Update to 1.1.04
PR: ports/157527 Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> Approved by: bapt (mentor)
This commit is contained in:
Julien Laffaye
parent
5a450bee81
commit
1ca81797c4
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=275282
@ -6,7 +6,7 @@
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#
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PORTNAME= velvet
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PORTVERSION= 0.7.55
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PORTVERSION= 1.1.04
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CATEGORIES= biology
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MASTER_SITES= http://www.ebi.ac.uk/~zerbino/velvet/
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DISTNAME= ${PORTNAME}_${PORTVERSION}
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@ -19,28 +19,34 @@ USE_GMAKE= yes
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ALL_TARGET= default
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MAXKMERLENGTH?= 31
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MAKE_ENV+= MAXKMERLENGTH=${MAXKMERLENGTH}
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VELVET_CATEGORIES?= 2
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MAKE_ENV+= MAXKMERLENGTH=${MAXKMERLENGTH} CATEGORIES=${VELVET_CATEGORIES}
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USE_PERL5_RUN= yes
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BINARIES= velvetg velveth
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SCRIPTS= contrib/VelvetOptimiser/VelvetOptimiser.pl \
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SCRIPTS= shuffleSequences_fasta.pl shuffleSequences_fastq.pl \
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contrib/VelvetOptimiser-2.1.7/VelvetOptimiser.pl \
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contrib/afg_handling/asmbly_splitter.pl \
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contrib/afg_handling/snp_view.pl \
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contrib/columbus_scripts/enlarge_exons.pl \
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contrib/columbus_scripts/gff2fasta.pl \
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contrib/columbus_scripts/merge_gtf_exons.pl \
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contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl \
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contrib/fasta2agp/fasta2agp.pl \
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contrib/extractContigReads/extractContigReads.pl \
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contrib/fasta2agp/fasta2agp.pl \
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contrib/observed-insert-length.pl/observed-insert-length.pl \
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contrib/shuffleSequences_fasta/shuffleSequences_fasta.pl
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PERLMOD_DIRS= contrib/VelvetOptimiser/VelvetOpt
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PERLMOD_FILES= contrib/VelvetOptimiser/VelvetOpt/Assembly.pm \
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contrib/VelvetOptimiser/VelvetOpt/Utils.pm \
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contrib/VelvetOptimiser/VelvetOpt/gwrap.pm \
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contrib/VelvetOptimiser/VelvetOpt/hwrap.pm
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contrib/select_paired/select_paired.pl \
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contrib/show_repeats/show_repeats.pl
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PERLMOD_DIRS= contrib/VelvetOptimiser-2.1.7/VelvetOpt
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PERLMOD_FILES= contrib/VelvetOptimiser-2.1.7/VelvetOpt/Assembly.pm \
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contrib/VelvetOptimiser-2.1.7/VelvetOpt/Utils.pm \
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contrib/VelvetOptimiser-2.1.7/VelvetOpt/gwrap.pm \
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contrib/VelvetOptimiser-2.1.7/VelvetOpt/hwrap.pm
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.if !defined(WITHOUT_PYTHON)
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USE_PYTHON= yes
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SCRIPTS+= contrib/layout/graph2.py
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SCRIPTS+= contrib/AssemblyAssembler1.3/AssemblyAssembler1.3.py
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.endif
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.for f in ${BINARIES} ${SCRIPTS}
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@ -53,19 +59,16 @@ PLIST_DIRS+= %%SITE_PERL%%/${d:T}
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PLIST_FILES+= %%SITE_PERL%%/${f:H:T}/${f:T}
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.endfor
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PORTDOCS= ChangeLog Manual.pdf
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PORTDOCS= ChangeLog Manual.pdf Columbus_manual.pdf
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post-patch:
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.for f in ${SCRIPTS}
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${REINPLACE_CMD} -e s,#!/usr/bin/perl,${PERL}, ${WRKSRC}/${f}
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.endfor
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.if !defined(WITHOUT_PYTHON)
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(IFS=''; ${REINPLACE_CMD} -e `${ECHO} '1i\'; ${ECHO} '#!${PYTHON_CMD}'` ${WRKSRC}/contrib/layout/graph2.py)
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${REINPLACE_CMD} -e s,#!/usr/bin/python,${PYTHON_CMD}, ${WRKSRC}/contrib/AssemblyAssembler1.3/AssemblyAssembler1.3.py
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.endif
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post-build:
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${REINPLACE_CMD} -e s,%%MAXKMERLENGTH%%,${MAXKMERLENGTH},g ${WRKSRC}/contrib/VelvetOptimiser/VelvetOptimiser.pl
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do-install:
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.for f in ${BINARIES}
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${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin
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@ -1,2 +1,2 @@
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SHA256 (velvet_0.7.55.tgz) = 315331f418c2de89c6c871cea3759d947320c0adbc763fea290ec78ece69b614
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SIZE (velvet_0.7.55.tgz) = 3475289
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SHA256 (velvet_1.1.04.tgz) = 7ae9855c3eabd1d222815a7132cdc9eeb387d83132390d020fc78491e6dcc9d6
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SIZE (velvet_1.1.04.tgz) = 7744134
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@ -1,5 +1,5 @@
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--- Makefile.orig 2009-09-02 22:21:01.000000000 +0900
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+++ Makefile 2009-10-27 22:05:49.000000000 +0900
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--- Makefile.orig 2011-03-30 14:34:09.000000000 +0900
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+++ Makefile 2011-06-02 20:28:04.000000000 +0900
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@@ -1,18 +1,18 @@
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-CC = gcc
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-CFLAGS = -Wall
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@ -27,12 +27,21 @@
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# CFLAGS = -Wall -m64
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# Sparc/Solaris users: uncomment the following line
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@@ -32,7 +32,7 @@
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@@ -35,7 +35,7 @@
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OBJ = obj/tightString.o obj/run.o obj/splay.o obj/splayTable.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/scaffold.o obj/kmerOccurenceTable.o obj/allocArray.o
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OBJDBG = $(subst obj,obj/dbg,$(OBJ))
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-default : cleanobj zlib obj velveth velvetg doc
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+default : cleanobj zlib obj velveth velvetg
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clean :
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-rm obj/*.o obj/dbg/*.o ./velvet*
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@@ -47,7 +47,7 @@
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-rm obj/*.o obj/dbg/*.o
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zlib :
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- cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o
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+# cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o
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velveth : $(OBJ)
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$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o $(Z_LIB_FILES)
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velveth : obj
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$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o $(Z_LIB_FILES)
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@ -1,92 +0,0 @@
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--- contrib/VelvetOptimiser/VelvetOptimiser.pl.orig 2009-09-14 23:44:19.000000000 +0900
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+++ contrib/VelvetOptimiser/VelvetOptimiser.pl 2009-10-30 22:13:45.000000000 +0900
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@@ -44,9 +44,10 @@
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my @hashvals;
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my %assemblies;
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my $readfile;
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+my $MAXKMERLENGTH = %%MAXKMERLENGTH%%;
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my $logfile = "logfile.txt";
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my $hashs = 19;
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-my $hashe = 129;
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+my $hashe = $MAXKMERLENGTH;
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my $ass_num = 1;
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my $interested = 1;
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@@ -311,26 +312,26 @@
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my $ass = shift;
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print STDERR "\tPlease type in the insert length for the short reads: ";
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#my $len = <>;
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- my $len = "200"; #do not ask for insert size!
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+ my $len = "auto"; #do not ask for insert size!
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chomp($len);
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- while($len =~ /\D+/){
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- print STDERR "\tThe length needs to be a number, please re-enter: ";
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- $len = <>;
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- chomp($len);
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- }
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+ #while($len =~ /\D+/){
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+ # print STDERR "\tThe length needs to be a number, please re-enter: ";
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+ # $len = <>;
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+ # chomp($len);
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+ #}
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print STDERR strftime("%b %e %H:%M:%S", localtime), " Running assembly with short insert length $len\n";
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print OUT strftime("%b %e %H:%M:%S", localtime), " Running assembly with short insert length $len\n";
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#re-write the pstringg with the new velvetg command..
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- my $vg = $ass->{pstringg};
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- if($vg =~ /ins_length /){
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- $vg =~ s/ins_length\s+\d+/ins_length $len/;
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- }
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- else {
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- $vg .= " -ins_length $len";
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- }
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+ #my $vg = $ass->{pstringg};
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+ #if($vg =~ /ins_length /){
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+ # $vg =~ s/ins_length\s+\d+/ins_length $len/;
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+ #}
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+ #else {
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+ # $vg .= " -ins_length $len";
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+ #}
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- $ass->{pstringg} = $vg;
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+ #$ass->{pstringg} = $vg;
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my $worked = VelvetOpt::gwrap::objectVelvetg($ass);
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if($worked){
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$ass->getAssemblyDetails();
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@@ -347,8 +348,8 @@
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my $usage = "\nVelvetOptimiser.pl: A script to run the Velvet assembler and optimise its output. Simon Gladman - CSIRO 2008, 2009.\n\n";
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$usage .= "Usage: VelvetOptimiser.pl <-f 'velveth parameters'> [-s <hash start>] [-e <hash end>] [-a <yes>]\n\n";
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$usage .= "Where:\t<-f 'velveth parameters'> is the parameter line normally passed to velveth in quotes.\n";
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-$usage .= "\t-s <hash start> The hash value you want velvet to start looking from. Default: 19. MUST BE ODD > 0 & <=31!\n";
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-$usage .= "\t-e <hash end> The hash value you want velvet to stop looking at. Default: 31. MUST BE ODD AND > START & <= 31!\n";
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+$usage .= "\t-s <hash start> The hash value you want velvet to start looking from. Default: 19. MUST BE ODD > 0 & <=$MAXKMERLENGTH!\n";
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+$usage .= "\t-e <hash end> The hash value you want velvet to stop looking at. Default: $MAXKMERLENGTH. MUST BE ODD AND > START & <= $MAXKMERLENGTH!\n";
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$usage .= "\t-a <yes> The final optimised assembly will include read tracking and amos file outputs (however, intermediate assemblies won't.)\n";
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$usage .= "\nIf the optimizer requires an insert length for some paired end data, it will ask for it when it gets to the optimization step.\n";
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@@ -390,9 +391,9 @@
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$hashs = $opts{'s'};
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print STDERR "\n\t\t's-Param' is >$hashs<\n";
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unless($hashs =~ /^\d+$/){ die "\tFatal error! Start hash not a number!\n$usage";}
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- if($hashs > 129){
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- print STDERR "\tStart hash value too high. New start hash value is 129.\n";
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- $hashs = 129;
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+ if($hashs > $MAXKMERLENGTH){
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+ print STDERR "\tStart hash value too high. New start hash value is $MAXKMERLENGTH.\n";
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+ $hashs = $MAXKMERLENGTH;
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}
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if(!&isOdd($hashs)){
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$hashs = $hashs - 1;
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@@ -404,9 +405,9 @@
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if($opts{'e'}){
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$hashe = $opts{'e'};
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unless($hashe =~ /^\d+$/){ die "\tFatal error! End hash not a number!\n$usage";}
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- if($hashe > 129 || $hashe < 1){
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- print STDERR "\tEnd hash value not in workable range. New end hash value is 129.\n";
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- $hashe = 129;
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+ if($hashe > $MAXKMERLENGTH || $hashe < 1){
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+ print STDERR "\tEnd hash value not in workable range. New end hash value is $MAXKMERLENGTH.\n";
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+ $hashe = $MAXKMERLENGTH;
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}
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if($hashe < $hashs){
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print STDERR "\tEnd hash value lower than start hash value. New end hash value = $hashs.\n";
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@ -1,11 +0,0 @@
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--- src/run.c.orig 2009-09-16 20:11:59.000000000 +0900
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+++ src/run.c 2009-10-27 22:27:27.000000000 +0900
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@@ -152,7 +152,7 @@
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double_strand);
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destroySplayTable(splayTable);
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- closedir(dir);
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+ if (dir) closedir(dir);
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free(filename);
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free(buf);
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