pax_global_header00006660000000000000000000000064141507035740014520gustar00rootroot0000000000000052 comment=d3f5a082af86f649d4c74c7fcc946188b1ac9fac andi-0.14/000077500000000000000000000000001415070357400123575ustar00rootroot00000000000000andi-0.14/.clang-format000066400000000000000000000003501415070357400147300ustar00rootroot00000000000000BasedOnStyle: LLVM IndentWidth: 4 TabWidth: 4 UseTab: Always AllowShortIfStatementsOnASingleLine: true AllowShortFunctionsOnASingleLine: false IndentCaseLabels: true AllowShortCaseLabelsOnASingleLine: true BreakBeforeBraces: Attach andi-0.14/.gitignore000066400000000000000000000014471415070357400143550ustar00rootroot00000000000000# Binary and automatically generated files *.o *.a andi andi_* randomSeed.dat seedms testRMQ src/config.h src/stamp-h1 src/config.hin src/config.hin~ #docs docs/doxygen_sqlite3.db docs/html/* docs/latex/* docs/andi.1 *.aux *.auxlock *.dep *.dpth *.toc *.out *.pdf *.backup *.bbl *.blg !andi-manual.pdf *.in !docs/andi.1.in !docs/manual/version.tex.in docs/manual/version.tex *.log **/Makefile configure.scan config.status depcomp install-sh aclocal.m4 **/.deps/ autom4te.cache/ README ChangeLog missing compile configure ar-lib src/.dirstamp # test files *.fasta cachegrind* callgrind* test.trs test-driver test_esa test_seq test_fasta test_process *.trs # Coverage *.gcda *.gcno *.gcov andi.sublime-* # for legacy git only: libs/RMQ/.deps/ libs/RMQ/Makefile Makefile # Profiling: gmon.out profile andi-0.14/.travis.yml000066400000000000000000000030411415070357400144660ustar00rootroot00000000000000language: cpp compiler: - gcc - clang arch: - amd64 - ppc64le sudo: false addons: apt: sources: - deadsnakes - ubuntu-toolchain-r-test packages: - cmake - libglib2.0-dev - libgsl0-dev install: - export LIBDIVDIR="$HOME/libdivsufsort" - pip install --user cpp-coveralls - wget https://github.com/y-256/libdivsufsort/archive/master.tar.gz - tar -xzvf master.tar.gz - cd libdivsufsort-master && mkdir build && cd build - cmake -DCMAKE_BUILD_TYPE="Release" -DCMAKE_INSTALL_PREFIX="$LIBDIVDIR" .. - make && make install script: - CONFIGURE_FLAGS="" - export LD_LIBRARY_PATH="$LIBDIVDIR:$LIBDIVDIR/lib" - export LIBRARY_PATH="$LIBDIVDIR:$LIBRARY_PATH" - cd $TRAVIS_BUILD_DIR - autoreconf -fvi -Im4 - export MYFLAGS="-fprofile-arcs -ftest-coverage -I$LIBDIVDIR/include" - if [ "${CC}" = "clang" ]; then export CONFIGURE_FLAGS="--disable-openmp"; fi - ./configure $CONFIGURE_FLAGS --enable-unit-tests LDFLAGS="-L$LIBDIVDIR/lib" CFLAGS="$MYFLAGS" CXXFLAGS="$MYFLAGS" - make - make check || cat ./test-suite.log || exit 1 - export MYFLAGS="-I$LIBDIVDIR/include" - ./configure $CONFIGURE_FLAGS --enable-unit-tests LDFLAGS="-L$LIBDIVDIR/lib" CFLAGS="$MYFLAGS" CXXFLAGS="$MYFLAGS" - make distcheck DISTCHECK_CONFIGURE_FLAGS="LDFLAGS=\"-L$LIBDIVDIR/lib\" CFLAGS=\"-I$LIBDIVDIR/include\" CXXFLAGS=\"-I$LIBDIVDIR/include\" $CONFIGURE_FLAGS" after_success: - if [ "$CXX" = "g++" ]; then coveralls --exclude libdivsufsort-master -E '^andi-.*' --exclude libs --exclude test --gcov `which gcov-4.8` --gcov-options '\-lp'; fi andi-0.14/COPYING000066400000000000000000001045131415070357400134160ustar00rootroot00000000000000 GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. 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But first, please read . andi-0.14/INSTALL000066400000000000000000000366001415070357400134150ustar00rootroot00000000000000Installation Instructions ************************* Copyright (C) 1994-1996, 1999-2002, 2004-2011 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. 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Run `configure --help' for more details. andi-0.14/Makefile.am000066400000000000000000000017651415070357400144240ustar00rootroot00000000000000ACLOCAL_AMFLAGS = ${ACLOCAL_FLAGS} -I m4 AM_DISTCHECK_CONFIGURE_FLAGS="--enable-unit-tests" .PHONY: all SUBDIRS = . libs opt src docs DIST_SUBDIRS = . libs opt src docs test # Conditionally build the tests if BUILD_TESTS SUBDIRS+= test AM_TESTS_ENVIRONMENT= \ RANDOM_SEED='@SEED@' ; export RANDOM_SEED ; XFAIL_TESTS= TESTS = $(XFAIL_TESTS) test/nan.sh test/low_homo.sh test/test_esa test/test_seq test/test_extra.sh test/test_random.sh test/test_join.sh test/test_process $(TESTS): src/andi endif # BUILD_TESTS dist_noinst_DATA = ChangeLog README.md dist_pdf_DATA = andi-manual.pdf dist_noinst_SCRIPTS= scripts/maf2phy.awk scripts/vmatch.sh scripts/_andi # Recreate the changelog, when the version string changes. ChangeLog: configure.ac echo "Missing Git" > ChangeLog; if test -d $(srcdir)/.git; then \ which git && git log --stat --date=short --abbrev-commit | grep --invert-match '^ [[:alnum:].]' | git stripspace > ChangeLog; \ fi .PHONY: code-docs code-docs: cd docs && $(MAKE) code-docs; andi-0.14/README.md000066400000000000000000000074611415070357400136460ustar00rootroot00000000000000[![Build Status](https://travis-ci.org/EvolBioInf/andi.svg?branch=master)](https://travis-ci.org/EvolBioInf/andi) [![Coverage Status](https://coveralls.io/repos/EvolBioInf/andi/badge.svg?branch=master)](https://coveralls.io/r/EvolBioInf/andi?branch=master) # About This is the `andi` program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because `andi` does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes. This readme covers all necessary instructions for the impatient to get `andi` up and running. For extensive instructions please consult the [manual](andi-manual.pdf). # Installation and Usage Stable versions of `andi` are available via package managers. For manual installation see below. For Debian and Ubuntu: sudo apt-get install andi For macOS with Homebrew: brew tap brewsci/bio brew install andi For ArchLinux with aura: sudo aura -A andi With a successful installation you can get the usage instructions via `--help` or the man page. $ andi --help $ man andi You can simply use `andi` with your genomes in `FASTA` format. $ andi S1.fasta S2.fasta 2 S1 0.0 0.1 s2 0.1 0.0 From this distance matrix the phylogeny can be inferred via neighbor-joining. Check the [manual](andi-manual.pdf) for a more thorough description. ## Manual installation If your system does not support one of the above package managers you have to manually build the latest [stable release](https://github.com/EvolBioInf/andi/releases) from a tarball. See the [manual](andi-manual.pdf) for extensive building instructions. This program has the following external dependencies: [libdivsufsort](https://github.com/y-256/libdivsufsort) and the [GSL](https://www.gnu.org/software/gsl/). Please make sure you installed both before attempting a build. If you did get the source, not as a tarball, but straight from the git repository, you will also need the autotools. Assuming you have installed all prerequisites, building is as easy as follows. $ autoreconf -fi -Im4 # optional when building from tarball $ ./configure $ make $ make install Excessive build instructions are located in `INSTALL`. # Links and Additional Resources The release of this software is accompanied by a paper from [Haubold et al.](http://bioinformatics.oxfordjournals.org/content/31/8/1169). It explains the used *anchor distance* strategy in great detail. The `maf2phy.awk` script used in the validation process is located under `scripts`. Simulations were done using our own [simK](http://guanine.evolbio.mpg.de/bioBox/) tool. For a demo visualising the internals of andi visit our [GitHub pages](http://evolbioinf.github.io/andi/). ## Data Sets 1. 29 E. coli and Shigella strains: [data](http://guanine.evolbio.mpg.de/andi/eco29.fasta.gz) 2. 109 E. coli ST131 strains ([paper](http://www.pnas.org/content/early/2014/03/28/1322678111.abstract)): * [99 newly sequenced strains](https://github.com/BeatsonLab-MicrobialGenomics/ST131_99) * [10 previously published strains](http://guanine.evolbio.mpg.de/andi/st131_extra.tgz) 3. 3085 Streptococcus pneumoniae strains ([paper](http://www.nature.com/ng/journal/v46/n3/full/ng.2895.html)): ftp://ftp.sanger.ac.uk/pub/pathogens/Streptococcus/pneumoniae/Maela_assemblies.tgz ## License Copyright © 2014 - 2021 Fabian Klötzl License GPLv3+: GNU GPL version 3 or later. This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. The full license text is available at . Some files may be licensed differently. ## Contact In case of bugs or unexpected errors don't hesitate to send me a mail: kloetzl@evolbio.mpg.de andi-0.14/andi-manual.pdf000066400000000000000000015365451415070357400152630ustar00rootroot00000000000000%PDF-1.5 % 8 0 obj << /Length 417 /Filter /FlateDecode >> stream xڝRn0>TzlcCOU(ͩno;`Ru+E"73A#&/$ݶb&[]%%k i%(@X͚=Cm;nma(,E#u.;Xhh\{?(duYʩ;J%tӌ}1ş*yʴ22k?vع1}n)'rM ',f艔2DIW}jEd}?oa%y ݕa 4,Р-0ܨWrvn})cnjG0K8ZLnި#W< ПwZ@L:8w(De5k4iU$s?E Ϯ~dzFsSuK`u#[];@ endstream endobj 6 0 obj << /Type /XObject /Subtype /Form /FormType 1 /PTEX.FileName (./andi_labels.pdf) /PTEX.PageNumber 1 /PTEX.InfoDict 16 0 R /BBox [0 0 793 639] /Resources << /XObject << /Xf1 17 0 R >>>> /Length 49 /Filter /FlateDecode >> stream x+r 26S030VIr *T0T0Bf endstream endobj 17 0 obj << /Type /XObject /Resources << /ExtGState << /GS2 18 0 R /GS1 19 0 R >> /Font << /F1 20 0 R >> >> /Subtype /Form /BBox [ 0 0 793 639] /Matrix [ 1 0 0 1 0 0] /Length 1617 /FormType 1 /Filter /FlateDecode >> stream xWKsGﯘcr0==ϣ- `CL֦I}im@I3_%FqOJ>qsx;< ZSPj%n/=~lrU*WyK)thk<rmgAh%,%1H"p$Al?(q*^j< '-Hc+c:&^X`a +FE8@ҢV ` :@cUyOJ'*^7XeNLNPHvc6 :迡:Hm;.oRZ@Eg EY),E>J f<Pr1Q/羚aŵk_VWm=)pJkP56 X_tg<͗0Sl:m<><^~R< ҉F %Ҥ-YW@ҋRl;.*.&Қ󪾑7wwbu; :I fy'Q6=Nm.Z}ܯh=6Ul$tA"=]J:_߶N~ 7_eZE}E]΢Qp7*lri r~yb -V5bO9\CnڀIZSL^xZ+:jB_iJvL WS[wzEciu~TS*zUEDlev?=E.HOBc#*ʹ4]7o~QzA?{ 꾬^qA>I&'a"^G7A$؜`$Xmxv񉮂wmr'~R;q`MQ endstream endobj 26 0 obj << /Length 1254 /Filter /FlateDecode >> stream xڍVKo8 W62(5bg\[IvGK=i2C+JȏGI跻5 //h}[~,J)&gj )!QSLVUrW&,X[)N̺g`,%4ʉyGv͑_9vTmQ9֪nVCxaFRLr1(J7f R}v6m~5 l'dW{ɌCOl~J@]ٸU4m"w;%ӽLe 3ikc V?LmAly@7cnkhɽotQL 7JCQBн;_RZ_M ؔ2v.g<jAQ^(z?lf4KmcY u֯GBhA4ڗLnb0J;]m .yUqH/\c0LHqQ˒hZ{HiOr3Iǹ@g * h {wۧxY&x~w ws d.pA.LޢEd غ91E?.]G 9{01˦'r@'HxQGvyZa\A7@F#KOX $AqҮ!h"@> ӳɃ (~=Cu Nאh/VjWʅOQJs.83E9n,KA>j===d .2,)H-Kx8 eVP,ʶ1a<̚P@cS9_~b05<=kmaz{Iwg0Mn3 cdc;qFũtXA>MwEtFopԶ#៮)f.dID2>e'۵Á{@\ XX'nPGQwJ'%\$u;JɔT+gV~u `݋)n :y&S4$mOWvDH 窫n'E1޾`NC$2s^`XFM8n9tHjƩǶp0eٹBQve`}\q%Sjf7)/}/J]kF :S3WEZ J[)^9?A endstream endobj 56 0 obj << /Length 748 /Filter /FlateDecode >> stream xXMs0WI+ kL&ę<=0q=qkp?}B$L3`0ݷ"h:H`fB5|δ@`)@ Ac (8L"?eu*3kdi #dpa"͒bߍ8W ~% x (k!bbJ >'dEŒ8!pZ*;hQ%X?xlU0oW^5ulN!PҐ=p'7z"q@E1ks#(ǚ[bZ&sy!z]/Yf3?uN?جQe(s'.z.‹,}r<"{2ޖ&0xMi>K?[X9 h:Θok!P$m .r'%(NP Y[䮆I̽;9]T5"$"fUWz5ej|Y|&ZUEB^.M]5&MC AYX|:j îGVļ%wxp'i?,We岑Jr1#όvۂp$7ryz[@6~3oD8"R'l|JM"yh{3~[%*[DzJ|Oqi2+?"ϗ=[_$]̤$āo}wD~s}Y- endstream endobj 80 0 obj << /Length 19 /Filter /FlateDecode >> stream x3PHW0Pp2Ac( endstream endobj 89 0 obj << /Length 2556 /Filter /FlateDecode >> stream xZIsWԀUF NA=JMC4U`6t~=(6^轾~1"D}]}~qJr(k/('B|},a_uyde1<=mQ"fCi4FzDvKIg[Ru5+rO"H `A))&u֍KESS-R)H5` VbaⰨFm mgƥ$nbvk[X1OǹXY X2^\blڨ`" l"K +XhڗFHzݿj o? r/1b֗^9 iJ2dOߍbFĔ5$ u΂_;x位vUQTHMI#u G(ѱ<͘sİQ,]|wc8kE]Lwڏe~<[TkrӪ,Lq)Q og0"~z}7W?dC($mL"!3Y s1IX tI8R,;M`J݉9Cb DS \z\Q[yXE7&cE}* #DeU?ٷǶKDqwTΊԬ_˭ZR٤s/ R#9I}R EERI*C p|3kCQ9 x!L}Kv{ k:[E.-b0`:%`c^`Hԕ34!W6iUZfjvY`L0?H2 )j*[dA^)aI|ba8ňı;<ȞKeUZQ/paS&+6流IYO% ƈ M۲-"dƮP< }>Bm"˽0vC0ĦVqc~ 1r<7 .hta:7e @G|Cby0X2 M%e,"ʏ6})>H G=L,(u'u@uL0 ỹF4ih\΁w+u.f$G{(s(tᅙ}"Z0JLl-0"NI_[_tGQNhHׅuzE-]Ƞ:A!]U 5nuY5S,E@>"T.1j8l/fva鷲 玼 ,]?x Y <Bghlo3^ &HXWn Kmmwet9]3)*xTRCcM2 MA1Y+#ݙ^$e\6ߧ5!p`!7h |#5re>~[+K)|#ۄ)mn1)}=b|2u΋f8a f'É,٦iGUgx1tR=P%_&V)z=J;FUzpc,f#ͯ0‰Ed'~R0Бr1@̝g@,nHN+!͂ ʼ&iʆp*3FwWm~q,KwYCJ2:}bguDJDmmgfސrP[Cax8ai MAS] $"7ܺZ> Ɂ3⮜Ƒhv]W) Cd ' φUOК23qI]ØYN˜!F68bT1 7Ǫvb!z# iy4Oz"ű(gD;b?{䰧2hƶ!ŌތbٝXԡRm) ܙ@10z &MshOZF!T0'k /G N6#{t7FnU#O}dE!auZL;nvo.kS\+f~e.P뉵PLϥ&P:/')j>\^5hP=OjdǻJ.UVL`lyLzߙ>`IXM͚%(Rlⅱa,ʲ*|vnAHZeJթðQʖi=p,PLM{Xª\_O*AP3~cFMMYŴ S'VmS0`lQ>I{҄۶bGB qI *?ܼ endstream endobj 120 0 obj << /Length 1435 /Filter /FlateDecode >> stream xڽXKs6W15S"ěH'3mǵm:=P$$qB*vtoi΁:hoPmл< {EBJ-מQH!!L}xWEy7YY,Y^j'R^6J],= záD̓#AguF\̸1a7`",`W:ͻv,bGqa[O\L˵}ϝCk";L"NHRx"-;ݜl_Sۼye߮>'"U(1io]|" lSd,DI3 lj H|v`ĕ") Ut]뷋O.⪬h0 ٷU\9}|*rjx8/!rD2 .ٙ] )6ڼI[GOYB2At7DUY,S{iֵ=ɊuYـžAv5aIȎPm|F= .y|QVO)O: tJ!׬' sNp@ڐ1 ٷ( _ֵ_$_>f ?` ܜR4 LGpr b.}l(`oY$^dŭOLv.I"Qo-^La0rqBٯG5C^?&=h(CՔ  1iVlCjξ\g7Nu֘.s,70ʞ`KBߜ>F|8VbxJXɷ1Z:^*]eBJ.mooG=xg6u0Wt<)Fz`ʇ`&`Ge^? d6Ddm.gMɴ4$ .kϐDc*\H$LevʎLif61CiYG^H7Nko;y^ u57sO5{)w)I?^<]6s$N%mB_]ܕ*/\Q<g74 ؍LTGG\r~q H3LS͚=Ӵ`|U飽ԋg(j,SLKuH:I!xW{V 0S]xZedEwC(R!/v킒4YspMkR]'U6OC˔}kC"LjI7@;-:fW1) EGT` endstream endobj 137 0 obj << /Length 3216 /Filter /FlateDecode >> stream xZmP@ UR]Kp-д " Ŗm۠o D{H9cD(L}wm£9nHI% j~ 8ȒmH4CX;:KYymZgP}ޑvV7"jGduds.G5TJQ]s۸;e+wܯ4ww7x>SVF S7خbʹVH4Qv7rz? 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AC_CHECK_FUNCS([floor pow sqrt strdup strerror]) AC_CHECK_FUNCS([strndup strcasecmp]) AC_CHECK_FUNCS([strchr strrchr strchrnul]) AC_CHECK_FUNCS([strtoul strtod]) AC_CHECK_FUNCS([reallocarray]) AM_CONDITIONAL([HAVE_REALLOCARRAY], [test "x$ac_cv_func_reallocarray" = xyes]) AM_CONDITIONAL([HAVE_STRCHRNUL], [test "x$ac_cv_func_strchrnul" = xyes]) AC_CONFIG_HEADERS([src/config.h:src/config.hin]) AC_CONFIG_FILES([ Makefile docs/andi.1 docs/Makefile libs/Makefile opt/Makefile src/Makefile test/Makefile ]) AC_OUTPUT andi-0.14/docs/000077500000000000000000000000001415070357400133075ustar00rootroot00000000000000andi-0.14/docs/Doxyfile000066400000000000000000002234061415070357400150240ustar00rootroot00000000000000# Doxyfile 1.7.6.1 # This file describes the settings to be used by the documentation system # doxygen (www.doxygen.org) for a project. # # All text after a hash (#) is considered a comment and will be ignored. # The format is: # TAG = value [value, ...] # For lists items can also be appended using: # TAG += value [value, ...] # Values that contain spaces should be placed between quotes (" "). #--------------------------------------------------------------------------- # Project related configuration options #--------------------------------------------------------------------------- # This tag specifies the encoding used for all characters in the config file # that follow. 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If set # to NO the shortest path that makes the file name unique will be used. FULL_PATH_NAMES = YES # If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag # can be used to strip a user-defined part of the path. Stripping is # only done if one of the specified strings matches the left-hand part of # the path. The tag can be used to show relative paths in the file list. # If left blank the directory from which doxygen is run is used as the # path to strip. STRIP_FROM_PATH = # The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of # the path mentioned in the documentation of a class, which tells # the reader which header file to include in order to use a class. # If left blank only the name of the header file containing the class # definition is used. Otherwise one should specify the include paths that # are normally passed to the compiler using the -I flag. STRIP_FROM_INC_PATH = # If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter # (but less readable) file names. This can be useful if your file system # doesn't support long names like on DOS, Mac, or CD-ROM. SHORT_NAMES = NO # If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen # will interpret the first line (until the first dot) of a JavaDoc-style # comment as the brief description. If set to NO, the JavaDoc # comments will behave just like regular Qt-style comments # (thus requiring an explicit @brief command for a brief description.) JAVADOC_AUTOBRIEF = NO # If the QT_AUTOBRIEF tag is set to YES then Doxygen will # interpret the first line (until the first dot) of a Qt-style # comment as the brief description. If set to NO, the comments # will behave just like regular Qt-style comments (thus requiring # an explicit \brief command for a brief description.) QT_AUTOBRIEF = NO # The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen # treat a multi-line C++ special comment block (i.e. a block of //! or /// # comments) as a brief description. This used to be the default behaviour. # The new default is to treat a multi-line C++ comment block as a detailed # description. Set this tag to YES if you prefer the old behaviour instead. MULTILINE_CPP_IS_BRIEF = NO # If the INHERIT_DOCS tag is set to YES (the default) then an undocumented # member inherits the documentation from any documented member that it # re-implements. INHERIT_DOCS = YES # If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce # a new page for each member. If set to NO, the documentation of a member will # be part of the file/class/namespace that contains it. SEPARATE_MEMBER_PAGES = NO # The TAB_SIZE tag can be used to set the number of spaces in a tab. # Doxygen uses this value to replace tabs by spaces in code fragments. TAB_SIZE = 8 # This tag can be used to specify a number of aliases that acts # as commands in the documentation. An alias has the form "name=value". # For example adding "sideeffect=\par Side Effects:\n" will allow you to # put the command \sideeffect (or @sideeffect) in the documentation, which # will result in a user-defined paragraph with heading "Side Effects:". # You can put \n's in the value part of an alias to insert newlines. ALIASES = # This tag can be used to specify a number of word-keyword mappings (TCL only). # A mapping has the form "name=value". For example adding # "class=itcl::class" will allow you to use the command class in the # itcl::class meaning. TCL_SUBST = # Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C # sources only. Doxygen will then generate output that is more tailored for C. # For instance, some of the names that are used will be different. The list # of all members will be omitted, etc. OPTIMIZE_OUTPUT_FOR_C = YES # Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java # sources only. Doxygen will then generate output that is more tailored for # Java. For instance, namespaces will be presented as packages, qualified # scopes will look different, etc. OPTIMIZE_OUTPUT_JAVA = NO # Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran # sources only. Doxygen will then generate output that is more tailored for # Fortran. OPTIMIZE_FOR_FORTRAN = NO # Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL # sources. Doxygen will then generate output that is tailored for # VHDL. OPTIMIZE_OUTPUT_VHDL = NO # Doxygen selects the parser to use depending on the extension of the files it # parses. With this tag you can assign which parser to use for a given extension. # Doxygen has a built-in mapping, but you can override or extend it using this # tag. The format is ext=language, where ext is a file extension, and language # is one of the parsers supported by doxygen: IDL, Java, Javascript, CSharp, C, # C++, D, PHP, Objective-C, Python, Fortran, VHDL, C, C++. For instance to make # doxygen treat .inc files as Fortran files (default is PHP), and .f files as C # (default is Fortran), use: inc=Fortran f=C. Note that for custom extensions # you also need to set FILE_PATTERNS otherwise the files are not read by doxygen. EXTENSION_MAPPING = # If you use STL classes (i.e. std::string, std::vector, etc.) but do not want # to include (a tag file for) the STL sources as input, then you should # set this tag to YES in order to let doxygen match functions declarations and # definitions whose arguments contain STL classes (e.g. func(std::string); v.s. # func(std::string) {}). This also makes the inheritance and collaboration # diagrams that involve STL classes more complete and accurate. BUILTIN_STL_SUPPORT = NO # If you use Microsoft's C++/CLI language, you should set this option to YES to # enable parsing support. CPP_CLI_SUPPORT = NO # Set the SIP_SUPPORT tag to YES if your project consists of sip sources only. # Doxygen will parse them like normal C++ but will assume all classes use public # instead of private inheritance when no explicit protection keyword is present. SIP_SUPPORT = NO # For Microsoft's IDL there are propget and propput attributes to indicate getter # and setter methods for a property. Setting this option to YES (the default) # will make doxygen replace the get and set methods by a property in the # documentation. This will only work if the methods are indeed getting or # setting a simple type. If this is not the case, or you want to show the # methods anyway, you should set this option to NO. IDL_PROPERTY_SUPPORT = YES # If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC # tag is set to YES, then doxygen will reuse the documentation of the first # member in the group (if any) for the other members of the group. By default # all members of a group must be documented explicitly. DISTRIBUTE_GROUP_DOC = NO # Set the SUBGROUPING tag to YES (the default) to allow class member groups of # the same type (for instance a group of public functions) to be put as a # subgroup of that type (e.g. under the Public Functions section). Set it to # NO to prevent subgrouping. Alternatively, this can be done per class using # the \nosubgrouping command. SUBGROUPING = YES # When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and # unions are shown inside the group in which they are included (e.g. using # @ingroup) instead of on a separate page (for HTML and Man pages) or # section (for LaTeX and RTF). INLINE_GROUPED_CLASSES = NO # When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and # unions with only public data fields will be shown inline in the documentation # of the scope in which they are defined (i.e. file, namespace, or group # documentation), provided this scope is documented. If set to NO (the default), # structs, classes, and unions are shown on a separate page (for HTML and Man # pages) or section (for LaTeX and RTF). INLINE_SIMPLE_STRUCTS = NO # When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum # is documented as struct, union, or enum with the name of the typedef. So # typedef struct TypeS {} TypeT, will appear in the documentation as a struct # with name TypeT. When disabled the typedef will appear as a member of a file, # namespace, or class. And the struct will be named TypeS. This can typically # be useful for C code in case the coding convention dictates that all compound # types are typedef'ed and only the typedef is referenced, never the tag name. TYPEDEF_HIDES_STRUCT = NO # The SYMBOL_CACHE_SIZE determines the size of the internal cache use to # determine which symbols to keep in memory and which to flush to disk. # When the cache is full, less often used symbols will be written to disk. # For small to medium size projects (<1000 input files) the default value is # probably good enough. For larger projects a too small cache size can cause # doxygen to be busy swapping symbols to and from disk most of the time # causing a significant performance penalty. # If the system has enough physical memory increasing the cache will improve the # performance by keeping more symbols in memory. Note that the value works on # a logarithmic scale so increasing the size by one will roughly double the # memory usage. The cache size is given by this formula: # 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0, # corresponding to a cache size of 2^16 = 65536 symbols. SYMBOL_CACHE_SIZE = 0 # Similar to the SYMBOL_CACHE_SIZE the size of the symbol lookup cache can be # set using LOOKUP_CACHE_SIZE. This cache is used to resolve symbols given # their name and scope. Since this can be an expensive process and often the # same symbol appear multiple times in the code, doxygen keeps a cache of # pre-resolved symbols. If the cache is too small doxygen will become slower. # If the cache is too large, memory is wasted. The cache size is given by this # formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range is 0..9, the default is 0, # corresponding to a cache size of 2^16 = 65536 symbols. LOOKUP_CACHE_SIZE = 0 #--------------------------------------------------------------------------- # Build related configuration options #--------------------------------------------------------------------------- # If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in # documentation are documented, even if no documentation was available. # Private class members and static file members will be hidden unless # the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES EXTRACT_ALL = YES # If the EXTRACT_PRIVATE tag is set to YES all private members of a class # will be included in the documentation. EXTRACT_PRIVATE = NO # If the EXTRACT_STATIC tag is set to YES all static members of a file # will be included in the documentation. EXTRACT_STATIC = NO # If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) # defined locally in source files will be included in the documentation. # If set to NO only classes defined in header files are included. EXTRACT_LOCAL_CLASSES = YES # This flag is only useful for Objective-C code. When set to YES local # methods, which are defined in the implementation section but not in # the interface are included in the documentation. # If set to NO (the default) only methods in the interface are included. EXTRACT_LOCAL_METHODS = NO # If this flag is set to YES, the members of anonymous namespaces will be # extracted and appear in the documentation as a namespace called # 'anonymous_namespace{file}', where file will be replaced with the base # name of the file that contains the anonymous namespace. By default # anonymous namespaces are hidden. EXTRACT_ANON_NSPACES = NO # If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all # undocumented members of documented classes, files or namespaces. # If set to NO (the default) these members will be included in the # various overviews, but no documentation section is generated. # This option has no effect if EXTRACT_ALL is enabled. HIDE_UNDOC_MEMBERS = NO # If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all # undocumented classes that are normally visible in the class hierarchy. # If set to NO (the default) these classes will be included in the various # overviews. This option has no effect if EXTRACT_ALL is enabled. HIDE_UNDOC_CLASSES = NO # If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all # friend (class|struct|union) declarations. # If set to NO (the default) these declarations will be included in the # documentation. HIDE_FRIEND_COMPOUNDS = NO # If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any # documentation blocks found inside the body of a function. # If set to NO (the default) these blocks will be appended to the # function's detailed documentation block. HIDE_IN_BODY_DOCS = NO # The INTERNAL_DOCS tag determines if documentation # that is typed after a \internal command is included. If the tag is set # to NO (the default) then the documentation will be excluded. # Set it to YES to include the internal documentation. INTERNAL_DOCS = NO # If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate # file names in lower-case letters. If set to YES upper-case letters are also # allowed. This is useful if you have classes or files whose names only differ # in case and if your file system supports case sensitive file names. Windows # and Mac users are advised to set this option to NO. CASE_SENSE_NAMES = YES # If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen # will show members with their full class and namespace scopes in the # documentation. If set to YES the scope will be hidden. HIDE_SCOPE_NAMES = NO # If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen # will put a list of the files that are included by a file in the documentation # of that file. SHOW_INCLUDE_FILES = YES # If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen # will list include files with double quotes in the documentation # rather than with sharp brackets. FORCE_LOCAL_INCLUDES = NO # If the INLINE_INFO tag is set to YES (the default) then a tag [inline] # is inserted in the documentation for inline members. INLINE_INFO = YES # If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen # will sort the (detailed) documentation of file and class members # alphabetically by member name. If set to NO the members will appear in # declaration order. SORT_MEMBER_DOCS = YES # If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the # brief documentation of file, namespace and class members alphabetically # by member name. If set to NO (the default) the members will appear in # declaration order. SORT_BRIEF_DOCS = NO # If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen # will sort the (brief and detailed) documentation of class members so that # constructors and destructors are listed first. If set to NO (the default) # the constructors will appear in the respective orders defined by # SORT_MEMBER_DOCS and SORT_BRIEF_DOCS. # This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO # and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO. SORT_MEMBERS_CTORS_1ST = NO # If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the # hierarchy of group names into alphabetical order. If set to NO (the default) # the group names will appear in their defined order. SORT_GROUP_NAMES = NO # If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be # sorted by fully-qualified names, including namespaces. If set to # NO (the default), the class list will be sorted only by class name, # not including the namespace part. # Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. # Note: This option applies only to the class list, not to the # alphabetical list. SORT_BY_SCOPE_NAME = NO # If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to # do proper type resolution of all parameters of a function it will reject a # match between the prototype and the implementation of a member function even # if there is only one candidate or it is obvious which candidate to choose # by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen # will still accept a match between prototype and implementation in such cases. STRICT_PROTO_MATCHING = NO # The GENERATE_TODOLIST tag can be used to enable (YES) or # disable (NO) the todo list. This list is created by putting \todo # commands in the documentation. GENERATE_TODOLIST = YES # The GENERATE_TESTLIST tag can be used to enable (YES) or # disable (NO) the test list. This list is created by putting \test # commands in the documentation. GENERATE_TESTLIST = YES # The GENERATE_BUGLIST tag can be used to enable (YES) or # disable (NO) the bug list. This list is created by putting \bug # commands in the documentation. GENERATE_BUGLIST = YES # The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or # disable (NO) the deprecated list. This list is created by putting # \deprecated commands in the documentation. GENERATE_DEPRECATEDLIST= YES # The ENABLED_SECTIONS tag can be used to enable conditional # documentation sections, marked by \if sectionname ... \endif. ENABLED_SECTIONS = # The MAX_INITIALIZER_LINES tag determines the maximum number of lines # the initial value of a variable or macro consists of for it to appear in # the documentation. If the initializer consists of more lines than specified # here it will be hidden. Use a value of 0 to hide initializers completely. # The appearance of the initializer of individual variables and macros in the # documentation can be controlled using \showinitializer or \hideinitializer # command in the documentation regardless of this setting. MAX_INITIALIZER_LINES = 30 # Set the SHOW_USED_FILES tag to NO to disable the list of files generated # at the bottom of the documentation of classes and structs. If set to YES the # list will mention the files that were used to generate the documentation. SHOW_USED_FILES = YES # If the sources in your project are distributed over multiple directories # then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy # in the documentation. The default is NO. SHOW_DIRECTORIES = NO # Set the SHOW_FILES tag to NO to disable the generation of the Files page. # This will remove the Files entry from the Quick Index and from the # Folder Tree View (if specified). The default is YES. SHOW_FILES = YES # Set the SHOW_NAMESPACES tag to NO to disable the generation of the # Namespaces page. # This will remove the Namespaces entry from the Quick Index # and from the Folder Tree View (if specified). The default is YES. SHOW_NAMESPACES = YES # The FILE_VERSION_FILTER tag can be used to specify a program or script that # doxygen should invoke to get the current version for each file (typically from # the version control system). Doxygen will invoke the program by executing (via # popen()) the command , where is the value of # the FILE_VERSION_FILTER tag, and is the name of an input file # provided by doxygen. Whatever the program writes to standard output # is used as the file version. See the manual for examples. FILE_VERSION_FILTER = # The LAYOUT_FILE tag can be used to specify a layout file which will be parsed # by doxygen. The layout file controls the global structure of the generated # output files in an output format independent way. The create the layout file # that represents doxygen's defaults, run doxygen with the -l option. # You can optionally specify a file name after the option, if omitted # DoxygenLayout.xml will be used as the name of the layout file. LAYOUT_FILE = # The CITE_BIB_FILES tag can be used to specify one or more bib files # containing the references data. This must be a list of .bib files. The # .bib extension is automatically appended if omitted. Using this command # requires the bibtex tool to be installed. See also # http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style # of the bibliography can be controlled using LATEX_BIB_STYLE. To use this # feature you need bibtex and perl available in the search path. CITE_BIB_FILES = #--------------------------------------------------------------------------- # configuration options related to warning and progress messages #--------------------------------------------------------------------------- # The QUIET tag can be used to turn on/off the messages that are generated # by doxygen. Possible values are YES and NO. If left blank NO is used. QUIET = NO # The WARNINGS tag can be used to turn on/off the warning messages that are # generated by doxygen. Possible values are YES and NO. If left blank # NO is used. WARNINGS = YES # If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings # for undocumented members. If EXTRACT_ALL is set to YES then this flag will # automatically be disabled. WARN_IF_UNDOCUMENTED = YES # If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for # potential errors in the documentation, such as not documenting some # parameters in a documented function, or documenting parameters that # don't exist or using markup commands wrongly. WARN_IF_DOC_ERROR = YES # The WARN_NO_PARAMDOC option can be enabled to get warnings for # functions that are documented, but have no documentation for their parameters # or return value. If set to NO (the default) doxygen will only warn about # wrong or incomplete parameter documentation, but not about the absence of # documentation. WARN_NO_PARAMDOC = NO # The WARN_FORMAT tag determines the format of the warning messages that # doxygen can produce. The string should contain the $file, $line, and $text # tags, which will be replaced by the file and line number from which the # warning originated and the warning text. Optionally the format may contain # $version, which will be replaced by the version of the file (if it could # be obtained via FILE_VERSION_FILTER) WARN_FORMAT = "$file:$line: $text" # The WARN_LOGFILE tag can be used to specify a file to which warning # and error messages should be written. If left blank the output is written # to stderr. WARN_LOGFILE = #--------------------------------------------------------------------------- # configuration options related to the input files #--------------------------------------------------------------------------- # The INPUT tag can be used to specify the files and/or directories that contain # documented source files. You may enter file names like "myfile.cpp" or # directories like "/usr/src/myproject". Separate the files or directories # with spaces. INPUT = ../src # This tag can be used to specify the character encoding of the source files # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is # also the default input encoding. Doxygen uses libiconv (or the iconv built # into libc) for the transcoding. See http://www.gnu.org/software/libiconv for # the list of possible encodings. INPUT_ENCODING = UTF-8 # If the value of the INPUT tag contains directories, you can use the # FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp # and *.h) to filter out the source-files in the directories. If left # blank the following patterns are tested: # *.c *.cc *.cxx *.cpp *.c++ *.d *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh # *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py # *.f90 *.f *.for *.vhd *.vhdl FILE_PATTERNS = # The RECURSIVE tag can be used to turn specify whether or not subdirectories # should be searched for input files as well. Possible values are YES and NO. # If left blank NO is used. RECURSIVE = NO # The EXCLUDE tag can be used to specify files and/or directories that should be # excluded from the INPUT source files. This way you can easily exclude a # subdirectory from a directory tree whose root is specified with the INPUT tag. # Note that relative paths are relative to the directory from which doxygen is # run. EXCLUDE = # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or # directories that are symbolic links (a Unix file system feature) are excluded # from the input. EXCLUDE_SYMLINKS = NO # If the value of the INPUT tag contains directories, you can use the # EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude # certain files from those directories. Note that the wildcards are matched # against the file with absolute path, so to exclude all test directories # for example use the pattern */test/* EXCLUDE_PATTERNS = # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names # (namespaces, classes, functions, etc.) that should be excluded from the # output. The symbol name can be a fully qualified name, a word, or if the # wildcard * is used, a substring. Examples: ANamespace, AClass, # AClass::ANamespace, ANamespace::*Test EXCLUDE_SYMBOLS = # The EXAMPLE_PATH tag can be used to specify one or more files or # directories that contain example code fragments that are included (see # the \include command). EXAMPLE_PATH = # If the value of the EXAMPLE_PATH tag contains directories, you can use the # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp # and *.h) to filter out the source-files in the directories. If left # blank all files are included. EXAMPLE_PATTERNS = # If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be # searched for input files to be used with the \include or \dontinclude # commands irrespective of the value of the RECURSIVE tag. # Possible values are YES and NO. If left blank NO is used. EXAMPLE_RECURSIVE = NO # The IMAGE_PATH tag can be used to specify one or more files or # directories that contain image that are included in the documentation (see # the \image command). IMAGE_PATH = # The INPUT_FILTER tag can be used to specify a program that doxygen should # invoke to filter for each input file. Doxygen will invoke the filter program # by executing (via popen()) the command , where # is the value of the INPUT_FILTER tag, and is the name of an # input file. Doxygen will then use the output that the filter program writes # to standard output. # If FILTER_PATTERNS is specified, this tag will be # ignored. INPUT_FILTER = # The FILTER_PATTERNS tag can be used to specify filters on a per file pattern # basis. # Doxygen will compare the file name with each pattern and apply the # filter if there is a match. # The filters are a list of the form: # pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further # info on how filters are used. If FILTER_PATTERNS is empty or if # non of the patterns match the file name, INPUT_FILTER is applied. FILTER_PATTERNS = # If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using # INPUT_FILTER) will be used to filter the input files when producing source # files to browse (i.e. when SOURCE_BROWSER is set to YES). FILTER_SOURCE_FILES = NO # The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file # pattern. A pattern will override the setting for FILTER_PATTERN (if any) # and it is also possible to disable source filtering for a specific pattern # using *.ext= (so without naming a filter). This option only has effect when # FILTER_SOURCE_FILES is enabled. FILTER_SOURCE_PATTERNS = #--------------------------------------------------------------------------- # configuration options related to source browsing #--------------------------------------------------------------------------- # If the SOURCE_BROWSER tag is set to YES then a list of source files will # be generated. Documented entities will be cross-referenced with these sources. # Note: To get rid of all source code in the generated output, make sure also # VERBATIM_HEADERS is set to NO. SOURCE_BROWSER = NO # Setting the INLINE_SOURCES tag to YES will include the body # of functions and classes directly in the documentation. INLINE_SOURCES = NO # Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct # doxygen to hide any special comment blocks from generated source code # fragments. Normal C and C++ comments will always remain visible. STRIP_CODE_COMMENTS = YES # If the REFERENCED_BY_RELATION tag is set to YES # then for each documented function all documented # functions referencing it will be listed. REFERENCED_BY_RELATION = NO # If the REFERENCES_RELATION tag is set to YES # then for each documented function all documented entities # called/used by that function will be listed. REFERENCES_RELATION = NO # If the REFERENCES_LINK_SOURCE tag is set to YES (the default) # and SOURCE_BROWSER tag is set to YES, then the hyperlinks from # functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will # link to the source code. # Otherwise they will link to the documentation. REFERENCES_LINK_SOURCE = YES # If the USE_HTAGS tag is set to YES then the references to source code # will point to the HTML generated by the htags(1) tool instead of doxygen # built-in source browser. The htags tool is part of GNU's global source # tagging system (see http://www.gnu.org/software/global/global.html). You # will need version 4.8.6 or higher. USE_HTAGS = NO # If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen # will generate a verbatim copy of the header file for each class for # which an include is specified. Set to NO to disable this. VERBATIM_HEADERS = YES #--------------------------------------------------------------------------- # configuration options related to the alphabetical class index #--------------------------------------------------------------------------- # If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index # of all compounds will be generated. Enable this if the project # contains a lot of classes, structs, unions or interfaces. ALPHABETICAL_INDEX = YES # If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then # the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns # in which this list will be split (can be a number in the range [1..20]) COLS_IN_ALPHA_INDEX = 5 # In case all classes in a project start with a common prefix, all # classes will be put under the same header in the alphabetical index. # The IGNORE_PREFIX tag can be used to specify one or more prefixes that # should be ignored while generating the index headers. IGNORE_PREFIX = #--------------------------------------------------------------------------- # configuration options related to the HTML output #--------------------------------------------------------------------------- # If the GENERATE_HTML tag is set to YES (the default) Doxygen will # generate HTML output. GENERATE_HTML = YES # The HTML_OUTPUT tag is used to specify where the HTML docs will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `html' will be used as the default path. HTML_OUTPUT = html # The HTML_FILE_EXTENSION tag can be used to specify the file extension for # each generated HTML page (for example: .htm,.php,.asp). If it is left blank # doxygen will generate files with .html extension. HTML_FILE_EXTENSION = .html # The HTML_HEADER tag can be used to specify a personal HTML header for # each generated HTML page. If it is left blank doxygen will generate a # standard header. Note that when using a custom header you are responsible # for the proper inclusion of any scripts and style sheets that doxygen # needs, which is dependent on the configuration options used. # It is advised to generate a default header using "doxygen -w html # header.html footer.html stylesheet.css YourConfigFile" and then modify # that header. Note that the header is subject to change so you typically # have to redo this when upgrading to a newer version of doxygen or when # changing the value of configuration settings such as GENERATE_TREEVIEW! HTML_HEADER = # The HTML_FOOTER tag can be used to specify a personal HTML footer for # each generated HTML page. If it is left blank doxygen will generate a # standard footer. HTML_FOOTER = # The HTML_STYLESHEET tag can be used to specify a user-defined cascading # style sheet that is used by each HTML page. It can be used to # fine-tune the look of the HTML output. If the tag is left blank doxygen # will generate a default style sheet. Note that doxygen will try to copy # the style sheet file to the HTML output directory, so don't put your own # style sheet in the HTML output directory as well, or it will be erased! HTML_STYLESHEET = # The HTML_EXTRA_FILES tag can be used to specify one or more extra images or # other source files which should be copied to the HTML output directory. Note # that these files will be copied to the base HTML output directory. Use the # $relpath$ marker in the HTML_HEADER and/or HTML_FOOTER files to load these # files. In the HTML_STYLESHEET file, use the file name only. Also note that # the files will be copied as-is; there are no commands or markers available. HTML_EXTRA_FILES = # The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. # Doxygen will adjust the colors in the style sheet and background images # according to this color. Hue is specified as an angle on a colorwheel, # see http://en.wikipedia.org/wiki/Hue for more information. # For instance the value 0 represents red, 60 is yellow, 120 is green, # 180 is cyan, 240 is blue, 300 purple, and 360 is red again. # The allowed range is 0 to 359. HTML_COLORSTYLE_HUE = 220 # The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of # the colors in the HTML output. For a value of 0 the output will use # grayscales only. A value of 255 will produce the most vivid colors. HTML_COLORSTYLE_SAT = 100 # The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to # the luminance component of the colors in the HTML output. Values below # 100 gradually make the output lighter, whereas values above 100 make # the output darker. The value divided by 100 is the actual gamma applied, # so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2, # and 100 does not change the gamma. HTML_COLORSTYLE_GAMMA = 80 # If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML # page will contain the date and time when the page was generated. Setting # this to NO can help when comparing the output of multiple runs. HTML_TIMESTAMP = YES # If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, # files or namespaces will be aligned in HTML using tables. If set to # NO a bullet list will be used. HTML_ALIGN_MEMBERS = YES # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML # documentation will contain sections that can be hidden and shown after the # page has loaded. For this to work a browser that supports # JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox # Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari). HTML_DYNAMIC_SECTIONS = NO # If the GENERATE_DOCSET tag is set to YES, additional index files # will be generated that can be used as input for Apple's Xcode 3 # integrated development environment, introduced with OSX 10.5 (Leopard). # To create a documentation set, doxygen will generate a Makefile in the # HTML output directory. Running make will produce the docset in that # directory and running "make install" will install the docset in # ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find # it at startup. # See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html # for more information. GENERATE_DOCSET = NO # When GENERATE_DOCSET tag is set to YES, this tag determines the name of the # feed. A documentation feed provides an umbrella under which multiple # documentation sets from a single provider (such as a company or product suite) # can be grouped. DOCSET_FEEDNAME = "Doxygen generated docs" # When GENERATE_DOCSET tag is set to YES, this tag specifies a string that # should uniquely identify the documentation set bundle. This should be a # reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen # will append .docset to the name. DOCSET_BUNDLE_ID = org.doxygen.Project # When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely identify # the documentation publisher. This should be a reverse domain-name style # string, e.g. com.mycompany.MyDocSet.documentation. DOCSET_PUBLISHER_ID = org.doxygen.Publisher # The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher. DOCSET_PUBLISHER_NAME = Publisher # If the GENERATE_HTMLHELP tag is set to YES, additional index files # will be generated that can be used as input for tools like the # Microsoft HTML help workshop to generate a compiled HTML help file (.chm) # of the generated HTML documentation. GENERATE_HTMLHELP = NO # If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can # be used to specify the file name of the resulting .chm file. You # can add a path in front of the file if the result should not be # written to the html output directory. CHM_FILE = # If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can # be used to specify the location (absolute path including file name) of # the HTML help compiler (hhc.exe). If non-empty doxygen will try to run # the HTML help compiler on the generated index.hhp. HHC_LOCATION = # If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag # controls if a separate .chi index file is generated (YES) or that # it should be included in the master .chm file (NO). GENERATE_CHI = NO # If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING # is used to encode HtmlHelp index (hhk), content (hhc) and project file # content. CHM_INDEX_ENCODING = # If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag # controls whether a binary table of contents is generated (YES) or a # normal table of contents (NO) in the .chm file. BINARY_TOC = NO # The TOC_EXPAND flag can be set to YES to add extra items for group members # to the contents of the HTML help documentation and to the tree view. TOC_EXPAND = NO # If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and # QHP_VIRTUAL_FOLDER are set, an additional index file will be generated # that can be used as input for Qt's qhelpgenerator to generate a # Qt Compressed Help (.qch) of the generated HTML documentation. GENERATE_QHP = NO # If the QHG_LOCATION tag is specified, the QCH_FILE tag can # be used to specify the file name of the resulting .qch file. # The path specified is relative to the HTML output folder. QCH_FILE = # The QHP_NAMESPACE tag specifies the namespace to use when generating # Qt Help Project output. For more information please see # http://doc.trolltech.com/qthelpproject.html#namespace QHP_NAMESPACE = org.doxygen.Project # The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating # Qt Help Project output. For more information please see # http://doc.trolltech.com/qthelpproject.html#virtual-folders QHP_VIRTUAL_FOLDER = doc # If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to # add. For more information please see # http://doc.trolltech.com/qthelpproject.html#custom-filters QHP_CUST_FILTER_NAME = # The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the # custom filter to add. For more information please see # # Qt Help Project / Custom Filters. QHP_CUST_FILTER_ATTRS = # The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this # project's # filter section matches. # # Qt Help Project / Filter Attributes. QHP_SECT_FILTER_ATTRS = # If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can # be used to specify the location of Qt's qhelpgenerator. # If non-empty doxygen will try to run qhelpgenerator on the generated # .qhp file. QHG_LOCATION = # If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files # will be generated, which together with the HTML files, form an Eclipse help # plugin. To install this plugin and make it available under the help contents # menu in Eclipse, the contents of the directory containing the HTML and XML # files needs to be copied into the plugins directory of eclipse. The name of # the directory within the plugins directory should be the same as # the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before # the help appears. GENERATE_ECLIPSEHELP = NO # A unique identifier for the eclipse help plugin. When installing the plugin # the directory name containing the HTML and XML files should also have # this name. ECLIPSE_DOC_ID = org.doxygen.Project # The DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) # at top of each HTML page. The value NO (the default) enables the index and # the value YES disables it. Since the tabs have the same information as the # navigation tree you can set this option to NO if you already set # GENERATE_TREEVIEW to YES. DISABLE_INDEX = NO # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index # structure should be generated to display hierarchical information. # If the tag value is set to YES, a side panel will be generated # containing a tree-like index structure (just like the one that # is generated for HTML Help). For this to work a browser that supports # JavaScript, DHTML, CSS and frames is required (i.e. any modern browser). # Windows users are probably better off using the HTML help feature. # Since the tree basically has the same information as the tab index you # could consider to set DISABLE_INDEX to NO when enabling this option. GENERATE_TREEVIEW = NO # The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values # (range [0,1..20]) that doxygen will group on one line in the generated HTML # documentation. Note that a value of 0 will completely suppress the enum # values from appearing in the overview section. ENUM_VALUES_PER_LINE = 4 # By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories, # and Class Hierarchy pages using a tree view instead of an ordered list. USE_INLINE_TREES = NO # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be # used to set the initial width (in pixels) of the frame in which the tree # is shown. TREEVIEW_WIDTH = 250 # When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open # links to external symbols imported via tag files in a separate window. EXT_LINKS_IN_WINDOW = NO # Use this tag to change the font size of Latex formulas included # as images in the HTML documentation. The default is 10. Note that # when you change the font size after a successful doxygen run you need # to manually remove any form_*.png images from the HTML output directory # to force them to be regenerated. FORMULA_FONTSIZE = 10 # Use the FORMULA_TRANPARENT tag to determine whether or not the images # generated for formulas are transparent PNGs. Transparent PNGs are # not supported properly for IE 6.0, but are supported on all modern browsers. # Note that when changing this option you need to delete any form_*.png files # in the HTML output before the changes have effect. FORMULA_TRANSPARENT = YES # Enable the USE_MATHJAX option to render LaTeX formulas using MathJax # (see http://www.mathjax.org) which uses client side Javascript for the # rendering instead of using prerendered bitmaps. Use this if you do not # have LaTeX installed or if you want to formulas look prettier in the HTML # output. When enabled you also need to install MathJax separately and # configure the path to it using the MATHJAX_RELPATH option. USE_MATHJAX = NO # When MathJax is enabled you need to specify the location relative to the # HTML output directory using the MATHJAX_RELPATH option. The destination # directory should contain the MathJax.js script. For instance, if the mathjax # directory is located at the same level as the HTML output directory, then # MATHJAX_RELPATH should be ../mathjax. The default value points to the # mathjax.org site, so you can quickly see the result without installing # MathJax, but it is strongly recommended to install a local copy of MathJax # before deployment. MATHJAX_RELPATH = http://www.mathjax.org/mathjax # The MATHJAX_EXTENSIONS tag can be used to specify one or MathJax extension # names that should be enabled during MathJax rendering. MATHJAX_EXTENSIONS = # When the SEARCHENGINE tag is enabled doxygen will generate a search box # for the HTML output. The underlying search engine uses javascript # and DHTML and should work on any modern browser. Note that when using # HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets # (GENERATE_DOCSET) there is already a search function so this one should # typically be disabled. For large projects the javascript based search engine # can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution. SEARCHENGINE = YES # When the SERVER_BASED_SEARCH tag is enabled the search engine will be # implemented using a PHP enabled web server instead of at the web client # using Javascript. Doxygen will generate the search PHP script and index # file to put on the web server. The advantage of the server # based approach is that it scales better to large projects and allows # full text search. The disadvantages are that it is more difficult to setup # and does not have live searching capabilities. SERVER_BASED_SEARCH = NO #--------------------------------------------------------------------------- # configuration options related to the LaTeX output #--------------------------------------------------------------------------- # If the GENERATE_LATEX tag is set to YES (the default) Doxygen will # generate Latex output. GENERATE_LATEX = YES # The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `latex' will be used as the default path. LATEX_OUTPUT = latex # The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be # invoked. If left blank `latex' will be used as the default command name. # Note that when enabling USE_PDFLATEX this option is only used for # generating bitmaps for formulas in the HTML output, but not in the # Makefile that is written to the output directory. LATEX_CMD_NAME = latex # The MAKEINDEX_CMD_NAME tag can be used to specify the command name to # generate index for LaTeX. If left blank `makeindex' will be used as the # default command name. MAKEINDEX_CMD_NAME = makeindex # If the COMPACT_LATEX tag is set to YES Doxygen generates more compact # LaTeX documents. This may be useful for small projects and may help to # save some trees in general. COMPACT_LATEX = NO # The PAPER_TYPE tag can be used to set the paper type that is used # by the printer. Possible values are: a4, letter, legal and # executive. If left blank a4wide will be used. PAPER_TYPE = a4 # The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX # packages that should be included in the LaTeX output. EXTRA_PACKAGES = # The LATEX_HEADER tag can be used to specify a personal LaTeX header for # the generated latex document. The header should contain everything until # the first chapter. If it is left blank doxygen will generate a # standard header. Notice: only use this tag if you know what you are doing! LATEX_HEADER = # The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for # the generated latex document. The footer should contain everything after # the last chapter. If it is left blank doxygen will generate a # standard footer. Notice: only use this tag if you know what you are doing! LATEX_FOOTER = # If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated # is prepared for conversion to pdf (using ps2pdf). The pdf file will # contain links (just like the HTML output) instead of page references # This makes the output suitable for online browsing using a pdf viewer. PDF_HYPERLINKS = YES # If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of # plain latex in the generated Makefile. Set this option to YES to get a # higher quality PDF documentation. USE_PDFLATEX = YES # If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. # command to the generated LaTeX files. This will instruct LaTeX to keep # running if errors occur, instead of asking the user for help. # This option is also used when generating formulas in HTML. LATEX_BATCHMODE = NO # If LATEX_HIDE_INDICES is set to YES then doxygen will not # include the index chapters (such as File Index, Compound Index, etc.) # in the output. LATEX_HIDE_INDICES = NO # If LATEX_SOURCE_CODE is set to YES then doxygen will include # source code with syntax highlighting in the LaTeX output. # Note that which sources are shown also depends on other settings # such as SOURCE_BROWSER. LATEX_SOURCE_CODE = NO # The LATEX_BIB_STYLE tag can be used to specify the style to use for the # bibliography, e.g. plainnat, or ieeetr. The default style is "plain". See # http://en.wikipedia.org/wiki/BibTeX for more info. LATEX_BIB_STYLE = plain #--------------------------------------------------------------------------- # configuration options related to the RTF output #--------------------------------------------------------------------------- # If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output # The RTF output is optimized for Word 97 and may not look very pretty with # other RTF readers or editors. GENERATE_RTF = NO # The RTF_OUTPUT tag is used to specify where the RTF docs will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `rtf' will be used as the default path. RTF_OUTPUT = rtf # If the COMPACT_RTF tag is set to YES Doxygen generates more compact # RTF documents. This may be useful for small projects and may help to # save some trees in general. COMPACT_RTF = NO # If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated # will contain hyperlink fields. The RTF file will # contain links (just like the HTML output) instead of page references. # This makes the output suitable for online browsing using WORD or other # programs which support those fields. # Note: wordpad (write) and others do not support links. RTF_HYPERLINKS = NO # Load style sheet definitions from file. Syntax is similar to doxygen's # config file, i.e. a series of assignments. You only have to provide # replacements, missing definitions are set to their default value. RTF_STYLESHEET_FILE = # Set optional variables used in the generation of an rtf document. # Syntax is similar to doxygen's config file. RTF_EXTENSIONS_FILE = #--------------------------------------------------------------------------- # configuration options related to the man page output #--------------------------------------------------------------------------- # If the GENERATE_MAN tag is set to YES (the default) Doxygen will # generate man pages GENERATE_MAN = NO # The MAN_OUTPUT tag is used to specify where the man pages will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `man' will be used as the default path. MAN_OUTPUT = man # The MAN_EXTENSION tag determines the extension that is added to # the generated man pages (default is the subroutine's section .3) MAN_EXTENSION = .3 # If the MAN_LINKS tag is set to YES and Doxygen generates man output, # then it will generate one additional man file for each entity # documented in the real man page(s). These additional files # only source the real man page, but without them the man command # would be unable to find the correct page. The default is NO. MAN_LINKS = NO #--------------------------------------------------------------------------- # configuration options related to the XML output #--------------------------------------------------------------------------- # If the GENERATE_XML tag is set to YES Doxygen will # generate an XML file that captures the structure of # the code including all documentation. GENERATE_XML = NO # The XML_OUTPUT tag is used to specify where the XML pages will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `xml' will be used as the default path. XML_OUTPUT = xml # The XML_SCHEMA tag can be used to specify an XML schema, # which can be used by a validating XML parser to check the # syntax of the XML files. XML_SCHEMA = # The XML_DTD tag can be used to specify an XML DTD, # which can be used by a validating XML parser to check the # syntax of the XML files. XML_DTD = # If the XML_PROGRAMLISTING tag is set to YES Doxygen will # dump the program listings (including syntax highlighting # and cross-referencing information) to the XML output. Note that # enabling this will significantly increase the size of the XML output. XML_PROGRAMLISTING = YES #--------------------------------------------------------------------------- # configuration options for the AutoGen Definitions output #--------------------------------------------------------------------------- # If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will # generate an AutoGen Definitions (see autogen.sf.net) file # that captures the structure of the code including all # documentation. Note that this feature is still experimental # and incomplete at the moment. GENERATE_AUTOGEN_DEF = NO #--------------------------------------------------------------------------- # configuration options related to the Perl module output #--------------------------------------------------------------------------- # If the GENERATE_PERLMOD tag is set to YES Doxygen will # generate a Perl module file that captures the structure of # the code including all documentation. Note that this # feature is still experimental and incomplete at the # moment. GENERATE_PERLMOD = NO # If the PERLMOD_LATEX tag is set to YES Doxygen will generate # the necessary Makefile rules, Perl scripts and LaTeX code to be able # to generate PDF and DVI output from the Perl module output. PERLMOD_LATEX = NO # If the PERLMOD_PRETTY tag is set to YES the Perl module output will be # nicely formatted so it can be parsed by a human reader. # This is useful # if you want to understand what is going on. # On the other hand, if this # tag is set to NO the size of the Perl module output will be much smaller # and Perl will parse it just the same. PERLMOD_PRETTY = YES # The names of the make variables in the generated doxyrules.make file # are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. # This is useful so different doxyrules.make files included by the same # Makefile don't overwrite each other's variables. PERLMOD_MAKEVAR_PREFIX = #--------------------------------------------------------------------------- # Configuration options related to the preprocessor #--------------------------------------------------------------------------- # If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will # evaluate all C-preprocessor directives found in the sources and include # files. ENABLE_PREPROCESSING = YES # If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro # names in the source code. If set to NO (the default) only conditional # compilation will be performed. Macro expansion can be done in a controlled # way by setting EXPAND_ONLY_PREDEF to YES. MACRO_EXPANSION = NO # If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES # then the macro expansion is limited to the macros specified with the # PREDEFINED and EXPAND_AS_DEFINED tags. EXPAND_ONLY_PREDEF = NO # If the SEARCH_INCLUDES tag is set to YES (the default) the includes files # pointed to by INCLUDE_PATH will be searched when a #include is found. SEARCH_INCLUDES = YES # The INCLUDE_PATH tag can be used to specify one or more directories that # contain include files that are not input files but should be processed by # the preprocessor. INCLUDE_PATH = # You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard # patterns (like *.h and *.hpp) to filter out the header-files in the # directories. If left blank, the patterns specified with FILE_PATTERNS will # be used. INCLUDE_FILE_PATTERNS = # The PREDEFINED tag can be used to specify one or more macro names that # are defined before the preprocessor is started (similar to the -D option of # gcc). The argument of the tag is a list of macros of the form: name # or name=definition (no spaces). If the definition and the = are # omitted =1 is assumed. To prevent a macro definition from being # undefined via #undef or recursively expanded use the := operator # instead of the = operator. PREDEFINED = # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then # this tag can be used to specify a list of macro names that should be expanded. # The macro definition that is found in the sources will be used. # Use the PREDEFINED tag if you want to use a different macro definition that # overrules the definition found in the source code. EXPAND_AS_DEFINED = # If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then # doxygen's preprocessor will remove all references to function-like macros # that are alone on a line, have an all uppercase name, and do not end with a # semicolon, because these will confuse the parser if not removed. SKIP_FUNCTION_MACROS = YES #--------------------------------------------------------------------------- # Configuration::additions related to external references #--------------------------------------------------------------------------- # The TAGFILES option can be used to specify one or more tagfiles. # Optionally an initial location of the external documentation # can be added for each tagfile. The format of a tag file without # this location is as follows: # # TAGFILES = file1 file2 ... # Adding location for the tag files is done as follows: # # TAGFILES = file1=loc1 "file2 = loc2" ... # where "loc1" and "loc2" can be relative or absolute paths or # URLs. If a location is present for each tag, the installdox tool # does not have to be run to correct the links. # Note that each tag file must have a unique name # (where the name does NOT include the path) # If a tag file is not located in the directory in which doxygen # is run, you must also specify the path to the tagfile here. TAGFILES = # When a file name is specified after GENERATE_TAGFILE, doxygen will create # a tag file that is based on the input files it reads. GENERATE_TAGFILE = # If the ALLEXTERNALS tag is set to YES all external classes will be listed # in the class index. If set to NO only the inherited external classes # will be listed. ALLEXTERNALS = NO # If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed # in the modules index. If set to NO, only the current project's groups will # be listed. EXTERNAL_GROUPS = YES # The PERL_PATH should be the absolute path and name of the perl script # interpreter (i.e. the result of `which perl'). PERL_PATH = /usr/bin/perl #--------------------------------------------------------------------------- # Configuration options related to the dot tool #--------------------------------------------------------------------------- # If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will # generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base # or super classes. Setting the tag to NO turns the diagrams off. Note that # this option also works with HAVE_DOT disabled, but it is recommended to # install and use dot, since it yields more powerful graphs. CLASS_DIAGRAMS = YES # You can define message sequence charts within doxygen comments using the \msc # command. Doxygen will then run the mscgen tool (see # http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the # documentation. The MSCGEN_PATH tag allows you to specify the directory where # the mscgen tool resides. If left empty the tool is assumed to be found in the # default search path. MSCGEN_PATH = # If set to YES, the inheritance and collaboration graphs will hide # inheritance and usage relations if the target is undocumented # or is not a class. HIDE_UNDOC_RELATIONS = YES # If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is # available from the path. This tool is part of Graphviz, a graph visualization # toolkit from AT&T and Lucent Bell Labs. The other options in this section # have no effect if this option is set to NO (the default) HAVE_DOT = NO # The DOT_NUM_THREADS specifies the number of dot invocations doxygen is # allowed to run in parallel. When set to 0 (the default) doxygen will # base this on the number of processors available in the system. You can set it # explicitly to a value larger than 0 to get control over the balance # between CPU load and processing speed. DOT_NUM_THREADS = 0 # By default doxygen will use the Helvetica font for all dot files that # doxygen generates. When you want a differently looking font you can specify # the font name using DOT_FONTNAME. You need to make sure dot is able to find # the font, which can be done by putting it in a standard location or by setting # the DOTFONTPATH environment variable or by setting DOT_FONTPATH to the # directory containing the font. DOT_FONTNAME = Helvetica # The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs. # The default size is 10pt. DOT_FONTSIZE = 10 # By default doxygen will tell dot to use the Helvetica font. # If you specify a different font using DOT_FONTNAME you can use DOT_FONTPATH to # set the path where dot can find it. DOT_FONTPATH = # If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen # will generate a graph for each documented class showing the direct and # indirect inheritance relations. Setting this tag to YES will force the # CLASS_DIAGRAMS tag to NO. CLASS_GRAPH = YES # If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen # will generate a graph for each documented class showing the direct and # indirect implementation dependencies (inheritance, containment, and # class references variables) of the class with other documented classes. COLLABORATION_GRAPH = YES # If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen # will generate a graph for groups, showing the direct groups dependencies GROUP_GRAPHS = YES # If the UML_LOOK tag is set to YES doxygen will generate inheritance and # collaboration diagrams in a style similar to the OMG's Unified Modeling # Language. UML_LOOK = NO # If set to YES, the inheritance and collaboration graphs will show the # relations between templates and their instances. TEMPLATE_RELATIONS = NO # If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT # tags are set to YES then doxygen will generate a graph for each documented # file showing the direct and indirect include dependencies of the file with # other documented files. INCLUDE_GRAPH = YES # If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and # HAVE_DOT tags are set to YES then doxygen will generate a graph for each # documented header file showing the documented files that directly or # indirectly include this file. INCLUDED_BY_GRAPH = YES # If the CALL_GRAPH and HAVE_DOT options are set to YES then # doxygen will generate a call dependency graph for every global function # or class method. Note that enabling this option will significantly increase # the time of a run. So in most cases it will be better to enable call graphs # for selected functions only using the \callgraph command. CALL_GRAPH = NO # If the CALLER_GRAPH and HAVE_DOT tags are set to YES then # doxygen will generate a caller dependency graph for every global function # or class method. Note that enabling this option will significantly increase # the time of a run. So in most cases it will be better to enable caller # graphs for selected functions only using the \callergraph command. CALLER_GRAPH = NO # If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen # will generate a graphical hierarchy of all classes instead of a textual one. GRAPHICAL_HIERARCHY = YES # If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES # then doxygen will show the dependencies a directory has on other directories # in a graphical way. The dependency relations are determined by the #include # relations between the files in the directories. DIRECTORY_GRAPH = YES # The DOT_IMAGE_FORMAT tag can be used to set the image format of the images # generated by dot. 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DOT_GRAPH_MAX_NODES = 50 # The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the # graphs generated by dot. A depth value of 3 means that only nodes reachable # from the root by following a path via at most 3 edges will be shown. Nodes # that lay further from the root node will be omitted. Note that setting this # option to 1 or 2 may greatly reduce the computation time needed for large # code bases. Also note that the size of a graph can be further restricted by # DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction. MAX_DOT_GRAPH_DEPTH = 0 # Set the DOT_TRANSPARENT tag to YES to generate images with a transparent # background. This is disabled by default, because dot on Windows does not # seem to support this out of the box. Warning: Depending on the platform used, # enabling this option may lead to badly anti-aliased labels on the edges of # a graph (i.e. they become hard to read). DOT_TRANSPARENT = NO # Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output # files in one run (i.e. multiple -o and -T options on the command line). This # makes dot run faster, but since only newer versions of dot (>1.8.10) # support this, this feature is disabled by default. DOT_MULTI_TARGETS = YES # If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will # generate a legend page explaining the meaning of the various boxes and # arrows in the dot generated graphs. GENERATE_LEGEND = YES # If the DOT_CLEANUP tag is set to YES (the default) Doxygen will # remove the intermediate dot files that are used to generate # the various graphs. DOT_CLEANUP = YES andi-0.14/docs/Makefile.am000066400000000000000000000015261415070357400153470ustar00rootroot00000000000000dist_man_MANS = andi.1 dist_noinst_DATA = Doxyfile # I intentionally do not list any of the manual files here. I neither want them # distributed nor installed. The reason is that building the manual requires # LaTeX with a whole bunch of packages installed. Plus, so many things can go # wrong, when building, so it's better to inspect the result. Thus, the manual # has to be build by hand and copied to the right place for distribution. .PHONY: code-docs code-docs: doxygen manual/version.tex: manual/version.tex.in $(top_srcdir)/configure.ac sed "s/VERSION/$(VERSION)/" manual/version.tex.in > manual/version.tex manual/andi-manual.pdf: manual/andi-manual.tex manual/version.tex @echo "error: manual rebuild of the manual required (no pun intended)." @exit 1 # maintainer-clean-local: # rm -f manual/*{aux,log,out,toc} manual/andi-manual.pdf andi-0.14/docs/andi.1.in000066400000000000000000000101701415070357400147100ustar00rootroot00000000000000.TH ANDI "1" "2020-01-09" "@VERSION@" "andi manual" .SH NAME andi \- estimates evolutionary distances .SH SYNOPSIS .B andi [\fIOPTIONS...\fR] \fIFILES\fR... .SH DESCRIPTION \fBandi\fR estimates the evolutionary distance between closely related genomes. For this \fBandi\fR reads the input sequences from \fIFASTA\fR files and computes the pairwise anchor distance. The idea behind this is explained in a paper by Haubold et al. (2015). .SH OUTPUT The output is a symmetrical distance matrix in \fIPHYLIP\fR format, with each entry representing divergence with a positive real number. A distance of zero means that two sequences are identical, whereas other values are estimates for the nucleotide substitution rate (Jukes-Cantor corrected). For technical reasons the comparison might fail and no estimate can be computed. In such cases \fInan\fR is printed. This either means that the input sequences were too short (<200bp) or too diverse (K>0.5) for our method to work properly. .SH OPTIONS .TP \fB\-b\fR \fIINT\fR, \fB\-\-bootstrap\fR=\fIINT\fR Compute multiple distance matrices, with \fIn-1\fR bootstrapped from the first. See the paper Klötzl & Haubold (2016) for a detailed explanation. .TP \fB--file-of-filenames\fR=\fIFILE\fR Usually, \fBandi\fR is called with the filenames as commandline arguments. With this option the filenames may also be read from a file itself, with one name per line. Use a single dash (\fB'-'\fR) to read from stdin. .TP \fB\-j\fR, \fB\-\-join\fR Use this mode if each of your \fIFASTA\fR files represents one assembly with numerous contigs. \fBandi\fR will then treat all of the contained sequences per file as a single genome. In this mode at least one filename must be provided via command line arguments. For the output the filename is used to identify each sequence. .TP \fB\-l\fR, \fB\-\-low-memory\fR In multithreaded mode, \fBandi\fR requires memory linear to the amount of threads. The low memory mode changes this to a constant demand independent from the used number of threads. Unfortunately, this comes at a significant runtime cost. .TP \fB\-m\fR \fIMODEL\fR, \fB\-\-model\fR=\fIMODEL\fR Set the nucleotide evolution model to one of 'Raw', 'JC', 'Kimura', or 'LogDet'. By default the Jukes-Cantor correction is used. .TP \fB\-p\fR \fIFLOAT\fR Significance of an anchor; default: 0.025. .TP \fB--progress\fR[=\fIWHEN\fR] Print a progress bar. \fIWHEN\fR can be 'auto' (default if omitted), 'always', or 'never'. .TP \fB\-t\fR \fIINT\fR, \fB\-\-threads\fR=\fIINT\fR The number of threads to be used; by default, all available processors are used. .br Multithreading is only available if \fBandi\fR was compiled with OpenMP support. .TP \fB\-\-truncate-names\fR By default \fBandi\fR outputs the full names of sequences, optionally padded with spaces, if they are shorter than ten characters. Names longer than ten characters may lead to problems with downstream tools. With this switch names will be truncated. .TP \fB\-v\fR, \fB\-\-verbose\fR Prints additional information, including the amount of found homology. Apply multiple times for extra verboseness. .TP \fB\-h\fR, \fB\-\-help\fR Prints the synopsis and an explanation of available options. .TP \fB\-\-version\fR Outputs version information and acknowledgments. .SH COPYRIGHT Copyright \(co 2014 - 2021 Fabian Klötzl License GPLv3+: GNU GPL version 3 or later. .br This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. The full license text is available at . .PP .SH ACKNOWLEDGMENTS 1) andi: Haubold, B. Klötzl, F. and Pfaffelhuber, P. (2015). andi: Fast and accurate estimation of evolutionary distances between closely related genomes, Bioinformatics 31.8. .br 2) Algorithms: Ohlebusch, E. (2013). Bioinformatics Algorithms. Sequence Analysis, Genome Rearrangements, and Phylogenetic Reconstruction. pp 118f. .br 3) SA construction: Mori, Y. (2005). libdivsufsort, unpublished. .br 4) Bootstrapping: Klötzl, F. and Haubold, B. (2016). Support Values for Genome Phylogenies, Life 6.1. .SH BUGS .SS Reporting Bugs Please report bugs to or at . andi-0.14/docs/manual/000077500000000000000000000000001415070357400145645ustar00rootroot00000000000000andi-0.14/docs/manual/andi-manual.tex000066400000000000000000000563361415070357400175110ustar00rootroot00000000000000\documentclass[a4paper, 10pt, english, DIV=12, BCOR=8mm]{scrbook} \usepackage[utf8x]{inputenc} \usepackage{babel} \usepackage{listings} \usepackage{xcolor} \usepackage{hyperref} \usepackage{siunitx} \usepackage[T1]{fontenc} \usepackage{isodate} \usepackage{graphicx} \usepackage{amsthm} \usepackage{acronym} \usepackage{amssymb} \usepackage{caption} \usepackage{subcaption} \usepackage{xspace} \usepackage{microtype} \bibliographystyle{alpha} \DeclareSIUnit\byte{B} \DeclareSIUnit\basepairs{bp} \DeclareSIUnit\bit{bit} \definecolor{oceangreen}{cmyk}{1,.0,.20,.78} \addtokomafont{sectioning}{\rmfamily\color{oceangreen}} \definecolor{bluekeywords}{rgb}{0.13,0.13,1} \definecolor{greencomments}{rgb}{0,0.5,0} \definecolor{turqusnumbers}{rgb}{0.17,0.57,0.69} \definecolor{redstrings}{rgb}{0.5,0,0} \definecolor{lightgray}{rgb}{0.9,0.9,0.9} \usepackage{libertine} \fontfamily{libertine} \selectfont %\usepackage[scaled]{berasans} \newcommand{\thymine}{\textsc{m}\oldstylenums{2}\xspace} \newcommand{\local}{\textsc{m}\oldstylenums{1}\xspace} \newcommand{\algo}[1]{\textsc{{#1}}} \newcommand{\andi}{\algo{andi}\xspace} \newcommand{\word}[1]{\textsf{\small#1}} \newcommand{\wchar}[1]{\textsf{\small#1}} \newcommand{\eco}{\textsc{eco}\oldstylenums{29}\xspace} \newcommand{\pneu}{\textsc{Pneu}\oldstylenums{3085}\xspace} \include{version} % Todos at the margin \newcommand{\todo}[1]{ \marginpar{\fbox{\begin{minipage}{0.9\marginparwidth} \scriptsize\sloppy\raggedright #1 \end{minipage}}} } \newtheorem{definition}{Definition} \lstset{backgroundcolor=\color{lightgray}} \lstdefinestyle{shell}{ language=bash, columns=flexible, xleftmargin=12pt, xrightmargin=12pt, breaklines=true, basicstyle=\small\ttfamily, morekeywords={make, tar, git, sudo, andi, time, man, head, cut, fneighbor, fretree, figtree, brew, aura, autoreconf, ls}, % literate={~} {$\sim$}{1} } \lstset{style=shell} \title{Documentation of \algo{andi}} \subtitle{Rapid Estimation of Evolutionary Distances between Genomes\\ {\small\url{https://github.com/EvolBioInf/andi}}} \author{Fabian Klötzl\\ \href{mailto:kloetzl@evolbio.mpg.de}{kloetzl@evolbio.mpg.de}} \date{Version \version, \isodate\today \\ \vspace*{2cm} \centering\includegraphics[width=0.8\textwidth]{andi_labels.pdf}} \begin{document} \maketitle \section*{Abstract} This is the documentation of the \andi program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because \andi does not compute full alignments, it is so efficient that it scales well up to thousands of bacterial genomes. This is scientific software. Please cite our paper \cite{andi} if you use \andi in your publication. Also refer to the paper for the internals of \andi. Additionally, there is a Master's thesis with even more in depth analysis of \andi \cite{kloetzl}. \vspace*{1cm} \section*{License} This document is release under the Creative Commons Attribution Share-Alike license. This means, you are free to copy and redistribute this document. You may even remix, tweak and build upon this document, as long as you credit me for the work I've done and release your document under the identical terms. The full legal code is available online: {\small\url{https://creativecommons.org/licenses/by-sa/4.0/legalcode}}. \tableofcontents \chapter{Installation} %%%%% \section{Package Manager} The easiest way to install \andi is via a package manager. This also handles all dependencies for you. \noindent Debian and Ubuntu: \begin{lstlisting} ~ % sudo apt-get install andi \end{lstlisting} \noindent macOS with homebrew: \begin{lstlisting} ~ % brew tap brewsci/bio ~ % brew install andi \end{lstlisting} \noindent ArchLinux AUR package with aura: \begin{lstlisting} ~ % aura -A andi \end{lstlisting} \andi is intended to be run in a \algo{Unix} commandline such as \lstinline$bash$ or \lstinline$zsh$. All examples in this document are also intended for that environment. You can verify that \andi was installed correctly by executing \lstinline$andi -h$. This should give you a list of all available options (see Section~\ref{sec:options}). \section{Source Package} \label{sub:regular} To build \andi from source, download the latest \href{https://github.com/EvolBioInf/andi/releases}{release} from GitHub. Please note, that \andi requires the \algo{Gnu Scientific Library} and \algo{libdivsufsort}\footnote{\url{https://github.com/y-256/libdivsufsort}} for optimal performance \cite{divsufsort}. Once you have downloaded the package, unzip it and change into the newly created directory. \begin{lstlisting} ~ % tar -xzvf andi-0.14.tar.gz ~ % cd andi-0.14 \end{lstlisting} \noindent Now build and install \andi. \begin{lstlisting} ~/andi-0.14 % ./configure ~/andi-0.14 % make ~/andi-0.14 % sudo make install \end{lstlisting} \noindent This installs \andi for all users on your system. If you do not have root privileges, you will find a working copy of \andi in the \lstinline$src$ subdirectory. For the rest of this documentation, it is assumed, that \andi is in your \textdollar\lstinline!PATH!. Now \andi should be ready for use. Try invoking the help. \begin{lstlisting} ~/andi-0.14 % ~/andi Usage: andi [OPTIONS...] FILES... FILES... can be any sequence of FASTA files. Use '-' as file name to read from stdin. Options: -b, --bootstrap=INT Print additional bootstrap matrices --file-of-filenames=FILE Read additional filenames from FILE; one per line -j, --join Treat all sequences from one file as a single genome -l, --low-memory Use less memory at the cost of speed -m, --model=MODEL Pick an evolutionary model of 'Raw', 'JC', 'Kimura', 'LogDet'; default: JC -p FLOAT Significance of an anchor; default: 0.025 --progress=WHEN Print a progress bar 'always', 'never', or 'auto'; default: auto -t, --threads=INT Set the number of threads; by default, all processors are used --truncate-names Truncate names to ten characters -v, --verbose Prints additional information -h, --help Display this help and exit --version Output version information and acknowledgments \end{lstlisting} \noindent \andi also comes with a man page, which can be accessed via \lstinline$man andi$. % But once you are done with this documentation, you will require it scarcely. \section{Installing from Git Repository} To build \andi from the \algo{Git} repo, you will also need the \algo{autotools}. Refer to your OS documentation for installation instructions. Once done, execute the following steps. \begin{lstlisting} ~ % git clone git@github.com:EvolBioInf/andi.git ~ % cd andi ~/andi % autoreconf -fi -Im4 \end{lstlisting} \noindent Continue with the \algo{Gnu} trinity as described in Section~\ref{sub:regular}. \chapter{Usage} %%%%% The input sequences for \andi should be in \algo{Fasta} format. Any number of files can be passed. Each file may contain more than one sequence. \begin{lstlisting} ~ % andi S1.fasta S2.fasta 2 S1 0.0000 0.0979 S2 0.0979 0.0000 \end{lstlisting} If no file argument is given, \andi reads the input from \algo{stdin}. This makes it convenient to use in \algo{Unix} pipelines. \begin{lstlisting} ~ % cat S1.fasta S2.fasta | andi 2 S1 0.0000 0.0979 S2 0.0979 0.0000 \end{lstlisting} The output of \andi is a matrix in \algo{Phylip} style: On the first line the number of compared sequences is given, \lstinline!2! in our example. Then the matrix is printed, where each line is preceded by the name of the $i$th sequence. Note that the matrix is symmetric and the main diagonal contains only zeros. The numbers themselves are evolutionary distances, estimated from substitution rates. \section{Input} \label{sec:join} As mentioned before, \andi reads in \algo{Fasta} files. It recognizes only the four standard bases and is case insensitive (RegEx: \lstinline![acgtACGT]!). All other residue symbols are excluded from the analysis and \andi prints a warning, when this happens. If instead of distinct sequences, a \algo{Fasta} file contains contigs belonging to a single taxon, \andi will treat them as a unit when switched into \algo{join} mode. This can be achieved by using the \lstinline!-j! or \lstinline!--join! command line switch. \begin{lstlisting} ~ % andi --join E_coli.fasta Shigella.fasta [Output] \end{lstlisting} When the \algo{join} mode is active, the file names are used to label the individual sequences. Thus, in \algo{join} mode, each genome has to be in its own file, and furthermore, at least one filename has to be given via the command line. If not enough file names are provided, \andi will try to read sequences from the standard input stream. This behaviour can be explicitly triggered by passing a single dash (\lstinline$-$) as a file name, which is useful in pipelines. If \andi seems to take unusually long, or requires huge amounts of memory, then you might have forgotten the \algo{join} switch. This makes \andi compare each contig instead of each genome, resulting in many more comparisons! Since version 0.12 \andi produces a progressmeter on the standard error stream. \andi tries to be smart about when to show or hide the progress bar. You can manually change this behaviour using the \lstinline!--progress! option. Starting with version 0.11 \andi supports an extra way of input. Instead of passing file names directly to \andi via the commandline arguments, the file names may also be read from a file itself. Using this new \lstinline$--file-of-filenames$ argument can work around limitations imposed be the shell. The following three snippets have the same functionality. \begin{lstlisting} ~ % andi --join *.fasta [Output] \end{lstlisting} \begin{lstlisting} ~ % ls *.fasta > filenames.txt ~ % andi --join --file-of-filenames filenames.txt [Output] \end{lstlisting} \begin{lstlisting} ~ % ls *.fasta | andi --join --file-of-filenames - [Output] \end{lstlisting} \section{Output} The output of \andi is written to \lstinline$stdout$. This makes it easy to use on the command line and within shell scripts. As seen before, the matrix, computed by \algo{andi}, is given in \algo{Phylip} format \cite{phylip}. \begin{lstlisting} ~ % cat S1.fasta S2.fasta | andi 2 S1 0.0000 0.0979 S2 0.0979 0.0000 \end{lstlisting} If the computation completed successfully, \andi exits with the status code 0. Otherwise, the value of \lstinline$errno$ is used as the exit code. \andi can also produce warnings and error messages for the user's convenience. These messages are printed to \lstinline$stderr$ and thus do not interfere with the normal output. \section{Options} \label{sec:options} \andi takes a small number of commandline options, of which even fewer are of interest on a day-to-day basis. If \lstinline$andi -h$ displays a \lstinline$-t$ option, then \andi was compiled with multi-threading support (implemented using \algo{OpenMP}). By default, \andi uses all available processors. However, to restrict the number of threads, use \lstinline$-t$. \begin{lstlisting} ~ % time andi ../test/1M.1.fasta -t 1 2 S1 0.0000 0.0995 S2 0.0995 0.0000 ./andi ../test/1M.1.fasta 0,60s user 0,01s system 99% cpu 0,613 total ~ % time andi ../test/1M.1.fasta -t 2 2 S1 0.0000 0.0995 S2 0.0995 0.0000 ./andi ../test/1M.1.fasta -t 2 0,67s user 0,03s system 195% cpu 0,362 total \end{lstlisting} In the above examples the runtime dropped from \SI{0.613}{\second}, to \SI{0.362}{\second} using two threads. Giving \andi more threads than input genomes leads to no further speed improvement. \, The other important option is \lstinline$--join$ (see Section~\ref{sec:join}). By default, the distances computed by \andi are \emph{Jukes-Cantor} corrected \cite{jukescantor}. Other evolutionary models are also implemented (Kimura \cite{kimura}, LogDet \cite{logdet}, raw). The \lstinline$--model$ parameter can be used to switch between them. Since version 0.9.4 \andi includes a bootstrapping method. It can be activated via the \lstinline$--bootstrap$ or \lstinline$-b$ switch. This option takes a numeric argument representing the number of matrices to create. The output can then be piped into \algo{phylip}. For more information on computing support values from distance matrices see \cite{afra}. \begin{lstlisting} ~ % andi -b 2 ../test/1M.1.fasta 2 S1 0.0000 0.1067 S2 0.1067 0.0000 2 S1 0.0000 0.1071 S2 0.1071 0.0000 \end{lstlisting} The original \algo{phylip} only supports distance matrices with names no longer than ten characters. However, this sometimes leads to problems with long accession numbers. Starting with version 0.11 \andi prints the full name of a sequence, even if it is longer than ten characters. If your downstream tools have trouble with this, use \lstinline$--truncate-names$ to reimpose the limit. Also new in version 0.11 is the \lstinline$--file-of-filenames$ option. See Section~\ref{sec:join} for details. \section{Example: \algo{eco29}} Here follows a real-world example of how to use \algo{andi}. It makes heavy use of the commandline and tools like \algo{Phylip}. If you prefer \algo{R}, check out this excellent blog post by Kathryn Holt.\footnote{\url{http://holtlab.net/2015/05/08/r-code-to-infer-tree-from-andi-output/}} As a data set we use \algo{eco29}; 29 genomes of \textit{E. Coli} and \textit{Shigella}. You can download the data from here: {\small{\url{http://guanine.evolbio.mpg.de/andi/eco29.fasta.gz}}}. The genomes have an average length of 4.9~million nucleotides amounting to a total \SI{138}{\mega\byte}. \algo{eco29} comes a single \algo{fasta} file, where each sequence is a genome. To calculate their pairwise distances, enter \begin{lstlisting} ~ % andi eco29.fasta > eco29.mat andi: The input sequences contained characters other than acgtACGT. These were automatically stripped to ensure correct results. \end{lstlisting} \noindent The \algo{eco29} data set includes non-canonical nucleotides, such as \word{Y}, \word{N}, and \word{P}, which get stripped from the input sequences. The resulting matrix is stored in \lstinline$eco29.mat$; Here is a small excerpt: \begin{lstlisting} ~ % head -n 5 eco29.mat | cut -d ' ' -f 1-5 29 gi|563845 0.0000e+00 1.8388e-02 1.8439e-02 2.6398e-02 gi|342360 1.8388e-02 0.0000e+00 4.4029e-04 2.6166e-02 gi|300439 1.8439e-02 4.4029e-04 0.0000e+00 2.6123e-02 gi|261117 2.6398e-02 2.6166e-02 2.6123e-02 0.0000e+00 \end{lstlisting} \noindent From this we compute a tree via neighbor-joining using a \algo{Phylip} wrapper called \algo{Embassy}.\footnote{\url{http://emboss.sourceforge.net/embassy/\#PHYLIP}} \begin{lstlisting} ~ % fneighbor -datafile eco29.mat -outfile eco29.phylipdump \end{lstlisting} \noindent To make this tree easier to read, we can midpoint-root it. \begin{lstlisting} ~ % fretree -spp 29 -intreefile eco29.treefile -outtreefile eco29.tree <0.5$) or sprout a lot of indels that make comparison difficult. \subsection*{Little Homology} Very few anchors were found and thus only a tiny part of the sequences is considered homologous. Expect that the given distance is erroneous. \subsection*{Too long name} If you added the \lstinline$--truncate-names$ switch and an input name is longer than ten characters, you will receive this warning. \chapter{DevOps} %%%%% \andi is written in C/C++; mostly C99 with some parts in C++11. The sources are released on \algo{GitHub} as \emph{free software} under the \textsc{Gnu General Public License version~3} \cite{GPL}. Prebundled packages using \algo{autoconf} are also available, with the latest release being {\version} at the time of writing. If you are interested in the internals of \algo{andi}, consult the paper \cite{andi} or my Master's thesis \cite{kloetzl}. Both explain the used approach in detail. The latter emphasizes the used algorithms, data structures and their efficient implementation. \section{Dependencies} Here is a complete list of dependencies required for developing \algo{andi}. \begin{itemize} \item A C and a C++11 compiler, \item the \algo{autotools}, \item the \algo{Gnu Scientific Library}, \item \algo{Pdflatex} with various packages for the manual, \item \algo{Git}, \item \algo{glib2} for the unit tests, \item \algo{doxygen}, \item and \algo{libdivsufsort}. \end{itemize} \section{Code Documentation} \emph{Every} function in \andi is documented using \algo{doxygen} style comments. To create the documentation run \lstinline$make code-docs$ in the main directory. You will then find the documentation under \lstinline$./docs$. \section{Unit Tests} The unit tests are located in the \andi repository under the \lstinline$./test$ directory. Because they require \algo{glib2}, and a C++11 compiler, they are deactivated by default. To enable them, execute \begin{lstlisting} ~/andi % ./configure --enable-unit-tests \end{lstlisting} \noindent during the installation process. You can then verify the build via \begin{lstlisting} ~/andi % make check \end{lstlisting} \noindent The unit tests are also checked each time a commit is sent to the repository. This is done via \algo{TravisCI}.\footnote{\url{https://travis-ci.org/EvolBioInf/andi}} Thus, a warning is produced, when the builds fail, or the unit tests did not run successfully. Currently, the unit tests cover more than 75\% of the code. This is computed via the \algo{Travis} builds and a service called \algo{Coveralls}.\footnote{\url{https://coveralls.io/r/EvolBioInf/andi}} \section{Known Issues} These minor issues are known. I intend to fix them, when I have time. \begin{enumerate} \item This code will not work under Windows. At two places Unix-only code is used: filepath-separators are assumed to be \lstinline$/$ and file-descriptors are used for I/O. \item Unit tests for the bootstrapped matrices are missing. \item Cached intervals are sometimes not “as deep as they could be”. If that got fixed \lstinline$get_match_cache$ could bail out on \lstinline$ij.lcp < CACHE_LENGTH$. However the \lstinline$esa_init_cache$ code is the most fragile part and should be handled with care. \end{enumerate} \section{Creating a Release} A release should be a stable version of \andi with significant improvements over the last version. dotdot releases should be avoided. %\subsection{Preparing a new Release} Once \andi is matured, the new features implemented, and all tests were run, a new release can be created. First, increase the version number in \lstinline$configure.ac$. Commit that change in git, and tag this commit with \lstinline$vX.y$. Tags should be annotated and signed, if possible. This manual then needs manual rebuilding. Ensure that \andi is ready for packaging with \algo{autoconf}. \begin{lstlisting} ~ % make distcheck make dist-gzip am__post_remove_distdir='@:' make[1]: Entering directory `/home/kloetzl/Projects/andi' if test -d "andi-0.9.1-beta"; then find "andi-0.9.1-beta" -type d ! -perm -200 -exec chmod u+w {} ';' && rm -rf "andi-0.9.1-beta" || { sleep 5 && rm -rf "andi-0.9.1-beta"; }; else :; fi test -d "andi-0.9.1-beta" || mkdir "andi-0.9.1-beta" (cd src && make top_distdir=../andi-0.9.1-beta distdir=../andi-0.9.1-beta/src \ am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir) ... Loads of output ... ================================================= andi-0.9.1-beta archives ready for distribution: andi-0.9.1-beta.tar.gz ================================================= \end{lstlisting} If the command does not build successfully, no tarballs will be created. This may necessitate further study of \algo{autoconf} and \algo{automake}. Also verify that the recent changes did not create a performance regression. This includes testing both ends of the scale: \eco and \pneu. Both should be reasonable close to previous releases. Create another commit, where you set the version number to the next release (e.\,g., \lstinline$vX.z-beta$). This assures that there is only one commit and build with that specific version. \backmatter %\addcontentsline{toc}{chapter}{Bibliography} \bibliography{references} \end{document} andi-0.14/docs/manual/andi_labels.pdf000066400000000000000000000054211415070357400175160ustar00rootroot00000000000000%PDF-1.4 % 5 0 obj <>stream x+r 26S030VIr *T0T0Bf endstream endobj 7 0 obj <>>>/MediaBox[0 0 793 639]>> endobj 2 0 obj <> endobj 1 0 obj <>/Font<>>>/Subtype/Form/BBox[0 0 793 639]/Matrix [1 0 0 1 0 0]/Length 1617/FormType 1/Filter/FlateDecode>>stream xWKsGﯘcr0==ϣ- `CL֦I}im@I3_%FqOJ>qsx;< ZSPj%n/=~lrU*WyK)thk<rmgAh%,%1H"p$Al?(q*^j< '-Hc+c:&^X`a +FE8@ҢV ` :@cUyOJ'*^7XeNLNPHvc6 :迡:Hm;.oRZ@Eg EY),E>J f<Pr1Q/羚aŵk_VWm=)pJkP56 X_tg<͗0Sl:m<><^~R< ҉F %Ҥ-YW@ҋRl;.*.&Қ󪾑7wwbu; :I fy'Q6=Nm.Z}ܯh=6Ul$tA"=]J:_߶N~ 7_eZE}E]΢Qp7*lri r~yb -V5bO9\CnڀIZSL^xZ+:jB_iJvL WS[wzEciu~TS*zUEDlev?=E.HOBc#*ʹ4]7o~QzA?{ 꾬^qA>I&'a"^G7A$؜`$Xmxv񉮂wmr'~R;q`MQ endstream endobj 3 0 obj <> endobj 4 0 obj <> endobj 6 0 obj <> endobj 8 0 obj <> endobj 9 0 obj <> endobj xref 0 10 0000000000 65535 f 0000000334 00000 n 0000000246 00000 n 0000002161 00000 n 0000002192 00000 n 0000000015 00000 n 0000002223 00000 n 0000000130 00000 n 0000002274 00000 n 0000002319 00000 n trailer <<2fd9b203f0cc5c36c5491af452364469>]/Info 9 0 R/Size 10>> %iText-5.4.5 startxref 2472 %%EOF andi-0.14/docs/manual/references.bib000066400000000000000000000100731415070357400173640ustar00rootroot00000000000000@misc{divsufsort, author="Yuta Mori", year="2005", title="Short description of improved two-stage suffix sorting algorithm", note="\url{http://homepage3.nifty.com/wpage/software/itssort.txt}" } @article{andi, author = {Haubold, Bernhard and Klötzl, Fabian and Pfaffelhuber, Peter}, title = {andi: Fast and accurate estimation of evolutionary distances between closely related genomes}, volume = {31}, number = {8}, pages = {1169-1175}, year = {2015}, doi = {10.1093/bioinformatics/btu815}, URL = {http://bioinformatics.oxfordjournals.org/content/31/8/1169.abstract}, eprint = {http://bioinformatics.oxfordjournals.org/content/31/8/1169.full.pdf+html}, journal = {Bioinformatics} } @book{Felsenstein, author={Joseph Felsenstein}, title={Inferring Phylogenies}, year={2004}, publisher={Sinauer Associates, Inc.} } @misc{GPL, author={{Free~Software~Foundation}}, year={2007}, title={Gnu General Public License}, note={\url{https://gnu.org/licenses/gpl.html}} } @misc{phylip, author={Felsenstein, J.}, year={2005}, title={PHYLIP (Phylogeny Inference Package)}, version={version 3.6}, howpublished={Distributed by the author}, note={Department of Genome Sciences, University of Washington.} } @InProceedings{LLVM, Author = {Chris Lattner and Vikram Adve}, Title = {{LLVM}: A Compilation Framework for Lifelong Program Analysis and Transformation}, Booktitle = "Code Generation and Optimization", Month = {Mar}, Year = {2004}, pages = {75--88}, Publisher={International Symposium on Code Generation and Optimization} } @article{ms, author = {Hudson, Richard R.}, title = {Generating samples under a Wright–Fisher neutral model of genetic variation}, volume = {18}, number = {2}, pages = {337-338}, year = {2002}, doi = {10.1093/bioinformatics/18.2.337}, URL = {http://bioinformatics.oxfordjournals.org/content/18/2/337.abstract}, eprint = {http://bioinformatics.oxfordjournals.org/content/18/2/337.full.pdf+html}, journal = {Bioinformatics} } @article{valgrind, author = {Nethercote, Nicholas and Seward, Julian}, title = {Valgrind: A Framework for Heavyweight Dynamic Binary Instrumentation}, journal = {SIGPLAN Not.}, issue_date = {June 2007}, volume = {42}, number = {6}, month = jun, year = {2007}, issn = {0362-1340}, pages = {89--100}, numpages = {12}, url = {http://doi.acm.org/10.1145/1273442.1250746}, doi = {10.1145/1273442.1250746}, acmid = {1250746}, publisher = {ACM}, keywords = {Memcheck, Valgrind, dynamic binary analysis, dynamic binary instrumentation, shadow values} } @misc{figtree, title="FigTree", author={Andrew Rambaut}, year={accessed 2015}, note={\url{http://tree.bio.ed.ac.uk/software/figtree/}} } @article{jukescantor, author={Jukes, T. H. and Cantor, C. R.}, year={1969}, title={Evolution of protein molecules}, journal={Mammalian protein metabolism}, volume={3}, pages={21-132}, publisher={Academic Press} } @mastersthesis{kloetzl, author={Fabian Kl{\"o}tzl}, school={University of L\"ubeck}, year={2015}, title={Efficient Estimation of Evolutionary Distances} } @article{afra, AUTHOR = {Klötzl, Fabian and Haubold, Bernhard}, TITLE = {Support Values for Genome Phylogenies}, JOURNAL = {Life}, VOLUME = {6}, YEAR = {2016}, NUMBER = {1}, PAGES = {11}, URL = {http://www.mdpi.com/2075-1729/6/1/11}, ISSN = {2075-1729}, DOI = {10.3390/life6010011} } @article{logdet, AUTHOR = {Lockhart, P.J. and M.A. Steel and M.D. Hendy and D. Penny}, TITLE = {Recovering Evolutionary Trees under a More Realistic Model of Sequence Evolution}, JOURNAL = {Molecular Biology and Evolution}, VOLUME = {11}, YEAR = {1994}, NUMBER = {4}, PAGES = {605-612}, DOI = {10.1093/oxfordjournals.molbev.a040136} } @article{kimura, AUTHOR = {Kimura, M.}, TITLE = {A Simple Method for Estimating Evolutionary Rate of Base Substitutions Through Comparative Studies of Nucleotide Sequences}, JOURNAL = {Journal of Molecular Evolution}, VOLUME = {16}, YEAR = {1980}, NUMBER = {2}, PAGES = {111-120}, DOI = {10.1007/BF01731581} } andi-0.14/docs/manual/version.tex.in000066400000000000000000000000401415070357400173720ustar00rootroot00000000000000 \newcommand{\version}{VERSION} andi-0.14/libs/000077500000000000000000000000001415070357400133105ustar00rootroot00000000000000andi-0.14/libs/Makefile.am000066400000000000000000000002551415070357400153460ustar00rootroot00000000000000# (C) 2015, Fabian Klötzl ISC License noinst_LIBRARIES= libpfasta.a libpfasta_a_SOURCES= pfasta.c pfasta.h libpfasta_a_CPPFLAGS= -I$(top_srcdir)/opt andi-0.14/libs/pfasta.c000066400000000000000000000402471415070357400147410ustar00rootroot00000000000000/* * Copyright (c) 2015-2020, Fabian Klötzl * * Permission to use, copy, modify, and/or distribute this software for any * purpose with or without fee is hereby granted, provided that the above * copyright notice and this permission notice appear in all copies. * * THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES * WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF * MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR * ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES * WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN * ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. * */ #include #include #include #include #include #include #include #include #include #include "pfasta.h" #define VERSION "v15" #ifdef __SSE2__ #include #endif #if __STDC_VERSION__ >= 201112L && !defined(__STDC_NO_THREADS__) #include #define PFASTA_THREADSAFE 1 #else #define thread_local #define PFASTA_THREADSAFE 0 #endif int pfasta_threadsafe() { return PFASTA_THREADSAFE ; } /** The following is the maximum length of an error string. It has to be * carefully chosen, so that all calls to PF_FAIL_STR succeed. For instance, * the line number can account for up to 20 characters. */ #define PF_ERROR_STRING_LENGTH 100 thread_local char errstr_buffer[PF_ERROR_STRING_LENGTH]; void *pfasta_reallocarray(void *ptr, size_t nmemb, size_t size); #define BUFFER_SIZE 16384 #define LIKELY(X) __builtin_expect((intptr_t)(X), 1) #define UNLIKELY(X) __builtin_expect((intptr_t)(X), 0) enum { NO_ERROR, E_EOF, E_ERROR, E_ERRNO, E_BUBBLE, E_STR, E_STR_CONST }; #define PF_FAIL_ERRNO(PP) \ do { \ (void)strerror_r(errno, errstr_buffer, PF_ERROR_STRING_LENGTH); \ (PP)->errstr = errstr_buffer; \ return_code = E_ERRNO; \ goto cleanup; \ } while (0) #define PF_FAIL_BUBBLE_CHECK(PP, CHECK) \ do { \ if (UNLIKELY(CHECK)) { \ return_code = CHECK; \ goto cleanup; \ } \ } while (0) #define PF_FAIL_BUBBLE(PP) \ do { \ if (UNLIKELY((PP)->errstr)) { \ return_code = E_BUBBLE; \ goto cleanup; \ } \ } while (0) #define PF_FAIL_STR_CONST(PP, STR) \ do { \ (PP)->errstr = (STR); \ return_code = E_STR_CONST; \ goto cleanup; \ } while (0) #define PF_FAIL_STR(PP, ...) \ do { \ (void)snprintf(errstr_buffer, PF_ERROR_STRING_LENGTH, __VA_ARGS__); \ (PP)->errstr = errstr_buffer; \ return_code = E_STR; \ goto cleanup; \ } while (0) int pfasta_read_name(struct pfasta_parser *pp, struct pfasta_record *pr); int pfasta_read_comment(struct pfasta_parser *pp, struct pfasta_record *pr); int pfasta_read_sequence(struct pfasta_parser *pp, struct pfasta_record *pr); static inline char *buffer_begin(struct pfasta_parser *pp); static inline char *buffer_end(struct pfasta_parser *pp); static inline int buffer_advance(struct pfasta_parser *pp, size_t steps); static inline int buffer_is_empty(const struct pfasta_parser *pp); static inline int buffer_is_eof(const struct pfasta_parser *pp); static inline int buffer_peek(struct pfasta_parser *pp); static inline int buffer_read(struct pfasta_parser *pp); typedef struct dynstr { char *str; size_t capacity, count; } dynstr; static inline char *dynstr_move(dynstr *ds); static inline int dynstr_init(dynstr *ds, struct pfasta_parser *pp); static inline size_t dynstr_len(const dynstr *ds); static inline void dynstr_free(dynstr *ds); static inline int dynstr_append(dynstr *ds, const char *str, size_t length, struct pfasta_parser *pp); static inline int my_isspace(int c) { // ascii whitespace return (c >= '\t' && c <= '\r') || (c == ' '); } const char *pfasta_version(void) { return VERSION; } int buffer_init(struct pfasta_parser *pp) { int return_code = 0; pp->buffer = malloc(BUFFER_SIZE); if (!pp->buffer) PF_FAIL_ERRNO(pp); int check = buffer_read(pp); PF_FAIL_BUBBLE_CHECK(pp, check); cleanup: return return_code; } int buffer_read(struct pfasta_parser *pp) { int return_code = NO_ERROR; ssize_t count = read(pp->file_descriptor, pp->buffer, BUFFER_SIZE); if (UNLIKELY(count < 0)) PF_FAIL_ERRNO(pp); if (UNLIKELY(count == 0)) { // EOF pp->fill_ptr = pp->buffer; pp->read_ptr = pp->buffer + 1; pp->errstr = "EOF (maybe error)"; // enable bubbling return E_EOF; } pp->read_ptr = pp->buffer; pp->fill_ptr = pp->buffer + count; cleanup: return return_code; } int buffer_peek(struct pfasta_parser *pp) { return LIKELY(pp->read_ptr < pp->fill_ptr) ? *(unsigned char *)pp->read_ptr : EOF; } char *buffer_begin(struct pfasta_parser *pp) { return pp->read_ptr; } char *buffer_end(struct pfasta_parser *pp) { return pp->fill_ptr; } inline int buffer_advance(struct pfasta_parser *pp, size_t steps) { int return_code = 0; pp->read_ptr += steps; if (UNLIKELY(pp->read_ptr >= pp->fill_ptr)) { assert(pp->read_ptr == pp->fill_ptr); int check = buffer_read(pp); // resets pointers PF_FAIL_BUBBLE_CHECK(pp, check); } cleanup: return return_code; } int buffer_is_empty(const struct pfasta_parser *pp) { return pp->read_ptr == pp->fill_ptr; } int buffer_is_eof(const struct pfasta_parser *pp) { return pp->read_ptr > pp->fill_ptr; } char *find_first_space(const char *begin, const char *end) { size_t offset = 0; size_t length = end - begin; #ifdef __SSE2__ typedef __m128i vec_type; static const size_t vec_size = sizeof(vec_type); const vec_type all_tab = _mm_set1_epi8('\t' - 1); const vec_type all_carriage = _mm_set1_epi8('\r' + 1); const vec_type all_space = _mm_set1_epi8(' '); size_t vec_offset = 0; size_t vec_length = (end - begin) / vec_size; for (; vec_offset < vec_length; vec_offset++) { vec_type chunk; memcpy(&chunk, begin + vec_offset * vec_size, vec_size); // isspace: \t <= char <= \r || char == space vec_type v1 = _mm_cmplt_epi8(all_tab, chunk); vec_type v2 = _mm_cmplt_epi8(chunk, all_carriage); vec_type v3 = _mm_cmpeq_epi8(chunk, all_space); unsigned int vmask = (_mm_movemask_epi8(v1) & _mm_movemask_epi8(v2)) | _mm_movemask_epi8(v3); if (UNLIKELY(vmask)) { offset += __builtin_ctz(vmask); offset += vec_offset * vec_size; return (char *)begin + offset; } } offset += vec_offset * vec_size; #endif for (; offset < length; offset++) { if (my_isspace(begin[offset])) break; } return (char *)begin + offset; } char *find_first_not_space(const char *begin, const char *end) { size_t offset = 0; size_t length = end - begin; for (; offset < length; offset++) { if (!my_isspace(begin[offset])) break; } return (char *)begin + offset; } size_t count_newlines(const char *begin, const char *end) { size_t offset = 0; size_t length = end - begin; size_t newlines = 0; for (; offset < length; offset++) { if (begin[offset] == '\n') newlines++; } return newlines; } static int copy_word(struct pfasta_parser *pp, dynstr *target) { int return_code = 0; int c; while (c = buffer_peek(pp), c != EOF && LIKELY(!my_isspace(c))) { char *end_of_word = find_first_space(buffer_begin(pp), buffer_end(pp)); size_t word_length = end_of_word - buffer_begin(pp); assert(word_length > 0); int check = dynstr_append(target, buffer_begin(pp), word_length, pp); PF_FAIL_BUBBLE_CHECK(pp, check); check = buffer_advance(pp, word_length); PF_FAIL_BUBBLE_CHECK(pp, check); } cleanup: return return_code; } static int skip_whitespace(struct pfasta_parser *pp) { int return_code = 0; while (my_isspace(buffer_peek(pp))) { char *split = find_first_not_space(buffer_begin(pp), buffer_end(pp)); // advance may clear the buffer. So count first … size_t newlines = count_newlines(buffer_begin(pp), split); int check = buffer_advance(pp, split - buffer_begin(pp)); PF_FAIL_BUBBLE_CHECK(pp, check); // … and then increase the counter. pp->line_number += newlines; } cleanup: return return_code; } struct pfasta_parser pfasta_init(int file_descriptor) { int return_code = 0; struct pfasta_parser pp = {0}; pp.line_number = 1; pp.file_descriptor = file_descriptor; int check = buffer_init(&pp); if (check && check != E_EOF) PF_FAIL_BUBBLE_CHECK(&pp, check); if (buffer_is_empty(&pp) || buffer_is_eof(&pp)) { PF_FAIL_STR(&pp, "File is empty."); } if (buffer_peek(&pp) != '>') { PF_FAIL_STR(&pp, "File must start with '>'."); } cleanup: // free buffer if necessary if (return_code) { pfasta_free(&pp); } pp.done = return_code || buffer_is_eof(&pp); return pp; } struct pfasta_record pfasta_read(struct pfasta_parser *pp) { int return_code = 0; struct pfasta_record pr = {0}; int check = pfasta_read_name(pp, &pr); PF_FAIL_BUBBLE_CHECK(pp, check); check = pfasta_read_comment(pp, &pr); PF_FAIL_BUBBLE_CHECK(pp, check); check = pfasta_read_sequence(pp, &pr); PF_FAIL_BUBBLE_CHECK(pp, check); cleanup: if (return_code) { pfasta_record_free(&pr); pfasta_free(pp); } pp->done = return_code || buffer_is_eof(pp); return pr; } int pfasta_read_name(struct pfasta_parser *pp, struct pfasta_record *pr) { int return_code = 0; dynstr name; dynstr_init(&name, pp); PF_FAIL_BUBBLE(pp); assert(!buffer_is_empty(pp)); if (buffer_peek(pp) != '>') { PF_FAIL_STR(pp, "Expected '>' but found '%c' on line %zu.", buffer_peek(pp), pp->line_number); } int check = buffer_advance(pp, 1); // skip > if (check == E_EOF) PF_FAIL_STR(pp, "Unexpected EOF in name on line %zu.", pp->line_number); PF_FAIL_BUBBLE(pp); check = copy_word(pp, &name); if (check == E_EOF) PF_FAIL_STR(pp, "Unexpected EOF in name on line %zu.", pp->line_number); PF_FAIL_BUBBLE(pp); if (dynstr_len(&name) == 0) PF_FAIL_STR(pp, "Empty name on line %zu.", pp->line_number); pr->name_length = dynstr_len(&name); pr->name = dynstr_move(&name); cleanup: if (return_code) { dynstr_free(&name); } return return_code; } int pfasta_read_comment(struct pfasta_parser *pp, struct pfasta_record *pr) { int return_code = 0; if (buffer_peek(pp) == '\n') { pr->comment_length = 0; pr->comment = NULL; return 0; } dynstr comment; dynstr_init(&comment, pp); PF_FAIL_BUBBLE(pp); assert(!buffer_is_empty(pp)); int check = buffer_advance(pp, 1); // skip first whitespace if (check == E_EOF) goto label_eof; PF_FAIL_BUBBLE(pp); assert(!buffer_is_empty(pp)); // get comment while (buffer_peek(pp) != '\n') { check = dynstr_append(&comment, buffer_begin(pp), 1, pp); PF_FAIL_BUBBLE_CHECK(pp, check); check = buffer_advance(pp, 1); if (check == E_EOF) goto label_eof; PF_FAIL_BUBBLE_CHECK(pp, check); } label_eof: if (buffer_is_eof(pp)) PF_FAIL_STR(pp, "Unexpected EOF in comment on line %zu.", pp->line_number); pr->comment_length = dynstr_len(&comment); pr->comment = dynstr_move(&comment); cleanup: if (return_code) { dynstr_free(&comment); } return return_code; } int pfasta_read_sequence(struct pfasta_parser *pp, struct pfasta_record *pr) { int return_code = 0; dynstr sequence; dynstr_init(&sequence, pp); PF_FAIL_BUBBLE(pp); assert(!buffer_is_empty(pp)); assert(!buffer_is_eof(pp)); assert(buffer_peek(pp) == '\n'); int check = skip_whitespace(pp); if (check == E_EOF) PF_FAIL_STR(pp, "Empty sequence on line %zu.", pp->line_number); PF_FAIL_BUBBLE_CHECK(pp, check); // Assume a line begins only with alpha, -, *, or more spaces char c; while (c = buffer_peek(pp), LIKELY(isalpha(c) || c == '-' || c == '*')) { int check = copy_word(pp, &sequence); if (UNLIKELY(check == E_EOF)) break; PF_FAIL_BUBBLE_CHECK(pp, check); // optimize for more common case ptrdiff_t length = buffer_end(pp) - buffer_begin(pp); if (LIKELY(length >= 2 && buffer_begin(pp)[0] == '\n' && buffer_begin(pp)[1] > ' ')) { pp->read_ptr++; // nasty hack pp->line_number += 1; } else { check = skip_whitespace(pp); if (UNLIKELY(check == E_EOF)) break; PF_FAIL_BUBBLE_CHECK(pp, check); } } if (dynstr_len(&sequence) == 0) PF_FAIL_STR(pp, "Empty sequence on line %zu.", pp->line_number); pr->sequence_length = dynstr_len(&sequence); pr->sequence = dynstr_move(&sequence); pp->errstr = NULL; // reset error cleanup: if (return_code) { dynstr_free(&sequence); } return return_code; } void pfasta_record_free(struct pfasta_record *pr) { if (!pr) return; free(pr->name); free(pr->comment); free(pr->sequence); pr->name = pr->comment = pr->sequence = NULL; } void pfasta_free(struct pfasta_parser *pp) { if (!pp) return; free(pp->buffer); pp->buffer = NULL; } /** @brief Creates a new string that can grow dynamically. * * @param ds - A reference to the dynstr container. * * @returns 0 iff successful. */ static inline int dynstr_init(dynstr *ds, struct pfasta_parser *pp) { int return_code = 0; *ds = (dynstr){NULL, 0, 0}; ds->str = malloc(61); if (!ds->str) PF_FAIL_ERRNO(pp); ds->str[0] = '\0'; ds->capacity = 61; ds->count = 0; cleanup: return return_code; } /** @brief A append more than one character to a string. * * @param ds - A reference to the dynstr container. * @param str - The new characters. * @param length - number of new characters to append * * @returns 0 iff successful. */ static inline int dynstr_append(dynstr *ds, const char *str, size_t length, struct pfasta_parser *pp) { int return_code = 0; size_t required = ds->count + length; if (UNLIKELY(required >= ds->capacity)) { char *neu = pfasta_reallocarray(ds->str, required / 2, 3); if (UNLIKELY(!neu)) { dynstr_free(ds); PF_FAIL_ERRNO(pp); } ds->str = neu; ds->capacity = (required / 2) * 3; } memcpy(ds->str + ds->count, str, length); ds->count = required; cleanup: return return_code; } /** @brief Frees a dynamic string. */ static inline void dynstr_free(dynstr *ds) { if (!ds) return; free(ds->str); *ds = (dynstr){NULL, 0, 0}; } /** @brief Returns the string as a standard `char*`. The internal reference is * then deleted. Hence the name *move* as in *move semantics*. * * @param ds - The dynamic string to move from. * * @returns a `char*` to a standard null-terminated string. */ static inline char *dynstr_move(dynstr *ds) { char *out = pfasta_reallocarray(ds->str, ds->count + 1, 1); if (!out) { out = ds->str; } out[ds->count] = '\0'; *ds = (dynstr){NULL, 0, 0}; return out; } /** @brief Returns the current length of the dynamic string. */ static inline size_t dynstr_len(const dynstr *ds) { return ds->count; } __attribute__((weak)) void *reallocarray(void *ptr, size_t nmemb, size_t size); /** * @brief Unsafe fallback in case reallocarray isn't provided by the stdlib. */ void *pfasta_reallocarray(void *ptr, size_t nmemb, size_t size) { if (reallocarray == NULL) { return realloc(ptr, nmemb * size); } else { return reallocarray(ptr, nmemb, size); } } andi-0.14/libs/pfasta.h000066400000000000000000000053631415070357400147460ustar00rootroot00000000000000/* * Copyright (c) 2015-2020, Fabian Klötzl * * Permission to use, copy, modify, and/or distribute this software for any * purpose with or without fee is hereby granted, provided that the above * copyright notice and this permission notice appear in all copies. * * THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES * WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF * MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR * ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES * WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN * ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. * */ #ifndef PFASTA_H #define PFASTA_H #ifdef __cplusplus extern "C" { #endif #include /** * There is no magic to this structure. Its just a container of three strings. * Feel free to duplicate or move them. But don't forget to free the data after * usage! */ struct pfasta_record { char *name, *comment, *sequence; size_t name_length, comment_length, sequence_length; }; /** * This structure holds a number of members to represent the state of the FASTA * parser. Please make sure that it is properly initialized before usage. * Always free this structure when the parser is done. */ struct pfasta_parser { const char *errstr; int done; /*< private -- do not touch! >*/ int file_descriptor; char *buffer; char *read_ptr, *fill_ptr; size_t line_number; }; /** * This function initializes a `pfasta_parser` struct with a parser bound to a * specific file descriptor. Iff an error occurred `errstr` is set to contain a * suitable message. Otherwise you can read data from it as long as `done` isn't * set. The parser should be freed after usage. * * Please note that the user is responsible for opening the file descriptor as * readable and closing after usage. */ struct pfasta_parser pfasta_init(int file_descriptor); /** * Using a properly initialized parser, this function can read FASTA sequences. * These are stored in the simple structure and returned. On error, the `errstr` * property of the parser is set. */ struct pfasta_record pfasta_read(struct pfasta_parser *pp); /** * This function frees the resources held by a pfasta record. */ void pfasta_record_free(struct pfasta_record *pr); /** * This function frees the resources held by a pfasta parser. */ void pfasta_free(struct pfasta_parser *pp); /** * Get a string defining the version of the pfasta library. */ const char *pfasta_version(void); /** * Returns 0 iff pfasta is not threadsafe. */ int pfasta_threadsafe(); #ifdef __cplusplus } #endif #endif /* PFASTA_H */ andi-0.14/m4/000077500000000000000000000000001415070357400126775ustar00rootroot00000000000000andi-0.14/m4/ax_cxx_compile_stdcxx_11.m4000066400000000000000000000123351415070357400200450ustar00rootroot00000000000000# ============================================================================ # http://www.gnu.org/software/autoconf-archive/ax_cxx_compile_stdcxx_11.html # ============================================================================ # # SYNOPSIS # # AX_CXX_COMPILE_STDCXX_11([ext|noext],[mandatory|optional]) # # DESCRIPTION # # Check for baseline language coverage in the compiler for the C++11 # standard; if necessary, add switches to CXXFLAGS to enable support. # # The first argument, if specified, indicates whether you insist on an # extended mode (e.g. -std=gnu++11) or a strict conformance mode (e.g. # -std=c++11). If neither is specified, you get whatever works, with # preference for an extended mode. # # The second argument, if specified 'mandatory' or if left unspecified, # indicates that baseline C++11 support is required and that the macro # should error out if no mode with that support is found. If specified # 'optional', then configuration proceeds regardless, after defining # HAVE_CXX11 if and only if a supporting mode is found. # # LICENSE # # Copyright (c) 2008 Benjamin Kosnik # Copyright (c) 2012 Zack Weinberg # Copyright (c) 2013 Roy Stogner # Copyright (c) 2014 Alexey Sokolov # Copyright (c) 2014, 2015 Google 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 any # warranty. #serial 7 m4_define([_AX_CXX_COMPILE_STDCXX_11_testbody], [[ template struct check { static_assert(sizeof(int) <= sizeof(T), "not big enough"); }; struct Base { virtual void f() {} }; struct Child : public Base { virtual void f() override {} }; typedef check> right_angle_brackets; int a; decltype(a) b; typedef check check_type; check_type c; check_type&& cr = static_cast(c); auto d = a; auto l = [](){}; // http://stackoverflow.com/questions/13728184/template-aliases-and-sfinae // Clang 3.1 fails with headers of libstd++ 4.8.3 when using std::function because of this namespace test_template_alias_sfinae { struct foo {}; template using member = typename T::member_type; template void func(...) {} template void func(member*) {} void test() { func(0); } } ]]) AC_DEFUN([AX_CXX_COMPILE_STDCXX_11], [dnl m4_if([$1], [], [], [$1], [ext], [], [$1], [noext], [], [m4_fatal([invalid argument `$1' to AX_CXX_COMPILE_STDCXX_11])])dnl m4_if([$2], [], [ax_cxx_compile_cxx11_required=true], [$2], [mandatory], [ax_cxx_compile_cxx11_required=true], [$2], [optional], [ax_cxx_compile_cxx11_required=false], [m4_fatal([invalid second argument `$2' to AX_CXX_COMPILE_STDCXX_11])]) AC_LANG_PUSH([C++])dnl ac_success=no AC_CACHE_CHECK(whether $CXX supports C++11 features by default, ax_cv_cxx_compile_cxx11, [AC_COMPILE_IFELSE([AC_LANG_SOURCE([_AX_CXX_COMPILE_STDCXX_11_testbody])], [ax_cv_cxx_compile_cxx11=yes], [ax_cv_cxx_compile_cxx11=no])]) if test x$ax_cv_cxx_compile_cxx11 = xyes; then ac_success=yes fi m4_if([$1], [noext], [], [dnl if test x$ac_success = xno; then for switch in -std=gnu++11 -std=gnu++0x; do cachevar=AS_TR_SH([ax_cv_cxx_compile_cxx11_$switch]) AC_CACHE_CHECK(whether $CXX supports C++11 features with $switch, $cachevar, [ac_save_CXXFLAGS="$CXXFLAGS" CXXFLAGS="$CXXFLAGS $switch" AC_COMPILE_IFELSE([AC_LANG_SOURCE([_AX_CXX_COMPILE_STDCXX_11_testbody])], [eval $cachevar=yes], [eval $cachevar=no]) CXXFLAGS="$ac_save_CXXFLAGS"]) if eval test x\$$cachevar = xyes; then CXXFLAGS="$CXXFLAGS $switch" ac_success=yes break fi done fi]) m4_if([$1], [ext], [], [dnl if test x$ac_success = xno; then for switch in -std=c++11 -std=c++0x; do cachevar=AS_TR_SH([ax_cv_cxx_compile_cxx11_$switch]) AC_CACHE_CHECK(whether $CXX supports C++11 features with $switch, $cachevar, [ac_save_CXXFLAGS="$CXXFLAGS" CXXFLAGS="$CXXFLAGS $switch" AC_COMPILE_IFELSE([AC_LANG_SOURCE([_AX_CXX_COMPILE_STDCXX_11_testbody])], [eval $cachevar=yes], [eval $cachevar=no]) CXXFLAGS="$ac_save_CXXFLAGS"]) if eval test x\$$cachevar = xyes; then CXXFLAGS="$CXXFLAGS $switch" ac_success=yes break fi done fi]) AC_LANG_POP([C++]) if test x$ax_cxx_compile_cxx11_required = xtrue; then if test x$ac_success = xno; then AC_MSG_ERROR([*** A compiler with support for C++11 language features is required.]) fi else if test x$ac_success = xno; then HAVE_CXX11=0 AC_MSG_NOTICE([No compiler with C++11 support was found]) else HAVE_CXX11=1 AC_DEFINE(HAVE_CXX11,1, [define if the compiler supports basic C++11 syntax]) fi AC_SUBST(HAVE_CXX11) fi ]) andi-0.14/opt/000077500000000000000000000000001415070357400131615ustar00rootroot00000000000000andi-0.14/opt/Makefile.am000066400000000000000000000003211415070357400152110ustar00rootroot00000000000000noinst_LIBRARIES= libcompat.a libcompat_a_SOURCES= compat-string.h compat-stdlib.h if !HAVE_STRCHRNUL libcompat_a_SOURCES+= strchrnul.c endif if !HAVE_REALLOCARRAY libcompat_a_SOURCES+= reallocarray.c endif andi-0.14/opt/compat-stdlib.h000066400000000000000000000001201415070357400160650ustar00rootroot00000000000000#include void *reallocarray(void *optr, size_t nmemb, size_t size); andi-0.14/opt/compat-string.h000066400000000000000000000001051415070357400161150ustar00rootroot00000000000000#ifndef HAVE_STRCHRNUL char *strchrnul(const char *s, int c); #endif andi-0.14/opt/reallocarray.c000066400000000000000000000023721415070357400160110ustar00rootroot00000000000000#include #include #include "compat-stdlib.h" /* * Copyright (c) 2008 Otto Moerbeek * * Permission to use, copy, modify, and distribute this software for any * purpose with or without fee is hereby granted, provided that the above * copyright notice and this permission notice appear in all copies. * * THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES * WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF * MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR * ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES * WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN * ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ /* * This is sqrt(SIZE_MAX+1), as s1*s2 <= SIZE_MAX * if both s1 < MUL_NO_OVERFLOW and s2 < MUL_NO_OVERFLOW */ #define MUL_NO_OVERFLOW ((size_t)1 << (sizeof(size_t) * 4)) void *reallocarray(void *optr, size_t nmemb, size_t size) { if ((nmemb >= MUL_NO_OVERFLOW || size >= MUL_NO_OVERFLOW) && nmemb > 0 && SIZE_MAX / nmemb < size) { errno = ENOMEM; return NULL; } return realloc(optr, size * nmemb); } andi-0.14/opt/strchrnul.c000066400000000000000000000004031415070357400153460ustar00rootroot00000000000000/* @brief Here follows a simple implementation of the GNU function `strchrnul`. * Please check the gnulib manual for details. */ #include char *strchrnul(const char *s, int c){ char *p = strchr(s,c); return p != NULL ? p : strchr(s, '\0'); } andi-0.14/scripts/000077500000000000000000000000001415070357400140465ustar00rootroot00000000000000andi-0.14/scripts/_andi000077500000000000000000000036141415070357400150520ustar00rootroot00000000000000#compdef andi # This file allows zsh to complete arguments for andi. As the syntax is # totally non-obvious, I'll explain the basics here. For details see # http://zsh.sourceforge.net/Doc/Release/Completion-System.html # Each line consists of three parts: (A){B}[C] # The B part performs brace expansion as on the commandline. Thus each # line with braces gets translated into multiple arguments! Also the # B part lists the relevant argument for which we are trying to set # the completion rules. The A part simply states that B shall not be # completed if A is already present. i.e. Most flags only make sense once, # with the exception of -v. The string C is simply the message that is # displayed to the user. local info="-h --help --version" local ret=1 local -a args args+=( "($info -b --bootstrap)"{-b+,--bootstrap=}'[Print additional bootstrap matrices]:int:' "($info)*--file-of-filenames=[Read additional filenames from file; one per line]:file:_files" "($info -j --join)"{-j,--join}'[Treat all sequences from one file as a single genome]' "($info -l --low-memory)"{-l,--low-memory}'[Use less memory at the cost of speed]' "($info -m --model)"{-m+,--model=}'[Pick an evolutionary model]:model:(( Raw\:Uncorrected\ distances JC\:Jukes\-Cantor\ corrected Kimura\:Kimura\-two\-parameter LogDet\:Logarithmic\ determinant ))' "($info)-p+[Significance of an anchor; default\: 0.025]:float:" "($info)--progress=[Show progress bar]:when:(always auto never)" "($info -t --threads)"{-t+,--threads=}'[The number of threads to be used; by default, all available processors are used]:num_threads:' "($info)--truncate-names[Print only the first ten characters of each name]" "($info)*"{-v,--verbose}'[Prints additional information]' '(- *)'{-h,--help}'[Display help and exit]' '(- *)--version[Output version information and acknowledgments]' '*:file:_files' ) _arguments -w -s -S $args[@] && ret=0 return ret andi-0.14/scripts/failed.zsh000077500000000000000000000012641415070357400160260ustar00rootroot00000000000000#!/usr/bin/zsh # Compute the number of failing comparisons for different distances. DISTS=(0.1 0.2 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7) LENGTH=100000 for dist in $DISTS; do echo "" > est_$dist.dist for (( i = 0; i < 1000; i++ )); do ../test/test_fasta -l $LENGTH -d $dist > temp.fa ../src/andi ./temp.fa > est.dist 2> /dev/null tail -n 1 est.dist >> est_$dist.dist done avg=$(cat est_$dist.dist | awk '"nan" !~ $2 {sum+=$2;c++}END{print sum/c}') sd=$(grep -v 'nan' est_$dist.dist | awk '{a[c++]=$2;aa+=$2}END{aa/=NR;for(c=0;c file.maf > file.phy"; exit(-1); } numName = 0; test = "mult=" n; }{ if(/^a/){ if($0 ~ test) open = 1; else open = 0; } if(open && /^s/){ if(!s[$2]) names[numNames++] = $2; s[$2] = s[$2] $7; } }END{ # check equal length of sequences len = -1; for(i=0;i 0){ if(length(s[name]) != len){ print "sequence length should be " len " but is in fact " length(s[name]); exit(-1); } }else len = length(s[name]); } print numNames, len; start = 1; l = 60; for(i=0;i /dev/null # In theory we have to calculate the anchors distance here using the previously # computed matches. But since vmatch is already significantly slower than andi, # we skip this step. done andi-0.14/src/000077500000000000000000000000001415070357400131465ustar00rootroot00000000000000andi-0.14/src/Makefile.am000066400000000000000000000007171415070357400152070ustar00rootroot00000000000000bin_PROGRAMS = andi andi_SOURCES = andi.c esa.c process.c sequence.c io.c global.h esa.h process.h sequence.h io.h dist_hack.h \ model.h model.c andi_CPPFLAGS = $(OPENMP_CFLAGS) -I$(top_srcdir)/libs -I$(top_srcdir)/opt -std=gnu99 andi_CFLAGS = $(OPENMP_CFLAGS) -Wall -Wextra -Wno-missing-field-initializers andi_LDADD = $(top_builddir)/libs/libpfasta.a $(top_builddir)/opt/libcompat.a .PHONY: perf perf: CFLAGS+= -g -O3 -ggdb -fno-omit-frame-pointer perf: andi andi-0.14/src/andi.c000066400000000000000000000254621415070357400142360ustar00rootroot00000000000000/** * @file * * This is the main file. It contains functions to parse the commandline * arguments, read files etc. * * @brief The main file * @author Fabian Klötzl * * @section License * * 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 at * http://www.gnu.org/copyleft/gpl.html * */ #include "global.h" #include "io.h" #include "process.h" #include "sequence.h" #include #include #include #include #include #include #include #include #include #include #ifdef _OPENMP #include #endif /* Global variables */ int FLAGS = 0; int THREADS = 1; long unsigned int BOOTSTRAP = 0; double ANCHOR_P_VALUE = 0.025; gsl_rng *RNG = NULL; int MODEL = M_JC; void usage(int); void version(void); /** * @brief The main function. * * The main function reads and parses the commandline arguments. Depending on * the set flags it reads the input files and forwards the contained sequences * to processing. Also it verifies the input for correctness and issues warnings * and errors. */ int main(int argc, char *argv[]) { struct option long_options[] = { {"version", no_argument, NULL, 0}, {"truncate-names", no_argument, NULL, 0}, {"file-of-filenames", required_argument, NULL, 0}, {"progress", optional_argument, NULL, 0}, {"help", no_argument, NULL, 'h'}, {"verbose", no_argument, NULL, 'v'}, {"join", no_argument, NULL, 'j'}, {"low-memory", no_argument, NULL, 'l'}, {"threads", required_argument, NULL, 't'}, {"bootstrap", required_argument, NULL, 'b'}, {"model", required_argument, NULL, 'm'}, {0, 0, 0, 0}}; #ifdef _OPENMP // Use all available processors by default. THREADS = omp_get_num_procs(); #endif enum { P_AUTO, P_NEVER, P_ALWAYS } progress = P_AUTO; struct string_vector file_names; string_vector_init(&file_names); // parse arguments while (1) { int option_index = 0; int c = getopt_long(argc, argv, "jvht:p:m:b:l", long_options, &option_index); if (c == -1) { break; } switch (c) { case 0: { const char *option_str = long_options[option_index].name; if (strcasecmp(option_str, "version") == 0) { version(); } if (strcasecmp(option_str, "truncate-names") == 0) { FLAGS |= F_TRUNCATE_NAMES; } if (strcasecmp(option_str, "file-of-filenames") == 0) { read_into_string_vector(optarg, &file_names); } if (strcasecmp(option_str, "progress") == 0) { if (!optarg || strcasecmp(optarg, "always") == 0) { progress = P_ALWAYS; } else if (strcasecmp(optarg, "auto") == 0) { progress = P_AUTO; } else if (strcasecmp(optarg, "never") == 0) { progress = P_NEVER; } else { warnx("invalid argument to --progress '%s'. Expected " "one of 'auto', 'always', or 'never'.", optarg); } } break; } case 'h': usage(EXIT_SUCCESS); break; case 'v': FLAGS |= FLAGS & F_VERBOSE ? F_EXTRA_VERBOSE : F_VERBOSE; break; case 'p': { errno = 0; char *end; double prop = strtod(optarg, &end); if (errno || end == optarg || *end != '\0') { soft_errx( "Expected a floating point number for -p argument, but " "'%s' was given. Skipping argument.", optarg); break; } if (prop <= 0.0 || prop >= 1.0) { soft_errx("A probability should be a value between 0 and " "1, exclusive; Ignoring -p %f argument.", prop); break; } ANCHOR_P_VALUE = prop; break; } case 'l': FLAGS |= F_LOW_MEMORY; break; case 'j': FLAGS |= F_JOIN; break; case 't': { #ifdef _OPENMP errno = 0; char *end; long unsigned int threads = strtoul(optarg, &end, 10); if (errno || end == optarg || *end != '\0') { warnx("Expected a number for -t argument, but '%s' was " "given. Ignoring -t argument.", optarg); break; } if (threads > (long unsigned int)omp_get_num_procs()) { warnx( "The number of threads to be used, is greater than the " "number of available processors; Ignoring -t %lu " "argument.", threads); break; } THREADS = threads; #else warnx( "This version of andi was built without OpenMP and thus " "does not support multi threading. Ignoring -t argument."); #endif break; } case 'b': { errno = 0; char *end; long unsigned int bootstrap = strtoul(optarg, &end, 10); if (errno || end == optarg || *end != '\0' || bootstrap == 0) { soft_errx( "Expected a positive number for -b argument, but '%s' " "was given. Ignoring -b argument.", optarg); break; } BOOTSTRAP = bootstrap - 1; break; } case 'm': { if (strcasecmp(optarg, "RAW") == 0) { MODEL = M_RAW; } else if (strcasecmp(optarg, "JC") == 0) { MODEL = M_JC; } else if (strcasecmp(optarg, "KIMURA") == 0) { MODEL = M_KIMURA; } else if (strcasecmp(optarg, "LOGDET") == 0) { MODEL = M_LOGDET; } else { soft_errx("Ignoring argument for --model. Expected Raw, " "JC, Kimura or LogDet"); } break; } case '?': /* intentional fall-through */ default: usage(EXIT_FAILURE); break; } } argc -= optind; argv += optind; // copy command line arguments into vector // std::copy, anyone? for (size_t i = 0; i < (unsigned int)argc; i++) { string_vector_push_back(&file_names, argv[i]); } // at least one file name must be given if (FLAGS & F_JOIN && string_vector_size(&file_names) == 0) { errx(1, "In join mode at least one filename needs to be supplied."); } size_t minfiles = FLAGS & F_JOIN ? 2 : 1; if (string_vector_size(&file_names) < minfiles) { // not enough files passed via arguments if (!isatty(STDIN_FILENO)) { // read from stdin in pipe string_vector_push_back(&file_names, "-"); } else { // print a helpful message on './andi' without args usage(EXIT_FAILURE); } } // parse fasta files dsa_t dsa; dsa_init(&dsa); for (size_t i = 0; i < string_vector_size(&file_names); i++) { char *file_name = string_vector_at(&file_names, i); if (FLAGS & F_JOIN) { read_fasta_join(file_name, &dsa); } else { read_fasta(file_name, &dsa); } } string_vector_free(&file_names); size_t n = dsa_size(&dsa); if (n < 2) { errx(1, "I am truly sorry, but with less than two sequences (%zu given) " "there is nothing to compare.", n); } RNG = gsl_rng_alloc(gsl_rng_default); if (!RNG) { err(1, "RNG allocation failed."); } // seed the random number generator with the current time // TODO: enable seeding for reproducibility gsl_rng_set(RNG, time(NULL)); // Warn about non ACGT residues. if (FLAGS & F_NON_ACGT) { warnx("The input sequences contained characters other than acgtACGT. " "These were automatically stripped to ensure correct results."); } // validate sequence correctness const seq_t *seq = dsa_data(&dsa); for (size_t i = 0; i < n; ++i, seq++) { if ((FLAGS & F_TRUNCATE_NAMES) && strlen(seq->name) > 10) { warnx("The sequence name '%s' is longer than ten characters. It " "will be truncated in the output to '%.10s'.", seq->name, seq->name); } const size_t LENGTH_LIMIT = (INT_MAX - 1) / 2; if (seq->len > LENGTH_LIMIT) { errx(1, "The sequence %s is too long. The technical limit is %zu.", seq->name, LENGTH_LIMIT); } if (seq->len == 0) { errx(1, "The sequence %s is empty.", seq->name); } if (seq->len < 1000) { FLAGS |= F_SHORT; } } if (FLAGS & F_SHORT) { soft_errx( "One of the given input sequences is shorter than a thousand " "nucleotides. This may result in inaccurate distances. Try an " "alignment instead."); } // determine whether to print a progress bar if (progress == P_AUTO) { progress = isatty(STDERR_FILENO) ? P_ALWAYS : P_NEVER; } if (progress == P_ALWAYS) { FLAGS |= F_PRINT_PROGRESS; } // compute distance matrix calculate_distances(dsa_data(&dsa), n); dsa_free(&dsa); gsl_rng_free(RNG); return FLAGS & F_SOFT_ERROR ? EXIT_FAILURE : EXIT_SUCCESS; } /** * @brief Prints the usage and then exits. */ void usage(int status) { const char str[] = { "Usage: andi [OPTIONS...] FILES...\n" "\tFILES... can be any sequence of FASTA files.\n" "\tUse '-' as file name to read from stdin.\n" "Options:\n" " -b, --bootstrap=INT Print additional bootstrap matrices\n" " --file-of-filenames=FILE Read additional filenames from FILE; " "one per line\n" " -j, --join Treat all sequences from one file as a single " "genome\n" " -l, --low-memory Use less memory at the cost of speed\n" " -m, --model=MODEL Pick an evolutionary model of 'Raw', 'JC', " "'Kimura', 'LogDet'; default: JC\n" " -p FLOAT Significance of an anchor; default: 0.025\n" " --progress=WHEN Print a progress bar 'always', 'never', or " "'auto'; default: auto\n" #ifdef _OPENMP " -t, --threads=INT Set the number of threads; by default, all " "processors are used\n" #endif " --truncate-names Truncate names to ten characters\n" " -v, --verbose Prints additional information\n" " -h, --help Display this help and exit\n" " --version Output version information and " "acknowledgments\n"}; fprintf(status == EXIT_SUCCESS ? stdout : stderr, "%s", str); exit(status); } /** * @brief This function just prints the version string and then aborts * the program. It conforms to the [GNU Coding * Standard](http://www.gnu.org/prep/standards/html_node/_002d_002dversion.html#g_t_002d_002dversion). */ void version(void) { const char str[] = { "andi " VERSION "\n" "Copyright (C) 2014 - 2020 Fabian Klötzl\n" "License GPLv3+: GNU GPL version 3 or later " "\n" "This is free software: you are free to change and redistribute it.\n" "There is NO WARRANTY, to the extent permitted by law.\n\n" "Acknowledgments:\n" "1) Andi: Haubold, B. Klötzl, F. and Pfaffelhuber, P. (2015). " "Fast and accurate estimation of evolutionary distances between " "closely related genomes, Bioinformatics.\n" "2) Algorithms: Ohlebusch, E. (2013). Bioinformatics Algorithms. " "Sequence Analysis, Genome Rearrangements, and Phylogenetic " "Reconstruction. pp 118f.\n" "3) SA construction: Mori, Y. (2005). libdivsufsort, unpublished.\n" "4) Bootstrapping: Klötzl, F. and Haubold, B. (2016). Support Values " "for Genome Phylogenies, Life 6.1.\n"}; printf("%s", str); exit(EXIT_SUCCESS); } andi-0.14/src/dist_hack.h000066400000000000000000000051061415070357400152520ustar00rootroot00000000000000/** @file * @brief This file is a preprocessor hack for the two functions `distMatrix` * and `distMatrixLM`. */ // clang-format off #ifdef FAST #define NAME distMatrix #define P_OUTER _Pragma("omp parallel for num_threads( THREADS) default(none) shared(progress_counter) firstprivate( stderr, M, sequences, n, print_progress)") #define P_INNER #else #undef NAME #undef P_OUTER #undef P_INNER #define NAME distMatrixLM #define P_OUTER #define P_INNER _Pragma("omp parallel for num_threads( THREADS) default(none) shared(progress_counter) firstprivate( stderr, M, sequences, n, print_progress, i, E, subject)") #endif // clang-format on /** @brief This function calls dist_andi for pairs of subjects and queries, and * thereby fills the distance matrix. * * This function is actually two functions. It is one template that gets * compiled into two functions via preprocessor hacks. The reason is DRY (Do not * Repeat Yourselves). * The two functions only differ by their name and pragmas; i.e. They run in * different parallel modes. * `distMatrix` is faster than `distMatrixLM` but needs more memory. * * @param sequences - The sequences to compare * @param n - The number of sequences * @param M - A matrix for additional output data */ void NAME(struct model *M, const seq_t *sequences, size_t n) { size_t i; size_t progress_counter = 0; int print_progress = FLAGS & F_PRINT_PROGRESS; if (print_progress) { fprintf(stderr, "Comparing %zu sequences: %5.1f%% (%zu/%zu)", n, 0.0, (size_t)0, n * n - n); } //#pragma P_OUTER for (i = 0; i < n; i++) { seq_subject subject; esa_s E; if (seq_subject_init(&subject, &sequences[i]) || esa_init(&E, &subject)) { errx(1, "Failed to create index for %s.", sequences[i].name); } // now compare every other sequence to i size_t j; P_INNER for (j = 0; j < n; j++) { if (j == i) { M(i, j) = (struct model){.seq_len = 9, .counts = {9}}; continue; } size_t ql = sequences[j].len; M(i, j) = dist_anchor(&E, sequences[j].S, ql, subject.threshold); #pragma omp atomic update progress_counter++; } if (print_progress) { size_t local_progress_counter; size_t num_comparisons = n * n - n; #pragma omp atomic read local_progress_counter = progress_counter; double progress = 100.0 * (double)local_progress_counter / num_comparisons; #pragma omp critical fprintf(stderr, "\rComparing %zu sequences: %5.1f%% (%zu/%zu)", n, progress, local_progress_counter, num_comparisons); } esa_free(&E); seq_subject_free(&subject); } if (print_progress) { fprintf(stderr, ", done.\n"); } } andi-0.14/src/esa.c000066400000000000000000000376451415070357400141010ustar00rootroot00000000000000/** * @file * @brief ESA functions * * This file contains various functions that operate on an enhanced suffix * array. The basic algorithms originate from the book of Ohlebusch * "Bioinformatics Algorithms" (2013). Most of these were heavily modified * for improved performance. One example is the lcp-cache. * * The ESA structure defined in esa.h contains a `cache` field. This cache is * used to quickly look up lcp-intervals. Consider the queries "AAGT" and * "AACG". In both cases the interval for "AA" has to be looked up in the * ESA. If we simply store the interval for "AA" in the cache, once and use it * for each query we are significantly faster (up to 7 times). */ #include "esa.h" #include "global.h" #include #include #include static void esa_init_cache_dfs(esa_s *, char *str, size_t pos, lcp_inter_t in); static void esa_init_cache_fill(esa_s *, char *str, size_t pos, lcp_inter_t in); static lcp_inter_t get_interval(const esa_s *, lcp_inter_t ij, char a); lcp_inter_t get_match(const esa_s *, const char *query, size_t qlen); static lcp_inter_t get_match_from(const esa_s *, const char *query, size_t qlen, saidx_t k, lcp_inter_t ij); static int esa_init_SA(esa_s *); static int esa_init_LCP(esa_s *); static int esa_init_CLD(esa_s *); /** @brief The prefix length up to which LCP-intervals are cached. */ const size_t CACHE_LENGTH = 10; /** @brief Map a code to the character. */ char code2char(ssize_t code) { switch (code & 0x3) { case 0: return 'A'; case 1: return 'C'; case 2: return 'G'; case 3: return 'T'; } return '\0'; } /** @brief Map a character to a two bit code. */ ssize_t char2code(const char c) { ssize_t result = -1; switch (c) { case 'A': result = 0; break; case 'C': result = 1; break; case 'G': result = 2; break; case 'T': result = 3; break; } return result; } #define R(CLD, i) ((CLD)[(i)]) #define L(CLD, i) ((CLD)[(i)-1]) /** @brief Fills the LCP-Interval cache. * * Traversing the virtual suffix tree, created by SA, LCP and CLD is rather * slow. Hence we create a cache, holding the LCP-interval for a prefix of a * certain length ::CACHE_LENGTH. This function it the entry point for the * cache filling routine. * * @param self - The ESA. * @returns 0 iff successful */ int esa_init_cache(esa_s *self) { lcp_inter_t *cache = malloc((1 << (2 * CACHE_LENGTH)) * sizeof(*cache)); CHECK_MALLOC(cache); self->cache = cache; char str[CACHE_LENGTH + 1]; str[CACHE_LENGTH] = '\0'; saidx_t m = L(self->CLD, self->len); lcp_inter_t ij = {.i = 0, .j = self->len - 1, .m = m, .l = self->LCP[m]}; esa_init_cache_dfs(self, str, 0, ij); return 0; } /** @brief Fills the cache — one char at a time. * * This function is a depth first search on the virtual suffix tree and fills * the cache. Or rather it calls it self until some value to cache is * calculated. This function is a recursive version of get_interval but with * more edge cases. * * @param C - The ESA. * @param str - The current prefix. * @param pos - The length of the prefix. * @param in - The LCP-interval of prefix[0..pos-1]. */ void esa_init_cache_dfs(esa_s *C, char *str, size_t pos, const lcp_inter_t in) { // we are not yet done, but the current strings do not exist in the subject. if (pos < CACHE_LENGTH && in.i == -1 && in.j == -1) { esa_init_cache_fill(C, str, pos, in); return; } // we are past the caching length if (pos >= CACHE_LENGTH) { esa_init_cache_fill(C, str, pos, in); return; } lcp_inter_t ij; // iterate over all nucleotides for (int code = 0; code < 4; ++code) { str[pos] = code2char(code); ij = get_interval(C, in, str[pos]); // fail early if (ij.i == -1 && ij.j == -1) { // if the current extension cannot be found, will with previous one esa_init_cache_fill(C, str, pos + 1, in); continue; } // singleton if (ij.i == ij.j) { // fix length ij.l = pos + 1; esa_init_cache_fill(C, str, pos + 1, ij); continue; } if (ij.l <= (ssize_t)(pos + 1)) { // Continue one level deeper // This is the usual case esa_init_cache_dfs(C, str, pos + 1, ij); continue; } // The LCP-interval is deeper than expected // Check if it still fits into the cache if ((size_t)ij.l >= CACHE_LENGTH) { // If the lcp-interval exceeds the cache depth, stop here and fill esa_init_cache_fill(C, str, pos + 1, in); continue; } /* At this point the prefix `str` of length `pos` has been found. * However, the call to `getInterval` above found an interval with * an LCP value bigger than `pos`. This means that not all elongations * (more precise: just one) of `str` appear in the subject. Thus fill * all values with the matched result to far and continue only with * the one special substring. */ esa_init_cache_fill(C, str, pos + 1, in); char non_acgt = 0; // fast forward size_t k = pos + 1; for (; k < (size_t)ij.l; k++) { // In some very edgy edge cases the lcp-interval `ij` // contains a `;` or another non-acgt character. Since we // cannot cache those, break. char c = C->S[C->SA[ij.i] + k]; if (char2code(c) < 0) { non_acgt = 1; break; } str[k] = c; } // We are skipping intervals here. Maybe for each of them we should also // fill the cache. However, I haven't yet figured out how to do that // properly and whether it is worth it. if (non_acgt) { esa_init_cache_fill(C, str, k, ij); } else { esa_init_cache_dfs(C, str, k, ij); } } } /** @brief Fills the cache with a given value. * * Given a prefix and a value this function fills the cache beyond this point * the value. * * @param C - The ESA. * @param str - The current prefix. * @param pos - The length of the prefix. * @param in - The LCP-interval of prefix[0..pos-1]. */ void esa_init_cache_fill(esa_s *C, char *str, size_t pos, lcp_inter_t in) { if (pos < CACHE_LENGTH) { for (int code = 0; code < 4; ++code) { str[pos] = code2char(code); esa_init_cache_fill(C, str, pos + 1, in); } } else { ssize_t code = 0; for (size_t i = 0; i < CACHE_LENGTH; ++i) { code <<= 2; code |= char2code(str[i]); } C->cache[code] = in; } } /** * @brief Initializes the FVC (first variant character) array. * * The FVC is of my own invention and simply defined as * `FVC[i] = S[SA[i]+LCP[i]]`. This expression is constantly used in * get_interval. By precomputing the result, we have less memory * accesses, less cache misses, and thus improved runtimes of up to 15% * faster matching. This comes at a negligible cost of increased memory. * * @param self - The ESA * @returns 0 iff successful */ int esa_init_FVC(esa_s *self) { size_t len = self->len; char *FVC = self->FVC = malloc(len); CHECK_MALLOC(FVC); const char *S = self->S; const int *SA = self->SA; const int *LCP = self->LCP; FVC[0] = '\0'; for (size_t i = len; i; i--, FVC++, SA++, LCP++) { *FVC = S[*SA + *LCP]; } return 0; } /** @brief Initializes an ESA. * * This function initializes an ESA with respect to the provided sequence. * @param C - The ESA to initialize. * @param S - The sequence * @returns 0 iff successful */ int esa_init(esa_s *C, const seq_subject *S) { if (!C || !S || !S->RS) return 1; *C = (esa_s){.S = S->RS, .len = S->RSlen}; int result; result = esa_init_SA(C); if (result) return result; result = esa_init_LCP(C); if (result) return result; result = esa_init_CLD(C); if (result) return result; result = esa_init_FVC(C); if (result) return result; result = esa_init_cache(C); if (result) return result; return 0; } /** @brief Free the private data of an ESA. */ void esa_free(esa_s *self) { free(self->SA); free(self->LCP); free(self->CLD); free(self->cache); free(self->FVC); *self = (esa_s){}; } /** * Computes the SA given a string S. To do so it uses libdivsufsort. * @param C The enhanced suffix array to use. Reads C->S, fills C->SA. * @returns 0 iff successful */ int esa_init_SA(esa_s *C) { // assert c.S if (!C || !C->S) { return 1; } C->SA = malloc(C->len * sizeof(*C->SA)); CHECK_MALLOC(C->SA); return divsufsort((const unsigned char *)C->S, C->SA, C->len); } /** @brief Initializes the CLD (child) array. * * See Ohlebusch. * * @param C - The ESA */ int esa_init_CLD(esa_s *C) { if (!C || !C->LCP) { return 1; } saidx_t *CLD = C->CLD = malloc((C->len + 1) * sizeof(*CLD)); CHECK_MALLOC(CLD); const saidx_t *LCP = C->LCP; typedef struct pair_s { saidx_t idx, lcp; } pair_t; pair_t *stack = malloc((C->len + 1) * sizeof(*stack)); CHECK_MALLOC(stack); pair_t *top = stack; // points at the topmost filled element pair_t last; R(CLD, 0) = C->len; top->idx = 0; top->lcp = -1; // iterate over all elements for (size_t k = 1; k < (size_t)(C->len + 1); k++) { while (LCP[k] < top->lcp) { // top->lcp is a leaf last = *top--; // link all elements of same lcp value in a chain while (top->lcp == last.lcp) { R(CLD, top->idx) = last.idx; last = *top--; } // store the l-index of last if (LCP[k] < top->lcp) { R(CLD, top->idx) = last.idx; } else { L(CLD, k) = last.idx; } } // continue one level deeper top++; top->idx = k; top->lcp = LCP[k]; } free(stack); return 0; } /** * This function computed the LCP array, given the suffix array. Thereto it uses * a special `phi` array, which makes it slightly faster than the original * linear-time algorithm by Kasai et al. * * @param C The enhanced suffix array to compute the LCP from. * @returns 0 iff successful */ int esa_init_LCP(esa_s *C) { const char *S = C->S; const saidx_t *SA = C->SA; saidx_t len = C->len; // Trivial safety checks if (!C || !S || !SA || len == 0) { return 1; } // Allocate new memory // The LCP array is one element longer than S. saidx_t *LCP = C->LCP = malloc((len + 1) * sizeof(*LCP)); CHECK_MALLOC(LCP); LCP[0] = -1; LCP[len] = -1; // Allocate temporary arrays saidx_t *PHI = malloc(len * sizeof(*PHI)); saidx_t *PLCP = PHI; CHECK_MALLOC(PHI); PHI[SA[0]] = -1; saidx_t k; ssize_t i; for (i = 1; i < len; i++) { PHI[SA[i]] = SA[i - 1]; } ssize_t l = 0; for (i = 0; i < len; i++) { k = PHI[i]; if (k != -1) { while (S[k + l] == S[i + l]) { l++; } PLCP[i] = l; l--; if (l < 0) l = 0; } else { PLCP[i] = -1; } } // unpermutate the LCP array for (i = 1; i < len; i++) { LCP[i] = PLCP[SA[i]]; } free(PHI); return 0; } /** @brief For the lcp-interval of string `w` compute the interval for `wa` * * Say, we already know the LCP-interval ij for a string `w`. Now we want to * check if `wa` may also be found in the ESA and thus in the subject. So we * look for the sub interval of `ij` in which all strings feature an `a` as * the next character. If such a sub interval is found, its boundaries are * returned. * * @param self - The ESA. * @param ij - The lcp-interval for `w`. * @param a - The next character. * @returns The lcp-interval one level deeper. */ static lcp_inter_t get_interval(const esa_s *self, lcp_inter_t ij, char a) { saidx_t i = ij.i; saidx_t j = ij.j; const saidx_t *SA = self->SA; const saidx_t *LCP = self->LCP; const char *S = self->S; const saidx_t *CLD = self->CLD; const char *FVC = self->FVC; // check for singleton or empty interval if (i == j) { if (S[SA[i] + ij.l] != a) { ij.i = ij.j = -1; } return ij; } int m = ij.m; int l = ij.l; char c = S[SA[i] + l]; goto SoSueMe; do { c = FVC[i]; SoSueMe: if (c == a) { /* found ! */ if (i != m - 1) { // found interval contains >1 element saidx_t n = L(CLD, m); ij = (lcp_inter_t){.i = i, .j = m - 1, .m = n, .l = LCP[n]}; } else { // empty or singleton // doing L(CLD, m) is not valid in this case! ij = (lcp_inter_t){.i = i, .j = i, .m = -1, .l = LCP[i]}; } return ij; } if (c > a) { break; } i = m; if (i == j) { break; // singleton interval, or `a` not found } m = R(CLD, m); } while (/*m != "bottom" && */ LCP[m] == l); // final sanity check if (i != ij.i ? FVC[i] == a : S[SA[i] + l] == a) { ij.i = i; ij.j = j; /* Also return the length of the LCP interval including `a` and * possibly even more characters. Note: l + 1 <= LCP[m] */ ij.l = LCP[m]; ij.m = m; } else { ij.i = ij.j = -1; } return ij; } /** @brief Compute the longest match of a query with the subject. * * The *longest match* is the core concept of `andi`. Its simply defined as the * longest prefix of a query Q appearing anywhere in the subject S. Talking * about genetic sequences, a match is a homologous region, likely followed by a * SNP. * * This function returns the interval for where the longest match of the query * can be found in the ESA. Thereto it expects a starting interval for the * search. * * @param C - The enhanced suffix array for the subject. * @param query - The query sequence. * @param qlen - The length of the query. Should correspond to `strlen(query)`. * @param k - The starting index into the query. * @param ij - The LCP interval for the string `query[0..k]`. * @returns The LCP interval for the longest prefix. */ lcp_inter_t get_match_from(const esa_s *C, const char *query, size_t qlen, saidx_t k, lcp_inter_t ij) { if (ij.i == -1 && ij.j == -1) { return ij; } // fail early on singleton intervals. if (ij.i == ij.j) { // try to extend the match. See line 513 below. saidx_t p = C->SA[ij.i]; size_t k = ij.l; const char *S = (const char *)C->S; for (; k < qlen && S[p + k]; k++) { if (S[p + k] != query[k]) { ij.l = k; return ij; } } ij.l = k; return ij; } saidx_t l, i, j; lcp_inter_t res = ij; const saidx_t *SA = C->SA; const char *S = C->S; // Loop over the query until a mismatch is found do { // Get the subinterval for the next character. ij = get_interval(C, ij, query[k]); i = ij.i; j = ij.j; // If our match cannot be extended further, return. if (i == -1 && j == -1) { res.l = k; return res; } res.i = ij.i; res.j = ij.j; l = qlen; if (i < j && ij.l < l) { /* Instead of making another look up we can use the LCP interval * calculated in get_interval */ l = ij.l; } // By definition, the kth letter of the query was matched. k++; // Extend the match for (int p = SA[i]; k < l; k++) { if (S[p + k] != query[k]) { res.l = k; return res; } } } while (k < (ssize_t)qlen); res.l = qlen; return res; } /** @brief Get a match. * * Given an ESA and a string Q find the longest prefix of Q that matches * somewhere in C. This search is done entirely via jumping around in the ESA, * and thus is slow. * * @param C - The ESA. * @param query - The query string — duh. * @param qlen - The length of the query. * @returns the lcp interval of the match. */ lcp_inter_t get_match(const esa_s *C, const char *query, size_t qlen) { // sanity checks if (!C || !query || !C->len || !C->SA || !C->LCP || !C->S || !C->CLD) { return (lcp_inter_t){-1, -1, -1, -1}; } saidx_t m = L(C->CLD, C->len); lcp_inter_t ij = {.i = 0, .j = C->len - 1, .m = m, .l = C->LCP[m]}; return get_match_from(C, query, qlen, 0, ij); } /** @brief Compute the LCP interval of a query. For a certain prefix length of * the query its LCP interval is retrieved from a cache. Hence this is faster * than the naive `get_match`. If the cache fails to provide a proper value, we * fall back to the standard search. * * @param C - The enhanced suffix array for the subject. * @param query - The query sequence. * @param qlen - The length of the query. Should correspond to `strlen(query)`. * @returns The LCP interval for the longest prefix. */ lcp_inter_t get_match_cached(const esa_s *C, const char *query, size_t qlen) { if (qlen <= CACHE_LENGTH) return get_match(C, query, qlen); ssize_t offset = 0; for (size_t i = 0; i < CACHE_LENGTH && offset >= 0; i++) { offset <<= 2; offset |= char2code(query[i]); } if (offset < 0) { return get_match(C, query, qlen); } lcp_inter_t ij = C->cache[offset]; if (ij.i == -1 && ij.j == -1) { return get_match(C, query, qlen); } return get_match_from(C, query, qlen, ij.l, ij); } andi-0.14/src/esa.h000066400000000000000000000036701415070357400140750ustar00rootroot00000000000000/** * @file * @brief This header contains the declarations for functions in esa.c. * */ #ifndef _ESA_H_ #define _ESA_H_ #include "config.h" #include "sequence.h" #include #include /** * @brief Represents LCP-Intervals. * * This struct is used to represent LCP-intervals. The member `i` should * coincide with the lower bound whereas `j` is the upper bound. Both bounds * are inclusive. So if `i == j` the interval contains exactly one element, * namely `i`. To represent an empty interval please use `i == j == -1`. * Other variants, such as `i == j == -2` can be used to indicate an error. * The common prefix length is denoted by l and should always be non-negative. * Variables of this type are often called `ij`. */ typedef struct { /** @brief The common prefix length */ saidx_t l; /** @brief lower bound */ saidx_t i; /** @brief upper bound */ saidx_t j; /** The new middle. */ saidx_t m; } lcp_inter_t; /** * @brief The ESA type. * * This structure holds arrays and objects associated with an enhanced * suffix array (ESA). */ typedef struct esa_s { /** The base string from which the ESA was generated. */ const char *S; /** The actual suffix array with indexes into S. */ saidx_t *SA; /** The LCP holds the number of letters up to which a suffix `S[SA[i]]` equals `S[SA[i-1]]`. Hence the name longest common prefix. For `i = 0` and `i = len` the LCP value is -1. */ saidx_t *LCP; /** The length of the string S. */ saidx_t len; /** A cache for lcp-intervals */ lcp_inter_t *cache; /** The FVC array holds the character after the LCP. */ char *FVC; /** This is the child array. */ saidx_t *CLD; } esa_s; lcp_inter_t get_match_cached(const esa_s *, const char *query, size_t qlen); lcp_inter_t get_match(const esa_s *, const char *query, size_t qlen); int esa_init(esa_s *, const seq_subject *S); void esa_free(esa_s *); #ifdef DEBUG char code2char(ssize_t code); #endif // DEBUG #endif andi-0.14/src/global.h000066400000000000000000000054511415070357400145640ustar00rootroot00000000000000/** * @file * @brief Global Definitions * * This file contains the declaration of global variables and * their related values. The actual definition is located in andi.c */ #ifndef _GLOBAL_H_ #define _GLOBAL_H_ #include #include "config.h" #include /** * The *global* variable ::FLAGS is used to set different options * for the execution of the program. Use `FLAGS & F_NAME` to check * if `F_NAME` was set. */ extern int FLAGS; /** * The *global* variable ::THREADS contains the number of threads the program * should use. */ extern int THREADS; /** * The ::ANCHOR_P_VALUE represents the probability that an anchor will be found, * if the two sequences are unrelated. I.e. it is the p-value for H_0: random * sequences. Its value can be set using the `-p` switch. */ extern double ANCHOR_P_VALUE; /** * The number of matrices that should be bootstrapped. */ extern long unsigned int BOOTSTRAP; /** * A global random number generator. Has to be seedable. */ extern gsl_rng *RNG; /** * The evolutionary model. */ extern int MODEL; enum { M_RAW, M_JC, M_KIMURA, M_LOGDET }; /** * This enum contains the available flags. Please note that all * available options are a power of 2. */ enum { F_NONE = 0, F_TRUNCATE_NAMES = 1, F_VERBOSE = 2, F_EXTRA_VERBOSE = 4, F_NON_ACGT = 8, F_JOIN = 16, F_LOW_MEMORY = 32, F_SHORT = 64, F_PRINT_PROGRESS = 128, F_SOFT_ERROR = 256 }; /** * @brief This macro is used to unify the checks for the return value of malloc. * * @param PTR - The pointer getting checked. */ #define CHECK_MALLOC(PTR) \ do { \ if (PTR == NULL) { \ err(errno, "Out of memory"); \ } \ } while (0) /** * @brief This macro is used to print a warning and make the program exit with * an failure exit code, later. */ #define soft_err(...) \ do { \ FLAGS |= F_SOFT_ERROR; \ warn(__VA_ARGS__); \ } while (0) /** * @brief This macro is used to print a warning and make the program exit with * an failure exit code, later. */ #define soft_errx(...) \ do { \ FLAGS |= F_SOFT_ERROR; \ warnx(__VA_ARGS__); \ } while (0) #endif andi-0.14/src/io.c000066400000000000000000000200621415070357400137210ustar00rootroot00000000000000/** * @file * @brief This file contains the definitions for various io methods. */ #define _GNU_SOURCE #include #include #include #include #include #include #include #include #include #include "global.h" #include "io.h" /** * @brief Access an element. * @param sv - The base vector. * @param index - The element index to access. * @returns the string at position `index`. */ char *string_vector_at(struct string_vector *sv, size_t index) { return sv->data[index]; } /** * @brief Access the underlying buffer. * @param sv - The base vector. * @returns the underlying buffer. */ char **string_vector_data(struct string_vector *sv) { return sv->data; } /** * @brief Free all data. * @param sv - The base vector. */ void string_vector_free(struct string_vector *sv) { size_t i = 0; for (; i < sv->size; i++) { free(sv->data[i]); } free(sv->data); } /** * @brief Initialise the vector. * @param sv - The base vector. */ void string_vector_init(struct string_vector *sv) { sv->data = malloc(sizeof(*sv->data) * 4); CHECK_MALLOC(sv->data); sv->capacity = 4; sv->size = 0; } /** * @brief Adds a copy to the end of the vector. * @param sv - The base vector. * @param str - The new string to add. */ void string_vector_push_back(struct string_vector *sv, const char *str) { string_vector_emplace_back(sv, strdup(str)); } /** * @brief Add a file name to the end of the vector, directly. * @param sv - The base vector. * @param str - The string to emplace. */ void string_vector_emplace_back(struct string_vector *sv, char *str) { if (sv->size < sv->capacity) { sv->data[sv->size++] = str; } else { char **ptr = reallocarray(sv->data, sv->capacity / 2, 3 * sizeof(*ptr)); CHECK_MALLOC(ptr); sv->data = ptr; sv->capacity = (sv->capacity / 2) * 3; sv->data[sv->size++] = str; } } /** * @brief Return the number of elements. * @param sv - The base vector. * @returns the size of the vector. */ size_t string_vector_size(const struct string_vector *sv) { return sv->size; } /** * @brief Read a *fof* and add its contents into a vector. * @param file_name - The file of file names aka. fof. * @param sv - The vector to add file names to. */ void read_into_string_vector(const char *file_name, struct string_vector *sv) { FILE *file = strcmp(file_name, "-") ? fopen(file_name, "r") : stdin; if (!file) { soft_err("%s", file_name); return; } while (1) { char *str = NULL; size_t buffer_size = 0; ssize_t check = getline(&str, &buffer_size, file); // EOF is set only *after* getline tried to read past it. if (check == -1 && feof(file) != 0) { free(str); break; // EOF } if (check == -1) { soft_err("%s", file_name); break; } char *nl = strchr(str, '\n'); if (nl) { *nl = '\0'; // remove newline character } // ignore empty lines if (strlen(str) == 0) { free(str); continue; } string_vector_emplace_back(sv, str); } int check = fclose(file); if (check != 0) { soft_err("%s", file_name); } } /** * @brief Joins all sequences from a file into a single long sequence. * * Apart from reading all sequences from a file, this function also * merges them into one long sequence. * * "I didn't learn joined up handwriting for nothing, you know." * ~ Gilderoy Lockhart * * @param file_name - The name of the file to be used for reading. The name is * also used to infer the sequence name. * @param dsa - (output parameter) An array that holds found sequences. */ void read_fasta_join(const char *file_name, dsa_t *dsa) { if (!file_name || !dsa) return; dsa_t single; dsa_init(&single); read_fasta(file_name, &single); if (dsa_size(&single) == 0) { return; } seq_t joined = dsa_join(&single); /* In join mode we try to be clever about the sequence name. Given the file * path we extract just the file name. ie. path/file.ext -> file * This obviously fails on Windows. */ const char *left = strrchr(file_name, '/'); // find the last path separator left = (left == NULL) ? file_name : left + 1; // left is the position one of to the right of the path separator const char *dot = strchrnul(left, '.'); // find the extension // copy only the file name, not its path or extension joined.name = strndup(left, dot - left); CHECK_MALLOC(joined.name); dsa_push(dsa, joined); dsa_free(&single); } /** * @brief This function reads sequences from a file. * @param file_name - The file to read. * @param dsa - (output parameter) An array that holds found sequences. */ void read_fasta(const char *file_name, dsa_t *dsa) { if (!file_name || !dsa) return; int file_descriptor = strcmp(file_name, "-") ? open(file_name, O_RDONLY) : STDIN_FILENO; if (file_descriptor < 0) { soft_err("%s", file_name); return; } struct pfasta_parser pp = pfasta_init(file_descriptor); if (pp.errstr) { soft_errx("%s: %s", file_name, pp.errstr); goto fail; } seq_t top = {}; while (!pp.done) { struct pfasta_record pr = pfasta_read(&pp); if (pp.errstr) { soft_errx("%s: %s", file_name, pp.errstr); goto fail; } int check = seq_init(&top, pr.sequence, pr.name); // skip broken sequences if (check != 0) continue; dsa_push(dsa, top); pfasta_record_free(&pr); } fail: pfasta_free(&pp); close(file_descriptor); } /** * @brief Prints the distance matrix. * * This function pretty prints the distance matrix. For small distances * scientific notation is used. * * @param D - The distance matrix * @param sequences - An array of pointers to the sequences. * @param n - The number of sequences. * @param warnings - Print warnings? Set to 0 for bootstrapped matrices. */ void print_distances(const struct model *D, const seq_t *sequences, size_t n, int warnings) { size_t i, j; int use_scientific = 0; double *DD = malloc(n * n * sizeof(*DD)); CHECK_MALLOC(DD); #define DD(X, Y) (DD[(X)*n + (Y)]) typedef double(estimate_fn)(const model *); estimate_fn *estimate; switch (MODEL) { case M_RAW: estimate = &estimate_RAW; break; default: /* intentional fall-through. This is just here to silence any * compiler warnings. The real default is set in andi.c.*/ case M_JC: estimate = &estimate_JC; break; case M_KIMURA: estimate = &estimate_KIMURA; break; case M_LOGDET: estimate = &estimate_LOGDET; break; } for (i = 0; i < n; i++) { for (j = 0; j < n; j++) { model datum = D(i, j); if (!(FLAGS & F_EXTRA_VERBOSE)) { datum = model_average(&D(i, j), &D(j, i)); } double dist = DD(i, j) = i == j ? 0.0 : estimate(&datum); if (dist > 0 && dist < 0.001) { use_scientific = 1; } if (isnan(dist) && warnings) { const char str[] = { "For the two sequences '%s' and '%s' the distance " "computation failed and is reported as nan. " "Please refer to the documentation for further details."}; soft_errx(str, sequences[i].name, sequences[j].name); } if (!isnan(dist) && i < j && warnings) { double coverage1 = model_coverage(&D(i, j)); double coverage2 = model_coverage(&D(j, i)); if (coverage1 < 0.2 || coverage2 < 0.2) { const char str[] = { "For the two sequences '%s' and '%s' very little " "homology was found (%f and %f, respectively)."}; soft_errx(str, sequences[i].name, sequences[j].name, coverage1, coverage2); } } } } printf("%zu\n", n); for (i = 0; i < n; i++) { // Print ten characters of the name. Pad with spaces, if // necessary. Truncate to exactly ten characters if requested by user. printf(FLAGS & F_TRUNCATE_NAMES ? "%-10.10s" : "%-10s", sequences[i].name); for (j = 0; j < n; j++) { // use scientific notation for small numbers printf(use_scientific ? " %1.4e" : " %1.4f", DD(i, j)); } printf("\n"); } free(DD); } /** * @brief Prints the coverage matrix. * @param D - The distance matrix * @param n - The number of sequences. */ void print_coverages(const struct model *D, size_t n) { size_t i, j; printf("\nCoverage:\n"); for (i = 0; i < n; i++) { for (j = 0; j < n; j++) { printf("%1.4e ", model_coverage(&D(i, j))); } printf("\n"); } } andi-0.14/src/io.h000066400000000000000000000022241415070357400137260ustar00rootroot00000000000000/** * @file * @brief This header contains function declarations for io procedures. */ #ifndef _IO_H_ #define _IO_H_ #include "model.h" #include "sequence.h" #include #include #include /** * This is a neat hack for dealing with matrices. */ #define D(X, Y) (D[(X)*n + (Y)]) #define M(X, Y) (M[(X)*n + (Y)]) void read_fasta(const char *, dsa_t *dsa); void read_fasta_join(const char *, dsa_t *dsa); void print_distances(const struct model *, const seq_t *, size_t, int); void print_coverages(const struct model *, size_t); /** * @brief A dynamically growing structure for file_names. */ struct string_vector { char **data; size_t capacity, size; }; char *string_vector_at(struct string_vector *, size_t); char **string_vector_data(struct string_vector *); void string_vector_free(struct string_vector *); void string_vector_init(struct string_vector *); void string_vector_push_back(struct string_vector *, const char *); void string_vector_emplace_back(struct string_vector *, char *); size_t string_vector_size(const struct string_vector *); void read_into_string_vector(const char *, struct string_vector *); #endif // _IO_H_ andi-0.14/src/model.c000066400000000000000000000221531415070357400144150ustar00rootroot00000000000000/** @file * @brief This file contains all functions for the mutation matrix and the * estimation of evolutionary distances thereof. */ #include "model.h" #include "global.h" #include #include #include #include /** * @brief Sum some mutation count specified by `summands`. Intended to be used * through the `model_sum` macro. * * @param MM - The mutation matrix. * @param summands - The mutations to add. * @returns The sum of mutations. */ static size_t model_sum_types(const model *MM, const int summands[]) { size_t total = 0; for (int i = 0; summands[i] != MUTCOUNTS; ++i) { total += MM->counts[summands[i]]; } return total; } #define model_sum(MM, ...) \ model_sum_types((MM), (int[]){__VA_ARGS__, MUTCOUNTS}) /** * @brief Average two mutation matrices. * * @param MM - One matrix * @param NN - Second matrix * @returns The average (sum) of two mutation matrices. */ model model_average(const model *MM, const model *NN) { model ret = *MM; for (int i = 0; i != MUTCOUNTS; ++i) { ret.counts[i] += NN->counts[i]; } ret.seq_len += NN->seq_len; return ret; } /** * @brief Compute the total number of nucleotides in the pairwise alignment. * * @param MM - The mutation matrix. * @returns The length of the alignment. */ size_t model_total(const model *MM) { size_t total = 0; for (size_t i = 0; i < MUTCOUNTS; ++i) { total += MM->counts[i]; } return total; } /** * @brief Compute the coverage of an alignment. * * @param MM - The mutation matrix. * @returns The relative coverage */ double model_coverage(const model *MM) { size_t covered = model_total(MM); size_t actual = MM->seq_len; return (double)covered / (double)actual; } /** * @brief Estimate the uncorrected distance of a pairwise alignment. * * @param MM - The mutation matrix. * @returns The uncorrected substitution rate. */ double estimate_RAW(const model *MM) { size_t nucl = model_total(MM); size_t SNPs = model_sum(MM, AtoC, AtoG, AtoT, CtoA, CtoG, CtoT, GtoA, GtoC, GtoT, TtoA, TtoC, TtoG); // Insignificant results. All abort the fail train. if (nucl <= 3) { return NAN; } return (double)SNPs / (double)nucl; } /** * @brief Compute the Jukes-Cantor distance. * * @param MM - The mutation matrix. * @returns The corrected JC distance. */ double estimate_JC(const model *MM) { double dist = estimate_RAW(MM); dist = -0.75 * log(1.0 - (4.0 / 3.0) * dist); // jukes cantor // fix negative zero return dist <= 0.0 ? 0.0 : dist; } /** @brief computes the evolutionary distance using K80. * * @param MM - The mutation matrix. * @returns The corrected Kimura distance. */ double estimate_KIMURA(const model *MM) { size_t nucl = model_total(MM); size_t transitions = model_sum(MM, AtoG, GtoA, CtoT, TtoC); size_t transversions = model_sum(MM, AtoC, CtoA, AtoT, TtoA, GtoC, CtoG, GtoT, TtoG); double P = (double)transitions / (double)nucl; double Q = (double)transversions / (double)nucl; double tmp = 1.0 - 2.0 * P - Q; double dist = -0.25 * log((1.0 - 2.0 * Q) * tmp * tmp); // fix negative zero return dist <= 0.0 ? 0.0 : dist; } /** @brief computes the evolutionary distance using LogDet. * * The LogDet distance between sequence X and and sequence Y * is given as * * -(1 / K) * (log(det(Fxy)) - 0.5 * log(det(Fxx * Fyy))) * * Where K is the number of character states, Fxy is the site-pattern * frequency matrix, and diagonal matrices Fxx and Fyy give the * frequencies of the different character states in sequences X and Y. * * Each i,j-th entry in Fxy is the proportion of homologous sites * where sequences X and Y have character states i and j, respectively. * * For our purposes, X is the Subject (From) sequence and Y is the * Query (To) sequence and matrix Fxy looks like * * To A C G T * From * A ( ) * C ( ) * G ( ) * T ( ) * * @param MM - The mutation matrix. * @returns The LogDet distance. */ double estimate_LOGDET(const model *MM) { double nucl = (double)model_total(MM); double P[MUTCOUNTS]; for (int i = 0; i < MUTCOUNTS; i++) { P[i] = MM->counts[i] / nucl; } double logDetFxxFyy = // log determinant of diagonal matrix of row sums log(model_sum(MM, AtoA, AtoC, AtoG, AtoT) / nucl) + log(model_sum(MM, CtoA, CtoC, CtoG, CtoT) / nucl) + log(model_sum(MM, GtoA, GtoC, GtoG, GtoT) / nucl) + log(model_sum(MM, TtoA, TtoC, TtoG, TtoT) / nucl) + // log determinant of diagonal matrix of column sums log(model_sum(MM, AtoA, CtoA, GtoA, TtoA) / nucl) + log(model_sum(MM, AtoC, CtoC, GtoC, TtoC) / nucl) + log(model_sum(MM, AtoG, CtoG, GtoG, TtoG) / nucl) + log(model_sum(MM, AtoT, CtoT, GtoT, TtoT) / nucl); // determinant of the site-pattern frequency matrix double detFxy = P[AtoA] * P[CtoC] * (P[GtoG] * P[TtoT] - P[TtoG] * P[GtoT]) - P[AtoA] * P[CtoG] * (P[GtoC] * P[TtoT] - P[TtoC] * P[GtoT]) + P[AtoA] * P[CtoT] * (P[GtoC] * P[TtoG] - P[TtoC] * P[GtoG]) - P[AtoC] * P[CtoA] * (P[GtoG] * P[TtoT] - P[TtoG] * P[GtoT]) + P[AtoC] * P[CtoG] * (P[GtoA] * P[TtoT] - P[TtoA] * P[GtoT]) - P[AtoC] * P[CtoT] * (P[GtoA] * P[TtoG] - P[TtoA] * P[GtoG]) + P[AtoG] * P[CtoA] * (P[GtoC] * P[TtoT] - P[TtoC] * P[GtoT]) - P[AtoG] * P[CtoC] * (P[GtoA] * P[TtoT] - P[TtoA] * P[GtoT]) + P[AtoG] * P[CtoT] * (P[GtoA] * P[TtoC] - P[TtoA] * P[GtoC]) - P[AtoT] * P[CtoA] * (P[GtoC] * P[TtoG] - P[TtoC] * P[GtoG]) + P[AtoT] * P[CtoC] * (P[GtoA] * P[TtoG] - P[TtoA] * P[GtoG]) - P[AtoT] * P[CtoG] * (P[GtoA] * P[TtoC] - P[TtoA] * P[GtoC]); double dist = -0.25 * (log(detFxy) - 0.5 * logDetFxxFyy); // fix negative zero return dist <= 0.0 ? 0.0 : dist; } /** @brief Bootstrap a mutation matrix. * * The classical bootstrapping process, as described by Felsenstein, resamples * all nucleotides of a MSA. As andi only computes a pairwise alignment, this * process boils down to a simple multinomial distribution. We just have to * resample the elements of the mutation matrix. See Klötzl & Haubold (2016) * for details. http://www.mdpi.com/2075-1729/6/1/11/htm * * @param datum - The original mutation matrix. * @returns A bootstrapped mutation matrix. */ model model_bootstrap(model datum) { size_t nucl = model_total(&datum); double p[MUTCOUNTS]; for (size_t i = 0; i < MUTCOUNTS; ++i) { p[i] = datum.counts[i] / (double)nucl; } gsl_ran_multinomial(RNG, MUTCOUNTS, nucl, p, datum.counts); return datum; } /** * @brief Given an anchor, classify nucleotides. * * For anchors we already know that the nucleotides of the subject and the query * are equal. Thus only one sequence has to be analysed. Most models don't * actually care about the individual nucleotides as long as they are equal in * the two sequences. For these models, we just assume equal distribution. * * @param MM - The mutation matrix * @param S - The subject * @param len - The anchor length */ void model_count_equal(model *MM, const char *S, size_t len) { if (MODEL == M_RAW || MODEL == M_JC || MODEL == M_KIMURA) { size_t fourth = len / 4; MM->counts[AtoA] += fourth; MM->counts[CtoC] += fourth; MM->counts[GtoG] += fourth; MM->counts[TtoT] += fourth + (len & 3); return; } // Fall-back algorithm for future models. Note, as this works on a // per-character basis it is slow. size_t local_counts[4] = {0}; for (; len--;) { char s = *S++; // ';!#' are all smaller than 'A' if (s < 'A') { // Technically, s can only be ';' at this point. continue; } // The four canonical nucleotides can be uniquely identified by the bits // 0x6: A -> 0, C → 1, G → 3, T → 2. Thus the order below is changed. local_counts[(s >> 1) & 3]++; } MM->counts[AtoA] += local_counts[0]; MM->counts[CtoC] += local_counts[1]; MM->counts[GtoG] += local_counts[3]; MM->counts[TtoT] += local_counts[2]; } /** @brief Convert a nucleotide to a 2bit representation. * * We want to map characters: * A → 0 * C → 1 * G → 2 * T → 3 * The trick used below is that the three lower bits of the * characters are unique. Thus, they can be used to compute the mapping * above. The mapping itself is done via tricky bitwise operations. * * @param c - input nucleotide * @returns 2bit representation. */ char nucl2bit(unsigned char c) { c &= 6; c ^= c >> 1; return c >> 1; } /** * @brief Count the substitutions and add them to the mutation matrix. * * @param MM - The mutation matrix. * @param S - The subject * @param Q - The query * @param len - The length of the alignment */ void model_count(model *MM, const char *S, const char *Q, size_t len) { size_t local_counts[MUTCOUNTS] = {0}; for (size_t i = 0; i < len; S++, Q++, i++) { char s = *S; char q = *Q; // Skip special characters. if (s < 'A' || q < 'A') { continue; } // Pick the correct two bits representing s and q. unsigned char foo = nucl2bit(s); unsigned char bar = nucl2bit(q); /* * Finally, we want to map the indices to the correct mutation. This is * done by utilising the mutation types in model.h. */ unsigned int index = (foo << 2) + bar; local_counts[index]++; } for (int i = 0; i != MUTCOUNTS; ++i) { MM->counts[i] += local_counts[i]; } } andi-0.14/src/model.h000066400000000000000000000030321415070357400144150ustar00rootroot00000000000000/** @file * @brief This header contains all structures and prototypes for creating a * mutation matrix and estimating distances trough an evolutionary model * thereof. */ #pragma once #include /** * This enum contains all possible mutations. The total number * of different possible mutations is MUTCOUNTS. */ enum { AtoA, AtoC, AtoG, AtoT, CtoA, CtoC, CtoG, CtoT, GtoA, GtoC, GtoG, GtoT, TtoA, TtoC, TtoG, TtoT, MUTCOUNTS }; /** @brief The mutation matrix. * * We need to keep track of the different types of mutations between two * sequences. For this the following matrix is filled. * * To A C G T * From * A ( ) * C ( ) * G ( ) * T ( ) * * The cells are absolute counts. Together with seq_len (the query length), * we can deduce the substitution rate and coverage. * * As libdivsufsort is 32 bit the sequence length is limited to (INT_MAX-1)/2. * We can thus use the same limit for the counts. */ typedef struct model { /** The absolute counts of mutation types. */ unsigned int counts[MUTCOUNTS]; /** The query length. */ unsigned int seq_len; } model; void model_count_equal(model *, const char *, size_t); void model_count(model *, const char *, const char *, size_t); model model_average(const model *, const model *); double model_coverage(const model *); double estimate_RAW(const model *); double estimate_JC(const model *); double estimate_KIMURA(const model *); double estimate_LOGDET(const model *); model model_bootstrap(model); andi-0.14/src/process.c000066400000000000000000000220241415070357400147700ustar00rootroot00000000000000 /** * @file * @brief This file contains various distance methods. */ #include "process.h" #include "esa.h" #include "global.h" #include "io.h" #include "model.h" #include "sequence.h" #include #include #include #include #ifdef _OPENMP #include #endif int calculate_bootstrap(const struct model *M, const seq_t *sequences, size_t n); typedef _Bool bool; #define false 0 #define true !false /** * @brief This structure captures properties of an anchor. */ struct anchor { /** The position on the subject. */ size_t pos_S; /** The position on the query. */ size_t pos_Q; /** The length of the exact match. */ size_t length; }; /** * @brief This is a structure of assorted variables needed for anchor finding. */ struct context { const esa_s *C; const char *query; size_t query_length; size_t threshold; }; /** * @brief Compute the length of the longest common prefix of two strings. * * @param S - One string. * @param Q - Another string. * @param remaining - The length of one of the strings. * @returns the length of the lcp. */ static inline size_t lcp(const char *S, const char *Q, size_t remaining) { size_t length = 0; while (length < remaining && S[length] == Q[length]) { length++; } return length; } /** * @brief Check whether the last anchor can be extended by a lucky anchor. * * Anchors are defined to be unique and of a minimum length. The uniqueness * requires us to search throw the suffix array for a second appearance of the * anchor. However, if a left anchor is already unique, we could be sloppy and * drop the uniqueness criterion for the second anchor. This way we can skip the * lookup and just compare characters directly. However, for a lucky anchor the * match still has to be longer than the threshold. * * @param ctx - Matching context of various variables. * @param last_match - The last anchor. * @param this_match - Input/Output variable for the current match. * @returns true iff the current match is a lucky anchor. */ static inline bool lucky_anchor(const struct context *ctx, const struct anchor *last_match, struct anchor *this_match) { size_t advance = this_match->pos_Q - last_match->pos_Q; size_t gap = this_match->pos_Q - last_match->pos_Q - last_match->length; size_t try_pos_S = last_match->pos_S + advance; if (try_pos_S >= (size_t)ctx->C->len || gap > ctx->threshold) { return false; } this_match->pos_S = try_pos_S; this_match->length = lcp(ctx->query + this_match->pos_Q, ctx->C->S + try_pos_S, ctx->query_length - this_match->pos_Q); return this_match->length >= ctx->threshold; } /** * @brief Check for a new anchor. * * Given the current context and starting position check if the new match is an * anchor. The latter requires uniqueness and a certain minimum length. * * @param ctx - Matching context of various variables. * @param last_match - (unused) * @param this_match - Input/Output variable for the current match. * @returns true iff an anchor was found. */ static inline bool anchor(const struct context *ctx, const struct anchor *last_match, struct anchor *this_match) { lcp_inter_t inter = get_match_cached(ctx->C, ctx->query + this_match->pos_Q, ctx->query_length - this_match->pos_Q); this_match->pos_S = ctx->C->SA[inter.i]; this_match->length = inter.l <= 0 ? 0 : inter.l; return inter.i == inter.j && this_match->length >= ctx->threshold; } /** * @brief Divergence estimation using the anchor technique. * * The dist_anchor() function estimates the divergence between two * DNA sequences. The subject is given as an ESA, whereas the query * is a simple string. This function then looks for *anchors* -- long * substrings that exist in both sequences. Then it manually checks for * mutations between those anchors. * * @param C - The enhanced suffix array of the subject. * @param query - The actual query string. * @param query_length - The length of the query string. Needed for speed * reasons. * @param threshold - Minimal length for an anchor. * @returns A matrix with estimates of base substitutions. */ model dist_anchor(const esa_s *C, const char *query, size_t query_length, size_t threshold) { struct model ret = {.seq_len = query_length, .counts = {0}}; struct anchor this_match = {0}; struct anchor last_match = {0}; bool last_was_right_anchor = false; size_t border = C->len / 2; struct context ctx = {C, query, query_length, threshold}; // Iterate over the complete query. while (this_match.pos_Q < query_length) { // Check for lucky anchors and fall back to normal strategy. if (lucky_anchor(&ctx, &last_match, &this_match) || anchor(&ctx, &last_match, &this_match)) { // We have reached a new anchor. size_t end_S = last_match.pos_S + last_match.length; size_t end_Q = last_match.pos_Q + last_match.length; // Check if this can be a right anchor to the last one. if (this_match.pos_S > end_S && this_match.pos_Q - end_Q == this_match.pos_S - end_S && (this_match.pos_S < border) == (last_match.pos_S < border)) { // classify nucleotides in the left qanchor model_count_equal(&ret, query + last_match.pos_Q, last_match.length); // Count the SNPs in between. model_count(&ret, C->S + end_S, query + end_Q, this_match.pos_Q - end_Q); last_was_right_anchor = true; } else { if (last_was_right_anchor) { // If the last was a right anchor, but with the current one, // we cannot extend, then add its length. model_count_equal(&ret, query + last_match.pos_Q, last_match.length); } else if (last_match.length >= threshold * 2) { // The last anchor wasn't neither a left or right anchor. // But, it was as long as an anchor pair. So still count it. model_count_equal(&ret, query + last_match.pos_Q, last_match.length); } last_was_right_anchor = false; } // Cache values for later last_match = this_match; } // Advance this_match.pos_Q += this_match.length + 1; } // Very special case: The sequences are identical if (last_match.length >= query_length) { model_count_equal(&ret, query, query_length); return ret; } // We might miss a few nucleotides if the last anchor was also a right // anchor. The logic is the same as a few lines above. if (last_was_right_anchor) { model_count_equal(&ret, query + last_match.pos_Q, last_match.length); } else if (last_match.length >= threshold * 2) { model_count_equal(&ret, query + last_match.pos_Q, last_match.length); } return ret; } /* * Include distMatrix and distMatrixLM. */ #define FAST #include "dist_hack.h" #undef FAST #include "dist_hack.h" /** * @brief Calculates and prints the distance matrix * @param sequences - An array of pointers to the sequences. * @param n - The number of sequences. */ void calculate_distances(seq_t *sequences, size_t n) { struct model *M = NULL; // The maximum number of sequences is near 457'845'052. size_t intermediate = SIZE_MAX / sizeof(*M) / n; if (intermediate < n) { size_t root = (size_t)sqrt(SIZE_MAX / sizeof(*M)); err(1, "Comparison is limited to %zu sequences (%zu given).", root, n); } M = malloc(n * n * sizeof(*M)); if (!M) { err(errno, "Could not allocate enough memory for the comparison " "matrix. Try using --join or --low-memory."); } // compute the distances if (FLAGS & F_LOW_MEMORY) { distMatrixLM(M, sequences, n); } else { distMatrix(M, sequences, n); } // print the results print_distances(M, sequences, n, 1); // print additional information. if (FLAGS & F_VERBOSE) { print_coverages(M, n); } // create new bootstrapped distance matrices if (BOOTSTRAP) { int res = calculate_bootstrap(M, sequences, n); if (res) { soft_errx("Bootstrapping failed."); } } free(M); } /** Yet another hack. */ #define B(X, Y) (B[(X)*n + (Y)]) /** @brief Computes a bootstrap from _pairwise_ alignments. * * Doing bootstrapping for alignments with only two sequences is easy. It boils * down to a simple multi-nomial process over the substitution matrix. * * @param M - the initial distance matrix * @param sequences - a list of the sequences, containing their lengths * @param n - the number of sequences * * The number of bootstrapped distance matrices to print is implicitly * passed via the global `BOOTSTRAP` variable. * * @returns 0 iff successful. */ int calculate_bootstrap(const struct model *M, const seq_t *sequences, size_t n) { if (!M || !sequences || !n) { return 1; } // B is the new bootstrap matrix struct model *B = malloc(n * n * sizeof(*B)); CHECK_MALLOC(B); // Compute a number of new distance matrices while (BOOTSTRAP--) { for (size_t i = 0; i < n; i++) { for (size_t j = i; j < n; j++) { if (i == j) { B(i, j) = (struct model){.seq_len = 1.0, .counts = {1.0}}; continue; } // Bootstrapping should only be used with averaged distances. model datum = model_average(&M(i, j), &M(j, i)); datum = model_bootstrap(datum); B(j, i) = B(i, j) = datum; } } print_distances(B, sequences, n, 0); } free(B); return 0; } andi-0.14/src/process.h000066400000000000000000000003321415070357400147730ustar00rootroot00000000000000/** * @file * @brief This file contains the declarations of functions in process.c * */ #ifndef _PROCESS_H_ #define _PROCESS_H_ #include "sequence.h" void calculate_distances(seq_t *sequences, size_t n); #endif andi-0.14/src/sequence.c000066400000000000000000000174171415070357400151340ustar00rootroot00000000000000/** * @file * @brief Sequence utilities * * This file contains utility functions for working with DNA sequences. */ #include #include #include #include #include #include "global.h" #include "sequence.h" #include void normalize(seq_t *S); double shustring_cum_prob(size_t x, double g, size_t l); size_t min_anchor_length(double p, double g, size_t l); /** Create a new dynamic array for sequences. */ int dsa_init(dsa_t *A) { // allocate at least 4 slots so the growth by 1.5 below doesn't get stuck // at 3 slots. A->data = malloc(sizeof(*A->data) * 4); CHECK_MALLOC(A->data); A->capacity = 4; A->size = 0; return 0; } /** Add a sequence to an array. */ void dsa_push(dsa_t *A, seq_t S) { if (A->size < A->capacity) { A->data[A->size++] = S; } else { // use the near-optimal growth factor of 1.5 seq_t *ptr = reallocarray(A->data, A->capacity / 2, sizeof(seq_t) * 3); CHECK_MALLOC(ptr); A->capacity = (A->capacity / 2) * 3; A->data = ptr; A->data[A->size++] = S; } } /** Frees the array and all sequences stored within. */ void dsa_free(dsa_t *A) { size_t i; for (i = 0; i < A->size; i++) { seq_free(&A->data[i]); } free(A->data); *A = (dsa_t){}; } /** Returns the number of sequences stored within an array. */ size_t dsa_size(const dsa_t *A) { return A->size; } /** Get the raw C array. */ seq_t *dsa_data(dsa_t *A) { return A->data; } /** * @brief Convert an array of multiple sequences into a single sequence. * * This function joins all sequences contained in an array into one * long sequence. The sequences are separated by a `!` character. The * caller has to free the initial array. * * @returns A new sequence representation the union of the array. */ seq_t dsa_join(dsa_t *A) { seq_t joined = {}; if (A->size == 0) { return joined; } if (A->size == 1) { /* If we are to join just one sequence, _move_ its contents. */ joined = A->data[0]; A->data[0] = (seq_t){}; return joined; } seq_t *data = A->data; seq_t *it = data; // Compute the total length size_t total = 0, i; for (i = 0; i < A->size; i++, it++) { total += it->len + 1; } // A single malloc for the whole new sequence char *ptr = malloc(total); CHECK_MALLOC(ptr); char *next = ptr; // Copy all old sequences and add a `!` in between it = data; memcpy(next, it->S, it->len); next += it->len; for (i = 1, it++; i < A->size; i++, it++) { *next++ = '!'; memcpy(next, it->S, it->len); next += it->len; } // Don't forget the null byte. *next = '\0'; joined.S = ptr; joined.len = total - 1; // subtract the null byte return joined; } /** * @brief Frees the memory of a given sequence. * @param S - The sequence to free. */ void seq_free(seq_t *S) { free(S->S); free(S->name); *S = (seq_t){}; } /** * @brief Compute the reverse complement. * @param str The master string. * @param len The length of the master string * @return The reverse complement. The caller has to free it! */ char *revcomp(const char *str, size_t len) { if (!str) return NULL; char *rev = malloc(len + 1); CHECK_MALLOC(rev); char *r = rev; const char *s = &str[len - 1]; rev[len] = '\0'; do { char c = *s--; char d; if (c < 'A') { d = ';'; // rosebud } else { d = c ^= c & 2 ? 4 : 21; } *r++ = d; } while (--len); return rev; } /** * @brief This function concatenates the reverse complement to a given master * string. A `#` sign is used as a separator. * @param s The master string. * @param len Its length. * @return The newly concatenated string. */ char *catcomp(char *s, size_t len) { if (!s) return NULL; char *rev = revcomp(s, len); char *temp = realloc(rev, 2 * len + 2); CHECK_MALLOC(temp); rev = temp; rev[len] = '#'; memcpy(rev + len + 1, s, len + 1); return rev; } /** * @brief Calculates the GC content of a sequence. * * This function computes the relative amount of G and C in the total sequence. */ double calc_gc(const seq_t *S) { size_t GC = 0; const char *p = S->S; for (; *p; p++) { if (*p == 'G' || *p == 'C') { GC++; } } return (double)GC / S->len; } /** @brief Prepares a sequences to be used as the subject in a comparison. */ int seq_subject_init(seq_subject *S, const seq_t *base) { S->gc = calc_gc(base); S->RS = catcomp(base->S, base->len); if (!S->RS) return 1; S->RSlen = 2 * base->len + 1; S->threshold = min_anchor_length(ANCHOR_P_VALUE, S->gc, S->RSlen); return 0; } /** @brief Frees some memory unused for when a sequence is only used as query. */ void seq_subject_free(seq_subject *S) { free(S->RS); S->RS = NULL; S->RSlen = 0; S->gc = 0.0; } /** @brief Initializes a sequences * * @returns 0 iff successful. */ int seq_init(seq_t *S, const char *seq, const char *name) { if (!S || !seq || !name) { return 1; } *S = (seq_t){.S = strdup(seq), .name = strdup(name)}; CHECK_MALLOC(S->S); CHECK_MALLOC(S->name); normalize(S); // recalculate the length because `normalize` might have stripped some // characters. S->len = strlen(S->S); return 0; } /** * @brief Restricts a sequence characters set to ACGT. * * This function strips a sequence of non ACGT characters and converts acgt to * the upper case equivalent. A flag is set if a non-canonical character was * encountered. */ void normalize(seq_t *S) { char *p, *q; char local_non_acgt = 0; for (p = q = S->S; *p; p++) { switch (*p) { case 'A': case 'C': case 'G': case 'T': case '!': *q++ = *p; break; case 'a': case 'c': case 'g': case 't': *q++ = toupper((unsigned char)*p); break; default: local_non_acgt = 1; break; } } *q = '\0'; if (local_non_acgt) { #pragma omp atomic FLAGS |= F_NON_ACGT; } } /** * @brief Calculates the minimum anchor length. * * Given some parameters calculate the minimum length for anchors according * to the distribution from Haubold et al. (2009). * * @param p - The probability with which an anchor will be created under a * random model. * @param g - The the relative amount of GC in the subject. * @param l - The length of the subject (includes revcomp). * @returns The minimum length of an anchor. */ size_t min_anchor_length(double p, double g, size_t l) { size_t x = 1; while (shustring_cum_prob(x, g / 2, l) < 1 - p) { x++; } return x; } /** * @brief Calculates the binomial coefficient of n and k. * * We could (and probably should) use gsl_sf_lnchoose(xx,kk) for this. * * @param n - The n part of the binomial coefficient. * @param k - analogue. * @returns (n choose k) */ size_t binomial_coefficient(size_t n, size_t k) { if (n <= 0 || k > n) { return 0; } if (k == 0 || k == n) { return 1; } if (k > n - k) { k = n - k; } size_t res = 1; for (size_t i = 1; i <= k; i++) { res *= n - k + i; res /= i; } return res; } /** * @brief Given `x` this function calculates the probability of a shustring * with a length less or equal to `x` under a random model. This means, it is * the cumulative probability. * * Let X be the longest shortest unique substring (shustring) at any position. * Then this function computes P{X <= x} with respect to the given parameter * set. See Haubold et al. (2009). Note that `x` includes the final mismatch. * Thus, `x` is `match length + 1`. * * @param x - The maximum length of a shustring. * @param p - The half of the relative amount of GC in the DNA. * @param l - The length of the subject. * @returns The probability of a certain shustring length. */ double shustring_cum_prob(size_t x, double p, size_t l) { double xx = (double)x; double ll = (double)l; size_t k; double s = 0.0; for (k = 0; k <= x; k++) { double kk = (double)k; double t = pow(p, kk) * pow(0.5 - p, xx - kk); s += pow(2, xx) * (t * pow(1 - t, ll)) * (double)binomial_coefficient(x, k); if (s >= 1.0) { s = 1.0; break; } } return s; } andi-0.14/src/sequence.h000066400000000000000000000026111415070357400151270ustar00rootroot00000000000000/** * @file * @brief Functions and structures for DNA sequences * */ #ifndef _SEQUENCE_H_ #define _SEQUENCE_H_ #include #include #include /** * @brief A structure for sequences. * * This structure is used to represent a DNA sequence of some kind. */ typedef struct seq_s { /** This is the DNAs forward strand as a string. */ char *S; /** The length of the forward strand. */ size_t len; /** A name for this sequence */ char *name; } seq_t; /** * @brief This structure enhances the usual sequence with its reverse * complement. */ typedef struct seq_subject { /** This member contains first the reverse strand and then the forward strand. */ char *RS; /** Corresponds to strlen(RS) */ size_t RSlen; /** * @brief GC-Content * * The relative amount of G or C in the DNA. */ double gc; /** The minimum length for an anchor. */ size_t threshold; } seq_subject; void seq_free(seq_t *S); int seq_subject_init(seq_subject *S, const seq_t *); void seq_subject_free(seq_subject *S); int seq_init(seq_t *S, const char *seq, const char *name); /** * @brief A dynamically growing structure for sequences. */ typedef struct dsa_s { seq_t *data; size_t capacity, size; } dsa_t; int dsa_init(dsa_t *A); void dsa_push(dsa_t *A, seq_t S); void dsa_free(dsa_t *A); size_t dsa_size(const dsa_t *A); seq_t *dsa_data(dsa_t *A); seq_t dsa_join(dsa_t *dsa); #endif andi-0.14/test/000077500000000000000000000000001415070357400133365ustar00rootroot00000000000000andi-0.14/test/Makefile.am000066400000000000000000000025571415070357400154030ustar00rootroot00000000000000check_PROGRAMS = test_esa test_seq test_fasta test_process dist_noinst_DATA = test_extra.sh test_random.sh test_join.sh nan.sh low_homo.sh test_seq_SOURCES = test_seq.c $(top_srcdir)/src/sequence.c test_seq_CPPFLAGS = -I$(top_srcdir)/src -I$(top_srcdir)/opt -DDEBUG -std=gnu99 test_seq_CFLAGS = -Wall -Wextra $(GLIB_CFLAGS) -Wno-missing-field-initializers test_seq_LDADD = $(GLIB_LIBS) $(top_builddir)/opt/libcompat.a test_process_SOURCES = test_process.c $(top_srcdir)/src/esa.c $(top_srcdir)/src/io.c $(top_srcdir)/src/model.c $(top_srcdir)/src/process.c $(top_srcdir)/src/sequence.c $(top_srcdir)/src/global.h test_process_CPPFLAGS = $(OPENMP_CFLAGS) -I$(top_srcdir)/src -I$(top_srcdir)/opt -I$(top_srcdir)/libs -DDEBUG -std=gnu99 test_process_CFLAGS = $(OPENMP_CFLAGS) -Wall -Wextra $(GLIB_CFLAGS) -Wno-missing-field-initializers test_process_LDADD = $(GLIB_LIBS) $(top_builddir)/opt/libcompat.a $(top_builddir)/libs/libpfasta.a test_esa_SOURCES = test_esa.c $(top_srcdir)/src/esa.c $(top_srcdir)/src/sequence.c $(top_srcdir)/src/esa.h test_esa_CPPFLAGS = $(OPENMP_CFLAGS) -I$(top_srcdir)/libs -I$(top_srcdir)/opt -I$(top_srcdir)/src -DDEBUG -std=gnu99 test_esa_CFLAGS = $(OPENMP_CFLAGS) -Wall -Wextra $(GLIB_CFLAGS) -Wno-missing-field-initializers test_esa_LDADD = $(GLIB_LIBS) $(top_builddir)/opt/libcompat.a test_fasta_SOURCES = test_fasta.cxx .PHONY: all all: $(check_PROGRAMS) andi-0.14/test/low_homo.sh000077500000000000000000000014131415070357400155170ustar00rootroot00000000000000#!/bin/bash -f SEED=${RANDOM_SEED:-0} SEED2=0 SEED3=0 if test $SEED -ne 0; then SEED=$((SEED + 1)) SEED2=$((SEED + 2)) SEED3=$((SEED + 3)) fi ./test/test_fasta -s $SEED -l 100000 > a_low.fa ./test/test_fasta -s $SEED2 -l 100000 > b_low.fa ./test/test_fasta -s $SEED3 -l 100 > both_low.fa cat both_low.fa a_low.fa | awk -v RS='>' '{if($1 == "S0")print ">"$0 > "S0_low.fa"}' cat both_low.fa b_low.fa | awk -v RS='>' '{if($1 == "S1")print ">"$0 > "S1_low.fa"}' # this is expected to trigger the low homology warning ./src/andi -j S0_low.fa S1_low.fa 2>&1 | grep 'homology' EXIT_VAL=$? if [[ EXIT_VAL -ge 1 ]]; then echo "Triggering low homology failed" >&2 grep '^>' a_low.fa b_low.fa both_low.fa fi rm -f a_low.fa b_low.fa both_low.fa S0_low.fa S1_low.fa exit $EXIT_VAL andi-0.14/test/nan.sh000077500000000000000000000007151415070357400144540ustar00rootroot00000000000000#!/bin/bash -f SEED=${RANDOM_SEED:-0} SEED2=0 if test $SEED -ne 0; then SEED=$((SEED + 1)) SEED2=$((SEED + 2)) fi ./test/test_fasta -s $SEED -l 10000 > a_nan.fa ./test/test_fasta -s $SEED2 -l 10000 > b_nan.fa # this is expected to trigger the nan warning ./src/andi -j a_nan.fa b_nan.fa 2>&1 | grep 'nan' EXIT_VAL=$? if [[ EXIT_VAL -ge 1 ]]; then echo "Triggering nan failed" >&2 grep '^>' a_nan.fa b_nan.fa fi rm -f a_nan.fa b_nan.fa exit $EXIT_VAL andi-0.14/test/test_esa.c000066400000000000000000000121261415070357400153130ustar00rootroot00000000000000#include "esa.h" #include #include "global.h" #include #include int FLAGS = F_NONE; int THREADS = 1; double ANCHOR_P_VALUE = 0.025; extern const int CACHE_LENGTH; char code3char( ssize_t code){ switch( code & 0x7){ case 0: return 'A'; case 1: return 'C'; case 2: return 'G'; case 3: return 'T'; case 4: return '!'; case 5: return ';'; case 6: return '#'; } return '\0'; } typedef struct { esa_s *C; seq_t *S; seq_subject subject; } esa_fixture; void assert_equal_lcp( const lcp_inter_t *a, const lcp_inter_t *b){ g_assert_cmpint( a->i, ==, b->i); g_assert_cmpint( a->j, ==, b->j); g_assert_cmpint( a->l, ==, b->l); } void assert_equal_cache_nocache( const esa_s *C, const char *str, size_t qlen){ lcp_inter_t a = get_match_cached(C, str, qlen); lcp_inter_t b = get_match(C, str, qlen); assert_equal_lcp( &a, &b); g_assert(strncmp(str, C->S + C->SA[a.i], a.l) == 0); g_assert( str[a.l] != C->S[ a.l + C->SA[a.i]] || str[a.l] == '\0'); } void setup( esa_fixture *ef, gconstpointer test_data){ ef->C = malloc( sizeof(esa_s)); ef->S = malloc( sizeof(seq_t)); g_assert( ef->C != NULL); g_assert( ef->S != NULL); const char *seq = { "TACGAGCACTGGTGGAATTGATGTC" "CAGTCTTATATGGCGCACCAGGCTG" "ATAGTAGTAGCAGTTTGCTTATCTC" "ATCGCGTGTTTCCGGATGACAGAGA" "TACGTGCACTGGTGGGATTGATGTC" "TAGTATTATATGGCGCACCAGGATG" "ATAGTAGTAGCAGTTTGCTTATCCC" "ATCGCGTGTTTGCGGATGACCGAGA" }; g_assert( seq_init( ef->S, seq, "S0" ) == 0); seq_subject_init( &ef->subject, ef->S); g_assert( ef->subject.RS != NULL); int check = esa_init( ef->C, &ef->subject); g_assert( check == 0); } void setup2( esa_fixture *ef, gconstpointer test_data){ ef->C = malloc( sizeof(esa_s)); ef->S = malloc( sizeof(seq_t)); g_assert( ef->C != NULL); g_assert( ef->S != NULL); const char *seq = { "TACGAGCACTGGTGGAATTGATGTC" "CAGTCTTATATGGCGCACCAGGCTG" "ATAGTAGTAGCAGTTTGCTTATCTC" "ATCGCGTGTTTCCGGATGACAGAGA" "!" "TACGTGCACTGGTGGGATTGATGTC" "TAGTATTATATGGCGCACCAGGATG" "ATAGTAGTAGCAGTTTGCTTATCCC" "ATCGCGTGTTTGCGGATGACCGAGA" }; g_assert( seq_init( ef->S, seq, "S0" ) == 0); seq_subject_init( &ef->subject, ef->S); g_assert( ef->subject.RS != NULL); int check = esa_init( ef->C, &ef->subject); g_assert( check == 0); } void teardown( esa_fixture *ef, gconstpointer test_data){ esa_free(ef->C); free(ef->C); seq_free(ef->S); free(ef->S); seq_subject_free(&ef->subject); } extern int count; void basic( esa_fixture *ef, gconstpointer test_data){ esa_s *C = ef->C; g_assert( C->SA); lcp_inter_t a = get_match_cached(C, "AAGACTGG", 8); lcp_inter_t b = get_match(C, "AAGACTGG", 8); assert_equal_lcp( &a, &b); g_assert(strncmp("AAGACTGG",C->S + C->SA[a.i], 8) == 0); a = get_match_cached(C, "AATTAAAA", 8); b = get_match(C, "AATTAAAA", 8); assert_equal_lcp( &a, &b); g_assert(strncmp("AATTAAAA",C->S + C->SA[a.i], a.l) == 0); a = get_match_cached(C, "ACCGAGAA", 8); b = get_match(C, "ACCGAGAA", 8); assert_equal_lcp( &a, &b); g_assert(strncmp("ACCGAGAA",C->S + C->SA[a.i], a.l) == 0); a = get_match_cached(C, "AAAAAAAAAAAA", 12); b = get_match(C, "AAAAAAAAAAAA", 12); assert_equal_lcp( &a, &b); g_assert(strncmp("AAAAAAAAAAAA",C->S + C->SA[a.i], a.l) == 0); //g_assert_cmpint(count, >=, 1 << (2*8)); } void normq_cached( esa_fixture *ef, gconstpointer test_data){ esa_s *C = ef->C; g_assert( C->SA); lcp_inter_t a, b; a = get_match_cached(C, "A", 1); b = get_match(C, "A", 1); assert_equal_lcp( &a, &b); a = get_match_cached(C, "C", 1); b = get_match(C, "C", 1); assert_equal_lcp( &a, &b); a = get_match_cached(C, "CT", 2); b = get_match(C, "CT", 2); assert_equal_lcp( &a, &b); a = get_match_cached(C, "AAGACTGG", 8); b = get_match(C, "AAGACTGG", 8); assert_equal_lcp( &a, &b); a = get_match_cached(C, "AATTAAAA", 8); b = get_match(C, "AATTAAAA", 8); assert_equal_lcp( &a, &b); a = get_match_cached(C, "ACCGAGAA", 8); b = get_match(C, "ACCGAGAA", 8); assert_equal_lcp( &a, &b); a = get_match_cached(C, "AAAAAAAAAAAA", 12); b = get_match(C, "AAAAAAAAAAAA", 12); assert_equal_lcp( &a, &b); a = get_match_cached(C, "!AAAAAAAAAAAA", 12); b = get_match(C, "!AAAAAAAAAAAA", 12); assert_equal_lcp( &a, &b); } size_t MAX_DEPTH = 11; void prefix_dfs( esa_s *C, char *str, size_t depth); void prefix( esa_fixture *ef, gconstpointer test_data){ esa_s *C = ef->C; char str[MAX_DEPTH+1]; str[MAX_DEPTH] = '\0'; prefix_dfs( C, str, 0); } void prefix_dfs( esa_s *C, char *str, size_t depth){ if( depth < MAX_DEPTH){ for( int code = 0; code < 4; ++code){ str[depth] = code2char(code); prefix_dfs( C, str, depth + 1); } } else { assert_equal_cache_nocache(C, str, depth); } } int main(int argc, char *argv[]) { g_test_init( &argc, &argv, NULL); g_test_add("/esa/basic", esa_fixture, NULL, setup, basic, teardown); g_test_add("/esa/sample cache", esa_fixture, NULL, setup, normq_cached, teardown); g_test_add("/esa/sample cache 2", esa_fixture, NULL, setup2, normq_cached, teardown); g_test_add("/esa/full cache", esa_fixture, NULL, setup, prefix, teardown); g_test_add("/esa/full cache 2", esa_fixture, NULL, setup2, prefix, teardown); return g_test_run(); } andi-0.14/test/test_extra.sh000077500000000000000000000020431415070357400160560ustar00rootroot00000000000000#!/bin/sh -f # Test if andi exists, and can be executed ./src/andi --version > /dev/null || exit 1 SEED=${RANDOM_SEED:-0} SEED2=0 SEED3=0 if test $SEED -ne 0; then SEED=$((SEED + 1)) SEED2=$((SEED + 2)) SEED3=$((SEED + 3)) fi # Test andi for more than just two sequences at a time ./test/test_fasta -s $SEED -l 100000 -d 0.01 -d 0.01 -d 0.01 -d 0.01 | ./src/andi > /dev/null || exit 1 # Test low-memory mode ./test/test_fasta -s $SEED2 -l 10000 > test_extra.fasta ./src/andi test_extra.fasta > extra.out ./src/andi test_extra.fasta --low-memory > extra_low_memory.out diff extra.out extra_low_memory.out || exit 1 # Test file of filenames ./test/test_fasta -s $SEED3 -l 10000 > test_extra.fasta echo "$PWD/test_extra.fasta" > fof.txt ./src/andi test_extra.fasta > extra.out ./src/andi --file-of-filenames fof.txt > fof.out cat fof.txt | ./src/andi --file-of-filenames - > fof2.out diff extra.out fof.out || exit 1 diff extra.out fof2.out || exit 1 rm -f test_extra.fasta extra.out extra_low_memory.out fof.out fof2.out fof.txt andi-0.14/test/test_fasta.cxx000066400000000000000000000051661415070357400162270ustar00rootroot00000000000000/** * This program can create genome sequences with a specific distance. */ #include #include #include #include #include using namespace std; void usage(); void print_seq( unsigned, unsigned, int, int, double); int main(int argc, char *argv[]){ random_device rd{}; auto seed = rd(); int length = 1000; int line_length = 70; int raw = 0; auto seqs = vector{0}; int check; while((check = getopt(argc, argv, "s:l:L:d:r")) != -1){ switch(check) { case 's': { seed = static_cast(stol(optarg)); if( seed == 0){ seed = rd(); } break; } case 'l': length = stoi(optarg); break; case 'L': line_length = stoi(optarg); break; case 'd': seqs.push_back(stod(optarg)); break; case 'r': raw = 1; break; case '?': default: usage(); return 1; } } if( seqs.size() < 2){ seqs.push_back(0.1); } if( !raw){ for(auto& dist : seqs) { auto d = dist; auto p = 0.75 - 0.75 * exp(-(4.0/3.0) * d); dist = p; } } auto base_seed = seed; for( int i=0; i< seqs.size(); i++){ cout << ">S" << i << " (base_seed: " << base_seed << ")" << endl; print_seq( base_seed, seed++, length, line_length, seqs[i]); } return 0; } static auto ACGT = "ACGT"; static auto NO_A = "CGT"; static auto NO_C = "AGT"; static auto NO_G = "ACT"; static auto NO_T = "ACG"; void print_seq( unsigned base_seed, unsigned mut_seed, int length, int line_length, double divergence){ char line[line_length+1]; line[line_length] = '\0'; auto base_rand = default_random_engine{base_seed}; auto base_dist = uniform_int_distribution{0,3}; auto base_acgt = [&]{return ACGT[base_dist(base_rand)];}; auto mut_rand = default_random_engine{mut_seed}; auto mut_dist = uniform_real_distribution{0,1}; auto mut = bind( mut_dist, mut_rand); auto mut_acgt = uniform_int_distribution{0,2}; auto mutate = [&](char c){ int idx = mut_acgt(mut_rand); switch(c){ case 'A': return NO_A[idx]; case 'C': return NO_C[idx]; case 'G': return NO_G[idx]; case 'T': return NO_T[idx]; default: return 'X'; } }; double nucleotides = (double)length; double mutations = nucleotides * divergence; for(int i= length, j; i > 0; i -= j){ j = min(line_length, i); for(auto k=0; k /dev/null || exit 1 SEED=${RANDOM_SEED:-0} SEED2=0 SEED3=0 if test $SEED -ne 0; then SEED=$((SEED + 1)) SEED2=$((SEED + 2)) SEED3=$((SEED + 3)) fi # Simple join test ./test/test_fasta -s $SEED -l 1000 -L 1000 -d 0.1 > p1_join.fasta ./test/test_fasta -s $SEED2 -l 1000 -L 1000 -d 0.1 > p2_join.fasta ./test/test_fasta -s $SEED3 -l 10000 -L 10000 -d 0.1 > p3_join.fasta head -qn 2 p1_join.fasta p2_join.fasta p3_join.fasta > S0_join.fasta tail -qn 2 p1_join.fasta p2_join.fasta p3_join.fasta > S1_join.fasta rm p1_join.fasta p2_join.fasta p3_join.fasta; RES=$(./src/andi -m RAW -t 1 -j S0_join.fasta S1_join.fasta | tail -n 1 | awk '{print ($2 - 0.1)}' | awk 'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) < 0.03}' ) if test $RES -ne 1; then echo "The last test computed a distance deviating more than three percent from its intended value." echo "See S0_join.fasta and S1_join.fasta for the used sequences." exit 1; fi SEED=${RANDOM_SEED:-0} SEED2=0 if test $SEED -ne 0; then SEED=$((SEED + 5)) SEED2=$((SEED + 6)) fi #unbalanced number of contigs ./test/test_fasta -s $SEED -l 1000 -L 1000 -d 0.1 > p2_join.fasta ./test/test_fasta -s $SEED2 -l 10000 -L 10000 -d 0.1 > p3_join.fasta head -qn 2 p3_join.fasta > S0_join.fasta tail -qn 2 p2_join.fasta p3_join.fasta > S1_join.fasta rm p2_join.fasta p3_join.fasta; RES=$(./src/andi -m RAW -t1 -j S0_join.fasta S1_join.fasta | tail -n 1 | awk '{print ($2 - 0.1)}' | awk 'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) < 0.03}' ) if test $RES -ne 1; then echo "The last test computed a distance deviating more than three percent from its intended value." echo "See S0_join.fasta and S1_join.fasta for the used sequences." exit 1; fi SEED=${RANDOM_SEED:-0} SEED2=0 SEED3=0 if test $SEED -ne 0; then SEED=$((SEED + 11)) SEED2=$((SEED + 12)) SEED3=$((SEED + 13)) fi #unbalanced number of contigs 2 ./test/test_fasta -s $SEED -l 1000 -L 1000 -d 0.1 > p1_join.fasta ./test/test_fasta -s $SEED2 -l 1000 -L 1000 -d 0.1 > p2_join.fasta ./test/test_fasta -s $SEED3 -l 10000 -L 10000 -d 0.1 > p3_join.fasta head -qn 2 p1_join.fasta p3_join.fasta > S0_join.fasta tail -qn 2 p1_join.fasta p2_join.fasta p3_join.fasta > S1_join.fasta rm p1_join.fasta p2_join.fasta p3_join.fasta; RES=$(./src/andi -mRAW -t 1 -j S0_join.fasta S1_join.fasta | tail -n 1 | awk '{print ($2 - 0.1)}' | awk 'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) < 0.03}' ) if test $RES -ne 1; then echo "The last test computed a distance deviating more than three percent from its intended value." echo "See S0_join.fasta and S1_join.fasta for the used sequences." exit 1; fi rm S0_join.fasta S1_join.fasta andi-0.14/test/test_process.c000066400000000000000000000016061415070357400162220ustar00rootroot00000000000000#include "global.h" #include "process.h" #include #include int FLAGS = 0; int THREADS = 1; long unsigned int BOOTSTRAP = 0; double ANCHOR_P_VALUE = 0.025; gsl_rng *RNG = NULL; int MODEL = M_JC; double shustring_cum_prob(size_t x, double g, size_t l); size_t min_anchor_length(double p, double g, size_t l); void test_shustring_cum_prob() { int len = 100000; double gc = 0.5; double p_value = 0.025; size_t threshold = min_anchor_length(p_value, gc, len); g_assert_cmpfloat(1 - p_value, <, shustring_cum_prob(threshold + 1, gc / 2, len)); g_assert_cmpfloat(1 - p_value, <=, shustring_cum_prob(threshold, gc / 2, len)); g_assert_cmpfloat(1 - p_value, >, shustring_cum_prob(threshold - 1, gc / 2, len)); } int main(int argc, char *argv[]) { g_test_init(&argc, &argv, NULL); g_test_add_func("/process/shustring_cum_prob", test_shustring_cum_prob); return g_test_run(); } andi-0.14/test/test_random.sh000077500000000000000000000044141415070357400162170ustar00rootroot00000000000000#!/bin/sh -f # This scripts test the accuracy of andi with random inputs. For that # it uses the small program test_random to generate pairs of sequences # with a given distance. By default, test_random creates a new set of # sequences each time it is called. Thus, this test has a small, but # non-zero probability of failing. That is a problem with Debian's # reproducible builds effort. So this script acts as a wrapper around # this issue. # # Simply calling this script via # % ./test/test_random.sh # checks a new test-case every time. But with the right parameter # % RANDOM_SEED=1729 ./test/test_random.sh # one specific set of sequences is validated. ./src/andi --help > /dev/null || exit 1 LENGTH=100000 # If RANDOM_SEED is set, use its value. Otherwise 0 is used to signal # to test_random that a new set of sequences shall be generated. SEED=${RANDOM_SEED:-0} for dist in 0.0 0.001 0.01 0.02 0.05 0.1 0.2 0.3 do for n in $(seq 10) do if test $SEED -ne 0; then SEED=$((SEED + 1)) fi res=$(./test/test_fasta -s $SEED -l $LENGTH -d $dist | tee ./test/test_random.fasta | ./src/andi -t 1 | tail -n 1 | awk -v dist=$dist '{print $2, dist}' | awk 'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) <= 0.055 && abs($1-$2) <= 0.055 * $2}') if test $res -ne 1; then echo "The last test computed a distance deviating more than five percent from its intended value." echo "See test_random.fasta for the used sequences." echo "./test/test_fasta -s $SEED -l $LENGTH -d $dist" head -n 1 ./test/test_random.fasta exit 1; fi done # raw for n in $(seq 10) do if test $SEED -ne 0; then SEED=$((SEED + 1)) fi res=$(./test/test_fasta -r -s $SEED -l $LENGTH -d $dist | tee ./test/test_random.fasta | ./src/andi -m RAW -t 1 | tail -n 1 | awk -v dist=$dist '{print $2, dist}' | awk 'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) <= 0.055 && abs($1-$2) <= 0.055 * $2}') if test $res -ne 1; then echo "The last test computed a distance deviating more than five percent from its intended value." echo "See test_random.fasta for the used sequences." echo "./test/test_fasta -r -s $SEED -l $LENGTH -d $dist" head -n 1 ./test/test_random.fasta exit 1; fi done done rm ./test/test_random.fasta andi-0.14/test/test_seq.c000066400000000000000000000033321415070357400153320ustar00rootroot00000000000000#include #include "global.h" #include #include #include "sequence.h" double ANCHOR_P_VALUE = 0.025; int FLAGS = F_NONE; void test_seq_basic(){ seq_t S; seq_init( &S, "ACGT", "name"); g_assert_cmpstr(S.S, ==, "ACGT"); g_assert_cmpstr(S.name, ==, "name"); g_assert_cmpuint(S.len, ==, 4); seq_free( &S); } void test_seq_full(){ seq_t S; seq_subject subject; seq_init( &S, "ACGTTGCA", "name"); int check = seq_subject_init( &subject, &S); g_assert_cmpint(check, ==, 0); g_assert_cmpstr(subject.RS, ==, "TGCAACGT#ACGTTGCA"); g_assert_cmpuint(subject.RSlen, ==, 8*2+1); g_assert( subject.gc == 0.5); seq_subject_free( &subject); seq_free( &S); } void test_seq_nonacgt(){ seq_t S; seq_subject subject; seq_init( &S, "11ACGTNN7682394689NNTGCA11", "name"); seq_subject_init( &subject, &S); g_assert_cmpstr(S.S, ==, "ACGTTGCA"); g_assert_cmpuint(S.len, ==, 8 ); g_assert( FLAGS & F_NON_ACGT); g_assert_cmpstr(subject.RS, ==, "TGCAACGT#ACGTTGCA"); g_assert_cmpuint(subject.RSlen, ==, 8*2+1); g_assert( subject.gc == 0.5); seq_subject_free( &subject); seq_free( &S); FLAGS = F_NONE; seq_init( &S, "@ACGT_!0TGCA ", "name"); seq_subject_init( &subject, &S); g_assert_cmpstr(S.S, ==, "ACGT!TGCA"); g_assert_cmpuint(S.len, ==, 9 ); g_assert( FLAGS & F_NON_ACGT); g_assert_cmpstr(subject.RS, ==, "TGCA;ACGT#ACGT!TGCA"); g_assert_cmpuint(subject.RSlen, ==, 9*2+1); seq_subject_free( &subject); seq_free( &S); FLAGS = F_NONE; } int main(int argc, char *argv[]) { g_test_init( &argc, &argv, NULL); g_test_add_func("/seq/basic", test_seq_basic); g_test_add_func("/seq/full", test_seq_full); g_test_add_func("/seq/non acgt", test_seq_nonacgt); return g_test_run(); }