Date: Sat, 23 Aug 2014 18:04:58 +0000 (UTC) From: Kurt Jaeger <pi@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r365765 - in head/biology: consed consed/files phrap phrap/files phred phred/files Message-ID: <201408231804.s7NI4wMx057360@svn.freebsd.org>
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Author: pi Date: Sat Aug 23 18:04:58 2014 New Revision: 365765 URL: http://svnweb.freebsd.org/changeset/ports/365765 QAT: https://qat.redports.org/buildarchive/r365765/ Log: update ports: biology/phrab biology/phred biology/consed Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to obtain the tarballs. PR: 191336 Submitted by: mzaki@m.u-tokyo.ac.jp (maintainer) Added: head/biology/consed/files/patch-installConsed.perl (contents, props changed) head/biology/consed/files/pkg-message.in (contents, props changed) head/biology/phrap/files/patch-alignments.c (contents, props changed) head/biology/phrap/files/patch-analyze_splices.c (contents, props changed) head/biology/phrap/files/patch-anomalies.c (contents, props changed) head/biology/phrap/files/patch-calf_utils.c (contents, props changed) head/biology/phrap/files/patch-call_subs.c (contents, props changed) head/biology/phrap/files/patch-cand_pairs.c (contents, props changed) head/biology/phrap/files/patch-contigs.c (contents, props changed) head/biology/phrap/files/patch-db.c (contents, props changed) head/biology/phrap/files/patch-names.c (contents, props changed) head/biology/phrap/files/patch-nodes.c (contents, props changed) head/biology/phrap/files/patch-pairs.c (contents, props changed) head/biology/phrap/files/patch-qual.c (contents, props changed) head/biology/phrap/files/patch-readin.c (contents, props changed) head/biology/phrap/files/patch-segments.c (contents, props changed) head/biology/phrap/files/patch-tig_node.c (contents, props changed) head/biology/phrap/files/patch-weibull.c (contents, props changed) head/biology/phrap/files/patch-words.c (contents, props changed) head/biology/phrap/pkg-plist (contents, props changed) head/biology/phred/files/pkg-message.in (contents, props changed) Deleted: head/biology/consed/files/patch-scripts_addReads2Consed.perl head/biology/consed/files/patch-scripts_determineReadTypes.perl head/biology/consed/pkg-plist.examples Modified: head/biology/consed/Makefile head/biology/consed/distinfo head/biology/consed/files/patch-scripts_phredPhrap head/biology/phrap/Makefile head/biology/phrap/distinfo head/biology/phrap/files/patch-makefile head/biology/phred/Makefile Modified: head/biology/consed/Makefile ============================================================================== --- head/biology/consed/Makefile Sat Aug 23 18:02:29 2014 (r365764) +++ head/biology/consed/Makefile Sat Aug 23 18:04:58 2014 (r365765) @@ -2,22 +2,68 @@ # $FreeBSD$ PORTNAME= consed -PORTVERSION= 16.0 +PORTVERSION= 27.0 CATEGORIES= biology -MASTER_SITES= http://www.phrap.org/consed/distributions/${PORTVERSION}/ +# MASTER_SITES= http://www.phrap.org/consed/distributions/${PORTVERSION}/ +MASTER_SITES= http://bozeman.mbt.washington.edu/consed/distributions/${PORTVERSION}/ DISTNAME= ${PORTNAME}_linux MAINTAINER= mzaki@m.u-tokyo.ac.jp COMMENT= Graphical tool for editing Phrap assemblies RUN_DEPENDS= phred:${PORTSDIR}/biology/phred \ - phrap:${PORTSDIR}/biology/phrap \ - phd2fasta:${PORTSDIR}/biology/phd2fasta + phrap:${PORTSDIR}/biology/phrap -USES= perl5 tar:Z +CONFLICTS_INSTALL= phd2fasta-[0-9]* + +SUB_FILES= pkg-message + +USES= perl5 shebangfix USE_LINUX= yes USE_LINUX_APPS= xorglibs ONLY_FOR_ARCHS= i386 amd64 +MYSHEBANG= bin/ace2Fasta.perl \ + bin/tagRepeats.perl \ + bin/selectRegions.perl \ + bin/selectOneRegion.perl \ + bin/revertToUneditedRead \ + bin/removeReads \ + bin/phredPhrap.orig \ + bin/phredPhrap \ + bin/phd2Ace.perl \ + bin/orderPrimerPairs.perl \ + bin/makeRegionsFile.perl \ + bin/makePhdBall.perl \ + bin/lib2Phd.perl \ + bin/fixContigEnd.perl \ + bin/findSequenceMatchesForConsed.perl \ + bin/revert_fof \ + bin/filter454Reads.perl \ + bin/fastq2Phrap.perl \ + bin/fasta2PhdBall.perl \ + bin/fasta2Phd.perl \ + bin/fasta2Ace.perl \ + bin/determineReadTypes.perl \ + bin/countEditedBases.perl \ + bin/bam2Ace.perl \ + bin/amplifyTranscripts.perl \ + bin/alignSolexaReads2Refs.perl \ + bin/alignRNA2Genomic.perl \ + bin/addSolexaReads.perl \ + bin/addSangerReads.perl \ + bin/addReads2Consed.perl \ + bin/add454Reads.perl \ + bin/ace2Oligos.perl \ + bin/transferConsensusTags.perl \ + bin/ace2fof \ + bin/ace2OligosWithComments.perl \ + bin/sff2phd.perl \ + bin/recover_consensus_tags \ + bin/phredPhrapWithPhdBalls \ + bin/cons.perl \ + bin/acestatus.pl \ + bin/aceContigs2Phds.perl \ + bin/sff2phd_Samborskyy RESTRICTED= Redistribution is not permitted in any form. You must request access permission via e-mail to get the tarball. Free for academic use. .if defined(PACKAGE_BUILDING) @@ -25,84 +71,13 @@ IGNORE= distribution files must be obta .endif NO_WRKSUBDIR= yes - -BUILD_WRKSRC= ${WRKSRC}/misc/mktrace -ALL_TARGET= mktrace - -BINARIES= consed mktrace sffinfo sff2scf -CONTRIBS= ace2OligosWithComments.perl ace2fof \ - aceContigs2Phds.perl acestatus.pl export_cons \ - mergeAces.perl recover_consensus_tags revert_fof -SCRIPTS= ace2Fasta.perl ace2Oligos.perl addReads2Consed.perl \ - amplifyTranscripts.perl catPhdFiles.perl \ - countEditedBases.perl determineReadTypes.perl fasta2Phd.perl \ - findSequenceMatchesForConsed.perl lib2Phd.perl \ - orderPrimerPairs.perl phd2Ace.perl phredPhrap removeReads \ - revertToUneditedRead tagRepeats.perl transferConsensusTags.perl -.for f in ${BINARIES} ${CONTRIBS} ${SCRIPTS} -PLIST_FILES+= bin/${f} -.endfor - -DATADIR= ${PREFIX}/lib/screenLibs -DATAFILES= primerCloneScreen.seq primerSubcloneScreen.seq \ - repeats.fasta singleVectorForRestrictionDigest.fasta -NULLFILES= vector.seq -.for f in ${DATAFILES} ${NULLFILES} -PORTDATA+= ${f}.dist -.endfor -PORTDOCS= README.txt - -NO_STAGE= yes - -OPTIONS_DEFINE= DOCS EXAMPLES - -.include <bsd.port.options.mk> - -.if ${PORT_OPTIONS:MEXAMPLES} -EXAMPLES= standard autofinish assembly_view polyphred -PLIST= ${PKGDIR}/pkg-plist.examples -.endif - -post-build: - (cd ${WRKSRC}/misc/454; ${CC} ${CFLAGS} sffinfo.c -o sffinfo) - (cd ${WRKSRC}/misc/454; ${CC} ${CFLAGS} sff2scf.c -o sff2scf) +NO_BUILD= yes do-install: - @${INSTALL_PROGRAM} ${WRKSRC}/consed_linux2.4 ${PREFIX}/bin/consed - @${INSTALL_PROGRAM} ${BUILD_WRKSRC}/mktrace ${PREFIX}/bin/ - @${INSTALL_PROGRAM} ${WRKSRC}/misc/454/sffinfo ${PREFIX}/bin/ - @${INSTALL_PROGRAM} ${WRKSRC}/misc/454/sff2scf ${PREFIX}/bin/ -.for f in ${BINARIES} - @${CHMOD} a-r ${PREFIX}/bin/${f} -.endfor -.for f in ${CONTRIBS} - @${INSTALL_SCRIPT} ${WRKSRC}/contributions/${f} ${PREFIX}/bin/ -.endfor -.for f in ${SCRIPTS} - @${INSTALL_SCRIPT} ${WRKSRC}/scripts/${f} ${PREFIX}/bin/ -.endfor - @${MKDIR} ${DATADIR} -.for f in ${DATAFILES} - @${INSTALL_DATA} ${WRKSRC}/misc/${f} ${DATADIR}/${f}.dist -.endfor -.for f in ${NULLFILES} - @${INSTALL_DATA} /dev/null ${DATADIR}/${f}.dist -.endfor -.if ${PORT_OPTIONS:MEXAMPLES} - @${MKDIR} ${EXAMPLESDIR} -.for dir in ${EXAMPLES} - @${CP} -R ${WRKSRC}/${dir} ${EXAMPLESDIR} -.endfor -.endif -.if ${PORT_OPTIONS:MDOCS} - @${MKDIR} ${DOCSDIR} -.for f in ${PORTDOCS} - @${INSTALL_DATA} ${WRKSRC}/${f} ${DOCSDIR} -.endfor -.endif -.if ! ${PORT_OPTIONS:MEXAMPLES} - @${ECHO_CMD} "Examples were not installed. You can define WITH_EXAMPLES=yes to install them." -.endif - @${ECHO_CMD} "You must set the CONSED_HOME environment variable to '${PREFIX}'" + ${MKDIR} ${STAGEDIR}${DATADIR} + ${LN} -sf ../../bin ${STAGEDIR}${DATADIR}/bin + (cd ${WRKSRC}; ${ENV} CC=${CC} ./installConsed.perl consed_linux32bit ${STAGEDIR}${DATADIR}) + ${LN} -sf ../../../etc/PhredPar/phredpar.dat ${STAGEDIR}${DATADIR}/lib/phredpar.dat + cd ${STAGEDIR}${PREFIX} && ${ECHO_CMD} ${MYSHEBANG} | ${XARGS} ${SED} -i '' ${_SHEBANG_REINPLACE_ARGS} .include <bsd.port.mk> Modified: head/biology/consed/distinfo ============================================================================== --- head/biology/consed/distinfo Sat Aug 23 18:02:29 2014 (r365764) +++ head/biology/consed/distinfo Sat Aug 23 18:04:58 2014 (r365765) @@ -1,2 +1,2 @@ -SHA256 (consed_linux.tar.Z) = ac9ce155ce46f7200accaa033c9b1ea1d8c071c68c2a82ab5f4b623d9ff6b117 -SIZE (consed_linux.tar.Z) = 27555099 +SHA256 (consed_linux.tar.gz) = 8038d2b94078ba918e97785fc7497252139029281000f1c54ff9dd1ec70e05fc +SIZE (consed_linux.tar.gz) = 34390726 Added: head/biology/consed/files/patch-installConsed.perl ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/consed/files/patch-installConsed.perl Sat Aug 23 18:04:58 2014 (r365765) @@ -0,0 +1,57 @@ +--- installConsed.perl.orig 2014-02-11 21:28:45.000000000 +0100 ++++ installConsed.perl 2014-08-23 19:27:23.000000000 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/local/bin/perl -w + + # installConsed.perl + +@@ -9,7 +9,7 @@ + # and this must be empty and must allow write access + + # edit this if you are using a different compiler than gcc +-$CC = "gcc"; ++$CC = $ENV{'CC'}; + + $szVersion = "25.0"; + +@@ -78,9 +78,9 @@ + $szHowToStartOver = "if you have had an error in the midst of this script, you have a problem because some things have been done and others not done. The cleanest solution is to go back to where nothing is done. To do that, type:\nrm -rf $szConsedHome/bin\nrm -rf $szConsedHome/lib\nrm -rf $szConsedHome/examples"; + + +-if ( -e "$szConsedHome/bin" ) { +- die "$szConsedHome/bin already exists\n$szHowToStartOver\n"; +-} ++#if ( -e "$szConsedHome/bin" ) { ++# die "$szConsedHome/bin already exists\n$szHowToStartOver\n"; ++#} + + if ( -e "$szConsedHome/lib" ) { + die "$szConsedHome/lib already exists\n$szHowToStartOver\n"; +@@ -91,7 +91,7 @@ + } + + +-&doCommand( "mkdir $szConsedHome/bin" ); ++#&doCommand( "mkdir $szConsedHome/bin" ); + &doCommand( "mkdir -p $szConsedHome/lib/screenLibs" ); + &doCommand( "mkdir $szConsedHome/examples" ); + &doCommand( "cp $szConsedExecutable $szConsedHome/bin" ); +@@ -101,7 +101,7 @@ + print "done\n"; + &doCommand( "cp README.txt $szConsedHome" ); + +-&doCommand( "chmod -R a+w $szConsedHome/examples/*" ); ++#&doCommand( "chmod -R a+w $szConsedHome/examples/*" ); + + &doCommand( "cp $szDownloadDirectory/scripts/* $szConsedHome/bin" ); + +@@ -112,7 +112,7 @@ + @aScreenLibs = split(' ', $szScreenLibs ); + foreach $szScreenFile ( @aScreenLibs ) { + print "about to cp $szDownloadDirectory/misc/$szScreenFile $szConsedHome/lib/screenLibs\n"; +- &doCommand( "cp $szDownloadDirectory/misc/$szScreenFile $szConsedHome/lib/screenLibs" ); ++ &doCommand( "cp $szDownloadDirectory/misc/$szScreenFile $szConsedHome/lib/screenLibs/$szScreenFile.sample" ); + } + + Modified: head/biology/consed/files/patch-scripts_phredPhrap ============================================================================== --- head/biology/consed/files/patch-scripts_phredPhrap Sat Aug 23 18:02:29 2014 (r365764) +++ head/biology/consed/files/patch-scripts_phredPhrap Sat Aug 23 18:04:58 2014 (r365765) @@ -1,36 +1,11 @@ ---- scripts/phredPhrap.orig 2007-09-26 04:02:20.000000000 +0900 -+++ scripts/phredPhrap 2007-12-11 17:32:27.000000000 +0900 -@@ -101,7 +101,7 @@ - - - # change this to reflect wherever you put the phredpar.dat file --$szPhredParameterFile = $szConsedHome . "/lib/phredpar.dat"; -+$szPhredParameterFile = $szConsedHome . "/etc/PhredPar/phredpar.dat"; - #$szPhredParameterFile = "/usr/local/common/lib/PhredPar/phredpar.dat"; - #$szPhredParameterFile = "/usr/local/etc/PhredPar/phredpar.dat"; - -@@ -207,7 +207,7 @@ - $chromatDirPath = "../chromat_dir"; - $phdDirPath = "../phd_dir"; +--- scripts/phredPhrap.orig 2014-02-12 05:28:45.000000000 +0900 ++++ scripts/phredPhrap 2014-06-22 03:07:33.000000000 +0900 +@@ -217,7 +217,7 @@ + #$solexaDirPath = "../solexa_dir"; + #$sffDirPath = "../sff_dir"; -$niceExe = "/bin/nice"; +$niceExe = "/usr/bin/nice"; $mvExe = "/bin/mv"; $lsExe = "/bin/ls"; $pwdExe = "/bin/pwd"; -@@ -568,11 +568,11 @@ - - # only uncomment the following 4 lines when you have customized - # determineReadTypes.perl --#print "\n\n--------------------------------------------------------\n"; --#print "Now running determineReadTypes.perl...\n"; --#print "--------------------------------------------------------\n\n\n"; -+print "\n\n--------------------------------------------------------\n"; -+print "Now running determineReadTypes.perl...\n"; -+print "--------------------------------------------------------\n\n\n"; - --#!system( "$determineReadTypes" ) || die "some problem running determineReadTypes.perl $!\n"; -+!system( "$determineReadTypes" ) || die "some problem running determineReadTypes.perl $!\n"; - - - print "\n\n--------------------------------------------------------\n"; Added: head/biology/consed/files/pkg-message.in ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/consed/files/pkg-message.in Sat Aug 23 18:04:58 2014 (r365765) @@ -0,0 +1,12 @@ +----------------------------------------------------------------------------- +CONSED installation directory: %%PREFIX%%/share/consed + + You must do either of following (see section 4.5 of README.txt): + 1) set CONSED_HOME environment variable to the location above + 2) make /usr/local/genome be a symlink targeting to the location above + +Example files are installed not as world writable, which README.txt assumes. +So you must copy the files to anywhere you have writable permissions. + +Now you can follow README.txt from section 4.12 +----------------------------------------------------------------------------- Modified: head/biology/phrap/Makefile ============================================================================== --- head/biology/phrap/Makefile Sat Aug 23 18:02:29 2014 (r365764) +++ head/biology/phrap/Makefile Sat Aug 23 18:04:58 2014 (r365765) @@ -1,11 +1,10 @@ -# Created by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp> # $FreeBSD$ PORTNAME= phrap -PORTVERSION= 0.990329 +PORTVERSION= 1.090518 CATEGORIES= biology MASTER_SITES= # put the tarball manually -DISTFILES= distrib.tar.Z +DISTFILES= distrib.tar.gz DIST_SUBDIR= ${PORTNAME} MAINTAINER= mzaki@m.u-tokyo.ac.jp @@ -19,19 +18,14 @@ IGNORE= distribution files must be obta NO_WRKSUBDIR= yes MAKEFILE= makefile -ALL_TARGET= all manyreads +ALL_TARGET= all -BINARIES= cluster cross_match cross_match.manyreads loco \ - phrap phrap.longreads phrap.manyreads swat +BINARIES= calf_merge pcluster cross_match loco phrap swat SCRIPTS= phrapview -.for f in ${BINARIES} ${SCRIPTS} -PLIST_FILES+= bin/${f} -.endfor -PORTDATA= BLOSUM50 BLOSUM62 PAM250 mat50 mat70 penalty2 vector.seq +PORTDATA= BLOSUM50 BLOSUM62 PAM250 mat50 mat70 mb_matrix penalty2 vector.seq PORTDOCS= general.doc phrap.doc swat.doc -NO_STAGE= yes .include <bsd.port.pre.mk> .for f in ${DISTFILES} @@ -42,21 +36,18 @@ IGNORE= you must request the source code do-install: .for f in ${BINARIES} - @${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin/ - @${CHMOD} a-r ${PREFIX}/bin/${f} # as required by the agreement + @${INSTALL_PROGRAM} ${WRKSRC}/${f} ${STAGEDIR}${PREFIX}/bin/ .endfor .for f in ${SCRIPTS} - @${INSTALL_SCRIPT} ${WRKSRC}/${f} ${PREFIX}/bin/ + @${INSTALL_SCRIPT} ${WRKSRC}/${f} ${STAGEDIR}${PREFIX}/bin/ .endfor - @${MKDIR} ${DATADIR} + @${MKDIR} ${STAGEDIR}${DATADIR} .for f in ${PORTDATA} - @${INSTALL_DATA} ${WRKSRC}/${f} ${DATADIR} + @${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${DATADIR} .endfor -.if ${PORT_OPTIONS:MDOCS} - @${MKDIR} ${DOCSDIR} + @${MKDIR} ${STAGEDIR}${DOCSDIR} .for f in ${PORTDOCS} - @${INSTALL_DATA} ${WRKSRC}/${f} ${DOCSDIR} + @${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${DOCSDIR} .endfor -.endif .include <bsd.port.post.mk> Modified: head/biology/phrap/distinfo ============================================================================== --- head/biology/phrap/distinfo Sat Aug 23 18:02:29 2014 (r365764) +++ head/biology/phrap/distinfo Sat Aug 23 18:04:58 2014 (r365765) @@ -1,2 +1,3 @@ -SHA256 (phrap/distrib.tar.Z) = e0be79818e3a8ca17391f42cc0ffbaf1a63299c8845a0b9ac3aaeb3cac641fcc -SIZE (phrap/distrib.tar.Z) = 366163 +MD5 (phrap/distrib.tar.gz) = 93ef3d1cca4d1a70ed16511d30a355ab +SHA256 (phrap/distrib.tar.gz) = 81f50c4410e8604cdefcc34ef6dc7b037be3bb45b94c439611a5590c1cf83665 +SIZE (phrap/distrib.tar.gz) = 333159 Added: head/biology/phrap/files/patch-alignments.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/phrap/files/patch-alignments.c Sat Aug 23 18:04:58 2014 (r365765) @@ -0,0 +1,10 @@ +--- ./alignments.c.orig 2009-04-18 23:07:41.000000000 +0200 ++++ ./alignments.c 2014-08-02 12:39:30.000000000 +0200 +@@ -591,6 +591,7 @@ + return adj_score; + } + ++void + print_alignment(profile) + Profile *profile; + { Added: head/biology/phrap/files/patch-analyze_splices.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/phrap/files/patch-analyze_splices.c Sat Aug 23 18:04:58 2014 (r365765) @@ -0,0 +1,88 @@ +--- ./analyze_splices.c.orig 2008-08-31 03:37:44.000000000 +0200 ++++ ./analyze_splices.c 2014-08-02 12:39:30.000000000 +0200 +@@ -146,6 +146,13 @@ + char *exon_seq; + double base_llr, intron_coeff; + ++void find_left_sites(Aligned_pair *, Cand_pair *, char *, char *); ++void find_right_sites(Aligned_pair *, Cand_pair *, char *, char *); ++void increment_splice_site(unsigned char *, unsigned char *, ++ Aligned_pair *, int, int, int, unsigned char *, int); ++void scan(Splice_site *, Aligned_pair *, unsigned char *, ++ int, int, int, int); ++ + set_splice_params() + { + int i, j; +@@ -186,6 +193,7 @@ + cases of large missing exons: want to make sure this part of read doesn't match somewhere else, instead + */ + ++void + append_cand_splice(strand, left_splice_site, right_splice_site, overlap, intron_length, left_pair, right_pair) + int strand, overlap, intron_length; + Splice_site *left_splice_site, *right_splice_site; +@@ -512,6 +520,7 @@ + return penalty; + } + ++void + check_best_site(pair, side, cand_pair) + Aligned_pair *pair; + int side; +@@ -560,6 +569,7 @@ + + int extend[3]; + ++void + find_left_sites(pair, cand_pair, seq1, seq2) + Aligned_pair *pair; + Cand_pair *cand_pair; +@@ -651,6 +661,7 @@ + + } + ++void + find_right_sites(pair, cand_pair, seq1, seq2) + Aligned_pair *pair; + Cand_pair *cand_pair; +@@ -816,6 +827,7 @@ + This doesn't really address multiple testing issue; + */ + ++void + increment_splice_site(seq1, seq2, pair, strand, side, loc, seq, type) + Aligned_pair *pair; + int strand, side, loc, type; +@@ -922,6 +934,7 @@ + + /* input: splice_site, c_len, pair, seq1, exon_seq, genome_overhang, cdna_overhang, base_llr, intron_coeff, max_i */ + ++void + scan(splice_site, pair, seq1, genome_overhang, cdna_overhang, max_i, test_len) + Splice_site *splice_site; + Aligned_pair *pair; +@@ -1098,6 +1111,7 @@ + return n_matches; + } + ++void + check_max_length(length) + int length; + { +@@ -1118,6 +1132,7 @@ + max_length = length; + } + ++void + filter_matches(i_ptr, n_p, pair_pointers, print_flag) + int i_ptr, n_p, print_flag; + Aligned_pair **pair_pointers; +@@ -1276,6 +1291,7 @@ + return seg_equiv1->start - seg_equiv2->start; + } + ++void + analyze_multiple(i_ptr, n_p, pair_pointers, print_flag) + int i_ptr, n_p, print_flag; + Aligned_pair **pair_pointers; Added: head/biology/phrap/files/patch-anomalies.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/phrap/files/patch-anomalies.c Sat Aug 23 18:04:58 2014 (r365765) @@ -0,0 +1,19 @@ +--- ./anomalies.c.orig 2008-11-10 06:02:00.000000000 +0100 ++++ ./anomalies.c 2014-08-02 12:39:30.000000000 +0200 +@@ -28,6 +28,8 @@ + extern Parameters *parameters; + extern int num_pairs, t_num_entries; + ++void visit_cand_pairs_dups(int, Cand_pair *); ++ + #define MAX_CHIMERA_GAP 30 /* maximum gap between distinct confirmed segments for + putative chimeras */ + compare_pair_entries(pair_1, pair_2) +@@ -830,6 +832,7 @@ + notify(" Done\n"); + } + ++void + visit_cand_pairs_dups(entry1, pair) + int entry1; + Cand_pair *pair; Added: head/biology/phrap/files/patch-calf_utils.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/phrap/files/patch-calf_utils.c Sat Aug 23 18:04:58 2014 (r365765) @@ -0,0 +1,19 @@ +--- ./calf_utils.c.orig 2008-11-04 23:21:50.000000000 +0100 ++++ ./calf_utils.c 2014-08-02 12:39:30.000000000 +0200 +@@ -28,6 +28,8 @@ + + extern void *malloc(), *realloc(); + ++void read_type_3(File_stat *, int); ++ + append_file_stat(file_name) + char *file_name; + { +@@ -110,6 +112,7 @@ + get_record_header(file_stat); + } + ++void + read_type_3(file_stat, new_rec_flag) + File_stat *file_stat; + int new_rec_flag; Added: head/biology/phrap/files/patch-call_subs.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/phrap/files/patch-call_subs.c Sat Aug 23 18:04:58 2014 (r365765) @@ -0,0 +1,19 @@ +--- ./call_subs.c.orig 1999-01-17 00:42:56.000000000 +0100 ++++ ./call_subs.c 2014-08-02 12:39:30.000000000 +0200 +@@ -26,15 +26,13 @@ + + extern Parameters *parameters; + ++void + call_write_exp_files(n_sing, n_contigs, contig_ptrs) + int n_sing, n_contigs; + Contig **contig_ptrs; + { + #if defined(GCPHRAP) + write_exp_files(n_sing, n_contigs, contig_ptrs); +- return; +-#else +- return; + #endif + } + Added: head/biology/phrap/files/patch-cand_pairs.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/phrap/files/patch-cand_pairs.c Sat Aug 23 18:04:58 2014 (r365765) @@ -0,0 +1,18 @@ +--- ./cand_pairs.c.orig 2008-08-31 03:02:56.000000000 +0200 ++++ ./cand_pairs.c 2014-08-02 12:39:30.000000000 +0200 +@@ -38,6 +38,7 @@ + + static int num_cand_pairs, num_dups, num_repeat_rejected_pairs; + ++void + cluster_pairs(entry1, entry2, start1, start2, reverse, rev_store_flag) + int entry1, entry2, start1, start2; + int reverse, rev_store_flag; +@@ -74,6 +75,7 @@ + set_equiv_class(entry, final_class); + } + ++void + make_new_cand_pair(entry1, entry2, start1, start2, reverse, rev_store_flag) + int entry1, entry2, start1, start2; + int reverse, rev_store_flag; Added: head/biology/phrap/files/patch-contigs.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/phrap/files/patch-contigs.c Sat Aug 23 18:04:58 2014 (r365765) @@ -0,0 +1,10 @@ +--- ./contigs.c.orig 2008-11-11 22:56:27.000000000 +0100 ++++ ./contigs.c 2014-08-02 12:39:30.000000000 +0200 +@@ -2115,6 +2115,7 @@ + contig1->base_segment = previous_base_segment; + } + ++void + write_contigs() + { + char *our_alloc(); Added: head/biology/phrap/files/patch-db.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/phrap/files/patch-db.c Sat Aug 23 18:04:58 2014 (r365765) @@ -0,0 +1,19 @@ +--- ./db.c.orig 2009-04-21 18:10:09.000000000 +0200 ++++ ./db.c 2014-08-02 12:39:30.000000000 +0200 +@@ -38,6 +38,8 @@ + int qseq_trans[256]; + int t_num_entries; + ++void size_conflict(SEQ_AREA,long int,char *); ++ + typedef long int POS; + static POS id_pos, descrip_pos, seq_pos, seq_length; + /* N.B. following needed by Bonfield code, so original "static" designation has +@@ -571,6 +573,7 @@ + (unsigned long int)db->seq_area_size, (unsigned long int)db->id_area_size, (unsigned long int)db->descrip_area_size); + } + ++void + size_conflict(size1, size2, label) + SEQ_AREA size1; + long int size2; Modified: head/biology/phrap/files/patch-makefile ============================================================================== --- head/biology/phrap/files/patch-makefile Sat Aug 23 18:02:29 2014 (r365764) +++ head/biology/phrap/files/patch-makefile Sat Aug 23 18:04:58 2014 (r365765) @@ -1,9 +1,9 @@ ---- makefile.orig 1999-03-11 15:13:20.000000000 +0900 -+++ makefile 2007-12-11 13:19:39.000000000 +0900 -@@ -23,8 +23,8 @@ - #*****************************************************************************/ - +--- ./makefile.orig 2009-06-02 17:45:34.000000000 +0200 ++++ ./makefile 2014-08-02 12:43:45.000000000 +0200 +@@ -25,8 +25,8 @@ # Makefile for swat, phrap, cross_match, phrapview; also swprobs (currently inactivated) + #CC= icc + #CFLAGS= -O2 -wd266,880 -CC= cc -CFLAGS= -O2 +CC?= cc @@ -11,17 +11,24 @@ LFLAGS= -lm SWATOBJS= swat.o weibull.o -@@ -55,11 +55,11 @@ +@@ -55,7 +55,7 @@ + + CALFOBJS= calf_merge.o calf_utils.o + +-all: swat phrap cross_match phrapview cluster loco calf_merge ++all: swat phrap cross_match phrapview pcluster loco calf_merge + + #manyreads: + # touch swat.h; +@@ -131,9 +131,9 @@ + $(CC) $(CFLAGS) -o $@ gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LFLAGS) + chmod o-r gccross_match + +-cluster: makefile $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) ++pcluster: makefile $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) + $(CC) $(CFLAGS) -o $@ $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) $(LFLAGS) +- chmod o-r cluster ++ chmod o-r pcluster - manyreads: - touch swat.h; -- make CFLAGS="-O2 -DMANYREADS" phrap cross_match; -+ make CFLAGS="$(CFLAGS) -DMANYREADS" phrap cross_match; - mv phrap phrap.manyreads; - mv cross_match cross_match.manyreads; - touch swat.h; -- make CFLAGS="-O2 -DLONGREADS" phrap; -+ make CFLAGS="$(CFLAGS) -DLONGREADS" phrap; - mv phrap phrap.longreads; - touch swat.h; - make phrap cross_match; + loco: makefile $(LOCOOBJS) $(SWOBJS) + $(CC) $(CFLAGS) -o $@ $(LOCOOBJS) $(SWOBJS) $(LFLAGS) Added: head/biology/phrap/files/patch-names.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/phrap/files/patch-names.c Sat Aug 23 18:04:58 2014 (r365765) @@ -0,0 +1,19 @@ +--- ./names.c.orig 2007-11-06 23:03:53.000000000 +0100 ++++ ./names.c 2014-08-02 12:39:30.000000000 +0200 +@@ -30,6 +30,8 @@ + + #define MAX_SUBCLONE_HIST 101 + ++void print_contig_chains(); ++ + set_delims() + { + subclone_delim = parameters->subclone_delim; +@@ -1014,6 +1016,7 @@ + + /* greedy algorithm for finding chains of contigs */ + /* NEED TO LOOK SYSTEMATICALLY FOR CIRCULAR CHAINS, AND BREAK THEM */ ++void + print_contig_chains() + { + Link *link; Added: head/biology/phrap/files/patch-nodes.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/phrap/files/patch-nodes.c Sat Aug 23 18:04:58 2014 (r365765) @@ -0,0 +1,19 @@ +--- ./nodes.c.orig 2008-08-31 03:44:15.000000000 +0200 ++++ ./nodes.c 2014-08-02 12:39:30.000000000 +0200 +@@ -31,6 +31,8 @@ + extern Parameters *parameters; /* exported */ + extern double *scaled_err_probs; + int *contig_graph_weights; ++ ++void nr_tarjan(int); + + set_contig_graph_weights() + { +@@ -679,6 +681,7 @@ + curr_state->calling_point = calling_point; + } + ++void + nr_tarjan(k) + int k; + { Added: head/biology/phrap/files/patch-pairs.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/phrap/files/patch-pairs.c Sat Aug 23 18:04:58 2014 (r365765) @@ -0,0 +1,91 @@ +--- ./pairs.c.orig 2009-04-23 00:12:20.000000000 +0200 ++++ ./pairs.c 2014-08-02 12:39:30.000000000 +0200 +@@ -37,6 +37,16 @@ + int single_domain; + double mask_frac; + ++void revise_qd_scores(Query_domain *); ++void visit_cand_pairs_scores( Cand_pair *); ++void merge_qds(Database *, int); ++void init_qd_trims(Query_domain *); ++void test_qd1_merges(Query_domain *, Query_domain *); ++void test_qd2_merges(Query_domain *, Query_domain *); ++void compare_query_domains(Query_domain *, Query_domain *); ++void print_score_list(int, Query_domain *); ++void print_pair(Aligned_pair *, FILE *, int); ++ + set_domain_vars() + { + single_domain = parameters->masklevel == 0 || parameters->masklevel == 101; +@@ -697,6 +707,7 @@ + */ + } + ++void + visit_cand_pairs_scores(cand_pair) + Cand_pair *cand_pair; + { +@@ -1423,6 +1434,7 @@ + + int trim_flag; + ++void + merge_qds(db, t_f) + Database *db; + int t_f; +@@ -1463,6 +1475,7 @@ + } + } + ++void + init_qd_trims(query_domain) + Query_domain *query_domain; + { +@@ -1476,6 +1489,7 @@ + init_qd_trims(query_domain->child[1]); + } + ++void + test_qd1_merges(query_domain1, query_domain2) + Query_domain *query_domain1, *query_domain2; + { +@@ -1486,6 +1500,7 @@ + test_qd1_merges(query_domain1->child[1], query_domain2); + } + ++void + test_qd2_merges(query_domain1, query_domain2) + Query_domain *query_domain1, *query_domain2; + { +@@ -1533,6 +1548,7 @@ + } + } + ++void + compare_query_domains(query_domain1, query_domain2) + Query_domain *query_domain1, *query_domain2; + { +@@ -1570,6 +1586,7 @@ + } + } + ++void + print_score_list(entry, query_domain) + int entry; + Query_domain *query_domain; +@@ -1732,6 +1749,7 @@ + } + } + ++void + print_pair(pair, fp, no_zero) + Aligned_pair *pair; + FILE *fp; +@@ -4125,6 +4143,7 @@ + notify("done"); + } + ++void + revise_qd_scores(query_domain) + Query_domain *query_domain; + { Added: head/biology/phrap/files/patch-qual.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/phrap/files/patch-qual.c Sat Aug 23 18:04:58 2014 (r365765) @@ -0,0 +1,82 @@ +--- ./qual.c.orig 2008-11-12 17:45:48.000000000 +0100 ++++ ./qual.c 2014-08-02 12:39:30.000000000 +0200 +@@ -44,6 +44,12 @@ + static int mismatch_LLR[256]; + double *scaled_err_probs; /* used for finding high-quality segments */ + ++void read_qual(Database *); ++void rescale_qual(Database *); ++void incr_diff_hist(unsigned char *, unsigned char *, ++ int, int, int, int, ++ int, int, int, int ); ++ + init_qual_arrays() + { + int i; +@@ -580,6 +586,7 @@ + } + + /* read in quality data */ ++void + read_qual(db) + Database *db; + { +@@ -876,6 +883,7 @@ + } + + /* NOT CORRECT WITH COMPRESSED QUAL */ ++void + rescale_qual(db) + Database *db; + { +@@ -1153,6 +1161,10 @@ + int conf_count[2], conf_max_score, conf_max_margin; /* # confirming reads */ + } Diffsegnode; + ++void append_diffdata(Diffsegnode *); ++void append_diffsegnode(Diffsegnode *, int, int, int, int, Diffsegnode *); ++void write_diffsegnode(Diffsegnode *); ++ + int data_type, data_length, data_qual, data_reverse, data_score, data_margin; + unsigned char *data_seq; + +@@ -1400,6 +1412,7 @@ + = n_align[i] = n_unalign[i] = n_p_unalign[i] = 0; + } + ++void + incr_diff_hist(seq, diff, length1, length2, start1, start2, end1, end2, reverse, ignore_ends) + unsigned char *seq; + unsigned char *diff; +@@ -1543,6 +1556,7 @@ + int node_index; + extern unsigned char area_comp_mat[]; + ++void + append_diffdata(diffsegnode) + Diffsegnode *diffsegnode; + { +@@ -1607,6 +1621,7 @@ + diffdata->count[!data_reverse] = 0; + } + ++void + append_diffsegnode(node, entry, seg_start, seg_end, conf_flag, data_node) + Diffsegnode *node, *data_node; /* latter is 0 if reading from global vars */ + int entry, seg_start, seg_end, conf_flag; +@@ -1724,6 +1739,7 @@ + strcpy(cdb, "CDSILRdi"); + } + ++void + write_diffsegnode(node) + Diffsegnode *node; + { +@@ -1800,6 +1816,7 @@ + write_diffsegnode(node->child[1]); + } + ++void + write_diffsegnodes() + { + int i; Added: head/biology/phrap/files/patch-readin.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/phrap/files/patch-readin.c Sat Aug 23 18:04:58 2014 (r365765) @@ -0,0 +1,10 @@ +--- ./readin.c.orig 2008-11-11 20:33:41.000000000 +0100 ++++ ./readin.c 2014-08-02 12:39:30.000000000 +0200 +@@ -31,6 +31,7 @@ + /* read in sequence files, initialize array of aligned read info, and log file of ancillary information, + and find pairwise matches */ + ++void + readin_and_match() + { + File *file; Added: head/biology/phrap/files/patch-segments.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/phrap/files/patch-segments.c Sat Aug 23 18:04:58 2014 (r365765) @@ -0,0 +1,18 @@ +--- ./segments.c.orig 2008-07-30 19:14:13.000000000 +0200 ++++ ./segments.c 2014-08-02 12:39:30.000000000 +0200 +@@ -112,6 +112,7 @@ + return head; + } + ++void + print_segments(head, index, complement) + Segment *head; + int index; +@@ -128,6 +129,7 @@ + } + } + ++void + old_print_segments(head, index1, index2, offset, rel_orient) + Segment *head; + int index1, index2, offset; Added: head/biology/phrap/files/patch-tig_node.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/phrap/files/patch-tig_node.c Sat Aug 23 18:04:58 2014 (r365765) @@ -0,0 +1,18 @@ +--- ./tig_node.c.orig 2007-11-06 23:02:49.000000000 +0100 ++++ ./tig_node.c 2014-08-02 12:39:30.000000000 +0200 +@@ -138,6 +138,7 @@ + tig_node->best_stack_length[0] = tig_node->best_stack_length[1] = 0; + } + ++void + alloc_edge(contig, orientation, pair, reverse) + Contig *contig; + int orientation, reverse; +@@ -176,6 +177,7 @@ + tig_node->edges[orientation] = edge; + } + ++void + find_best_paths(gap_cutoff, LLR_reject_cutoff, LLR_join_cutoff) + int gap_cutoff, LLR_reject_cutoff, LLR_join_cutoff; + { Added: head/biology/phrap/files/patch-weibull.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/phrap/files/patch-weibull.c Sat Aug 23 18:04:58 2014 (r365765) @@ -0,0 +1,18 @@ +--- ./weibull.c.orig 2008-07-29 20:06:24.000000000 +0200 ++++ ./weibull.c 2014-08-02 12:39:30.000000000 +0200 +@@ -77,6 +77,7 @@ + z_cutoff = Z_CUTOFF; + } + ++void + update_hist(score_entry, z_flag) + Score_entry *score_entry; + int z_flag; +@@ -103,6 +104,7 @@ + score2_sums[length] += score * score; + } + ++void + prune_hist(score_entry) + Score_entry *score_entry; + { Added: head/biology/phrap/files/patch-words.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/phrap/files/patch-words.c Sat Aug 23 18:04:58 2014 (r365765) @@ -0,0 +1,64 @@ +--- ./words.c.orig 2009-04-22 20:48:22.000000000 +0200 ++++ ./words.c 2014-08-02 12:39:30.000000000 +0200 +@@ -59,6 +59,12 @@ + static unsigned char *long_word_array; + static int n_skips[3]; + ++void print_word_counts(); ++void set_lower_upper(); ++void set_index_words(int,int,int); ++void find_external_word_matches(int, unsigned char *); ++void quicksort(SEQ_AREA, SEQ_AREA, int, int, SEQ_AREA *); ++void new_lookup_words(unsigned char *, int, SEQ_AREA, SEQ_AREA, int, int); + + typedef struct sw_edge { + int curr0, curr1, curr2; +@@ -323,6 +329,7 @@ + + /* only used when DNA_flag == 2 */ + ++void + set_lower_upper() + { + unsigned int word_int, word_reduced, last_word_reduced; +@@ -540,6 +547,7 @@ + /* + other input: total_length, num_entries, complexity_flag, alphabet_size, residues, minmatch, nlogn_diff, mod_value, index_shift */ + ++void + set_index_words(pass, trans_type, index_type) + int pass, trans_type, index_type; + { +@@ -1070,7 +1078,7 @@ + refinement in Sedgwick, but using bookkeeping of matching leading parts + of words in a block to substantially improve + efficiency) */ +- ++void + quicksort(left, right, k_start, maxcheck, seq_offsets) + SEQ_AREA left, right; + int k_start, maxcheck; +@@ -1532,6 +1540,7 @@ + + */ + ++void + find_external_word_matches(e1, seq) + int e1; + unsigned char *seq; +@@ -1776,6 +1785,7 @@ *** DIFF OUTPUT TRUNCATED AT 1000 LINES ***
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