_.Clear() ; Hit *h = res_.add_hit() ; unsigned bsize = read_uint32() ; unsigned refid = read_uint32() ; if( refid < refseqs_.size() ) h->set_sequence( refseqs_[ refid ] ) ; if( !genome_.empty() ) h->set_genome_name( genome_ ) ; h->set_start_pos( read_uint32() ) ; int namelen = read_uint8() ; int mapq = read_uint8() ; if( mapq < 255 ) h->set_map_quality( mapq ) ; read_uint16() ; // BIN int cigarlen = read_uint16() ; int flags = read_uint16() ; int seqlen = read_uint32() ; read_uint32() ; // MATE RID read_uint32() ; // MATE POS read_uint32() ; // INS SIZE read_string( namelen-1, res_.mutable_read()->mutable_seqid() ) ; read_uint8() ; unsigned aln_len = 0 ; for( int i = 0 ; i != cigarlen ; ++i ) { int cig = read_uint32() ; h->add_cigar( cig ) ; switch( cigar_op( cig ) ) { case Hit::Match: case Hit::Mismatch: case Hit::Delete: case Hit::Skip: aln_len += cigar_len( cig ) ; break ; case Hit::Insert: case Hit::SoftClip: case Hit::HardClip: case Hit::Pad: break ; } } h->set_aln_length( flags & 0x10 ? -aln_len : aln_len ) ; if( flags & 0x10 ) reverse( h->mutable_cigar()->begin(), h->mutable_cigar()->end() ) ; if( flags & 0x10 ) { string seq ; for( int i = 0 ; i != seqlen ; ++i ) { static char bases_rev[] = "=TG.C...A......N" ; uint8_t code = read_uint8() ; seq.push_back( bases_rev[ (code >> 4) & 0xf ] ) ; if( ++i == seqlen ) break ; seq.push_back( bases_rev[ code & 0xf ] ) ; } res_.mutable_read()->mutable_sequence()->assign( seq.rbegin(), seq.rend() ) ; } else { for( int i = 0 ; i != seqlen ; ++i ) { static char bases_fwd[] = "=AC.G...T......N" ; uint8_t code = read_uint8() ; res_.mutable_read()->mutable_sequence()->push_back( bases_fwd[ (code >> 4) & 0xf ] ) ; if( ++i == seqlen ) break ; res_.mutable_read()->mutable_sequence()->push_back( bases_fwd[ code & 0xf ] ) ; } } string qual ; read_string( seqlen, &qual ) ; bool has_qual = false ; for( unsigned i = 0 ; i != qual.size() ; ++i ) if( (uint8_t)qual[i] != 0xff ) has_qual = true ; if( has_qual ) { if( flags & 0x10 ) res_.mutable_read()->mutable_quality()->assign( qual.rbegin(), qual.rend() ) ; else res_.mutable_read()->set_quality( qual ) ; } bsize -= 32 + namelen + 4*cigarlen + ((seqlen+1)/2) + seqlen ; while( bsize ) { char tag0 = read_uint8() ; char tag1 = read_uint8() ; char type = read_uint8() ; bsize -= 3 ; int ival = 0 ; string sval ; switch( type ) { case 'A': case 'c': case 'C': ival = read_uint8() ; bsize -= 1 ; break ; case 's': case 'S': ival = read_uint16() ; bsize -= 2 ; break ; case 'i': case 'I': ival = read_uint32() ; bsize -= 4 ; break ; case 'f': throw "can't decode float" ; case 'Z': --bsize ; while( char c = read_uint8() ) { sval.push_back( c ) ; --bsize ; } break ; case 'H': throw "can't decode HEX string" ; default: throw string( "can't decode shit " ) + tag0 + tag1 + ':' + type ; } if( tag0 == 'U' && tag1 == 'Q' ) h->set_score( ival ) ; if( tag0 == 'A' && tag1 == 'S' && !h->has_score() ) h->set_score( ival ) ; } if( flags & 4 ) res_.mutable_hit()->RemoveLast() ; while( buf_ && !buf_size_ ) if( !is_->Next( &buf_, &buf_size_ ) ) buf_ = 0 ; state_ = buf_ && buf_size_ ? have_output : end_of_stream ; return res_ ; } } ; // namespace std::pair< PipeInputStream*, std::string > make_PipeInputStream( const std::string& p ) { console.output( Console::notice, "piping from " + p ) ; int fds[2] ; throw_errno_if_minus1( pipe( fds ), "creating pipe" ) ; pid_t chld = throw_errno_if_minus1( fork(), "forking pipe process" ) ; if( chld == 0 ) { throw_errno_if_minus1( dup2( fds[1], 1 ), "duplicating file descriptor" ) ; if( fds[1] != 1 ) throw_errno_if_minus1( close( fds[1] ), "closing fd" ) ; throw_errno_if_minus1( close( fds[0] ), "closing fd" ) ; const char *c = p.c_str() ; while( *c && isspace( *c ) ) ++c ; execl( "/bin/sh", "sh", "-c", c, (char*)0 ) ; } throw_errno_if_minus1( close( fds[1] ), "closing fd" ) ; return std::make_pair( new PipeInputStream( fds[0], chld ), "" ) ; } std::pair< PipeOutputStream*, std::string > make_PipeOutputStream( const std::string& p ) { console.output( Console::notice, "piping to " + p ) ; int fds[2] ; throw_errno_if_minus1( pipe( fds ), "creating pipe" ) ; pid_t chld = throw_errno_if_minus1( fork(), "forking pipe process" ) ; if( chld == 0 ) { throw_errno_if_minus1( dup2( fds[0], 0 ), "duplicating file descriptor" ) ; if( fds[0] != 0 ) throw_errno_if_minus1( close( fds[0] ), "closing fd" ) ; throw_errno_if_minus1( close( fds[1] ), "closing fd" ) ; const char *c = p.c_str() ; while( *c && isspace( *c ) ) ++c ; execl( "/bin/sh", "sh", "-c", c, (char*)0 ) ; } throw_errno_if_minus1( close( fds[0] ), "closing fd" ) ; return std::make_pair( new PipeOutputStream( fds[1], chld ), "" ) ; } zero_copy_output_buf::~zero_copy_output_buf() { sync() ; } int zero_copy_output_buf::sync() { if( epptr() != pptr() ) { os_->BackUp( epptr() - pptr() ) ; setp( 0, 0 ) ; } return 0 ; } zero_copy_output_buf::int_type zero_copy_output_buf::overflow( zero_copy_output_buf::int_type c ) { sync() ; void *buf ; int len ; if( !os_->Next( &buf, &len ) ) return traits_type::eof() ; setp( static_cast( buf ), static_cast( buf ) + len ) ; return traits_type::eq_int_type( c, traits_type::eof() ) ? traits_type::not_eof( c ) : sputc( c ) ; } anfo-0.98/src/util.cc0000644000371600007640000000757411447113464011423 00000000000000// Copyright 2009 Udo Stenzel // This file is part of ANFO // // ANFO is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // Anfo is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with Anfo. If not, see . #ifdef HAVE_CONFIG_H #include "../config.h" #endif #include "util.h" #include #include #include #include volatile int exit_with = 0 ; std::string program_name ; Console console ; int wrap_main( int argc, const char * argv[], int (*main1)( int, const char *[] ) ) { program_name = argv[0] ; try { return main1( argc, argv ) ; } catch( const std::string& e ) { perr( e ) ; } catch( const char *e ) { perr( e ) ; } catch( char *e ) { perr( e ) ; } catch( const Exception& e ) { perr( e ) ; } catch( const std::exception& e ) { perr( e.what() ) ; } catch( ... ) { perr( "Oh noes!" ) ; } return 1 ; } void set_proc_title( const char *title ) { extern char* __progname_full ; extern char* __progname ; static char* pe = 0 ; static char* pa = 0 ; if( !pe ) { char* p = __progname ; pa = __progname_full ; for( pe = pa ; pe[0] || pe[1] ; ++pe ) ; while( *p && pa != pe ) *pa++ = *p++ ; if( pa != pe ) *pa++ = ':' ; if( pa != pe ) *pa++ = ' ' ; } char* pf = pa ; if( pf != pe ) { while( *title && pf != pe ) *pf++ = *title++ ; while( pf != pe ) *pf++ = 0 ; } } int mktempfile( std::string* name ) { const char *suffix = "/anfo_sort_XXXXXX" ; const char *base = getenv("ANFO_TEMP") ; if( !base ) base = getenv("TMPDIR") ; if( !base ) base = getenv("TEMP") ; if( !base ) base = getenv("TMP") ; if( !base ) base = "." ; char n1[ strlen(base) + strlen(suffix) + 1 ] ; char *n2 = n1 ; while( *base ) *n2++ = *base++ ; while( *suffix ) *n2++ = *suffix++ ; *n2 = 0 ; int fd = throw_errno_if_minus1( mkstemp( n1 ), "making temp file" ) ; throw_errno_if_minus1( unlink( n1 ), "unlinking temp name" ) ; if( name ) *name = n1 ; return fd ; } namespace { const char *describe[] = { "[debug] ", "[info] ", "[notice] ", "[warning] ", "[error] ", "[critical] " } ; } ; void Console::output( Loglevel l, const std::string& s ) { if( l < loglevel ) return ; if( fd_ < 0 ) { std::clog << s << std::endl ; } if( s.empty() ) return ; mywrite( fd_, "\r\e[K", 4 ) ; mywrite( fd_, describe[l], strlen( describe[l] ) ) ; mywrite( fd_, s.data(), s.size() ) ; if( s[ s.size()-1 ] != '\n' ) mywrite( fd_, "\n", 1 ) ; update() ; } void Console::update() { if( fd_ < 0 ) return ; int width = 79 ; struct winsize ws; if( 0 == ioctl( fd_, TIOCGWINSZ, &ws ) ) width = ws.ws_col-1 ; std::string line = "\r\e[K" ; for( Chans::const_iterator ch = chans_.begin() ; width >= 3 && ch != chans_.end() ; ++ch ) { line.push_back( '[' ) ; line.append( ch->second.substr( 0, width-2 ) ) ; line.push_back( ']' ) ; line.push_back( ' ' ) ; width -= ch->second.size()+3 ; } mywrite( fd_, line.data(), line.size() - (line[line.size()-1] == ' ') ) ; } void Console::free_chan( int c ) { for( Chans::iterator i = chans_.begin() ; i != chans_.end() ; ++i ) { if( i->first == c ) { chans_.erase(i) ; update() ; return ; } } } void Console::progress( int c, Loglevel l, const std::string& s ) { if( l < loglevel ) return ; for( Chans::iterator i = chans_.begin() ; i != chans_.end() ; ++i ) { if( i->first == c ) { i->second = s ; update() ; return ; } } chans_.push_front( make_pair( c, s ) ) ; update() ; } anfo-0.98/src/anfo-elk.cc0000644000371600007640000004764111447113463012140 00000000000000// Copyright 2009 Udo Stenzel // This file is part of ANFO // // ANFO is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // Anfo is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with Anfo. If not, see . //! \page anfo-elk ELK extension to control ANFO. //! The idea: use the ELK interpreter as a scripting engine for //! golfing ANFO files. //! //! \todo Deal with scheme ports somehow. #ifdef HAVE_CONFIG_H #include "../config.h" #endif #include "anfo_common.h" #include "ducttape.h" #include "index.h" #include "misc_streams.h" #include "output_streams.h" #include "stream.h" #include "util.h" #include #include #include #include #include #include // Somewhat silly workaround for linking problems: protobuf needs // pthread, but doesn't automtically link it; we don't need it, and Elk // won't provide it. So here's a dependency on libpthread, it gets // linked and protobuf is happy again. #include pthread_once_t anfo_elk_once_control = PTHREAD_ONCE_INIT; extern "C" void anfo_elk_init_routine() {} using namespace std ; using namespace streams ; using namespace google::protobuf::io ; // generic interfacing to ELK: primitive procedures typedef Object (*P)() ; // the wrapped stream type: construction, destruction, predicates static int t_stream ; struct StreamWrapper { Object o_ ; StreamHolder h_ ; StreamWrapper( StreamHolder h ) : h_(h) {} } ; extern "C" Object terminate_stream( Object o ) { ((StreamWrapper*)POINTER(o))->~StreamWrapper() ; Deregister_Object( o ) ; return Void ; } extern "C" Object p_delete_stream( Object o ) { StreamWrapper* s = (StreamWrapper*)POINTER(o) ; if( !s->h_ ) Primitive_Error( "BUG: double deletion of stream" ) ; StreamHolder().swap( s->h_ ) ; Deregister_Object( o ) ; return Void ; } Object wrap_stream( StreamHolder h ) { Object o = Alloc_Object( sizeof( StreamWrapper ), t_stream, 0 ) ; StreamWrapper *w = new( POINTER(o) ) StreamWrapper( h ) ; Register_Object( o, const_cast("anfostreams") , terminate_stream, 0 ) ; w->h_->get_state() ; return o ; } string object_to_string( Object o, const string& def = "" ) { if( TYPE(o) == T_Symbol ) o = SYMBOL(o)->name ; return TYPE(o) == T_String ? string( STRING(o)->data, STRING(o)->size ) : def ; } pair< ZeroCopyOutputStream*, string > open_any_output_zc( Object o ) { switch( TYPE(o) ) { case T_Symbol: case T_String: { string nm = object_to_string(o) ; if( !nm.empty() && nm[0] == '|' ) return make_PipeOutputStream( nm.substr(1) ) ; else { FileOutputStream *s = new FileOutputStream( throw_errno_if_minus1( open( nm.c_str(), O_WRONLY | O_CREAT | O_TRUNC, 0666 ), "opening file" ) ) ; s->SetCloseOnDelete( true ) ; return make_pair( s, nm ) ; } } case T_Fixnum: return make_pair( new FileOutputStream( Get_Exact_Integer( o ) ), "" ) ; case T_Boolean: if( !Truep(o) ) return make_pair( new FileOutputStream( 1 ), "" ) ; default: throw "can't handle file argument" ; } } pair< std::ostream*, string > open_any_output_std( Object o ) { pair< ZeroCopyOutputStream*, string > p = open_any_output_zc( o ) ; return make_pair( new zero_copy_ostream( p.first ), p.second ) ; } // note: this is only used to initialize the "region filters". Use of a // scheme data structure might be beneficial here. pair< std::istream*, string > open_any_input_std( Object o ) { switch( TYPE(o) ) { case T_Symbol: case T_String: return make_pair( new ifstream( object_to_string(o).c_str() ), object_to_string(o) ) ; case T_Boolean: if( !Truep(o) ) return make_pair( new istream( cin.rdbuf() ), "" ) ; default: break ; } throw "can't handle file argument" ; } inline StreamHolder obj_to_stream( Object o ) // , bool sol = false , int ori = 33 ) { Check_Type( o, t_stream ) ; StreamHolder& h = ((StreamWrapper*)POINTER(o))->h_ ; if( !h ) Primitive_Error( "BUG: use of deleted stream" ) ; return h ; } vector obj_to_genomes( Object o ) { vector r ; if( TYPE(o) == T_String || TYPE(o) == T_Symbol ) r.push_back( object_to_string( o ) ) ; else for( ; TYPE(o) == T_Pair ; o = Cdr(o) ) r.push_back( object_to_string( Car(o) ) ) ; return r ; } Object wrap_streams( StreamBundle *m_, int argc, Object *argv ) { Holder< StreamBundle > m( m_ ) ; for( Object *o = argv ; o != argv + argc ; ++o ) m->add_stream( obj_to_stream( *o ) ) ; return wrap_stream( m ) ; } #define WRAP( fun, proto, args ) \ Object wrap_##fun proto ; \ Object fun proto { \ Object err = False ; \ try { return wrap_##fun args ; } \ catch( const std::string& e ) { err = Make_String( e.data(), e.size() ) ; } \ catch( const char *e ) { err = Make_String( e, strlen(e) ) ; } \ catch( const Exception& e ) { stringstream ss ; ss << e ; string s = ss.str() ; err = Make_String( s.data(), s.size() ) ; } \ catch( const std::exception& e ) { string s = e.what() ; err = Make_String( s.data(), s.size() ) ; } \ catch( ... ) { err = Make_String( "unhandled C++ exception", 23 ) ; } \ if( TYPE(err) == T_String ) Primitive_Error( "~s", err ) ; \ return Void ; \ } \ Object wrap_##fun proto extern "C" { Object p_is_stream( Object d ) { return TYPE(d) == t_stream ? True : False; } int compare_stream_wrappers( Object a, Object b ) { return obj_to_stream(a) == obj_to_stream(b) ; } int print_stream_wrapper( Object o, Object p, int, int, int ) { StreamWrapper *w = (StreamWrapper*)POINTER(o) ; Printf( p, "#[anfo-stream %s %p]", w && w->h_ ? w->h_->type_name().c_str() : "Null", w ? (const void*)(w->h_) : 0 ) ; return 0 ; } // misc. ANFO primitves SYMDESCR verbosity_syms[] = { { (char*) "debug", Console::debug }, { (char*) "info", Console::info }, { (char*) "notice", Console::notice }, { (char*) "warning", Console::warning }, { (char*) "error", Console::error }, { (char*) "critical", Console::critical }, { 0, 0 } } ; WRAP( p_set_verbosity, ( Object v ), (v) ) { if( TYPE(v) == T_Symbol ) console.loglevel = (Console::Loglevel) Symbols_To_Bits( v, 0, verbosity_syms ) ; else console.loglevel = (Console::Loglevel) Get_Integer( v ) ; return Void ; } WRAP( p_use_mmap, ( Object v ), (v) ) { Metagenome::nommap = !Truep( v ) ; return Void ; } // ANFO stream constructors // Output WRAP( p_write_native, ( Object f, Object c ), (f,c) ) { return wrap_stream( new ChunkedWriter( open_any_output_zc( f ), Get_Integer( c ) ) ) ; } WRAP( p_write_text, ( Object f ), (f) ) { return wrap_stream( new TextWriter( open_any_output_std( f ) ) ) ; } WRAP( p_write_sam, ( Object f ), (f) ) { return wrap_stream( new SamWriter( open_any_output_std( f ) ) ) ; } WRAP( p_write_glz, ( Object f ), (f) ) { return wrap_stream( new GlzWriter( open_any_output_zc( f ) ) ) ; } WRAP( p_write_3aln, ( Object f ), (f) ) { return wrap_stream( new ThreeAlnWriter( open_any_output_std( f ) ) ) ; } WRAP( p_write_fastq, ( Object f ), (f) ) { return wrap_stream( new FastqWriter( open_any_output_std( f ), true ) ) ; } WRAP( p_write_table, ( Object f ), (f) ) { return wrap_stream( new TableWriter( open_any_output_std( f ) ) ) ; } WRAP( p_write_fasta, ( Object f ), (f) ) { return wrap_stream( new FastaAlnWriter( open_any_output_std( f ) ) ) ; } WRAP( p_write_wig, ( Object f ), (f) ) { return wrap_stream( new WigCoverageWriter( open_any_output_std( f ) ) ) ; } // Processors WRAP( p_duct_tape, ( Object n, Object p ), (n,p) ) { return wrap_stream( new DuctTaper( object_to_string( n, "contig" ), Get_Double(p) ) ) ; } WRAP( p_add_alns, ( Object c, Object s ), (c,s) ) { return wrap_stream( new GenTextAlignment( Get_Integer( c ), Truep( s ) ) ) ; } WRAP( p_rmdup, ( Object s, Object i, Object q ), (s,i,q) ) { return wrap_stream( new RmdupStream( Get_Double(s), Get_Double(i), Get_Integer(q) ) ) ; } WRAP( p_trim, ( Object l, Object r, Object m ), (l,r,m) ) { return wrap_stream( new Housekeeper( obj_to_genomes( l ), obj_to_genomes( r ), Get_Integer( m ) ) ) ; } // Evaluators WRAP( p_stats, (), () ) { return wrap_stream( new StatStream() ) ; } WRAP( p_mismatches, (), () ) { return wrap_stream( new MismatchStats() ) ; } WRAP( p_divergence, ( Object p, Object s, Object b ), (p,s,b) ) { return wrap_stream( new DivergenceStream( object_to_string(p), object_to_string(s), Get_Integer(b) ) ) ; } // Filters WRAP( p_sort_by_pos, ( Object mem, Object handles, Object genomes ), (mem,handles,genomes) ) { return wrap_stream( new SortingStream( Get_Integer( mem ), Get_Integer( handles ), by_genome_coordinate( obj_to_genomes( genomes ) ) ) ) ; } WRAP( p_sort_by_name, ( Object mem, Object handles ), (mem,handles) ) { return wrap_stream( new SortingStream( Get_Integer( mem ), Get_Integer( handles ) ) ) ; } WRAP( p_filter_by_score, ( Object slope, Object len, Object genomes ), (slope,len,genomes) ) { return wrap_stream( new ScoreFilter( Get_Double( slope ), Get_Double( len ), obj_to_genomes( genomes ) ) ) ; } WRAP( p_filter_tot_score, ( Object slope, Object len, Object genomes ), (slope,len,genomes) ) { return wrap_stream( new TotalScoreFilter( Get_Double( slope ), Get_Double( len ), obj_to_genomes( genomes ) ) ) ; } WRAP( p_filter_by_qual, ( Object qual ), (qual) ) { return wrap_stream( new QualFilter( Get_Double( qual ) ) ) ; } WRAP( p_filter_chain, ( Object left, Object right, Object file ), (left,right,file) ) { return wrap_stream( new AgreesWithChain( object_to_string(left), object_to_string(right), open_any_input_std( file ) ) ) ; } WRAP( p_mask_by_qual, ( Object qual ), (qual) ) { return wrap_stream( new QualMasker( Get_Integer( qual ) ) ) ; } WRAP( p_filter_by_mapq, ( Object mapq, Object genomes ), (mapq,genomes) ) { return wrap_stream( new MapqFilter( obj_to_genomes( genomes ), Get_Integer( mapq ) ) ) ; } WRAP( p_require_best_hit, ( Object genomes, Object sequences ), (genomes,sequences) ) { return wrap_stream( new RequireBestHit( obj_to_genomes( genomes ), obj_to_genomes( sequences ) ) ) ; } WRAP( p_require_hit, ( Object genomes, Object sequences ), (genomes,sequences) ) { return wrap_stream( new RequireHit( obj_to_genomes( genomes ), obj_to_genomes( sequences ) ) ) ; } WRAP( p_ignore_hit, ( Object genomes, Object sequences ), (genomes,sequences) ) { return wrap_stream( new IgnoreHit( obj_to_genomes( genomes ), obj_to_genomes( sequences ) ) ) ; } WRAP( p_only_genome, ( Object g ), (g) ) { return wrap_stream( new OnlyGenome( obj_to_genomes( g ) ) ) ; } WRAP( p_filter_by_len, ( Object l, Object h ), (l,h) ) { return wrap_stream( new LengthFilter( Get_Integer( l ), Truep(h) ? Get_Integer( h ) : numeric_limits::max() ) ) ; } WRAP( p_filter_by_gc, ( Object l, Object h ), (l,h) ) { return wrap_stream( new GcFilter( Get_Integer( l ), Get_Integer( h ) ) ) ; } WRAP( p_filter_multi, ( Object m ), (m) ) { return wrap_stream( new MultiFilter( Get_Integer( m ) ) ) ; } WRAP( p_subsample, ( Object r ), (r) ) { return wrap_stream( new Subsample( Get_Double( r ) ) ) ; } WRAP( p_edit_header, ( Object e ), (e) ) { return wrap_stream( new RepairHeaderStream( object_to_string( e, "" ) ) ) ; } WRAP( p_inside_region, ( Object f ), (f) ) { return wrap_stream( new InsideRegion( open_any_input_std( f ) ) ) ; } WRAP( p_outside_region, ( Object f ), (f) ) { return wrap_stream( new OutsideRegion( open_any_input_std( f ) ) ) ; } WRAP( p_sanitize, (), ( ) ) { return wrap_stream( new Sanitizer() ) ; } WRAP( p_get_summary, ( Object o ), (o) ) { return obj_to_stream( o )->get_summary() ; } // Mergers (I'll drop the unholy mega-merge here, that's far better // scripted in Scheme) WRAP( p_merge, ( int argc, Object *argv ), (argc,argv) ) { return wrap_streams( new MergeStream, argc, argv ) ; } WRAP( p_join, ( int argc, Object *argv ), (argc,argv) ) { return wrap_streams( new NearSortedJoin, argc, argv ) ; } WRAP( p_concat, ( int argc, Object *argv ), (argc,argv) ) { return wrap_streams( new ConcatStream, argc, argv ) ; } WRAP( p_read_file, ( Object fn, Object sol_scores, Object origin, Object genome, Object name ), (fn,sol_scores,origin,genome,name) ) { bool sol = Truep( sol_scores ) ; int ori = Get_Integer( origin ) ; string g ; if( TYPE(genome) == T_Symbol ) genome = SYMBOL(genome)->name ; if( TYPE(genome) == T_String ) g.assign( STRING(genome)->data, STRING(genome)->size ) ; switch( TYPE(fn) ) { case T_Symbol: case T_String: { string nm = object_to_string(fn) ; if( !nm.empty() && nm[nm.size()-1] == '|' ) return wrap_stream( new UniversalReader( object_to_string( name, "" ), make_PipeInputStream( nm.substr(0,nm.size()-1) ).first, sol, ori, g ) ) ; else return wrap_stream( new UniversalReader( object_to_string(fn), 0, sol, ori, g ) ) ; } case T_Fixnum: return wrap_stream( new UniversalReader( object_to_string( name, "" ), new FileInputStream( Get_Integer(fn) ), sol, ori, g ) ) ; case T_Boolean: if( !Truep(fn) ) return wrap_stream( new UniversalReader( object_to_string( name, "" ), new FileInputStream(0), sol, ori, g ) ) ; default: throw "can't handle file argument ~s" ; } } // Composition //! \brief top-level ELK call. //! Gets exactly one input stream and one output stream, transfers //! between them. Returns results extracted from them. WRAP( p_anfo_run, ( Object inpo, Object outo ), (inpo,outo) ) { StreamHolder inp = obj_to_stream( inpo ) ; StreamHolder out = obj_to_stream( outo ) ; out->put_header( inp->fetch_header() ) ; while( inp->get_state() == Stream::have_output && out->get_state() == Stream::need_input ) out->put_result( inp->fetch_result() ) ; out->put_footer( inp->fetch_footer() ) ; return Null ; } //! \brief output stream replication //! Gets many streams as argument, bundles them up so they all receive //! the same input. WRAP( p_tee, ( int argc, Object *argv ), (argc,argv) ) { Holder< FanOut > f( new FanOut ) ; for( Object *o = argv ; o != argv+argc ; ++o ) f->add_stream( obj_to_stream( *o ) ) ; return wrap_stream( f ) ; } //! \brief stream composition. //! Gets many streams as argument, ties them into a chain and returns a //! new stream. WRAP( p_chain, ( int argc, Object *argv ), (argc,argv) ) { Holder< Compose > c( new Compose ) ; for( Object *o = argv ; o != argv+argc ; ++o ) c->add_stream( obj_to_stream( *o ) ) ; return wrap_stream( c ) ; } WRAP( p_glob, ( Object path ), (path) ) { glob_t the_glob ; throw_errno_if_minus1( glob( Get_String( path ), GLOB_MARK, 0, &the_glob ), "globbing" ) ; GC_Node ; Object r = Null ; GC_Link( r ) ; for( int i = the_glob.gl_pathc ; i != 0 ; --i ) r = Cons( Make_String( the_glob.gl_pathv[i-1], strlen( the_glob.gl_pathv[i-1] ) ), r ) ; GC_Unlink ; globfree( &the_glob ) ; return r ; } Object p_version() { return Make_String( PACKAGE_VERSION, strlen(PACKAGE_VERSION) ) ; } Object p_limit_core( Object amt ) { struct rlimit lim ; getrlimit( RLIMIT_AS, &lim ) ; lim.rlim_cur = 1024*1024 * Get_Integer( amt ) ; setrlimit( RLIMIT_AS, &lim ) ; return Void ; } // init code void elk_init_libanfo() { t_stream = Define_Type( 0, "anfo-stream", 0, sizeof( StreamWrapper ), compare_stream_wrappers, compare_stream_wrappers, print_stream_wrapper, 0 ) ; Define_Primitive( (P)p_is_stream, "anfo-stream?", 1, 1, EVAL ) ; Define_Primitive( (P)p_set_verbosity, "set-verbosity!", 1, 1, EVAL ) ; Define_Primitive( (P)p_use_mmap, "use-mmap!", 1, 1, EVAL ) ; Define_Primitive( (P)p_limit_core, "limit-core!", 1, 1, EVAL ) ; Define_Primitive( (P)p_get_summary, "get-summary", 1, 1, EVAL ) ; Define_Primitive( (P)p_read_file, "prim-read-file", 5, 5, EVAL ) ; Define_Primitive( (P)p_write_native, "prim-write-native", 2, 2, EVAL ) ; Define_Primitive( (P)p_write_text, "prim-write-text", 1, 1, EVAL ) ; Define_Primitive( (P)p_write_sam, "prim-write-sam", 1, 1, EVAL ) ; Define_Primitive( (P)p_write_glz, "prim-write-glz", 1, 1, EVAL ) ; Define_Primitive( (P)p_write_3aln, "prim-write-threealn", 1, 1, EVAL ) ; Define_Primitive( (P)p_write_fastq, "prim-write-fastq", 1, 1, EVAL ) ; Define_Primitive( (P)p_write_table, "prim-write-table", 1, 1, EVAL ) ; Define_Primitive( (P)p_write_fasta, "prim-write-fasta", 1, 1, EVAL ) ; Define_Primitive( (P)p_write_wig, "prim-write-wiggle", 1, 1, EVAL ) ; Define_Primitive( (P)p_duct_tape, "prim-duct-tape", 2, 2, EVAL ) ; Define_Primitive( (P)p_add_alns, "prim-add-alns", 2, 2, EVAL ) ; Define_Primitive( (P)p_rmdup, "prim-rmdup", 3, 3, EVAL ) ; Define_Primitive( (P)p_trim, "prim-trim", 3, 3, EVAL ) ; Define_Primitive( (P)p_filter_by_len, "prim-filter-length", 2, 2, EVAL ) ; Define_Primitive( (P)p_filter_by_gc, "prim-filter-gc", 2, 2, EVAL ) ; Define_Primitive( (P)p_filter_by_qual, "prim-filter-qual", 1, 1, EVAL ) ; Define_Primitive( (P)p_mask_by_qual, "prim-mask-qual", 1, 1, EVAL ) ; Define_Primitive( (P)p_filter_multi, "prim-filter-multi", 1, 1, EVAL ) ; Define_Primitive( (P)p_subsample, "prim-subsample", 1, 1, EVAL ) ; Define_Primitive( (P)p_sanitize, "prim-sanitize", 0, 0, EVAL ) ; Define_Primitive( (P)p_edit_header, "prim-edit-header", 1, 1, EVAL ) ; Define_Primitive( (P)p_filter_by_score, "prim-filter-score", 3, 3, EVAL ) ; Define_Primitive( (P)p_filter_tot_score, "prim-filter-total-score",3,3,EVAL) ; Define_Primitive( (P)p_filter_by_mapq, "prim-filter-mapq", 2, 2, EVAL ) ; Define_Primitive( (P)p_filter_chain, "prim-filter-chain", 3, 3, EVAL ) ; // redesign? Define_Primitive( (P)p_inside_region, "prim-inside-region", 1, 1, EVAL ) ; // redesign? Define_Primitive( (P)p_outside_region, "prim-outside-region", 1, 1, EVAL ) ; // redesign? Define_Primitive( (P)p_require_best_hit, "prim-require-bht", 2, 2, EVAL ) ; Define_Primitive( (P)p_require_hit, "prim-require-hit", 2, 2, EVAL ) ; Define_Primitive( (P)p_ignore_hit, "prim-ignore-hit", 2, 2, EVAL ) ; Define_Primitive( (P)p_only_genome, "prim-only-genomes", 1, 1, EVAL ) ; Define_Primitive( (P)p_sort_by_pos, "prim-sort-pos", 3, 3, EVAL ) ; Define_Primitive( (P)p_sort_by_name, "prim-sort-name", 2, 2, EVAL ) ; Define_Primitive( (P)p_merge, "prim-merge", 1, MANY, VARARGS ) ; Define_Primitive( (P)p_join, "prim-join", 1, MANY, VARARGS ) ; Define_Primitive( (P)p_concat, "prim-concat", 1, MANY, VARARGS ) ; Define_Primitive( (P)p_stats, "prim-stats", 0, 0, EVAL ) ; Define_Primitive( (P)p_divergence, "prim-divergence", 3, 3, EVAL ) ; Define_Primitive( (P)p_mismatches, "prim-mismatches", 0, 0, EVAL ) ; Define_Primitive( (P)p_delete_stream, "prim-delete-stream", 1, 1, EVAL ) ; Define_Primitive( (P)p_anfo_run, "prim-anfo-run", 2, 2, EVAL ) ; Define_Primitive( (P)p_tee, "prim-tee", 1, MANY, VARARGS ) ; Define_Primitive( (P)p_chain, "prim-chain", 1, MANY, VARARGS ) ; // not exactly Anfo, but damn practical Define_Primitive( (P)p_glob, "glob", 1, 1, EVAL ) ; Define_Primitive( (P)p_version, "anfo-version", 0, 0, EVAL ) ; // part of the aforementioned workaround pthread_once( &anfo_elk_once_control, anfo_elk_init_routine ) ; } void elk_finit_libanfo() { // force GC to run d'tors, makes sure nothing was forgotten Terminate_Type( t_stream ) ; } } // extern C anfo-0.98/src/fastlz.h0000644000371600007640000000675611447112753011614 00000000000000/* FastLZ - lightning-fast lossless compression library Copyright (C) 2007 Ariya Hidayat (ariya@kde.org) Copyright (C) 2006 Ariya Hidayat (ariya@kde.org) Copyright (C) 2005 Ariya Hidayat (ariya@kde.org) Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef FASTLZ_H #define FASTLZ_H #define FASTLZ_VERSION 0x000100 #define FASTLZ_VERSION_MAJOR 0 #define FASTLZ_VERSION_MINOR 0 #define FASTLZ_VERSION_REVISION 0 #define FASTLZ_VERSION_STRING "0.1.0" #if defined (__cplusplus) extern "C" { #endif /** Compress a block of data in the input buffer and returns the size of compressed block. The size of input buffer is specified by length. The minimum input buffer size is 16. The output buffer must be at least 5% larger than the input buffer and can not be smaller than 66 bytes. If the input is not compressible, the return value might be larger than length (input buffer size). The input buffer and the output buffer can not overlap. */ int fastlz_compress(const void* input, int length, void* output); /** Decompress a block of compressed data and returns the size of the decompressed block. If error occurs, e.g. the compressed data is corrupted or the output buffer is not large enough, then 0 (zero) will be returned instead. The input buffer and the output buffer can not overlap. Decompression is memory safe and guaranteed not to write the output buffer more than what is specified in maxout. */ int fastlz_decompress(const void* input, int length, void* output, int maxout); /** Compress a block of data in the input buffer and returns the size of compressed block. The size of input buffer is specified by length. The minimum input buffer size is 16. The output buffer must be at least 5% larger than the input buffer and can not be smaller than 66 bytes. If the input is not compressible, the return value might be larger than length (input buffer size). The input buffer and the output buffer can not overlap. Compression level can be specified in parameter level. At the moment, only level 1 and level 2 are supported. Level 1 is the fastest compression and generally useful for short data. Level 2 is slightly slower but it gives better compression ratio. Note that the compressed data, regardless of the level, can always be decompressed using the function fastlz_decompress above. */ int fastlz_compress_level(int level, const void* input, int length, void* output); #if defined (__cplusplus) } #endif #endif /* FASTLZ_H */ anfo-0.98/src/fastlz.c0000644000371600007640000003252011447112753011573 00000000000000/* FastLZ - lightning-fast lossless compression library Copyright (C) 2007 Ariya Hidayat (ariya@kde.org) Copyright (C) 2006 Ariya Hidayat (ariya@kde.org) Copyright (C) 2005 Ariya Hidayat (ariya@kde.org) Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #if !defined(FASTLZ__COMPRESSOR) && !defined(FASTLZ_DECOMPRESSOR) /* * Always check for bound when decompressing. * Generally it is best to leave it defined. */ #define FASTLZ_SAFE /* * Give hints to the compiler for branch prediction optimization. */ #if defined(__GNUC__) && (__GNUC__ > 2) #define FASTLZ_EXPECT_CONDITIONAL(c) (__builtin_expect((c), 1)) #define FASTLZ_UNEXPECT_CONDITIONAL(c) (__builtin_expect((c), 0)) #else #define FASTLZ_EXPECT_CONDITIONAL(c) (c) #define FASTLZ_UNEXPECT_CONDITIONAL(c) (c) #endif /* * Use inlined functions for supported systems. */ #if defined(__GNUC__) || defined(__DMC__) || defined(__POCC__) || defined(__WATCOMC__) || defined(__SUNPRO_C) #define FASTLZ_INLINE inline #elif defined(__BORLANDC__) || defined(_MSC_VER) || defined(__LCC__) #define FASTLZ_INLINE __inline #else #define FASTLZ_INLINE #endif /* * Prevent accessing more than 8-bit at once, except on x86 architectures. */ #if !defined(FASTLZ_STRICT_ALIGN) #define FASTLZ_STRICT_ALIGN #if defined(__i386__) || defined(__386) /* GNU C, Sun Studio */ #undef FASTLZ_STRICT_ALIGN #elif defined(__i486__) || defined(__i586__) || defined(__i686__) /* GNU C */ #undef FASTLZ_STRICT_ALIGN #elif defined(_M_IX86) /* Intel, MSVC */ #undef FASTLZ_STRICT_ALIGN #elif defined(__386) #undef FASTLZ_STRICT_ALIGN #elif defined(_X86_) /* MinGW */ #undef FASTLZ_STRICT_ALIGN #elif defined(__I86__) /* Digital Mars */ #undef FASTLZ_STRICT_ALIGN #endif #endif /* * FIXME: use preprocessor magic to set this on different platforms! */ typedef unsigned char flzuint8; typedef unsigned short flzuint16; typedef unsigned int flzuint32; /* prototypes */ int fastlz_compress(const void* input, int length, void* output); int fastlz_compress_level(int level, const void* input, int length, void* output); int fastlz_decompress(const void* input, int length, void* output, int maxout); #define MAX_COPY 32 #define MAX_LEN 264 /* 256 + 8 */ #define MAX_DISTANCE 8192 #if !defined(FASTLZ_STRICT_ALIGN) #define FASTLZ_READU16(p) *((const flzuint16*)(p)) #else #define FASTLZ_READU16(p) ((p)[0] | (p)[1]<<8) #endif #define HASH_LOG 13 #define HASH_SIZE (1<< HASH_LOG) #define HASH_MASK (HASH_SIZE-1) #define HASH_FUNCTION(v,p) { v = FASTLZ_READU16(p); v ^= FASTLZ_READU16(p+1)^(v>>(16-HASH_LOG));v &= HASH_MASK; } #undef FASTLZ_LEVEL #define FASTLZ_LEVEL 1 #undef FASTLZ_COMPRESSOR #undef FASTLZ_DECOMPRESSOR #define FASTLZ_COMPRESSOR fastlz1_compress #define FASTLZ_DECOMPRESSOR fastlz1_decompress static FASTLZ_INLINE int FASTLZ_COMPRESSOR(const void* input, int length, void* output); static FASTLZ_INLINE int FASTLZ_DECOMPRESSOR(const void* input, int length, void* output, int maxout); #include "fastlz.c" #undef FASTLZ_LEVEL #define FASTLZ_LEVEL 2 #undef MAX_DISTANCE #define MAX_DISTANCE 8191 #define MAX_FARDISTANCE (65535+MAX_DISTANCE-1) #undef FASTLZ_COMPRESSOR #undef FASTLZ_DECOMPRESSOR #define FASTLZ_COMPRESSOR fastlz2_compress #define FASTLZ_DECOMPRESSOR fastlz2_decompress static FASTLZ_INLINE int FASTLZ_COMPRESSOR(const void* input, int length, void* output); static FASTLZ_INLINE int FASTLZ_DECOMPRESSOR(const void* input, int length, void* output, int maxout); #include "fastlz.c" int fastlz_compress(const void* input, int length, void* output) { /* for short block, choose fastlz1 */ if(length < 65536) return fastlz1_compress(input, length, output); /* else... */ return fastlz2_compress(input, length, output); } int fastlz_decompress(const void* input, int length, void* output, int maxout) { /* magic identifier for compression level */ int level = ((*(const flzuint8*)input) >> 5) + 1; if(level == 1) return fastlz1_decompress(input, length, output, maxout); if(level == 2) return fastlz2_decompress(input, length, output, maxout); /* unknown level, trigger error */ return 0; } int fastlz_compress_level(int level, const void* input, int length, void* output) { if(level == 1) return fastlz1_compress(input, length, output); if(level == 2) return fastlz2_compress(input, length, output); return 0; } #else /* !defined(FASTLZ_COMPRESSOR) && !defined(FASTLZ_DECOMPRESSOR) */ static FASTLZ_INLINE int FASTLZ_COMPRESSOR(const void* input, int length, void* output) { const flzuint8* ip = (const flzuint8*) input; const flzuint8* ip_bound = ip + length - 2; const flzuint8* ip_limit = ip + length - 12; flzuint8* op = (flzuint8*) output; const flzuint8* htab[HASH_SIZE]; const flzuint8** hslot; flzuint32 hval; flzuint32 copy; /* sanity check */ if(FASTLZ_UNEXPECT_CONDITIONAL(length < 4)) { if(length) { /* create literal copy only */ *op++ = length-1; ip_bound++; while(ip <= ip_bound) *op++ = *ip++; return length+1; } else return 0; } /* initializes hash table */ for (hslot = htab; hslot < htab + HASH_SIZE; hslot++) *hslot = ip; /* we start with literal copy */ copy = 2; *op++ = MAX_COPY-1; *op++ = *ip++; *op++ = *ip++; /* main loop */ while(FASTLZ_EXPECT_CONDITIONAL(ip < ip_limit)) { const flzuint8* ref; flzuint32 distance; /* minimum match length */ flzuint32 len = 3; /* comparison starting-point */ const flzuint8* anchor = ip; /* check for a run */ #if FASTLZ_LEVEL==2 if(ip[0] == ip[-1] && FASTLZ_READU16(ip-1)==FASTLZ_READU16(ip+1)) { distance = 1; ip += 3; ref = anchor - 1 + 3; goto match; } #endif /* find potential match */ HASH_FUNCTION(hval,ip); hslot = htab + hval; ref = htab[hval]; /* calculate distance to the match */ distance = anchor - ref; /* update hash table */ *hslot = anchor; /* is this a match? check the first 3 bytes */ if(distance==0 || #if FASTLZ_LEVEL==1 (distance >= MAX_DISTANCE) || #else (distance >= MAX_FARDISTANCE) || #endif *ref++ != *ip++ || *ref++!=*ip++ || *ref++!=*ip++) goto literal; #if FASTLZ_LEVEL==2 /* far, needs at least 5-byte match */ if(distance >= MAX_DISTANCE) { if(*ip++ != *ref++ || *ip++!= *ref++) goto literal; len += 2; } match: #endif /* last matched byte */ ip = anchor + len; /* distance is biased */ distance--; if(!distance) { /* zero distance means a run */ flzuint8 x = ip[-1]; while(ip < ip_bound) if(*ref++ != x) break; else ip++; } else for(;;) { /* safe because the outer check against ip limit */ if(*ref++ != *ip++) break; if(*ref++ != *ip++) break; if(*ref++ != *ip++) break; if(*ref++ != *ip++) break; if(*ref++ != *ip++) break; if(*ref++ != *ip++) break; if(*ref++ != *ip++) break; if(*ref++ != *ip++) break; while(ip < ip_bound) if(*ref++ != *ip++) break; break; } /* if we have copied something, adjust the copy count */ if(copy) /* copy is biased, '0' means 1 byte copy */ *(op-copy-1) = copy-1; else /* back, to overwrite the copy count */ op--; /* reset literal counter */ copy = 0; /* length is biased, '1' means a match of 3 bytes */ ip -= 3; len = ip - anchor; /* encode the match */ #if FASTLZ_LEVEL==2 if(distance < MAX_DISTANCE) { if(len < 7) { *op++ = (len << 5) + (distance >> 8); *op++ = (distance & 255); } else { *op++ = (7 << 5) + (distance >> 8); for(len-=7; len >= 255; len-= 255) *op++ = 255; *op++ = len; *op++ = (distance & 255); } } else { /* far away, but not yet in the another galaxy... */ if(len < 7) { distance -= MAX_DISTANCE; *op++ = (len << 5) + 31; *op++ = 255; *op++ = distance >> 8; *op++ = distance & 255; } else { distance -= MAX_DISTANCE; *op++ = (7 << 5) + 31; for(len-=7; len >= 255; len-= 255) *op++ = 255; *op++ = len; *op++ = 255; *op++ = distance >> 8; *op++ = distance & 255; } } #else if(FASTLZ_UNEXPECT_CONDITIONAL(len > MAX_LEN-2)) while(len > MAX_LEN-2) { *op++ = (7 << 5) + (distance >> 8); *op++ = MAX_LEN - 2 - 7 -2; *op++ = (distance & 255); len -= MAX_LEN-2; } if(len < 7) { *op++ = (len << 5) + (distance >> 8); *op++ = (distance & 255); } else { *op++ = (7 << 5) + (distance >> 8); *op++ = len - 7; *op++ = (distance & 255); } #endif /* update the hash at match boundary */ HASH_FUNCTION(hval,ip); htab[hval] = ip++; HASH_FUNCTION(hval,ip); htab[hval] = ip++; /* assuming literal copy */ *op++ = MAX_COPY-1; continue; literal: *op++ = *anchor++; ip = anchor; copy++; if(FASTLZ_UNEXPECT_CONDITIONAL(copy == MAX_COPY)) { copy = 0; *op++ = MAX_COPY-1; } } /* left-over as literal copy */ ip_bound++; while(ip <= ip_bound) { *op++ = *ip++; copy++; if(copy == MAX_COPY) { copy = 0; *op++ = MAX_COPY-1; } } /* if we have copied something, adjust the copy length */ if(copy) *(op-copy-1) = copy-1; else op--; #if FASTLZ_LEVEL==2 /* marker for fastlz2 */ *(flzuint8*)output |= (1 << 5); #endif return op - (flzuint8*)output; } static FASTLZ_INLINE int FASTLZ_DECOMPRESSOR(const void* input, int length, void* output, int maxout) { const flzuint8* ip = (const flzuint8*) input; const flzuint8* ip_limit = ip + length; flzuint8* op = (flzuint8*) output; flzuint8* op_limit = op + maxout; flzuint32 ctrl = (*ip++) & 31; int loop = 1; do { const flzuint8* ref = op; flzuint32 len = ctrl >> 5; flzuint32 ofs = (ctrl & 31) << 8; if(ctrl >= 32) { #if FASTLZ_LEVEL==2 flzuint8 code; #endif len--; ref -= ofs; if (len == 7-1) #if FASTLZ_LEVEL==1 len += *ip++; ref -= *ip++; #else do { code = *ip++; len += code; } while (code==255); code = *ip++; ref -= code; /* match from 16-bit distance */ if(FASTLZ_UNEXPECT_CONDITIONAL(code==255)) if(FASTLZ_EXPECT_CONDITIONAL(ofs==(31 << 8))) { ofs = (*ip++) << 8; ofs += *ip++; ref = op - ofs - MAX_DISTANCE; } #endif #ifdef FASTLZ_SAFE if (FASTLZ_UNEXPECT_CONDITIONAL(op + len + 3 > op_limit)) return 0; if (FASTLZ_UNEXPECT_CONDITIONAL(ref-1 < (flzuint8 *)output)) return 0; #endif if(FASTLZ_EXPECT_CONDITIONAL(ip < ip_limit)) ctrl = *ip++; else loop = 0; if(ref == op) { /* optimize copy for a run */ flzuint8 b = ref[-1]; *op++ = b; *op++ = b; *op++ = b; for(; len; --len) *op++ = b; } else { #if !defined(FASTLZ_STRICT_ALIGN) const flzuint16* p; flzuint16* q; #endif /* copy from reference */ ref--; *op++ = *ref++; *op++ = *ref++; *op++ = *ref++; #if !defined(FASTLZ_STRICT_ALIGN) /* copy a byte, so that now it's word aligned */ if(len & 1) { *op++ = *ref++; len--; } /* copy 16-bit at once */ q = (flzuint16*) op; op += len; p = (const flzuint16*) ref; for(len>>=1; len > 4; len-=4) { *q++ = *p++; *q++ = *p++; *q++ = *p++; *q++ = *p++; } for(; len; --len) *q++ = *p++; #else for(; len; --len) *op++ = *ref++; #endif } } else { ctrl++; #ifdef FASTLZ_SAFE if (FASTLZ_UNEXPECT_CONDITIONAL(op + ctrl > op_limit)) return 0; if (FASTLZ_UNEXPECT_CONDITIONAL(ip + ctrl > ip_limit)) return 0; #endif *op++ = *ip++; for(--ctrl; ctrl; ctrl--) *op++ = *ip++; loop = FASTLZ_EXPECT_CONDITIONAL(ip < ip_limit); if(loop) ctrl = *ip++; } } while(FASTLZ_EXPECT_CONDITIONAL(loop)); return op - (flzuint8*)output; } #endif /* !defined(FASTLZ_COMPRESSOR) && !defined(FASTLZ_DECOMPRESSOR) */ anfo-0.98/src/anfo.cc0000644000371600007640000002223511447113464011360 00000000000000// Copyright 2009 Udo Stenzel // This file is part of ANFO // // ANFO is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // Anfo is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with Anfo. If not, see . #ifdef HAVE_CONFIG_H #include "../config.h" #endif #include "anfo_common.h" #include "compress_stream.h" #include "concurrent_stream.h" #include "conffile.h" #include "index.h" #include "misc_streams.h" #include "stream.h" #include "util.h" #include "output.pb.h" #include #include #include #include #include #include #include #include #include #include #include #if HAVE_UNISTD_H #include #endif #if HAVE_SYS_STAT_H #include #endif #if HAVE_FCNTL_H #include #endif using namespace config ; using namespace std ; using namespace google::protobuf::io ; using namespace streams ; //! \page anfo_standalone Standalone ANFO executable //! What's not obvious from the command line help: ANFO can run in //! multiple threads. If you have an SMP machine, that is definitely //! what you want, but even a single CPU machine can benefit from //! multithreading while the index is being (implicitly) fetched to //! memory. The -p option can request any number of worker //! threads for aligning and indexing, and you get a main (control and //! IO) thread in addition. //! //! \todo We want an E-value... //! \todo We want more than just the best match. Think about a sensible //! way to configure this. //! \page finding_alns How to find everything we need //! We look for best hits globally and specifically on one genome. They //! will be discovered in the order of decreasing score. After setup, //! we can operate in a loop of cleaning out the stuff we don't need //! anymore and finding more alignments. //! //! Cleanup: //! - If we don't have a best hit, everything is needed. //! - If we don't have a hit to a different species, alignments to any //! different species are needed. //! - If we don't have a hit to a different order, alignments to any //! different order are needed. //! - If we don't have a hit to the human genome, alignments to the //! human genome are needed. //! - If we don't have the second best hit, non-overlapping alignments //! to the human genome are needed. //! - If we didn't hit a different chromosome, alignments to different //! chromosomes are needed. //! - If we didn't hit a different class (autosomes, sex chromosomes, //! organelles), those are needed. //! //! We're done if nothing is left to align or no alignment is found (or //! if we got everything, which means everything is thrown out nothing //! is left). //! //! Assignment: //! For every alignment, just check if it fits anywhere, then store it //! appropriately. Expand the two we were interested in. //! //! \todo Actually implement search for multiple alignments in its full generality... WRAPPED_MAIN { GOOGLE_PROTOBUF_VERIFY_VERSION ; enum option_tags { opt_none, opt_version, opt_housekeep, opt_index, opt_genome } ; std::vector< pair< int, string > > more_opts ; const char* config_file = 0 ; const char* output_file = 0 ; int nthreads = 1 ; int solexa_scale = 0 ; int clobber = 0 ; int fastq_origin = 33 ; int task_id = 0 ; if( const char *t = getenv( "SGE_TASK_ID" ) ) task_id = atoi( t ) -1 ; if( const char *t = getenv( "NSLOTS" ) ) nthreads = atoi( t ) ; struct poptOption options[] = { { "version", 'V', POPT_ARG_NONE, 0, opt_version, "Print version number and exit", 0 }, { "config", 'c', POPT_ARG_STRING, &config_file, opt_none, "Read config from FILE", "FILE" }, { "output", 'o', POPT_ARG_STRING, &output_file, opt_none, "Write output to FILE", "FILE" }, { "housekeeping",'H', POPT_ARG_NONE, 0, opt_housekeep,"Perform housekeeping (e.g. trimming)", 0 }, { "index", 'i', POPT_ARG_STRING, 0, opt_index, "Use FILE as index according to config", "FILE" }, { "genome", 'g', POPT_ARG_STRING, 0, opt_genome, "Use FILE as genome according to config", "FILE" }, { "threads", 'p', POPT_ARG_INT, &nthreads, opt_none, "Run next step in N parallel worker threads", "N" }, { "clobber", 'C', POPT_ARG_NONE, &clobber, opt_none, "Overwrite existing output file", 0 }, { "nommap", 0 , POPT_ARG_NONE, &Metagenome::nommap, opt_none, "Don't use mmap(), read() indexes instead", 0 }, { "solexa-scale", 0 , POPT_ARG_NONE, &solexa_scale, opt_none, "Quality scores use Solexa formula", 0 }, { "fastq-origin", 0 , POPT_ARG_INT, &fastq_origin, opt_none, "Quality 0 encodes as ORI, not 33", "ORI" }, { "quiet", 'q', POPT_ARG_VAL, &console.loglevel, Console::error, "Suppress most output", 0 }, { "verbose", 'v', POPT_ARG_VAL, &console.loglevel, Console::info, "Produce more output", 0 }, POPT_AUTOHELP POPT_TABLEEND } ; poptContext pc = poptGetContext( "anfo", argc, argv, options, 0 ) ; poptSetOtherOptionHelp( pc, "[OPTION...] [sequence-file...]" ) ; poptReadDefaultConfig( pc, 0 ) ; if( argc <= 1 ) { poptPrintHelp( pc, stderr, 0 ) ; return 1 ; } for( int rc = poptGetNextOpt( pc ) ; rc > 0 ; rc = poptGetNextOpt(pc) ) switch( rc ) { case opt_version: std::cout << poptGetInvocationName(pc) << ", revision " << PACKAGE_VERSION << std::endl ; return 0 ; case opt_housekeep: more_opts.push_back( make_pair( rc + (nthreads << 4), string() ) ) ; break ; case opt_index: case opt_genome: more_opts.push_back( make_pair( rc + (nthreads << 4), poptGetOptArg( pc ) ) ) ; break ; default: std::clog << poptGetInvocationName(pc) << ": " << poptStrerror( rc ) << ' ' << poptBadOption( pc, 0 ) << std::endl ; return 1 ; } if( !output_file ) throw "no output file" ; if( nthreads <= 0 ) throw "invalid thread number" ; // no-op if output exists and overwriting wasn't asked for if( !clobber && 0 == access( output_file, F_OK ) ) return 0 ; Config conf = get_default_config( config_file ) ; Holder< StreamBundle > comp = new Compose() ; { Holder< StreamBundle > ins = new ConcatStream() ; if( poptPeekArg( pc ) ) { while( const char* arg = poptGetArg( pc ) ) ins->add_stream( new UniversalReader( arg, 0, solexa_scale, fastq_origin ) ) ; } else { ins->add_stream( new UniversalReader( "-", 0, solexa_scale, fastq_origin ) ) ; } comp->add_stream( ins ) ; } poptFreeContext( pc ) ; for( size_t i = 0 ; i != more_opts.size() ; ++i ) { if( (more_opts[i].first & 0xf) == opt_housekeep ) { comp->add_stream( new Housekeeper( conf ) ) ; } else if( (more_opts[i].first & 0xf) == opt_genome ) { if( !conf.has_aligner() ) throw "no aligner configuration---cannot start." ; if( more_opts[i].first > 0x1F ) { vector< StreamHolder > v ; for( int k = 0 ; k != (more_opts[i].first >> 4) ; ++k ) v.push_back( new Mapper( conf.aligner(), more_opts[i].second ) ) ; comp->add_stream( new ConcurrentStream( v.begin(), v.end() ) ) ; } else comp->add_stream( new Mapper( conf.aligner(), more_opts[i].second ) ) ; } else { if( more_opts[i].first > 0x1F ) { vector< StreamHolder > v ; for( int k = 0 ; k != (more_opts[i].first >> 4) ; ++k ) v.push_back( new Indexer( conf, more_opts[i].second ) ) ; comp->add_stream( new ConcurrentStream( v.begin(), v.end() ) ) ; } else comp->add_stream( new Indexer( conf, more_opts[i].second ) ) ; } } std::string of = output_file ; of.append( ".#new#" ) ; StreamHolder outs = new ChunkedWriter( of.c_str(), 25 ) ; // prefer speed over compression { output::Header ohdr ; *ohdr.mutable_config() = conf ; ohdr.set_version( PACKAGE_VERSION ) ; for( const char **arg = argv ; arg != argv+argc ; ++arg ) *ohdr.add_command_line() = *arg ; if( const char *jobid = getenv( "SGE_JOB_ID" ) ) ohdr.set_sge_job_id( atoi( jobid ) ) ; if( const char *taskid = getenv( "SGE_TASK_ID" ) ) ohdr.set_sge_task_id( atoi( taskid ) ) ; comp->put_header( ohdr ) ; } outs->put_header( comp->fetch_header() ) ; while( !exit_with && comp->get_state() == Stream::have_output && outs->get_state() == Stream::need_input ) outs->put_result( comp->fetch_result() ) ; { output::Footer ofoot = comp->fetch_footer() ; exit_with |= ofoot.exit_code() ; ofoot.set_exit_code( exit_with ) ; outs->put_footer( ofoot ) ; } if( !exit_with ) { // "mv -f" rename( of.c_str(), output_file ) ; if( 0 == access( of.c_str(), F_OK ) ) { unlink( output_file ) ; rename( of.c_str(), output_file ) ; } } return 0 ; } anfo-0.98/src/anfo-tool.cc0000644000371600007640000006241611447113463012337 00000000000000// Copyright 2009 Udo Stenzel // This file is part of ANFO // // ANFO is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // Anfo is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with Anfo. If not, see . #ifdef HAVE_CONFIG_H #include "../config.h" #endif #include "compress_stream.h" #include "ducttape.h" #include "misc_streams.h" #include "output_streams.h" #include "stream.h" #include "util.h" #include #include #include #include using namespace std ; using namespace output ; using namespace streams ; //! \page anfo_stream stream-like operations on ANFO files //! //! This program builds a chain out of a variety of filters for ANFO //! streams, allowing various filters, merging and format conversions to //! be applied. The options on the command line are read from left to //! right. Those that name filters will build a chain of filters to be //! applied to every input file until a merge operation (merge, //! mega-merge, or concat) is reached, then they build up a chain to be //! applied to the result of the merge. Some filters will write a file //! containing a subset of the alignments. Afterwards, all the input //! files are "sucked" through the filter pipeline, driven by the //! calculation of a few statistics, which are printed at the end. struct ParamBlock { float slope ; float intercept ; const char* genome ; const char* arg ; ParamBlock( float s, float i, const char* g, const char* a ) : slope(s), intercept(i), genome(g), arg(a) {} } ; typedef void (*G)( ostream&, const ParamBlock& ) ; template< typename S > struct FilterParams : public ParamBlock { typedef S* (*F)( const ParamBlock& ) ; F maker ; G describe ; FilterParams( const ParamBlock& p, const char* a, F m, G d ) : ParamBlock(p.slope, p.intercept, p.genome, a), maker(m), describe(d) {} } ; typedef std::vector< FilterParams< Stream > > FilterStack ; float parse_float( const char* a ) { char *e ; float f = strtod( a, &e ) ; if( a && *a && !*e ) return f ; throw "expected real number, but found \"" + string(a) + "\"" ; } int parse_int( const char* a ) { char *e ; int i = strtol( a, &e, 10 ) ; if( a && *a && !*e ) return i ; throw "expected integer, but found \"" + string(a) + "\"" ; } int parse_int( const char* a, int d ) { char *e ; if( !a || !*a ) return d ; int i = strtol( a, &e, 10 ) ; if( !*e ) return i ; throw "expected integer, but found \"" + string(a) + "\"" ; } vector split_string( const string& s ) { if( s.empty() ) return vector() ; vector t ; for( string::size_type r, l = 0 ; ; l = r+1 ) { r = min( s.find( ':', l ), s.find( ',', l ) ) ; t.push_back( s.substr( l, r-l ) ) ; if( r == string::npos ) break ; } return t ; } vector split_string( const char* s ) { return s ? split_string( string(s) ) : vector() ; } bool is_stdout( const char* a ) { return !a || 0 == strcmp( a, "-" ) ; } const char* parse_fn( const char* a ) { return is_stdout( a ) ? "" : a ; } pair< ZeroCopyOutputStream*, string > make_output_stream_zc( const char* a ) { return is_stdout( a ) ? make_pair( new FileOutputStream( 1 ), "" ) : make_pair( new FileOutputStream( throw_errno_if_minus1( creat( a, 0666 ), "opening", a ) ) , a ) ; } pair< ostream*, string > make_output_stream_std( const char* a ) { return is_stdout( a ) ? make_pair( new ostream( cout.rdbuf() ), "" ) : make_pair( static_cast( new ofstream( a ) ), a ) ; } pair< istream*, string > make_input_stream_std( const char* a ) { return is_stdout( a ) ? make_pair( new istream( cin.rdbuf() ), "" ) : make_pair( static_cast( new ifstream( a ) ), a ) ; } Stream* mk_sort_by_pos( const ParamBlock& p ) { return new SortingStream( parse_int( p.arg, 1024 ), 256, by_genome_coordinate( split_string( p.genome ) ) ) ; } void desc_sort_by_pos( ostream& ss, const ParamBlock& p ) { ss << "sort by position on genomes [" ; vector gs = split_string( p.genome ) ; if( !gs.empty() ) { copy( gs.begin(), gs.end()-1, ostream_iterator( ss, ", " ) ) ; ss << gs.back() ; } ss << "], using " << + parse_int( p.arg, 1024 ) << " MB" ; } Stream* mk_sort_by_name( const ParamBlock& p ) { return new SortingStream( parse_int( p.arg, 1024 ) ) ; } void desc_sort_by_name( ostream& ss, const ParamBlock& p ) { ss << "sort by sequence id, using " << parse_int( p.arg, 1024 ) << " MB" ; } Stream* mk_filter_by_length( const ParamBlock& p ) { return new LengthFilter( parse_int( p.arg ) ) ; } void desc_filter_by_length( ostream& ss, const ParamBlock& p ) { ss << "remove alignments shorter than " << parse_int( p.arg ) ; } Stream* mk_filter_by_score( const ParamBlock& p ) { return new ScoreFilter( p.slope, p.intercept, split_string( p.genome ) ) ; } void desc_filter_by_score( ostream& ss, const ParamBlock& p ) { ss << "remove alignments to " << (p.genome?p.genome:"any genome") << " scoring worse than ( " << p.slope << " * ( L - " << p.intercept << " ) )" ; } Stream* mk_filter_by_mapq( const ParamBlock& p ) { return new MapqFilter( split_string( p.genome ), parse_int( p.arg ) ) ; } void desc_filter_by_mapq( ostream& ss, const ParamBlock& p ) { ss << "remove alignments where MAPQ" ; if( p.genome ) ss << " on genome " << p.genome ; ss << " is below " << parse_int( p.arg ) ; } Stream* mk_filter_by_hit( const ParamBlock& p ) { return new OnlyGenome( split_string( p.genome ) ) ; } void desc_filter_by_hit( ostream& ss, const ParamBlock& p ) { ss << "remove hits" ; if( p.genome && *p.genome ) ss << " to genomes other than " << p.genome ; } Stream* mk_delete_hit( const ParamBlock& p ) { return new IgnoreHit( split_string( p.genome ), split_string( p.arg ) ) ; } void desc_delete_hit( ostream& ss, const ParamBlock& p ) { ss << "delete hits" ; if( p.arg && *p.arg ) ss << " to sequence " << p.arg ; if( p.genome && *p.genome ) ss << " in genome " << p.genome ; } Stream* mk_require_hit( const ParamBlock& p ) { return new RequireHit( split_string( p.genome ), split_string( p.arg ) ) ; } void desc_require_hit( ostream& ss, const ParamBlock& p ) { ss << "delete records without hits" ; if( p.arg && *p.arg ) ss << " to sequence " << p.arg ; if( p.genome && *p.genome ) ss << " in genome " << p.genome ; } Stream* mk_filter_qual( const ParamBlock& p ) { return new QualFilter( parse_float( p.arg ) ) ; } void desc_filter_qual( ostream& ss, const ParamBlock& p ) { ss << "remove reads with avg. quality below " << parse_float( p.arg ) ; } Stream* mk_mask_qual( const ParamBlock& p ) { return new QualMasker( parse_int( p.arg ) ) ; } void desc_mask_qual( ostream& ss, const ParamBlock& p ) { ss << "mask bases with quality below " << parse_int( p.arg ) ; } Stream* mk_filter_multi( const ParamBlock& p ) { return new MultiFilter( parse_int( p.arg, 2 ) ) ; } void desc_filter_multi( ostream& ss, const ParamBlock& p ) { ss << "retain only sequences that were seen at least " << parse_int( p.arg, 2 ) << " times" ; } Stream* mk_subsample( const ParamBlock& p ) { return new Subsample( parse_float( p.arg ) ) ; } void desc_subsample( ostream& ss, const ParamBlock& p ) { ss << "subsample a " << parse_float(p.arg) << " fraction of sequences" ; } Stream* mk_edit_header( const ParamBlock& p ) { return new RepairHeaderStream( p.arg ? p.arg : "" ) ; } void desc_edit_header( ostream& ss, const ParamBlock& p ) { ss << "invoke " << (p.arg?p.arg:" text editor ") << " on stream's header" ; } Stream* mk_rmdup( const ParamBlock& p ) { return new RmdupStream( p.slope, p.intercept, parse_int( p.arg, 127 ) ) ; } void desc_rmdup( ostream& ss, const ParamBlock& p ) { ss << "coalesce duplicates as long as score is no worse than ( " << p.slope << " * ( L - " << p.intercept << " ) ), " << "limit Q score to " << parse_int( p.arg, 127 ) ; } Stream* mk_add_alns( const ParamBlock& p ) { return new GenTextAlignment( parse_int( p.arg, 0 ), false ) ; } void desc_add_alns( ostream& ss, const ParamBlock& p ) { ss << "add textual alignments with " << parse_int( p.arg, 0 ) << "nt of context." ; } Stream* mk_regions_only( const ParamBlock& p ) { return new InsideRegion( make_input_stream_std( p.arg ) ) ; } void desc_regions_only( ostream& ss, const ParamBlock& p ) { ss << "keep results only in regions read from " << p.arg ; } Stream* mk_not_regions( const ParamBlock& p ) { return new OutsideRegion( make_input_stream_std( p.arg ) ) ; } void desc_not_regions( ostream& ss, const ParamBlock& p ) { ss << "keep results outside regions read from " << p.arg ; } StreamBundle* mk_merge( const ParamBlock& ) { return new MergeStream() ; } void desc_merge( ostream& ss, const ParamBlock& ) { ss << "merge sorted streams" ; } StreamBundle* mk_join( const ParamBlock& ) { return new NearSortedJoin() ; } void desc_join( ostream& ss, const ParamBlock& ) { ss << "join near-sorted streams and retain best hits to each genome" ; } StreamBundle* mk_concat( const ParamBlock& ) { return new ConcatStream() ; } void desc_concat( ostream& ss, const ParamBlock& ) { ss << "concatenate streams" ; } Stream* mk_output( const ParamBlock& p ) { return is_stdout( p.arg ) ? new ChunkedWriter( 1, 99, "" ) : new ChunkedWriter( p.arg, 99 ) ; } void desc_output( ostream& ss, const ParamBlock& p ) { ss << "write native output to " << parse_fn( p.arg ) ; } Stream* mk_output_text( const ParamBlock& p ) { return new TextWriter( make_output_stream_std( p.arg ) ) ; } void desc_output_text( ostream& ss, const ParamBlock& p ) { ss << "write in text format to " << parse_fn( p.arg ) ; } Stream* mk_output_sam( const ParamBlock& p ) { return new SamWriter( make_output_stream_std( p.arg ) ) ; } void desc_output_sam( ostream& ss, const ParamBlock& p ) { ss << "write alignments in SAM format to " << parse_fn( p.arg ) ; } Stream* mk_output_glz( const ParamBlock& p ) { return new GlzWriter( make_output_stream_zc( p.arg ) ) ; } void desc_output_glz( ostream& ss, const ParamBlock& p ) { ss << "write contigs in GLZ format to " << parse_fn( p.arg ) ; } Stream* mk_output_3aln( const ParamBlock& p ) { return new ThreeAlnWriter( make_output_stream_std( p.arg ) ) ; } void desc_output_3aln( ostream& ss, const ParamBlock& p ) { ss << "write contigs in 3ALN format to " << parse_fn( p.arg ) ; } Stream* mk_output_fasta( const ParamBlock& p ) { return new FastaAlnWriter( make_output_stream_std( p.arg ) ) ; } void desc_output_fasta( ostream& ss, const ParamBlock& p ) { ss << "write best alignments(!) in FASTA format to " << parse_fn( p.arg ) ; } Stream* mk_output_fastq( const ParamBlock& p ) { return new FastqWriter( make_output_stream_std( p.arg ), true ) ; } void desc_output_fastq( ostream& ss, const ParamBlock& p ) { ss << "write sequences(!) in FASTQ format to " << parse_fn( p.arg ) ; } Stream* mk_output_table( const ParamBlock& p ) { return new TableWriter( make_output_stream_std( p.arg ) ) ; } void desc_output_table( ostream& ss, const ParamBlock& p ) { ss << "write useless table to " << parse_fn( p.arg ) ; } Stream* mk_output_wiggle( const ParamBlock& p ) { return new WigCoverageWriter( make_output_stream_std( p.arg ) ) ; } void desc_output_wiggle( ostream& ss, const ParamBlock& p ) { ss << "write depth-of-coverage in WIG format to " << parse_fn( p.arg ) ; } Stream* mk_duct_tape( const ParamBlock& p ) { return new DuctTaper( p.arg ? p.arg : "contig" ) ; } void desc_duct_tape( ostream& ss, const ParamBlock& p ) { ss << "mock-assemble hits" ; if( p.genome ) ss << " to genome " << p.genome ; ss << ", name contigs '" << (p.arg ? p.arg : "contig" ) << '\'' ; } Stream* mk_sanitize( const ParamBlock& ) { return new Sanitizer() ; } void desc_sanitize( ostream& ss, const ParamBlock& ) { ss << "remove debugging information" ; } const char *poptGetOptArg1( poptContext con ) { const char *p = poptGetOptArg( con ) ; if( !p || *p != '-' || !p[1] ) return p ; console.output( Console::warning, string("poptGetOptArg: ") + p + " treated as parameter" ) ; return p ; } struct optdef { FilterParams::F filter_maker ; FilterParams::F merge_maker ; FilterParams::F output_maker ; G description ; } ; WRAPPED_MAIN { GOOGLE_PROTOBUF_VERIFY_VERSION ; enum { opt_none, opt_sort_pos, opt_sort_name, opt_filter_length, opt_filter_score, opt_filter_mapq, opt_filter_hit, opt_delete_hit, opt_require_hit, opt_filter_qual, opt_mask_qual, opt_subsample, opt_sanitize, opt_filter_multi, opt_regions_only, opt_not_regions, opt_edit_header, opt_add_alns, opt_rmdup, opt_duct_tape, opt_merge, opt_join, opt_concat, opt_output, opt_output_text, opt_output_sam, opt_output_glz, opt_output_3aln, opt_output_fasta, opt_output_fastq, opt_output_table, opt_output_wiggle, opt_version, } ; struct optdef optdefs[] = { { 0, 0, 0, 0 }, { mk_sort_by_pos, 0, 0, desc_sort_by_pos }, { mk_sort_by_name, 0, 0, desc_sort_by_name }, { mk_filter_by_length, 0, 0, desc_filter_by_length }, { mk_filter_by_score, 0, 0, desc_filter_by_score }, { mk_filter_by_mapq, 0, 0, desc_filter_by_mapq }, { mk_filter_by_hit, 0, 0, desc_filter_by_hit }, { mk_delete_hit, 0, 0, desc_delete_hit }, { mk_require_hit, 0, 0, desc_require_hit }, { mk_filter_qual, 0, 0, desc_filter_qual }, { mk_mask_qual, 0, 0, desc_mask_qual }, { mk_subsample, 0, 0, desc_subsample }, { mk_sanitize, 0, 0, desc_sanitize }, { mk_filter_multi, 0, 0, desc_filter_multi }, { mk_regions_only, 0, 0, desc_regions_only }, { mk_not_regions, 0, 0, desc_not_regions }, { mk_edit_header, 0, 0, desc_edit_header }, { mk_add_alns, 0, 0, desc_add_alns }, { mk_rmdup, 0, 0, desc_rmdup }, { mk_duct_tape, 0, 0, desc_duct_tape }, { 0, mk_merge, 0, desc_merge }, { 0, mk_join, 0, desc_join }, { 0, mk_concat, 0, desc_concat }, { 0, 0, mk_output, desc_output }, { 0, 0, mk_output_text, desc_output_text }, { 0, 0, mk_output_sam, desc_output_sam }, { 0, 0, mk_output_glz, desc_output_glz }, { 0, 0, mk_output_3aln, desc_output_3aln }, { 0, 0, mk_output_fasta, desc_output_fasta }, { 0, 0, mk_output_fastq, desc_output_fastq }, { 0, 0, mk_output_table, desc_output_table }, { 0, 0, mk_output_wiggle, desc_output_wiggle }, { 0, 0, 0, 0 } } ; ParamBlock param( 7.5, 20.0, 0, 0 ) ; int POPT_ARG_DFLT = POPT_ARG_FLOAT | POPT_ARGFLAG_SHOW_DEFAULT ; int core_limit = 0, dry_run = 0 ; struct poptOption options[] = { { "sort-pos", 's', POPT_ARG_INT, 0, opt_sort_pos, "sort by alignment position [using merging_filter( ParamBlock(0,0,0,0), 0, mk_concat, desc_concat ) ; typedef std::deque< FilterStack > FilterStacks ; FilterStacks filters_terminal ; filters_terminal.push_back( FilterStack() ) ; poptContext pc = poptGetContext( "anfo", argc, argv, options, 0 ) ; poptSetOtherOptionHelp( pc, "[OPTION...] [sequence-file...]" ) ; poptReadDefaultConfig( pc, 0 ) ; if( argc <= 1 ) { poptPrintHelp( pc, stderr, 0 ) ; return 1 ; } for( int rc = poptGetNextOpt( pc ) ; rc != -1 ; rc = poptGetNextOpt(pc) ) { if( rc == opt_version ) { std::cout << poptGetInvocationName(pc) << ", revision " << PACKAGE_VERSION << std::endl ; return 0 ; } else if( rc >= 0 && optdefs[rc].filter_maker ) { filters_current->push_back( FilterParams< Stream >( param, poptGetOptArg1( pc ), optdefs[rc].filter_maker, optdefs[rc].description ) ); } else if( rc >= 0 && optdefs[rc].merge_maker ) { // make sure we are still creating input filters if( filters_current != &filters_initial ) throw "merge-like commands cannot not follow merge- or output-like commands" ; merging_filter = FilterParams< StreamBundle >( param, poptGetOptArg1( pc ), optdefs[rc].merge_maker, optdefs[rc].description ) ; // from now on we build output filters filters_current = &filters_terminal.back() ; } else if( rc >= 0 && optdefs[rc].output_maker ) { // make sure we are creating output filters if( filters_current == &filters_initial ) filters_current = &filters_terminal.back() ; // create filter filters_current->push_back( FilterParams< Stream >( param, poptGetOptArg( pc ), optdefs[rc].output_maker, optdefs[rc].description ) ) ; // start new output stream filters_terminal.push_back( FilterStack() ) ; filters_current = &filters_terminal.back() ; } else { std::clog << poptGetInvocationName(pc) << ": " << poptStrerror( rc ) << ' ' << poptBadOption( pc, 0 ) << std::endl ; return 1 ; } } if( core_limit ) { struct rlimit lim ; getrlimit( RLIMIT_AS, &lim ) ; lim.rlim_cur = 1024*1024 * (long)core_limit ; setrlimit( RLIMIT_AS, &lim ) ; } // iterate over non-option arguments, glob everything glob_t the_glob ; the_glob.gl_pathv = 0 ; the_glob.gl_pathc = 0 ; int glob_flag = GLOB_NOSORT | GLOB_NOCHECK ; while( const char* arg = poptGetArg( pc ) ) { switch( glob( arg, glob_flag, 0, &the_glob ) ) { case 0: break ; case GLOB_NOSPACE: throw "out of memory while globbing " + std::string(arg) ; case GLOB_ABORTED: throw "read error on " + std::string(arg) ; default: throw "strange error from glob()" ; } glob_flag |= GLOB_APPEND ; } // give a report of the filter stack (because it's so easy to get // wrong) console.output( Console::notice, "Input files:" ) ; if( the_glob.gl_pathc ) for( char **arg = the_glob.gl_pathv ; arg != the_glob.gl_pathv + the_glob.gl_pathc ; ++arg ) { if( !strcmp( *arg, "-" ) ) console.output( Console::notice, " " ) ; else console.output( Console::notice, " " + string(*arg) ) ; } else console.output( Console::notice, " " ) ; if( !filters_initial.empty() ) { console.output( Console::notice, "For every input file:" ) ; for( FilterStack::const_iterator i = filters_initial.begin() ; i != filters_initial.end() ; ++i ) { stringstream s ; (i->describe)( s << " ", *i ) ; console.output( Console::notice, s.str() ) ; } } { stringstream s ; merging_filter.describe( s, merging_filter ) ; console.output( Console::notice, s.str() ) ; } // last filter stack is not empty (== missing output filter) or only // one filter stack (== no output at all)? --> add a writer for // stdout to last filter. else remove the empty one if( !filters_terminal.back().empty() || filters_terminal.size() == 1 ) filters_terminal.back().push_back( FilterParams< Stream >( param, 0, mk_output_text, desc_output_text ) ) ; else filters_terminal.pop_back() ; for( FilterStacks::const_iterator i = filters_terminal.begin() ; i != filters_terminal.end() ; ++i ) { console.output( Console::notice, "Filter a copy of the result as follows:" ) ; for( FilterStack::const_iterator j = i->begin() ; j != i->end() ; ++j ) { stringstream s ; (j->describe)( s << " ", *j ) ; console.output( Console::notice, s.str() ) ; } } poptFreeContext( pc ) ; if( !dry_run ) { Holder< StreamBundle > merging_stream( (merging_filter.maker)( merging_filter ) ) ; // iterate over glob results if( the_glob.gl_pathc ) { vector< Holder< Compose > > cs ; for( char **arg = the_glob.gl_pathv ; arg != the_glob.gl_pathv + the_glob.gl_pathc ; ++arg ) { Holder< Compose > c( new Compose ) ; c->add_stream( strcmp( *arg, "-" ) ? new UniversalReader( *arg ) : new UniversalReader( "", new FileInputStream(0) ) ) ; for( FilterStack::const_iterator i = filters_initial.begin() ; i != filters_initial.end() ; ++i ) c->add_stream( (i->maker)( *i ) ) ; cs.push_back( c ) ; } for( vector< Holder< Compose > >::const_iterator i = cs.begin(), ie = cs.end() ; i != ie ; ++i ) merging_stream->add_stream( *i ) ; } else merging_stream->add_stream( new UniversalReader( "", new FileInputStream(0) ) ) ; FanOut out ; for( FilterStacks::const_iterator i = filters_terminal.begin() ; i != filters_terminal.end() ; ++i ) { Holder< Compose > c( new Compose ) ; for( FilterStack::const_iterator j = i->begin() ; j != i->end() ; ++j ) c->add_stream( (j->maker)( *j ) ) ; out.add_stream( c ) ; } return transfer( *merging_stream, out ) ; } return 0 ; } anfo-0.98/src/dnaindex.cc0000644000371600007640000003362511447113506012231 00000000000000// Copyright 2009 Udo Stenzel // This file is part of ANFO // // ANFO is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // Anfo is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with Anfo. If not, see . /*! \page DNA indexer * * Scans a dna file, creating an index of fixed-size words. We need a * two-level index and want to keep it simple. To this end, we'll store * plain arrays in the index files so they can be directly mmaped. That * makes them inherently unportable between different architectures, but * we'll have to live with that. So, this is what an index file looks * like: * * - The signature "IDX1" in ASCII. * - The length of the meta information. * - The metainformation of type config::CompactIndex, serialized in * binary protocol buffer format. * - The first level array itself. Every DNA-word is converted to an * index by assigning 0,1,2,3 to A,C,T,G and writing nucleotides LSB * to MSB. The entry at that position is an offset into the second * level array. * - The size of the second level array in words. * - The second level array. This is a dense array of offsets into a * compact genome. Entries in the first level array point to the * begin of the subarray of indices where their key can be found. * * All words are 32bit unsigned integers written LSB first. No such * word can overflow, since we limit ourselves to genomes no larger than * 4G bases. The index file can be larger than 4G (and often will be). * If so, they are only useful on 64bit platforms. * * This code probably makes little to no sense on a 32bit machine. * Anyway, we take care that a 32bit version will still work, though * limiting the index size to comfortably fit into the address space * will make it impossible to index more than roughly a quarter billion * bases. * * We use (unsigned long long int) to store words cut out from the * genome. Assuming it has at least 64 bits of storage, this limits the * word size to no less than 16 bases. (No problem, more than that is * probably impractical anyway.) */ #ifdef HAVE_CONFIG_H #include "../config.h" #endif #include "index.h" #include "util.h" #include "config.pb.h" #include #include #include #include #include #include #include #include template< typename G > struct mk_dense_word { public: mk_dense_word( G consume_word ) : consume_( consume_word ) {} void operator()( int w, uint32_t offs, Oligo dna ) { go( w, offs, dna, 0 ) ; } private: G consume_ ; void go( int w, uint32_t offs, Oligo dna, uint32_t acc ) { while( w ) { // Loop over set bits in ambiguity codes. Special cased and // unrolled for speed. Note that we need recursion, but we can // avoid it in the most common case of not having any ambiguity // code. int nt = dna & 0xf ; dna >>= 4 ; acc <<= 2 ; --w ; switch ( nt ) { case 0: break ; // not supposed actually occur case 1: acc |= 0 ; break ; case 2: acc |= 1 ; break ; case 3: go( w, offs, dna, acc | 0 ) ; acc |= 1 ; break ; case 4: acc |= 2 ; break ; case 5: go( w, offs, dna, acc | 0 ) ; acc |= 2 ; break ; case 6: go( w, offs, dna, acc | 1 ) ; acc |= 2 ; break ; case 7: go( w, offs, dna, acc | 0 ) ; go( w, offs, dna, acc | 1 ) ; acc |= 2 ; break ; case 8: acc |= 3 ; break ; case 9: go( w, offs, dna, acc | 0 ) ; acc |= 3 ; break ; case 10: go( w, offs, dna, acc | 1 ) ; acc |= 3 ; break ; case 11: go( w, offs, dna, acc | 0 ) ; go( w, offs, dna, acc | 1 ) ; acc |= 3 ; break ; case 12: go( w, offs, dna, acc | 2 ) ; acc |= 3 ; break ; case 13: go( w, offs, dna, acc | 0 ) ; go( w, offs, dna, acc | 2 ) ; acc |= 3 ; break ; case 14: go( w, offs, dna, acc | 1 ) ; go( w, offs, dna, acc | 2 ) ; acc |= 3 ; break ; case 15: go( w, offs, dna, acc | 0 ) ; go( w, offs, dna, acc | 1 ) ; go( w, offs, dna, acc | 2 ) ; acc |= 3 ; break ; } } // No more bases to add, we can finally do something with this word. consume_( offs, acc ) ; } } ; //! \brief makes C++ happy //! Type inference only works for functions, not objects. Don't you //! just love C++? //! \internal template< typename G > mk_dense_word make_dense_word( G g ) { return mk_dense_word( g ) ; } //! \brief checks for self-overlapping seeds //! \internal //! We define a seed as useless if for any n in the range 1..o dropping //! the first n bases from the seed results in the same value as //! dropping the last n bases. //! \param w seed to test //! \param l length of the seed //! \param o max. overlap length to check //! \return true iff the seed is good (i.e. doesn't self-overlap) inline bool check_repeat( uint32_t w, uint32_t l, uint32_t o ) { uint32_t mask = (1 << (2*l))-1, v = w ; for( ; o ; --o ) { mask >>= 2 ; v >>= 2 ; if( v == (w & mask) ) return false ; } return true ; } //! \brief counts words in a genome //! This is passed as a worker to CompactGenome::scan_words, it only //! counts the words and stores the counts in what later becomes the //! first level index. //! \internal class count_word { private: public: uint32_t *base_ ; uint32_t cutoff_ ; uint32_t stride_ ; uint32_t size_ ; uint32_t repeat_ ; uint64_t &total_ ; count_word( uint32_t *b, uint32_t c, uint32_t s, uint32_t sz, uint32_t r, uint64_t &t ) : base_(b), cutoff_(c), stride_(s), size_(sz), repeat_(r), total_(t) {} void operator()( uint32_t off, uint32_t ix ) const { if( off % stride_ == 0 && check_repeat( ix, size_, repeat_ ) ) { uint32_t x = ++base_[ix] ; if( x <= cutoff_ ) { ++total_ ; if( x == cutoff_ ) total_ -= cutoff_ ; } if( std::numeric_limits::max() / 4 <= total_ ) throw "Sorry, but a bigger machine is needed for this kind of index." ; } } } ; //! \brief stores words in an index //! This is passed as a worker to CompactGenome::scan_words, it stores //! the words in the second level index, which must have been correctly //! allocated beforehand. //! \internal class store_word { private: uint32_t *index_1l_ ; uint32_t *index_2l_ ; uint32_t stride_ ; uint32_t size_ ; uint32_t repeat_ ; public: store_word( uint32_t s, uint32_t *i1, uint32_t *i2, uint32_t sz, uint32_t r ) : index_1l_(i1), index_2l_(i2), stride_(s), size_(sz), repeat_(r) {} void operator()( uint32_t off, uint32_t ix ) { if( off % stride_ == 0 && check_repeat( ix, size_, repeat_ ) ) { uint32_t& p = index_1l_[ (uint64_t)ix ] ; if( p ) index_2l_[ (uint64_t)(--p) ] = off ; } } } ; struct noop { void operator()( uint32_t ) const {} } ; struct put_gap { google::protobuf::RepeatedField *gaps_ ; put_gap( google::protobuf::RepeatedField *gaps ) : gaps_(gaps) {} void operator()( uint32_t g ) const { gaps_->Add(g) ; } } ; WRAPPED_MAIN { GOOGLE_PROTOBUF_VERIFY_VERSION ; enum option_tags { opt_none, opt_version } ; const char* output_file = 0 ; const char* description = 0 ; const char* genome_name = 0 ; unsigned wordsize = 12 ; unsigned cutoff = std::numeric_limits::max() ; unsigned repeat = std::numeric_limits::max() ; unsigned stride = 4 ; int verbose = 0 ; int histogram = 0 ; int slice = 0 ; int slices = 1 ; config::Config mi ; struct poptOption options[] = { { "version", 'V', POPT_ARG_NONE, 0, opt_version, "Print version number and exit", 0 }, { "output", 'o', POPT_ARG_STRING, &output_file, opt_none, "Output index to FILE", "FILE" }, { "genome", 'g', POPT_ARG_STRING, &genome_name, opt_none, "Read genome GENOME", "GENOME" }, { "description", 'd', POPT_ARG_STRING, &description, opt_none, "Add TEXT as description to index", "TEXT" }, { "wordsize", 's', POPT_ARG_INT | POPT_ARGFLAG_SHOW_DEFAULT, &wordsize, opt_none, "Index words of length SIZE", "SIZE" }, { "stride", 'S', POPT_ARG_INT | POPT_ARGFLAG_SHOW_DEFAULT, &stride, opt_none, "Index every Nth word", "N" }, { "limit", 'l', POPT_ARG_INT, &cutoff, opt_none, "Do not index words more frequent than LIM", "LIM" }, { "repetitive", 'r', POPT_ARG_INT, &repeat, opt_none, "Do not index words that self-overlap N bases", "N" }, { "slice", 'x', POPT_ARG_INT, &slice, opt_none, "Process slice N if creating a split index", "N" }, { "numslice", 'x', POPT_ARG_INT, &slice, opt_none, "Process slice N if creating a split index", "N" }, { "histogram", 'h', POPT_ARG_NONE, &histogram, opt_none, "Produce histogram of word frequencies", 0 }, { "verbose", 'v', POPT_ARG_NONE, &verbose, opt_none, "Make more noise while working", 0 }, POPT_AUTOHELP POPT_TABLEEND } ; poptContext pc = poptGetContext( "dnaindex", argc, argv, options, 0 ) ; poptSetOtherOptionHelp( pc, "[OPTION...]" ) ; poptReadDefaultConfig( pc, 0 ) ; if( argc <= 1 ) { poptPrintHelp( pc, stderr, 0 ) ; return 1 ; } for( int rc = poptGetNextOpt( pc ) ; rc > 0 ; rc = poptGetNextOpt(pc) ) switch( rc ) { case opt_version: std::cout << poptGetInvocationName(pc) << ", revision " << PACKAGE_VERSION << std::endl ; return 0 ; default: std::clog << poptGetInvocationName(pc) << ": " << poptStrerror( rc ) << ' ' << poptBadOption( pc, 0 ) << std::endl ; return 1 ; } if( !genome_name ) throw "missing --genome option" ; if( poptGetArg( pc ) ) throw "unexpected non-option argument" ; GenomeHolder genome = Metagenome::find_genome( genome_name ) ; if( repeat == std::numeric_limits::max() ) repeat = wordsize >> 1 ; uint64_t first_level_len = (1 << (2 * wordsize)) + 1 ; if( std::numeric_limits::max() <= first_level_len || std::numeric_limits::max() / 4 <= first_level_len ) throw "integer overflow in size calculation; cannot handle this word size" ; uint32_t *base = (uint32_t*)malloc( 4 * first_level_len ) ; throw_errno_if_null( base, "allocating first level index" ) ; // we will scan over the dna twice: once to count occurences of // words, once to actually store pointers. // First scan: only count words. We'll have to go over the whole // table again to convert counts into offsets. uint64_t total0 = 0; genome->scan_words( wordsize, make_dense_word( count_word( base, cutoff, stride, wordsize, repeat, total0 ) ), noop(), slice, slices, "Counting" ) ; std::clog << "Need to store " << total0 << " pointers." << std::endl ; // Histogram of word frequencies. if( histogram ) { std::map< int, int > hist ; for( unsigned *p = base+3 ; p != base+3+first_level_len ; ++p ) ++hist[ *p ] ; int max = 0 ; for( std::map< int,int >::const_iterator i = hist.begin() ; i != hist.end() ; ++i ) if( max < i->second ) max = i->second ; for( std::map< int,int >::const_iterator i = hist.begin() ; i != hist.end() ; ++i ) std::cout << i->first << '\t' << i->second << '\t' << std::string( 50*i->second / max, '*' ) << std::endl ; } // sum up occurences and replace counts by pointers into array. // For practical reasons, pointers (actually indices) will be set to // the *end* of the allocated range and count down when writing // second-level-pointers. // // Whenever we decide to ignore some oligo because it occurs too // often, we store the index 0. An additional pass needs to replace // the zeros by sensible values. uint64_t total = 0 ; for( uint32_t *p = base ; p != base + first_level_len ; ++p ) { if( *p < cutoff ) { total += *p ; *p = total ; } else { *p = 0 ; } } if( total0 != total ) throw "logic error: totals are not equal" ; uint32_t *lists = (uint32_t*)malloc( 4 * total ) ; throw_errno_if_null( lists, "allocating second level index" ) ; madvise( lists, 4 * total, MADV_WILLNEED ) ; config::CompactIndex ci ; // Second scan: we actually store the offsets now. genome->scan_words( wordsize, make_dense_word( store_word( stride, base, lists, wordsize, repeat ) ), put_gap( ci.mutable_gap() ), slice, slices, "Indexing" ) ; std::clog << "Found " << ci.gap_size() << " gap symbols" << std::endl ; // need to fix 0-entries in 1L index uint32_t last = total ; for( uint32_t *p = base + first_level_len ; p != base ; ) { --p ; if( !*p ) *p = last ; else last = *p ; } ci.set_genome_name( genome_name ) ; ci.set_wordsize( wordsize ) ; ci.set_stride( stride ) ; ci.set_indexsize( total ) ; if( cutoff != std::numeric_limits::max() ) ci.set_cutoff( cutoff ) ; std::string metainfo ; if( !ci.SerializeToString( &metainfo ) ) throw "error when serializing metainfo" ; // Note to self: creating and mmapping a sparse file, then filling // it in random order is an exceptionally bad idea... std::clog << "Writing " << genome->name() << "..." << std::endl ; std::stringstream output_path ; if( output_file ) output_path << output_file ; else output_path << genome->name() << '_' << wordsize << ".idx" ; int fd = throw_errno_if_minus1( creat( output_path.str().c_str(), 0644 ), "opening", output_path.str().c_str() ) ; uint32_t sig = FixedIndex::signature, len = metainfo.size() ; metainfo.append( "\0\0\0" ) ; mywrite( fd, &sig, 4 ) ; mywrite( fd, &len, 4 ) ; mywrite( fd, metainfo.data(), (len+3)&~3 ) ; mywrite( fd, base, 4 * first_level_len ) ; mywrite( fd, lists, 4 * total ) ; close( fd ) ; return 0 ; } anfo-0.98/src/fa2dna.cc0000644000371600007640000002664411447113072011573 00000000000000// Copyright 2009 Udo Stenzel // This file is part of ANFO // // ANFO is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // Anfo is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with Anfo. If not, see . /*! * \page fasta_to_dna FASTA to DNA file converter * * \c fa2dna reads a set of FASTA files with one ore more DNA or RNA * sequences, possibly containing ambiguity codes, from files or stdin, * writes it in a compact representation into a new file and writes meta * information into another file. * * We chop the genome into contigs. Every sequence start also starts a * new contig, stretches of more than 2 Ns (configurable, but more Ns * become nonsensical quite quickly) separate contigs and are not * stored. Ambiguity codes are recognized, and so is 'U' for uracil. * * A "compact genome" is a file encoding DNA as 4 bits per nucleotide. * The bits code for A,C,T,G from LSB to MSB. Combinations of bits form * ambiguity codes (0 is a gap, used as terminator only, 15 is an N), * two left rotations therefore reverse-complement a single nucleotide. * In a byte, the first nucleotide occupies the 4 LSBs. * * The "compact genome" starts with the ACSII-signature "DNA1", then the * offset to the internal metadata, then the length of the metadata, followed * by the raw DNA. Finally the metadata is attached, in the form of a * binary protocol buffer message of type config::Genome. * * In the DNA part, each contig is prepended with a single gap, then the * contigs are concatenated, then a final single gap is appended. The * DNA is written out with two nucleotides per byte, and the final byte * is padded with a gap if necessary. Note that every contig is always * preceded and succeeded by a gap; this is done so we can \c mmap a * genome into memory and operate on pointers into it in the knowledge * that every contig is terminated by a gap in either direction. * * \todo A genome may or may not contain information about taxonomy, and * this info may apply to the genome or just some sequences. Add * support to either set a taxid or look it up in some sort of * data base. */ #ifdef HAVE_CONFIG_H #include "../config.h" #endif #include "conffile.h" #include "config.pb.h" #include "index.h" #include "sequence.h" #include "util.h" #include #include #include #include //! \brief decodes a FASTA file //! //! This class is a state machine that recognizes a FASTA file. //! Nucleotides are split into contigs and written out to an \c ostream, //! names and coordinates are remembered and can later be written to a //! config file. //! //! \todo The state machine is implemented using a pointer to member //! functions. This is straight-forward, but also a bit hard to //! read and it may be slower than necessary. This could be //! enhanced by including a loop in each of the involved //! functions. class FastaDecoder { private: void (FastaDecoder::*state_)( char ) ; unsigned position_ ; unsigned source_position_ ; unsigned num_n_ ; uint8_t one_nt_ ; const unsigned max_n_ ; bool verbose_ ; std::ostream& dna_ ; config::Genome cur_genome_ ; config::Sequence *cur_sequence_ ; config::Contig *cur_contig_ ; public: //! \brief sets up a fresh decoder //! The decoder is initialized with an output stream, a genome //! metadata structure and some parameters. The output stream //! is assumed to be empty, which means that a signature is //! written first and all coordinates will be relative to the //! current position. The metadata should be properly //! initialized, if it contains sequence definitions, they will //! be lost. //! //! \param dna output stream for compact DNA data //! \param genome metadata about genome, will be filled in //! \param maxn maximum number of Ns in a row that is not a gap //! \param verbose whether to produce progress reports to \c //! stderr FastaDecoder( std::ostream& dna, const config::Genome &genome, unsigned maxn = 2, bool verbose = false ) : state_( &FastaDecoder::s_idle ), position_( 24 ), num_n_( 0 ), one_nt_( 0 ) , max_n_( maxn ), verbose_( verbose ), dna_( dna ) , cur_genome_( genome ), cur_sequence_( 0 ), cur_contig_( 0 ) { uint32_t dummy = 0, signature = CompactGenome::signature ; dna_.write( (const char*)&signature, 4 ) ; dna_.write( (const char*)&dummy, 4 ) ; dna_.write( (const char*)&dummy, 4 ) ; cur_genome_.clear_sequence() ; cur_genome_.set_maxn( maxn ) ; } void finish() { step( 0 ) ; if( verbose_ ) std::clog << "\33[K" << std::flush ; uint32_t ix_start = dna_.tellp() ; if( !cur_genome_.SerializeToOstream( &dna_ ) ) throw "couldn't serialize config" ; uint32_t ix_len = (uint32_t)dna_.tellp() - ix_start ; dna_.seekp( 4 ) ; dna_.write( (char*)&ix_start, 4 ) ; dna_.write( (char*)&ix_len, 4 ) ; } void consume( std::istream& s ) { int c ; while( (c = s.get()) != std::istream::traits_type::eof() ) step( c ) ; } void step( char c ) { (this->*state_)( c ) ; } void report() const { if( verbose_ ) std::clog << cur_sequence_->name() << " @ " << source_position_ << "\33[K\r" << std::flush ; } void begin_new_sequence() { source_position_ = 0 ; cur_sequence_ = cur_genome_.add_sequence() ; } void finish_sequence() { cur_sequence_ = 0 ; } void begin_new_contig() { put_nt( '-' ) ; num_n_ = 0 ; cur_contig_ = cur_sequence_->add_contig() ; cur_contig_->set_offset( position_ ) ; cur_contig_->set_range_start( source_position_ ) ; report() ; } void finish_contig() { cur_contig_->set_range_end( source_position_ ) ; report() ; } void finish_genome() { put_nt( '-' ) ; cur_genome_.set_total_size( position_ ) ; if( position_ & 1 ) put_nt( '-' ) ; } void put_nt( char c ) { if( c == 'n' || c == 'N' ) { ++num_n_ ; } else { for( ; num_n_ ; --num_n_ ) put_nt_( '-' ) ; put_nt_( c ) ; } } void put_nt_( char c ) { if( position_ & 1 ) { dna_.put( (to_ambicode(c) << 4) | one_nt_ ) ; } else { one_nt_ = to_ambicode(c) ; } ++position_ ; if( !(position_ & 0xfffff ) ) report() ; } void s_idle( char c ) { if( c == '>' ) { begin_new_sequence() ; state_ = &FastaDecoder::s_name ; } } void s_name( char c ) { if( !c ) finish_genome() ; else if( std::isspace(c) || c == '\n' ) { if( c == '\n' ) state_ = &FastaDecoder::s_seq_begin ; else state_ = &FastaDecoder::s_info ; } else cur_sequence_->mutable_name()->push_back( c ) ; } void s_info( char c ) { if( !c ) finish_genome() ; else if( c == '\n' ) state_ = &FastaDecoder::s_seq_begin ; } void s_seq_begin( char c ) { if( !c ) finish_genome() ; else if( c == ';' ) state_ = &FastaDecoder::s_info ; else if( c == '>' ) { begin_new_sequence() ; state_ = &FastaDecoder::s_name ; } else if( c == 'n' || c == 'N' ) { if( num_n_ == max_n_ ) { ++source_position_ ; num_n_ = 0 ; state_ = &FastaDecoder::s_contig_gap ; } else { ++source_position_ ; put_nt( c ) ; } } else if( encodes_nuc( c ) ) { begin_new_contig() ; ++source_position_ ; put_nt( c ) ; state_ = &FastaDecoder::s_sequence ; } } void s_sequence( char c ) { if( !c ) { source_position_ -= num_n_ ; finish_contig() ; finish_sequence() ; finish_genome() ; } else if( (c == 'N' || c == 'n') && num_n_ == max_n_ ) { source_position_ -= num_n_ ; finish_contig() ; source_position_ += num_n_+1 ; num_n_ = 0 ; state_ = &FastaDecoder::s_contig_gap ; } else if( encodes_nuc( c ) ) { ++source_position_ ; put_nt( c ) ; } else if( c == '>' ) { source_position_ -= num_n_ ; finish_contig() ; finish_sequence() ; begin_new_sequence() ; state_ = &FastaDecoder::s_name ; } } void s_contig_gap( char c ) { if( !c ) { finish_sequence() ; finish_genome() ; } else if( c == '>' ) { finish_sequence() ; begin_new_sequence() ; state_ = &FastaDecoder::s_name ; } else if( encodes_nuc( c ) && c != 'n' && c != 'N' ) { begin_new_contig() ; ++source_position_ ; put_nt( c ) ; state_ = &FastaDecoder::s_sequence ; } else if( c == 'n' || c == 'N' ) { ++source_position_ ; } } } ; std::string drop_suffix( const std::string& suf, const std::string& s ) { if( s.substr( s.size()-suf.size() ) == suf ) return s.substr( 0, s.size()-suf.size() ) ; else return s ; } WRAPPED_MAIN { GOOGLE_PROTOBUF_VERIFY_VERSION ; enum option_tags { opt_none, opt_version } ; const char* output_file = 0 ; const char* description = 0 ; const char* genome_name = 0 ; int max_num_n = 2 ; int verbose = 0 ; int taxid = 0 ; struct poptOption options[] = { { "version", 'V', POPT_ARG_NONE, 0, opt_version, "Print version number and exit", 0 }, { "output", 'o', POPT_ARG_STRING, &output_file, opt_none, "Write DNA output to FILE", "FILE" }, { "maxn", 'm', POPT_ARG_INT, &max_num_n, opt_none, "Treat N consecutive Ns as separator", "N" }, { "genome", 'g', POPT_ARG_STRING, &genome_name, opt_none, "Set genome name to NAME", "NAME" }, { "taxid", 0 , POPT_ARG_INT, &taxid, opt_none, "Set numeric taxid of genome to T", "T" }, { "description", 'd', POPT_ARG_STRING, &description, opt_none, "Add TEXT as description to genome", "TEXT" }, { "verbose", 'v', POPT_ARG_NONE, &verbose, opt_none, "Make more noise while working", 0 }, POPT_AUTOHELP POPT_TABLEEND } ; poptContext pc = poptGetContext( "fa2dna", argc, argv, options, 0 ) ; poptSetOtherOptionHelp( pc, "[OPTION...] [FASTA-file...]" ) ; poptReadDefaultConfig( pc, 0 ) ; if( argc <= 1 ) { poptPrintHelp( pc, stderr, 0 ) ; return 1 ; } for( int rc = poptGetNextOpt( pc ) ; rc > 0 ; rc = poptGetNextOpt(pc) ) switch( rc ) { case opt_version: std::cout << poptGetInvocationName(pc) << ", revision " << PACKAGE_VERSION << std::endl ; return 0 ; default: std::clog << argv[0] << ": " << poptStrerror( rc ) << ' ' << poptBadOption( pc, 0 ) << std::endl ; return 1 ; } if( !genome_name ) throw "missing --genome option" ; config::Genome g ; if( description ) g.set_description( description ) ; if( taxid ) g.set_taxid( taxid ) ; if( genome_name ) g.set_name( genome_name ) ; else if( !poptPeekArg( pc ) ) g.set_name( "genome" ) ; else g.set_name( drop_suffix( ".fa", drop_suffix( ".fas", drop_suffix( ".fna", poptPeekArg( pc ))))) ; std::ofstream output_stream( (output_file ? output_file : (g.name() + ".dna")).c_str(), std::ios::trunc ) ; FastaDecoder fd( output_stream, g, max_num_n, verbose ) ; if( !poptPeekArg( pc ) ) fd.consume( std::cin ) ; while( const char* arg = poptGetArg( pc ) ) { if( strcmp(arg,"-") ) { std::ifstream str( arg ) ; fd.consume( str ) ; } else fd.consume( std::cin ) ; } fd.finish() ; return 0 ; } anfo-0.98/src/file-info.cc0000644000371600007640000000604111447113463012301 00000000000000// Copyright 2009 Udo Stenzel // This file is part of ANFO // // ANFO is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // Anfo is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with Anfo. If not, see . #ifdef HAVE_CONFIG_H #include "../config.h" #endif #include "align_fwd.h" #include "conffile.h" #include "config.pb.h" #include "index.h" #include "stream.h" #include "util.h" #include #include #include #include #include WRAPPED_MAIN { GOOGLE_PROTOBUF_VERIFY_VERSION ; for( int argi = 1 ; argi != argc ; ++argi ) { std::cout << argv[argi] << ": " ; std::ifstream fd( argv[argi] ) ; uint32_t sig ; fd.read( (char*)&sig, 4 ) ; if( sig == CompactGenome::signature ) { std::cout << "DNA file" << std::endl ; uint32_t off = 0, len = 0 ; fd.read( (char*)&off, 4 ) ; fd.read( (char*)&len, 4 ) ; char buf[ len ] ; fd.seekg( off ) ; fd.read( (char*)buf, len ) ; config::Genome g ; g.ParseFromArray( buf, len ) ; google::protobuf::io::OstreamOutputStream os( &std::cout ) ; google::protobuf::TextFormat::Print( g, &os ) ; } else if( sig == FixedIndex::signature || (sig & 0xffffff) == (FixedIndex::signature & 0xffffff) ) { std::cout << "inverted list index" << ( sig == FixedIndex::signature ? "" : " (legacy format)" ) << std::endl ; uint32_t len = 0 ; fd.read( (char*)&len, 4 ) ; char buf[ len ] ; fd.read( (char*)buf, len ) ; config::CompactIndex ci ; ci.ParseFromArray( buf, len ) ; google::protobuf::io::OstreamOutputStream os( &std::cout ) ; google::protobuf::TextFormat::Print( ci, &os ) ; } else { config::Config conf ; Holder< streams::Stream > af( new streams::UniversalReader( argv[argi] ) ) ; try { conf = af->fetch_header().config() ; if( conf.has_aligner() ) std::cout << "ANFO stream file" << std::endl ; } catch(...) {} if( !conf.IsInitialized() ) try { conf = parse_text_config( argv[argi] ) ; std::cout << "ANFO configuration file" << std::endl ; } catch(...) { } if( conf.has_aligner() ) { google::protobuf::io::OstreamOutputStream os( &std::cout ) ; google::protobuf::TextFormat::Print( conf, &os ) ; std::cout << adna_parblock( conf.aligner() ) ; } else if( af->get_state() == streams::Stream::have_output ) { std::cout << "FastA/FastQ sequence file(?)" << std::endl ; } else std::cout << "unknown\n" ; } std::cout << std::endl ; } return 0 ; } anfo-0.98/src/index-test.cc0000644000371600007640000001047211447113465012522 00000000000000// Copyright 2009 Udo Stenzel // This file is part of ANFO // // ANFO is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // Anfo is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with Anfo. If not, see . //! \page index_test Testing the indexing phase //! This binary just runs the indexer on whatever input it is given, //! printing the resulting seeds in various detail. If the input looks //! as if it contains a coordinate (simulated data does), this program //! will check whether a seed in the correct region is found at all. #ifdef HAVE_CONFIG_H #include "../config.h" #endif #include "compress_stream.h" #include "conffile.h" #include "index.h" #include "stream.h" #include "util.h" #include #include #include #include #include using namespace config ; using namespace std ; using namespace google::protobuf::io ; struct Subject { string chrom, seq ; int start, len ; bool strand ; } ; istream& operator >> ( istream& s, Subject& t ) { string strand ; s >> t.chrom >> strand >> t.start >> t.len >> t.seq ; t.strand = !strand.empty() && strand[0] == '-' ; return s ; } WRAPPED_MAIN { GOOGLE_PROTOBUF_VERIFY_VERSION ; enum option_tags { opt_none, opt_version } ; FixedIndex::LookupParams params ; params.cutoff = numeric_limits::max() ; const char *index_name = "hg18" ; struct poptOption options[] = { { "version", 'V', POPT_ARG_NONE, 0, opt_version, "Print version number and exit", 0 }, { "index", 'i', POPT_ARG_STRING, &index_name, 0, "Use INX as index", "INX" }, POPT_AUTOHELP POPT_TABLEEND } ; console.loglevel = Console::info ; poptContext pc = poptGetContext( "anfo", argc, argv, options, 0 ) ; poptSetOtherOptionHelp( pc, "[OPTION...] [sequence-file...]" ) ; poptReadDefaultConfig( pc, 0 ) ; if( argc <= 1 ) { poptPrintHelp( pc, stderr, 0 ) ; return 1 ; } for( int rc = poptGetNextOpt( pc ) ; rc > 0 ; rc = poptGetNextOpt(pc) ) switch( rc ) { case opt_version: std::cout << poptGetInvocationName(pc) << ", revision " << PACKAGE_VERSION << std::endl ; return 0 ; default: std::clog << poptGetInvocationName(pc) << ": " << poptStrerror( rc ) << ' ' << poptBadOption( pc, 0 ) << std::endl ; return 1 ; } FixedIndex index( index_name ) ; GenomeHolder genome = Metagenome::find_genome( index.metadata().genome_name() ) ; vector subjects ; while( const char* arg = poptGetArg( pc ) ) { ifstream ifs( arg ) ; Subject subj ; while( ifs >> subj ) subjects.push_back( subj ) ; } // for( params.wordsize = lower_limit ; params.wordsize <= 12 ; ++params.wordsize ) { // for( params.stride = 4 ; params.stride <= 8 ; params.stride *= 2 ) { params.wordsize = 12 ; params.stride = 4 ; for( params.allow_mismatches = 0 ; params.allow_mismatches != 2 ; ++params.allow_mismatches ) { for( int min_seed_len = 12 ; min_seed_len <= 20 ; min_seed_len+=4 ) { cout << params.allow_mismatches << '\t' << min_seed_len << '\t' << flush ; unsigned total_seeds = 0, total_seqs = 0, total_hits = 0 ; for( vector::const_iterator subj = subjects.begin() ; subj != subjects.end() ; ++subj ) { PreSeeds seeds ; int num_useless ; index.lookupS( subj->seq, seeds, params, &num_useless ) ; output::Seeds ss ; total_seeds += combine_seeds( seeds, min_seed_len, &ss ) ; ++total_seqs ; unsigned left = genome->find_pos( subj->chrom, subj->start ) - genome->get_base() ; for( int i = 0 ; i != ss.ref_positions_size() ; ++i ) { unsigned ref = ss.ref_positions(i) ; int qry = ss.query_positions(i) ; if( subj->strand == (qry < 0) && ref >= left && ref < left+subj->len ) { ++total_hits ; break ; } } } cout << total_seqs << '\t' << total_seeds << '\t' << total_hits << endl ; } } poptFreeContext( pc ) ; return 0 ; } anfo-0.98/src/anfo.scm.in0000644000371600007640000002264211447113464012164 00000000000000; ELK extension for Anfo ; ; Loads the Anfo library and provides a wrappers/ convenience functions. ; TODO: decide whether output streams should return anything. ; bind missing "calculating" streams. ; take the returning of results out of the C code (mostly...) (require 'srfi-89) (load "__LIBDIR__/libanfo.la") (define *default-compression* 99) (define *default-handles-limit* 128) (define *default-mem-limit* 512) (define *default-origin* 33) (define *default-solexa-scale* #f) ; sets sensible verbosity, but also makes sure that libanfo was actually loaded (set-verbosity! 'warning) ; invokes continuation on stream, extracts a result, frees the stream ; The stream is always freed, even on non-local exit. The result is ; only extracted in the normal control flow. (define (bracket-stream stream) (lambda (cont) (dynamic-wind (lambda () #f) (lambda () (let ((rs (cont stream)) (r0 (get-summary stream))) (if r0 (cons r0 rs) rs))) (lambda () (prim-delete-stream stream))))) (define chop: 'chop:) (define compress: 'compress:) (define context: 'context:) (define editor: 'editor:) (define genome: 'genome:) (define genomes: 'genomes:) (define handles: 'handles:) (define intercept: 'intercept:) (define label: 'label:) (define left: 'left:) (define max: 'max:) (define mem: 'mem:) (define min: 'min:) (define name: 'name:) (define num: 'num:) (define origin: 'origin:) (define primary: 'primary:) (define prior: 'prior:) (define quality: 'quality:) (define right: 'right:) (define score: 'score:) (define secondary: 'secondary:) (define sequences: 'sequences:) (define slope: 'slope:) (define solexa: 'solexa:) (define strict: 'strict:) (define (write-fasta file) (bracket-stream (prim-write-fasta file))) (define (write-fastq file) (bracket-stream (prim-write-fastq file))) (define (write-glz file) (bracket-stream (prim-write-glz file))) (define (write-sam file) (bracket-stream (prim-write-sam file))) (define (write-table file) (bracket-stream (prim-write-table file))) (define (write-text file) (bracket-stream (prim-write-text file))) (define (write-threealn file) (bracket-stream (prim-write-threealn file))) (define (write-wiggle file) (bracket-stream (prim-write-wiggle file))) (define* (duct-tape (label: lbl "contig") (prior: pri 0.0)) (bracket-stream (prim-duct-tape lbl pri))) (define* (add-alns (context: ctx 0) (strict: str #f)) (bracket-stream (prim-add-alns ctx str))) (define* (read-file in (solexa: sol *default-solexa-scale*) (origin: ori *default-origin*) (genome: gen "") (name: nam #f)) (bracket-stream (prim-read-file in sol ori gen nam))) (define (filter-chain left right file) (bracket-stream (prim-filter-chain left right file))) (define (filter-qual qual) (bracket-stream (prim-filter-qual qual))) (define (inside-region file) (bracket-stream (prim-inside-region file))) (define (mask-qual qual) (bracket-stream (prim-mask-qual qual))) (define (outside-region file) (bracket-stream (prim-outside-region file))) (define (sanitize) (bracket-stream (prim-sanitize))) (define (subsample rate) (bracket-stream (prim-subsample rate))) (define* (filter-length (min: min 0) (max: max #f)) (bracket-stream (prim-filter-length min max))) (define* (filter-gc (min: min 0) (max: max 100)) (bracket-stream (prim-filter-gc min max))) (define* (filter-multi (num: num 2)) (bracket-stream (prim-filter-multi num))) (define* (edit-header (editor: editor #f)) (bracket-stream (prim-edit-header editor))) (define* (filter-score (slope: slope 7.5) (intercept: intercept 20) (genomes: genomes '())) (bracket-stream (prim-filter-score slope intercept genomes))) (define* (filter-total-score (slope: slope 7.5) (intercept: intercept 20) (genomes: genomes '(hg18 pt2))) (bracket-stream (prim-filter-total-score slope intercept genomes))) (define* (filter-mapq mapq (genomes '())) (bracket-stream (prim-filter-mapq mapq genomes))) (define* (require-best-hit (genomes: g '()) (sequences: s '())) (bracket-stream (prim-require-bht g s))) (define* (require-hit (genomes: g '()) (sequences: s '())) (bracket-stream (prim-require-hit g s))) (define* (ignore-hit (genomes: g '()) (sequences: s '())) (bracket-stream (prim-ignore-hit g s))) (define* (only-genomes (genomes '())) (bracket-stream (prim-only-genomes genomes))) (define* (sort-pos genomes (mem: m *default-mem-limit*) (handles: h *default-handles-limit*)) (bracket-stream (prim-sort-pos m h genomes))) (define* (sort-name (mem: m *default-mem-limit*) (handles: h *default-handles-limit*)) (bracket-stream (prim-sort-name m h))) (define* (rmdup (slope: slope 7.5) (intercept: intercept 20) (quality: qual 40)) (bracket-stream (prim-rmdup slope intercept qual))) (define* (trim (left: left '()) (right: right '()) (score: score 4)) (bracket-stream (prim-trim left right score))) (define (stats) (let* ((p (lambda (lo hi) (+ lo (* hi 65536 32768)))) (fun (lambda (total mapped mapped_u different bases_gc_lo bases_gc_hi bases_gc_m_lo bases_gc_m_hi bases_lo bases_hi bases_2_lo bases_2_hi bases_m_lo bases_m_hi bases_m2_lo bases_m2_hi) `(( total . ,total ) ( mapped . ,mapped ) ( mapuniq . ,mapped_u ) ( distinct . ,different ) ( gc-raw . ,(* 100 (/ (p bases_gc_lo bases_gc_hi) (p bases_lo bases_hi)))) ( gc-mapped . ,(* 100 (/ (p bases_gc_m_lo bases_gc_m_hi) (p bases_m_lo bases_m_hi)))) ( bases . ,(p bases_lo bases_hi)) ( bases-m2 . ,(p bases_2_lo bases_2_hi)) ( mapbases . ,(p bases_m_lo bases_m_hi)) ( mapbases-m2 . ,(p bases_m2_lo bases_m2_hi)))))) (fmap (lambda (args) (apply fun args)) (bracket-stream (prim-stats))))) (define (mismatches) (bracket-stream (prim-mismatches))) (define (vector-dot v w) (let loop ((s 0) (l (vector->list v)) (r (vector->list w))) (if (or (null? l) (null? r)) s (loop (+ s (* (car l) (car r))) (cdr l) (cdr r))))) (define (vector-mul v x) (apply vector (map (lambda (y) (* y x)) (vector->list v)))) (define (mat-times-vector m v) (apply vector (map (lambda (w) (vector-dot w v)) (vector->list m)))) (define* (divergence (primary: p) (secondary: s) (chop: c)) (let ((fun (lambda (b) (let* ((d1 (vector-dot b '#(3 -1 3 -1 -1))) (e (/ (* (- (vector-ref b 2) (vector-ref b 3)) 3) d1)) (d (- (* 4 e) 3)) (a (vector-mul (mat-times-vector `#( #( ,(- e 3) 0 ,e 0 0 ) #( 0 ,(- e 3) 0 ,e ,e ) #( ,(* 3 e) 0 ,(- (* 3 e) 3) 0 0 ) #( 0 ,e 0 ,(- e 3) ,e ) #( 0 ,(* 2 e) 0 ,(* 2 e) ,(- (* 2 e) 3) ) ) b) (/ 1 d)))) `(( error-rate . ,e ) ( corrected-div . ,(/ (* 2 (vector-ref a 3)) (+ (vector-ref a 1) (vector-ref a 3)))) ( corrected-counts . ,a ) ( raw-div . ,(/ (* 2 (vector-ref b 3)) (+ (vector-ref b 1) (vector-ref b 3)))) ( raw-counts . ,b )))))) (fmap fun (bracket-stream (prim-divergence p s c))))) (define* (write-file out (compress: comp *default-compression*)) (bracket-stream (prim-write-native out comp))) (define write-native write-file) (define (anfo-with-input in) (cond ((procedure? in) in) (else (bracket-stream (prim-read-file in *default-solexa-scale* *default-origin* "" #f))))) (define (anfo-with-output out) (cond ((procedure? out) out) ((string? out) (bracket-stream (prim-write-native out *default-compression*))) (else (error 'anfo-with-output "object does not denote an output stream: ~s" out)))) (define (anfo-with-many-inputs args cont) (anfo-with-many anfo-with-input args cont)) (define (anfo-with-many-outputs args cont) (anfo-with-many anfo-with-output args cont)) (define (anfo-with-many-filters args cont) (anfo-with-many (lambda (x) x) args cont)) (define (anfo-with-many fun args cont) (if (null? args) (cont '()) ((fun (car args)) (lambda (s) (anfo-with-many fun (cdr args) (lambda (ss) (cont (cons s ss)))))))) (define (tee . args) (lambda (cont) (anfo-with-many-outputs args (lambda (outs) ((bracket-stream (apply prim-tee outs)) cont))))) (define (chain . args) (lambda (cont) (anfo-with-many-filters args (lambda (outs) ((bracket-stream (apply prim-chain outs)) cont))))) (define (merge . args) (lambda (cont) (anfo-with-many-inputs args (lambda (outs) ((bracket-stream (apply prim-merge outs)) cont))))) (define (join . args) (lambda (cont) (anfo-with-many-inputs args (lambda (outs) ((bracket-stream (apply prim-join outs)) cont))))) (define (concat . args) (lambda (cont) (anfo-with-many-inputs args (lambda (outs) ((bracket-stream (apply prim-concat outs)) cont))))) (define (anfo-run . args) ((anfo-with-input (car args)) (lambda (in-stream) ((anfo-with-output (apply chain (cdr args))) (lambda (out-stream) (prim-anfo-run in-stream out-stream)))))) (define (fmap fun stream) (lambda (cont) (let ((rs (stream cont))) (cons (fun (car rs)) (cdr rs))))) (provide 'anfo) (autoload 'pp 'pp.scm) anfo-0.98/man/0000777000371600007640000000000011447127355010176 500000000000000anfo-0.98/man/fa2dna.10000644000371600007640000000434311447112754011330 00000000000000.\" ANFO short read aligner .\" (C) 2009 Udo Stenzel .\" .\" This program is free software; you can redistribute it and/or modify .\" it under the terms of the GNU General Public License as published by .\" the Free Software Foundation; either version 3 of the License, or (at .\" your option) any later version. See the COPYING file for details. .\" Process this file with .\" groff -man -Tascii patman.1 .\" .TH FA2DNA 1 "OCTOBER 2009" Applications "User Manuals" .SH NAME fa2dna \- format fasta database for use with ANFO .SH SYNOPSIS .B fa2dna [ .I option .B | .I file .B ... ] .SH DESCRIPTION .B fa2dna reads one or more files in fasta format and reformats them into a database suitable for .BR anfo (1). The input file(s) can contain more than one sequence, and each sequence can be broken up into multiple contigs by a stretch of Ns. All IUPAC ambiguity codes are fully supported. .SH OPTIONS .IP "-V, --version" Print version number and exit. .IP "-o file, --output file" Write output to .IR file . file should end in .IR .dna , because .B anfo and some downstream tools might stumble over a different extension. Default is the genome name with the .I .dna extension. .IP "-m N, --maxn N" Sets the maximum number of .IR N s to be interpreted as IUPAC ambiguity codes to .IR N ; any longer stretch is interpreted as separing contigs. Default is 2. .IP "-g name, --genome name" Sets the genome name to .IR name . This name is stored in the output file and will be used by .B anfo to identify the matched genome in its output. The genome should be a prefix of the output file name to allow downstream tools to find it. The name should be short, but unique, something like "hg18" or "pt2" for human or chimpanzee genomes would work fine. .IP "-d text, --description text" Adds .I text as description to the metadata. This is purely informational. .IP "-v, --verbose" Causes a progress indicator to be printed. .SH FILES .I /etc/popt .RS The system wide configuration file for .BR popt (3). .B fa2dna identifies itself as "fa2dna" to popt. .RE .I ~/.popt .RS Per user configuration file for .BR popt (3). .RE .SH BUGS None known. .SH AUTHOR Udo Stenzel .SH "SEE ALSO" .BR anfo "(1), " fa2dna "(1) " popt "(3), " fasta (5) anfo-0.98/man/dnaindex.10000644000371600007640000000650611447112754011772 00000000000000.\" ANFO short read aligner .\" (C) 2009 Udo Stenzel .\" .\" This program is free software; you can redistribute it and/or modify .\" it under the terms of the GNU General Public License as published by .\" the Free Software Foundation; either version 3 of the License, or (at .\" your option) any later version. See the COPYING file for details. .\" Process this file with .\" groff -man -Tascii patman.1 .\" .TH DNAINDEX 1 "OCTOBER 2009" Applications "User Manuals" .SH NAME dnaindex \- index dna file for use with ANFO .SH SYNOPSIS .B dnaindex [ .I option .B ... ] .SH DESCRIPTION .B dnaindex builds an index for a dna file. Dna files must be indexed to be useable with .BR anfo (1), it is possible to have multiple indices for the same dna file. .SH OPTIONS .IP "-V, --version" Print version number and exit. .IP "-o file, --output file" Write output to .IR file ". " file customarily ends in .IR .idx . Default is .IR genomename_wordsize.idx . .IP "-g file, --genome file" Read the genome from .IR file . This file name is also stored in the resulting index so it can be found automatically whenever the index is used. It is therefore best if .I file is just a file name without path. .IP "-G dir, --genome-dir dir" Add .I dir to the genome search path. This is useful if the genome to be indexed is not yet in the place where it will later be used. .IP "-d text, --description text" Add .I text as description to the index. This is purely informative. .IP "-s size, --wordsize size" Set the wordsize to .IR size . A smaller wordsize increases precision at the expense of higher computational investment. The default is 12, which with a stride of 8 yields a good compromise. .IP "-S num, --stride num" Set the stride to .IR num . Only one out of .I num possible words of dna is actually indexed. A smaller stride increases precicion at the expense of a bigger index. The default is 8, which in conjunction with a wordsize of 12 yields a good compromise. .IP "-l lim, --limit lim" Prevents the indexing of words that occur more often than .I lim times. This can be used to ignore repetitive seeds and save the space to store them. A good default depends on the size of the genome being indexed, something like 500 works for the human genome with wordsize 12 and stride 8. .IP "-h, --histogram" Produce a histogram of word frequencies. This can be used to get an indea how the frequency distribution to select an appropriate value for .IR --limit . .IP "-v, --verbose" Print a progress indicator during operation. .SH "NOTES" .B dnaindex is limited to genomes no longer than 4 gigabases due to its use of 32 bit indices. The index is quite large, so depending on parameters, a 64 bit platform is needed for genomes in the gigabase range. If a genome contains IUPAC ambiguity codes, the affected seeds need to be expanded. If there are many ambiguity codes in a small region, that results in an unacceptably large index. .SH ENVIRONMENT .IP ANFO_PATH Colon separated list of directories searched for genome files. .SH FILES .I /etc/popt .RS The system wide configuration file for .BR popt (3). .B dnaindex identifies itself as "dnaindex" to popt. .RE .I ~/.popt .RS Per user configuration file for .BR popt (3). .RE .SH BUGS None known. .SH AUTHOR Udo Stenzel .SH "SEE ALSO" .BR anfo "(1), " fa2dna "(1), " popt "(3), " fasta (5) anfo-0.98/man/anfo-sge.10000644000371600007640000000641311447112754011674 00000000000000.\" ANFO short read aligner .\" (C) 2009 Udo Stenzel .\" .\" This program is free software; you can redistribute it and/or modify .\" it under the terms of the GNU General Public License as published by .\" the Free Software Foundation; either version 3 of the License, or (at .\" your option) any later version. See the COPYING file for details. .\" Process this file with .\" groff -man -Tascii patman.1 .\" .TH ANFO 1 "OCTOBER 2009" Applications "User Manuals" .SH NAME anfo-sge \- version of ANFO for hostile grid engines .SH SYNOPSIS .B anfo [ .I option .B | .I file .B ... ] .SH DESCRIPTION .B anfo-sge is a castrated version of .B anfo intended to be run in hostile environments, such as a misconfigured Sun Grid Engine. It has provisions to split up both indices and input files and doesn't use pthreads. Chances are, unless your pthreads implementation is unusable, you do not want to use this version, but .B anfo instead. If run as an array task, the total number of tasks must be evenly divisible by the number of slices in the index. Each task then picks one slice of the index and one slice of the input and processes it in the ordinary way. All output files must be merged (e.g. using the .I mega-merge operation of .BR anfo-tool ") " to get the correct final result. .SH OPTIONS .IP "-V, --version" Print version number and exit. .IP "-o file, --output file" Write output to .IR file ". " file will be written in the native .B anfo binary format, which can be operated upon using .B anfo-tool or the bindings to .BR guile . .IP "-c conffile, --config conffile" Read configuration from .IR conffile . This file configures which indices are used, and by extension to which genomes an alignment is made, what parameters to use in the aligner and can set paths. See the example file. .IP "--solexa-scale" When reading FastQ files, use the Solexa scale (log-odds-ratios) instead of the standard Phread scale (probabilities). If you use Solexa/Illumina sequencers, refer to your documentation whether you need this, otherwise you don't. .IP "--fastq-origin ori" Set origin for FastQ decoding to .IR ori . The standard and default is 33, but it must be set to 64 for some versions of the Solexa/Illumina software. If you use Solexa/Illumina sequencers, refer to your documentation whether you need this, otherwise you don't. .IP "-q, --quiet" Suppress all output except fatal errors. .IP "--sge-task-last id" Set the highest task number to .IR id , overriding the environment variable .IR SGE_TASK_LAST . .SH ENVIRONMENT .IP ANFO_PATH Colon separated list of directories searched for genome and index files. .IP TASK_ID Task identifier given by SGE. Determines which slice of the total workload is to be processed. .IP SGE_TASK_LAST Set by the SGE, determines how to slide the total workload. .SH FILES .I /etc/popt .RS The system wide configuration file for .BR popt (3). .B anfo-sge identifies itself as "anfo" to popt. .RE .I ~/.popt .RS Per user configuration file for .BR popt (3). .RE .I /usr/share/doc/anfo/example/*.cfg .RS Example configuration files to be used with .BR anfo . .RE .SH BUGS None known. .SH AUTHOR Udo Stenzel .SH "SEE ALSO" http://bioinf.eva.mpg.de/anfo .BR anfo-tool "(1), " anfo "(1), " fa2dna "(1), " dnaindex "(1), " popt "(3), " fasta (5) anfo-0.98/man/anfo-tool.10000644000371600007640000002400611447112754012071 00000000000000.\" ANFO short read aligner .\" (C) 2009 Udo Stenzel .\" .\" This program is free software; you can redistribute it and/or modify .\" it under the terms of the GNU General Public License as published by .\" the Free Software Foundation; either version 3 of the License, or (at .\" your option) any later version. See the COPYING file for details. .\" Process this file with .\" groff -man -Tascii patman.1 .\" .TH ANFO-TOOL 1 "OCTOBER 2009" Applications "User Manuals" .SH NAME anfo-tool \- process native ANFO binary files .SH SYNOPSIS .B anfo-tool [ .I option .B | .I pattern .B ... ] .SH DESCRIPTION .B anfo-tool is used to filter, process and convert the files created by .BR anfo . Every pattern on the command line is wildcard expanded, then for every input file (or the standard input, if no pattern is given), .B anfo-tool builds a chain of input filters, it then merges these input streams in one of several ways, splits the result up into multiple output streams, each of which can have a chain of output filter applied. .SH OPTIONS .SS General Options These options apply globally and modify the behavior of the whole program. They can be placed anywhere in the command line. .IP "-V, --version" Print version number and exit. .IP "-q, --quiet" Suppress all output except fatal error messages. .IP "-v, --verbose" Produce more output, including progress indicators for most operations. .IP "--debug" Produce debugging output in addition to progress information. .IP "-n, --dry-run" Parse command line, optionally print a description of the intended operations, then exit. .IP "--vmem X" Limit virtual memory to .I X megabytes. If memory runs out, .I anfo-tool tries to free up memory by forgetting about big files, e.g. genomes. Use this option to avoid swapping or out-of-memory conditions when operations involve big or multiple genomes. .SS Setting Parameters A parameter can be set multiple times on the command line and will overwrite previous settings. Any filter option that needs a parameter picks up the last definition that appeared before the filter option. .IP "--set-slope S" Set the slope parameter to .IR S . The .I slope is used together with the .I intercept where filters apply to alignment scores; alignments scoring no worse than .I slope * (length - intercept) are considered good. The default is 7.5. .IP "--set-intercept L" Set the intercept parameter to .IR L . The .I intercept is used together with the .I slope where filters apply to alignment scores; alignments scoring no worse than .I slope * (length - intercept) are considered good. The default is 20. .IP "--set-context C" Set the context parameter to .IR C . The context is the number of surrounding bases of the reference included when printing alignments in text form. The default is 0. .IP "--set-genome G" Set the genome parameter to .IR G . Many filters will only consider the best alignments to this specific genome if it is set. If no genome is set, the globally best alignment is used. .IP "--clear-genome" Clear the genome parameter. Filters apply to the globally best alignment afterwards. .SS Filter Options Filters can be applied before merging the inputs or after splitting the back up. .IP "-s, --sort-pos=n" Sort by alignment position while buffering no more than .I n MiB in memory. If a genome is set, alignments to that genome are used. .IP "-S, --sort-name=n" Sort by read name while buffering no more than .I n MiB in memory. .IP "-l, --filter-length=L" Retain alignments only for reads of at least .I L bases length. The reads themselves are kept. .IP "-f, --filter-score" Retain alignments only if their score is good enough. .IR Uses slope and intercept . .IP "--filter-mapq=Q" Remove alignments with mapping quality below .IR Q . .IP "-h, --filter-hit=SEQ" Keep only reads that have a hit to a sequence named .IR SEQ . If .I SEQ is empty, reads are kept if they have any hit. If the .I genome parameter is set, only hits to that genome count. .IP "--delete-hit=SEQ" Delete alignments to .IR SEQ . If .I SEQ is empty, all alignments are deleted. If the .I genome parameter is set, only alignments to that genome are deleted. .IP "--filter-qual=Q" Mask out bases with quality below .IR Q . Such a base is replaced by the .I N ambiguity code. .IP "--multiplicity=N" Keep only reads of molecules that have been sequenced at least .I N times. Reads are considered to come from the same original molecule if their aligned coordinates are identical. .IP "--subsample=F" Subsample a fraction .I F of the results. Every read is independently and randomly choosen to be kept or not. .IP "--inside-regions=FILE" Read a list of regions from .IR FILE , then keep only alignments that overlap an annotated region. .IP "--outside-regions=FILE" Read a list of regions from .IR FILE , then keep only alignments that do not overlap an annotated region. .SS "Special Filters" .IP "-d, --rmdup=Q" Remove PCR duplicates, clamp quality scores to .IR Q . Two reads are considered to be duplicates, if their aligned coordinates are identical. If a .I genome is set, the best alignment to that genome is used, else the globally best alignment. Both alignments must be good, as determined by .IR slope and intercept . For a set of duplicates, a consensus is called, generally increasing the quality scores. If a resulting quality score exceeds .IR Q , it is set to .IR Q . This filter requires the input to be sorted by alignment coordinate on the selected .IR genome . .IR "--duct-tape=NAME" Duct-tape overlapping alignments into contigs and call a consensus for them. If a .I genome is set, alignments to that genome are used, else the globally best alignments. This filter requires input to be sorted by alignment coordinate on the genome. Output is a set of contigs, every position gets assigned a consensus base, a quality score and likelihoods for every possible diallele. (It is called duct-taping because it kind of looks like an assembly, but is not nearly as solid.) .IP "--edit-header=ED" Invoke the editor .I ED on the text representaion of the stream's header. This can be used to clean up header that have accumulated too much cruft. .SS "Merging Filters" Exactly one merging filter should be given on the command line, all filter options occuring before that are part of the input filter chains, all further filters become output chains. If no merging filter is given, .I "--concat" is assumed, and all filters are input filters. .IP "-c, --concat" Concatenate all input streams in the order they appear on the command line. .IP "-m, --merge" Merge sorted input streams, producing a sorted result. All inputs must be sorted in the same way. .IP "-j, --join" Join input streams and retain the single best hits to each genome. Every input stream must contain a record for every read, reads are buffered in memory until all of their hits are collected. This way, joining works well if all inputs are nearly in the same order. If reads are missing from some streams, joining them will waste memory. .IP "--mega-merge" Merge many streams such as those produced by running .BR anfo-sge . Streams that operated on the same reads are joined, then everything is merged. .SS "Output Options" If an output option is given on the command line, the current output filter chain is ended and a new one is started. If no output option is given, a textual representation of the final stream is written to .IR stdout . All output options accept .I - to write to stdout. .IP "-o, --output FILE" Write native binary stream (a compressed protobuf message) to .IR FILE . Writing a binary stream and reading it back in is lossless. .IP "--output-text FILE" Write protobuf text stream to .IR FILE . If the necessary genomes are available, a textual representation of the alignments is included. If the .I context parameter is set, that many additional bases of the reference upstream and downstream from the alignment are included. .IP "--output-sam=FILE" Write alignments in SAM format to .IR FILE . .IP "--output-glz FILE" Write contigs in GLZ 0.9 format to .IR FILE . Generating GLZ only works after application of .IR --duct-tape , every contigs becomes a GLZ record. .IP "--output-3aln FILE" Write contigs in a table based format to .IR FILE . The format is still subject to change, see the source code for detailed documentation. .IP "--output-fasta FILE" Write alignments(!) in FastA format to .IR FILE . Alignments are writte as pair of reference and query sequence, aligned coordinates are indicated in the description of the query sequence. If the .I context parameter is set, that many additional bases of the reference upstream and downstream from the alignment are included. This format is not suggested for any serious use, it exists to support legacy applications. .IP "--output-fastq FILE" Write sequences(!) in FastQ format to .IR FILE . Writing FastQ effectively reconstitutes the input to .B ANFO if no filtering was done on the results. .IP "--output-table FILE" Write per-alignment statistics to .IR FILE . The file has three colums:Âsequence length, alignment score, difference to next best alignment. It is mainly useful to analyze/visualize the distribution of alignment scores. .IP "--stats FILE" Write simple statistics to .IR FILE . This results in some simple summary statistics of a whole stream: number of aligned sequences, average length, GC content. .SH ENVIRONMENT .IP ANFO_PATH Colon separated list of directories searched for genome and index files. .IP ANFO_TEMP Temporary space used for sorting of large files. .SH FILES .I /etc/popt .RS The system wide configuration file for .BR popt (3). .B anfo-tool identifies itself as "anfo-tool" to popt. .RE .I ~/.popt .RS Per user configuration file for .BR popt (3). .RE .SH BUGS The command line of this tools is way too complicated and its semantics are counterintuitive. Using .B anfo-tool is probably best avoided in most cases, the .B guile bindings should provide a much more scalable and easier to understand interface. .SH AUTHOR Udo Stenzel .SH "SEE ALSO" .BR anfo "(1), " fa2dna "(1) " popt "(3), " fasta (5) anfo-0.98/man/file-info.10000644000371600007640000000204611447112754012043 00000000000000.\" ANFO short read aligner .\" (C) 2009 Udo Stenzel .\" .\" This program is free software; you can redistribute it and/or modify .\" it under the terms of the GNU General Public License as published by .\" the Free Software Foundation; either version 3 of the License, or (at .\" your option) any later version. See the COPYING file for details. .\" Process this file with .\" groff -man -Tascii patman.1 .\" .TH FILE-INFO 1 "OCTOBER 2009" Applications "User Manuals" .SH NAME fa2dna \- format fasta database for use with ANFO .SH SYNOPSIS .B file-info [ .I file .B ... ] .SH DESCRIPTION .B file-info reads one or more files in various formats that .BR anfo (1) understands, and for each file prints to stdout .IP \(bu 4 the type of file if it was identified, .IP \(bu 4 a textual form of the configuration, if a configuration is contained in it, .IP \(bu 4 the substitution matrix and other alignment parameters, if an aligner configuration was contained. .SH BUGS None known. .SH AUTHOR Udo Stenzel .SH "SEE ALSO" .BR anfo (1) anfo-0.98/man/Makefile.am0000644000371600007640000000011511447112754012140 00000000000000dist_man1_MANS = fa2dna.1 dnaindex.1 anfo-sge.1 anfo-tool.1 file-info.1 anfo-0.98/man/Makefile.in0000644000371600007640000002533311447120210012144 00000000000000# Makefile.in generated by automake 1.10.2 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, # 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. # This Makefile.in is free software; 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