author: Kurt Jaeger <pi@FreeBSD.org> 2014-08-23 18:04:58 +0000
committer: Kurt Jaeger <pi@FreeBSD.org> 2014-08-23 18:04:58 +0000
commit: 690da7ea383f1f7ba029563658b17f1a2544007b (patch)
tree: 23e972a9950cc8d2fbf2c0128d929e3655a093ab /biology
parent: 652bbb78d901c4cafc5ebcb47f5de9e22c3bee34 (diff)
download: ports-690da7ea383f1f7ba029563658b17f1a2544007b.tar.gz
ports-690da7ea383f1f7ba029563658b17f1a2544007b.zip
31 files changed, 735 insertions, 1187 deletions
diff --git a/biology/consed/Makefile b/biology/consed/Makefile
index 4debb50ee96d..971c930d5e15 100644
--- a/biology/consed/Makefile
+++ b/biology/consed/Makefile
@@ -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>
diff --git a/biology/consed/distinfo b/biology/consed/distinfo
index 6c2724276ef8..828556d8cd5e 100644
--- a/biology/consed/distinfo
+++ b/biology/consed/distinfo
@@ -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
diff --git a/biology/consed/files/patch-installConsed.perl b/biology/consed/files/patch-installConsed.perl
new file mode 100644
index 000000000000..057ea5d13a90
--- /dev/null
+++ b/biology/consed/files/patch-installConsed.perl
@@ -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" );
+ }
+ 
+ 
diff --git a/biology/consed/files/patch-scripts_addReads2Consed.perl b/biology/consed/files/patch-scripts_addReads2Consed.perl
deleted file mode 100644
index 094a7028a701..000000000000
--- a/biology/consed/files/patch-scripts_addReads2Consed.perl
+++ /dev/null
@@ -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";
- 
diff --git a/biology/consed/files/patch-scripts_determineReadTypes.perl b/biology/consed/files/patch-scripts_determineReadTypes.perl
deleted file mode 100644
index 70405b43cca2..000000000000
--- a/biology/consed/files/patch-scripts_determineReadTypes.perl
+++ /dev/null
@@ -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";
- 
- $szVersion = "001205";
- 
diff --git a/biology/consed/files/patch-scripts_phredPhrap b/biology/consed/files/patch-scripts_phredPhrap
index 5ac28e3d808a..b0543e7b5ed6 100644
--- a/biology/consed/files/patch-scripts_phredPhrap
+++ b/biology/consed/files/patch-scripts_phredPhrap
@@ -1,36 +1,11 @@
---- scripts/phredPhrap.orig	2007-09-26 04:02:20.000000000 +0900
-+++ scripts/phredPhrap	2007-12-11 17:32:27.000000000 +0900
-@@ -101,7 +101,7 @@
- 
- 
- # change this to reflect wherever you put the phredpar.dat file
--$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";
diff --git a/biology/consed/files/pkg-message.in b/biology/consed/files/pkg-message.in
new file mode 100644
index 000000000000..a82e3e3dfa80
--- /dev/null
+++ b/biology/consed/files/pkg-message.in
@@ -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
+-----------------------------------------------------------------------------
diff --git a/biology/consed/pkg-plist.examples b/biology/consed/pkg-plist.examples
deleted file mode 100644
index 5fc178a1cb63..000000000000
--- a/biology/consed/pkg-plist.examples
+++ /dev/null
@@ -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
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q423.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q426.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q426.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q427.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q441.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q441.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q444.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q444.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q452.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q452.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q469.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q469.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q472.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q472.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q474.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q474.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q479.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q479.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q482.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q482.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q488.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q488.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q494.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp02q494.x1r1p17_e87.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q210.y3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q220.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q222.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q222.y3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q226.y3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q233.y3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q240.y3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q245.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q251.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q251.y3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q256.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q256.y3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q266.x1r1p14_e79.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q266.y1u1_e195.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q266.y3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q268.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q268.y3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q275.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q275.y3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q283.y3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q288.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q288.y3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q307.x4.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q312.x4.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q318.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q329.x4.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q330.x4.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q330.x5.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q335.x4.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q335.x5.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q350.x4.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q350.x5.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q357.x5.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q357.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q364.x4.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q364.x5.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q364.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q368.x4.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q380.x4.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q380.x5.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q380.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q387.x4.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q387.x5.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q393.x5.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp03q393.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q104.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q104.y1u1_e134.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q104.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q110.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q110.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q112.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q112.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q136.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q136.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q137.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q137.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q138.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q138.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q141.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q142.x1u2_e247.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q142.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q145.x1r1p12_e70.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q145.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q145.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q155.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q155.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q171.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q171.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q179.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q180.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q180.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q202.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q206.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q206.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q207.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q207.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q214.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q214.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q219.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q219.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q222.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q222.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q224.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q234.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q237.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q239.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q239.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q241.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q241.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q246.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q246.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q254.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q257.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q257.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q260.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q260.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q295.y1u1_e21.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q317.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q317.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q328.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q331.x1u1_e146.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q331.y1u1_e137.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q331.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q332.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q339.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q343.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q347.y1u1_e193.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q347.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q350.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q372.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q375.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q385.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q390.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q409.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q422.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q429.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q429.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q451.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q451.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q458.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q458.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q464.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q472.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a1_fp04q483.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q105.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q108.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q108.x1r1p12_e69.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q108.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q116.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q116.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q116.y1u1_e143.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q117.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q117.x1r2p51_e249.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q117.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q127.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q127.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q150.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q150.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q152.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q152.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q167.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q167.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q178.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q187.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q187.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q189.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q201.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q201.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q208.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q210.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q210.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q217.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q217.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q219.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q219.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q220.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q220.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q226.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q226.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q227.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q227.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q233.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q233.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q246.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q246.y1u1_e75.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q263.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q263.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q268.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q268.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q268.y1u1_e65.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q273.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q273.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q283.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q283.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q284.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q286.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q334.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q334.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q339.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q339.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q345.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q345.y1u1_e139.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q345.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q348.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q348.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q363.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q365.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q365.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q367.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q367.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q374.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q374.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q379.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q379.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q390.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q390.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q404.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q404.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q405.x1u1_e61.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q405.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q405.y1u1_e62.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q405.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q409.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q409.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q420.x1u1_e136.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q420.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q420.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q421.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q421.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q424.x1u1_e80.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q424.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q424.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q425.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q425.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q441.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q441.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q443.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q443.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q453.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q453.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q455.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q455.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q461.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q461.y1u1_e135.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q461.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q464.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q464.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q471.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q471.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q474.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q474.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q477.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q477.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q480.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q480.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q482.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q482.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q484.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q484.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q485.x3.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp01q485.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q105.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q105.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q107.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q107.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q110.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q110.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q112.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q112.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q124.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q124.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q126.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q126.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q134.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q134.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q143.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q144.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q145.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q145.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q147.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q147.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q150.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q150.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q161.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q165.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q173.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q173.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q175.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q175.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q177.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q177.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q187.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q187.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q188.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q189.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q189.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q209.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q210.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q210.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q214.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q222.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q222.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q231.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q231.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q234.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q234.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q238.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q238.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q240.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q240.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q242.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q242.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q243.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q243.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q248.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q248.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q250.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q253.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q253.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q264.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q264.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q266.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q266.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q268.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q268.x1u1_e131.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q268.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q273.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q289.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q290.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q290.x1r2p46_e235.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q290.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q291.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q291.x1r1p25_e153.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q291.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q291.y1u1_e142.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q294.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q295.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q309.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q309.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q314.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q314.y1u1_e64.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q319.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q319.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q321.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q321.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q331.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q336.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q336.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q344.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q344.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q347.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q349.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q349.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q354.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q354.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q358.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q358.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q359.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q359.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q360.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q360.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q363.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q369.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q369.x1r2p51_e248.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q369.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q370.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q370.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q375.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q375.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q381.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q381.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q386.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q386.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q388.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q388.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q419.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q419.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q425.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q425.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q427.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q427.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q428.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q428.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q430.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q430.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q435.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q435.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q438.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q438.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q440.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q440.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q444.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q444.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q445.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q445.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q445.y1u1_e140.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q446.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q446.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q451.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q451.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q464.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q464.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q465.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q465.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q475.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q475.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q480.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q480.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q483.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q483.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q488.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q488.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp02q494.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q102.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q104.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q107.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q108.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q112.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q119.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q126.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q127.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q127.x1u1_e132.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q127.y1u1_e129.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q133.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q136.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q138.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q138.y1u1_e128.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q146.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q152.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q153.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q156.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q159.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q161.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q164.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q171.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q172.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q173.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q177.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q177.x1r2p62_e291.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q177.y1u2_e289.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q183.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q187.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q189.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q210.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q210.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q211.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q211.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q212.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q212.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q216.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q216.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q218.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q218.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q218.y1u1_e138.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q225.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q225.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q227.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q227.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q229.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q238.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q238.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q238.y1u1_e67.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q275.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q275.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q280.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q280.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q284.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q284.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q286.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q286.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q287.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q287.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q293.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q293.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q303.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q306.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q315.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q338.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q338.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q341.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q341.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q342.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q342.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q342.y1u1_e66.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q343.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q343.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q344.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q344.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q346.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q346.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q349.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q349.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q350.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q350.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q355.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q355.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q368.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q368.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q368.y1u1_e81.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q370.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q370.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q372.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q372.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q376.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q376.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q378.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q378.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q379.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q379.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q380.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q382.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q382.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q383.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q383.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q386.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q386.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q392.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q392.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q403.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q403.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q404.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q404.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q405.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q405.x1u1_e130.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q405.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q407.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q407.x1u1_e182.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q409.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q409.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q413.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q413.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q415.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q415.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q416.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q418.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q418.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q419.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q419.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q423.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q423.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q432.y1u2_e254.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q433.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q433.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q436.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q436.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q437.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q437.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q445.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q445.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q455.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q455.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q457.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q457.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q459.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q459.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q462.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q462.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q465.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q465.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q469.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q474.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q474.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q483.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q483.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q485.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q485.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q488.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q489.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q489.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q493.x1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q493.x1r1p28_e160.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp03q493.y1.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q103.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q103.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q107.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q107.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q114.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q114.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q121.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q121.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q122.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q122.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q125.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q125.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q132.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q132.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q133.x1u1_e141.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q133.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q133.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q142.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q142.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q146.x1r1p15_e83.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q146.x1u1_e82.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q146.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q146.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q149.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q149.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q151.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q151.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q160.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q160.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q166.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q166.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q169.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q169.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q170.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q170.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q171.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q171.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q172.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q172.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q175.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q182.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q182.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q202.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q202.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q210.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q210.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q211.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q211.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q216.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q216.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q219.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q219.y1u1_e145.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q219.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q226.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q229.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q229.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q234.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q234.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q243.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q243.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q253.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q253.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q256.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q256.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q265.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q265.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q273.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q273.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q274.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q274.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q282.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q282.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q286.x2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q286.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q291.y2.phd.1
-share/examples/consed/assembly_view/phd_dir/djs736a2_fp04q293.x2.phd.1
-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
diff --git a/biology/phrap/Makefile b/biology/phrap/Makefile
index 6fa03617ccc1..de2be50a3c56 100644
--- a/biology/phrap/Makefile
+++ b/biology/phrap/Makefile
@@ -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>
diff --git a/biology/phrap/distinfo b/biology/phrap/distinfo
index 3d39a84a04c2..78f1935d26e9 100644
--- a/biology/phrap/distinfo
+++ b/biology/phrap/distinfo
@@ -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
diff --git a/biology/phrap/files/patch-alignments.c b/biology/phrap/files/patch-alignments.c
new file mode 100644
index 000000000000..986799024563
--- /dev/null
+++ b/biology/phrap/files/patch-alignments.c
@@ -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;
+ {
diff --git a/biology/phrap/files/patch-analyze_splices.c b/biology/phrap/files/patch-analyze_splices.c
new file mode 100644
index 000000000000..bb3f5fe42475
--- /dev/null
+++ b/biology/phrap/files/patch-analyze_splices.c
@@ -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;
diff --git a/biology/phrap/files/patch-anomalies.c b/biology/phrap/files/patch-anomalies.c
new file mode 100644
index 000000000000..508d4cd9de69
--- /dev/null
+++ b/biology/phrap/files/patch-anomalies.c
@@ -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;
diff --git a/biology/phrap/files/patch-calf_utils.c b/biology/phrap/files/patch-calf_utils.c
new file mode 100644
index 000000000000..9a09fb4d1c49
--- /dev/null
+++ b/biology/phrap/files/patch-calf_utils.c
@@ -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;
diff --git a/biology/phrap/files/patch-call_subs.c b/biology/phrap/files/patch-call_subs.c
new file mode 100644
index 000000000000..8ee1379afc28
--- /dev/null
+++ b/biology/phrap/files/patch-call_subs.c
@@ -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
+ }
+ 
diff --git a/biology/phrap/files/patch-cand_pairs.c b/biology/phrap/files/patch-cand_pairs.c
new file mode 100644
index 000000000000..6765364b7544
--- /dev/null
+++ b/biology/phrap/files/patch-cand_pairs.c
@@ -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;
diff --git a/biology/phrap/files/patch-contigs.c b/biology/phrap/files/patch-contigs.c
new file mode 100644
index 000000000000..a2f99c774dc9
--- /dev/null
+++ b/biology/phrap/files/patch-contigs.c
@@ -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();
diff --git a/biology/phrap/files/patch-db.c b/biology/phrap/files/patch-db.c
new file mode 100644
index 000000000000..ae100313b440
--- /dev/null
+++ b/biology/phrap/files/patch-db.c
@@ -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;
diff --git a/biology/phrap/files/patch-makefile b/biology/phrap/files/patch-makefile
index 7fccdb3846a1..2a83cd9e1e44 100644
--- a/biology/phrap/files/patch-makefile
+++ b/biology/phrap/files/patch-makefile
@@ -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)
diff --git a/biology/phrap/files/patch-names.c b/biology/phrap/files/patch-names.c
new file mode 100644
index 000000000000..4b6ef3dd9526
--- /dev/null
+++ b/biology/phrap/files/patch-names.c
@@ -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;
diff --git a/biology/phrap/files/patch-nodes.c b/biology/phrap/files/patch-nodes.c
new file mode 100644
index 000000000000..50af42003571
--- /dev/null
+++ b/biology/phrap/files/patch-nodes.c
@@ -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;
+ {
diff --git a/biology/phrap/files/patch-pairs.c b/biology/phrap/files/patch-pairs.c
new file mode 100644
index 000000000000..d81b915fda34
--- /dev/null
+++ b/biology/phrap/files/patch-pairs.c
@@ -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;
+ {
diff --git a/biology/phrap/files/patch-qual.c b/biology/phrap/files/patch-qual.c
new file mode 100644
index 000000000000..5c7627f1eb3a
--- /dev/null
+++ b/biology/phrap/files/patch-qual.c
@@ -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;
diff --git a/biology/phrap/files/patch-readin.c b/biology/phrap/files/patch-readin.c
new file mode 100644
index 000000000000..0e30d7872bd6
--- /dev/null
+++ b/biology/phrap/files/patch-readin.c
@@ -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;
diff --git a/biology/phrap/files/patch-segments.c b/biology/phrap/files/patch-segments.c
new file mode 100644
index 000000000000..950899da7b15
--- /dev/null
+++ b/biology/phrap/files/patch-segments.c
@@ -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;
diff --git a/biology/phrap/files/patch-tig_node.c b/biology/phrap/files/patch-tig_node.c
new file mode 100644
index 000000000000..d2506b8beeda
--- /dev/null
+++ b/biology/phrap/files/patch-tig_node.c
@@ -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;
+ {
diff --git a/biology/phrap/files/patch-weibull.c b/biology/phrap/files/patch-weibull.c
new file mode 100644
index 000000000000..1e8de65cb2b6
--- /dev/null
+++ b/biology/phrap/files/patch-weibull.c
@@ -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;
+ {
diff --git a/biology/phrap/files/patch-words.c b/biology/phrap/files/patch-words.c
new file mode 100644
index 000000000000..ed36f2bee041
--- /dev/null
+++ b/biology/phrap/files/patch-words.c
@@ -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;
diff --git a/biology/phrap/pkg-plist b/biology/phrap/pkg-plist
new file mode 100644
index 000000000000..e1faf40459ee
--- /dev/null
+++ b/biology/phrap/pkg-plist
@@ -0,0 +1,9 @@
+@mode 111
+bin/calf_merge
+bin/pcluster
+bin/cross_match
+bin/loco
+bin/phrap
+bin/phrapview
+bin/swat
+@mode
diff --git a/biology/phred/Makefile b/biology/phred/Makefile
index 61027fcfe259..06f673b57574 100644
--- a/biology/phred/Makefile
+++ b/biology/phred/Makefile
@@ -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>
diff --git a/biology/phred/files/pkg-message.in b/biology/phred/files/pkg-message.in
new file mode 100644
index 000000000000..04ae9ab3ef43
--- /dev/null
+++ b/biology/phred/files/pkg-message.in
@@ -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
+-----------------------------------------------------------------------------
author	Kurt Jaeger <pi@FreeBSD.org>	2014-08-23 18:04:58 +0000
committer	Kurt Jaeger <pi@FreeBSD.org>	2014-08-23 18:04:58 +0000
commit	690da7ea383f1f7ba029563658b17f1a2544007b (patch)
tree	23e972a9950cc8d2fbf2c0128d929e3655a093ab /biology
parent	652bbb78d901c4cafc5ebcb47f5de9e22c3bee34 (diff)
download	ports-690da7ea383f1f7ba029563658b17f1a2544007b.tar.gz ports-690da7ea383f1f7ba029563658b17f1a2544007b.zip