pax_global_header00006660000000000000000000000064123301264660014515gustar00rootroot0000000000000052 comment=a77b93546f17fc606650ef1bcedd09e6162cb2de bambamc-bambamc_0_0_50/000077500000000000000000000000001233012646600147655ustar00rootroot00000000000000bambamc-bambamc_0_0_50/.gitignore000066400000000000000000000007661233012646600167660ustar00rootroot00000000000000*.o *~ INSTALL Makefile.in aclocal.m4 autom4te.cache config.guess config.h.in config.sub configure depcomp doconfig.sh doconfig32.sh install-sh ltmain.sh missing recomp.sh src/Makefile.in Makefile compile config.h config.log config.status doconfig48.sh doconfig49.sh libtool m4/libtool.m4 m4/ltoptions.m4 m4/ltsugar.m4 m4/ltversion.m4 m4/lt~obsolete.m4 maccombined.sh src/.deps/ stamp-h1 ubuntu.sh src/*.lo src/*.la src/bambamc/BamBam_Config.h bambamc.pc src/bamreadertest src/bamwritertest src/.libs/ bambamc-bambamc_0_0_50/AUTHORS000066400000000000000000000000351233012646600160330ustar00rootroot00000000000000Please see the COPYING file. bambamc-bambamc_0_0_50/COPYING000066400000000000000000000006401233012646600160200ustar00rootroot00000000000000The hashing code in the source file src/bambamc/BamBam_Hash.c is by Bob Jenkins. This code is in the public domain (please see the corresponding remarks in src/bambamc/BamBam_Hash.c). The rest of the code is by German Tischler and distributed under version 3 of the GNU General Public License (see file GPLv3, which is part of the distribution). The single source files denote the respective copyright ownerships. bambamc-bambamc_0_0_50/ChangeLog000066400000000000000000000001601233012646600165340ustar00rootroot00000000000000bambamc (0.0.50) * add support for null quality pointers when constructing alignments using PutAlignment bambamc-bambamc_0_0_50/GPLv3000066400000000000000000001045131233012646600156070ustar00rootroot00000000000000 GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The GNU General Public License is a free, copyleft license for software and other kinds of works. 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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 . bambamc-bambamc_0_0_50/INSTALL000066400000000000000000000366051233012646600160300ustar00rootroot00000000000000Installation Instructions ************************* Copyright (C) 1994-1996, 1999-2002, 2004-2013 Free Software Foundation, Inc. Copying and distribution of this file, with or without modification, are permitted in any medium without royalty provided the copyright notice and this notice are preserved. This file is offered as-is, without warranty of any kind. Basic Installation ================== Briefly, the shell commands `./configure; make; make install' should configure, build, and install this package. The following more-detailed instructions are generic; see the `README' file for instructions specific to this package. Some packages provide this `INSTALL' file but do not implement all of the features documented below. The lack of an optional feature in a given package is not necessarily a bug. More recommendations for GNU packages can be found in *note Makefile Conventions: (standards)Makefile Conventions. The `configure' shell script attempts to guess correct values for various system-dependent variables used during compilation. It uses those values to create a `Makefile' in each directory of the package. It may also create one or more `.h' files containing system-dependent definitions. Finally, it creates a shell script `config.status' that you can run in the future to recreate the current configuration, and a file `config.log' containing compiler output (useful mainly for debugging `configure'). It can also use an optional file (typically called `config.cache' and enabled with `--cache-file=config.cache' or simply `-C') that saves the results of its tests to speed up reconfiguring. Caching is disabled by default to prevent problems with accidental use of stale cache files. If you need to do unusual things to compile the package, please try to figure out how `configure' could check whether to do them, and mail diffs or instructions to the address given in the `README' so they can be considered for the next release. If you are using the cache, and at some point `config.cache' contains results you don't want to keep, you may remove or edit it. The file `configure.ac' (or `configure.in') is used to create `configure' by a program called `autoconf'. You need `configure.ac' if you want to change it or regenerate `configure' using a newer version of `autoconf'. The simplest way to compile this package is: 1. `cd' to the directory containing the package's source code and type `./configure' to configure the package for your system. Running `configure' might take a while. While running, it prints some messages telling which features it is checking for. 2. Type `make' to compile the package. 3. 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Run `configure --help' for more details. bambamc-bambamc_0_0_50/Makefile.am000066400000000000000000000002021233012646600170130ustar00rootroot00000000000000EXTRA_DIST = configure GPLv3 SUBDIRS = src ACLOCAL_AMFLAGS=-I m4 pkgconfigdir = $(libdir)/pkgconfig pkgconfig_DATA = bambamc.pc bambamc-bambamc_0_0_50/NEWS000066400000000000000000000000001233012646600154520ustar00rootroot00000000000000bambamc-bambamc_0_0_50/README000066400000000000000000000005641233012646600156520ustar00rootroot00000000000000This package contains mainly a lightwight C implementation of the read name collation code from the larger bambam C++ project (see ftp://ftp.sanger.ac.uk/pub/users/gt1). The gibhub repository does not contain the final configure script but only the source files passed to autoconf/automake. Please use autoreconf -i -f to obtain a set of working configuration scripts. bambamc-bambamc_0_0_50/README.md000066400000000000000000000001431233012646600162420ustar00rootroot00000000000000bambamc ======= lightweight C implementation of name collating BAM file input and BAM file output bambamc-bambamc_0_0_50/bambamc.pc.in000066400000000000000000000003371233012646600173030ustar00rootroot00000000000000prefix=@prefix@ exec_prefix=@exec_prefix@ libdir=@libdir@ includedir=@includedir@ Name: bambamc Description: bambamc Requires: @ZLIBREQ@ Version: @VERSION@ Libs: -L${libdir} -lbambamc @ZLIBPKGLIBS@ Cflags: -I${includedir} bambamc-bambamc_0_0_50/bumpversion.sh000066400000000000000000000022131233012646600176700ustar00rootroot00000000000000#! /bin/bash VERSION=`grep AC_INIT < configure.in | awk -F',' '{print $2}'` FIRST=`echo $VERSION | awk -F'.' '{print $1}'` SECOND=`echo $VERSION | awk -F'.' '{print $2}'` THIRD=`echo $VERSION | awk -F'.' '{print $3}'` NEXTTHIRD=`expr ${THIRD} + 1` awk -v first=${FIRST} -v second=${SECOND} -v third=${THIRD} '/^AC_INIT/ {gsub(first"."second"."third,first"."second"."third+1);print} ; !/^AC_INIT/{print}' < configure.in | \ awk -v first=${FIRST} -v second=${SECOND} -v third=${THIRD} '/^LIBRARY_VERSION=/ {gsub("="first"."third"."second,"="first":"third+1":"second);print} ; !/^LIBRARY_VERSION=/{print}' \ > configure.in.tmp mv configure.in.tmp configure.in pushd ../bambamc-debian git checkout master git pull pushd debian export DEBEMAIL=gt1@sanger.ac.uk export DEBFULLNAME="German Tischler" dch --distribution unstable -v ${FIRST}.${SECOND}.${NEXTTHIRD} dch --release # dch --release -v ${FIRST}.${SECOND}.${NEXTTHIRD}-1 popd git add debian/changelog git commit git push popd git add configure.in git commit git push TAG=bambamc_${FIRST}_${SECOND}_${NEXTTHIRD} git tag -a ${TAG} -m "bambamc version ${FIRST}_${SECOND}_${NEXTTHIRD}" git push origin ${TAG} bambamc-bambamc_0_0_50/configure.in000066400000000000000000000101371233012646600173000ustar00rootroot00000000000000AC_INIT(bambamc,0.0.50,[gt1@sanger.ac.uk],[bambamc],[http://www.sanger.ac.uk]) LIBRARY_VERSION=0:50:0 AC_CANONICAL_SYSTEM AC_PROG_LIBTOOL AM_CONFIG_HEADER(config.h) AM_INIT_AUTOMAKE AC_CONFIG_MACRO_DIR([m4]) # check for c99 compiler CFLAGS_SAVE="${CFLAGS}" CPPFLAGS_SAVE="${CPPFLAGS}" CFLAGS="" CPPFLAGS="" AC_PROG_CC_C99 C99CFLAGS="${CFLAGS}" C99CPPFLAGS="${CPPFLAGS}" CFLAGS="${CFLAGS_SAVE}" CPPFLAGS="${CPPFLAGS_SAVE}" # AC_MSG_NOTICE([C99: :${C99CFLAGS}: :${C99CPPFLAGS}:]) AM_PROG_CC_C_O AC_LANG_ASSERT([C]) AC_HEADER_STDC PKG_PROG_PKG_CONFIG PKG_CHECK_MODULES([zlib],[zlib >= 0],[zlibpkg=yes],[zlibpkg=no]) if [[ "${zlibpkg}" = "yes" ]] ; then PKG_CHECK_MODULES([zlib],[zlib >= 0]) LIBSSAVE="${LIBS}" LIBS="${LIBS} ${zlib_LIBS}" CPPFLAGSSAVE="${CPPFLAGS}" CPPFLAGS="${CPPFLAGS} ${zlib_CFLAGS}" AC_MSG_CHECKING([whether we can compile a zlib program]) AC_TRY_LINK([#include #include ],[ z_stream strm; memset ( &strm , 0, sizeof(z_stream) ); strm.zalloc = Z_NULL; strm.zfree = Z_NULL; strm.opaque = Z_NULL; deflateInit(&strm,Z_DEFAULT_COMPRESSION); ],[zlib=yes],[zlib=no]) AC_MSG_RESULT([${zlib}]) LIBS="${LIBSSAVE}" CPPFLAGS="${CPPFLAGSSAVE}" if [[ "$zlib" = "no" ]] ; then AC_MSG_ERROR([Required library zlib not found.]); else ZLIBREQ=zlib ZLIBCPPFLAGS="${zlib_CFLAGS}" ZLIBLIBS="${zlib_LIBS}" ZLIBPKGLBIS= fi else AC_MSG_WARN([zlib pkgconfig file is not installed. Trying if -lz for LIBS is enough.]) LIBSSAVE="${LIBS}" LIBS="${LIBS} -lz" AC_MSG_CHECKING([whether we can compile a zlib program]) AC_TRY_LINK([#include #include ],[ z_stream strm; memset ( &strm , 0, sizeof(z_stream) ); strm.zalloc = Z_NULL; strm.zfree = Z_NULL; strm.opaque = Z_NULL; deflateInit(&strm,Z_DEFAULT_COMPRESSION); ],[zlib=yes],[zlib=no]) AC_MSG_RESULT([${zlib}]) LIBS="${LIBSSAVE}" if [[ "$zlib" = "no" ]] ; then AC_MSG_ERROR([Required library zlib not found.]); else ZLIBREQ= ZLIBCPPFLAGS= ZLIBLIBS="-lz" ZLIBPKGLIBS="-lz" fi fi if test "${CC}" = "gcc" ; then CPPFLAGS="${CPPFLAGS} -W -Wall" fi if test "${CC}" = "cl.exe" ; then CPPFLAGS="${CPPFLAGS} -W1" # -Wall fi AC_ARG_ENABLE(optimization, AS_HELP_STRING([--enable-optimization],[use compiler optimization (default yes)]), [optimization=${enableval}],[optimization=yes]) AC_ARG_ENABLE(debug, AS_HELP_STRING([--enable-debug],[use compiler debug flags (default no)]), [debug=${enableval}],[debug=no]) AC_ARG_ENABLE(profile, AS_HELP_STRING([--enable-profile],[use compiler profiling flags (default no)]), [profile=${enableval}],[profile=no]) AC_ARG_ENABLE(fast, AS_HELP_STRING([--enable-fast],[disable evaluation of assertions (default no)]), [fast=${enableval}],[fast=no]) if test "${fast}" = "yes" ; then CPPFLAGS="${CPPFLAGS} -DNDEBUG" fi if test "${debug}" = "yes" ; then CFLAGS="${CFLAGS} -g -O0 -rdynamic" else if test "${profile}" = "yes" ; then CFLAGS="${CFLAGS} -g -pg -rdynamic" else if test "${optimization}" = "yes" ; then case ${CC} in gcc) CFLAGS="${CFLAGS} -O3 -rdynamic" ;; *-mingw32msvc-gcc) CFLAGS="${CFLAGS} -O3 -rdynamic" ;; cl.exe) CFLAGS="${CFLAGS} -O2 -Ob2 -Ot -Oy" ;; esac fi fi fi AC_CHECK_FUNC([_mkdir],[have_mkdir=yes],[have_mkdir=no]) AC_CHECK_HEADER([direct.h],[have_direct_h=yes],[have_direct_h=no]) if test "${have_mkdir}" = "yes" -a "${have_direct_h}" = "yes" ; then AC_MSG_CHECKING([whether we can compile a program using _mkdir]) AC_TRY_LINK([#include ],[_mkdir("tmpdir");],[have_mkdir=yes],[have_mkdir=no]) AC_MSG_RESULT([${have_mkdir}]) fi if test "${have_mkdir}" = "yes" ; then HAVEWINDOWS_MKDIR="#define HAVEWINDOWS_MKDIR" else HAVEWINDOWS_MKDIR= fi PACKAGE_NAME=${PACKAGE} PACKAGE_VERSION=${VERSION} AC_SUBST([PACKAGE_NAME]) AC_SUBST([PACKAGE_VERSION]) AC_SUBST([ZLIBCPPFLAGS]) AC_SUBST([ZLIBLIBS]) AC_SUBST([ZLIBPKGLIBS]) AC_SUBST([ZLIBREQ]) AC_SUBST([LIBRARY_VERSION]) AC_SUBST([HAVEWINDOWS_MKDIR]) AC_OUTPUT(Makefile src/Makefile ubuntu.sh bambamc.pc src/bambamc/BamBam_Config.h) bambamc-bambamc_0_0_50/m4/000077500000000000000000000000001233012646600153055ustar00rootroot00000000000000bambamc-bambamc_0_0_50/m4/keepme.m4000066400000000000000000000000001233012646600170030ustar00rootroot00000000000000bambamc-bambamc_0_0_50/release.sh000066400000000000000000000014021233012646600167360ustar00rootroot00000000000000#! /bin/bash VERSION=`grep . **/ #include #include BamBam_AlignmentPut * BamBam_AlignmentPut_Delete(BamBam_AlignmentPut * aput) { if ( aput ) { if ( aput->calignment ) { BamBam_BamSingleAlignment_Delete(aput->calignment); aput->calignment = 0; } BamBam_CharBuffer_Delete(aput->charbuffer); aput->charbuffer = 0; free(aput); } return 0; } BamBam_AlignmentPut * BamBam_AlignmentPut_New() { BamBam_AlignmentPut * aput = 0; aput = (BamBam_AlignmentPut *)malloc(sizeof(BamBam_AlignmentPut)); if ( ! aput ) BamBam_AlignmentPut_Delete(aput); aput->charbuffer = BamBam_CharBuffer_New(); if ( ! aput->charbuffer ) return BamBam_AlignmentPut_Delete(aput); aput->calignment = BamBam_BamSingleAlignment_New(); if ( ! aput->calignment ) return BamBam_AlignmentPut_Delete(aput); return aput; } /* reg2bin as defined in sam file format spec */ static int reg2bin(uint32_t beg, uint32_t end) { --end; if (beg>>14 == end>>14) return ((1ul<<15)-1ul)/7ul + (beg>>14); if (beg>>17 == end>>17) return ((1ul<<12)-1ul)/7ul + (beg>>17); if (beg>>20 == end>>20) return ((1ul<<9)-1ul)/7ul + (beg>>20); if (beg>>23 == end>>23) return ((1ul<<6)-1ul)/7ul + (beg>>23); if (beg>>26 == end>>26) return ((1ul<<3)-1ul)/7ul + (beg>>26); return 0; } int BamBam_CharBuffer_PutAlignmentC( BamBam_AlignmentPut * aput, /* flags */ int32_t const flags, /* target (chromosome) id */ int32_t const tid, /* position on chromosome (0 based) */ uint64_t const rpos, /* mate target id */ int32_t const mtid, /* position of mate on mate target id */ uint64_t const rmpos, /* sequence name */ char const * name, /* query sequence (read) */ char const * query, /* quality string */ char const * qual, /* cigar operations */ char const * cigar, /* mapping quality */ int32_t const rqual, /* insert size */ int32_t const isize ) { /* buffer */ BamBam_CharBuffer * buffer = aput->charbuffer; BamBam_BamSingleAlignment * alignment = aput->calignment; int ret = 0; uint64_t i = 0; uint64_t const qlen = strlen(query); uint64_t const quallen = qlen; uint64_t const namelen = strlen(name); uint64_t ncigar = 0; uint64_t bin = 0; int64_t endpos = rpos; static char const cmap[5] = {1,2,4,8,15}; /* * CharBuffer: buffer,buffersize,bufferfill * BamBam_BamSingleAlignment: data,dataav,dataused */ assert ( ! buffer->buffer ); buffer->buffer = alignment->data; buffer->buffersize = alignment->dataav; buffer->bufferfill = alignment->dataused; alignment->data = 0; alignment->dataav = 0; alignment->dataused = 0; BamBam_CharBuffer_Reset(buffer); /* core data */ BamBam_CharBuffer_PushLE(buffer,(int32_t)tid,ret); if ( ret < 0 ) return ret; BamBam_CharBuffer_PushLE(buffer,(int32_t)rpos,ret); if ( ret < 0 ) return ret; /* bin_mq_nl, bin will be written later */ BamBam_CharBuffer_PushLE(buffer,(uint32_t)((rqual<<8)|(namelen+1)),ret); if ( ret < 0 ) return ret; /* flag_nc, number of cigar operations will be written later */ BamBam_CharBuffer_PushLE(buffer,(uint32_t)(flags<<16),ret); if ( ret < 0 ) return ret; /* length of query sequence */ BamBam_CharBuffer_PushLE(buffer,(int32_t)qlen,ret); if ( ret < 0 ) return ret; BamBam_CharBuffer_PushLE(buffer,(int32_t)mtid,ret); if ( ret < 0 ) return ret; BamBam_CharBuffer_PushLE(buffer,(int32_t)rmpos,ret); if ( ret < 0 ) return ret; BamBam_CharBuffer_PushLE(buffer,(int32_t)isize,ret); if ( ret < 0 ) return ret; /* copy read name */ BamBam_CharBuffer_PushString(buffer,name,ret); if ( ret < 0 ) return ret; /* terminating zero */ BamBam_CharBuffer_PushCharQuick(buffer,0,ret); if ( ret < 0 ) return ret; /* if cigar string is "*", then skip it */ if ( ret >= 0 && cigar[0] && (!cigar[1]) && (cigar[0] == '*') ) { ++cigar; } /* encode cigar string */ while ( ret >= 0 && *cigar ) { uint64_t num = 0; uint32_t op = 0; uint32_t store = 0; assert ( isdigit(cigar[0]) ); while ( (*cigar) && isdigit(*cigar) ) { num *= 10; num += (*(cigar++)) - '0'; } assert ( *cigar ); switch ( *cigar ) { case 'M': op = BAMBAMC_CMATCH; endpos += num; break; case 'I': op = BAMBAMC_CINS; break; case 'D': op = BAMBAMC_CDEL; endpos += num; break; case 'N': op = BAMBAMC_CREF_SKIP; endpos += num; break; case 'S': op = BAMBAMC_CSOFT_CLIP; break; case 'H': op = BAMBAMC_CHARD_CLIP; break; case 'P': op = BAMBAMC_CPAD; endpos += num; break; case '=': op = BAMBAMC_CEQUAL; endpos += num; break; case 'X': op = BAMBAMC_CDIFF; endpos += num; break; default: op = '*'; break; } cigar++; /* fprintf(stderr,"op: %u cmatch: %u num: %llu\n", op, BAMBAMC_CMATCH, (unsigned long long)num); */ store = op | (num << 4); BamBam_CharBuffer_PushLE(buffer,store,ret); ++ncigar; } /* put number of cigar operations */ buffer->buffer[12] = ((ncigar>>0) & 0xFFu); buffer->buffer[13] = ((ncigar>>8) & 0xFFu); if ( ret < 0 ) return ret; /* encode query string */ for ( i = 0; i < qlen/2 && ret >= 0; ++i ) { BamBam_CharBuffer_PushCharQuick( buffer, (cmap[(int)(BamBam_MapBase((int)(query[2*i+0])))] << 4) | (cmap[(int)(BamBam_MapBase((int)(query[2*i+1])))] << 0), ret); } if ( qlen % 2 && ret >= 0 ) BamBam_CharBuffer_PushCharQuick(buffer,((cmap[(int)(BamBam_MapBase((int)(query[qlen-1])))] << 4)),ret); if ( ret < 0 ) return ret; /* encode quality */ if ( qual ) { for ( i = 0; i < quallen && ret >= 0; ++i ) BamBam_CharBuffer_PushCharQuick(buffer,qual[i]-33,ret); } /* no quality given */ else { for ( i = 0; i < quallen && ret >= 0; ++i ) BamBam_CharBuffer_PushCharQuick(buffer,255,ret); } if ( ret < 0 ) return ret; /* set bin */ bin = reg2bin(rpos, endpos); buffer->buffer[10] = (bin>>0)&0xFFu; buffer->buffer[11] = (bin>>8)&0xFFu; /* swap buffers */ alignment->data = buffer->buffer; alignment->dataav = buffer->buffersize; alignment->dataused = buffer->bufferfill; buffer->buffer = 0; buffer->buffersize = 0; buffer->bufferfill = 0; return ret; } int BamBam_CharBuffer_PutAuxNumberC(BamBam_AlignmentPut * aput, char const * tag, char const type, void const * pvalue) { /* buffer */ BamBam_CharBuffer * buffer = aput->charbuffer; BamBam_BamSingleAlignment * alignment = aput->calignment; int ret = 0; /* * swap buffers */ assert ( ! buffer->buffer ); buffer->buffer = alignment->data; buffer->buffersize = alignment->dataav; buffer->bufferfill = alignment->dataused; alignment->data = 0; alignment->dataav = 0; alignment->dataused = 0; assert ( strlen(tag) == 2 ); /* put tag */ BamBam_CharBuffer_PushString(buffer,tag,ret); if ( ret < 0 ) return ret; /* put type */ BamBam_CharBuffer_PushCharQuick(buffer,type,ret); if ( ret < 0 ) return ret; switch ( type ) { case 'A': { int8_t const value = *((int8_t*)pvalue); BamBam_CharBuffer_PushLE(buffer,value,ret); break; } case 'c': { int8_t const value = *((int8_t*)pvalue); BamBam_CharBuffer_PushLE(buffer,value,ret); break; } case 'C': { uint8_t const value = *((uint8_t*)pvalue); BamBam_CharBuffer_PushLE(buffer,value,ret); break; } case 's': { int16_t const value = *((int16_t*)pvalue); BamBam_CharBuffer_PushLE(buffer,value,ret); break; } case 'S': { uint16_t const value = *((uint16_t*)pvalue); BamBam_CharBuffer_PushLE(buffer,value,ret); break; } case 'i': { int32_t const value = *((int32_t*)pvalue); BamBam_CharBuffer_PushLE(buffer,value,ret); break; } case 'I': { uint32_t const value = *((uint32_t*)pvalue); BamBam_CharBuffer_PushLE(buffer,value,ret); break; } case 'f': { uint32_t const value = *((uint32_t*)pvalue); BamBam_CharBuffer_PushLE(buffer,value,ret); break; } } /* swap buffers */ alignment->data = buffer->buffer; alignment->dataav = buffer->buffersize; alignment->dataused = buffer->bufferfill; buffer->buffer = 0; buffer->buffersize = 0; buffer->bufferfill = 0; return ret; } bambamc-bambamc_0_0_50/src/bambamc/BamBam_BamAlignmentPut.h000066400000000000000000000040621233012646600235370ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAM_BAMALIGNMENTPUT_H) #define BAMBAM_BAMALIGNMENTPUT_H #include #include #include #include #include typedef struct _BamBam_AlignmentPut { BamBam_CharBuffer * charbuffer; BamBam_BamSingleAlignment * calignment; } BamBam_AlignmentPut; extern BamBam_AlignmentPut * BamBam_AlignmentPut_New() BAMBAM_WARN_IF_UNUSEDRESULT; extern BamBam_AlignmentPut * BamBam_AlignmentPut_Delete(BamBam_AlignmentPut * aput); extern int BamBam_CharBuffer_PutAlignmentC( BamBam_AlignmentPut * aput, /* flags */ int32_t const flags, /* target (chromosome) id */ int32_t const tid, /* position on chromosome (0 based) */ uint64_t const rpos, /* mate target id */ int32_t const mtid, /* position of mate on mate target id */ uint64_t const rmpos, /* sequence name */ char const * name, /* query sequence (read) */ char const * query, /* quality string */ char const * qual, /* cigar operations */ char const * cigar, /* mapping quality */ int32_t const rqual, /* insert size */ int32_t const isize ) BAMBAM_WARN_IF_UNUSEDRESULT; extern int BamBam_CharBuffer_PutAuxNumberC(BamBam_AlignmentPut * aput, char const * tag, char const type, void const * rvalue) BAMBAM_WARN_IF_UNUSEDRESULT; #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_BamCollationHash.c000066400000000000000000000030011233012646600236430ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include void BamBam_BamCollationHash_Delete(BamBam_BamCollationHash * hash) { if ( hash ) { free(hash->entries); free(hash); } } BamBam_BamCollationHash * BamBam_BamCollationHash_New(unsigned int sizelog) { BamBam_BamCollationHash * hash = 0; uint64_t i; hash = (BamBam_BamCollationHash *)malloc(sizeof(BamBam_BamCollationHash)); if ( ! hash ) return 0; hash->entries = 0; hash->tablesize = 1ull << sizelog; hash->tablemask = hash->tablesize-1; hash->entries = (BamBam_BamCollationHashEntry **)malloc(hash->tablesize*(sizeof(BamBam_BamCollationHashEntry *))); if ( ! hash->entries ) { free(hash); return 0; } for ( i = 0; i < hash->tablesize; ++i ) hash->entries[i] = 0; return hash; } bambamc-bambamc_0_0_50/src/bambamc/BamBam_BamCollationHash.h000066400000000000000000000024011233012646600236530ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAM_BAMCOLLATIONHASH_H) #define BAMBAM_BAMCOLLATIONHASH_H #include #include typedef struct _BamBam_BamCollationHash { BamBam_BamCollationHashEntry ** entries; uint64_t tablesize; uint64_t tablemask; } BamBam_BamCollationHash; extern BamBam_BamCollationHash * BamBam_BamCollationHash_New(unsigned int sizelog) BAMBAM_WARN_IF_UNUSEDRESULT; extern void BamBam_BamCollationHash_Delete(BamBam_BamCollationHash * hash); #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_BamCollationHashEntry.c000066400000000000000000000070641233012646600247020ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include #include #include int BamBam_BamHashEntry_Compare(BamBam_BamCollationHashEntry const * A, BamBam_BamCollationHashEntry const * B) { int cmpres = strcmp(A->qname,B->qname); int Amate1 = (BamBam_BamCollationHashEntry_GetFlags(A) & BAMBAMC_FREAD1) != 0; int Bmate1 = (BamBam_BamCollationHashEntry_GetFlags(B) & BAMBAMC_FREAD1) != 0; if ( cmpres != 0 ) return cmpres; else if ( Amate1 < Bmate1 ) return -1; else if ( Amate1 > Bmate1 ) return 1; else return 0; } int BamBam_BamHashEntry_CompareVerbose(BamBam_BamCollationHashEntry const * A, BamBam_BamCollationHashEntry const * B) { int cmpres = strcmp(A->qname,B->qname); int Amate1 = (BamBam_BamCollationHashEntry_GetFlags(A) & BAMBAMC_FREAD1) != 0; int Bmate1 = (BamBam_BamCollationHashEntry_GetFlags(B) & BAMBAMC_FREAD1) != 0; fprintf(stderr,"Comparing %s and %s result %d\n", A->qname, B->qname, cmpres); if ( cmpres != 0 ) return cmpres; else if ( Amate1 < Bmate1 ) return -1; else if ( Amate1 > Bmate1 ) return 1; else return 0; } int BamBam_BamHashEntry_CompareVoidPtr(const void * VA, const void * VB) { BamBam_BamCollationHashEntry const ** A = (BamBam_BamCollationHashEntry const **)VA; BamBam_BamCollationHashEntry const ** B = (BamBam_BamCollationHashEntry const **)VB; return BamBam_BamHashEntry_Compare(*A,*B); } void BamBam_BamCollationHashEntry_Delete(BamBam_BamCollationHashEntry * hashentry) { if ( hashentry ) { if ( hashentry->entry ) BamBam_BamSingleAlignment_Delete(hashentry->entry); free(hashentry->qname); free(hashentry); } } uint32_t BamBam_BamCollationHashEntry_GetFlags(BamBam_BamCollationHashEntry const * hashentry) { return BamBam_BamSingleAlignment_GetFlags(hashentry->entry); } BamBam_BamCollationHashEntry * BamBam_BamCollationHashEntry_NewDup(BamBam_BamSingleAlignment * alignment) { BamBam_BamSingleAlignment * entry = 0; BamBam_BamCollationHashEntry * hashentry = 0; char const * qname = 0; entry = BamBam_BamSingleAlignment_Clone(alignment); if ( ! entry ) return 0; hashentry = (BamBam_BamCollationHashEntry *)malloc(sizeof(BamBam_BamCollationHashEntry)); if ( ! hashentry ) { BamBam_BamSingleAlignment_Delete(entry); return 0; } hashentry->entry = entry; hashentry->qnamelen = 0; hashentry->qname = 0; qname = BamBam_BamSingleAlignment_GetReadName(entry); if ( ! qname ) { BamBam_BamSingleAlignment_Delete(entry); free(hashentry); return 0; } hashentry->qname = BamBam_StrDup(qname); if ( ! hashentry->qname ) { BamBam_BamSingleAlignment_Delete(entry); free(hashentry); return 0; } hashentry->qnamelen = strlen(hashentry->qname); hashentry->hashvalue = hashDefaultSeed((uint8_t const *)hashentry->qname,hashentry->qnamelen); return hashentry; } bambamc-bambamc_0_0_50/src/bambamc/BamBam_BamCollationHashEntry.h000066400000000000000000000037511233012646600247060ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAM_BAMCOLLATIONHASHENTRY_H) #define BAMBAM_BAMCOLLATIONHASHENTRY_H #include #include #include #include #include typedef struct _BamBam_BamCollationHashEntry { BamBam_BamSingleAlignment * entry; char * qname; unsigned int qnamelen; uint32_t hashvalue; } BamBam_BamCollationHashEntry; extern int BamBam_BamHashEntry_Compare(BamBam_BamCollationHashEntry const * A, BamBam_BamCollationHashEntry const * B) BAMBAM_WARN_IF_UNUSEDRESULT; extern int BamBam_BamHashEntry_CompareVerbose(BamBam_BamCollationHashEntry const * A, BamBam_BamCollationHashEntry const * B) BAMBAM_WARN_IF_UNUSEDRESULT; extern int BamBam_BamHashEntry_CompareVoidPtr(const void * VA, const void * VB) BAMBAM_WARN_IF_UNUSEDRESULT; extern void BamBam_BamCollationHashEntry_Delete(BamBam_BamCollationHashEntry * hashentry); extern uint32_t BamBam_BamCollationHashEntry_GetFlags(BamBam_BamCollationHashEntry const * hashentry) BAMBAM_WARN_IF_UNUSEDRESULT; extern BamBam_BamCollationHashEntry * BamBam_BamCollationHashEntry_NewDup(BamBam_BamSingleAlignment * alignment) BAMBAM_WARN_IF_UNUSEDRESULT; #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_BamCollationOutputVector.c000066400000000000000000000062531233012646600254570ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include #include void BamBam_BamCollationOutputVector_PushFront(BamBam_BamCollationOutputVector * outputvector, BamBam_BamCollationHashEntry * entry) { assert (outputvector->outputvectorfill < outputvector->outputvectorsize ); if ( outputvector->outputvectorlow == 0 ) { outputvector->outputvectorlow += outputvector->outputvectorsize; outputvector->outputvectorhigh += outputvector->outputvectorsize; } outputvector->outputvector[(--outputvector->outputvectorlow) % outputvector->outputvectorsize] = entry; outputvector->outputvectorfill++; } void BamBam_BamCollationOutputVector_PushBack(BamBam_BamCollationOutputVector * outputvector, BamBam_BamCollationHashEntry * entry) { assert (outputvector->outputvectorfill < outputvector->outputvectorsize ); outputvector->outputvector[(outputvector->outputvectorhigh++) % outputvector->outputvectorsize] = entry; outputvector->outputvectorfill++; } BamBam_BamCollationHashEntry * BamBam_BamCollationOutputVector_PopFront(BamBam_BamCollationOutputVector * outputvector) { assert ( outputvector->outputvectorfill ); BamBam_BamCollationHashEntry * entry = outputvector->outputvector[(outputvector->outputvectorlow++) % outputvector->outputvectorsize]; outputvector->outputvectorfill--; return entry; } BamBam_BamCollationOutputVector * BamBam_BamCollationOutputVector_New(unsigned int const vectorsizelog) { BamBam_BamCollationOutputVector * outputvector = 0; outputvector = (BamBam_BamCollationOutputVector *)malloc(sizeof(BamBam_BamCollationOutputVector)); if ( ! outputvector ) return 0; outputvector->outputvectorsize = 1ull<outputvectorlow = 0; outputvector->outputvectorhigh = 0; outputvector->outputvectorfill = 0; outputvector->outputvector = (BamBam_BamCollationHashEntry **)malloc((outputvector->outputvectorsize)*sizeof(BamBam_BamCollationHashEntry *)); return outputvector; } void BamBam_BamCollationOutputVector_Delete(BamBam_BamCollationOutputVector * outputvector) { uint64_t i; for ( i = outputvector->outputvectorlow; i != outputvector->outputvectorhigh; ++i ) { if ( outputvector->outputvector[i % outputvector->outputvectorsize] ) { BamBam_BamCollationHashEntry_Delete(outputvector->outputvector[i%outputvector->outputvectorsize]); outputvector->outputvector[i%outputvector->outputvectorsize] = 0; } } free(outputvector->outputvector); free(outputvector); } bambamc-bambamc_0_0_50/src/bambamc/BamBam_BamCollationOutputVector.h000066400000000000000000000035241233012646600254620ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAM_BAMCOLLATIONOUTPUTVECTOR_H) #define BAMBAM_BAMCOLLATIONOUTPUTVECTOR_H #include #include typedef struct _BamBam_BamCollationOutputVector { BamBam_BamCollationHashEntry ** outputvector; uint64_t outputvectorsize; uint64_t outputvectorfill; uint64_t outputvectorlow; uint64_t outputvectorhigh; } BamBam_BamCollationOutputVector; extern void BamBam_BamCollationOutputVector_PushBack(BamBam_BamCollationOutputVector * outputvector, BamBam_BamCollationHashEntry * entry); extern void BamBam_BamCollationOutputVector_PushFront(BamBam_BamCollationOutputVector * outputvector, BamBam_BamCollationHashEntry * entry); extern BamBam_BamCollationHashEntry * BamBam_BamCollationOutputVector_PopFront(BamBam_BamCollationOutputVector * outputvector) BAMBAM_WARN_IF_UNUSEDRESULT; extern BamBam_BamCollationOutputVector * BamBam_BamCollationOutputVector_New(unsigned int const vectorsizelog) BAMBAM_WARN_IF_UNUSEDRESULT; extern void BamBam_BamCollationOutputVector_Delete(BamBam_BamCollationOutputVector * outputvector); #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_BamCollationTempFileGenerator.c000066400000000000000000000067511233012646600263530ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include #include #include #include void BamBam_BamCollationTempFileGenerator_Print(FILE * file, BamBam_BamCollationTempFileGenerator const * gen) { fprintf(file,"BamBam_BamCollationTempFileGenerator(prefix=%s,nextid=%llu,tempfilenames=",gen->prefix,(unsigned long long)gen->nextid); BamBam_List_Print(file,gen->tempfilenames); fprintf(file,")"); } /* for getpid */ #include #include char * BamBam_ComputeTempFileName(char const * prefix, uint64_t const id) { char * sid = 0; char * spid = 0; unsigned int tempnamelen = 0; char * tempname = 0; sid = BamBam_FormatNumberMinLen(id,6); if ( ! sid ) return 0; spid = BamBam_FormatNumber(getpid()); if ( ! spid ) { free(sid); return 0; } tempnamelen = strlen(prefix) + 1 + /* _ */ strlen(spid) + 1 + /* _ */ strlen(sid) + 1 /* NUL */ ; tempname = (char *)malloc(tempnamelen); if ( ! tempname ) { free(sid); free(spid); return 0; } snprintf(tempname,tempnamelen,"%s_%s_%s", prefix, spid, sid); free(sid); free(spid); return tempname; } void freeTempFile(void * vtmpfilename) { if ( vtmpfilename ) { char * tmpfilename = (char *)vtmpfilename; unlink(tmpfilename); free(tmpfilename); } else { fprintf(stderr,"freeTempFile() called for NULL pointer.\n"); } } char * BamBam_BamCollationTempFileGenerator_GetNextTempFileName(BamBam_BamCollationTempFileGenerator * gen) { uint64_t id; char * tmpfilename = 0; BamBam_ListNode * listnode = 0; id = (gen->nextid)++; tmpfilename = BamBam_ComputeTempFileName(gen->prefix,id); if ( ! tmpfilename ) return 0; listnode = BamBam_ListNode_New(); if ( ! listnode ) { free(tmpfilename); return 0; } listnode->entry = tmpfilename; listnode->bamBamListFreeFunction = freeTempFile; listnode->bamBamListPrintFunction = BamBam_PrintStringFunction; BamBam_ListNode_PushBack(gen->tempfilenames,listnode); return tmpfilename; } BamBam_BamCollationTempFileGenerator * BamBam_BamCollationTempFileGenerator_New(char const * prefix) { BamBam_BamCollationTempFileGenerator * gen = 0; gen = (BamBam_BamCollationTempFileGenerator *)malloc(sizeof(BamBam_BamCollationTempFileGenerator)); if ( ! gen ) return 0; gen->prefix = BamBam_StrDup(prefix); if ( ! gen->prefix ) { free(gen); return 0; } gen->nextid = 0; gen->tempfilenames = BamBam_List_New(); if ( ! gen->tempfilenames ) { free(gen->prefix); free(gen); return 0; } return gen; } void BamBam_BamCollationTempFileGenerator_Delete(BamBam_BamCollationTempFileGenerator * gen) { if ( gen ) { BamBam_List_Delete(gen->tempfilenames); free(gen->prefix); free(gen); } } bambamc-bambamc_0_0_50/src/bambamc/BamBam_BamCollationTempFileGenerator.h000066400000000000000000000033401233012646600263470ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAM_BAMCOLLATIONTEMPFILEGENERATOR_H) #define BAMBAM_BAMCOLLATIONTEMPFILEGENERATOR_H #include #include #include typedef struct _BamBam_BamCollationTempFileGenerator { char * prefix; uint64_t nextid; BamBam_List * tempfilenames; } BamBam_BamCollationTempFileGenerator; extern void BamBam_BamCollationTempFileGenerator_Print(FILE * file, BamBam_BamCollationTempFileGenerator const * gen); extern char * BamBam_ComputeTempFileName(char const * prefix, uint64_t const id) BAMBAM_WARN_IF_UNUSEDRESULT; extern char * BamBam_BamCollationTempFileGenerator_GetNextTempFileName(BamBam_BamCollationTempFileGenerator * gen) BAMBAM_WARN_IF_UNUSEDRESULT; extern BamBam_BamCollationTempFileGenerator * BamBam_BamCollationTempFileGenerator_New(char const * prefix) BAMBAM_WARN_IF_UNUSEDRESULT; extern void BamBam_BamCollationTempFileGenerator_Delete(BamBam_BamCollationTempFileGenerator * gen); #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_BamCollationVector.c000066400000000000000000000110661233012646600242340ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include #include BamBam_BamCollationVector * BamBam_BamCollationVector_New(unsigned int sizelog) { BamBam_BamCollationVector * vector = 0; uint64_t i; vector = (BamBam_BamCollationVector *)malloc(sizeof(BamBam_BamCollationVector)); if ( ! vector ) return 0; vector->entries = 0; vector->tablesize = 1ull << sizelog; vector->fill = 0; vector->entries = (BamBam_BamCollationHashEntry **)malloc(vector->tablesize*(sizeof(BamBam_BamCollationHashEntry *))); if ( ! vector->entries ) { free(vector); return 0; } for ( i = 0; i < vector->tablesize; ++i ) vector->entries[i] = 0; return vector; } int BamBam_BamCollationVector_PushBack(BamBam_BamCollationVector * vector, BamBam_BamCollationHashEntry * entry) { vector->entries[vector->fill++] = entry; return (vector->fill == vector->tablesize); } void BamBam_BamCollationVector_Erase(BamBam_BamCollationVector * vector) { uint64_t i; for ( i = 0; i < vector->fill; ++i ) BamBam_BamCollationHashEntry_Delete(vector->entries[i]); vector->fill = 0; } int BamBam_BamCollationVector_Sort( BamBam_BamCollationVector * vector, BamBam_BamCollationOutputVector * outputvector, BamBam_BamCollationTempFileGenerator * gen ) { uint64_t i, j; qsort ( &(vector->entries[0]), vector->fill, sizeof(BamBam_BamCollationHashEntry *), BamBam_BamHashEntry_CompareVoidPtr ); j = 0; for ( i = 0; i < vector->fill; ) { if ( i+1 < vector->fill && strcmp(vector->entries[i]->qname,vector->entries[i+1]->qname) == 0 && (((BamBam_BamCollationHashEntry_GetFlags(vector->entries[i]) & BAMBAMC_FREAD1) && (BamBam_BamCollationHashEntry_GetFlags(vector->entries[i+1]) & BAMBAMC_FREAD2)) || ((BamBam_BamCollationHashEntry_GetFlags(vector->entries[i]) & BAMBAMC_FREAD2) && (BamBam_BamCollationHashEntry_GetFlags(vector->entries[i+1]) & BAMBAMC_FREAD1))) ) { /* fprintf(stderr,"Found pair %s %s\n", vector->entries[i]->qname, vector->entries[i+1]->qname); */ BamBam_BamCollationOutputVector_PushBack(outputvector,vector->entries[i ]); BamBam_BamCollationOutputVector_PushBack(outputvector,vector->entries[i+1]); i += 2; } else { vector->entries[j++] = vector->entries[i]; i++; } } vector->fill = j; if ( vector->fill ) { char * tmpfilename = BamBam_BamCollationTempFileGenerator_GetNextTempFileName(gen); #if 0 BamBam_GzipWriter * gzipfile = 0; int status = -1; if ( ! tmpfilename ) return -1; gzipfile = BamBam_GzipWriter_New(tmpfilename,1); if ( ! gzipfile ) return -1; for ( i = 0; i < vector->fill; ++i ) { int const r = BamBam_BamSingleAlignment_StoreAlignment(vector->entries[i]->entry,gzipfile); if ( r < 0 ) { BamBam_GzipWriter_Delete(gzipfile,&status); return -1; } } BamBam_GzipWriter_Delete(gzipfile,&status); if ( status < 0 ) return -1; #else BamBam_BgzfCompressor * gzipfile = 0; int status = -1; if ( ! tmpfilename ) return -1; gzipfile = BamBam_BgzfCompressor_New(tmpfilename,1); if ( ! gzipfile ) return -1; for ( i = 0; i < vector->fill; ++i ) { int const r = BamBam_BamSingleAlignment_StoreAlignmentBgzf(vector->entries[i]->entry,gzipfile); if ( r < 0 ) { BamBam_BgzfCompressor_Delete(gzipfile); return -1; } } status = BamBam_BgzfCompressor_Terminate(gzipfile); if ( status < 0 ) { BamBam_BgzfCompressor_Delete(gzipfile); return -1; } BamBam_BgzfCompressor_Delete(gzipfile); #endif } return 0; } void BamBam_BamCollationVector_Delete(BamBam_BamCollationVector * vector) { if ( vector ) { uint64_t i; for ( i = 0; i < vector->fill; ++i ) if ( vector->entries[i] ) BamBam_BamCollationHashEntry_Delete(vector->entries[i]); free(vector->entries); free(vector); } } bambamc-bambamc_0_0_50/src/bambamc/BamBam_BamCollationVector.h000066400000000000000000000034571233012646600242460ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAM_BAMCOLLATIONVECTOR_H) #define BAMBAM_BAMCOLLATIONVECTOR_H #include #include #include #include typedef struct _BamBam_BamCollationVector { BamBam_BamCollationHashEntry ** entries; uint64_t tablesize; uint64_t fill; } BamBam_BamCollationVector; extern BamBam_BamCollationVector * BamBam_BamCollationVector_New(unsigned int sizelog) BAMBAM_WARN_IF_UNUSEDRESULT; extern int BamBam_BamCollationVector_PushBack(BamBam_BamCollationVector * vector, BamBam_BamCollationHashEntry * entry) BAMBAM_WARN_IF_UNUSEDRESULT; extern void BamBam_BamCollationVector_Erase(BamBam_BamCollationVector * vector); extern int BamBam_BamCollationVector_Sort( BamBam_BamCollationVector * vector, BamBam_BamCollationOutputVector * outputvector, BamBam_BamCollationTempFileGenerator * gen ) BAMBAM_WARN_IF_UNUSEDRESULT; extern void BamBam_BamCollationVector_Delete(BamBam_BamCollationVector * vector); #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_BamCollator.c000066400000000000000000000576571233012646600227240ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include #include #include #include #include #include void BamBam_BamCollator_MergeHeapEntrySwap(BamBam_MergeHeapEntry * A, BamBam_MergeHeapEntry * B) { { uint64_t t = B->fileid; B->fileid = A->fileid; A->fileid = t; } { BamBam_BamCollationHashEntry * t = B->hashentry; B->hashentry = A->hashentry; A->hashentry = t; } } void BamBam_BamCollator_MergeHeapPrint(BamBam_BamCollator * collator) { uint64_t p; for ( p = 0; p < collator->mergeheapfill; ++p ) fprintf(stderr,"HEAP[%llu]=%s\n",(unsigned long long)p,collator->mergeheap[p].hashentry->qname); } void BamBam_BamCollator_MergeHeapCheck(BamBam_BamCollator * collator) { uint64_t p; for ( p = 1; p < collator->mergeheapfill; ++p ) { uint64_t const parent = (p-1)/2; BamBam_MergeHeapEntry * Pp = &(collator->mergeheap[p]); BamBam_MergeHeapEntry * Pparent = &(collator->mergeheap[parent]); assert ( BamBam_BamHashEntry_Compare( Pparent->hashentry, Pp->hashentry ) <= 0 ); } } static unsigned int BamBam_BamCollator_MergeHeapMinimum2(BamBam_BamCollator * collator, unsigned int p0, unsigned int p1) { BamBam_MergeHeapEntry * Pp0 = &(collator->mergeheap[p0]); BamBam_MergeHeapEntry * Pp1 = &(collator->mergeheap[p1]); if ( BamBam_BamHashEntry_Compare( Pp0->hashentry, Pp1->hashentry ) <= 0 ) return p0; else return p1; } static unsigned int BamBam_BamCollator_MergeHeapMinimum3(BamBam_BamCollator * collator, unsigned int p0, unsigned int p1, unsigned int p2) { return BamBam_BamCollator_MergeHeapMinimum2(collator,p0,BamBam_BamCollator_MergeHeapMinimum2(collator,p1,p2)); } BamBam_MergeHeapEntry * BamBam_BamCollator_MergeHeapMinimum(BamBam_BamCollator * collator) { assert ( collator->mergeheapfill ); return &(collator->mergeheap[0]); } void BamBam_BamCollator_MergeHeapDeleteMinimum(BamBam_BamCollator * collator) { BamBam_MergeHeapEntry * first; BamBam_MergeHeapEntry * last; unsigned int p = 0; assert ( collator->mergeheapfill ); /* swap first and last element, then delete the former minimum */ first = &(collator->mergeheap[0]); last = &(collator->mergeheap[collator->mergeheapfill-1]); BamBam_BamCollator_MergeHeapEntrySwap(first,last); BamBam_BamCollationHashEntry_Delete(last->hashentry); collator->mergeheapfill -= 1; /* push former last element down the heap until the heap property holds */ while ( 2*p+1 < collator->mergeheapfill ) { /* both children exist */ if ( 2*p+2 < collator->mergeheapfill ) { /* find minimum of this node and both children */ unsigned int const mini = BamBam_BamCollator_MergeHeapMinimum3(collator,p,2*p+1,2*p+2); /* if minimum is this node, then heap property holds */ if ( mini == p ) { break; } /* otherwise swap minimum with this node and recurse into corresponding subtree */ else { BamBam_MergeHeapEntry * Pp = &(collator->mergeheap[p]); BamBam_MergeHeapEntry * Pc = &(collator->mergeheap[mini]); BamBam_BamCollator_MergeHeapEntrySwap(Pp,Pc); p = mini; } } /* only left child exists */ else { /* if minimum is this node, then heap property holds */ if ( BamBam_BamCollator_MergeHeapMinimum2(collator,p,2*p+1) == p ) { break; } /* otherwise swap and recurse */ else { BamBam_MergeHeapEntry * Pp = &(collator->mergeheap[p]); BamBam_MergeHeapEntry * Pl = &(collator->mergeheap[2*p+1]); BamBam_BamCollator_MergeHeapEntrySwap(Pp,Pl); p = 2*p+1; } } } } void BamBam_BamCollator_MergeHeapInsert(BamBam_BamCollator * collator, BamBam_BamCollationHashEntry * hashentry, unsigned int fileid) { unsigned int p; int swapped = 1; /* insert new element at the end of the heap */ p = collator->mergeheapfill++; assert ( collator->mergeheapfill <= collator->nummergefiles ); collator->mergeheap [ p ] . hashentry = hashentry; collator->mergeheap [ p ] . fileid = fileid; /* move it up */ while ( p && swapped ) { unsigned int parent = (p-1)/2; BamBam_MergeHeapEntry * Pp = &(collator->mergeheap[p]); BamBam_MergeHeapEntry * Pparent = &(collator->mergeheap[parent]); if ( BamBam_BamHashEntry_Compare( Pp->hashentry, Pparent->hashentry ) < 0 ) { BamBam_BamCollator_MergeHeapEntrySwap(Pp,Pparent); } else { swapped = 0; } p = parent; } } #include BamBam_BamCollationHashEntry * BamBam_BamCollator_GetNextRead(BamBam_BamCollator * collator) { while ( (collator->state==BAMBAM_COLLATE_READING_INPUT) && !collator->outputvector->outputvectorfill ) { if ( (collator->alignment = BamBam_SamBamFileDecoder_DecodeAlignment(collator->decoder)) ) { BamBam_BamCollationHashEntry * nhashentry = 0; BamBam_BamCollationHashEntry * ohashentry = 0; nhashentry = BamBam_BamCollationHashEntry_NewDup(collator->alignment); if ( ! nhashentry ) { collator->state = BAMBAM_COLLATE_FAILED; } else { uint32_t nhashentryflags; nhashentryflags = BamBam_BamCollationHashEntry_GetFlags(nhashentry); /* single end? */ if ( !(nhashentryflags & BAMBAMC_FPAIRED) ) { BamBam_BamCollationOutputVector_PushBack(collator->outputvector,nhashentry); } /* pair */ else { ohashentry = collator->hash->entries[ nhashentry->hashvalue & collator->hash->tablemask ]; /* fprintf(stderr,"Got name %s\n", hashentry->qname); */ /* hash place is empty */ if ( ! ohashentry ) { collator->hash->entries[ nhashentry->hashvalue & collator->hash->tablemask ] = nhashentry; } else { uint32_t ohashentryflags = BamBam_BamCollationHashEntry_GetFlags(ohashentry); if ( ohashentry->hashvalue == nhashentry->hashvalue && ! strcmp(ohashentry->qname,nhashentry->qname) && ( ((nhashentryflags & BAMBAMC_FREAD1) && (ohashentryflags & BAMBAMC_FREAD2)) || ((nhashentryflags & BAMBAMC_FREAD2) && (ohashentryflags & BAMBAMC_FREAD1)) ) ) { /* found pair */ collator->hash->entries[ nhashentry->hashvalue & collator->hash->tablemask ] = 0; if ( (ohashentryflags & BAMBAMC_FREAD1) != 0 ) { BamBam_BamCollationOutputVector_PushBack(collator->outputvector,ohashentry); BamBam_BamCollationOutputVector_PushBack(collator->outputvector,nhashentry); } else { BamBam_BamCollationOutputVector_PushBack(collator->outputvector,nhashentry); BamBam_BamCollationOutputVector_PushBack(collator->outputvector,ohashentry); } } else { int vecfull; /* not pair, push previous entry out */ vecfull = BamBam_BamCollationVector_PushBack(collator->vector,ohashentry); if ( vecfull ) { int sortok; sortok = BamBam_BamCollationVector_Sort(collator->vector,collator->outputvector,collator->gen); if ( sortok < 0 ) { collator->state = BAMBAM_COLLATE_FAILED; } BamBam_BamCollationVector_Erase(collator->vector); } collator->hash->entries[ nhashentry->hashvalue & collator->hash->tablemask ] = nhashentry; } } } } } /* no more alignments in input file */ else { /* handle alignments left in hash table */ unsigned int i = 0; int sortok; for ( i = 0; collator->state != BAMBAM_COLLATE_FAILED && i < collator->hash->tablesize; ++i ) if ( collator->hash->entries[i] ) { int vecfull; int sortok; BamBam_BamCollationHashEntry * hashentry = collator->hash->entries[i]; collator->hash->entries[i] = 0; /* push entry out */ vecfull = BamBam_BamCollationVector_PushBack(collator->vector,hashentry); if ( vecfull ) { /* fprintf(stderr,"erasing full vector.\n"); */ sortok = BamBam_BamCollationVector_Sort(collator->vector,collator->outputvector,collator->gen); if ( sortok < 0 ) collator->state = BAMBAM_COLLATE_FAILED; BamBam_BamCollationVector_Erase(collator->vector); } } sortok = BamBam_BamCollationVector_Sort(collator->vector,collator->outputvector,collator->gen); if ( sortok < 0 ) collator->state = BAMBAM_COLLATE_FAILED; BamBam_BamCollationVector_Erase(collator->vector); collator->state = BAMBAM_COLLATE_MERGING; } } while ( (collator->state==BAMBAM_COLLATE_MERGING) && !collator->outputvector->outputvectorfill ) { /* tempfiles not yet open, open them */ if ( ! collator->mergefiles ) { unsigned int numtempfiles; BamBam_ListNode * node = 0; unsigned int k = 0; numtempfiles = BamBam_List_Size(collator->gen->tempfilenames); collator->mergefiles = (BamBam_GzipFileDecoder **)malloc(numtempfiles * sizeof(BamBam_GzipFileDecoder *)); if ( ! collator->mergefiles ) collator->state = BAMBAM_COLLATE_FAILED; else { collator->nummergefiles = numtempfiles; for ( k = 0; k < numtempfiles; ++k ) collator->mergefiles[k] = 0; node = collator->gen->tempfilenames->first; k = 0; while ( node ) { char const * filename = (char const *)(node->entry); collator->mergefiles[k] = BamBam_GzipFileDecoder_New(filename); if ( ! collator->mergefiles[k] ) collator->state = BAMBAM_COLLATE_FAILED; node = node->next; k++; } /* if we managed to open all temporary files, then allocate heap */ if ( collator->state != BAMBAM_COLLATE_FAILED ) { collator->mergeheap = (BamBam_MergeHeapEntry *)malloc(numtempfiles * sizeof(BamBam_MergeHeapEntry)); if ( ! collator->mergeheap ) collator->state = BAMBAM_COLLATE_FAILED; else { for ( k = 0; k < numtempfiles; ++k ) { collator->mergeheap[k].hashentry = 0; collator->mergeheap[k].fileid = numtempfiles; } collator->mergeheapfill = 0; } for ( k = 0; (collator->state != BAMBAM_COLLATE_FAILED) && k < numtempfiles; ++k ) { if ( (collator->alignment = BamBam_GzipFileDecoder_DecodeAlignment(collator->mergefiles[k])) ) { BamBam_BamCollationHashEntry * nhashentry = 0; nhashentry = BamBam_BamCollationHashEntry_NewDup(collator->alignment); if ( ! nhashentry ) collator->state = BAMBAM_COLLATE_FAILED; else BamBam_BamCollator_MergeHeapInsert(collator,nhashentry,k); } else { fprintf(stderr,"WARNING: temp %llu file seems empty.\n", (unsigned long long)k); } } if ( collator->state != BAMBAM_COLLATE_FAILED ) { /* BamBam_BamCollator_MergeHeapPrint(collator); */ BamBam_BamCollator_MergeHeapCheck(collator); } } } } else { if ( collator->mergeheapfill ) { BamBam_MergeHeapEntry * mini = BamBam_BamCollator_MergeHeapMinimum(collator); BamBam_BamCollationHashEntry * hashentry = mini->hashentry; unsigned int const fileid = mini->fileid; BamBam_BamCollationOutputVector_PushBack(collator->outputvector,hashentry); mini->hashentry = 0; BamBam_BamCollator_MergeHeapDeleteMinimum(collator); if ( (collator->alignment = BamBam_GzipFileDecoder_DecodeAlignment(collator->mergefiles[fileid])) ) { BamBam_BamCollationHashEntry * nhashentry = 0; nhashentry = BamBam_BamCollationHashEntry_NewDup(collator->alignment); if ( ! nhashentry ) { collator->state = BAMBAM_COLLATE_FAILED; } else { BamBam_BamCollator_MergeHeapInsert(collator,nhashentry,fileid); } } } else collator->state = BAMBAM_COLLATE_DONE; } } if ( collator->outputvector->outputvectorfill ) { #if 0 int len = -1; BamBam_BamCollationHashEntry *entry = BamBam_BamCollationOutputVector_PopFront(collator->outputvector); len = BamBam_PutAlignmentBuffer(entry->entry,&(collator->bufferA),&(collator->bufferALength),'\n'); fwrite(collator->bufferA,1,len,stdout); /* fprintf(stdout,"%s\n", entry->qname); */ BamBam_BamCollationHashEntry_Delete(entry); return 1; #endif return BamBam_BamCollationOutputVector_PopFront(collator->outputvector); } else { return 0; } } enum tmpdirstate { BAMBAM_TMPDIR_FAILED = 1, BAMBAM_TMPDIR_CREATED = 2, BAMBAM_TMPDIR_WASPRESENT = 3 }; #include #if defined(HAVEWINDOWS_MKDIR) #include #endif /* for stat() */ #include #include #include #include static int BamBam_CreateTempDir(char const * tmpdirname) { struct stat sb; int statret = stat(tmpdirname,&sb); if ( statret == -1 && errno == ENOENT ) { #if defined(HAVEWINDOWS_MKDIR) if ( ! _mkdir(tmpdirname) ) #else if ( ! mkdir(tmpdirname, 0700) ) #endif { return BAMBAM_TMPDIR_CREATED; } else { return BAMBAM_TMPDIR_FAILED; } } /* it exists, check whether it is a directory */ else { if ( S_ISDIR(sb.st_mode) ) { return BAMBAM_TMPDIR_WASPRESENT; } else { return BAMBAM_TMPDIR_FAILED; } } } static char const * BamBam_BamCollator_InputFormatToMode(char const * inputformat) { if ( strcmp(inputformat,"bam") == 0 ) return "rb"; else if ( strcmp(inputformat,"sam") == 0 ) return "r"; else return 0; } BamBam_BamCollator * BamBam_BamCollator_Delete(BamBam_BamCollator * collator) { if ( collator ) { BamBam_BamHeaderInfo_Delete(collator->headerinfo); BamBam_BamHeaderInfo_Delete(collator->parsedheaderinfo); free(collator->headerline); free(collator->bamheadertext); free(collator->filteredbamheadertext); free(collator->vn); free(collator->so); free(collator->bufferA); free(collator->bufferB); unsigned int k; if ( collator->mergefiles ) { for ( k = 0; k < collator->nummergefiles; ++k ) if ( collator->mergefiles[k] ) { BamBam_GzipFileDecoder_Delete(collator->mergefiles[k]); collator->mergefiles[k] = 0; } free(collator->mergefiles); collator->mergefiles = 0; } if ( collator->mergeheap ) { if ( collator->mergeheapfill ) BamBam_BamCollator_MergeHeapDeleteMinimum(collator); free(collator->mergeheap); collator->mergeheap = 0; } if ( collator->tmpdirstate == BAMBAM_TMPDIR_CREATED ) rmdir(collator->tempdirname); if ( collator->decoder ) BamBam_SamBamFileDecoder_Delete(collator->decoder); BamBam_BamCollationOutputVector_Delete(collator->outputvector); BamBam_BamCollationTempFileGenerator_Delete(collator->gen); BamBam_BamCollationVector_Delete(collator->vector); BamBam_BamCollationHash_Delete(collator->hash); free(collator->tempdirname); free(collator->tempprefix); BamBam_BamCollationHashEntry_Delete(collator->entryA); BamBam_BamCollationHashEntry_Delete(collator->entryB); free(collator); } return 0; } char const * BamBam_findNextTab(char const * t) { char const * nexttab = t; while ( *nexttab && *nexttab != '\n' && *nexttab != '\t' ) ++nexttab; return nexttab; } char const * BamBam_skipTab(char const * t) { if ( *t && *t == '\t' ) return t+1; else return t; } char const * BamBam_nextField(char const * t) { return BamBam_skipTab(BamBam_findNextTab(t)); } BamBam_BamCollator * BamBam_BamCollator_New( char const * tempdirname, unsigned int const hashsizelog, unsigned int const vectorsizelog, char const * inputformat, char const * inputfilename ) { BamBam_BamCollator * collator = 0; size_t tempdirnamelen = 0; size_t tempfileprefixlen = 0; char const * tempadd = "/file"; char const * mode = BamBam_BamCollator_InputFormatToMode(inputformat); char const * hfilters[] = { "HD", "SQ", 0 }; int i; tempdirnamelen = strlen(tempdirname); tempfileprefixlen = tempdirnamelen + strlen(tempadd) + 1; collator = (BamBam_BamCollator *)malloc(sizeof(BamBam_BamCollator)); if ( ! collator ) return BamBam_BamCollator_Delete(collator); memset(collator,0,sizeof(BamBam_BamCollator)); collator->state = BAMBAM_COLLATE_READING_INPUT; collator->tmpdirstate = BamBam_CreateTempDir(tempdirname); if ( collator->tmpdirstate == BAMBAM_TMPDIR_FAILED ) return BamBam_BamCollator_Delete(collator); collator->tempdirname = BamBam_StrDup(tempdirname); if ( ! collator->tempdirname ) return BamBam_BamCollator_Delete(collator); collator->tempprefix = (char *)malloc(tempfileprefixlen); if ( ! collator->tempprefix ) return BamBam_BamCollator_Delete(collator); snprintf(collator->tempprefix,tempfileprefixlen,"%s%s",tempdirname,tempadd); collator->hash = BamBam_BamCollationHash_New(hashsizelog); if ( ! collator->hash ) return BamBam_BamCollator_Delete(collator); collator->vector = BamBam_BamCollationVector_New(vectorsizelog); if ( ! collator->vector ) return BamBam_BamCollator_Delete(collator); collator->gen = BamBam_BamCollationTempFileGenerator_New(collator->tempprefix); if ( ! collator->gen ) return BamBam_BamCollator_Delete(collator); collator->outputvector = BamBam_BamCollationOutputVector_New(vectorsizelog); if ( ! collator->outputvector ) return BamBam_BamCollator_Delete(collator); collator->decoder = BamBam_SamBamFileDecoder_New(inputfilename,mode); if ( ! collator->decoder ) return BamBam_BamCollator_Delete(collator); collator->bamheadertext = BamBam_StrDup(collator->decoder->header->headertext); if ( ! collator->bamheadertext ) return BamBam_BamCollator_Delete(collator); collator->filteredbamheadertext = BamBam_filterHeader(collator->bamheadertext,&hfilters[0]); if ( ! collator->filteredbamheadertext ) return BamBam_BamCollator_Delete(collator); /* parse header into header info structure, if we have a header text */ if ( collator->bamheadertext && (strlen(collator->bamheadertext) != 0) ) { char const * s = collator->bamheadertext; while ( (! collator->headerline) && *s ) { if ( BamBam_getLineLength(s) >= 4 && s[0] == '@' && s[1] == 'H' && s[2] == 'D' && s[3] == '\t' ) { collator->headerline = (char *)malloc(BamBam_getLineLength(s)+1); if ( ! collator->headerline ) return BamBam_BamCollator_Delete(collator); memset(collator->headerline,0,BamBam_getLineLength(s)+1); memcpy(collator->headerline,s,BamBam_getLineLength(s)); } s = BamBam_nextLine(s); } if ( collator->headerline ) { char const * t = collator->headerline; while ( *t && *t != '\n' ) { char const * nexttab = BamBam_findNextTab(t); /* version number */ if ( nexttab-t >= 3 && t[0] == 'V' && t[1] == 'N' && t[2] == ':' ) { collator->vn = (char *)malloc((nexttab-t)-3+1); if ( ! collator->vn ) return BamBam_BamCollator_Delete(collator); memset(collator->vn,0,(nexttab-t)-3+1); memcpy(collator->vn,t+3,(nexttab-t)-3); } /* sort order */ if ( nexttab-t >= 3 && t[0] == 'S' && t[1] == 'O' && t[2] == ':' ) { collator->so = (char *)malloc((nexttab-t)-3+1); if ( ! collator->so ) return BamBam_BamCollator_Delete(collator); memset(collator->so,0,(nexttab-t)-3+1); memcpy(collator->so,t+3,(nexttab-t)-3); } t = BamBam_nextField(t); } } if ( ! collator->vn ) { collator->vn = BamBam_StrDup("1.4"); if ( ! collator->vn ) return BamBam_BamCollator_Delete(collator); } if ( ! collator->so ) { collator->so = BamBam_StrDup("unknown"); if ( ! collator->so ) return BamBam_BamCollator_Delete(collator); } collator->parsedheaderinfo = BamBam_BamHeaderInfo_New(collator->vn, collator->so, collator->filteredbamheadertext); if ( ! collator->parsedheaderinfo ) return BamBam_BamCollator_Delete(collator); s = collator->bamheadertext; while ( *s ) { if ( BamBam_getLineLength(s) >= 4 && s[0] == '@' && s[1] == 'S' && s[2] == 'Q' && s[3] == '\t' ) { char const * t = s; char * sn = 0; long ln = -1; while ( *t && *t != '\n' ) { char const * nexttab = BamBam_findNextTab(t); /* sequence name */ if ( nexttab-t >= 3 && t[0] == 'S' && t[1] == 'N' && t[2] == ':' ) { sn = (char *)malloc((nexttab-t)-3+1); if ( ! sn ) return BamBam_BamCollator_Delete(collator); memset(sn,0,(nexttab-t)-3+1); memcpy(sn,t+3,(nexttab-t)-3); } /* sequence length */ if ( nexttab-t >= 3 && t[0] == 'L' && t[1] == 'N' && t[2] == ':' ) { ln = 0; char const * tt = t+3; while ( isdigit(*tt) ) { ln *= 10; ln += *tt-'0'; tt++; } } t = BamBam_nextField(t); } if ( sn && ln != -1 ) { if ( BamBam_BamHeaderInfo_AddChromosome(collator->parsedheaderinfo,sn,ln) ) { free(sn); return BamBam_BamCollator_Delete(collator); } } free(sn); } s = BamBam_nextLine(s); } if ( BamBam_BamHeaderInfo_ProduceHeaderText(collator->parsedheaderinfo) < 0 ) return BamBam_BamCollator_Delete(collator); } if ( ! collator->vn ) { collator->vn = BamBam_StrDup("1.4"); if ( ! collator->vn ) return BamBam_BamCollator_Delete(collator); } if ( ! collator->so ) { collator->so = BamBam_StrDup("unknown"); if ( ! collator->so ) return BamBam_BamCollator_Delete(collator); } collator->headerinfo = BamBam_BamHeaderInfo_New(collator->vn, collator->so, collator->filteredbamheadertext); if ( ! collator->headerinfo ) return BamBam_BamCollator_Delete(collator); for ( i = 0; i < collator->decoder->header->n_ref; ++i ) { if ( BamBam_BamHeaderInfo_AddChromosome(collator->headerinfo, collator->decoder->header->chromosomevec[i]->name,collator->decoder->header->chromosomevec[i]->length) ) return BamBam_BamCollator_Delete(collator); } if ( BamBam_BamHeaderInfo_ProduceHeaderText(collator->headerinfo) < 0 ) return BamBam_BamCollator_Delete(collator); return collator; } int BamBam_BamCollator_Get(BamBam_BamCollator * collator, BamBam_BamCollationHashEntry ** entryA, BamBam_BamCollationHashEntry ** entryB) { BamBam_BamCollationHashEntry * peekA = 0; BamBam_BamCollationHashEntry * peekB = 0; *entryA = 0; *entryB = 0; peekA = BamBam_BamCollator_GetNextRead(collator); peekB = BamBam_BamCollator_GetNextRead(collator); /* no alignments left */ if ( ! peekA ) { return 0; } /* only one alignment left (orphan) */ else if ( ! peekB ) { if ( BamBam_BamCollationHashEntry_GetFlags(peekA) & BAMBAMC_FREAD2 ) *entryB = peekA; else *entryA = peekA; return 1; } else { assert ( peekA ); assert ( peekB ); /* pair */ if ( (peekA->hashvalue == peekB->hashvalue) && (!strcmp(peekA->qname,peekB->qname)) && ( ((BamBam_BamCollationHashEntry_GetFlags(peekA) & BAMBAMC_FREAD1) &&(BamBam_BamCollationHashEntry_GetFlags(peekB) & BAMBAMC_FREAD2)) || ((BamBam_BamCollationHashEntry_GetFlags(peekB) & BAMBAMC_FREAD1) &&(BamBam_BamCollationHashEntry_GetFlags(peekA) & BAMBAMC_FREAD2)) ) ) { if ( BamBam_BamCollationHashEntry_GetFlags(peekA) & BAMBAMC_FREAD1 ) { *entryA = peekA; *entryB = peekB; } else { *entryA = peekB; *entryB = peekA; } return 2; } /* orphan */ else { if ( BamBam_BamCollationHashEntry_GetFlags(peekA) & BAMBAMC_FREAD2 ) *entryB = peekA; else *entryA = peekA; /* return alignment to queue */ BamBam_BamCollationOutputVector_PushFront(collator->outputvector,peekB); return 1; } } } bambamc-bambamc_0_0_50/src/bambamc/BamBam_BamCollator.h000066400000000000000000000064551233012646600227170ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAM_BAMCOLLATOR_H) #define BAMBAM_BAMCOLLATOR_H #include #include #include #include #include #include #include #include #include typedef struct _BamBam_BamCollator { int state; int tmpdirstate; char * tempdirname; char * tempprefix; BamBam_BamCollationHash * hash; BamBam_BamCollationVector * vector; BamBam_BamCollationTempFileGenerator * gen; BamBam_BamCollationOutputVector * outputvector; BamBam_SamBamFileDecoder * decoder; /* header text */ char * bamheadertext; char * filteredbamheadertext; char * headerline; char * vn; char * so; BamBam_BamHeaderInfo * parsedheaderinfo; BamBam_BamHeaderInfo * headerinfo; BamBam_BamSingleAlignment * alignment; uint64_t nummergefiles; BamBam_GzipFileDecoder ** mergefiles; BamBam_MergeHeapEntry * mergeheap; uint64_t mergeheapfill; char * bufferA; unsigned int bufferALength; char * bufferB; unsigned int bufferBLength; int keepOrphans; BamBam_BamCollationHashEntry * entryA; BamBam_BamCollationHashEntry * entryB; } BamBam_BamCollator; extern void BamBam_BamCollator_MergeHeapEntrySwap(BamBam_MergeHeapEntry * A, BamBam_MergeHeapEntry * B); extern void BamBam_BamCollator_MergeHeapPrint(BamBam_BamCollator * collator); extern void BamBam_BamCollator_MergeHeapCheck(BamBam_BamCollator * collator); extern BamBam_MergeHeapEntry * BamBam_BamCollator_MergeHeapMinimum(BamBam_BamCollator * collator) BAMBAM_WARN_IF_UNUSEDRESULT; extern void BamBam_BamCollator_MergeHeapDeleteMinimum(BamBam_BamCollator * collator); extern void BamBam_BamCollator_MergeHeapInsert(BamBam_BamCollator * collator, BamBam_BamCollationHashEntry * hashentry, unsigned int fileid); extern BamBam_BamCollationHashEntry * BamBam_BamCollator_GetNextRead(BamBam_BamCollator * collator) BAMBAM_WARN_IF_UNUSEDRESULT; extern BamBam_BamCollator * BamBam_BamCollator_Delete(BamBam_BamCollator * collator); extern BamBam_BamCollator * BamBam_BamCollator_New( char const * tempdirname, unsigned int const hashsizelog, unsigned int const vectorsizelog, char const * inputformat, char const * inputfilename ) BAMBAM_WARN_IF_UNUSEDRESULT; extern int BamBam_BamCollator_Get( BamBam_BamCollator * collator, BamBam_BamCollationHashEntry ** entryA, BamBam_BamCollationHashEntry ** entryB) BAMBAM_WARN_IF_UNUSEDRESULT; #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_BamCollatorInterface.c000066400000000000000000000121411233012646600245200ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include #include BamBam_List collatorList; #include int BamBam_AllocBamCollator(char const * filename, char const * filetype, char const * tempdirname, int const keepOrphans) { BamBam_BamCollator * collator = BamBam_BamCollator_New(tempdirname,16,16,filetype,filename); unsigned int id = -1; if ( ! collator ) return id; collator->keepOrphans = keepOrphans; BamBam_ListNode * node = BamBam_ListNode_New(); if ( ! node ) { BamBam_BamCollator_Delete(collator); return id; } node->entry = collator; id = BamBam_List_Size(&collatorList); BamBam_ListNode_PushBack(&collatorList,node); return id; } #include BamBam_BamCollator * BamBam_GetBamCollator(int id) { BamBam_ListNode * node; if ( id < 0 ) return 0; if ( id >= (int)(BamBam_List_Size(&collatorList)) ) return 0; node = collatorList.first; while ( id ) { assert ( node ); node = node->next; --id; } if ( ! node ) return 0; return node->entry; } void BamBam_FreeBamCollator(int const id) { if ( id >= 0 && id < (int)(BamBam_List_Size(&collatorList)) ) { int tid = id; BamBam_ListNode * node; node = collatorList.first; while ( tid ) { assert ( node ); node = node->next; --tid; } if ( node ) { BamBam_BamCollator_Delete((BamBam_BamCollator *)(node->entry)); node->entry = 0; } } } static void BamBam_ParseFastQ(char const * text, BamBam_FastQRead * reada, char const term) { /* at line */ assert ( *text == '@' ); text++; reada->name = text; reada->namelength = 0; while ( *text != term ) reada->namelength++, text++; assert ( *text == term ); text++; /* sequence line */ reada->seqlength = 0; reada->seq = text; while ( *text != term ) reada->seqlength++, text++; assert ( *text == term ); text++; /* plus line */ while ( *text != term ) text++; assert ( *text == term ); text++; /* quality line */ reada->qual = text; } #include int BamBam_ReadPair(int const id, BamBam_FastQRead * const reada, BamBam_FastQRead * const readb, void ** aligna, void ** alignb, char const term) { BamBam_BamCollator * collator = BamBam_GetBamCollator(id); int getret = 0; int ret = BAMBAM_ALIGNMENT_TYPE_UNDEFINED; if ( !collator ) return ret; while ( ret == BAMBAM_ALIGNMENT_TYPE_UNDEFINED ) { if ( aligna ) *aligna = 0; if ( alignb ) *alignb = 0; BamBam_BamCollationHashEntry_Delete(collator->entryA); collator->entryA = 0; BamBam_BamCollationHashEntry_Delete(collator->entryB); collator->entryB = 0; getret = BamBam_BamCollator_Get(collator, &(collator->entryA), &(collator->entryB)); /* a pair */ if ( getret == 2 ) { if ( aligna ) *aligna = collator->entryA->entry; if ( alignb ) *alignb = collator->entryB->entry; ret = BAMBAM_ALIGNMENT_TYPE_COMPLETE_PAIR; } /* single end */ else if ( getret == 1 && collator->entryA && (!((BamBam_BamCollationHashEntry_GetFlags(collator->entryA)) & BAMBAMC_FPAIRED)) ) { if ( aligna ) *aligna = collator->entryA->entry; ret = BAMBAM_ALIGNMENT_TYPE_SINGLE; } /* orphan, kept */ else if ( getret == 1 && collator->keepOrphans ) { if ( collator->entryA ) { if ( aligna ) *aligna = collator->entryA->entry; ret = BAMBAM_ALIGNMENT_TYPE_ORPHAN1_PAIR; } else { *alignb = collator->entryB->entry; ret = BAMBAM_ALIGNMENT_TYPE_ORPHAN2_PAIR; } } /* orphan, not kept */ else if ( getret == 1 && ! collator->keepOrphans ) { BamBam_BamCollationHashEntry_Delete(collator->entryA); collator->entryA = 0; BamBam_BamCollationHashEntry_Delete(collator->entryB); collator->entryB = 0; } /* nothing */ else { assert ( getret == 0 ); ret = BAMBAM_ALIGNMENT_TYPE_NONE; } if ( aligna && *aligna ) { int const lena = BamBam_PutAlignmentFastQBuffer(*aligna,&(collator->bufferA),&(collator->bufferALength),term); if ( lena < 0 ) ret = BAMBAM_ALIGNMENT_TYPE_NONE; else BamBam_ParseFastQ(collator->bufferA,reada,term); } if ( alignb && *alignb ) { int const lenb = BamBam_PutAlignmentFastQBuffer(*alignb,&(collator->bufferB),&(collator->bufferBLength),term); if ( lenb < 0 ) ret = BAMBAM_ALIGNMENT_TYPE_NONE; else BamBam_ParseFastQ(collator->bufferB,readb,term); } } return ret; } bambamc-bambamc_0_0_50/src/bambamc/BamBam_BamCollatorInterface.h000066400000000000000000000024571233012646600245360ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAM_BAMCOLLATORINTERFACE_H) #define BAMBAM_BAMCOLLATORINTERFACE_H #include #include extern int BamBam_AllocBamCollator(char const * filename, char const * filetype, char const * tempdirname, int const keepOrphans) BAMBAM_WARN_IF_UNUSEDRESULT; extern void BamBam_FreeBamCollator(int const id); extern int BamBam_ReadPair(int const id, BamBam_FastQRead * const reada, BamBam_FastQRead * const readb, void ** aligna, void ** alignb, char const term) BAMBAM_WARN_IF_UNUSEDRESULT; #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_BamFileDecoder.c000066400000000000000000000042271233012646600232730ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include BamBam_BamSingleAlignment * BamBam_BamFileDecoder_DecodeAlignment(BamBam_BamFileDecoder * object) { int const r = BamBam_BamSingleAlignment_LoadAlignment(object->alignment,object->reader); if ( r > 0 ) return object->alignment; else return 0; } BamBam_BamFileDecoder * BamBam_BamFileDecoder_Delete(BamBam_BamFileDecoder * object) { if ( object ) { if ( object->alignment ) { BamBam_BamSingleAlignment_Delete(object->alignment); object->alignment = 0; } if ( object->reader ) { BamBam_GzipReader_Delete(object->reader); object->reader = 0; } if ( object->header ) { BamBam_BamFileHeader_Delete(object->header); object->header = 0; } free(object); } return 0; } BamBam_BamFileDecoder * BamBam_BamFileDecoder_New(char const * filename) { BamBam_BamFileDecoder * object = 0; object = (BamBam_BamFileDecoder *)malloc(sizeof(BamBam_BamFileDecoder)); if ( ! object ) return BamBam_BamFileDecoder_Delete(object); object->reader = BamBam_GzipReader_New(filename); if ( ! object->reader ) return BamBam_BamFileDecoder_Delete(object); object->header = BamBam_BamFileHeader_New_BAM(object->reader); if ( ! object->header ) return BamBam_BamFileDecoder_Delete(object); object->alignment = BamBam_BamSingleAlignment_New(); if ( ! object->alignment ) return BamBam_BamFileDecoder_Delete(object); return object; } bambamc-bambamc_0_0_50/src/bambamc/BamBam_BamFileDecoder.h000066400000000000000000000025471233012646600233030ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAM_BAMFILEDECODER_H) #define BAMBAM_BAMFILEDECODER_H #include #include typedef struct _BamBam_BamFileDecoder { BamBam_GzipReader * reader; BamBam_BamFileHeader * header; BamBam_BamSingleAlignment * alignment; } BamBam_BamFileDecoder; extern BamBam_BamSingleAlignment * BamBam_BamFileDecoder_DecodeAlignment(BamBam_BamFileDecoder * object); extern BamBam_BamFileDecoder * BamBam_BamFileDecoder_Delete(BamBam_BamFileDecoder * object); extern BamBam_BamFileDecoder * BamBam_BamFileDecoder_New(char const * filename); #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_BamFileHeader.c000066400000000000000000000550661233012646600231250ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include #include #include #include #include #include #include #include static int chromosomeCompareNames(uint8_t const * unamea, uint8_t const * unameb) { while ( *unamea && *unameb ) { if ( isdigit(*unamea) && isdigit(*unameb) ) { int numa = 0, numb = 0; while ( *unamea && isdigit(*unamea) ) { numa *= 10; numa += (*unamea-'0'); unamea++; } while ( *unameb && isdigit(*unameb) ) { numb *= 10; numb += (*unameb-'0'); unameb++; } if ( numa != numb ) return numa-numb; } else if ( *unamea != *unameb ) { return (int)(*unamea) - (int)(*unameb); } else { unamea++, unameb++; } } return (int)(*unamea) - (int)(*unameb); } static int chromosomeNameComparison(void const * va, void const * vb) { BamBam_Chromosome * a = *((BamBam_Chromosome**)(va)); BamBam_Chromosome * b = *((BamBam_Chromosome**)(vb)); char const * namea = a->name; char const * nameb = b->name; uint8_t const * unamea = (uint8_t const *)(namea); uint8_t const * unameb = (uint8_t const *)(nameb); return chromosomeCompareNames(unamea,unameb); } BamBam_BamFileHeader * BamBam_BamFileHeader_Delete(BamBam_BamFileHeader * object) { if ( object ) { if ( object->headertext ) { free(object->headertext); object->headertext = 0; } if ( object->sortorder ) { free(object->sortorder); object->sortorder = 0; } if ( object->version ) { free(object->version); object->version = 0; } if ( object->headerlines ) { char ** h = object->headerlines; for ( ; *h ; ++h ) free(*h); free (object->headerlines); object->headerlines = 0; } if ( object->chromosomevec ) { free(object->chromosomevec); object->chromosomevec = 0; } if ( object->sortedchromosomevec ) { free(object->sortedchromosomevec); object->sortedchromosomevec = 0; } if ( object->chromosomes ) { BamBam_List_Delete(object->chromosomes); } if ( object->text ) { free(object->text); object->text = 0; } free(object); } return 0; } static void chromosomeDelete(void * chromosome) { BamBam_Chromosome_Delete((BamBam_Chromosome *)chromosome); } static BamBam_BamFileHeader * parseHeaderText(BamBam_BamFileHeader * header) { int headerlines = 0; char const * c = header->text; unsigned int i; char ** hc = 0; while ( *c ) { headerlines++; c = BamBam_nextLine(c); } header->headerlines = (char **)malloc((headerlines+1) * sizeof(char const *)); if ( ! header->headerlines ) { return BamBam_BamFileHeader_Delete(header); } for ( i = 0; (int)i < headerlines; ++i ) header->headerlines[i] = 0; header->headerlines[headerlines] = 0; headerlines = 0; c = header->text; while ( *c ) { int const len = BamBam_getLineLength(c); header->headerlines[headerlines] = malloc(len+1); if ( ! header->headerlines[headerlines] ) return BamBam_BamFileHeader_Delete(header); header->headerlines[headerlines][len] = 0; memcpy(header->headerlines[headerlines],c,len); headerlines++; c = BamBam_nextLine(c); } for ( hc = header->headerlines; *hc; ++hc ) { if ( strlen(*hc) >= 4 && !strncmp("@HD\t",*hc,4) ) header->hdline = *hc; } if ( header->hdline ) { for ( c = header->hdline; *c; ++c ) if ( c[0] == '\t' && c[1] == 'S' && c[2] == 'O' && c[3] == ':' ) { char const * d = c+4; char const * e = d; while ( *e != 0 && *e != '\t' ) ++e; if ( e-d ) { header->sortorder = (char *)malloc((e-d)+1); if ( ! header->sortorder ) { return BamBam_BamFileHeader_Delete(header); } header->sortorder[e-d] = 0; memcpy(header->sortorder,d,e-d); } } else if ( c[0] == '\t' && c[1] == 'V' && c[2] == 'N' && c[3] == ':' ) { char const * d = c+4; char const * e = d; while ( *e != 0 && *e != '\t' ) ++e; if ( e-d ) { header->version = (char *)malloc((e-d)+1); if ( ! header->version ) { return BamBam_BamFileHeader_Delete(header); } header->version[e-d] = 0; memcpy(header->version,d,e-d); } } } if ( ! header->version ) { header->version = BamBam_StrDup("1.4"); if ( ! header->version ) return BamBam_BamFileHeader_Delete(header); } if ( ! header->sortorder ) { header->sortorder = BamBam_StrDup("unknown"); if ( ! header->sortorder ) return BamBam_BamFileHeader_Delete(header); } return header; } static int findChromosomeByName( BamBam_Chromosome const ** sc, unsigned int const numchr, char const * name ) { int left = 0; int right = numchr; while ( right > left ) { unsigned int const mid = left + (right-left)/2; int const r = chromosomeCompareNames((uint8_t const *)name,(uint8_t const *)(sc[mid]->name)); if ( r == 0 ) return mid; else if ( r < 0 ) right = mid; else left = mid+1; } return -1; } int BamBam_BamFileHeader_FindChromosomeIdByName(BamBam_BamFileHeader const * header, char const * name) { return findChromosomeByName((BamBam_Chromosome const **)header->sortedchromosomevec,header->n_ref,name); } BamBam_Chromosome const * BamBam_BamFileHeader_FindChromosomeByName(BamBam_BamFileHeader const * header, char const * name) { int const r = BamBam_BamFileHeader_FindChromosomeIdByName(header,name); if ( r < 0 ) return 0; else return header->sortedchromosomevec[r]; } BamBam_BamFileHeader * BamBam_BamFileHeader_New_SAM(FILE * reader) { BamBam_BamFileHeader * header = 0; BamBam_CharBuffer * buffer = 0; int headerTextComplete = 0; int r = 0; char ** hc = 0; BamBam_ListNode * node = 0; size_t i; header = (BamBam_BamFileHeader *)malloc(sizeof(BamBam_BamFileHeader)); if ( ! header ) return BamBam_BamFileHeader_Delete(header); memset(header,0,sizeof(BamBam_BamFileHeader)); buffer = BamBam_CharBuffer_New(); if ( ! buffer ) return BamBam_BamFileHeader_Delete(header); while ( !headerTextComplete ) { int c = -1; c = getc(reader); if ( c < 0 || c != '@' ) { headerTextComplete = 1; if ( c >= 0 ) ungetc(c,reader); } else { while ( c >= 0 && c != '\n' ) { BamBam_CharBuffer_PushCharQuick(buffer,c,r); if ( r < 0 ) { BamBam_CharBuffer_Delete(buffer); return BamBam_BamFileHeader_Delete(header); } c = getc(reader); } if ( c < 0 ) { BamBam_CharBuffer_Delete(buffer); return BamBam_BamFileHeader_Delete(header); } BamBam_CharBuffer_PushCharQuick(buffer,'\n',r); if ( r < 0 ) { BamBam_CharBuffer_Delete(buffer); return BamBam_BamFileHeader_Delete(header); } } } BamBam_CharBuffer_PushCharQuick(buffer,0,r); if ( r < 0 ) { BamBam_CharBuffer_Delete(buffer); return BamBam_BamFileHeader_Delete(header); } /* fprintf(stderr,"::HEADER::\n%s::ENDHEADER::\n",(char const *)buffer->buffer); */ header->text = (char *)buffer->buffer; buffer->buffer = 0; header->l_text = buffer->bufferfill; BamBam_CharBuffer_Delete(buffer); header = parseHeaderText(header); if (! header ) return BamBam_BamFileHeader_Delete(header); header->chromosomes = BamBam_List_New(); if ( !header->chromosomes ) return BamBam_BamFileHeader_Delete(header); for ( hc = header->headerlines; *hc; ++hc ) { if ( strlen(*hc) >= 4 && !strncmp("@SQ\t",*hc,4) ) { BamBam_Chromosome * chr = 0; BamBam_ListNode * node = 0; char const * c = *hc; c += 3; char * sn = 0; int32_t ln = -1; while ( *c ) { while ( *c && *c == '\t' ) ++c; if ( *c ) { char const * ce = c; while ( *ce && *ce != '\t' ) ++ce; if ( ce-c >= 3 && !strncmp(c,"SN:",3) ) { sn = malloc((ce-c)-3+1); if ( ! sn ) { free(sn); sn = 0; return BamBam_BamFileHeader_Delete(header); } sn [ (ce-c)-3 ] = 0; memcpy(sn,c+3,(ce-c)-3); } else if ( ce-c >= 3 && !strncmp(c,"LN:",3) ) { char const * p = c+3; ln = 0; while ( p != ce ) { ln*=10; ln+=(*(p++))-'0'; } } c = ce; } } /* missing information, broken header */ if ( ! sn || ln < 0 ) { if ( sn ) { free(sn); sn = 0; } return BamBam_BamFileHeader_Delete(header); } /* fprintf(stderr,"Seq %s %d\n", sn,ln); */ chr = BamBam_Chromosome_New(sn,ln); free(sn); sn = 0; if ( ! chr ) { return BamBam_BamFileHeader_Delete(header); } chr->headerline = BamBam_StrDup(*hc); if ( ! chr->headerline ) { fprintf(stderr,"Failed to allocate memory for sequence meta data in BAM header.\n"); BamBam_Chromosome_Delete(chr); return BamBam_BamFileHeader_Delete(header); } node = BamBam_ListNode_New(); if ( ! node ) { fprintf(stderr,"Failed to allocate memory for sequence meta data in BAM header.\n"); BamBam_Chromosome_Delete(chr); return BamBam_BamFileHeader_Delete(header); } node->entry = chr; node->bamBamListFreeFunction = chromosomeDelete; BamBam_ListNode_PushBack(header->chromosomes,node); header->n_ref++; } } header->chromosomevec = (BamBam_Chromosome **)malloc(header->n_ref * sizeof(BamBam_Chromosome *)); if ( ! header->chromosomevec ) { return BamBam_BamFileHeader_Delete(header); } header->sortedchromosomevec = (BamBam_Chromosome **)malloc(header->n_ref * sizeof(BamBam_Chromosome *)); if ( ! header->sortedchromosomevec ) { return BamBam_BamFileHeader_Delete(header); } i = 0; for ( node = header->chromosomes->first; node; node = node->next ) { BamBam_Chromosome * chr = (BamBam_Chromosome *)node->entry; header->sortedchromosomevec[i] = chr; header->chromosomevec[i++] = chr; } qsort(header->sortedchromosomevec, header->n_ref, sizeof(BamBam_Chromosome *),chromosomeNameComparison); #if 0 for ( i = 0; (int)i < (int)header->n_ref; ++i ) { BamBam_Chromosome * chr = header->sortedchromosomevec[i]; fprintf(stderr,"seq[%d] = %s %d\n", (int)i, chr->name, (int)chr->length); } #endif header->headertext = BamBam_StrDup(header->text); if ( ! header->headertext ) { return BamBam_BamFileHeader_Delete(header); } return header; } BamBam_BamFileHeader * BamBam_BamFileHeader_New_BAM(BamBam_GzipReader * reader) { BamBam_BamFileHeader * header = 0; char magic[4]; static char const expMagic[4] = {'B','A','M',1}; unsigned int i; int l; char ** hc = 0; BamBam_CharBuffer * htextbuf = 0; header = (BamBam_BamFileHeader *)malloc(sizeof(BamBam_BamFileHeader)); if ( ! header ) return BamBam_BamFileHeader_Delete(header); memset(header,0,sizeof(BamBam_BamFileHeader)); magic[0] = BamBam_GzipReader_Getc(reader); magic[1] = BamBam_GzipReader_Getc(reader); magic[2] = BamBam_GzipReader_Getc(reader); magic[3] = BamBam_GzipReader_Getc(reader); for ( i = 0; i < sizeof(expMagic)/sizeof(expMagic[0]); ++i ) if ( magic[i] != expMagic[i] ) { fprintf(stderr,"Stream is not a BAM file (magic is wrong).\n"); return BamBam_BamFileHeader_Delete(header); } if ( BamBam_GzipReader_GetInt32(reader,&(header->l_text)) ) { fprintf(stderr,"Failed to read length of plain text in BAM header.\n"); return BamBam_BamFileHeader_Delete(header); } header->text = (char *)malloc(header->l_text); if ( header->l_text && (! header->text) ) { fprintf(stderr,"Failed to allocate memory for plain text in BAM header.\n"); return BamBam_BamFileHeader_Delete(header); } l = BamBam_GzipReader_Read(reader,header->text,header->l_text); if ( l != header->l_text ) { fprintf(stderr,"Failed to read plain text in BAM header.\n"); return BamBam_BamFileHeader_Delete(header); } /* terminate by zero if not already so */ if ( (!l) || (header->text[l-1]) ) { char * ztext = malloc(l+1); if ( ! ztext ) { fprintf(stderr,"Failed to allocate memory for plain text in BAM header.\n"); return BamBam_BamFileHeader_Delete(header); } memcpy(ztext,header->text,l); ztext[l] = 0; free(header->text); header->text = ztext; header->l_text = l+1; l += 1; } assert ( l == header->l_text ); assert ( (header->l_text != 0) && (header->text[header->l_text-1] == 0) ); if ( BamBam_GzipReader_GetInt32(reader,&(header->n_ref)) ) { fprintf(stderr,"Failed to read number of references in BAM header.\n"); return BamBam_BamFileHeader_Delete(header); } header->chromosomes = BamBam_List_New(); if ( ! header->chromosomes ) { return BamBam_BamFileHeader_Delete(header); } header->chromosomevec = (BamBam_Chromosome **)malloc(header->n_ref * sizeof(BamBam_Chromosome *)); if ( ! header->chromosomevec ) { return BamBam_BamFileHeader_Delete(header); } header->sortedchromosomevec = (BamBam_Chromosome **)malloc(header->n_ref * sizeof(BamBam_Chromosome *)); if ( ! header->sortedchromosomevec ) { return BamBam_BamFileHeader_Delete(header); } for ( i = 0; i < (unsigned int)(header->n_ref); ++i ) { int32_t chrnamelen = -1; char * chrname = 0; int32_t chrlen = -1; BamBam_Chromosome * chr = 0; BamBam_ListNode * node = 0; if ( BamBam_GzipReader_GetInt32(reader,&(chrnamelen)) ) { fprintf(stderr,"Failed to read sequence name length in BAM header.\n"); return BamBam_BamFileHeader_Delete(header); } chrname = (char*)malloc(chrnamelen); if ( ! chrname ) { fprintf(stderr,"Failed to allocate space for chromosome name while reading BAM header.\n"); return BamBam_BamFileHeader_Delete(header); } if ( BamBam_GzipReader_Read(reader,chrname,chrnamelen) != chrnamelen ) { fprintf(stderr,"Failed to read chromosome name while reading BAM header.\n"); free(chrname); return BamBam_BamFileHeader_Delete(header); } if ( BamBam_GzipReader_GetInt32(reader,&(chrlen)) ) { fprintf(stderr,"Failed to read sequence length in BAM header.\n"); free(chrname); return BamBam_BamFileHeader_Delete(header); } chr = BamBam_Chromosome_New(chrname,chrlen); free(chrname); if ( !chr ) { fprintf(stderr,"Failed to allocate memory for sequence meta data in BAM header.\n"); return BamBam_BamFileHeader_Delete(header); } node = BamBam_ListNode_New(); if ( ! node ) { fprintf(stderr,"Failed to allocate memory for sequence meta data in BAM header.\n"); BamBam_Chromosome_Delete(chr); return BamBam_BamFileHeader_Delete(header); } node->entry = chr; node->bamBamListFreeFunction = chromosomeDelete; BamBam_ListNode_PushBack(header->chromosomes,node); header->chromosomevec[i] = chr; header->sortedchromosomevec[i] = chr; } qsort(header->sortedchromosomevec, header->n_ref, sizeof(BamBam_Chromosome *),chromosomeNameComparison); /* check binary search */ for ( i = 0; i < (unsigned int)(header->n_ref); ++i ) { int r = -1; #if 0 fprintf(stderr,"%s\t%llu\n", header->sortedchromosomevec[i]->name, (unsigned long long)header->sortedchromosomevec[i]->length); #endif r = findChromosomeByName((BamBam_Chromosome const **)header->sortedchromosomevec,header->n_ref,header->sortedchromosomevec[i]->name); assert ( r == (int)i ); /* fprintf(stderr,"%d == %d\n", r, i); */ } header = parseHeaderText(header); if ( ! header ) return BamBam_BamFileHeader_Delete(header); htextbuf = BamBam_CharBuffer_New(); if ( ! htextbuf ) return BamBam_BamFileHeader_Delete(header); if ( header->hdline ) { int r = 0; BamBam_CharBuffer * buffer = htextbuf; BamBam_CharBuffer_PushString(buffer,header->hdline,r); if ( r < 0 ) { BamBam_CharBuffer_Delete(htextbuf); return BamBam_BamFileHeader_Delete(header); } BamBam_CharBuffer_PushString(buffer,"\n",r); if ( r < 0 ) { BamBam_CharBuffer_Delete(htextbuf); return BamBam_BamFileHeader_Delete(header); } } else { int r = 0; BamBam_CharBuffer * buffer = htextbuf; BamBam_CharBuffer_PushString(buffer,"@HD\tVN:",r); if ( r < 0 ) { BamBam_CharBuffer_Delete(htextbuf); return BamBam_BamFileHeader_Delete(header); } BamBam_CharBuffer_PushString(buffer,header->version,r); if ( r < 0 ) { BamBam_CharBuffer_Delete(htextbuf); return BamBam_BamFileHeader_Delete(header); } BamBam_CharBuffer_PushString(buffer,"\tSO:",r); if ( r < 0 ) { BamBam_CharBuffer_Delete(htextbuf); return BamBam_BamFileHeader_Delete(header); } BamBam_CharBuffer_PushString(buffer,header->sortorder,r); if ( r < 0 ) { BamBam_CharBuffer_Delete(htextbuf); return BamBam_BamFileHeader_Delete(header); } BamBam_CharBuffer_PushString(buffer,"\n",r); if ( r < 0 ) { BamBam_CharBuffer_Delete(htextbuf); return BamBam_BamFileHeader_Delete(header); } } #if 0 for ( i = 0; i < (unsigned int)(header->n_ref); ++i ) { BamBam_Chromosome const * chr = header->chromosomevec[i]; int r = 0; BamBam_CharBuffer * buffer = htextbuf; BamBam_CharBuffer_PushString(buffer,"@SQ\tSN:",r); if ( r < 0 ) { BamBam_CharBuffer_Delete(htextbuf); return BamBam_BamFileHeader_Delete(header); } BamBam_CharBuffer_PushString(buffer,chr->name,r); if ( r < 0 ) { BamBam_CharBuffer_Delete(htextbuf); return BamBam_BamFileHeader_Delete(header); } BamBam_CharBuffer_PushString(buffer,"\tLN:",r); if ( r < 0 ) { BamBam_CharBuffer_Delete(htextbuf); return BamBam_BamFileHeader_Delete(header); } BamBam_CharBuffer_PushNumber(buffer,chr->length,r); if ( r < 0 ) { BamBam_CharBuffer_Delete(htextbuf); return BamBam_BamFileHeader_Delete(header); } BamBam_CharBuffer_PushString(buffer,"\n",r); if ( r < 0 ) { BamBam_CharBuffer_Delete(htextbuf); return BamBam_BamFileHeader_Delete(header); } } #endif /* copy rest of the lines without SQ and HD lines */ for ( hc = header->headerlines; *hc; ++hc ) { /* fprintf(stderr, "Checking %s\n", *hc); */ if ( strlen(*hc) >= 4 && strncmp("@HD\t",*hc,4) && strncmp("@SQ\t",*hc,4) ) { int r = 0; BamBam_CharBuffer * buffer = htextbuf; BamBam_CharBuffer_PushString(buffer,*hc,r); if ( r < 0 ) { BamBam_CharBuffer_Delete(htextbuf); return BamBam_BamFileHeader_Delete(header); } BamBam_CharBuffer_PushString(buffer,"\n",r); if ( r < 0 ) { BamBam_CharBuffer_Delete(htextbuf); return BamBam_BamFileHeader_Delete(header); } } else if ( strlen(*hc) >= 4 && strncmp("@SQ\t",*hc,4) == 0 ) { char const * line = *hc; /* fprintf(stderr,"Here: %s\n", line); */ while ( *line ) { char const * field = line; char const * fielde = field; while ( (*fielde) && (*fielde != '\t') ) ++fielde; /* fprintf(stderr, "field length %d\n", (fielde-field)); */ if ( fielde-field >= 3 && field[0] == 'S' && field[1] == 'N' && field[2] == ':' ) { char const * name = field + 3; char const * namee = fielde; char * cname = (char *)malloc(namee-name+1); int r = -1, q = 0; BamBam_CharBuffer * buffer = htextbuf; if ( ! cname ) { BamBam_CharBuffer_Delete(htextbuf); return BamBam_BamFileHeader_Delete(header); } memcpy(cname,name,namee-name); cname[namee-name] = 0; r = findChromosomeByName((BamBam_Chromosome const **)header->sortedchromosomevec,header->n_ref,cname); if ( r < 0 ) { fprintf(stderr,"Chromosome %s in text index is not in binary header\n",cname); free(cname); BamBam_CharBuffer_Delete(htextbuf); return BamBam_BamFileHeader_Delete(header); } assert ( strcmp(header->sortedchromosomevec[r]->name,cname) == 0 ); free(cname); cname = 0; header->sortedchromosomevec[r]->headerline = BamBam_StrDup(*hc); if ( ! header->sortedchromosomevec[r]->headerline ) { fprintf(stderr,"Unable to allocate space for header line\n"); BamBam_CharBuffer_Delete(htextbuf); return BamBam_BamFileHeader_Delete(header); } BamBam_CharBuffer_PushString(buffer,*hc,q); if ( q < 0 ) { BamBam_CharBuffer_Delete(htextbuf); return BamBam_BamFileHeader_Delete(header); } BamBam_CharBuffer_PushString(buffer,"\n",q); if ( q < 0 ) { BamBam_CharBuffer_Delete(htextbuf); return BamBam_BamFileHeader_Delete(header); } } line = fielde; if ( *line ) { assert ( *line == '\t' ); ++line; } } } } for ( i = 0; i < (unsigned int)(header->n_ref); ++i ) if ( ! header->chromosomevec[i]->headerline ) { /* fprintf(stderr,"Sequence %s is in binary header but not in text\n", header->chromosomevec[i]->name); */ BamBam_Chromosome const * chr = header->chromosomevec[i]; int r = 0; BamBam_CharBuffer * buffer = htextbuf; BamBam_CharBuffer_PushString(buffer,"@SQ\tSN:",r); if ( r < 0 ) { BamBam_CharBuffer_Delete(htextbuf); return BamBam_BamFileHeader_Delete(header); } BamBam_CharBuffer_PushString(buffer,chr->name,r); if ( r < 0 ) { BamBam_CharBuffer_Delete(htextbuf); return BamBam_BamFileHeader_Delete(header); } BamBam_CharBuffer_PushString(buffer,"\tLN:",r); if ( r < 0 ) { BamBam_CharBuffer_Delete(htextbuf); return BamBam_BamFileHeader_Delete(header); } BamBam_CharBuffer_PushNumber(buffer,chr->length,r); if ( r < 0 ) { BamBam_CharBuffer_Delete(htextbuf); return BamBam_BamFileHeader_Delete(header); } BamBam_CharBuffer_PushString(buffer,"\n",r); if ( r < 0 ) { BamBam_CharBuffer_Delete(htextbuf); return BamBam_BamFileHeader_Delete(header); } } /* push terminator symbol */ if ( BamBam_CharBuffer_PushChar(htextbuf,0) < 0 ) { BamBam_CharBuffer_Delete(htextbuf); return BamBam_BamFileHeader_Delete(header); } header->headertext = BamBam_StrDup((char const *)(htextbuf->buffer)); if ( ! header->headertext ) { BamBam_CharBuffer_Delete(htextbuf); return BamBam_BamFileHeader_Delete(header); } BamBam_CharBuffer_Delete(htextbuf); /* fprintf(stderr,"%s",header->headertext); */ return header; } bambamc-bambamc_0_0_50/src/bambamc/BamBam_BamFileHeader.h000066400000000000000000000041421233012646600231170ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAM_BAMFILEHEADER_H) #define BAMBAM_BAMFILEHEADER_H #include #include #include #include typedef struct _BamBam_BamFileHeader { /* length of orignal text */ int32_t l_text; /* original text */ char * text; /* number of chromosomes/references */ int32_t n_ref; /* linked list of chromosomes */ BamBam_List * chromosomes; /* chromosomes in numerical id order */ BamBam_Chromosome ** chromosomevec; /* chromosomes in name sorted order */ BamBam_Chromosome ** sortedchromosomevec; /* single header lines */ char ** headerlines; /* HD header line */ char const * hdline; /* sort order (coordinate or queryname) */ char * sortorder; /* bam file version */ char * version; /* processed header text */ char * headertext; } BamBam_BamFileHeader; extern BamBam_BamFileHeader * BamBam_BamFileHeader_New_SAM(FILE * reader); extern BamBam_BamFileHeader * BamBam_BamFileHeader_New_BAM(BamBam_GzipReader * reader); extern BamBam_BamFileHeader * BamBam_BamFileHeader_Delete(BamBam_BamFileHeader * object); extern BamBam_Chromosome const * BamBam_BamFileHeader_FindChromosomeByName(BamBam_BamFileHeader const * header, char const * name); extern int BamBam_BamFileHeader_FindChromosomeIdByName(BamBam_BamFileHeader const * header, char const * name); #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_BamFlagBase.h000066400000000000000000000026061233012646600225760ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAM_BAMFLAGS) #define BAMBAM_BAMFLAGS enum bam_flags { BAMBAMC_FPAIRED = (1u << 0), BAMBAMC_FPROPER_PAIR = (1u << 1), BAMBAMC_FUNMAP = (1u << 2), BAMBAMC_FMUNMAP = (1u << 3), BAMBAMC_FREVERSE = (1u << 4), BAMBAMC_FMREVERSE = (1u << 5), BAMBAMC_FREAD1 = (1u << 6), BAMBAMC_FREAD2 = (1u << 7), BAMBAMC_FSECONDARY = (1u << 8), BAMBAMC_FQCFAIL = (1u << 9), BAMBAMC_FDUP = (1u << 10) }; enum bambam_cigar_operators { BAMBAMC_CMATCH = 0, BAMBAMC_CINS = 1, BAMBAMC_CDEL = 2, BAMBAMC_CREF_SKIP = 3, BAMBAMC_CSOFT_CLIP = 4, BAMBAMC_CHARD_CLIP = 5, BAMBAMC_CPAD = 6, BAMBAMC_CEQUAL = 7, BAMBAMC_CDIFF = 8 }; #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_BamHeaderInfo.c000066400000000000000000000117001233012646600231240ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include #include #include #include int BamBam_BamHeaderInfo_ProduceHeaderText(BamBam_BamHeaderInfo * info) { int ret = 0; BamBam_ListNode * node = 0; BamBam_CharBuffer * buffer = info->cb; BamBam_CharBuffer_Reset(buffer); BamBam_CharBuffer_PushString(buffer,"@HD\tVN:",ret); if ( ret < 0 ) return -1; BamBam_CharBuffer_PushString(buffer,info->version,ret); if ( ret < 0 ) return -1; BamBam_CharBuffer_PushString(buffer,"\tSO:",ret); if ( ret < 0 ) return -1; BamBam_CharBuffer_PushString(buffer,info->sortorder,ret); if ( ret < 0 ) return -1; BamBam_CharBuffer_PushString(buffer,"\n",ret); if ( ret < 0 ) return -1; node = info->chrlist->first; while ( ret >= 0 && node ) { BamBam_Chromosome const * chr = (BamBam_Chromosome const *)(node->entry); BamBam_CharBuffer_PushString(buffer,"@SQ\tSN:",ret); if ( ret < 0 ) return -1; BamBam_CharBuffer_PushString(buffer,chr->name,ret); if ( ret < 0 ) return -1; BamBam_CharBuffer_PushString(buffer,"\tLN:",ret); if ( ret < 0 ) return -1; BamBam_CharBuffer_PushNumber(buffer,chr->length,ret); if ( ret < 0 ) return -1; BamBam_CharBuffer_PushString(buffer,"\n",ret); if ( ret < 0 ) return -1; node = node->next; } if ( info->plaintext ) BamBam_CharBuffer_PushString(buffer,info->plaintext,ret); if ( ret < 0 ) return -1; return ret; } BamBam_BamHeaderInfo * BamBam_BamHeaderInfo_Delete(BamBam_BamHeaderInfo * info) { if ( info ) { free(info->plaintext); free(info->version); free(info->sortorder); BamBam_List_Delete(info->chrlist); BamBam_CharBuffer_Delete(info->cb); free(info); } return 0; } BamBam_BamHeaderInfo * BamBam_BamHeaderInfo_New(char const * version, char const * sortorder, char const * plaintext) { BamBam_BamHeaderInfo * info = 0; info = (BamBam_BamHeaderInfo *)malloc(sizeof(BamBam_BamHeaderInfo)); if ( ! info ) return BamBam_BamHeaderInfo_Delete(info); memset(info,0,sizeof(BamBam_BamHeaderInfo)); info->sortorder = BamBam_StrDup(sortorder); if ( ! info->sortorder ) return BamBam_BamHeaderInfo_Delete(info); info->version = BamBam_StrDup(version); if ( ! info->version ) return BamBam_BamHeaderInfo_Delete(info); if ( plaintext ) { info->plaintext = BamBam_StrDup(plaintext); if ( ! info->plaintext ) return BamBam_BamHeaderInfo_Delete(info); } else { info->plaintext = 0; } info->cb = BamBam_CharBuffer_New(); if ( ! info->cb ) return BamBam_BamHeaderInfo_Delete(info); info->chrlist = BamBam_List_New(); if ( ! info->chrlist ) return BamBam_BamHeaderInfo_Delete(info); return info; } static void BamBam_Chromosome_NodeDelete(void * node) { if ( node ) { BamBam_Chromosome_Delete((BamBam_Chromosome *)node); } } int BamBam_BamHeaderInfo_AddChromosome(BamBam_BamHeaderInfo * info, char const * name, uint64_t len) { BamBam_Chromosome * chr = BamBam_Chromosome_New(name,len); if ( ! chr ) return -1; BamBam_ListNode * node = BamBam_ListNode_New(); if ( ! node ) { BamBam_Chromosome_Delete(chr); return -1; } node->entry = chr; node->bamBamListFreeFunction = BamBam_Chromosome_NodeDelete; node->bamBamListPrintFunction = 0; BamBam_ListNode_PushBack(info->chrlist,node); return 0; } int BamBam_BamHeaderInfo_WriteBamHeader(BamBam_BamHeaderInfo * info, BamBam_BgzfCompressor * writer) { static char const magic[4] = { 'B', 'A', 'M', 1 }; int32_t numseq = BamBam_List_Size(info->chrlist); BamBam_ListNode const * node = 0; if ( BamBam_BamHeaderInfo_ProduceHeaderText(info) < 0 ) return -1; if ( BamBam_BgzfCompressor_Write(writer,(uint8_t const *)&magic[0],4) < 0 ) return -1; if ( BamBam_BgzfCompressor_PutInt32(writer,info->cb->bufferfill) < 0 ) return -1; if ( BamBam_BgzfCompressor_Write(writer,info->cb->buffer,info->cb->bufferfill) < 0 ) return -1; if ( BamBam_BgzfCompressor_PutInt32(writer,numseq) < 0 ) return -1; for ( node = info->chrlist->first; node; node = node->next ) { BamBam_Chromosome const * chr = (BamBam_Chromosome *)node->entry; assert ( chr ); if ( BamBam_BgzfCompressor_PutLenStringZ(writer,chr->name) < 0 ) return -1; if ( BamBam_BgzfCompressor_PutInt32(writer,chr->length) < 0 ) return -1; } return 0; } bambamc-bambamc_0_0_50/src/bambamc/BamBam_BamHeaderInfo.h000066400000000000000000000034021233012646600231310ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAM_BAMHEADERINFO_H) #define BAMBAM_BAMHEADERINFO_H #include #include #include #include typedef struct _BamBam_BamHeaderInfo { char * version; char * sortorder; char * plaintext; BamBam_List * chrlist; BamBam_CharBuffer * cb; } BamBam_BamHeaderInfo; extern int BamBam_BamHeaderInfo_ProduceHeaderText(BamBam_BamHeaderInfo * info) BAMBAM_WARN_IF_UNUSEDRESULT; extern BamBam_BamHeaderInfo * BamBam_BamHeaderInfo_Delete(BamBam_BamHeaderInfo * info); extern BamBam_BamHeaderInfo * BamBam_BamHeaderInfo_New(char const * version, char const * sortorder, char const * plaintext) BAMBAM_WARN_IF_UNUSEDRESULT; extern int BamBam_BamHeaderInfo_AddChromosome(BamBam_BamHeaderInfo * info, char const * name, uint64_t len) BAMBAM_WARN_IF_UNUSEDRESULT; extern int BamBam_BamHeaderInfo_WriteBamHeader(BamBam_BamHeaderInfo * info, BamBam_BgzfCompressor * writer) BAMBAM_WARN_IF_UNUSEDRESULT; #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_BamSingleAlignment.c000066400000000000000000001003721233012646600242040ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include #include #include #include #if defined(_linux) #include #endif #include static uint32_t getNumLength(uint32_t num, uint32_t const base) { uint32_t len; if ( ! num ) return 1; len = 0; while ( num ) { len++; num /= base; } return len; } static int32_t decodeInt(uint8_t const * D, unsigned int length) { int32_t v = 0; unsigned int i; for ( i = 0; i < length; ++i ) v |= ((*(D++)) << (i*8)); return v; } static uint32_t decodeUInt(uint8_t const * D, unsigned int length) { uint32_t v = 0; unsigned int i; for ( i = 0; i < length; ++i ) v |= ((*(D++)) << (i*8)); return v; } static uint64_t getPrimLengthByType(uint8_t const c) { switch ( c ) { case 'A': case 'c': case 'C': return sizeof(int8_t); case 's': case 'S': return sizeof(int16_t); case 'i': case 'I': return sizeof(int32_t); case 'f': return sizeof(float); default: return 0; } } static int64_t getAuxLength(uint8_t const * D) { switch ( D[2] ) { case 'A': case 'c': case 'C': case 's': case 'S': case 'i': case 'I': case 'f': return 2+1+getPrimLengthByType(D[2]); case 'H': { uint64_t len = 2+1; D += len; while ( *D ) len++, D++; len++; return len; } case 'B': { uint8_t const eltype = D[3]; uint32_t const numel = decodeUInt(D+4,4); return 2/*tag*/+1/*B*/+1/*type*/+4/* array length */+numel*getPrimLengthByType(eltype); } default: { return -1; } } } union numberpun { float fvalue; uint32_t uvalue; }; static int auxValueToString(uint8_t const * D, BamBam_CharBuffer * buffer) { int r = 0; switch ( D[2] ) { case 'A': { r = BamBam_CharBuffer_PushChar(buffer,D[3]); break; } case 'c': { int8_t const v = ((int8_t const *)(D+3))[0]; if ( r >= 0 && v < 0 ) BamBam_CharBuffer_PushCharQuick(buffer,'-',r); if ( r >= 0 ) BamBam_CharBuffer_PushNumber(buffer,(v>=0)?v:-v,r); break; } case 'C': { uint8_t const v = (D+3)[0]; if ( r >= 0 ) BamBam_CharBuffer_PushNumber(buffer,v,r); break; } case 's': { int16_t const v = decodeInt(D+3,2); if ( r >= 0 && v < 0 ) BamBam_CharBuffer_PushCharQuick(buffer,'-',r); if ( r >= 0 ) BamBam_CharBuffer_PushNumber(buffer,(v>=0)?v:-v,r); break; } case 'S': { uint16_t const v = decodeUInt(D+3,2); if ( r >= 0 ) BamBam_CharBuffer_PushNumber(buffer,v,r); break; } case 'i': { int32_t const v = decodeInt(D+3,4); if ( r >= 0 && v < 0 ) BamBam_CharBuffer_PushCharQuick(buffer,'-',r); if ( r >= 0 ) BamBam_CharBuffer_PushNumber(buffer,(v>=0)?v:-v,r); break; } case 'I': { uint32_t const v = decodeUInt(D+3,4); if ( r >= 0 ) BamBam_CharBuffer_PushNumber(buffer,v,r); break; } case 'f': { static size_t const tmpsize = 32; uint32_t const u = decodeUInt(D+3,4); float v; char * tmpmem = 0; union numberpun np; np.uvalue = u; v = np.fvalue; tmpmem = (char *)alloca(tmpsize); memset(tmpmem,0,tmpsize); snprintf(tmpmem,tmpsize-1,"%f",v); BamBam_CharBuffer_PushString(buffer,tmpmem,r); break; } case 'H': { uint8_t const * p = D+3; while ( *p && (r >= 0) ) BamBam_CharBuffer_PushCharQuick(buffer,*(p++),r); break; } case 'Z': { uint8_t const * p = D+3; while ( *p && (r >= 0) ) BamBam_CharBuffer_PushCharQuick(buffer,*(p++),r); break; } case 'B': { uint8_t const type = D[3]; uint32_t const len = decodeUInt(D+4,4); uint8_t const * p = D+8; uint64_t i; if ( r >= 0 ) BamBam_CharBuffer_PushCharQuick(buffer,type,r); for ( i = 0; (r >= 0) && i < len; ++i ) { if ( r >= 0 ) BamBam_CharBuffer_PushCharQuick(buffer,',',r); switch ( type ) { case 'A': { r = BamBam_CharBuffer_PushChar(buffer,*p); p += 1; break; } case 'c': { int8_t const v = ((int8_t const *)p)[0]; if ( r >= 0 && v < 0 ) BamBam_CharBuffer_PushCharQuick(buffer,'-',r); if ( r >= 0 ) BamBam_CharBuffer_PushNumber(buffer,(v>=0)?v:-v,r); p += 1; break; } case 'C': { uint8_t const v = p[0]; if ( r >= 0 ) BamBam_CharBuffer_PushNumber(buffer,v,r); p += 1; break; } case 's': { int16_t const v = decodeInt(p,2); if ( r >= 0 && v < 0 ) BamBam_CharBuffer_PushCharQuick(buffer,'-',r); if ( r >= 0 ) BamBam_CharBuffer_PushNumber(buffer,(v>=0)?v:-v,r); p += 2; break; } case 'S': { uint16_t const v = decodeUInt(p,2); if ( r >= 0 ) BamBam_CharBuffer_PushNumber(buffer,v,r); p += 2; break; } case 'i': { int32_t const v = decodeInt(p,4); if ( r >= 0 && v < 0 ) BamBam_CharBuffer_PushCharQuick(buffer,'-',r); if ( r >= 0 ) BamBam_CharBuffer_PushNumber(buffer,(v>=0)?v:-v,r); p += 4; break; } case 'I': { uint32_t const v = decodeUInt(p,4); if ( r >= 0 ) BamBam_CharBuffer_PushNumber(buffer,v,r); p += 4; break; } case 'f': { static size_t const tmpsize = 32; uint32_t const u = decodeUInt(p,4); float v; char * tmpmem = 0; union numberpun np; np.uvalue = u; v = np.fvalue; tmpmem = (char *)alloca(tmpsize); memset(tmpmem,0,tmpsize); snprintf(tmpmem,tmpsize-1,"%f",v); BamBam_CharBuffer_PushString(buffer,tmpmem,r); p += 4; break; } case 'Z': { while ( *p && (r >= 0) ) BamBam_CharBuffer_PushCharQuick(buffer,*(p++),r); if ( r >= 0 ) { assert ( ! *p ); } p += 1; break; } } } break; } /* unknown data type */ default: { r = -1; } } return r; } static int auxToString(uint8_t const * D, BamBam_CharBuffer * buffer) { int r = 0; if ( r >= 0 ) BamBam_CharBuffer_PushCharQuick(buffer,D[0],r); if ( r >= 0 ) BamBam_CharBuffer_PushCharQuick(buffer,D[1],r); if ( r >= 0 ) BamBam_CharBuffer_PushCharQuick(buffer,':',r); if ( r >= 0 ) BamBam_CharBuffer_PushCharQuick(buffer,D[2],r); if ( r >= 0 ) BamBam_CharBuffer_PushCharQuick(buffer,':',r); if ( r >= 0 ) r = auxValueToString(D,buffer); return r; } int BamBam_BamSingleAlignment_DecodeAuxSingle( BamBam_BamSingleAlignment * algn, uint8_t const * p, int reset) { int r = 0; if ( reset ) BamBam_CharBuffer_Reset(algn->auxbuffer); if ( r >= 0 ) r = auxToString(p,algn->auxbuffer); return r; } char const * BamBam_BamSingleAlignment_DecodeAux(BamBam_BamSingleAlignment * algn) { int r = 0; int first = 1; uint8_t const * data = BamBam_BamSingleAlignment_GetEncodedAux(algn); uint8_t const * datae = algn->data + algn->dataused; BamBam_CharBuffer_Reset(algn->auxbuffer); while ( r >= 0 && data < datae && *data ) { if ( first ) { first = 0; } else { if ( r >= 0 ) r = BamBam_CharBuffer_PushChar(algn->auxbuffer,'\t'); } if ( r >= 0 ) r = BamBam_BamSingleAlignment_DecodeAuxSingle(algn,data,0); data += getAuxLength(data); } if ( r >= 0 ) { r = BamBam_CharBuffer_PushChar(algn->auxbuffer,0); algn->auxbuffer->bufferfill -= 1; } if ( r >= 0 ) return (char const *)algn->auxbuffer->buffer; else return 0; } uint8_t const * BamBam_BamSingleAlignment_FindAux(BamBam_BamSingleAlignment const * algn, char const tag[2]) { uint8_t const * data = BamBam_BamSingleAlignment_GetEncodedAux(algn); uint8_t const * datae = algn->data + algn->dataused; while ( data < datae && *data ) { if ( data[0] == tag[0] && data[1] == tag[1] ) return data; data += getAuxLength(data); } return 0; } uint64_t BamBam_BamSingleAlignment_GetAuxLength(BamBam_BamSingleAlignment const * algn) { uint8_t const * dataa = BamBam_BamSingleAlignment_GetEncodedAux(algn); uint8_t const * data = dataa; uint8_t const * datae = algn->data + algn->dataused; while ( data < datae && *data ) data += getAuxLength(data); return data-dataa; } static uint32_t getCigarStringLength(uint8_t const * D, uint32_t ncigar) { uint32_t length = 0; uint32_t i; #if 0 static char const * opc = "MIDNSHP=X???????"; #endif for ( i = 0; i < ncigar; ++i, D+=4 ) { uint32_t const oppair = decodeUInt(D,4); uint32_t const len = (oppair>>4)&((1ul <<28)-1); #if 0 uint32_t const op = oppair & 0xF; uint8_t const c = op[opc]; #endif length += (1+getNumLength(len,10)); } return length; } int32_t BamBam_BamSingleAlignment_GetRefId(BamBam_BamSingleAlignment const * data) { return decodeInt(data->data + 0, 4); } int32_t BamBam_BamSingleAlignment_GetPos(BamBam_BamSingleAlignment const * data) { return decodeInt(data->data + 4, 4); } uint32_t BamBam_BamSingleAlignment_GetBinMQNL(BamBam_BamSingleAlignment const * data) { return decodeUInt(data->data + 8, 4); } uint32_t BamBam_BamSingleAlignment_GetBin(BamBam_BamSingleAlignment const * data) { return (BamBam_BamSingleAlignment_GetBinMQNL(data) >> 16) & 0xFFFFU; } uint32_t BamBam_BamSingleAlignment_GetMQ(BamBam_BamSingleAlignment const * data) { return (BamBam_BamSingleAlignment_GetBinMQNL(data) >> 8) & 0xFFU; } uint32_t BamBam_BamSingleAlignment_GetNL(BamBam_BamSingleAlignment const * data) { return (BamBam_BamSingleAlignment_GetBinMQNL(data) >> 0) & 0xFFU; } uint32_t BamBam_BamSingleAlignment_GetFlagNC(BamBam_BamSingleAlignment const * data) { return decodeUInt(data->data + 12, 4); } uint32_t BamBam_BamSingleAlignment_GetFlags(BamBam_BamSingleAlignment const * data) { return (BamBam_BamSingleAlignment_GetFlagNC(data)>>16)&0xFFFFUL; } uint32_t BamBam_BamSingleAlignment_GetNC(BamBam_BamSingleAlignment const * data) { return (BamBam_BamSingleAlignment_GetFlagNC(data)>>0)&0xFFFFUL; } int32_t BamBam_BamSingleAlignment_GetLSeq(BamBam_BamSingleAlignment const * data) { return decodeInt(data->data + 16, 4); } int32_t BamBam_BamSingleAlignment_GetNextRefID(BamBam_BamSingleAlignment const * data) { return decodeInt(data->data + 20, 4); } int32_t BamBam_BamSingleAlignment_GetNextPos(BamBam_BamSingleAlignment const * data) { return decodeInt(data->data + 24, 4); } int32_t BamBam_BamSingleAlignment_GetTLen(BamBam_BamSingleAlignment const * data) { return decodeInt(data->data + 28, 4); } char const * BamBam_BamSingleAlignment_GetReadName(BamBam_BamSingleAlignment const * data) { return (char const *)(data->data + 32); } uint8_t const * BamBam_BamSingleAlignment_GetEncodedCigar(BamBam_BamSingleAlignment const * data) { return ((uint8_t const *)BamBam_BamSingleAlignment_GetReadName(data)) + BamBam_BamSingleAlignment_GetNL(data); } uint8_t const * BamBam_BamSingleAlignment_GetEncodedQuery(BamBam_BamSingleAlignment const * data) { return BamBam_BamSingleAlignment_GetEncodedCigar(data) + 4 * BamBam_BamSingleAlignment_GetNC(data); } uint8_t const * BamBam_BamSingleAlignment_GetEncodedQual(BamBam_BamSingleAlignment const * data) { return BamBam_BamSingleAlignment_GetEncodedQuery(data) + (BamBam_BamSingleAlignment_GetLSeq(data)+1)/2; } uint8_t const * BamBam_BamSingleAlignment_GetEncodedAux(BamBam_BamSingleAlignment const * data) { return BamBam_BamSingleAlignment_GetEncodedQual(data) + (BamBam_BamSingleAlignment_GetLSeq(data)); } int BamBam_BamSingleAlignment_DecodeQueryRc(BamBam_BamSingleAlignment * algn, int const rc) { /* length of query */ int32_t lseq = BamBam_BamSingleAlignment_GetLSeq(algn); int32_t i; static char const * mapping = "=ACMGRSVTWYHKDBN"; static char const * rmapping = "=TGKCYSBAWRDMHVN"; /* * reverse complements for ambiguity codes: * M={A,C} -> K={G,T} * R={A,G} -> Y={C,T} * S={C,G} -> S={C,G} * V={A,C,G} -> B={C,G,T} * W={A,T} -> W={A,T} * Y={C,T} -> R={A,G} * H={A,C,T} -> D={A,G,T} * K={G,T} -> M={A,C} * D={A,G,T} -> H={A,C,T} * B={C,G,T} -> V={A,C,G} */ if ( lseq > algn->queryspace ) { free(algn->query); algn->query = 0; algn->query = (char *)malloc(lseq+1); if ( ! algn->query ) return -1; algn->queryspace = lseq; } algn->query[lseq] = 0; if ( ! rc ) { char * out = algn->query; uint8_t const * in = BamBam_BamSingleAlignment_GetEncodedQuery(algn); for ( i = 0; i < lseq/2; ++i, ++in ) { *(out++) = mapping[(int)((*in) >> 4) & 0xF]; *(out++) = mapping[(int)((*in) >> 0) & 0xF]; } if ( lseq & 1 ) *(out++) = mapping[(int)((*in) >> 4) & 0xF]; } else { char * out = algn->query + lseq; uint8_t const * in = BamBam_BamSingleAlignment_GetEncodedQuery(algn); for ( i = 0; i < lseq/2; ++i, ++in ) { *(--out) = rmapping[(int)((*in) >> 4) & 0xF]; *(--out) = rmapping[(int)((*in) >> 0) & 0xF]; } if ( lseq & 1 ) *(--out) = rmapping[(int)((*in) >> 4) & 0xF]; } return lseq; } int BamBam_BamSingleAlignment_DecodeQuery(BamBam_BamSingleAlignment * algn) { int const rc = (BamBam_BamSingleAlignment_GetFlags(algn) & BAMBAMC_FREVERSE) != 0; return BamBam_BamSingleAlignment_DecodeQueryRc(algn,rc); } int BamBam_BamSingleAlignment_DecodeQualRc(BamBam_BamSingleAlignment * algn, int const rc) { int32_t lseq = BamBam_BamSingleAlignment_GetLSeq(algn); int32_t i; if ( lseq > algn->qualspace ) { free(algn->qual); algn->qual = 0; algn->qual = (char *)malloc(lseq+1); if ( ! algn->qual ) return -1; algn->qualspace = lseq; } algn->qual[lseq] = 0; if ( ! rc ) { char * out = algn->qual; uint8_t const * in = BamBam_BamSingleAlignment_GetEncodedQual(algn); for ( i = 0; i < lseq; ++i ) *(out++) = *(in++)+33; } else { char * out = algn->qual + lseq; uint8_t const * in = BamBam_BamSingleAlignment_GetEncodedQual(algn); for ( i = 0; i < lseq; ++i ) *(--out) = (*(in++))+33; } return lseq; } int BamBam_BamSingleAlignment_DecodeQual(BamBam_BamSingleAlignment * algn) { int const rc = (BamBam_BamSingleAlignment_GetFlags(algn) & BAMBAMC_FREVERSE) != 0; return BamBam_BamSingleAlignment_DecodeQualRc(algn,rc); } int BamBam_BamSingleAlignment_DecodeCigarRc(BamBam_BamSingleAlignment * algn, int const rc) { uint8_t const * ecigar = BamBam_BamSingleAlignment_GetEncodedCigar(algn); uint32_t const ncigar = BamBam_BamSingleAlignment_GetNC(algn); int32_t const cigstrlen = getCigarStringLength(ecigar,ncigar); uint32_t i; static char const * opc = "MIDNSHP=X???????"; char * out = 0; if ( cigstrlen > algn->cigarspace ) { free(algn->cigar); algn->cigar = 0; algn->cigar = (char *)malloc(cigstrlen+1); if ( ! algn->cigar ) return -1; algn->cigarspace = cigstrlen; } algn->cigar[cigstrlen] = 0; out = algn->cigar; if ( ! rc ) for ( i = 0; i < ncigar; ++i, ecigar += 4 ) { uint32_t const oppair = decodeUInt(ecigar,4); uint32_t len = (oppair>>4)&((1ul <<28)-1); uint32_t const op = oppair & 0xF; uint8_t const c = op[opc]; if ( !len ) (*(out++)) = '0'; else { uint32_t const numlen = getNumLength(len,10); char * pout = out + numlen; uint32_t j; for ( j = 0; j < numlen; ++j ) { *(--pout) = '0'+(len%10); len /= 10; } out += numlen; } *(out++) = c; } else { ecigar += 4*ncigar; for ( i = 0; i < ncigar; ++i ) { ecigar -= 4; uint32_t const oppair = decodeUInt(ecigar,4); uint32_t len = (oppair>>4)&((1ul <<28)-1); uint32_t const op = oppair & 0xF; uint8_t const c = op[opc]; if ( !len ) (*(out++)) = '0'; else { uint32_t const numlen = getNumLength(len,10); char * pout = out + numlen; uint32_t j; for ( j = 0; j < numlen; ++j ) { *(--pout) = '0'+(len%10); len /= 10; } out += numlen; } *(out++) = c; } } return cigstrlen; } int BamBam_BamSingleAlignment_DecodeCigar(BamBam_BamSingleAlignment * algn) { int const rc = (BamBam_BamSingleAlignment_GetFlags(algn) & BAMBAMC_FREVERSE) != 0; return BamBam_BamSingleAlignment_DecodeCigarRc(algn,rc); } int32_t BamBam_BamSingleAlignment_DecodeQueryQualCigarRc( BamBam_BamSingleAlignment * algn, int rc, int32_t * querylen, int32_t * cigarlen) { int32_t r = 0; if ( r >= 0 ) { r = BamBam_BamSingleAlignment_DecodeQueryRc(algn,rc); *querylen = r; } if ( r >= 0 ) { r = BamBam_BamSingleAlignment_DecodeQualRc(algn,rc); if ( r != *querylen ) r = -1; } if ( r >= 0 ) { r = BamBam_BamSingleAlignment_DecodeCigarRc(algn,rc); *cigarlen = r; } return r; } int32_t BamBam_BamSingleAlignment_DecodeQueryQualCigar( BamBam_BamSingleAlignment * algn, int32_t * querylen, int32_t * cigarlen ) { int const rc = (BamBam_BamSingleAlignment_GetFlags(algn) & BAMBAMC_FREVERSE) != 0; return BamBam_BamSingleAlignment_DecodeQueryQualCigarRc(algn,rc,querylen,cigarlen); } int BamBam_BamSingleAlignment_StoreAlignment(BamBam_BamSingleAlignment const * data, BamBam_GzipWriter * writer) { /* put length of entry */ if ( BamBam_GzipWriter_PutInt32(writer,data->dataused) < 0 ) return -1; /* put entry */ if ( BamBam_GzipWriter_Write(writer,(char const *)(data->data),data->dataused) != (int64_t)(data->dataused) ) return -1; return 0; } int BamBam_BamSingleAlignment_StoreAlignmentBgzf(BamBam_BamSingleAlignment const * data, BamBam_BgzfCompressor * writer) { uint8_t used[4] = { (data->dataused >> 0) & 0xFFu, (data->dataused >> 8) & 0xFFu, (data->dataused >> 16) & 0xFFu, (data->dataused >> 24) & 0xFFu }; if ( BamBam_BgzfCompressor_Write(writer,&used[0],4) < 0 ) return -1; if ( BamBam_BgzfCompressor_Write(writer,data->data,data->dataused) < 0 ) return -1; return 0; } static uint8_t const bambamc_qnameValidTable[256] = { 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1, 0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1, 1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 }; int BamBam_BamSingleAlignment_LoadAlignment(BamBam_BamSingleAlignment * data, BamBam_GzipReader * reader) { int32_t reclen = -1; char const * ca = 0; char const * cc = 0; char const * ce = 0; uint8_t const * ue = 0; uint8_t const * ecigar; uint32_t ncigar; uint32_t i = 0; uint64_t ciglen = 0; int32_t pos = 0; uint64_t lseq = 0; uint8_t const * quala = 0; uint8_t const * qualc = 0; uint8_t const * quale = 0; uint8_t const * auxa = 0; uint8_t const * auxc = 0; uint64_t alen = 0; if ( BamBam_GzipReader_Peek(reader) < 0 ) { /* fprintf(stderr,"EOF.\n"); */ return 0; } /* assume block is valid until it turns out otherwise */ data->valid = bambamc_alignment_validity_ok; /* read length of alignment block */ if ( BamBam_GzipReader_GetInt32(reader,&reclen) < 0 ) return -1; if ( reclen < 32 ) { data->valid = bambamc_alignment_validity_block_too_small; return -1; } /* increase size of memory block if needed */ if ( (int32_t)data->dataav < reclen ) { free(data->data); data->data = (uint8_t *)malloc(reclen); if ( ! data->data ) return -1; data->dataav = reclen; } /* read block */ if ( BamBam_GzipReader_Read(reader,(char*)data->data,reclen) != reclen ) return -1; data->dataused = reclen; if ( reclen < 32 ) { data->valid = bambamc_alignment_validity_block_too_small; return -1; } /* compute length of query name */ ca = BamBam_BamSingleAlignment_GetReadName(data); cc = ca; ce = ((char const *)data->data) + data->dataused; ue = ((uint8_t *)data->data) + data->dataused; while ( cc != ce && *cc ) { if ( ! bambamc_qnameValidTable[*cc] ) { data->valid = bambamc_alignment_validity_queryname_contains_illegal_symbols; return -1; } ++cc; } if ( cc == ce ) { data->valid = bambamc_alignment_validity_queryname_extends_over_block; return -1; } assert ( ! *cc ); if ( (cc-ca)+1 != BamBam_BamSingleAlignment_GetNL(data) ) { data->valid = bambamc_alignment_validity_queryname_length_inconsistent; return -1; } if ( cc == ca ) { data->valid = bambamc_alignment_validity_queryname_empty; return -1; } if ( ue-BamBam_BamSingleAlignment_GetEncodedCigar(data) < BamBam_BamSingleAlignment_GetNC(data)*sizeof(uint32_t) ) { data->valid = bambamc_alignment_validity_cigar_extends_over_block; return -1; } if ( ue-BamBam_BamSingleAlignment_GetEncodedQuery(data) < (BamBam_BamSingleAlignment_GetLSeq(data)+1)/2 ) { data->valid = bambamc_alignment_validity_sequence_extends_over_block; return -1; } if ( ue-BamBam_BamSingleAlignment_GetEncodedQual(data) < BamBam_BamSingleAlignment_GetLSeq(data) ) { data->valid = bambamc_alignment_validity_quality_extends_over_block; return -1; } if ( !(BamBam_BamSingleAlignment_GetFlags(data) & BAMBAMC_FUNMAP) ) { ecigar = BamBam_BamSingleAlignment_GetEncodedCigar(data); ncigar = BamBam_BamSingleAlignment_GetNC(data); for ( i = 0; i < ncigar; ++i ) { uint32_t const oppair = decodeUInt(ecigar + i*sizeof(uint32_t),4); uint32_t len = (oppair>>4)&((1ul <<28)-1); uint32_t const op = oppair & 0xF; if ( op > (uint32_t)BAMBAMC_CDIFF ) { data->valid = bambamc_alignment_validity_unknown_cigar_op; return -1; } switch ( op ) { case BAMBAMC_CMATCH: case BAMBAMC_CINS: case BAMBAMC_CSOFT_CLIP: case BAMBAMC_CEQUAL: case BAMBAMC_CDIFF: ciglen += len; break; } } if ( ciglen != BamBam_BamSingleAlignment_GetLSeq(data) ) { data->valid = bambamc_alignment_validity_cigar_is_inconsistent_with_sequence_length; return -1; } } pos = BamBam_BamSingleAlignment_GetPos(data); if ( pos < -1 || pos > (((1ll<<29)-1)-1) ) { data->valid = bambamc_alignment_validity_invalid_mapping_position; return -1; } pos = BamBam_BamSingleAlignment_GetNextPos(data); if ( pos < -1 || pos > (((1ll<<29)-1)-1) ) { data->valid = bambamc_alignment_validity_invalid_next_mapping_position; return -1; } pos = BamBam_BamSingleAlignment_GetTLen(data); if ( pos < ((-(1ll<<29))+1) || pos > ((1ll<<29)-1) ) { data->valid = bambamc_alignment_validity_invalid_tlen; return -1; } lseq = BamBam_BamSingleAlignment_GetLSeq(data); quala = BamBam_BamSingleAlignment_GetEncodedQual(data); quale = quala + lseq; for ( qualc = quala; qualc != quale; ++qualc ) if ( (int)(*qualc) > (int)('~'-33) ) { if ( *qualc == 255 ) { if ( qualc - quala ) { data->valid = bambamc_alignment_validity_invalid_quality_value; return -1; } while ( qualc != quale ) if ( *(qualc++) != 255 ) { data->valid = bambamc_alignment_validity_invalid_quality_value; return -1; } /* go back by one to leave loop above */ --qualc; } else { data->valid = bambamc_alignment_validity_invalid_quality_value; return -1; } } auxa = BamBam_BamSingleAlignment_GetEncodedAux(data); auxc = auxa; while ( auxc != ue ) { uint64_t lauxlen = 0; if ( (ue-auxc) < 3 ) { data->valid = bambamc_alignment_validity_invalid_auxiliary_data; return -1; } switch ( auxc[2] ) { case 'A': if ( ue-auxc < 3+1 ) { data->valid = bambamc_alignment_validity_invalid_auxiliary_data; return -1; } if ( auxc[3] < '!' || auxc[3] > '~' ) { data->valid = bambamc_alignment_validity_invalid_auxiliary_data; return -1; } lauxlen = 3+1; break; case 'c': case 'C': if ( ue-auxc < 3+1 ) { data->valid = bambamc_alignment_validity_invalid_auxiliary_data; return -1; } lauxlen = 3+1; break; case 's': case 'S': if ( ue-auxc < 3+2 ) { data->valid = bambamc_alignment_validity_invalid_auxiliary_data; return -1; } lauxlen = 3+2; break; case 'i': case 'I': case 'f': if ( ue-auxc < 3+4 ) { data->valid = bambamc_alignment_validity_invalid_auxiliary_data; return -1; } lauxlen = 3+4; break; case 'B': { if ( ue-auxc < 3+1/*data type*/+4/*array length*/ ) { data->valid = bambamc_alignment_validity_invalid_auxiliary_data; return -1; } /* length of array */ alen = decodeUInt(auxc+4,4); /* valid element data types */ switch ( auxc[3] ) { case 'c': case 'C': if ( (ue-auxc) < (3+1+4+ 1*alen) ) { data->valid = bambamc_alignment_validity_invalid_auxiliary_data; return -1; } lauxlen = 3+1+4+ 1*alen; break; case 's': case 'S': if ( (ue-auxc) < (3+1+4+ 2*alen) ) { data->valid = bambamc_alignment_validity_invalid_auxiliary_data; return -1; } lauxlen = 3+1+4+ 2*alen; break; case 'i': case 'I': case 'f': if ( (ue-auxc) < (3+1+4+ 4*alen) ) { data->valid = bambamc_alignment_validity_invalid_auxiliary_data; return -1; } lauxlen = 3+1+4+ 4*alen; break; default: { data->valid = bambamc_alignment_validity_invalid_auxiliary_data; return -1; } } break; } case 'Z': { uint8_t const * p = auxc+3; while ( p != ue && *p ) ++p; /* if terminator byte 0 is not inside block */ if ( p == ue ) { data->valid = bambamc_alignment_validity_invalid_auxiliary_data; return -1; } assert ( ! *p ); lauxlen = (p-auxc)+1; break; } case 'H': { uint8_t const * p = auxc+3; while ( p != ue && *p ) ++p; /* if terminator byte 0 is not inside block */ if ( p == ue ) { data->valid = bambamc_alignment_validity_invalid_auxiliary_data; return -1; } assert ( ! *p ); lauxlen = (p-auxc)+1; break; } default: { data->valid = bambamc_alignment_validity_invalid_auxiliary_data; return -1; } break; } auxc = auxc + lauxlen; } /* typedef enum _bambamc_alignment_validity { bambamc_alignment_validity_invalid_refseq = 15, bambamc_alignment_validity_invalid_next_refseq = 16, } bambamc_alignment_validity; */ return 1; } BamBam_BamSingleAlignment * BamBam_BamSingleAlignment_Delete(BamBam_BamSingleAlignment * data) { if ( data ) { if ( data->auxbuffer ) { BamBam_CharBuffer_Delete(data->auxbuffer); data->auxbuffer = 0; } if ( data->cigar ) { free(data->cigar); data->cigar = 0; data->cigarspace = 0; } if ( data->query ) { free(data->query); data->query = 0; data->queryspace = 0; } if ( data->qual ) { free(data->qual); data->qual = 0; data->qualspace = 0; } if ( data->data ) { free(data->data); data->data = 0; } free(data); } return 0; } BamBam_BamSingleAlignment * BamBam_BamSingleAlignment_New() { BamBam_BamSingleAlignment * data = 0; data = (BamBam_BamSingleAlignment *)malloc(sizeof(BamBam_BamSingleAlignment)); if ( ! data ) return BamBam_BamSingleAlignment_Delete(data); memset(data,0,sizeof(BamBam_BamSingleAlignment)); data->auxbuffer = BamBam_CharBuffer_New(); if ( ! data->auxbuffer ) return BamBam_BamSingleAlignment_Delete(data); return data; } BamBam_BamSingleAlignment * BamBam_BamSingleAlignment_NewClone(uint8_t const * block, uint32_t const blocksize) { BamBam_BamSingleAlignment * data = 0; data = (BamBam_BamSingleAlignment *)malloc(sizeof(BamBam_BamSingleAlignment)); if ( ! data ) return BamBam_BamSingleAlignment_Delete(data); memset(data,0,sizeof(BamBam_BamSingleAlignment)); data->auxbuffer = BamBam_CharBuffer_New(); if ( ! data->auxbuffer ) return BamBam_BamSingleAlignment_Delete(data); if ( blocksize ) { data->data = (uint8_t *)malloc(blocksize); if ( ! data->data ) return BamBam_BamSingleAlignment_Delete(data); memcpy(data->data,block,blocksize); data->dataav = blocksize; data->dataused = blocksize; } return data; } BamBam_BamSingleAlignment * BamBam_BamSingleAlignment_Clone(BamBam_BamSingleAlignment const * o) { BamBam_BamSingleAlignment * data = 0; /* return null if o is null */ if ( ! o ) return 0; /* return null if o claims to have space for alignment data but pointer is null */ if ( (!(o->data)) && o->dataav ) return 0; data = (BamBam_BamSingleAlignment *)malloc(sizeof(BamBam_BamSingleAlignment)); if ( ! data ) return BamBam_BamSingleAlignment_Delete(data); /* erase newly allocated space */ memset(data,0,sizeof(BamBam_BamSingleAlignment)); /* copy alignment data if there is any */ if ( o->data ) { data->dataav = o->dataav; data->dataused = o->dataused; data->data = (uint8_t *)malloc(data->dataav); if ( ! data->data ) return BamBam_BamSingleAlignment_Delete(data); memcpy(data->data,o->data,data->dataav); } if ( o->query ) { data->query = (char *)malloc(o->queryspace); if ( ! data->query ) return BamBam_BamSingleAlignment_Delete(data); memcpy(data->query,o->query,o->queryspace); data->queryspace = o->queryspace; } if ( o->qual ) { data->qual = (char *)malloc(o->qualspace); if ( ! data->qual ) return BamBam_BamSingleAlignment_Delete(data); memcpy(data->qual,o->qual,o->qualspace); data->qualspace = o->qualspace; } if ( o->cigar ) { data->cigar = (char *)malloc(o->cigarspace); if ( ! data->cigar ) return BamBam_BamSingleAlignment_Delete(data); memcpy(data->cigar,o->cigar,o->cigarspace); data->cigarspace = o->cigarspace; } if ( o->auxbuffer ) { data->auxbuffer = BamBam_CharBuffer_Clone(o->auxbuffer); if ( ! data->auxbuffer ) return BamBam_BamSingleAlignment_Delete(data); } return data; } char const * BamBam_Alignment_Validity_Str(bambamc_alignment_validity const code) { switch ( code ) { case bambamc_alignment_validity_ok: return "Alignment valid"; case bambamc_alignment_validity_block_too_small: return "Alignment block is too small to hold fixed size data"; case bambamc_alignment_validity_queryname_extends_over_block: return "Null terminated query name extends beyond block boundary"; case bambamc_alignment_validity_queryname_length_inconsistent: return "Length of null terminated query name is inconsistent with alignment header"; case bambamc_alignment_validity_cigar_extends_over_block: return "Cigar data extends beyond block boundary"; case bambamc_alignment_validity_sequence_extends_over_block: return "Sequence data extends beyond block boundary"; case bambamc_alignment_validity_quality_extends_over_block: return "Quality data extends beyond block boundary"; case bambamc_alignment_validity_cigar_is_inconsistent_with_sequence_length: return "Cigar operations are inconsistent with length of query sequence"; case bambamc_alignment_validity_unknown_cigar_op: return "Unknown/invalid cigar operator"; case bambamc_alignment_validity_queryname_contains_illegal_symbols: return "Query name contains illegal symbols"; case bambamc_alignment_validity_queryname_empty: return "Query name is the empty string"; case bambamc_alignment_validity_invalid_mapping_position: return "Invalid leftmost mapping position"; case bambamc_alignment_validity_invalid_next_mapping_position: return "Invalid next segment mapping position"; case bambamc_alignment_validity_invalid_tlen: return "Invalid observed template length"; case bambamc_alignment_validity_invalid_quality_value: return "Quality string contains invalid quality value"; case bambamc_alignment_validity_invalid_refseq: return "Invalid/unknown reference sequence identifier"; case bambamc_alignment_validity_invalid_next_refseq: return "Invalid/unknown next segment reference sequence identifier"; case bambamc_alignment_validity_invalid_auxiliary_data: return "Invalid auxiliary tag data"; default: return "Unknown alignment validity value."; }; } bambamc-bambamc_0_0_50/src/bambamc/BamBam_BamSingleAlignment.h000066400000000000000000000142611233012646600242120ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAM_BAMSINGLEALIGNMENT_H) #define BAMBAM_BAMSINGLEALIGNMENT_H #include #include #include #include #include typedef enum _bambamc_alignment_validity { bambamc_alignment_validity_ok = 0, bambamc_alignment_validity_block_too_small = 1, bambamc_alignment_validity_queryname_extends_over_block = 2, bambamc_alignment_validity_queryname_length_inconsistent = 3, bambamc_alignment_validity_cigar_extends_over_block = 4, bambamc_alignment_validity_sequence_extends_over_block = 5, bambamc_alignment_validity_quality_extends_over_block = 6, bambamc_alignment_validity_cigar_is_inconsistent_with_sequence_length = 7, bambamc_alignment_validity_unknown_cigar_op = 8, bambamc_alignment_validity_queryname_contains_illegal_symbols = 9, bambamc_alignment_validity_queryname_empty = 10, bambamc_alignment_validity_invalid_mapping_position = 11, bambamc_alignment_validity_invalid_next_mapping_position = 12, bambamc_alignment_validity_invalid_tlen = 13, bambamc_alignment_validity_invalid_quality_value = 14, bambamc_alignment_validity_invalid_refseq = 15, bambamc_alignment_validity_invalid_next_refseq = 16, bambamc_alignment_validity_invalid_auxiliary_data = 17, bambamc_alignment_valididy_record_length_negative = 18 } bambamc_alignment_validity; typedef struct _BamBam_BamSingleAlignment { uint8_t * data; uint32_t dataav; uint32_t dataused; char * query; int32_t queryspace; char * qual; int32_t qualspace; char * cigar; int32_t cigarspace; bambamc_alignment_validity valid; BamBam_CharBuffer * auxbuffer; } BamBam_BamSingleAlignment; extern BamBam_BamSingleAlignment * BamBam_BamSingleAlignment_Delete(BamBam_BamSingleAlignment * data); extern BamBam_BamSingleAlignment * BamBam_BamSingleAlignment_New(); extern BamBam_BamSingleAlignment * BamBam_BamSingleAlignment_NewClone(uint8_t const * block, uint32_t const blocksize); extern BamBam_BamSingleAlignment * BamBam_BamSingleAlignment_Clone(BamBam_BamSingleAlignment const * o); extern int BamBam_BamSingleAlignment_LoadAlignment(BamBam_BamSingleAlignment * data, BamBam_GzipReader * reader); extern int BamBam_BamSingleAlignment_StoreAlignment(BamBam_BamSingleAlignment const * data, BamBam_GzipWriter * writer); extern int BamBam_BamSingleAlignment_StoreAlignmentBgzf(BamBam_BamSingleAlignment const * data, BamBam_BgzfCompressor * writer); extern int32_t BamBam_BamSingleAlignment_GetRefId(BamBam_BamSingleAlignment const * data); extern int32_t BamBam_BamSingleAlignment_GetPos(BamBam_BamSingleAlignment const * data); extern uint32_t BamBam_BamSingleAlignment_GetBinMQNL(BamBam_BamSingleAlignment const * data); extern uint32_t BamBam_BamSingleAlignment_GetBin(BamBam_BamSingleAlignment const * data); extern uint32_t BamBam_BamSingleAlignment_GetMQ(BamBam_BamSingleAlignment const * data); extern uint32_t BamBam_BamSingleAlignment_GetNL(BamBam_BamSingleAlignment const * data); extern uint32_t BamBam_BamSingleAlignment_GetFlagNC(BamBam_BamSingleAlignment const * data); extern uint32_t BamBam_BamSingleAlignment_GetFlags(BamBam_BamSingleAlignment const * data); extern uint32_t BamBam_BamSingleAlignment_GetNC(BamBam_BamSingleAlignment const * data); extern int32_t BamBam_BamSingleAlignment_GetLSeq(BamBam_BamSingleAlignment const * data); extern int32_t BamBam_BamSingleAlignment_GetNextRefID(BamBam_BamSingleAlignment const * data); extern int32_t BamBam_BamSingleAlignment_GetNextPos(BamBam_BamSingleAlignment const * data); extern int32_t BamBam_BamSingleAlignment_GetTLen(BamBam_BamSingleAlignment const * data); extern char const * BamBam_BamSingleAlignment_GetReadName(BamBam_BamSingleAlignment const * data); extern uint8_t const * BamBam_BamSingleAlignment_GetEncodedCigar(BamBam_BamSingleAlignment const * data); extern uint8_t const * BamBam_BamSingleAlignment_GetEncodedQuery(BamBam_BamSingleAlignment const * data); extern uint8_t const * BamBam_BamSingleAlignment_GetEncodedQual(BamBam_BamSingleAlignment const * data); extern uint8_t const * BamBam_BamSingleAlignment_GetEncodedAux(BamBam_BamSingleAlignment const * data); extern int BamBam_BamSingleAlignment_DecodeQueryRc(BamBam_BamSingleAlignment * algn, int const rc); extern int BamBam_BamSingleAlignment_DecodeQualRc(BamBam_BamSingleAlignment * algn, int const rc); extern int BamBam_BamSingleAlignment_DecodeCigarRc(BamBam_BamSingleAlignment * algn, int const rc); extern int BamBam_BamSingleAlignment_DecodeQuery(BamBam_BamSingleAlignment * algn); extern int BamBam_BamSingleAlignment_DecodeQual(BamBam_BamSingleAlignment * algn); extern int BamBam_BamSingleAlignment_DecodeCigar(BamBam_BamSingleAlignment * algn); extern int32_t BamBam_BamSingleAlignment_DecodeQueryQualCigarRc( BamBam_BamSingleAlignment * algn, int32_t rc, int32_t * querylen, int32_t * cigarlen); extern int32_t BamBam_BamSingleAlignment_DecodeQueryQualCigar( BamBam_BamSingleAlignment * algn, int32_t * querylen, int32_t * cigarlen); extern int BamBam_BamSingleAlignment_DecodeAuxSingle(BamBam_BamSingleAlignment * algn, uint8_t const * p, int reset); extern char const * BamBam_BamSingleAlignment_DecodeAux(BamBam_BamSingleAlignment * algn); extern uint8_t const * BamBam_BamSingleAlignment_FindAux(BamBam_BamSingleAlignment const * algn, char const tag[2]); extern uint64_t BamBam_BamSingleAlignment_GetAuxLength(BamBam_BamSingleAlignment const * algn); extern char const * BamBam_Alignment_Validity_Str(bambamc_alignment_validity const code); #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_BamWriter.c000066400000000000000000000062241233012646600224010ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include #include #include #include #include BamBam_BamWriter * BamBam_BamWriter_Delete(BamBam_BamWriter * writer, int * termstatus) { if ( writer ) { if ( writer->aput ) { BamBam_AlignmentPut_Delete(writer->aput); writer->aput = 0; } if ( writer->bgzf ) { int const r = BamBam_BgzfCompressor_Terminate(writer->bgzf); if ( termstatus ) *termstatus = r; BamBam_BgzfCompressor_Delete(writer->bgzf); writer->bgzf = 0; } free( writer ); } return 0; } BamBam_BamWriter * BamBam_BamWriter_New( BamBam_BamHeaderInfo * info, char const * filename, int compressionLevel) { BamBam_BamWriter * writer = (BamBam_BamWriter *)malloc(sizeof(BamBam_BamWriter)); char mode[3] = "w1\0"; assert ( mode[2] == 0 ); if ( !writer ) return BamBam_BamWriter_Delete(writer,0); memset(writer,0,sizeof(BamBam_BamWriter)); if ( compressionLevel < 0 || compressionLevel > 9 ) return BamBam_BamWriter_Delete(writer,0); mode[1] = compressionLevel + '0'; writer->bgzf = BamBam_BgzfCompressor_New(filename,compressionLevel); if ( BamBam_BamHeaderInfo_WriteBamHeader(info,writer->bgzf) < 0 ) return BamBam_BamWriter_Delete(writer,0); writer->aput = BamBam_AlignmentPut_New(); if ( ! writer->aput ) return BamBam_BamWriter_Delete(writer,0); return writer; } int BamBam_BamWriter_PutAlignment( BamBam_BamWriter * writer, /* flags */ int32_t const flags, /* target (chromosome) id */ int32_t const tid, /* position on chromosome (0 based) */ uint64_t const rpos, /* mate target id */ int32_t const mtid, /* position of mate on mate target id */ uint64_t const rmpos, /* sequence name */ char const * name, /* query sequence (read) */ char const * query, /* quality string */ char const * qual, /* cigar operations */ char const * cigar, /* mapping quality */ int32_t const rqual, /* insert size */ int32_t const isize ) { return BamBam_CharBuffer_PutAlignmentC(writer->aput,flags,tid,rpos,mtid,rmpos,name,query,qual,cigar,rqual,isize); } int BamBam_BamWriter_PutAuxNumber(BamBam_BamWriter * writer, char const * tag, char const type, void const * rvalue) { return BamBam_CharBuffer_PutAuxNumberC(writer->aput,tag,type,rvalue); } int BamBam_BamWriter_Commit(BamBam_BamWriter * writer) { return BamBam_BamSingleAlignment_StoreAlignmentBgzf(writer->aput->calignment,writer->bgzf); } bambamc-bambamc_0_0_50/src/bambamc/BamBam_BamWriter.h000066400000000000000000000041201233012646600223770ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAM_BAMWRITER_H) #define BAMBAM_BAMWRITER_H #include #include typedef struct _BamBam_BamWriter { BamBam_AlignmentPut * aput; BamBam_BgzfCompressor * bgzf; } BamBam_BamWriter; extern BamBam_BamWriter * BamBam_BamWriter_Delete(BamBam_BamWriter * writer, int * termstatus); extern BamBam_BamWriter * BamBam_BamWriter_New( BamBam_BamHeaderInfo * info, char const * filename, int compressionLevel) BAMBAM_WARN_IF_UNUSEDRESULT; extern int BamBam_BamWriter_PutAlignment( BamBam_BamWriter * writer, /* flags */ int32_t const flags, /* target (chromosome) id */ int32_t const tid, /* position on chromosome (0 based) */ uint64_t const rpos, /* mate target id */ int32_t const mtid, /* position of mate on mate target id */ uint64_t const rmpos, /* sequence name */ char const * name, /* query sequence (read) */ char const * query, /* quality string */ char const * qual, /* cigar operations */ char const * cigar, /* mapping quality */ int32_t const rqual, /* insert size */ int32_t const isize ) BAMBAM_WARN_IF_UNUSEDRESULT; extern int BamBam_BamWriter_PutAuxNumber(BamBam_BamWriter * writer, char const * tag, char const type, void const * rvalue) BAMBAM_WARN_IF_UNUSEDRESULT; extern int BamBam_BamWriter_Commit(BamBam_BamWriter * writer); #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_BgzfCompressor.c000066400000000000000000000211721233012646600234510ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include static const char BamBam_GzipHeaderData[18] = { (char)BAMBAMC_LZ_ID1, (char)BAMBAMC_LZ_ID2, BAMBAMC_LZ_CM, BAMBAMC_LZ_FEXTRA, 0,0,0,0, /* modification time, not given */ 0, /* XFL */ (char)BAMBAMC_LZ_OS_UNKNOWN, 6,0, /* XLEN, number 6 as little endian */ 'B', 'C', /* extra data block tag */ 2,0, /* length of extra field, 2 as little endian */ 0,0 /* extra field: blocksize-1 including block header and footer, to be filled */ }; static unsigned int const BAMBAMC_LZ_HEADERSIZE = sizeof(BamBam_GzipHeaderData); static unsigned int const BAMBAMC_LZ_FOOTERSIZE = 8; #include #include #include #include static int BamBam_BgzfCompressor_FlushInternal(BamBam_BgzfCompressor * object, int level) { uint32_t insize = object->inbufferfill; z_stream strm; do { int zret = -1; memset ( &strm , 0, sizeof(z_stream) ); strm.zalloc = Z_NULL; strm.zfree = Z_NULL; strm.opaque = Z_NULL; zret = deflateInit2(&strm, level, Z_DEFLATED, -15 /* window size */, 8 /* mem level, gzip default */, Z_DEFAULT_STRATEGY); if ( zret != Z_OK ) return -1; strm.avail_in = insize; strm.next_in = object->inbuffer; strm.avail_out = BAMBAMC_LZ_MAXBUFSIZE - (BAMBAMC_LZ_HEADERSIZE+BAMBAMC_LZ_FOOTERSIZE); strm.next_out = object->outbuffer + BAMBAMC_LZ_HEADERSIZE; zret = deflate(&strm,Z_FINISH); /* everything compressed, write block to file */ if ( zret == Z_STREAM_END ) { /* size of compressed data */ uint32_t const payloadsize = (BAMBAMC_LZ_MAXBUFSIZE - (BAMBAMC_LZ_HEADERSIZE+BAMBAMC_LZ_FOOTERSIZE)) - strm.avail_out; /* blocksize stored in extended header */ uint16_t const headblocksize = sizeof(BamBam_GzipHeaderData)/*header*/+8/*footer*/+payloadsize-1; /* remaining uncompressed bytes */ uint32_t const rembytes = object->inbufferfill - insize; /* pointer to uncompressed rest */ Bytef const * remp = object->inbuffer + insize; /* empty crc */ uint32_t crc = crc32(0,0,0); /* nextout ptr */ Bytef * nextout = strm.next_out; /* total size of compressed block */ int32_t compsize = -1; deflateEnd(&strm); /* copy header into its place */ memcpy(object->outbuffer,BamBam_GzipHeaderData,sizeof(BamBam_GzipHeaderData)); /* put block size (2 byte little endian) */ object->outbuffer[16] = (headblocksize >> 0) & 0xFFu; object->outbuffer[17] = (headblocksize >> 8) & 0xFFu; /* compute crc */ crc = crc32(crc, object->inbuffer, insize); /* put crc */ *(nextout++) = (crc >> 0) & 0xFFu; *(nextout++) = (crc >> 8) & 0xFFu; *(nextout++) = (crc >> 16) & 0xFFu; *(nextout++) = (crc >> 24) & 0xFFu; /* put uncompressed size */ *(nextout++) = (insize >> 0) & 0xFFu; *(nextout++) = (insize >> 8) & 0xFFu; *(nextout++) = (insize >> 16) & 0xFFu; *(nextout++) = (insize >> 24) & 0xFFu; /* write block */ compsize = nextout-object->outbuffer; if ( fwrite(object->outbuffer,compsize,1,object->file) != 1 ) return -1; /* move uncompressed rest (if any) to start of buffer */ if ( rembytes ) memmove(object->inbuffer,remp,rembytes); object->inbufferfill = rembytes; return compsize; } /* output buffer too small for compressed stream, reduce size of input (and try again) */ else if ( zret == Z_OK ) { fprintf(stderr,"Bad compression, reducing.\n"); deflateEnd(&strm); insize -= ((insize >= 1024) ? 1024 : insize); } /* other zlib error, give up */ else { deflateEnd(&strm); return -1; } } while ( insize ); return -1; } int BamBam_BgzfCompressor_Flush(BamBam_BgzfCompressor * object) { while ( object->inbufferfill ) { int const r = BamBam_BgzfCompressor_FlushInternal(object,object->level); if ( r < 0 ) return -1; } return 0; } int BamBam_BgzfCompressor_Terminate(BamBam_BgzfCompressor * object) { int r = -1; /* flush */ r = BamBam_BgzfCompressor_Flush(object); if ( r < 0 ) return -1; /* write empty block, default compression (EOF block) */ r = BamBam_BgzfCompressor_FlushInternal(object,Z_DEFAULT_COMPRESSION); if ( r < 0 ) return -1; /* flush the underlying file/stream */ if ( fflush(object->file) != 0 ) return -1; return 0; } int BamBam_BgzfCompressor_Write(BamBam_BgzfCompressor * object, uint8_t const * data, uint32_t len) { /* loop until all data is in buffer */ while ( len ) { uint32_t const space = BAMBAMC_LZ_MAXBUFSIZE - object->inbufferfill; uint32_t const towrite = (len <= space) ? len : space; /* if there is no space, then try to flush out some data */ if ( ! space ) { int const r = BamBam_BgzfCompressor_FlushInternal(object,object->level); if ( r < 0 ) return -1; } else { assert ( towrite ); /* copy data */ memcpy(object->inbuffer+object->inbufferfill,data,towrite); /* update counters */ object->inbufferfill += towrite; data += towrite; len -= towrite; } } return 0; } static BamBam_BgzfCompressor * BamBam_BgzfCompressor_Setup(BamBam_BgzfCompressor * object, int const level) { object->level = level; object->inbuffer = (Bytef *)malloc(BAMBAMC_LZ_MAXBUFSIZE); if ( ! object->inbuffer ) return BamBam_BgzfCompressor_Delete(object); object->outbuffer = (Bytef *)malloc(BAMBAMC_LZ_MAXBUFSIZE); if ( ! object->outbuffer ) return BamBam_BgzfCompressor_Delete(object); object->inbufferfill = 0; return object; } BamBam_BgzfCompressor * BamBam_BgzfCompressor_New(char const * filename, int const level) { if ( strcmp(filename,"-") == 0 ) return BamBam_BgzfCompressor_NewFP(stdout,level); else return BamBam_BgzfCompressor_NewFilename(filename,level); } BamBam_BgzfCompressor * BamBam_BgzfCompressor_NewFilename(char const * filename, int const level) { BamBam_BgzfCompressor * object = 0; object = (BamBam_BgzfCompressor *)malloc(sizeof(BamBam_BgzfCompressor)); if ( ! object ) return BamBam_BgzfCompressor_Delete(object); memset(object,0,sizeof(BamBam_BgzfCompressor)); object->closefile = fopen(filename,"wb"); if ( ! object->closefile ) return BamBam_BgzfCompressor_Delete(object); object->file = object->closefile; return BamBam_BgzfCompressor_Setup(object,level); } BamBam_BgzfCompressor * BamBam_BgzfCompressor_NewFP(FILE * rfile, int const level) { BamBam_BgzfCompressor * object = 0; object = (BamBam_BgzfCompressor *)malloc(sizeof(BamBam_BgzfCompressor)); if ( ! object ) return BamBam_BgzfCompressor_Delete(object); memset(object,0,sizeof(BamBam_BgzfCompressor)); object->file = rfile; if ( ! object->file ) return BamBam_BgzfCompressor_Delete(object); return BamBam_BgzfCompressor_Setup(object,level); } BamBam_BgzfCompressor * BamBam_BgzfCompressor_Delete(BamBam_BgzfCompressor * object) { if ( object ) { if ( object->file ) { fflush(object->file); object->file = 0; } if ( object->closefile ) { fclose(object->closefile); object->closefile = 0; } if ( object->inbuffer ) { free(object->inbuffer); object->inbuffer = 0; } if ( object->outbuffer ) { free(object->outbuffer); object->outbuffer = 0; } free(object); } return 0; } int BamBam_BgzfCompressor_PutInt32(BamBam_BgzfCompressor * object, int32_t const v) { uint8_t data[4] = { (v >> 0) & 0xFFu, (v >> 8) & 0xFFu, (v >> 16) & 0xFFu, (v >> 24) & 0xFFu }; return BamBam_BgzfCompressor_Write(object,&data[0],4); } int BamBam_BgzfCompressor_PutStringZ(BamBam_BgzfCompressor * object, char const * c) { uint32_t const len = strlen(c); return BamBam_BgzfCompressor_Write(object,(uint8_t const *)c,len+1); } int BamBam_BgzfCompressor_PutLenStringZ(BamBam_BgzfCompressor * object, char const * c) { uint32_t const len = strlen(c); int r = -1; /* put length */ r = BamBam_BgzfCompressor_PutInt32(object,len+1); if ( r < 0 ) return -1; /* put string */ r = BamBam_BgzfCompressor_PutStringZ(object,c); if ( r < 0 ) return -1; return 0; } bambamc-bambamc_0_0_50/src/bambamc/BamBam_BgzfCompressor.h000066400000000000000000000056201233012646600234560ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAMC_BGZFCOMPRESSOR_H) #define BAMBAMC_BGZFCOMPRESSOR_H #include #include #include #include /* gzip/zlib header flags */ enum bambamc_gzipheader_flags { BAMBAMC_LZ_FTEXT = (1u << 0), BAMBAMC_LZ_FHCRC = (1u << 1), BAMBAMC_LZ_FEXTRA = (1u << 2), BAMBAMC_LZ_FNAME = (1u << 3), BAMBAMC_LZ_FCOMMENT = (1u << 4), BAMBAMC_LZ_FRES0 = (1u<<5), BAMBAMC_LZ_FRES1 = (1u<<6), BAMBAMC_LZ_FRES2 = (1u<<7), BAMBAMC_LZ_FRES = ((1u<<5)|(1u<<6)|(1u<<7)) }; /* gzip header id */ #define BAMBAMC_LZ_ID1 0x1F #define BAMBAMC_LZ_ID2 0x8B /* compression method */ #define BAMBAMC_LZ_CM 8 /* compression method: deflate */ /* unknown operation system id */ #define BAMBAMC_LZ_OS_UNKNOWN 255 /* maximum buffer size */ #define BAMBAMC_LZ_MAXBUFSIZE (64*1024) typedef struct _BamBam_BgzfCompressor { FILE * file; FILE * closefile; int level; Bytef * inbuffer; uint32_t inbufferfill; Bytef * outbuffer; } BamBam_BgzfCompressor; extern BamBam_BgzfCompressor * BamBam_BgzfCompressor_New(char const * filename, int const level) BAMBAM_WARN_IF_UNUSEDRESULT; extern BamBam_BgzfCompressor * BamBam_BgzfCompressor_NewFilename(char const * filename, int const level) BAMBAM_WARN_IF_UNUSEDRESULT; extern BamBam_BgzfCompressor * BamBam_BgzfCompressor_NewFP(FILE * rfile, int const level) BAMBAM_WARN_IF_UNUSEDRESULT; extern BamBam_BgzfCompressor * BamBam_BgzfCompressor_Delete(BamBam_BgzfCompressor * object); extern int BamBam_BgzfCompressor_Flush(BamBam_BgzfCompressor * object) BAMBAM_WARN_IF_UNUSEDRESULT; extern int BamBam_BgzfCompressor_Write(BamBam_BgzfCompressor * object, uint8_t const * data, uint32_t len) BAMBAM_WARN_IF_UNUSEDRESULT; extern int BamBam_BgzfCompressor_PutInt32(BamBam_BgzfCompressor * object, int32_t const v) BAMBAM_WARN_IF_UNUSEDRESULT; extern int BamBam_BgzfCompressor_PutStringZ(BamBam_BgzfCompressor * object, char const * const c) BAMBAM_WARN_IF_UNUSEDRESULT; extern int BamBam_BgzfCompressor_PutLenStringZ(BamBam_BgzfCompressor * object, char const * const c) BAMBAM_WARN_IF_UNUSEDRESULT; extern int BamBam_BgzfCompressor_Terminate(BamBam_BgzfCompressor * object) BAMBAM_WARN_IF_UNUSEDRESULT; #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_CharBuffer.c000066400000000000000000000051051233012646600225110ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include #include #include #include BamBam_CharBuffer * BamBam_CharBuffer_Clone(BamBam_CharBuffer const * o) { BamBam_CharBuffer * charbuffer = BamBam_CharBuffer_New(); if ( ! charbuffer ) return 0; charbuffer->buffer = (uint8_t *)malloc(o->buffersize); if ( ! charbuffer->buffer ) { BamBam_CharBuffer_Delete(charbuffer); return 0; } memcpy(charbuffer->buffer,o->buffer,o->buffersize); charbuffer->buffersize = o->buffersize; charbuffer->bufferfill = o->bufferfill; return charbuffer; } BamBam_CharBuffer * BamBam_CharBuffer_New() { BamBam_CharBuffer * charbuffer = 0; charbuffer = (BamBam_CharBuffer *)malloc(sizeof(BamBam_CharBuffer)); if ( ! charbuffer ) return 0; memset(charbuffer,0,sizeof(BamBam_CharBuffer)); return charbuffer; } void BamBam_CharBuffer_Reset(BamBam_CharBuffer * buffer) { buffer->bufferfill = 0; } int BamBam_CharBuffer_PushChar(BamBam_CharBuffer * buffer, uint8_t c) { if ( buffer->bufferfill == buffer->buffersize ) { uint64_t newbuffersize = (buffer->buffersize) ? (2*buffer->buffersize) : 1; uint8_t * newbuffer = 0; newbuffer = (uint8_t *)malloc(newbuffersize*sizeof(uint8_t)); if ( ! newbuffer ) return -1; memcpy(newbuffer,buffer->buffer,buffer->bufferfill); free(buffer->buffer); buffer->buffer = newbuffer; buffer->buffersize = newbuffersize; } assert ( buffer->bufferfill < buffer->buffersize ); buffer->buffer [ buffer->bufferfill ++ ] = c; return 0; } void BamBam_CharBuffer_Delete(BamBam_CharBuffer * buffer) { if ( buffer ) { free(buffer->buffer); free(buffer); } } int BamBam_MapBase(uint8_t const c) { switch ( c ) { case 'A': return 0; case 'C': return 1; case 'G': return 2; case 'T': return 3; default: return 4; } } bambamc-bambamc_0_0_50/src/bambamc/BamBam_CharBuffer.h000066400000000000000000000053751233012646600225270ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAM_CHARBUFFER_H) #define BAMBAM_CHARBUFFER_H #include #if defined(_linux) #include #endif #include typedef struct _BamBam_CharBuffer { uint8_t * buffer; uint64_t buffersize; uint64_t bufferfill; } BamBam_CharBuffer; #include extern BamBam_CharBuffer * BamBam_CharBuffer_New() BAMBAM_WARN_IF_UNUSEDRESULT; extern int BamBam_CharBuffer_PushChar(BamBam_CharBuffer * buffer, uint8_t c) BAMBAM_WARN_IF_UNUSEDRESULT; extern void BamBam_CharBuffer_Reset(BamBam_CharBuffer * buffer); extern void BamBam_CharBuffer_Delete(BamBam_CharBuffer * buffer); extern int BamBam_MapBase(uint8_t const c); extern BamBam_CharBuffer * BamBam_CharBuffer_Clone(BamBam_CharBuffer const * o) BAMBAM_WARN_IF_UNUSEDRESULT; #define BamBam_CharBuffer_PushCharQuick(buffer,c,ret) \ do { \ if (buffer->bufferfill < buffer->buffersize) \ { \ buffer->buffer[buffer->bufferfill++] = c; \ } \ else \ ret = BamBam_CharBuffer_PushChar(buffer,c); \ } while(0); #define BamBam_CharBuffer_PushLE(buffer,n,ret) \ do { \ unsigned int i; \ for ( i = 0; i < 8*sizeof(n); i += 8 ) \ { \ BamBam_CharBuffer_PushCharQuick(buffer,(uint8_t)(((uint8_t)(n >> i))&0xFFu),ret); \ if ( ret < 0 ) \ { \ ret = -1; \ break; \ } \ } \ } while(0); #define BamBam_CharBuffer_PushString(buffer,s,ret) \ do { \ char const * c = s; \ while ( *c ) \ { \ BamBam_CharBuffer_PushCharQuick(buffer,*(c++),ret); \ if ( ret < 0 ) \ { \ break; \ } \ } \ } while(0); #define BamBam_CharBuffer_PushNumber(buffer,n,ret) \ do { \ uint64_t tn = n; \ unsigned int numlen = 0; \ unsigned int i = 0; \ char * c = 0; \ if ( !tn ) numlen = 1; \ while ( tn ) \ tn /= 10, numlen++; \ c = (char *)alloca(numlen); \ tn = n; \ while ( i < numlen ) \ { \ c[numlen-i-1] = (tn % 10)+'0'; \ i++; \ tn /= 10; \ } \ for ( i = 0; ret >= 0 && i < numlen; ++i ) \ ret = BamBam_CharBuffer_PushChar(buffer,c[i]); \ } while(0); #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_Chromosome.c000066400000000000000000000025631233012646600226220ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include #include #include #include BamBam_Chromosome * BamBam_Chromosome_New(char const * rname, uint64_t const rlength) { BamBam_Chromosome * chr = (BamBam_Chromosome *)malloc(sizeof(BamBam_Chromosome)); if ( ! chr ) return 0; memset(chr,0,sizeof(BamBam_Chromosome)); chr->name = BamBam_StrDup(rname); if ( ! chr->name ) { free(chr); return 0; } chr->length = rlength; return chr; } void BamBam_Chromosome_Delete(BamBam_Chromosome * chr) { if ( chr ) { free(chr->headerline); free(chr->name); free(chr); } } bambamc-bambamc_0_0_50/src/bambamc/BamBam_Chromosome.h000066400000000000000000000022321233012646600226200ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAM_CHROMOSOME_H) #define BAMBAM_CHROMOSOME_H #include #include typedef struct _BamBam_Chromosome { char * name; uint64_t length; char * headerline; } BamBam_Chromosome; BamBam_Chromosome * BamBam_Chromosome_New(char const * rname, uint64_t const rlength) BAMBAM_WARN_IF_UNUSEDRESULT; void BamBam_Chromosome_Delete(BamBam_Chromosome * chr); #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_CollatorState.h000066400000000000000000000017231233012646600232710ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAM_COLLATORSTATE_H) #define BAMBAM_COLLATORSTATE_H enum BamBam_CollatorState { BAMBAM_COLLATE_READING_INPUT, BAMBAM_COLLATE_MERGING, BAMBAM_COLLATE_DONE, BAMBAM_COLLATE_FAILED }; #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_Config.h.in000066400000000000000000000015271233012646600223250ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAMC_CONFIG_H) #define BAMBAMC_CONFIG_H @HAVEWINDOWS_MKDIR@ #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_FastQRead.h000066400000000000000000000023311233012646600223170ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(FASTQREAD_H) #define FASTQREAD_H enum alignment_type { BAMBAM_ALIGNMENT_TYPE_UNDEFINED = -2, BAMBAM_ALIGNMENT_TYPE_NONE = -1, BAMBAM_ALIGNMENT_TYPE_SINGLE = 1, BAMBAM_ALIGNMENT_TYPE_COMPLETE_PAIR = 2, BAMBAM_ALIGNMENT_TYPE_ORPHAN1_PAIR = 3, BAMBAM_ALIGNMENT_TYPE_ORPHAN2_PAIR = 4 }; typedef struct _BamBam_FastQRead { char const * name; unsigned int namelength; char const * seq; unsigned int seqlength; char const * qual; } BamBam_FastQRead; #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_FormatAlignment.c000066400000000000000000000105501233012646600235710ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include #include #include #include static uint64_t BamBam_GetFastqNameLineLength(unsigned int const qnamelen, uint32_t const flags) { return 1 /* @ */ + qnamelen + (( flags & BAMBAMC_FPAIRED ) ? 2 : 0) /* /[12] */ + 1 /* \n */; } static uint64_t BamBam_GetFastqSeqLineLength(unsigned int const seqlen) { return seqlen + 1; } static uint64_t BamBam_GetFastqPlusLineLength() { return 1 /* + */ + 1 /* \n */; } static uint64_t BamBam_GetFastqQualLineLength(unsigned int const seqlen) { return seqlen + 1; } static uint64_t BamBam_GetFastqEntryLength(unsigned int const qnamelen, unsigned int const seqlen, uint32_t const flags) { return BamBam_GetFastqNameLineLength(qnamelen,flags) + BamBam_GetFastqSeqLineLength(seqlen) + BamBam_GetFastqPlusLineLength(qnamelen) + BamBam_GetFastqQualLineLength(seqlen); } /** * put fastq @ line **/ static char * BamBam_PutAtLine( char const * qname, unsigned int const qnamelen, uint32_t const flags, char * opc, char const term ) { static int spaceTable[256]; static int spaceTableInitialized = 0; char const * qnamee = qname+qnamelen; if ( ! spaceTableInitialized ) { int i; for ( i = 0; i < 256; ++i ) spaceTable[i] = isspace(i); spaceTableInitialized = 1; } *(opc++) = '@'; /* paired? add /1 or /2 before first space or at end of line */ if ( flags & BAMBAMC_FPAIRED ) { while ( qname != qnamee && !spaceTable[(int)((uint8_t)(*qname))] ) *(opc++) = *(qname++); *(opc++) = '/'; if ( flags & BAMBAMC_FREAD1 ) *(opc++) = '1'; else *(opc++) = '2'; while ( qname != qnamee ) *(opc++) = *(qname++); } else { while ( qname != qnamee ) *(opc++) = *(qname++); } *(opc++) = term; return opc; } static char * BamBam_PutPlusLine(char * opc, char const term) { *opc++ = '+'; *opc++ = term; return opc; } static char * BamBam_PutAlignmentFastQ(BamBam_BamSingleAlignment const * alignment, char * opc, char const term) { char const * qname = BamBam_BamSingleAlignment_GetReadName(alignment); uint32_t const flags = BamBam_BamSingleAlignment_GetFlags(alignment); int32_t const seqlen = BamBam_BamSingleAlignment_GetLSeq(alignment); /* @ line */ opc = BamBam_PutAtLine(qname,strlen(qname),flags,opc,term); /* seq line */ memcpy(opc,alignment->query,seqlen); opc += seqlen; *(opc++) = term; /* + line */ opc = BamBam_PutPlusLine(opc,term); /* quality */ memcpy(opc,alignment->qual,seqlen); opc += seqlen; *(opc++) = term; return opc; } static uint64_t BamBam_GetFastQAlignmentLength(BamBam_BamSingleAlignment const * alignment) { int32_t const seqlen = BamBam_BamSingleAlignment_GetLSeq(alignment); uint32_t const flags = BamBam_BamSingleAlignment_GetFlags(alignment); char const * qname = BamBam_BamSingleAlignment_GetReadName(alignment); unsigned int const qnamelen = strlen(qname); return BamBam_GetFastqEntryLength(qnamelen, seqlen, flags); } int BamBam_PutAlignmentFastQBuffer( BamBam_BamSingleAlignment * alignment, char ** buffer, unsigned int * bufferlen, char const term ) { unsigned int const neededlength = BamBam_GetFastQAlignmentLength(alignment); char * endptr = 0; if ( neededlength > *bufferlen ) { free(*buffer); *buffer = 0; *bufferlen = 0; *buffer = (char *)malloc(neededlength); if ( ! *buffer ) return -1; *bufferlen = neededlength; } if ( BamBam_BamSingleAlignment_DecodeQuery(alignment) < 0 ) return -1; if ( BamBam_BamSingleAlignment_DecodeQual(alignment) < 0 ) return -1; endptr = BamBam_PutAlignmentFastQ(alignment,*buffer,term); return endptr - *buffer; } bambamc-bambamc_0_0_50/src/bambamc/BamBam_FormatAlignment.h000066400000000000000000000021551233012646600236000ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAM_FORMATALIGNMENT_H) #define BAMBAM_FORMATALIGNMENT_H #include #include #include #include extern int BamBam_PutAlignmentFastQBuffer(BamBam_BamSingleAlignment * alignment, char ** buffer, unsigned int * bufferlen, char const term); #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_FormatNumber.c000066400000000000000000000047211233012646600231060ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include #include #include #if defined(_linux) #include #endif #include char * BamBam_ConstructNumberFormatString(int numlen) { int lennumlen = 0; int tnumlen = 0; unsigned int fslen = 0; char * fs = 0; tnumlen = numlen; while ( tnumlen ) { tnumlen /= 10; lennumlen++; } fslen = 6 + lennumlen + 1; fs = (char *)malloc(fslen); if ( ! fs ) return 0; snprintf(fs,fslen,"%%0%dllu",numlen); return fs; } char * BamBam_FormatNumberMinLenAlt(uint64_t const num, int const minlen) { /* length of number in decimal repr */ int numlen = 0; /* tmp */ uint64_t tnum; /* string on stack */ char * s = 0; char * t = 0; if ( !num ) numlen = 1; else { /* count number of digits */ tnum = num; while ( tnum ) { tnum /= 10; numlen++; } } numlen = (numlen >= minlen) ? numlen : minlen; s = (char *)alloca(numlen+1); s[numlen] = 0; t = s + numlen; tnum = num; while ( t != s ) { *(--t) = '0' + (tnum%10); tnum /= 10; } return BamBam_StrDup(s); } char * BamBam_FormatNumberMinLen(uint64_t const num, int minlen) { uint64_t tnum; int numlen; char * smem = 0; char * fs = 0; tnum = num; numlen = 0; while ( tnum ) { tnum /= 10; numlen++; } if ( ! numlen ) numlen = 1; numlen = (numlen >= minlen) ? numlen : minlen; smem = (char *)malloc(numlen+1); if ( ! smem ) return 0; fs = BamBam_ConstructNumberFormatString(numlen); if ( ! fs ) { free(smem); return 0; } snprintf(smem,numlen+1,fs,(unsigned long long)num); free(fs); return smem; } char * BamBam_FormatNumber(uint64_t const num) { return BamBam_FormatNumberMinLen(num,-1); } bambamc-bambamc_0_0_50/src/bambamc/BamBam_FormatNumber.h000066400000000000000000000023211233012646600231050ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAM_FORMATNUMBER_H) #define BAMBAM_FORMATNUMBER_H #include #include #include #include #include extern char * BamBam_ConstructNumberFormatString(int numlen) BAMBAM_WARN_IF_UNUSEDRESULT; extern char * BamBam_FormatNumberMinLen(uint64_t const num, int minlen) BAMBAM_WARN_IF_UNUSEDRESULT; extern char * BamBam_FormatNumber(uint64_t const num) BAMBAM_WARN_IF_UNUSEDRESULT; #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_GzipFileDecoder.c000066400000000000000000000036641233012646600235110ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include BamBam_BamSingleAlignment * BamBam_GzipFileDecoder_DecodeAlignment(BamBam_GzipFileDecoder * object) { int const r = BamBam_BamSingleAlignment_LoadAlignment(object->alignment,object->reader); if ( r > 0 ) return object->alignment; else return 0; } BamBam_GzipFileDecoder * BamBam_GzipFileDecoder_Delete(BamBam_GzipFileDecoder * object) { if ( object ) { if ( object->alignment ) { BamBam_BamSingleAlignment_Delete(object->alignment); object->alignment = 0; } if ( object->reader ) { BamBam_GzipReader_Delete(object->reader); object->reader = 0; } free(object); } return 0; } BamBam_GzipFileDecoder * BamBam_GzipFileDecoder_New(char const * filename) { BamBam_GzipFileDecoder * object = 0; object = (BamBam_GzipFileDecoder *)malloc(sizeof(BamBam_GzipFileDecoder)); if ( ! object ) return BamBam_GzipFileDecoder_Delete(object); object->reader = BamBam_GzipReader_New(filename); if ( ! object->reader ) return BamBam_GzipFileDecoder_Delete(object); object->alignment = BamBam_BamSingleAlignment_New(); if ( ! object->alignment ) return BamBam_GzipFileDecoder_Delete(object); return object; } bambamc-bambamc_0_0_50/src/bambamc/BamBam_GzipFileDecoder.h000066400000000000000000000025221233012646600235060ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAM_GZIPFILEDECODER_H) #define BAMBAM_GZIPFILEDECODER_H #include #include typedef struct _BamBam_GzipFileDecoder { BamBam_GzipReader * reader; BamBam_BamSingleAlignment * alignment; } BamBam_GzipFileDecoder; extern BamBam_BamSingleAlignment * BamBam_GzipFileDecoder_DecodeAlignment(BamBam_GzipFileDecoder * object); extern BamBam_GzipFileDecoder * BamBam_GzipFileDecoder_Delete(BamBam_GzipFileDecoder * object); extern BamBam_GzipFileDecoder * BamBam_GzipFileDecoder_New(char const * filename); #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_GzipReader.c000066400000000000000000000057571233012646600225530ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include #include #include #include BamBam_GzipReader * BamBam_GzipReader_New_Filename(char const * filename) { BamBam_GzipReader * object = 0; object = (BamBam_GzipReader *)malloc(sizeof(BamBam_GzipReader)); if ( ! object ) return BamBam_GzipReader_Delete(object); memset(object,0,sizeof(BamBam_GzipReader)); object->file = gzopen(filename,"rb"); if ( ! object->file ) return BamBam_GzipReader_Delete(object); return object; } BamBam_GzipReader * BamBam_GzipReader_New_Fd(int fd) { BamBam_GzipReader * object = 0; object = (BamBam_GzipReader *)malloc(sizeof(BamBam_GzipReader)); if ( ! object ) return BamBam_GzipReader_Delete(object); memset(object,0,sizeof(BamBam_GzipReader)); object->file = gzdopen(fd,"rb"); if ( ! object->file ) return BamBam_GzipReader_Delete(object); return object; } BamBam_GzipReader * BamBam_GzipReader_New(char const * filename) { if ( !filename || !strcmp(filename,"-") ) return BamBam_GzipReader_New_Fd(STDIN_FILENO); else return BamBam_GzipReader_New_Filename(filename); } BamBam_GzipReader * BamBam_GzipReader_Delete(BamBam_GzipReader * object) { if ( object ) { if ( object->file ) { gzclose(object->file); object->file = 0; } free(object); } return 0; } int BamBam_GzipReader_Peek(BamBam_GzipReader * object) { int c = -1; if ( ! object || ! object->file ) return -1; c = gzgetc(object->file); if ( c < 0 ) return -1; if ( gzungetc(c,object->file) < 0 ) return -1; return c; } int BamBam_GzipReader_Getc(BamBam_GzipReader * object) { return gzgetc(object->file); } int BamBam_GzipReader_GetInt32(BamBam_GzipReader * object, int32_t * v) { int i = 0; *v = 0; for ( i = 0; i < 4; ++i ) { int const c = BamBam_GzipReader_Getc(object); if ( c < 0 ) return -1; *v |= ((int32_t)c) << (i*8); } return 0; } int BamBam_GzipReader_GetUInt32(BamBam_GzipReader * object, uint32_t * v) { int i = 0; *v = 0; for ( i = 0; i < 4; ++i ) { int const c = BamBam_GzipReader_Getc(object); if ( c < 0 ) return -1; *v |= ((uint32_t)c) << (i*8); } return 0; } int BamBam_GzipReader_Read(BamBam_GzipReader * object, char * c, int l) { return gzread(object->file,c,l); } bambamc-bambamc_0_0_50/src/bambamc/BamBam_GzipReader.h000066400000000000000000000031221233012646600225400ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAMC_GZIPREADER_H) #define BAMBAMC_GZIPREADER_H #include #include typedef struct _BamBam_GzipReader { gzFile file; } BamBam_GzipReader; extern BamBam_GzipReader * BamBam_GzipReader_New_Filename(char const * filename); extern BamBam_GzipReader * BamBam_GzipReader_New_Fd(int fd); extern BamBam_GzipReader * BamBam_GzipReader_New(char const * filename); extern BamBam_GzipReader * BamBam_GzipReader_Delete(BamBam_GzipReader * object); extern int BamBam_GzipReader_Peek(BamBam_GzipReader * object); extern int BamBam_GzipReader_Getc(BamBam_GzipReader * object); extern int BamBam_GzipReader_GetInt32(BamBam_GzipReader * object, int32_t * v); extern int BamBam_GzipReader_GetUInt32(BamBam_GzipReader * object, uint32_t * v); extern int BamBam_GzipReader_Read(BamBam_GzipReader * object, char * c, int l); #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_GzipWriter.c000066400000000000000000000062501233012646600226120ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include #include #include #include BamBam_GzipWriter * BamBam_GzipWriter_New_Filename(char const * filename, int level) { BamBam_GzipWriter * object = 0; char modestr[4] = { 'w', 'b', '0', 0 }; if ( level < 0 || level > 9 ) return 0; modestr[2] = level + '0'; object = (BamBam_GzipWriter *)malloc(sizeof(BamBam_GzipWriter)); if ( ! object ) return BamBam_GzipWriter_Delete(object,0); memset(object,0,sizeof(BamBam_GzipWriter)); object->file = gzopen(filename,&modestr[0]); if ( ! object->file ) return BamBam_GzipWriter_Delete(object,0); return object; } BamBam_GzipWriter * BamBam_GzipWriter_New_Fd(int fd, int level) { BamBam_GzipWriter * object = 0; char modestr[4] = { 'w', 'b', '0', 0 }; if ( level < 0 || level > 9 ) return 0; modestr[2] = level + '0'; object = (BamBam_GzipWriter *)malloc(sizeof(BamBam_GzipWriter)); if ( ! object ) return BamBam_GzipWriter_Delete(object,0); memset(object,0,sizeof(BamBam_GzipWriter)); object->file = gzdopen(fd,&modestr[0]); if ( ! object->file ) return BamBam_GzipWriter_Delete(object,0); return object; } BamBam_GzipWriter * BamBam_GzipWriter_New(char const * filename, int level) { if ( !filename || !strcmp(filename,"-") ) return BamBam_GzipWriter_New_Fd(STDIN_FILENO,level); else return BamBam_GzipWriter_New_Filename(filename,level); } BamBam_GzipWriter * BamBam_GzipWriter_Delete(BamBam_GzipWriter * object, int * state) { if ( state ) *state = 0; if ( object ) { if ( object->file ) { int const r = gzclose(object->file); if ( state ) { if ( r == Z_OK ) *state = 0; else *state = -1; } object->file = 0; } free(object); } return 0; } int BamBam_GzipWriter_Putc(BamBam_GzipWriter * object, int c) { return gzputc(object->file,c); } int BamBam_GzipWriter_PutInt32(BamBam_GzipWriter * object, int32_t v) { int i = 0; for ( i = 0; i < 4; ++i ) { int const c = BamBam_GzipWriter_Putc(object, (v >> (8*i)) & 0xFF); if ( c < 0 ) return -1; } return 0; } int BamBam_GzipWriter_PutUInt32(BamBam_GzipWriter * object, uint32_t v) { int i = 0; for ( i = 0; i < 4; ++i ) { int const c = BamBam_GzipWriter_Putc(object, (v >> (8*i)) & 0xFF); if ( c < 0 ) return -1; } return 0; } int BamBam_GzipWriter_Write(BamBam_GzipWriter * object, char const * c, int l) { return gzwrite(object->file,c,l); } bambamc-bambamc_0_0_50/src/bambamc/BamBam_GzipWriter.h000066400000000000000000000031271233012646600226170ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAMC_GZIPWRITER_H) #define BAMBAMC_GZIPWRITER_H #include #include typedef struct _BamBam_GzipWriter { gzFile file; } BamBam_GzipWriter; extern BamBam_GzipWriter * BamBam_GzipWriter_New_Filename(char const * filename, int level); extern BamBam_GzipWriter * BamBam_GzipWriter_New_Fd(int fd, int level); extern BamBam_GzipWriter * BamBam_GzipWriter_New(char const * filename, int level); extern BamBam_GzipWriter * BamBam_GzipWriter_Delete(BamBam_GzipWriter * object, int * state); extern int BamBam_GzipWriter_Putc(BamBam_GzipWriter * object, int c); extern int BamBam_GzipWriter_PutInt32(BamBam_GzipWriter * object, int32_t const v); extern int BamBam_GzipWriter_PutUInt32(BamBam_GzipWriter * object, uint32_t const v); extern int BamBam_GzipWriter_Write(BamBam_GzipWriter * object, char const * c, int l); #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_Hash.c000066400000000000000000000103501233012646600213630ustar00rootroot00000000000000/* * This file contains an adaption of some of Bob Jenkins' hash functions * For licensing please see Bob Jenkins's remarks below. */ #include /*-------------------------------------------------------------------- mix -- mix 3 32-bit values reversibly. For every delta with one or two bit set, and the deltas of all three high bits or all three low bits, whether the original value of a,b,c is almost all zero or is uniformly distributed, * If mix() is run forward or backward, at least 32 bits in a,b,c have at least 1/4 probability of changing. * If mix() is run forward, every bit of c will change between 1/3 and 2/3 of the time. (Well, 22/100 and 78/100 for some 2-bit deltas.) mix() was built out of 36 single-cycle latency instructions in a structure that could supported 2x parallelism, like so: a -= b; a -= c; x = (c>>13); b -= c; a ^= x; b -= a; x = (a<<8); c -= a; b ^= x; c -= b; x = (b>>13); ... Unfortunately, superscalar Pentiums and Sparcs can't take advantage of that parallelism. They've also turned some of those single-cycle latency instructions into multi-cycle latency instructions. Still, this is the fastest good hash I could find. There were about 2^^68 to choose from. I only looked at a billion or so. --------------------------------------------------------------------*/ #define mix(a,b,c) do { a -= b; a -= c; a ^= (c>>13); b -= c; b -= a; b ^= (a<<8); c -= a; c -= b; c ^= (b>>13); a -= b; a -= c; a ^= (c>>12); \ b -= c; b -= a; b ^= (a<<16); c -= a; c -= b; c ^= (b>>5); a -= b; a -= c; a ^= (c>>3); b -= c; b -= a; b ^= (a<<10); c -= a; c -= b; c ^= (b>>15); } while(0); /* -------------------------------------------------------------------- hash() -- hash a variable-length key into a 32-bit value k : the key (the unaligned variable-length array of bytes) len : the length of the key, counting by bytes level : can be any 4-byte value Returns a 32-bit value. Every bit of the key affects every bit of the return value. Every 1-bit and 2-bit delta achieves avalanche. About 36+6len instructions. The best hash table sizes are powers of 2. There is no need to do mod a prime (mod is sooo slow!). If you need less than 32 bits, use a bitmask. For example, if you need only 10 bits, do h = (h & hashmask(10)); In which case, the hash table should have hashsize(10) elements. If you are hashing n strings (uint8_t **)k, do it like this: for (i=0, h=0; i= 12) { a += (k[0] +((uint32_t)k[1]<<8) +((uint32_t)k[2]<<16) +((uint32_t)k[3]<<24)); b += (k[4] +((uint32_t)k[5]<<8) +((uint32_t)k[6]<<16) +((uint32_t)k[7]<<24)); c += (k[8] +((uint32_t)k[9]<<8) +((uint32_t)k[10]<<16)+((uint32_t)k[11]<<24)); mix(a,b,c); k += 12; len -= 12; } /*------------------------------------- handle the last 11 bytes */ c += length; switch(len) /* all the case statements fall through */ { case 11: c+=((uint32_t)k[10]<<24); case 10: c+=((uint32_t)k[9]<<16); case 9 : c+=((uint32_t)k[8]<<8); /* the first byte of c is reserved for the length */ case 8 : b+=((uint32_t)k[7]<<24); case 7 : b+=((uint32_t)k[6]<<16); case 6 : b+=((uint32_t)k[5]<<8); case 5 : b+=k[4]; case 4 : a+=((uint32_t)k[3]<<24); case 3 : a+=((uint32_t)k[2]<<16); case 2 : a+=((uint32_t)k[1]<<8); case 1 : a+=k[0]; /* case 0: nothing left to add */ } mix(a,b,c); /*-------------------------------------------- report the result */ return c; } uint32_t hashDefaultSeed(uint8_t const * k, uint32_t length) { return hash(k,length,0xb979379e); } bambamc-bambamc_0_0_50/src/bambamc/BamBam_Hash.h000066400000000000000000000021101233012646600213630ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(EVAHASH_H) #define EVAHASH_H #include #include extern uint32_t hash(uint8_t const * k, uint32_t length, uint32_t initval /* = 0xb979379e */) BAMBAM_WARN_IF_UNUSEDRESULT; extern uint32_t hashDefaultSeed(uint8_t const * k, uint32_t length) BAMBAM_WARN_IF_UNUSEDRESULT; #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_LineBuffer.c000066400000000000000000000126171233012646600225310ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include #include #include #include #include BamBam_LineBuffer * BamBam_LineBuffer_New(FILE * rfile, int initsize) { BamBam_LineBuffer * object = 0; size_t iobytes = 0; object = (BamBam_LineBuffer *)malloc(sizeof(BamBam_LineBuffer)); if ( ! object ) return BamBam_LineBuffer_Delete(object); memset(object,0,sizeof(BamBam_LineBuffer)); object->file = rfile; if ( ! object->file ) return BamBam_LineBuffer_Delete(object); object->buffer = (char *)malloc(initsize); if ( ! object->buffer ) return BamBam_LineBuffer_Delete(object); object->bufsize = initsize; object->bufferptra = object->buffer; object->bufferptre = object->buffer + object->bufsize; object->bufferptrout = object->buffer; iobytes = fread(object->bufferptra,1,object->bufsize,object->file); object->bufferptrin = object->bufferptra + iobytes; if ( ferror(object->file) ) return BamBam_LineBuffer_Delete(object); if ( feof(object->file) ) object->eof = 1; return object; } BamBam_LineBuffer * BamBam_LineBuffer_Delete(BamBam_LineBuffer * object) { if ( object ) { if ( object->buffer ) { free(object->buffer); object->buffer = 0; } if ( object->tmpbuf ) { free(object->tmpbuf); object->tmpbuf = 0; } free(object); } return 0; } int BamBam_LineBuffer_GetLine(BamBam_LineBuffer * object, char const **a, char const **e) { while ( 1 ) { /* end of line pointer */ char * lineend = object->bufferptrout; /* search for end of buffer or line end */ while ( lineend != object->bufferptrin && *(lineend) != '\n' ) ++lineend; /* we reached the end of the data currently in memory */ if ( lineend == object->bufferptrin ) { /* reached end of file, return what we have */ if ( object->eof ) { /* this is the last line we will return */ if ( object->bufferptrout != object->bufferptrin ) { /* if file ends with a newline */ if ( object->bufferptrin[-1] == '\n' ) { *a = object->bufferptrout; *e = object->bufferptrin-1; object->bufferptrout = object->bufferptrin; return 0; } /* otherwise we append an artifical newline */ else { uint64_t const numbytes = lineend - object->bufferptrout; char * tmpbuf = (char *)malloc(numbytes+1); if ( ! tmpbuf ) return -1; memcpy(tmpbuf,object->bufferptrout,numbytes); tmpbuf[numbytes] = '\n'; free(object->buffer); object->buffer = tmpbuf; object->bufsize = numbytes+1; object->bufferptra = tmpbuf; object->bufferptre = tmpbuf + object->bufsize; object->bufferptrin = object->bufferptre; object->bufferptrout = object->bufferptre; *a = object->bufferptra; *e = object->bufferptre - 1; return 0; } } else { return -1; } } /* we need to read more data */ else { /* do we need to extend the buffer? */ if ( object->bufferptrout == object->bufferptra && object->bufferptrin == object->bufferptre ) { unsigned int const newbufsize = object->bufsize ? 2*object->bufsize : 1; char * newbuf = realloc(object->buffer,newbufsize); if ( newbuf ) { /* fprintf(stderr,"extended buffer to %d bytes\n", newbufsize); */ object->bufferptre = newbuf + newbufsize; object->bufferptrout = newbuf + (object->bufferptrout - object->bufferptra); object->bufferptrin = newbuf + (object->bufferptrin - object->bufferptra); object->bufferptra = newbuf; object->buffer = newbuf; object->bufsize = newbufsize; } else { return -1; } } else { /* move data to front and fill rest of buffer */ uint64_t const used = object->bufferptrin - object->bufferptrout; uint64_t const unused = object->bufsize - used; size_t iobytes = 0; memmove(object->bufferptra, object->bufferptrout,used); object->bufferptrout = object->bufferptra; object->bufferptrin = object->bufferptrout + used; iobytes = fread(object->bufferptrin,1,unused,object->file); if ( ferror(object->file) ) return -1; if ( feof(object->file) ) object->eof = 1; /* fprintf(stderr,"Got %d bytes\n", iobytes); */ object->bufferptrin += iobytes; } } } else { *a = object->bufferptrout; *e = lineend; assert ( *lineend == '\n' ); object->bufferptrout = lineend+1; return 0; } } return -1; } void BamBam_LineBuffer_PutBack(BamBam_LineBuffer * object, char const *a) { object->bufferptrout = (char *)a; } bambamc-bambamc_0_0_50/src/bambamc/BamBam_LineBuffer.h000066400000000000000000000027541233012646600225370ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAMC_LINEBUFFER_H) #define BAMBAMC_LINEBUFFER_H #include #include typedef struct _BamBam_LineBuffer { FILE * file; char * buffer; unsigned int bufsize; int eof; char * tmpbuf; char * bufferptra; char * bufferptrin; char * bufferptrout; char * bufferptre; } BamBam_LineBuffer; extern BamBam_LineBuffer * BamBam_LineBuffer_New(FILE * rfile, int initsize) BAMBAM_WARN_IF_UNUSEDRESULT; extern int BamBam_LineBuffer_GetLine(BamBam_LineBuffer * object, char const **a, char const **e) BAMBAM_WARN_IF_UNUSEDRESULT; extern void BamBam_LineBuffer_PutBack(BamBam_LineBuffer * object, char const *a); extern BamBam_LineBuffer * BamBam_LineBuffer_Delete(BamBam_LineBuffer * object); #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_LineParsing.c000066400000000000000000000055061233012646600227220ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include #include #include #include #include #include char const * BamBam_findLineEnd(char const * s) { while ( *s && (*s != '\n') ) ++s; return s; } char const * BamBam_skipEndOfLine(char const * s) { if ( ! *s ) return s; while ( *s && isspace(*s) ) s++; return s; } char const * BamBam_nextLine(char const * s) { return BamBam_skipEndOfLine(BamBam_findLineEnd(s)); } unsigned int BamBam_getLineLength(char const * s) { return BamBam_findLineEnd(s)-s; } int BamBam_copyLine(char const * s, BamBam_CharBuffer * buffer) { unsigned int const l = BamBam_getLineLength(s); unsigned int i = 0; int ret = 0; for ( i = 0; (! ret) && i < l; ++i ) ret = BamBam_CharBuffer_PushChar(buffer,s[i]); if ( ! ret ) ret = BamBam_CharBuffer_PushChar(buffer,'\n'); return ret; } int BamBam_isValidLine(char const * s, char const ** filtered) { char const * sa; char const * se; if ( ! *s ) return 0; if ( s[0] != '@' ) return 0; sa = s+1; se = sa; while ( *se && *se != '\n' && *se != '\t' ) ++se; while ( *filtered ) { char const * filter = *filtered; if ( (strlen(filter) == (size_t)(se-sa)) && memcmp(filter,sa,se-sa) == 0 ) return 0; ++filtered; } return 1; } char * BamBam_filterHeader(char const * header, char const ** filters) { BamBam_CharBuffer * buffer = BamBam_CharBuffer_New(); char * filtered = 0; int ret = 0; if ( ! buffer ) return 0; while ( *header ) { if ( BamBam_isValidLine(header,filters) ) { ret = BamBam_copyLine(header,buffer); if ( ret < 0 ) { BamBam_CharBuffer_Delete(buffer); return 0; } } header = BamBam_nextLine(header); } /* append terminator */ ret = BamBam_CharBuffer_PushChar(buffer,0); if ( ret < 0 ) { BamBam_CharBuffer_Delete(buffer); return 0; } filtered = BamBam_StrDup((char const *)(buffer->buffer)); if ( ! filtered ) { BamBam_CharBuffer_Delete(buffer); return 0; } BamBam_CharBuffer_Delete(buffer); return filtered; } bambamc-bambamc_0_0_50/src/bambamc/BamBam_LineParsing.h000066400000000000000000000025251233012646600227250ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAM_LINEPARSING_H) #define BAMBAM_LINEPARSING_H #include #include extern char const * BamBam_findLineEnd(char const * s); extern char const * BamBam_skipEndOfLine(char const * s); extern char const * BamBam_nextLine(char const * s); extern unsigned int BamBam_getLineLength(char const * s); extern int BamBam_copyLine(char const * s, BamBam_CharBuffer * buffer); extern int BamBam_isValidLine(char const * s, char const ** filtered); extern char * BamBam_filterHeader(char const * header, char const ** filters); #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_List.c000066400000000000000000000035571233012646600214260ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include void BamBam_ListNode_PushBack(BamBam_List * list, BamBam_ListNode * listnode) { if ( ! list->last ) { list->first = list->last = listnode; } else { list->last->next = listnode; list->last = listnode; } } void BamBam_ListNode_PushFront(BamBam_List * list, BamBam_ListNode * listnode) { if ( ! list->last ) { list->first = list->last = listnode; } else { listnode->next = list->first; list->first = listnode; } } BamBam_List * BamBam_List_New() { BamBam_List * list = 0; list = (BamBam_List *)malloc(sizeof(BamBam_List)); if ( ! list ) return 0; list->first = 0; list->last = 0; return list; } void BamBam_List_Delete(BamBam_List * list) { if ( list ) { if ( list->first ) BamBam_ListNode_DeleteRec(list->first); free (list); } } void BamBam_List_Print(FILE * file, BamBam_List const * list) { if ( list ) { BamBam_ListNode_PrintRec(file,list->first); } } uint64_t BamBam_List_Size(BamBam_List * list) { uint64_t length = 0; BamBam_ListNode * node = list->first; while ( node ) { length++; node = node->next; } return length; }bambamc-bambamc_0_0_50/src/bambamc/BamBam_List.h000066400000000000000000000026741233012646600214320ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAM_LIST_HPP) #define BAMBAM_LIST_HPP #include #include #include typedef struct _BamBam_List { BamBam_ListNode * first; BamBam_ListNode * last; } BamBam_List; extern void BamBam_ListNode_PushBack(BamBam_List * list, BamBam_ListNode * listnode); extern void BamBam_ListNode_PushFront(BamBam_List * list, BamBam_ListNode * listnode); extern BamBam_List * BamBam_List_New() BAMBAM_WARN_IF_UNUSEDRESULT; extern void BamBam_List_Delete(BamBam_List * list); extern void BamBam_List_Print(FILE * file, BamBam_List const * list); extern uint64_t BamBam_List_Size(BamBam_List * list) BAMBAM_WARN_IF_UNUSEDRESULT; #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_ListNode.c000066400000000000000000000041121233012646600222200ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include void BamBam_PrintStringFunction(FILE * file, void const * vstr) { char const * str = (char const *)vstr; fprintf(file,"%s",str); } void BamBam_ListNode_Print(FILE * file, BamBam_ListNode const * node) { if ( node ) { if ( node->bamBamListPrintFunction ) { node->bamBamListPrintFunction(file,node->entry); } else { fprintf(file,""); } } else { fprintf(file,""); } } void BamBam_ListNode_PrintRec(FILE * file, BamBam_ListNode const * node) { if ( node ) { fprintf(file,"Node("); BamBam_ListNode_Print(file,node); fprintf(file,");"); BamBam_ListNode_PrintRec(file,node->next); } } BamBam_ListNode * BamBam_ListNode_New() { BamBam_ListNode * node = 0; node = (BamBam_ListNode *)malloc(sizeof(BamBam_ListNode)); if ( ! node ) return 0; node->next = 0; node->entry = 0; node->bamBamListFreeFunction = 0; node->bamBamListPrintFunction = 0; return node; } void BamBam_ListNode_Delete(BamBam_ListNode * node) { if ( node ) { if ( node->bamBamListFreeFunction ) node->bamBamListFreeFunction(node->entry); free(node); } } void BamBam_ListNode_DeleteRec(BamBam_ListNode * node) { if ( node ) { if ( node->next ) { BamBam_ListNode_DeleteRec(node->next); node->next = 0; } BamBam_ListNode_Delete(node); } } bambamc-bambamc_0_0_50/src/bambamc/BamBam_ListNode.h000066400000000000000000000031731233012646600222330ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAM_LISTNODE_H) #define BAMBAM_LISTNODE_H #include #include #include typedef void (*bamBamListFreeFunction)(void *); typedef void (*bamBamListPrintFunction)(FILE * file, void const *); typedef struct _BamBam_ListNode { struct _BamBam_ListNode * next; void * entry; bamBamListFreeFunction bamBamListFreeFunction; bamBamListPrintFunction bamBamListPrintFunction; } BamBam_ListNode; extern void BamBam_PrintStringFunction(FILE * file, void const * vstr); extern void BamBam_ListNode_Print(FILE * file, BamBam_ListNode const * node); extern void BamBam_ListNode_PrintRec(FILE * file, BamBam_ListNode const * node); extern BamBam_ListNode * BamBam_ListNode_New() BAMBAM_WARN_IF_UNUSEDRESULT; extern void BamBam_ListNode_Delete(BamBam_ListNode * node); extern void BamBam_ListNode_DeleteRec(BamBam_ListNode * node); #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_MergeHeapEntry.h000066400000000000000000000020021233012646600233570ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAM_MERGEHEAPENTRY_H) #define BAMBAM_MERGEHEAPENTRY_H #include typedef struct _BamBam_MergeHeapEntry { BamBam_BamCollationHashEntry * hashentry; uint64_t fileid; } BamBam_MergeHeapEntry; #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_SamBamFileDecoder.c000066400000000000000000000050461233012646600237340ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include BamBam_SamBamFileDecoder * BamBam_SamBamFileDecoder_Delete(BamBam_SamBamFileDecoder * object) { if ( object ) { if ( object->bamdecoder ) BamBam_BamFileDecoder_Delete(object->bamdecoder); if ( object->samdecoder ) BamBam_SamFileDecoder_Delete(object->samdecoder); } free(object); return 0; } BamBam_BamSingleAlignment * BamBam_SamBamFileDecoder_DecodeAlignment(BamBam_SamBamFileDecoder * object) { if ( object && object->bamdecoder ) return BamBam_BamFileDecoder_DecodeAlignment(object->bamdecoder); else if ( object && object->samdecoder ) return BamBam_SamFileDecoder_LoadAlignment(object->samdecoder); else return 0; } static int BamBam_SamBamFileDecoder_ContainsLetter(char const * s, char const c) { while ( *s ) if ( *s == c ) return 1; else ++s; return 0; } BamBam_SamBamFileDecoder * BamBam_SamBamFileDecoder_New(char const * filename, char const * mode) { BamBam_SamBamFileDecoder * object = 0; if ( ! BamBam_SamBamFileDecoder_ContainsLetter(mode,'r') ) return 0; object = (BamBam_SamBamFileDecoder *)malloc(sizeof(BamBam_SamBamFileDecoder)); if ( ! object ) return BamBam_SamBamFileDecoder_Delete(object); memset(object,0,sizeof(BamBam_SamBamFileDecoder)); if ( BamBam_SamBamFileDecoder_ContainsLetter(mode,'b') ) { object->bamdecoder = BamBam_BamFileDecoder_New(filename); if ( ! object->bamdecoder || ! object->bamdecoder->header ) return BamBam_SamBamFileDecoder_Delete(object); object->header = object->bamdecoder->header; } else { object->samdecoder = BamBam_SamFileDecoder_New(filename); if ( ! object->samdecoder || ! object->samdecoder->header ) return BamBam_SamBamFileDecoder_Delete(object); object->header = object->samdecoder->header; } return object; } bambamc-bambamc_0_0_50/src/bambamc/BamBam_SamBamFileDecoder.h000066400000000000000000000026401233012646600237360ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAM_SAMBAMFILEDECODER_H) #define BAMBAM_SAMBAMFILEDECODER_H #include #include typedef struct _BamBam_SamBamFileDecoder { BamBam_BamFileDecoder * bamdecoder; BamBam_SamFileDecoder * samdecoder; BamBam_BamFileHeader * header; } BamBam_SamBamFileDecoder; extern BamBam_BamSingleAlignment * BamBam_SamBamFileDecoder_DecodeAlignment(BamBam_SamBamFileDecoder * object); extern BamBam_SamBamFileDecoder * BamBam_SamBamFileDecoder_Delete(BamBam_SamBamFileDecoder * object); extern BamBam_SamBamFileDecoder * BamBam_SamBamFileDecoder_New(char const * filename, char const * mode); #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_SamFileDecoder.c000066400000000000000000000106071233012646600233130ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include BamBam_BamSingleAlignment * BamBam_SamFileDecoder_LoadAlignment(BamBam_SamFileDecoder * object) { char const * pa = 0; char const * pe = 0; char const * p = 0; unsigned int col = 0; int r = 0; if ( BamBam_LineBuffer_GetLine(object->lb,&pa,&pe) ) return 0; assert ( *pe == '\n' ); p = pa; while ( p != pe && col < BAMBAMC_SAMFILEDECODER_MANDATORYCOLUMNS ) { char const * pc = p; while ( p != pe && *p != '\t' ) ++p; object->fields[col][0] = pc; object->fields[col][1] = p; /* skip over tab */ if ( p != pe ) ++p; col += 1; } if ( col != BAMBAMC_SAMFILEDECODER_MANDATORYCOLUMNS || BamBam_SamInfo_parseSamLine(&object->fields[0],object->saminfo) < 0 ) { fprintf(stderr, "Defect SAM line: "); fwrite(pa,pe-pa,1,stderr); fprintf(stderr,"\n"); return 0; } r = BamBam_CharBuffer_PutAlignmentC( object->aput, object->saminfo->flag, BamBam_BamFileHeader_FindChromosomeIdByName(object->header,object->saminfo->rname), object->saminfo->pos-1, BamBam_BamFileHeader_FindChromosomeIdByName(object->header,object->saminfo->rnext), object->saminfo->pnext-1, object->saminfo->qname, object->saminfo->seq, object->saminfo->qual, object->saminfo->cigar, object->saminfo->mapq, object->saminfo->tlen ); if ( r < 0 ) return 0; #if 0 fprintf(stderr, "ok: "); fwrite(pa,pe-pa,1,stderr); fprintf(stderr,"\n"); #endif return object->aput->calignment; } BamBam_SamFileDecoder * BamBam_SamFileDecoder_Delete(BamBam_SamFileDecoder * object) { if ( object ) { if ( object->closefile ) { fclose(object->closefile); } if ( object->header ) { BamBam_BamFileHeader_Delete(object->header); } if ( object->lb ) { BamBam_LineBuffer_Delete(object->lb); } if ( object->saminfo ) { BamBam_SamInfo_Delete(object->saminfo); } if ( object->aput ) { BamBam_AlignmentPut_Delete(object->aput); } free(object); } return 0; } BamBam_SamFileDecoder * BamBam_SamFileDecoder_NewInternal(BamBam_SamFileDecoder * object, FILE * file) { BamBam_SamInfo_initSamCharTables(); object->header = BamBam_BamFileHeader_New_SAM(file); if ( ! object->header ) return BamBam_SamFileDecoder_Delete(object); object->lb = BamBam_LineBuffer_New(file,1024); if ( ! object->lb ) return BamBam_SamFileDecoder_Delete(object); object->saminfo = BamBam_SamInfo_New(); if ( ! object->saminfo ) return BamBam_SamFileDecoder_Delete(object); object->aput = BamBam_AlignmentPut_New(); if ( ! object->aput ) return BamBam_SamFileDecoder_Delete(object); return object; } BamBam_SamFileDecoder * BamBam_SamFileDecoder_NewFilename(char const * filename) { BamBam_SamFileDecoder * object = 0; object = (BamBam_SamFileDecoder *)malloc(sizeof(BamBam_SamFileDecoder)); if ( ! object ) return BamBam_SamFileDecoder_Delete(object); memset(object,0,sizeof(BamBam_SamFileDecoder)); object->closefile = fopen(filename,"rb"); if ( ! object->closefile ) return BamBam_SamFileDecoder_Delete(object); return BamBam_SamFileDecoder_NewInternal(object,object->closefile); } BamBam_SamFileDecoder * BamBam_SamFileDecoder_NewFd(FILE * file) { BamBam_SamFileDecoder * object = 0; object = (BamBam_SamFileDecoder *)malloc(sizeof(BamBam_SamFileDecoder)); if ( ! object ) return BamBam_SamFileDecoder_Delete(object); memset(object,0,sizeof(BamBam_SamFileDecoder)); return BamBam_SamFileDecoder_NewInternal(object,file); } BamBam_SamFileDecoder * BamBam_SamFileDecoder_New(char const * filename) { if ( strcmp(filename,"-") == 0 ) return BamBam_SamFileDecoder_NewFd(stdin); else return BamBam_SamFileDecoder_NewFilename(filename); } bambamc-bambamc_0_0_50/src/bambamc/BamBam_SamFileDecoder.h000066400000000000000000000033311233012646600233140ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAMC_SAMFILEDECODER_H) #define BAMBAMC_SAMFILEDECODER_H #include #include #include #include #define BAMBAMC_SAMFILEDECODER_MANDATORYCOLUMNS 11 typedef struct _BamBam_SamFileDecoder { FILE * closefile; BamBam_BamFileHeader * header; BamBam_LineBuffer * lb; BamBam_SamInfo * saminfo; BamBam_SamInfo_cptrpair fields[BAMBAMC_SAMFILEDECODER_MANDATORYCOLUMNS]; BamBam_AlignmentPut * aput; } BamBam_SamFileDecoder; extern BamBam_BamSingleAlignment * BamBam_SamFileDecoder_LoadAlignment(BamBam_SamFileDecoder * object); extern BamBam_SamFileDecoder * BamBam_SamFileDecoder_Delete(BamBam_SamFileDecoder * object); extern BamBam_SamFileDecoder * BamBam_SamFileDecoder_NewFd(FILE * file); extern BamBam_SamFileDecoder * BamBam_SamFileDecoder_NewFilename(char const * filename); extern BamBam_SamFileDecoder * BamBam_SamFileDecoder_New(char const * filename); #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_SamInfo.c000066400000000000000000000350751233012646600220470ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include #include #include #include #include #include BamBam_SamInfo * BamBam_SamInfo_Delete(BamBam_SamInfo * object) { if ( object ) { if ( object->qname ) { free(object->qname); object->qname = 0; } if ( object->rname ) { free(object->rname); object->rname = 0; } if ( object->cigar ) { free(object->cigar); object->cigar = 0; } if ( object->rnext ) { free(object->rnext); object->rnext = 0; } if ( object->seq ) { free(object->seq); object->seq = 0; } if ( object->qual ) { free(object->qual); object->qual = 0; } free(object); } return 0; } BamBam_SamInfo * BamBam_SamInfo_New() { BamBam_SamInfo * object = 0; object = (BamBam_SamInfo *)malloc(sizeof(BamBam_SamInfo)); if ( ! object ) return BamBam_SamInfo_Delete(object); memset(object,0,sizeof(BamBam_SamInfo)); return object; } static int BamBam_SamInfo_parseStringField(BamBam_SamInfo_cptrpair field, char ** str, unsigned int * maxlen, bambamc_sam_field_status * defined) { unsigned int const fieldlen = field[1]-field[0]; /* undefined by default */ *defined = bambamc_sam_field_undefined; if ( fieldlen > *maxlen ) { char * newstr = realloc(*str,fieldlen+1); if ( ! newstr ) return -1; *str = newstr; if ( ! *str ) return -1; *maxlen = fieldlen; } if ( fieldlen == 1 && field[0][0] == '*' ) { (*str)[0] = '*'; (*str)[1] = 0; } else { memcpy(*str,field[0],fieldlen); (*str)[fieldlen] = 0; *defined = bambamc_sam_field_undefined; } return 0; } static int BamBam_SamInfo_parseNumberField(BamBam_SamInfo_cptrpair field, int32_t * str, bambamc_sam_field_status * defined) { char const * p = field[0]; uint32_t const fieldlen = field[1]-field[0]; *defined = bambamc_sam_field_undefined; if ( fieldlen > 1 && p[0] == '-' ) { int32_t num = 0; ++p; while ( p != field[1] ) if ( isdigit(*p) ) { num *= 10; num += (*p-'0'); ++p; } else { return -1; } *defined = bambamc_sam_field_defined; *str = -num; } else { int32_t num = 0; while ( p != field[1] ) if ( isdigit(*p) ) { num *= 10; num += (*p-'0'); ++p; } else { return -1; } *defined = bambamc_sam_field_defined; *str = num; } return 0; } static char BamBam_SamInfo_qnameValid[256]; static char BamBam_SamInfo_qnameValidInitialised = 0; static char BamBam_SamInfo_rnameFirstValid[256]; static char BamBam_SamInfo_rnameFirstValidInitialised = 0; static char BamBam_SamInfo_rnameOtherValid[256]; static char BamBam_SamInfo_rnameOtherValidInitialised = 0; static char BamBam_SamInfo_seqValid[256]; static char BamBam_SamInfo_seqValidInitialised = 0; static char BamBam_SamInfo_qualValid[256]; static char BamBam_SamInfo_qualValidInitialised = 0; static int BamBam_SamInfo_tablesInitialised = 0; void BamBam_SamInfo_initSamCharTables() { if ( ! BamBam_SamInfo_tablesInitialised ) { int i = 0; memset(&BamBam_SamInfo_qnameValid[0],0,sizeof(BamBam_SamInfo_qnameValid)); memset(&BamBam_SamInfo_rnameFirstValid[0],0,sizeof(BamBam_SamInfo_rnameFirstValid)); memset(&BamBam_SamInfo_rnameOtherValid[0],0,sizeof(BamBam_SamInfo_rnameOtherValid)); memset(&BamBam_SamInfo_seqValid[0],0,sizeof(BamBam_SamInfo_seqValid)); memset(&BamBam_SamInfo_qualValid[0],0,sizeof(BamBam_SamInfo_qualValid)); for ( i = '!'; i <= '?'; ++i ) BamBam_SamInfo_qnameValid[i] = 1; for ( i = 'A'; i <= '~'; ++i ) BamBam_SamInfo_qnameValid[i] = 1; for ( i = '!'; i <= '('; ++i ) BamBam_SamInfo_rnameFirstValid[i] = 1; BamBam_SamInfo_rnameFirstValid[')'] = 1; for ( i = '+'; i <= '<'; ++i ) BamBam_SamInfo_rnameFirstValid[i] = 1; for ( i = '>'; i <= '~'; ++i ) BamBam_SamInfo_rnameFirstValid[i] = 1; for ( i = '!'; i <= '~'; ++i ) BamBam_SamInfo_rnameOtherValid[i] = 1; for ( i = 'A'; i <= 'Z'; ++i ) BamBam_SamInfo_seqValid[i] = 1; for ( i = 'a'; i <= 'z'; ++i ) BamBam_SamInfo_seqValid[i] = 1; BamBam_SamInfo_seqValid['='] = 1; BamBam_SamInfo_seqValid['.'] = 1; for ( i = '!'; i <= '~'; ++i ) BamBam_SamInfo_qualValid[i] = 1; BamBam_SamInfo_qnameValidInitialised = 1; BamBam_SamInfo_rnameFirstValidInitialised = 1; BamBam_SamInfo_rnameOtherValidInitialised = 1; BamBam_SamInfo_seqValidInitialised = 1; BamBam_SamInfo_qualValidInitialised = 1; BamBam_SamInfo_tablesInitialised = 1; } } int BamBam_SamInfo_parseSamLine(BamBam_SamInfo_cptrpair * fields, BamBam_SamInfo * saminfo) { if ( BamBam_SamInfo_parseStringField(fields[0], &(saminfo->qname), &(saminfo->qnamemax), &(saminfo->qnamedefined)) < 0 ) { fprintf(stderr,"Unable to parse column 0: "); fwrite(fields[0][0],fields[0][1]-fields[0][0],1,stderr); fprintf(stderr,"\n"); return -1; } else { saminfo->qnamelen = fields[0][1] - fields[0][0]; } if ( BamBam_SamInfo_parseNumberField(fields[1], &(saminfo->flag), &(saminfo->flagdefined)) < 0 ) { fprintf(stderr,"Unable to parse column 1: "); fwrite(fields[1][0],fields[1][1]-fields[1][0],1,stderr); fprintf(stderr,"\n"); return -1; } if ( BamBam_SamInfo_parseStringField(fields[2], &(saminfo->rname), &(saminfo->rnamemax), &(saminfo->rnamedefined)) < 0 ) { fprintf(stderr,"Unable to parse column 2: "); fwrite(fields[2][0],fields[2][1]-fields[2][0],1,stderr); fprintf(stderr,"\n"); return -1; } if ( BamBam_SamInfo_parseNumberField(fields[3], &(saminfo->pos), &(saminfo->posdefined)) < 0 ) { fprintf(stderr,"Unable to parse column 3: "); fwrite(fields[3][0],fields[3][1]-fields[3][0],1,stderr); fprintf(stderr,"\n"); return -1; } if ( BamBam_SamInfo_parseNumberField(fields[4], &(saminfo->mapq), &(saminfo->mapqdefined)) < 0 ) { fprintf(stderr,"Unable to parse column 4: "); fwrite(fields[4][0],fields[4][1]-fields[4][0],1,stderr); fprintf(stderr,"\n"); return -1; } if ( BamBam_SamInfo_parseStringField(fields[5], &(saminfo->cigar), &(saminfo->cigarmax), &(saminfo->cigardefined)) < 0 ) { fprintf(stderr,"Unable to parse column 5: "); fwrite(fields[5][0],fields[5][1]-fields[5][0],1,stderr); fprintf(stderr,"\n"); return -1; } if ( BamBam_SamInfo_parseStringField(fields[6], &(saminfo->rnext), &(saminfo->rnextmax), &(saminfo->rnextdefined)) < 0 ) { fprintf(stderr,"Unable to parse column 6: "); fwrite(fields[6][0],fields[6][1]-fields[6][0],1,stderr); fprintf(stderr,"\n"); return -1; } if ( BamBam_SamInfo_parseNumberField(fields[7], &(saminfo->pnext), &(saminfo->pnextdefined)) < 0 ) { fprintf(stderr,"Unable to parse column 7: "); fwrite(fields[7][0],fields[7][1]-fields[7][0],1,stderr); fprintf(stderr,"\n"); return -1; } if ( BamBam_SamInfo_parseNumberField(fields[8], &(saminfo->tlen), &(saminfo->tlendefined)) < 0 ) { fprintf(stderr,"Unable to parse column 8: "); fwrite(fields[8][0],fields[8][1]-fields[8][0],1,stderr); fprintf(stderr,"\n"); return -1; } if ( BamBam_SamInfo_parseStringField(fields[9], &(saminfo->seq), &(saminfo->seqmax), &(saminfo->seqdefined)) < 0 ) { fprintf(stderr,"Unable to parse column 9: "); fwrite(fields[9][0],fields[9][1]-fields[9][0],1,stderr); fprintf(stderr,"\n"); return -1; } else { saminfo->seqlen = fields[9][1] - fields[9][0]; } if ( BamBam_SamInfo_parseStringField(fields[10], &(saminfo->qual), &(saminfo->qualmax), &(saminfo->qualdefined)) < 0 ) { fprintf(stderr,"Unable to parse column 10: "); fwrite(fields[10][0],fields[10][1]-fields[10][0],1,stderr); fprintf(stderr,"\n"); return -1; } else { saminfo->seqlen = fields[10][1] - fields[10][0]; } if ( saminfo->qnamedefined == bambamc_sam_field_defined ) { int ok = 1; char const * p = saminfo->qname; while ( *p ) { ok = ok && BamBam_SamInfo_qnameValid[(int)*p]; ++p; } if ( !ok ) { fprintf(stderr,"Invalid name %s\n", saminfo->qname); return -1; } if ( p == saminfo->qname ) { fprintf(stderr,"Invalid name %s\n", saminfo->qname); return -1; } } if ( saminfo->flagdefined == bambamc_sam_field_defined ) { if ( saminfo->flag < 0 || saminfo->flag >= (int32_t)(1u<<16) ) { fprintf(stderr,"Invalid flag field %d\n", saminfo->flag); return -1; } } else { fprintf(stderr,"Invalid undefined flag field.\n"); return -1; } if ( saminfo->rnamedefined == bambamc_sam_field_defined ) { int ok = 1; char const * p = saminfo->rname; if ( !*p ) { fprintf(stderr,"Invalid empty rname field.\n"); return -1; } ok = ok && BamBam_SamInfo_rnameFirstValid[(int)*p]; ++p; while ( *p ) { ok = ok && BamBam_SamInfo_rnameOtherValid[(int)*p]; ++p; } if ( ! ok ) { fprintf(stderr,"Invalid rname field %s.\n", saminfo->rname); return -1; } } if ( saminfo->posdefined == bambamc_sam_field_defined ) { if ( saminfo->pos < 0 || saminfo->pos >= (int32_t)(1u<<29) ) { fprintf(stderr,"Invalid pos field %d\n", saminfo->pos); return -1; } } else { fprintf(stderr,"Invalid undefined pos field\n"); return -1; } if ( saminfo->mapqdefined == bambamc_sam_field_defined ) { if ( saminfo->mapq < 0 || saminfo->mapq >= (int32_t)(1u<<8) ) { fprintf(stderr,"Invalid mapping quality %d\n", saminfo->mapq); return -1; } } else { fprintf(stderr,"Invalid undefined mapping quality.\n"); return -1; } if ( saminfo->cigardefined == bambamc_sam_field_defined ) { char const * p = saminfo->cigar; unsigned int exseqlen = 0; while ( *p ) { unsigned int num = 0; if ( ! isdigit(*p) ) { fprintf(stderr,"Invalid cigar string: %s\n", saminfo->cigar); return -1; } while ( isdigit(*p) ) { num *= 10; num += (*p)-'0'; ++p; } switch ( *(p++) ) { case 'M': case 'I': case 'S': case '=': case 'X': exseqlen += num; break; case 'D': case 'N': case 'H': case 'P': break; default: fprintf(stderr,"Invalid cigar operator %c\n", *(p-1)); return -1; } } if ( ! (saminfo->flag & BAMBAMC_FUNMAP) ) { if ( exseqlen != strlen(saminfo->seq) ) { fprintf(stderr,"Invalid cigar string %s for sequence %s\n", saminfo->cigar, saminfo->seq); return -1; } } } if ( saminfo->rnextdefined == bambamc_sam_field_defined ) { int ok = 1; char const * p = saminfo->rnext; if ( !*p ) { fprintf(stderr,"Invalid empty rnext field.\n"); return -1; } if ( *p == '=' && !p[1] ) { } else { ok = ok && BamBam_SamInfo_rnameFirstValid[(int)*p]; ++p; while ( *p ) { ok = ok && BamBam_SamInfo_rnameOtherValid[(int)*p]; ++p; } if ( ! ok ) { fprintf(stderr,"Invalid rnext field %s.\n", saminfo->rnext); return -1; } } } if ( saminfo->pnextdefined == bambamc_sam_field_defined ) { if ( saminfo->pnext < 0 || saminfo->pnext >= (int32_t)(1u<<29) ) { fprintf(stderr,"Invalid pnext field %d\n", saminfo->pnext); return -1; } } else { fprintf(stderr,"Invalid undefined pnext field.\n"); return -1; } if ( saminfo->tlendefined == bambamc_sam_field_defined ) { if ( saminfo->tlen < ((-((int32_t)(1u<<29)))+1) || saminfo->tlen >= (int32_t)(1u<<29) ) { fprintf(stderr,"Invalid tlen field %d\n", saminfo->tlen); return -1; } } else { fprintf(stderr,"Invalid undefined tlen field\n"); return -1; } if ( saminfo->seqdefined == bambamc_sam_field_defined ) { int ok = 1; char const * p = saminfo->seq; while ( *p ) { ok = ok && BamBam_SamInfo_seqValid[(int)*p]; ++p; } if ( !ok ) { fprintf(stderr,"Invalid sequence string %s\n", saminfo->seq); return -1; } if ( p == saminfo->seq ) { fprintf(stderr,"Invalid empty sequence string %s\n", saminfo->seq); return -1; } } if ( saminfo->qualdefined == bambamc_sam_field_defined ) { int ok = 1; char const * p = saminfo->qual; while ( *p ) { ok = ok && BamBam_SamInfo_qualValid[(int)*p]; ++p; } if ( !ok ) { fprintf(stderr,"Invalid quality string %s\n", saminfo->qual); return -1; } if ( p == saminfo->qual ) { fprintf(stderr,"Invalid empty quality string %s\n", saminfo->qual); return -1; } } if ( saminfo->qualdefined == bambamc_sam_field_defined && saminfo->seqdefined == bambamc_sam_field_defined ) { if ( saminfo->seqlen != saminfo->quallen ) { fprintf(stderr,"Sequence length %u does not match length of quality string %u\n", saminfo->seqlen, saminfo->quallen); return -1; } } if ( saminfo->seqdefined == bambamc_sam_field_defined && saminfo->qualdefined == bambamc_sam_field_undefined ) { if ( saminfo->qualmax < saminfo->seqlen ) { char * newqual = realloc(saminfo->qual,saminfo->seqlen+1); if ( ! newqual ) { fprintf(stderr,"Failed to allocate memory for quality string.\n"); return -1; } saminfo->qual = newqual; saminfo->qualmax = saminfo->seqlen; } saminfo->qual[saminfo->seqlen] = 0; memset(saminfo->qual,255,saminfo->seqlen); } if ( saminfo->rnamedefined && saminfo->rnextdefined && saminfo->rnext && saminfo->rnext[0] == '=' && saminfo->rnext[1] == 0 ) { unsigned int const rnamelen = strlen(saminfo->rname); if ( saminfo->rnextmax < rnamelen ) { char * newrnext = realloc(saminfo->rnext,rnamelen+1); if ( ! newrnext ) { fprintf(stderr,"Failed to allocate memory for rnext.\n"); return -1; } saminfo->rnext = newrnext; saminfo->rnextmax = rnamelen; strcpy(saminfo->rnext,saminfo->rname); } } /* fprintf(stdout,"Got name %s\n", saminfo->qname); fprintf(stdout,"Got flag %d\n", saminfo->flag); fprintf(stdout,"Got rname %s\n", saminfo->rname); fprintf(stdout,"Got pos %d\n", saminfo->pos); fprintf(stdout,"Got mapq %d\n", saminfo->mapq); fprintf(stdout,"Got cigar %s\n", saminfo->cigar); fprintf(stdout,"Got rnext %s\n", saminfo->rnext); fprintf(stdout,"Got pnext %d\n", saminfo->pnext); fprintf(stdout,"Got tlen %d\n", saminfo->tlen); fprintf(stdout,"Got seq %s\n", saminfo->seq); fprintf(stdout,"Got qual %s\n", saminfo->qual); */ return 0; } bambamc-bambamc_0_0_50/src/bambamc/BamBam_SamInfo.h000066400000000000000000000042051233012646600220430ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAMC_SAMINFO_H) #define BAMBAMC_SAMINFO_H #include typedef enum _bambamc_sam_field_status { bambamc_sam_field_undefined = 0, bambamc_sam_field_defined = 1 } bambamc_sam_field_status; typedef char const * BamBam_SamInfo_cptrpair[2]; typedef struct _BamBam_SamInfo { char * qname; unsigned int qnamemax; bambamc_sam_field_status qnamedefined; unsigned int qnamelen; int32_t flag; bambamc_sam_field_status flagdefined; char * rname; unsigned int rnamemax; bambamc_sam_field_status rnamedefined; int32_t pos; bambamc_sam_field_status posdefined; int32_t mapq; bambamc_sam_field_status mapqdefined; char * cigar; unsigned int cigarmax; bambamc_sam_field_status cigardefined; char * rnext; unsigned int rnextmax; bambamc_sam_field_status rnextdefined; int32_t pnext; bambamc_sam_field_status pnextdefined; int32_t tlen; bambamc_sam_field_status tlendefined; char * seq; unsigned int seqmax; bambamc_sam_field_status seqdefined; unsigned int seqlen; char * qual; unsigned int qualmax; bambamc_sam_field_status qualdefined; unsigned int quallen; } BamBam_SamInfo; extern BamBam_SamInfo * BamBam_SamInfo_Delete(BamBam_SamInfo * object); extern BamBam_SamInfo * BamBam_SamInfo_New(); extern void BamBam_SamInfo_initSamCharTables(); extern int BamBam_SamInfo_parseSamLine(BamBam_SamInfo_cptrpair * fields, BamBam_SamInfo * saminfo); #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_StrDup.c000066400000000000000000000024261233012646600217260ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include #include #include char * BamBam_StrDup(char const * s) { size_t const len = strlen(s); char * c = (char *)malloc(len+1); if ( ! c ) return 0; memcpy(c,s,len); c[len] = 0; return c; } char * BamBam_StrCat(char const * sa, char const * sb) { size_t const lena = strlen(sa); size_t const lenb = strlen(sb); char * c = (char *)malloc(lena+lenb+1); if ( ! c ) return 0; memcpy(c+0 ,sa,lena); memcpy(c+lena,sb,lenb); c[lena+lenb] = 0; return c; } bambamc-bambamc_0_0_50/src/bambamc/BamBam_StrDup.h000066400000000000000000000016561233012646600217370ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAMC_STRDUP_H) #define BAMBAMC_STRDUP_H extern char * BamBam_StrDup(char const * s); extern char * BamBam_StrCat(char const * sa, char const * sb); #endif bambamc-bambamc_0_0_50/src/bambamc/BamBam_Unused.h000066400000000000000000000017241233012646600217550ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #if ! defined(BAMBAM_UNUSED_H) #define BAMBAM_UNUSED_H #if defined(__GNUC__) #define BAMBAM_WARN_IF_UNUSEDRESULT __attribute__ ((warn_unused_result)) #else #define BAMBAM_WARN_IF_UNUSEDRESULT #endif #endif bambamc-bambamc_0_0_50/src/test/000077500000000000000000000000001233012646600165335ustar00rootroot00000000000000bambamc-bambamc_0_0_50/src/test/bamreadertest.c000066400000000000000000000070151233012646600215240ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include #include #include #include #include int runCollationTest() { BamBam_BamCollator * col = 0; int cnt = 0; BamBam_BamCollationHashEntry * entryA = 0; BamBam_BamCollationHashEntry * entryB = 0; char * bufferA = 0, * bufferB = 0; unsigned int bufferAlen = 0, bufferBlen = 0; int aok, bok; /* allocate collator */ col = BamBam_BamCollator_New("tmpdir",16,16,"bam","-"); if ( ! col ) { fprintf(stderr,"Failed to open bam file.\n"); return EXIT_FAILURE; } /* get pairs */ while ( (cnt = BamBam_BamCollator_Get(col,&entryA,&entryB)) ) { if ( cnt == 2 ) { assert ( entryA ); assert ( entryB ); /* fprintf(stdout,"%s\t%s\n", entryA->qname, entryB->qname); */ aok = BamBam_PutAlignmentFastQBuffer(entryA->entry,&bufferA,&bufferAlen,'\n'); bok = BamBam_PutAlignmentFastQBuffer(entryB->entry,&bufferB,&bufferBlen,'\n'); if ( aok >= 0 && bok >= 0 ) { fwrite(bufferA,aok,1,stdout); fwrite(bufferB,bok,1,stdout); } } BamBam_BamCollationHashEntry_Delete(entryA); BamBam_BamCollationHashEntry_Delete(entryB); } free(bufferA); free(bufferB); BamBam_BamCollator_Delete(col); return 0; } void lineBufferTest() { char const * pa = 0; char const * pe = 0; unsigned int numlines = 0; BamBam_LineBuffer * lb = BamBam_LineBuffer_New(stdin,1024); assert ( lb ); while ( ! BamBam_LineBuffer_GetLine(lb,&pa,&pe) ) { if ( pe != pa && pa[0] == '@' ) { fprintf(stderr,"Header line: "); fwrite(pa,pe-pa,1,stderr); fprintf(stderr,"\n"); } else { BamBam_LineBuffer_PutBack(lb,pa); break; } } while ( ! BamBam_LineBuffer_GetLine(lb,&pa,&pe) ) { fprintf(stderr,"Non header line: "); fwrite(pa,pe-pa,1,stderr); fprintf(stderr,"\n"); } BamBam_LineBuffer_Delete(lb); fprintf(stderr,"number of lines is %u\n", numlines); } void samBamSamTest() { uint64_t c = 0; BamBam_SamBamFileDecoder * samdec = BamBam_SamBamFileDecoder_New("-","rb"); BamBam_BamSingleAlignment * algn = 0; assert ( samdec ); while ( (algn = BamBam_SamBamFileDecoder_DecodeAlignment(samdec)) ) { char const * name = BamBam_BamSingleAlignment_GetReadName(algn); fprintf(stderr,"%s\n", name); if ( ++c % (1024*1024) == 0 ) fprintf(stderr,"%d\n", (int)(c/(1024*1024)) ); } BamBam_SamBamFileDecoder_Delete(samdec); } #if defined(_WIN32) # include # include # define SET_BINARY_MODE(handle) _setmode(_fileno(handle), O_BINARY) #else # define SET_BINARY_MODE(handle) ((void)0) #endif int main(/* int argc, char * argv[] */) { SET_BINARY_MODE(stdin); SET_BINARY_MODE(stdout); runCollationTest(); /* lineBufferTest(); */ // samBamSamTest(); return EXIT_SUCCESS; } bambamc-bambamc_0_0_50/src/test/bamwritertest.c000066400000000000000000000043201233012646600215720ustar00rootroot00000000000000/** bambamc Copyright (C) 2009-2013 German Tischler Copyright (C) 2011-2013 Genome Research Limited 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 . **/ #include #include #include #include int testLibBamFree(char const * filename) { int r = -1; BamBam_BamHeaderInfo * hi = 0; BamBam_BamWriter * writer = 0; int const compressionLevel = 1; int status = -1; hi = BamBam_BamHeaderInfo_New("1.4","unknown",0); assert ( hi ); r = BamBam_BamHeaderInfo_AddChromosome(hi, "chr1",10000); assert ( ! r ); writer = BamBam_BamWriter_New(hi,filename,compressionLevel); assert ( writer ); r = BamBam_BamWriter_PutAlignment( writer, 0, 0, 5000, -1, 0, "readname", "ACGTTGCA", "HHHHHHHH", "8M", 60, 100); assert ( r >= 0 ); int val = 61; r = BamBam_BamWriter_PutAuxNumber(writer,"AS",'i',&val); assert ( r >= 0 ); r = BamBam_BamWriter_Commit(writer); assert ( r >= 0 ); r = BamBam_BamWriter_PutAlignment( writer, 0, 0, 5000, -1, 0, "readname_noqual", "ACGTTGCA", 0, "8M", 60, 100); assert ( r >= 0 ); r = BamBam_BamWriter_Commit(writer); assert ( r >= 0 ); BamBam_BamWriter_Delete(writer,&status); assert ( status >= 0 ); BamBam_BamHeaderInfo_Delete(hi); return 0; } #if defined(_WIN32) # include # include # define SET_BINARY_MODE(handle) _setmode(_fileno(handle), O_BINARY) #else # define SET_BINARY_MODE(handle) ((void)0) #endif int main() { SET_BINARY_MODE(stdin); SET_BINARY_MODE(stdout); return testLibBamFree("-"); return 0; } bambamc-bambamc_0_0_50/ubuntu.sh.in000077500000000000000000000002721233012646600172540ustar00rootroot00000000000000make distclean sh configure --prefix=/usr make sudo checkinstall --pkgname @PACKAGE_NAME@ --pkgversion @PACKAGE_VERSION@ --backup=no --default --deldoc \ --maintainer="German Tischler"