svn commit: r365765 - in head/biology: consed consed/files phrap phrap/files phred phred/files
Kurt Jaeger
pi at FreeBSD.org
Sat Aug 23 18:05:04 UTC 2014
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 at 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= ${PORTNAME}_linux
MAINTAINER= mzaki at m.u-tokyo.ac.jp
COMMENT= Graphical tool for editing Phrap assemblies
RUN_DEPENDS= phred:${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 at 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 at 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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