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update ports:

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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)
This commit is contained in:
Kurt Jaeger 2014-08-23 18:04:58 +00:00
parent 652bbb78d9
commit 690da7ea38
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=365765
31 changed files with 735 additions and 1187 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

139
biology/consed/Makefile
View file

@ -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 obtained via the authors
.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>

4
biology/consed/distinfo
View file

@ -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

57
biology/consed/files/patch-installConsed.perl Normal file
View file

@ -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" );
}

11
biology/consed/files/patch-scripts_addReads2Consed.perl
View file

@ -1,11 +0,0 @@
--- scripts/addReads2Consed.perl.orig 2007-09-26 04:02:19.000000000 +0900
+++ scripts/addReads2Consed.perl 2007-12-11 17:27:20.000000000 +0900
@@ -71,7 +71,7 @@
$szVectorFile = $szConsedHome . "/lib/screenLibs/vector.seq";
# change this to reflect wherever you put the phred parameter file
-$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";

11
biology/consed/files/patch-scripts_determineReadTypes.perl
View file

@ -1,11 +0,0 @@
--- scripts/determineReadTypes.perl.orig Tue Aug 31 03:14:13 2004
+++ scripts/determineReadTypes.perl Wed Jul 13 17:00:22 2005
@@ -177,7 +177,7 @@
# you can remove or comment out this line when you are satisfied with
# your customized version of this file.
-die "You must edit determineReadTypes.perl--please read README.txt that came with consed. Look under INSTALLING CONSED. Also look at the comments at the beginning of determineReadTypes.perl Then, and only then, comment out the line in determineReadTypes.perl that begins with \"die\" and has this error message\n by putting a # in front of that line";
+#die "You must edit determineReadTypes.perl--please read README.txt that came with consed. Look under INSTALLING CONSED. Also look at the comments at the beginning of determineReadTypes.perl Then, and only then, comment out the line in determineReadTypes.perl that begins with \"die\" and has this error message\n by putting a # in front of that line";
$szVersion = "001205";

35
biology/consed/files/patch-scripts_phredPhrap
View file

@ -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";

12
biology/consed/files/pkg-message.in Normal file
View file

@ -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
-----------------------------------------------------------------------------

990
biology/consed/pkg-plist.examples
View file

@ -1,990 +0,0 @@
share/examples/consed/assembly_view/edit_dir/.consedrc
share/examples/consed/assembly_view/edit_dir/.consedrc_mini
share/examples/consed/assembly_view/edit_dir/assembly_view.030319.170348.fasta
share/examples/consed/assembly_view/edit_dir/assembly_view.030319.170348.fasta.log
share/examples/consed/assembly_view/edit_dir/assembly_view.fasta.screen.ace.1
share/examples/consed/assembly_view/edit_dir/assembly_view.fasta.screen.ace.1.aview
share/examples/consed/assembly_view/edit_dir/doNotShowInAssemblyView.fof
share/examples/consed/assembly_view/edit_dir/fragSizes.txt
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q102.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q124.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q124.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q126.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q126.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q131.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q131.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q134.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q144.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q144.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q148.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q148.x1r1p24_e150.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q148.x1u1_e133.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q148.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q149.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q149.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q156.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q161.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q161.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q192.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q192.x1r1p30_e173.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q192.x1r1p33_e178.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q192.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q203.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q203.x1r2p46_e234.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q203.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q206.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q206.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q207.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q207.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q210.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q211.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q212.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q212.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q215.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q215.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q232.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q243.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q243.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q247.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q265.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q267.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q267.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q270.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q270.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q277.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q277.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q279.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q282.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q282.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q287.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q287.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q293.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q293.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q305.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q307.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q307.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q322.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q351.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q351.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q352.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q352.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q362.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q362.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q363.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q370.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q378.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q378.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q379.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q379.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q381.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q381.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q403.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q403.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q405.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q405.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q407.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q407.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q409.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q409.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q415.x1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q415.y1.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q423.x1.phd.1
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share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q293.y2.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q294.y2.phd.1
share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q296.y2.phd.1
share/examples/consed/autofinish/edit_dir/.consedrc.bu
share/examples/consed/autofinish/edit_dir/autoPCRAmplify.fof
share/examples/consed/autofinish/edit_dir/autoPCRAmplify.txt
share/examples/consed/autofinish/edit_dir/autoPCRAmplify2.txt
share/examples/consed/autofinish/edit_dir/autofinish.contigs
share/examples/consed/autofinish/edit_dir/autofinish.contigs.log
share/examples/consed/autofinish/edit_dir/autofinish.fasta
share/examples/consed/autofinish/edit_dir/autofinish.fasta.log
share/examples/consed/autofinish/edit_dir/autofinish.fasta.screen
share/examples/consed/autofinish/edit_dir/autofinish.fasta.screen.ace.1
share/examples/consed/autofinish/edit_dir/autofinish.fasta.screen.contigs
share/examples/consed/autofinish/edit_dir/autofinish.fasta.screen.contigs.qual
share/examples/consed/autofinish/edit_dir/autofinish.fasta.screen.log
share/examples/consed/autofinish/edit_dir/autofinish.fasta.screen.problems
share/examples/consed/autofinish/edit_dir/autofinish.fasta.screen.problems.qual
share/examples/consed/autofinish/edit_dir/autofinish.fasta.screen.qual
share/examples/consed/autofinish/edit_dir/autofinish.fasta.screen.singlets
share/examples/consed/autofinish/edit_dir/autofinish.fasta.screen.view
share/examples/consed/autofinish/edit_dir/autofinish.fof
share/examples/consed/autofinish/edit_dir/autofinish.newtags
share/examples/consed/autofinish/edit_dir/autofinishNewChromats.fof
share/examples/consed/autofinish/edit_dir/autofinish_to_alu.cross
share/examples/consed/autofinish/edit_dir/librariesInfo.txt_hide
share/examples/consed/autofinish/phd_dir/djs228_1013.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_1029.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_1033.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_1034.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_1051.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_1094.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_1141.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_1153.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_1211.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_1248.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_1273.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_1331.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_1336.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_1343.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_1418.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_1422.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_168.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_1680.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_1740.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_1777.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_1803.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_1919.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_1929.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_2019.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_2078.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_2083.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_2116.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_2151.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_2222.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_2273.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_2282.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_2338.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_2346.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_2390.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_2417.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_2436.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_2529.s2.phd.1
share/examples/consed/autofinish/phd_dir/djs228_2632.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_2659.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_2664.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_2714.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_2751.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_2813.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_2854.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_2862.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_2894.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_2912.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_2933.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_2949.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_3085.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_3196.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_331.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_426.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_433.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_434.s3.phd.1
share/examples/consed/autofinish/phd_dir/djs228_441.s3.phd.1
share/examples/consed/autofinish/phd_dir/djs228_474.s2.phd.1
share/examples/consed/autofinish/phd_dir/djs228_481.s2.phd.1
share/examples/consed/autofinish/phd_dir/djs228_523.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_539.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_560.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_671.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_671.s2.phd.1
share/examples/consed/autofinish/phd_dir/djs228_715.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_844.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_891.s1.phd.1
share/examples/consed/autofinish/phd_dir/djs228_892.s1.phd.1
share/examples/consed/polyphred/chromat_dir/ca-21.s
share/examples/consed/polyphred/chromat_dir/ca-22.r
share/examples/consed/polyphred/chromat_dir/ca-22.s
share/examples/consed/polyphred/chromat_dir/ca-23.s
share/examples/consed/polyphred/chromat_dir/ca-9.r
share/examples/consed/polyphred/chromat_dir/ca-9.s
share/examples/consed/polyphred/chromat_dir/va-1.x
share/examples/consed/polyphred/chromat_dir/va-13.x
share/examples/consed/polyphred/chromat_dir/va-16.x
share/examples/consed/polyphred/chromat_dir/va-23.x
share/examples/consed/polyphred/edit_dir/core
share/examples/consed/polyphred/edit_dir/example2.contigs
share/examples/consed/polyphred/edit_dir/example2.contigs.log
share/examples/consed/polyphred/edit_dir/example2.fasta
share/examples/consed/polyphred/edit_dir/example2.fasta.log
share/examples/consed/polyphred/edit_dir/example2.fasta.screen
share/examples/consed/polyphred/edit_dir/example2.fasta.screen.ace.1
share/examples/consed/polyphred/edit_dir/example2.fasta.screen.contigs
share/examples/consed/polyphred/edit_dir/example2.fasta.screen.contigs.qual
share/examples/consed/polyphred/edit_dir/example2.fasta.screen.log
share/examples/consed/polyphred/edit_dir/example2.fasta.screen.polyphred.out
share/examples/consed/polyphred/edit_dir/example2.fasta.screen.qual
share/examples/consed/polyphred/edit_dir/example2.fasta.screen.singlets
share/examples/consed/polyphred/edit_dir/example2.fasta.screen.view
share/examples/consed/polyphred/edit_dir/example2.newtags
share/examples/consed/polyphred/edit_dir/example2.phrap.out
share/examples/consed/polyphred/edit_dir/example2.screen.out
share/examples/consed/polyphred/edit_dir/example2_to_alu.cross
share/examples/consed/polyphred/edit_dir/phd.fof
share/examples/consed/polyphred/edit_dir/problem_reads
share/examples/consed/polyphred/edit_dir/problem_reads.qual
share/examples/consed/polyphred/phd_dir/ca-21.s.phd.1
share/examples/consed/polyphred/phd_dir/ca-22.r.phd.1
share/examples/consed/polyphred/phd_dir/ca-22.s.phd.1
share/examples/consed/polyphred/phd_dir/ca-23.s.phd.1
share/examples/consed/polyphred/phd_dir/ca-9.r.phd.1
share/examples/consed/polyphred/phd_dir/ca-9.s.phd.1
share/examples/consed/polyphred/phd_dir/va-1.x.phd.1
share/examples/consed/polyphred/phd_dir/va-13.x.phd.1
share/examples/consed/polyphred/phd_dir/va-16.x.phd.1
share/examples/consed/polyphred/phd_dir/va-23.x.phd.1
share/examples/consed/polyphred/poly_dir/ca-21.s.poly
share/examples/consed/polyphred/poly_dir/ca-22.r.poly
share/examples/consed/polyphred/poly_dir/ca-22.s.poly
share/examples/consed/polyphred/poly_dir/ca-23.s.poly
share/examples/consed/polyphred/poly_dir/ca-9.r.poly
share/examples/consed/polyphred/poly_dir/ca-9.s.poly
share/examples/consed/polyphred/poly_dir/va-1.x.poly
share/examples/consed/polyphred/poly_dir/va-13.x.poly
share/examples/consed/polyphred/poly_dir/va-16.x.poly
share/examples/consed/polyphred/poly_dir/va-23.x.poly
share/examples/consed/standard/chromat_dir/djs74-1180.s1
share/examples/consed/standard/chromat_dir/djs74-1432.s1
share/examples/consed/standard/chromat_dir/djs74-1532.s1
share/examples/consed/standard/chromat_dir/djs74-1802.s1
share/examples/consed/standard/chromat_dir/djs74-1803.s1
share/examples/consed/standard/chromat_dir/djs74-1861.s1
share/examples/consed/standard/chromat_dir/djs74-1871.s1
share/examples/consed/standard/chromat_dir/djs74-2231.s1
share/examples/consed/standard/chromat_dir/djs74-2350.s1
share/examples/consed/standard/chromat_dir/djs74-2361.s1
share/examples/consed/standard/chromat_dir/djs74-237.s1
share/examples/consed/standard/chromat_dir/djs74-2516.s1
share/examples/consed/standard/chromat_dir/djs74-2664.s1
share/examples/consed/standard/chromat_dir/djs74-2679.s1
share/examples/consed/standard/chromat_dir/djs74-2689.s1
share/examples/consed/standard/chromat_dir/djs74-2931.s1
share/examples/consed/standard/chromat_dir/djs74-3174.s1
share/examples/consed/standard/chromat_dir/djs74-423.s1
share/examples/consed/standard/chromat_dir/djs74-561.s1
share/examples/consed/standard/chromat_dir/djs74-564.s1
share/examples/consed/standard/chromat_dir/djs74-690.x1
share/examples/consed/standard/chromat_dir/djs74-824.s1
share/examples/consed/standard/chromat_dir/djs74-932.s1
share/examples/consed/standard/chromat_dir/djs74-996.s2
share/examples/consed/standard/chromats_to_add/djs74-1455.s1
share/examples/consed/standard/chromats_to_add/djs74-1465.s1
share/examples/consed/standard/chromats_to_add/djs74-2282.s1
share/examples/consed/standard/chromats_to_add/djs74-2712.s1
share/examples/consed/standard/chromats_to_add/djs74-2861.s1
share/examples/consed/standard/chromats_to_add/djs74-536.s2
share/examples/consed/standard/chromats_to_add/djs74-568.s1
share/examples/consed/standard/chromats_to_add/djs74-649.x1
share/examples/consed/standard/chromats_to_add/djs74-867.s1
share/examples/consed/standard/edit_dir/custom_navigation.nav
share/examples/consed/standard/edit_dir/fragSizes.txt
share/examples/consed/standard/edit_dir/reads_to_add.fof
share/examples/consed/standard/edit_dir/reads_to_remove.fof
share/examples/consed/standard/edit_dir/standard.030328.142354.fasta
share/examples/consed/standard/edit_dir/standard.030328.142354.fasta.log
share/examples/consed/standard/edit_dir/standard.contigs
share/examples/consed/standard/edit_dir/standard.contigs.log
share/examples/consed/standard/edit_dir/standard.fasta
share/examples/consed/standard/edit_dir/standard.fasta.log
share/examples/consed/standard/edit_dir/standard.fasta.screen
share/examples/consed/standard/edit_dir/standard.fasta.screen.ace.1
share/examples/consed/standard/edit_dir/standard.fasta.screen.ace.1.aview
share/examples/consed/standard/edit_dir/standard.fasta.screen.contigs
share/examples/consed/standard/edit_dir/standard.fasta.screen.contigs.qual
share/examples/consed/standard/edit_dir/standard.fasta.screen.log
share/examples/consed/standard/edit_dir/standard.fasta.screen.problems
share/examples/consed/standard/edit_dir/standard.fasta.screen.problems.qual
share/examples/consed/standard/edit_dir/standard.fasta.screen.qual
share/examples/consed/standard/edit_dir/standard.fasta.screen.singlets
share/examples/consed/standard/edit_dir/standard.fasta.screen.view
share/examples/consed/standard/edit_dir/standard.newtags
share/examples/consed/standard/edit_dir/standard.phrap.out
share/examples/consed/standard/edit_dir/standard.screen.out
share/examples/consed/standard/edit_dir/standardNewChromats.fof
share/examples/consed/standard/edit_dir/standard_to_alu.cross
share/examples/consed/standard/phd_dir/djs74-1180.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-1432.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-1532.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-1802.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-1803.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-1861.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-1871.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-2231.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-2350.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-2361.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-237.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-2516.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-2664.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-2679.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-2689.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-2931.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-3174.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-423.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-423.s1.phd.2
share/examples/consed/standard/phd_dir/djs74-561.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-564.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-690.x1.phd.1
share/examples/consed/standard/phd_dir/djs74-824.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-932.s1.phd.1
share/examples/consed/standard/phd_dir/djs74-996.s2.phd.1
@dirrm share/examples/consed/assembly_view/chromat_dir
@dirrm share/examples/consed/assembly_view/edit_dir
@dirrm share/examples/consed/assembly_view/phd_dir
@dirrm share/examples/consed/assembly_view
@dirrm share/examples/consed/autofinish/chromat_dir
@dirrm share/examples/consed/autofinish/edit_dir
@dirrm share/examples/consed/autofinish/phd_dir
@dirrm share/examples/consed/autofinish
@dirrm share/examples/consed/polyphred/chromat_dir
@dirrm share/examples/consed/polyphred/edit_dir
@dirrm share/examples/consed/polyphred/phd_dir
@dirrm share/examples/consed/polyphred/poly_dir
@dirrm share/examples/consed/polyphred
@dirrm share/examples/consed/standard/chromat_dir
@dirrm share/examples/consed/standard/chromats_to_add
@dirrm share/examples/consed/standard/edit_dir
@dirrm share/examples/consed/standard/phd_dir
@dirrm share/examples/consed/standard
@dirrm share/examples/consed

31
biology/phrap/Makefile
View file

@ -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 obtained via the authors
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 \(${DISTFILES}\) via e-mail, place it m
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>

5
biology/phrap/distinfo
View file

@ -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

10
biology/phrap/files/patch-alignments.c Normal file
View file

@ -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;
{

88
biology/phrap/files/patch-analyze_splices.c Normal file
View file

@ -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;

19
biology/phrap/files/patch-anomalies.c Normal file
View file

@ -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;

19
biology/phrap/files/patch-calf_utils.c Normal file
View file

@ -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;

19
biology/phrap/files/patch-call_subs.c Normal file
View file

@ -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
}

18
biology/phrap/files/patch-cand_pairs.c Normal file
View file

@ -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;

10
biology/phrap/files/patch-contigs.c Normal file
View file

@ -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();

19
biology/phrap/files/patch-db.c Normal file
View file

@ -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;

43
biology/phrap/files/patch-makefile
View file

@ -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 @@
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;
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
loco: makefile $(LOCOOBJS) $(SWOBJS)
$(CC) $(CFLAGS) -o $@ $(LOCOOBJS) $(SWOBJS) $(LFLAGS)

19
biology/phrap/files/patch-names.c Normal file
View file

@ -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;

19
biology/phrap/files/patch-nodes.c Normal file
View file

@ -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;
{

91
biology/phrap/files/patch-pairs.c Normal file
View file

@ -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;
{

82
biology/phrap/files/patch-qual.c Normal file
View file

@ -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;

10
biology/phrap/files/patch-readin.c Normal file
View file

@ -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;

18
biology/phrap/files/patch-segments.c Normal file
View file

@ -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;

18
biology/phrap/files/patch-tig_node.c Normal file
View file

@ -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;
{

18
biology/phrap/files/patch-weibull.c Normal file
View file

@ -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;
{

64
biology/phrap/files/patch-words.c Normal file
View file

@ -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 @@
int known_match_size, target_match_size, offset1, sub_check, reuse;
extern int num_pairs;
+void
new_lookup_words(seq1, trans_type, sa_l_lower, sa_u_upper, ss_displace, n_lc)
int trans_type, ss_displace, n_lc;
SEQ_AREA sa_l_lower, sa_u_upper;
@@ -2850,6 +2860,7 @@
for (i = 0; i < 5; i++) num_merge_words[i] = 0;
}
+void
print_word_counts()
{
int i;

9
biology/phrap/pkg-plist Normal file
View file

@ -0,0 +1,9 @@
@mode 111
bin/calf_merge
bin/pcluster
bin/cross_match
bin/loco
bin/phrap
bin/phrapview
bin/swat
@mode

28
biology/phred/Makefile
View file

@ -11,6 +11,8 @@ EXTRACT_SUFX= .tar.Z
MAINTAINER= mzaki@m.u-tokyo.ac.jp
COMMENT= Base calling and quality value assignment on DNA sequencing
SUB_FILES= pkg-message
RESTRICTED= Redistribution is not permitted in any form. You must request the tarball via e-mail. Free for academic use.
.if defined(PACKAGE_BUILDING)
IGNORE= distribution files must be obtained via the authors
@ -20,21 +22,13 @@ NO_WRKSUBDIR= yes
ALL_TARGET= phred daev
BINMODE= 0111 # avoid copying binaries as required by the agreement
BINARIES= phred daev
.for f in ${BINARIES}
PLIST_FILES+= bin/${f}
.endfor
DATADIR= ${PREFIX}/etc/PhredPar
DATAFILES= phredpar.dat
.for f in ${DATAFILES}
PORTDATA+= ${f}.dist
.endfor
PORTDOCS= NEWS PHRED.DOC DAEV.DOC
NO_STAGE= yes
.include <bsd.port.pre.mk>
.for f in ${DISTFILES}
@ -45,23 +39,15 @@ IGNORE= you must request the source code \(${f}\) via e-mail, place it manually
do-install:
.for f in ${BINARIES}
@${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin/
@${INSTALL_PROGRAM} ${WRKSRC}/${f} ${STAGEDIR}${PREFIX}/bin/
.endfor
@${MKDIR} ${DATADIR}
@${MKDIR} ${STAGEDIR}${DATADIR}
.for f in ${DATAFILES}
@${INSTALL_DATA} ${WRKSRC}/${f} ${DATADIR}/${f}.dist
@${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${DATADIR}/${f}.sample
.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
@${ECHO} "---------------------------------------------------------------------------"
@${ECHO} "You must set PHRED_PARAMETER_FILE environment variable."
@${ECHO} ""
@${ECHO} "The default parameter file in the distribution is located at:"
@${ECHO} " ${DATADIR}/phredpar.dat.dist"
@${ECHO} "---------------------------------------------------------------------------"
.include <bsd.port.post.mk>

6
biology/phred/files/pkg-message.in Normal file
View file

@ -0,0 +1,6 @@
-----------------------------------------------------------------------------
You must set PHRED_PARAMETER_FILE environment variable.
The default parameter file in the distribution is located at:
%%DATADIR%%/phredpar.dat
-----------------------------------------------------------------------------