===========================================================
.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
canu-2.0+dfsg/addCopyrights.pl-415- if ($doForReal) {
canu-2.0+dfsg/addCopyrights.pl:416: my $perms = `stat -f %p $file`; chomp $perms; $perms = substr($perms, -3);
canu-2.0+dfsg/addCopyrights.pl-417-
##############################################
canu-2.0+dfsg/addCopyrights.pl-421-
canu-2.0+dfsg/addCopyrights.pl:422: system("chmod $perms $file");
canu-2.0+dfsg/addCopyrights.pl-423-
##############################################
canu-2.0+dfsg/documentation/source/commands/updateDocs.sh-1-for file in `ls *.rst`; do
canu-2.0+dfsg/documentation/source/commands/updateDocs.sh:2: cmd=`echo $file |sed s/.rst//g`
canu-2.0+dfsg/documentation/source/commands/updateDocs.sh-3- export PATH=$PATH:../../../Darwin-amd64/bin
canu-2.0+dfsg/documentation/source/commands/updateDocs.sh:4: OUTPUT=`$cmd 2>&1 |awk '{print " "$0}'`
canu-2.0+dfsg/documentation/source/commands/updateDocs.sh-5- echo "$cmd" > $file
##############################################
canu-2.0+dfsg/documentation/source/faq.rst-118-
canu-2.0+dfsg/documentation/source/faq.rst:119: canu -p asm -d asm correctedErrorRate=0.3 utgGraphDeviation=50 -nanopore-corrected r5/r5.correctedReads.fasta.gz
canu-2.0+dfsg/documentation/source/faq.rst-120-
##############################################
canu-2.0+dfsg/documentation/source/parameter-reference.rst-282-
canu-2.0+dfsg/documentation/source/parameter-reference.rst:283: For example, in Sun Grid Engine, `/scratch/$JOB_ID-$SGE_TASK_ID` will use both the numeric
canu-2.0+dfsg/documentation/source/parameter-reference.rst:284: job ID and the numeric task ID. In SLURM, `/scratch/$SLRUM_JOBID` accomplishes the same.
canu-2.0+dfsg/documentation/source/parameter-reference.rst-285-
canu-2.0+dfsg/documentation/source/parameter-reference.rst-286- If specified on the command line, be sure to escape the dollar sign, otherwise the shell will try
canu-2.0+dfsg/documentation/source/parameter-reference.rst:287: to expand it before Canu sees the option: `stageDirectory=/scratch/\$JOB_ID-\$SGE_TASK_ID`.
canu-2.0+dfsg/documentation/source/parameter-reference.rst-288-
##############################################
canu-2.0+dfsg/documentation/source/quick-start.rst-155- canu \
canu-2.0+dfsg/documentation/source/quick-start.rst:156: -p asm -d yeast \
canu-2.0+dfsg/documentation/source/quick-start.rst-157- genomeSize=12.1m \
##############################################
canu-2.0+dfsg/documentation/source/quick-start.rst-171- canu \
canu-2.0+dfsg/documentation/source/quick-start.rst:172: -p asm -d ecoliTrio \
canu-2.0+dfsg/documentation/source/quick-start.rst-173- genomeSize=5m \
##############################################
canu-2.0+dfsg/documentation/source/quick-start.rst-191- canu \
canu-2.0+dfsg/documentation/source/quick-start.rst:192: -p asm -d ecoliHap \
canu-2.0+dfsg/documentation/source/quick-start.rst-193- genomeSize=5m \
##############################################
canu-2.0+dfsg/src/bogart-analysis/bogart-build-fasta.pl-103-
canu-2.0+dfsg/src/bogart-analysis/bogart-build-fasta.pl:104: system($cmd);
canu-2.0+dfsg/src/bogart-analysis/bogart-build-fasta.pl-105-
##############################################
canu-2.0+dfsg/src/bogart-analysis/bogart-build-fasta.pl-114-print R "#!/bin/sh\n";
canu-2.0+dfsg/src/bogart-analysis/bogart-build-fasta.pl:115:print R "idx=`printf %03d \$SGE_TASK_ID`\n";
canu-2.0+dfsg/src/bogart-analysis/bogart-build-fasta.pl-116-print R "utgcns -f -g ../$prefix.gkpStore -t $FILE.tigStore 1 \$idx > $FILE.tigStore/seqDB.v002.p\${idx}.utg.err 2>&1\n";
##############################################
canu-2.0+dfsg/src/bogart-analysis/bogart-build-fasta.pl-142-if ($withSGE) {
canu-2.0+dfsg/src/bogart-analysis/bogart-build-fasta.pl:143: #system("qsub -cwd -j y -o /dev/null -l memory=2g -t 1-9 -q servers.q,black.q $FILE.sge.sh");
canu-2.0+dfsg/src/bogart-analysis/bogart-build-fasta.pl-144- exit;
canu-2.0+dfsg/src/bogart-analysis/bogart-build-fasta.pl-145-} else {
canu-2.0+dfsg/src/bogart-analysis/bogart-build-fasta.pl:146: system("sh $FILE.tmp.sh");
canu-2.0+dfsg/src/bogart-analysis/bogart-build-fasta.pl-147-}
##############################################
canu-2.0+dfsg/src/bogart-analysis/bogart-build-fasta.pl-162-
canu-2.0+dfsg/src/bogart-analysis/bogart-build-fasta.pl:163: system($cmd);
canu-2.0+dfsg/src/bogart-analysis/bogart-build-fasta.pl-164-}
##############################################
canu-2.0+dfsg/src/bogart-analysis/bogart-build-fasta.pl-175-
canu-2.0+dfsg/src/bogart-analysis/bogart-build-fasta.pl:176: system($cmd);
canu-2.0+dfsg/src/bogart-analysis/bogart-build-fasta.pl-177-}
##############################################
canu-2.0+dfsg/src/bogart-analysis/bogart-build-fasta.pl-189-
canu-2.0+dfsg/src/bogart-analysis/bogart-build-fasta.pl:190: system($cmd);
canu-2.0+dfsg/src/bogart-analysis/bogart-build-fasta.pl-191-}
##############################################
canu-2.0+dfsg/src/bogart-analysis/bogart-build-fasta.pl-200-
canu-2.0+dfsg/src/bogart-analysis/bogart-build-fasta.pl:201: system($cmd);
canu-2.0+dfsg/src/bogart-analysis/bogart-build-fasta.pl-202-}
##############################################
canu-2.0+dfsg/src/bogart-analysis/count-bubbles.pl-51-
canu-2.0+dfsg/src/bogart-analysis/count-bubbles.pl:52: system($cmd);
canu-2.0+dfsg/src/bogart-analysis/count-bubbles.pl-53-}
##############################################
canu-2.0+dfsg/src/bogart-analysis/count-bubbles.pl-64-
canu-2.0+dfsg/src/bogart-analysis/count-bubbles.pl:65: system($cmd);
canu-2.0+dfsg/src/bogart-analysis/count-bubbles.pl-66-}
##############################################
canu-2.0+dfsg/src/bogart-analysis/examine-mapping-ideal.pl-50-
canu-2.0+dfsg/src/bogart-analysis/examine-mapping-ideal.pl:51: system($cmd);
canu-2.0+dfsg/src/bogart-analysis/examine-mapping-ideal.pl-52-}
##############################################
canu-2.0+dfsg/src/bogart-analysis/examine-mapping.pl-48-
canu-2.0+dfsg/src/bogart-analysis/examine-mapping.pl:49: system($cmd);
canu-2.0+dfsg/src/bogart-analysis/examine-mapping.pl-50-}
##############################################
canu-2.0+dfsg/src/bogart-analysis/show-false-best-edges-from-mapping.pl-28-
canu-2.0+dfsg/src/bogart-analysis/show-false-best-edges-from-mapping.pl:29:my $asm = shift @ARGV;
canu-2.0+dfsg/src/bogart-analysis/show-false-best-edges-from-mapping.pl-30-
##############################################
canu-2.0+dfsg/src/bogart/findOverlappingReads.pl-88-
canu-2.0+dfsg/src/bogart/findOverlappingReads.pl:89:system("ovStoreDump -G $gkpStore -O $ovlStore -p $readID");
canu-2.0+dfsg/src/bogart/findOverlappingReads.pl-90-print "\n";
##############################################
canu-2.0+dfsg/src/bogart/plotErrorProfile.pl-69-
canu-2.0+dfsg/src/bogart/plotErrorProfile.pl:70:system("gnuplot $name.gp");
##############################################
canu-2.0+dfsg/src/bogus/bogus-run.sh-28-
canu-2.0+dfsg/src/bogus/bogus-run.sh:29:OUT=`echo $FAS | tr '/' ' ' | awk '{ print $NF}' | sed s/.fasta//`
canu-2.0+dfsg/src/bogus/bogus-run.sh-30-
##############################################
canu-2.0+dfsg/src/bogus/bogus-run.sh-40-
canu-2.0+dfsg/src/bogus/bogus-run.sh:41:if [ `cat $REF | wc -l` != 2 ] ; then
canu-2.0+dfsg/src/bogus/bogus-run.sh-42- echo "REFERENCE is multi-line FASTA, sequence must be on one line."
##############################################
canu-2.0+dfsg/src/bogus/bogusness-run.pl-105-
canu-2.0+dfsg/src/bogus/bogusness-run.pl:106: system($cmd);
canu-2.0+dfsg/src/bogus/bogusness-run.pl-107-}
##############################################
canu-2.0+dfsg/src/bogus/bogusness-run.pl-117-
canu-2.0+dfsg/src/bogus/bogusness-run.pl:118: system($cmd);
canu-2.0+dfsg/src/bogus/bogusness-run.pl-119-}
##############################################
canu-2.0+dfsg/src/bogus/bogusness-run.pl-135-
canu-2.0+dfsg/src/bogus/bogusness-run.pl:136: system($cmd);
canu-2.0+dfsg/src/bogus/bogusness-run.pl-137-}
##############################################
canu-2.0+dfsg/src/bogus/bogusness-run.pl-196-
canu-2.0+dfsg/src/bogus/bogusness-run.pl:197:system("mkdir $prefix.jbrowse");
canu-2.0+dfsg/src/bogus/bogusness-run.pl-198-
##############################################
canu-2.0+dfsg/src/bogus/bogusness-run.pl-224-
canu-2.0+dfsg/src/bogus/bogusness-run.pl:225:system("sh $prefix.jbrowse/create.sh");
##############################################
canu-2.0+dfsg/src/meryl/meryl-import.C-206- for (uint32 ii=0; kstr[ii]; ii++)
canu-2.0+dfsg/src/meryl/meryl-import.C:207: kmerF.addR(kstr[ii]);
canu-2.0+dfsg/src/meryl/meryl-import.C-208-
##############################################
canu-2.0+dfsg/src/overlapBasedTrimming/generate-random-chimeric-fragments.pl-69-
canu-2.0+dfsg/src/overlapBasedTrimming/generate-random-chimeric-fragments.pl:70:system("$leaff --errors $readLength 10000 1 0.01 $genome > sample3.fasta");
canu-2.0+dfsg/src/overlapBasedTrimming/generate-random-chimeric-fragments.pl:71:system("$leaff -f sample3.fasta -R -C -W > sample1.fasta");
canu-2.0+dfsg/src/overlapBasedTrimming/generate-random-chimeric-fragments.pl:72:system("$leaff --errors $readLength 10000 1 0.01 $genome > sample2.fasta");
canu-2.0+dfsg/src/overlapBasedTrimming/generate-random-chimeric-fragments.pl-73-
##############################################
canu-2.0+dfsg/src/overlapBasedTrimming/test-random-chimeric-fragments.pl-104- if (($numMatches > 1) || ($badMatches > 0)) {
canu-2.0+dfsg/src/overlapBasedTrimming/test-random-chimeric-fragments.pl:105: my $ovl = `/work/wgs/FreeBSD-amd64/bin/overlapStore -g /work/test/test.gkpStore -dp $iid /work/test/0-overlaptrim/test.obtStore`;
canu-2.0+dfsg/src/overlapBasedTrimming/test-random-chimeric-fragments.pl-106-
##############################################
canu-2.0+dfsg/src/overlapInCore-analysis/analyze-true-vs-test.pl-309-print "overlapStoreBuild -g $testPrefix/test.gkpStore -o all.true.filtered-overlaps.ovlStore -F 1 all.true.filtered-overlaps.ovb\n";
canu-2.0+dfsg/src/overlapInCore-analysis/analyze-true-vs-test.pl:310:system("overlapStoreBuild -g $testPrefix/test.gkpStore -o all.true.filtered-overlaps.ovlStore -F 1 all.true.filtered-overlaps.ovb");
canu-2.0+dfsg/src/overlapInCore-analysis/analyze-true-vs-test.pl-311-
canu-2.0+dfsg/src/overlapInCore-analysis/analyze-true-vs-test.pl-312-print "overlapStoreBuild -g $testPrefix/test.gkpStore -o all.true.filtered-overlaps+false.ovlStore -F 1 all.true.filtered-overlaps.ovb all.false.filtered-overlaps.ovb\n";
canu-2.0+dfsg/src/overlapInCore-analysis/analyze-true-vs-test.pl:313:system("overlapStoreBuild -g $testPrefix/test.gkpStore -o all.true.filtered-overlaps+false.ovlStore -F 1 all.true.filtered-overlaps.ovb all.false.filtered-overlaps.ovb");
canu-2.0+dfsg/src/overlapInCore-analysis/analyze-true-vs-test.pl-314-
##############################################
canu-2.0+dfsg/src/overlapInCore-analysis/analyze-true-vs-test.pl-487-
canu-2.0+dfsg/src/overlapInCore-analysis/analyze-true-vs-test.pl:488:system("awk '{ print \$1 }' computed-overlaps.bestE.true.dat | sort -n | uniq -c > computed-overlaps.bestE.true.eratehist");
canu-2.0+dfsg/src/overlapInCore-analysis/analyze-true-vs-test.pl:489:system("awk '{ print \$1 }' computed-overlaps.bestE.near.dat | sort -n | uniq -c > computed-overlaps.bestE.near.eratehist");
canu-2.0+dfsg/src/overlapInCore-analysis/analyze-true-vs-test.pl:490:system("awk '{ print \$1 }' computed-overlaps.bestE.false.dat | sort -n | uniq -c > computed-overlaps.bestE.false.eratehist");
canu-2.0+dfsg/src/overlapInCore-analysis/analyze-true-vs-test.pl-491-
canu-2.0+dfsg/src/overlapInCore-analysis/analyze-true-vs-test.pl:492:system("awk '{ print \$1 }' computed-overlaps.bestC.true.dat | sort -n | uniq -c > computed-overlaps.bestC.true.eratehist");
canu-2.0+dfsg/src/overlapInCore-analysis/analyze-true-vs-test.pl:493:system("awk '{ print \$1 }' computed-overlaps.bestC.near.dat | sort -n | uniq -c > computed-overlaps.bestC.near.eratehist");
canu-2.0+dfsg/src/overlapInCore-analysis/analyze-true-vs-test.pl:494:system("awk '{ print \$1 }' computed-overlaps.bestC.false.dat | sort -n | uniq -c > computed-overlaps.bestC.false.eratehist");
canu-2.0+dfsg/src/overlapInCore-analysis/analyze-true-vs-test.pl-495-
canu-2.0+dfsg/src/overlapInCore-analysis/analyze-true-vs-test.pl:496:system("awk '{ print \$1 }' computed-overlaps.other.true.dat | sort -n | uniq -c > computed-overlaps.other.true.eratehist");
canu-2.0+dfsg/src/overlapInCore-analysis/analyze-true-vs-test.pl:497:system("awk '{ print \$1 }' computed-overlaps.other.false.dat | sort -n | uniq -c > computed-overlaps.other.false.eratehist");
canu-2.0+dfsg/src/overlapInCore-analysis/analyze-true-vs-test.pl-498-
##############################################
canu-2.0+dfsg/src/overlapInCore-analysis/filterTrue.pl-484-
canu-2.0+dfsg/src/overlapInCore-analysis/filterTrue.pl:485:system("awk '{ print \$1 }' computed-overlaps.bestE.true.dat | sort -n | uniq -c > computed-overlaps.bestE.true.eratehist");
canu-2.0+dfsg/src/overlapInCore-analysis/filterTrue.pl:486:system("awk '{ print \$1 }' computed-overlaps.bestE.near.dat | sort -n | uniq -c > computed-overlaps.bestE.near.eratehist");
canu-2.0+dfsg/src/overlapInCore-analysis/filterTrue.pl:487:system("awk '{ print \$1 }' computed-overlaps.bestE.false.dat | sort -n | uniq -c > computed-overlaps.bestE.false.eratehist");
canu-2.0+dfsg/src/overlapInCore-analysis/filterTrue.pl-488-
canu-2.0+dfsg/src/overlapInCore-analysis/filterTrue.pl:489:system("awk '{ print \$1 }' computed-overlaps.bestC.true.dat | sort -n | uniq -c > computed-overlaps.bestC.true.eratehist");
canu-2.0+dfsg/src/overlapInCore-analysis/filterTrue.pl:490:system("awk '{ print \$1 }' computed-overlaps.bestC.near.dat | sort -n | uniq -c > computed-overlaps.bestC.near.eratehist");
canu-2.0+dfsg/src/overlapInCore-analysis/filterTrue.pl:491:system("awk '{ print \$1 }' computed-overlaps.bestC.false.dat | sort -n | uniq -c > computed-overlaps.bestC.false.eratehist");
canu-2.0+dfsg/src/overlapInCore-analysis/filterTrue.pl-492-
canu-2.0+dfsg/src/overlapInCore-analysis/filterTrue.pl:493:system("awk '{ print \$1 }' computed-overlaps.other.true.dat | sort -n | uniq -c > computed-overlaps.other.true.eratehist");
canu-2.0+dfsg/src/overlapInCore-analysis/filterTrue.pl:494:system("awk '{ print \$1 }' computed-overlaps.other.false.dat | sort -n | uniq -c > computed-overlaps.other.false.eratehist");
canu-2.0+dfsg/src/overlapInCore-analysis/filterTrue.pl-495-
##############################################
canu-2.0+dfsg/src/overlapInCore/liboverlap/prefixEditDistance-matchLimit.sh-2-
canu-2.0+dfsg/src/overlapInCore/liboverlap/prefixEditDistance-matchLimit.sh:3:bgn=`expr $SGE_TASK_ID + 0`
canu-2.0+dfsg/src/overlapInCore/liboverlap/prefixEditDistance-matchLimit.sh:4:end=`expr $SGE_TASK_ID + 1`
canu-2.0+dfsg/src/overlapInCore/liboverlap/prefixEditDistance-matchLimit.sh-5-
##############################################
canu-2.0+dfsg/src/overlapInCore/overlapImport.C-175- fprintf(stderr, " -unaligned as unaligned regions on each read\n");
canu-2.0+dfsg/src/overlapInCore/overlapImport.C:176: fprintf(stderr, " -paf as miniasm Pairwise mApping Format\n");
canu-2.0+dfsg/src/overlapInCore/overlapImport.C-177- fprintf(stderr, "\n");
##############################################
canu-2.0+dfsg/src/pipelines/bogart-sweep.pl-29-my $wrk = "/work/canuassemblies/sent";
canu-2.0+dfsg/src/pipelines/bogart-sweep.pl:30:my $asm = "test";
canu-2.0+dfsg/src/pipelines/bogart-sweep.pl-31-
canu-2.0+dfsg/src/pipelines/bogart-sweep.pl:32:system("mkdir -p $wrk") if (! -d $wrk);
canu-2.0+dfsg/src/pipelines/bogart-sweep.pl-33-
##############################################
canu-2.0+dfsg/src/pipelines/bogart-sweep.pl-110-
canu-2.0+dfsg/src/pipelines/bogart-sweep.pl:111: system("mkdir -p $path") if (! -d $path);
canu-2.0+dfsg/src/pipelines/bogart-sweep.pl-112-
##############################################
canu-2.0+dfsg/src/pipelines/bogart-sweep.pl-174-
canu-2.0+dfsg/src/pipelines/bogart-sweep.pl:175: system("sh $wrk/$path/bogart.sh");
canu-2.0+dfsg/src/pipelines/bogart-sweep.pl:176: system("qsub -q vomit.q -cwd -j y -o /dev/null $wrk/$path/utgcns.sh > /dev/null 2>&1");
canu-2.0+dfsg/src/pipelines/bogart-sweep.pl-177-}
##############################################
canu-2.0+dfsg/src/pipelines/canu.pl-96-my $cmd = undef; # Temporary string passed to system().
canu-2.0+dfsg/src/pipelines/canu.pl:97:my $asm = undef; # Name of our assembly.
canu-2.0+dfsg/src/pipelines/canu.pl-98-my $asmAuto = undef; # If set, the name was auto-discovered.
##############################################
canu-2.0+dfsg/src/pipelines/canu.pl-182- elsif ($arg eq "-p") {
canu-2.0+dfsg/src/pipelines/canu.pl:183: $asm = shift @ARGV;
canu-2.0+dfsg/src/pipelines/canu.pl-184- addCommandLineOption("-p '$asm'");
##############################################
canu-2.0+dfsg/src/pipelines/canu.pl-297-
canu-2.0+dfsg/src/pipelines/canu.pl:298:# If no $asm or $dir, see if there is an assembly here. If so, set $asm to what was found.
canu-2.0+dfsg/src/pipelines/canu.pl-299-
##############################################
canu-2.0+dfsg/src/pipelines/canu.pl-304- while (<F>) {
canu-2.0+dfsg/src/pipelines/canu.pl:305: $asm = $1 if (m/^(.*).seqStore$/);
canu-2.0+dfsg/src/pipelines/canu.pl-306- }
##############################################
canu-2.0+dfsg/src/pipelines/canu.pl-312-addCommandLineError("ERROR: Assembly name prefix (-p) not supplied.\n") if (!defined($asm));
canu-2.0+dfsg/src/pipelines/canu.pl:313:addCommandLineError("ERROR: Assembly name prefix (-p) cannot contain the path delimiter '/'.\n") if ($asm =~ m!/!);
canu-2.0+dfsg/src/pipelines/canu.pl:314:addCommandLineError("ERROR: Assembly name prefix (-p) cannot contain spaces.\n") if ($asm =~ m!\s!);
canu-2.0+dfsg/src/pipelines/canu.pl-315-
##############################################
canu-2.0+dfsg/src/pipelines/canu.pl-423-#my $nOBT = getNumberOfReadsInStore($asm, "obt"); # Number of corrected reads ready for OBT.
canu-2.0+dfsg/src/pipelines/canu.pl:424:#my $nAsm = getNumberOfReadsInStore($asm, "utg"); # Number of trimmed reads ready for assembly.
canu-2.0+dfsg/src/pipelines/canu.pl-425-
##############################################
canu-2.0+dfsg/src/pipelines/canu.pl-436-
canu-2.0+dfsg/src/pipelines/canu.pl:437:#if ($nCor + $nOBT + $nAsm > 0) {
canu-2.0+dfsg/src/pipelines/canu.pl-438-if (-e "./$asm.seqStore/info") {
##############################################
canu-2.0+dfsg/src/pipelines/canu.pl-756-sub overlap ($$) {
canu-2.0+dfsg/src/pipelines/canu.pl:757: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu.pl-758- my $tag = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm-63-sub utgcns ($$$) {
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm:64: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm-65- my $ctgjobs = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm-89- print F " tag=\"utg\"\n";
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm:90: print F " jobid=`expr \$jobid - $ctgjobs`\n";
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm-91- print F "fi\n";
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm-92- print F "\n";
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm:93: print F "jobid=`printf %04d \$jobid`\n";
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm-94- print F "\n";
##############################################
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm-140-sub partitionTigs ($$) {
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm:141: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm-142- my $tag = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm-170-sub computeNumberOfConsensusJobs ($$) {
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm:171: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm-172- my $tag = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm-196-sub estimateMemoryNeededForConsensusJobs ($) {
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm:197: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm-198- my $minMem = 0;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm-266-sub consensusConfigure ($) {
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm:267: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm-268- my $bin = getBinDirectory();
##############################################
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm-316-sub consensusCheck ($) {
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm:317: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm-318- my $attempt = getGlobal("canuIteration");
##############################################
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm-429-sub purgeFiles ($$$$$$) {
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm:430: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm-431- my $tag = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm-482-sub consensusLoad ($) {
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm:483: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm-484- my $bin = getBinDirectory();
##############################################
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm-583-sub consensusAnalyze ($) {
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm:584: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm-585- my $bin = getBinDirectory();
##############################################
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm-622-sub alignGFA ($) {
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm:623: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Consensus.pm-624- my $attempt = getGlobal("canuIteration");
##############################################
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm-67-sub getCorCov ($$) {
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm:68: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm-69- my $typ = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm-87-sub getCorIdentity ($) {
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm:88: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm-89- my $bin = getBinDirectory();
##############################################
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm-105-sub setupCorrectionParameters ($) {
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm:106: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm-107- my $bin = getBinDirectory();
##############################################
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm-130-sub buildCorrectionLayoutsConfigure ($) {
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm:131: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm-132- my $bin = getBinDirectory();
##############################################
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm-229-sub buildCorrectionLayoutsCheck ($) {
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm:230: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm-231- my $bin = getBinDirectory();
##############################################
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm-251-sub filterCorrectionLayouts ($) {
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm:252: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm-253- my $bin = getBinDirectory();
##############################################
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm-308-sub generateCorrectedReadsConfigure ($) {
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm:309: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm-310- my $bin = getBinDirectory();
##############################################
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm-331- if (! -e "$path/$asm.readsToCorrect.stats") {
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm:332: caExit("failed to find `$path/$asm.readsToCorrect.stats` to read maximum estimated memory needed for correction", undef);
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm-333- }
##############################################
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm-536-sub generateCorrectedReadsCheck ($) {
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm:537: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm-538- my $attempt = getGlobal("canuIteration");
##############################################
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm-618-sub loadCorrectedReads ($) {
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm:619: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm-620- my $bin = getBinDirectory();
##############################################
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm-746-sub dumpCorrectedReads ($) {
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm:747: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/CorrectReads.pm-748- my $bin = getBinDirectory();
##############################################
canu-2.0+dfsg/src/pipelines/canu/Defaults.pm-1190-
canu-2.0+dfsg/src/pipelines/canu/Defaults.pm:1191: system("cd /tmp && $minimap --version > /tmp/minimap2-$$.err 2>&1");
canu-2.0+dfsg/src/pipelines/canu/Defaults.pm-1192-
##############################################
canu-2.0+dfsg/src/pipelines/canu/Defaults.pm-1238-
canu-2.0+dfsg/src/pipelines/canu/Defaults.pm:1239: system("cd /tmp && $gnuplot < /dev/null /tmp/gnuplot-$$-test.gp > /tmp/gnuplot-$$-test.err 2>&1");
canu-2.0+dfsg/src/pipelines/canu/Defaults.pm-1240-
##############################################
canu-2.0+dfsg/src/pipelines/canu/Defaults.pm-1316-
canu-2.0+dfsg/src/pipelines/canu/Defaults.pm:1317: system("cd /tmp && $gnuplot < /dev/null /tmp/gnuplot-$$-test.gp > /tmp/gnuplot-$$-test.err 2>&1");
canu-2.0+dfsg/src/pipelines/canu/Defaults.pm-1318-
##############################################
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-180- #
canu-2.0+dfsg/src/pipelines/canu/Execution.pm:181: exec($process);
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-182- } elsif ($! =~ /No more processes/) {
##############################################
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-373- $string .= "fi\n";
canu-2.0+dfsg/src/pipelines/canu/Execution.pm:374: $string .= "jobid=`expr -- \$baseid + \$offset`\n";
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-375- $string .= "if [ x\$$taskenv = x ]; then\n";
##############################################
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-477- $string .= "echo \"Found java:\"\n";
canu-2.0+dfsg/src/pipelines/canu/Execution.pm:478: $string .= "echo \" \" `which $javaPath`\n";
canu-2.0+dfsg/src/pipelines/canu/Execution.pm:479: $string .= "echo \" \" `$javaPath -showversion 2>&1 | head -n 1`\n";
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-480- $string .= "echo \"\"\n";
##############################################
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-482- $string .= "echo \" \" $canu\n";
canu-2.0+dfsg/src/pipelines/canu/Execution.pm:483: $string .= "echo \" \" `$canu -version`\n";
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-484- $string .= "echo \"\"\n";
##############################################
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-514-sub setWorkDirectory ($$) {
canu-2.0+dfsg/src/pipelines/canu/Execution.pm:515: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-516- my $rootdir = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-605- my $jobType = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Execution.pm:606: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-607-
##############################################
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-610- if ($jobType eq "canu") {
canu-2.0+dfsg/src/pipelines/canu/Execution.pm:611: return("canu_" . $asm . ((defined(getGlobal("gridOptionsJobName"))) ? ("_" . getGlobal("gridOptionsJobName")) : ("")));
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-612- }
##############################################
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-615-
canu-2.0+dfsg/src/pipelines/canu/Execution.pm:616: my $jobName = "${jobType}_" . $asm . ((defined(getGlobal("gridOptionsJobName"))) ? ("_" . getGlobal("gridOptionsJobName")) : (""));
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-617- my %jobs;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-669-sub submitScript ($$) {
canu-2.0+dfsg/src/pipelines/canu/Execution.pm:670: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-671- my $jobHold = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-971-sub buildGridJob ($$$$$$$$$) {
canu-2.0+dfsg/src/pipelines/canu/Execution.pm:972: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-973- my $jobType = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-1177-sub submitOrRunParallelJob ($$$$@) {
canu-2.0+dfsg/src/pipelines/canu/Execution.pm:1178: my $asm = shift @_; # Name of the assembly
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-1179-
##############################################
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-1537-
canu-2.0+dfsg/src/pipelines/canu/Execution.pm:1538: my $rc = 0xffff & system($cmd);
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-1539-
##############################################
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-1567-
canu-2.0+dfsg/src/pipelines/canu/Execution.pm:1568: my $rc = 0xffff & system($cmd);
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-1569-
##############################################
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-1601-
canu-2.0+dfsg/src/pipelines/canu/Execution.pm:1602: my $path = `which \"$exec\" 2> /dev/null`;
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-1603-
##############################################
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-1613-sub caExit ($$) {
canu-2.0+dfsg/src/pipelines/canu/Execution.pm:1614: my $asm = getGlobal("onExitNam");
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-1615- my $msg = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-1661-sub caFailure ($$) {
canu-2.0+dfsg/src/pipelines/canu/Execution.pm:1662: my $asm = getGlobal("onExitNam");
canu-2.0+dfsg/src/pipelines/canu/Execution.pm-1663- my $msg = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-104-sub configureCloud ($$) {
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm:105: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-106- my $dir = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-199- if (isOS() eq "DNANEXUS") {
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm:200: $exists = `$dx describe --name \"$link\" 2> /dev/null`;
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-201- }
##############################################
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-221- if (isOS() eq "DNANEXUS") {
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm:222: $exists = `$dx describe --name \"$path\" 2> /dev/null`;
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-223- }
##############################################
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-245- $code .= "${indent}if [ ! -e $file ] ; then\n";
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm:246: $code .= "${indent} $var=`$dx describe --name \"$pr:$ns/$path/$file\" 2> /dev/null`\n";
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-247- $code .= "${indent}fi\n";
##############################################
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-456- $code .= "${indent}if [ -e \"./$file\" ] ; then\n";
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm:457: $code .= "${indent} fold=`dirname \"$path/$file\"`\n";
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm:458: $code .= "${indent} name=`basename \"$file\"`\n";
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-459- $code .= "${indent}\n";
##############################################
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-466- $code .= "${indent} ! $ua --do-not-compress --wait-on-close --project \"$pr\" --folder \"$ns/\$fold/\" --name \"\$name\" \"./$file\" ; do\n";
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm:467: $code .= "${indent} retries=`expr \$retries - 1`\n";
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-468- $code .= "${indent} echo \"Failed to stash file '$file', wait $retryDelay seconds and try again (\$retries times left).\"\n";
##############################################
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-517- $code .= "${indent} ! $ua --do-not-compress --wait-on-close --project \"$pr\" --folder \"$ns/$folder/\" $files ; do\n";
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm:518: $code .= "${indent} retries=`expr \$retries - 1`\n";
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-519- $code .= "${indent} echo \"Failed to stash files '$files', wait $retryDelay seconds and try again (\$retries times left).\"\n";
##############################################
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-575- # $code .= "${indent}if [ ! -e \"./$name\" ] ; then\n";
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm:576: # $code .= "${indent} mkdir -p `dirname \"./$name\"`\n";
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-577- # $code .= "${indent} $da download --output \"./$name\" \"$link\"\n";
##############################################
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-598- $code .= "${indent}if [ ! -e \"./$name\" ] ; then\n";
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm:599: $code .= "${indent} mkdir -p `dirname \"./$name\"`\n";
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-600- $code .= "${indent} $da download --output \"./$name\" \"$link\"\n";
##############################################
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-623-sub stashSeqStore ($) {
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm:624: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-625- my $files;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-669-sub fetchSeqStore ($) {
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm:670: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-671-
##############################################
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-691-sub fetchSeqStoreShellCode ($$$) {
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm:692: my $asm = shift @_; # The name of the assembly.
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-693- my $path = shift @_; # The subdir we're running in; 'unitigging/4-unitigger', etc.
##############################################
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-720-sub stashSeqStorePartitions ($$$$) {
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm:721: my $asm = shift @_; # The name of the assembly.
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-722- my $base = shift @_; # The subdir we're running in; 'unitigging/4-unitigger', etc.
##############################################
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-761-sub stashOvlStore ($$) {
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm:762: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-763- my $base = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-801-sub stashOvlStoreShellCode ($$) {
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm:802: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-803- my $base = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-846-sub fetchOvlStore ($$) {
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm:847: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-848- my $base = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-870-sub fetchOvlStoreShellCode ($$$) {
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm:871: my $asm = shift @_; # The name of the assembly.
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-872- my $path = shift @_; # The subdir we're running in; 'unitigging/4-unitigger', etc.
##############################################
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-905- my $base = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm:906: my $asm = shift @_; # The name of the assembly.
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-907- my $type = shift @_; # Type of store: 'corStore' or 'ctgStore' or 'utgStore'.
##############################################
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-921- my $path = shift @_; # The subdir we're running in; 'unitigging', etc.
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm:922: my $asm = shift @_; # The name of the assembly.
canu-2.0+dfsg/src/pipelines/canu/Grid_Cloud.pm-923- my $type = shift @_; # Type of store: 'corStore' or 'ctgStore' or 'utgStore'.
##############################################
canu-2.0+dfsg/src/pipelines/canu/HaplotypeReads.pm-71-sub haplotypeReadsExist ($@) {
canu-2.0+dfsg/src/pipelines/canu/HaplotypeReads.pm:72: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/HaplotypeReads.pm-73- my @haplotypes = @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/HaplotypeReads.pm-97-sub haplotypeSplitReads ($$%) {
canu-2.0+dfsg/src/pipelines/canu/HaplotypeReads.pm:98: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/HaplotypeReads.pm-99- my $merSize = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/HaplotypeReads.pm-215-sub haplotypeCountConfigure ($%) {
canu-2.0+dfsg/src/pipelines/canu/HaplotypeReads.pm:216: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/HaplotypeReads.pm-217- my %haplotypeReads = @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/HaplotypeReads.pm-662-sub haplotypeCountCheck ($) {
canu-2.0+dfsg/src/pipelines/canu/HaplotypeReads.pm:663: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/HaplotypeReads.pm-664- my $attempt = getGlobal("canuIteration");
##############################################
canu-2.0+dfsg/src/pipelines/canu/HaplotypeReads.pm-773-sub haplotypeMergeCheck ($@) {
canu-2.0+dfsg/src/pipelines/canu/HaplotypeReads.pm:774: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/HaplotypeReads.pm-775- my @haplotypes = @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/HaplotypeReads.pm-859-sub haplotypeSubtractCheck ($@) {
canu-2.0+dfsg/src/pipelines/canu/HaplotypeReads.pm:860: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/HaplotypeReads.pm-861- my @haplotypes = @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/HaplotypeReads.pm-958-sub haplotypeReadsConfigure ($@) {
canu-2.0+dfsg/src/pipelines/canu/HaplotypeReads.pm:959: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/HaplotypeReads.pm-960- my $haplotypes = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/HaplotypeReads.pm-1096-sub haplotypeReadsCheck ($@) {
canu-2.0+dfsg/src/pipelines/canu/HaplotypeReads.pm:1097: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/HaplotypeReads.pm-1098- my @haplotypes = @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Meryl.pm-64-sub merylParameters ($$) {
canu-2.0+dfsg/src/pipelines/canu/Meryl.pm:65: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Meryl.pm-66- my $tag = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Meryl.pm-106-sub merylGenerateHistogram ($$) {
canu-2.0+dfsg/src/pipelines/canu/Meryl.pm:107: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Meryl.pm-108- my $tag = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Meryl.pm-237- my $path = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Meryl.pm:238: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Meryl.pm-239- my $name = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Meryl.pm-316-sub merylConfigure ($$) {
canu-2.0+dfsg/src/pipelines/canu/Meryl.pm:317: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Meryl.pm-318- my $tag = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Meryl.pm-489- print F "\n";
canu-2.0+dfsg/src/pipelines/canu/Meryl.pm:490: print F "jobid=`printf %02d \$jobid`\n";
canu-2.0+dfsg/src/pipelines/canu/Meryl.pm-491- print F "\n";
##############################################
canu-2.0+dfsg/src/pipelines/canu/Meryl.pm-665- print F "if [ ! -e ./$name.ignore.gz ] ; then\n";
canu-2.0+dfsg/src/pipelines/canu/Meryl.pm:666: print F " numKmers=`wc -l < ./$name.dump`\n";
canu-2.0+dfsg/src/pipelines/canu/Meryl.pm:667: print F " totKmers=`$bin/meryl statistics ./$name | grep present | awk '{ print \$2 }'`\n";
canu-2.0+dfsg/src/pipelines/canu/Meryl.pm-668- print F "\n";
##############################################
canu-2.0+dfsg/src/pipelines/canu/Meryl.pm-751-sub merylCountCheck ($$) {
canu-2.0+dfsg/src/pipelines/canu/Meryl.pm:752: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Meryl.pm-753- my $tag = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Meryl.pm-857-sub merylProcessCheck ($$) {
canu-2.0+dfsg/src/pipelines/canu/Meryl.pm:858: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Meryl.pm-859- my $tag = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Output.pm-60-sub generateOutputs ($) {
canu-2.0+dfsg/src/pipelines/canu/Output.pm:61: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Output.pm-62- my $bin = getBinDirectory();
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapBasedTrimming.pm-61-sub trimReads ($) {
canu-2.0+dfsg/src/pipelines/canu/OverlapBasedTrimming.pm:62: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapBasedTrimming.pm-63- my $bin = getBinDirectory();
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapBasedTrimming.pm-131-sub splitReads ($) {
canu-2.0+dfsg/src/pipelines/canu/OverlapBasedTrimming.pm:132: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapBasedTrimming.pm-133- my $bin = getBinDirectory();
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapBasedTrimming.pm-202-sub loadTrimmedReads ($) {
canu-2.0+dfsg/src/pipelines/canu/OverlapBasedTrimming.pm:203: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapBasedTrimming.pm-204- my $bin = getBinDirectory();
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapBasedTrimming.pm-261-sub dumpTrimmedReads ($) {
canu-2.0+dfsg/src/pipelines/canu/OverlapBasedTrimming.pm:262: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapBasedTrimming.pm-263- my $bin = getBinDirectory();
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapErrorAdjustment.pm-62-sub loadReadLengths ($$$) {
canu-2.0+dfsg/src/pipelines/canu/OverlapErrorAdjustment.pm:63: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapErrorAdjustment.pm-64- my $maxID = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapErrorAdjustment.pm-111-sub loadNumberOfOverlaps ($$$) {
canu-2.0+dfsg/src/pipelines/canu/OverlapErrorAdjustment.pm:112: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapErrorAdjustment.pm-113- my $maxID = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapErrorAdjustment.pm-154-sub readErrorDetectionConfigure ($) {
canu-2.0+dfsg/src/pipelines/canu/OverlapErrorAdjustment.pm:155: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapErrorAdjustment.pm-156- my $bin = getBinDirectory();
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapErrorAdjustment.pm-295-
canu-2.0+dfsg/src/pipelines/canu/OverlapErrorAdjustment.pm:296: print F "jobid=`printf %05d \$jobid`\n";
canu-2.0+dfsg/src/pipelines/canu/OverlapErrorAdjustment.pm-297- print F "\n";
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapErrorAdjustment.pm-332-sub readErrorDetectionCheck ($) {
canu-2.0+dfsg/src/pipelines/canu/OverlapErrorAdjustment.pm:333: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapErrorAdjustment.pm-334- my $attempt = getGlobal("canuIteration");
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapErrorAdjustment.pm-444-sub overlapErrorAdjustmentConfigure ($) {
canu-2.0+dfsg/src/pipelines/canu/OverlapErrorAdjustment.pm:445: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapErrorAdjustment.pm-446- my $bin = getBinDirectory();
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapErrorAdjustment.pm-596-
canu-2.0+dfsg/src/pipelines/canu/OverlapErrorAdjustment.pm:597: print F "jobid=`printf %05d \$jobid`\n";
canu-2.0+dfsg/src/pipelines/canu/OverlapErrorAdjustment.pm-598- print F "\n";
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapErrorAdjustment.pm-636-sub overlapErrorAdjustmentCheck ($) {
canu-2.0+dfsg/src/pipelines/canu/OverlapErrorAdjustment.pm:637: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapErrorAdjustment.pm-638- my $attempt = getGlobal("canuIteration");
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapErrorAdjustment.pm-726-sub updateOverlapStore ($) {
canu-2.0+dfsg/src/pipelines/canu/OverlapErrorAdjustment.pm:727: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapErrorAdjustment.pm-728- my $bin = getBinDirectory();
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapInCore.pm-59-sub overlapConfigure ($$$) {
canu-2.0+dfsg/src/pipelines/canu/OverlapInCore.pm:60: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapInCore.pm-61- my $tag = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapInCore.pm-271- my $base = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapInCore.pm:272: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapInCore.pm-273- my @statsJobs = @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapInCore.pm-321-sub overlapCheck ($$$) {
canu-2.0+dfsg/src/pipelines/canu/OverlapInCore.pm:322: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapInCore.pm-323- my $tag = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapMMap.pm-53-sub setParameters ($$) {
canu-2.0+dfsg/src/pipelines/canu/OverlapMMap.pm:54: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapMMap.pm-55- my $base = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapMMap.pm-92-sub mmapConfigure ($$$) {
canu-2.0+dfsg/src/pipelines/canu/OverlapMMap.pm:93: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapMMap.pm-94- my $tag = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapMMap.pm-372-
canu-2.0+dfsg/src/pipelines/canu/OverlapMMap.pm:373: print F "for ii in `ls ./queries/\$qry` ; do\n";
canu-2.0+dfsg/src/pipelines/canu/OverlapMMap.pm-374- print F " echo Fetch blocks/\$ii\n";
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapMMap.pm-393-
canu-2.0+dfsg/src/pipelines/canu/OverlapMMap.pm:394: print F "for file in `ls queries/\$qry/*.fasta`; do\n";
canu-2.0+dfsg/src/pipelines/canu/OverlapMMap.pm-395- print F " $minimap \\\n";
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapMMap.pm-498-sub mmapPrecomputeCheck ($$$) {
canu-2.0+dfsg/src/pipelines/canu/OverlapMMap.pm:499: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapMMap.pm-500- my $tag = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapMMap.pm-587-sub mmapCheck ($$$) {
canu-2.0+dfsg/src/pipelines/canu/OverlapMMap.pm:588: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapMMap.pm-589- my $tag = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-73-sub fetchOverlapData ($$@) {
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm:74: my $asm = shift @_; # Not actually used.
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-75- my $base = shift @_; # What stage we're in, 'correction', 'trimming', etc.
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-101-sub fetchOverlapDataShellCode ($$) {
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm:102: my $asm = shift @_; # Not actually used.
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-103- my $base = shift @_; # What stage we're in, 'correction', 'trimming', etc.
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-131- my $base = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm:132: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-133- my $tag = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-183- my $base = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm:184: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-185- my $tag = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-229- my $base = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm:230: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-231- my $tag = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-272- print F "\n";
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm:273: print F "jobname=`printf %04d \$jobid`\n";
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-274- print F "\n";
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-289- print F "\n";
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm:290: print F "inputs=`\$bin/ovStoreConfig -describe ./$asm.ovlStore.config -listinputs \$jobid`\n";
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-291- print F "\n";
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-351- print F "\n";
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm:352: print F "jobname=`printf %04d \$jobid`\n";
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-353- print F "\n";
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-367- print F "\n";
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm:368: print F "inputs=`\$bin/ovStoreConfig -describe ./$asm.ovlStore.config -listslices \$jobid`\n";
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-369- print F "\n";
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-395- print F "\n";
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm:396: print F "jobid=`printf %04d \$jobid`\n";
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-397- print F "\n";
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-437- my $base = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm:438: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-439- my $tag = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-537- my $base = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm:538: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-539- my $tag = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-626- my $base = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm:627: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-628-
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-685- my $base = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm:686: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-687- my @what = @_; # types of data to delete
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-747-sub createOverlapStore ($$) {
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm:748: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapStore.pm-749- my $tag = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Report.pm-56-sub loadReport ($) {
canu-2.0+dfsg/src/pipelines/canu/Report.pm:57: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Report.pm-58- my $tag;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Report.pm-119-sub saveReport ($) {
canu-2.0+dfsg/src/pipelines/canu/Report.pm:120: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Report.pm-121- my $tag;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Report.pm-193-sub generateReport ($) {
canu-2.0+dfsg/src/pipelines/canu/Report.pm:194: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Report.pm-195-
##############################################
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm-57-sub getNumberOfReadsInStore ($$) {
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm:58: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm-59- my $tag = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm-94-sub getNumberOfBasesInStore ($$) {
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm:95: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm-96- my $tag = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm-123-sub getSequenceStoreStats ($) {
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm:124: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm-125- my $bin = getBinDirectory();
##############################################
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm-182-sub getSizeOfSequenceStore ($) {
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm:183: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm-184- my $size = 0;
##############################################
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm-202- my $tag = shift @_;
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm:203: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm-204-
##############################################
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm-211- my $base = shift @_;
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm:212: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm-213- my $bin = getBinDirectory();
##############################################
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm-307- my $tag = shift @_;
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm:308: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm-309- my $bin = getBinDirectory();
##############################################
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm-414- my $base;
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm:415: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm-416- my $tag = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm-465- my $nOBT = getNumberOfReadsInStore($asm, "obt"); # Number of corrected reads ready for OBT.
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm:466: my $nAsm = getNumberOfReadsInStore($asm, "utg"); # Number of trimmed reads ready for assembly.
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm-467-
##############################################
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm-472- ($nOBT == 0) && # But no corrected reads.
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm:473: ($nAsm == 0)) { # And no trimmed reads!
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm-474-
##############################################
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm-498- (($tag eq "obt") && ($nOBT == 0)) ||
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm:499: (($tag eq "utg") && ($nAsm == 0))) {
canu-2.0+dfsg/src/pipelines/canu/SequenceStore.pm-500-
##############################################
canu-2.0+dfsg/src/pipelines/canu/Unitig.pm-65-sub reportUnitigSizes ($$$) {
canu-2.0+dfsg/src/pipelines/canu/Unitig.pm:66: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Unitig.pm-67- my $version = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/Unitig.pm-163-sub unitig_bogart ($) {
canu-2.0+dfsg/src/pipelines/canu/Unitig.pm:164: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Unitig.pm-165-
##############################################
canu-2.0+dfsg/src/pipelines/canu/Unitig.pm-186- print F " -O ../$asm.ovlStore \\\n";
canu-2.0+dfsg/src/pipelines/canu/Unitig.pm:187: print F " -o ./$asm \\\n";
canu-2.0+dfsg/src/pipelines/canu/Unitig.pm-188- print F " -gs " . getGlobal("genomeSize") . " \\\n";
##############################################
canu-2.0+dfsg/src/pipelines/canu/Unitig.pm-214-sub unitig ($) {
canu-2.0+dfsg/src/pipelines/canu/Unitig.pm:215: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Unitig.pm-216- my $path = "unitigging/4-unitigger";
##############################################
canu-2.0+dfsg/src/pipelines/canu/Unitig.pm-315-sub unitigCheck ($) {
canu-2.0+dfsg/src/pipelines/canu/Unitig.pm:316: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/Unitig.pm-317- my $attempt = getGlobal("canuIteration");
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapMhap.pm-68-sub mhapConfigure ($$$) {
canu-2.0+dfsg/src/pipelines/canu/OverlapMhap.pm:69: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapMhap.pm-70- my $tag = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapMhap.pm-463-
canu-2.0+dfsg/src/pipelines/canu/OverlapMhap.pm:464: print F "for ii in `ls ./queries/\$qry` ; do\n";
canu-2.0+dfsg/src/pipelines/canu/OverlapMhap.pm-465- print F " echo Fetch blocks/\$ii\n";
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapMhap.pm-593-sub mhapPrecomputeCheck ($$$) {
canu-2.0+dfsg/src/pipelines/canu/OverlapMhap.pm:594: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapMhap.pm-595- my $tag = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/canu/OverlapMhap.pm-685-sub mhapCheck ($$$) {
canu-2.0+dfsg/src/pipelines/canu/OverlapMhap.pm:686: my $asm = shift @_;
canu-2.0+dfsg/src/pipelines/canu/OverlapMhap.pm-687- my $tag = shift @_;
##############################################
canu-2.0+dfsg/src/pipelines/dx-canu/src/canu-job-launcher.sh-32-initialize_region() {
canu-2.0+dfsg/src/pipelines/dx-canu/src/canu-job-launcher.sh:33: region_type=`cat dnanexus-job.json | jq .region | sed s/,//g | sed s/\"//g | awk -F ":" '{print $1}'`
canu-2.0+dfsg/src/pipelines/dx-canu/src/canu-job-launcher.sh-34-
##############################################
canu-2.0+dfsg/src/pipelines/dx-canu/src/canu-job-launcher.sh-103- canuPath=`which canu`
canu-2.0+dfsg/src/pipelines/dx-canu/src/canu-job-launcher.sh:104: canuPath=`dirname $canuPath`
canu-2.0+dfsg/src/pipelines/dx-canu/src/canu-job-launcher.sh-105-
##############################################
canu-2.0+dfsg/src/pipelines/dx-canu/src/canu-job-launcher.sh-124- echo "."
canu-2.0+dfsg/src/pipelines/dx-canu/src/canu-job-launcher.sh:125: echo "Fetch '$script_name' into '`dirname $script_path`/'."
canu-2.0+dfsg/src/pipelines/dx-canu/src/canu-job-launcher.sh-126- echo "."
canu-2.0+dfsg/src/pipelines/dx-canu/src/canu-job-launcher.sh-127-
canu-2.0+dfsg/src/pipelines/dx-canu/src/canu-job-launcher.sh:128: mkdir -p `dirname $script_path/$script_name`
canu-2.0+dfsg/src/pipelines/dx-canu/src/canu-job-launcher.sh-129- cd $script_path
##############################################
canu-2.0+dfsg/src/pipelines/dx-canu/src/canu-job-launcher.sh-189- rn=${read_files_name[$ll]}
canu-2.0+dfsg/src/pipelines/dx-canu/src/canu-job-launcher.sh:190: rl=`dx-jobutil-parse-link "$rf"`
canu-2.0+dfsg/src/pipelines/dx-canu/src/canu-job-launcher.sh-191-
##############################################
canu-2.0+dfsg/src/pipelines/dx-trio/src/canu-job-launcher.sh-32-initialize_region() {
canu-2.0+dfsg/src/pipelines/dx-trio/src/canu-job-launcher.sh:33: region_type=`cat dnanexus-job.json | jq .region | sed s/,//g | sed s/\"//g | awk -F ":" '{print $1}'`
canu-2.0+dfsg/src/pipelines/dx-trio/src/canu-job-launcher.sh-34-
##############################################
canu-2.0+dfsg/src/pipelines/dx-trio/src/canu-job-launcher.sh-103- canuPath=`which canu`
canu-2.0+dfsg/src/pipelines/dx-trio/src/canu-job-launcher.sh:104: canuPath=`dirname $canuPath`
canu-2.0+dfsg/src/pipelines/dx-trio/src/canu-job-launcher.sh-105-
##############################################
canu-2.0+dfsg/src/pipelines/dx-trio/src/canu-job-launcher.sh-124- echo "."
canu-2.0+dfsg/src/pipelines/dx-trio/src/canu-job-launcher.sh:125: echo "Fetch '$script_name' into '`dirname $script_path`/'."
canu-2.0+dfsg/src/pipelines/dx-trio/src/canu-job-launcher.sh-126- echo "."
canu-2.0+dfsg/src/pipelines/dx-trio/src/canu-job-launcher.sh-127-
canu-2.0+dfsg/src/pipelines/dx-trio/src/canu-job-launcher.sh:128: mkdir -p `dirname $script_path/$script_name`
canu-2.0+dfsg/src/pipelines/dx-trio/src/canu-job-launcher.sh-129- cd $script_path
##############################################
canu-2.0+dfsg/src/pipelines/dx-trio/src/canu-job-launcher.sh-192- rn=${read_files_name[$ll]}
canu-2.0+dfsg/src/pipelines/dx-trio/src/canu-job-launcher.sh:193: rl=`dx-jobutil-parse-link "$rf"`
canu-2.0+dfsg/src/pipelines/dx-trio/src/canu-job-launcher.sh-194-
##############################################
canu-2.0+dfsg/src/pipelines/dx-trio/src/canu-job-launcher.sh-203- rn=${hapa_files_name[$ll]}
canu-2.0+dfsg/src/pipelines/dx-trio/src/canu-job-launcher.sh:204: rl=`dx-jobutil-parse-link "$rf"`
canu-2.0+dfsg/src/pipelines/dx-trio/src/canu-job-launcher.sh-205-
##############################################
canu-2.0+dfsg/src/pipelines/dx-trio/src/canu-job-launcher.sh-218- rn=${hapb_files_name[$ll]}
canu-2.0+dfsg/src/pipelines/dx-trio/src/canu-job-launcher.sh:219: rl=`dx-jobutil-parse-link "$rf"`
canu-2.0+dfsg/src/pipelines/dx-trio/src/canu-job-launcher.sh-220-
##############################################
canu-2.0+dfsg/src/pipelines/object-store-simulator.pl-230- exit(1);
canu-2.0+dfsg/src/pipelines/object-store-simulator.pl:231: #system("mkdir -p $STASH/" . dirname($path) . " 2> /dev/null");
canu-2.0+dfsg/src/pipelines/object-store-simulator.pl:232: #system("cp -fp \"$file\" \"$STASH/$path\" 2> /dev/null");
canu-2.0+dfsg/src/pipelines/object-store-simulator.pl-233- }
##############################################
canu-2.0+dfsg/src/pipelines/object-store-simulator.pl-243-
canu-2.0+dfsg/src/pipelines/object-store-simulator.pl:244: system("mkdir -p $STASH/$project:$folder 2> /dev/null");
canu-2.0+dfsg/src/pipelines/object-store-simulator.pl:245: system("cp -fp \"$file\" \"$STASH/$project:$folder/$name\" 2> /dev/null");
canu-2.0+dfsg/src/pipelines/object-store-simulator.pl-246-
##############################################
canu-2.0+dfsg/src/pipelines/object-store-simulator.pl-252-
canu-2.0+dfsg/src/pipelines/object-store-simulator.pl:253: system("mkdir -p $STASH/$project:$folder 2> /dev/null");
canu-2.0+dfsg/src/pipelines/object-store-simulator.pl:254: system("cp -fp \"$file\" \"$STASH/$project:$folder/$file\" 2> /dev/null");
canu-2.0+dfsg/src/pipelines/object-store-simulator.pl-255- }
##############################################
canu-2.0+dfsg/src/pipelines/object-store-simulator.pl-302-
canu-2.0+dfsg/src/pipelines/object-store-simulator.pl:303: system("cp -fp \"$STASH/$path\" \"$file\" 2> /dev/null");
canu-2.0+dfsg/src/pipelines/object-store-simulator.pl-304-}
##############################################
canu-2.0+dfsg/src/pipelines/parallel-ovl-store-test.sh-20-
canu-2.0+dfsg/src/pipelines/parallel-ovl-store-test.sh:21:for ii in `seq 1 $jobs` ; do
canu-2.0+dfsg/src/pipelines/parallel-ovl-store-test.sh:22: name=`printf %03d $ii`
canu-2.0+dfsg/src/pipelines/parallel-ovl-store-test.sh-23- $bin/overlapImport -G test.seqStore -o $name.ovb -random $size
##############################################
canu-2.0+dfsg/src/pipelines/parallel-ovl-store-test.sh-29-
canu-2.0+dfsg/src/pipelines/parallel-ovl-store-test.sh:30:buckets=`grep Will config.err | grep buckets | awk '{ print $9 }'`
canu-2.0+dfsg/src/pipelines/parallel-ovl-store-test.sh-31-
##############################################
canu-2.0+dfsg/src/pipelines/parallel-ovl-store-test.sh-37-
canu-2.0+dfsg/src/pipelines/parallel-ovl-store-test.sh:38:for ii in `seq 1 $jobs` ; do
canu-2.0+dfsg/src/pipelines/parallel-ovl-store-test.sh:39: name=`printf %03d $ii`
canu-2.0+dfsg/src/pipelines/parallel-ovl-store-test.sh-40- $bin/ovStoreBucketizer -G test.seqStore -O test.ovlStore -C config -i $name.ovb -job $ii
##############################################
canu-2.0+dfsg/src/pipelines/parallel-ovl-store-test.sh-48-
canu-2.0+dfsg/src/pipelines/parallel-ovl-store-test.sh:49:for ii in `seq 1 $buckets` ; do
canu-2.0+dfsg/src/pipelines/parallel-ovl-store-test.sh-50- echo ""
##############################################
canu-2.0+dfsg/src/pipelines/simple-repeat-test.pl-86-if (! -e "reads.s.fastq") {
canu-2.0+dfsg/src/pipelines/simple-repeat-test.pl:87: system("fastqSimulate -f reads.genome.fasta -o readsL -l $readLenL -x $coverageL -em 0.005 -ei 0 -ed 0 -se");
canu-2.0+dfsg/src/pipelines/simple-repeat-test.pl:88: system("fastqSimulate -f reads.genome.fasta -o readsM -l $readLenM -x $coverageM -em 0.005 -ei 0 -ed 0 -se");
canu-2.0+dfsg/src/pipelines/simple-repeat-test.pl:89: system("fastqSimulate -f reads.genome.fasta -o readsS -l $readLenS -x $coverageS -em 0.005 -ei 0 -ed 0 -se");
canu-2.0+dfsg/src/pipelines/simple-repeat-test.pl-90-}
##############################################
canu-2.0+dfsg/src/pipelines/simple-repeat-test.pl-100-
canu-2.0+dfsg/src/pipelines/simple-repeat-test.pl:101:system($canu);
canu-2.0+dfsg/src/pipelines/simple-repeat-test.pl-102-
##############################################
canu-2.0+dfsg/src/stores/ovStoreDump.C-870- fprintf(stderr, " -unaligned as unaligned regions on each read\n");
canu-2.0+dfsg/src/stores/ovStoreDump.C:871: fprintf(stderr, " -paf as miniasm Pairwise mApping Format\n");
canu-2.0+dfsg/src/stores/ovStoreDump.C-872- fprintf(stderr, " -gfa as Graphical Fragment Assembly format\n");
##############################################
canu-2.0+dfsg/src/utgcns/libpbutgcns/README.md-37- # cns: the output file name
canu-2.0+dfsg/src/utgcns/libpbutgcns/README.md:38: > tmp=/tmp cap=asm utg=utg.lst nproc=4 cns=utg_consensus.fa pbutgcns_wf.sh
canu-2.0+dfsg/src/utgcns/libpbutgcns/README.md-39-
##############################################
canu-2.0+dfsg/src/utility/kmers.H-95- //
canu-2.0+dfsg/src/utility/kmers.H:96: void addR(char base) { _mer = (((_mer << 2) & _fullMask) | (((base >> 1) & 0x03llu) ) ); };
canu-2.0+dfsg/src/utility/kmers.H-97- void addL(char base) { _mer = (((_mer >> 2) & _leftMask) | (((base >> 1) & 0x03llu) ^ 0x02llu) << _leftShift); };
##############################################
canu-2.0+dfsg/src/utility/kmers.H-228-
canu-2.0+dfsg/src/utility/kmers.H:229: _fmer.addR(_buffer[_bufferPos]); // A valid base, so push it onto
canu-2.0+dfsg/src/utility/kmers.H-230- _rmer.addL(_buffer[_bufferPos]); // the kmer.
##############################################
canu-2.0+dfsg/src/utility/kmers.H-276- } else {
canu-2.0+dfsg/src/utility/kmers.H:277: _fmer.addR(_buffer[_bufferPos]); // A valid base, so push it onto
canu-2.0+dfsg/src/utility/kmers.H-278- _rmer.addL(_buffer[_bufferPos]); // the kmer.
##############################################
canu-2.0+dfsg/src/utility/kmers.H-297- else {
canu-2.0+dfsg/src/utility/kmers.H:298: _fmer.addR(_buffer[_bufferPos]); // A valid base, so push it onto
canu-2.0+dfsg/src/utility/kmers.H-299- _rmer.addL(_buffer[_bufferPos]); // the kmer.
##############################################
canu-2.0+dfsg/src/utility/libbacktrace/dwarf.c-936-static int
canu-2.0+dfsg/src/utility/libbacktrace/dwarf.c:937:add_unit_addr (struct backtrace_state *state, uintptr_t base_address,
canu-2.0+dfsg/src/utility/libbacktrace/dwarf.c-938- struct unit_addrs addrs,
##############################################
canu-2.0+dfsg/src/utility/libbacktrace/dwarf.c-1315- a.u = u;
canu-2.0+dfsg/src/utility/libbacktrace/dwarf.c:1316: if (!add_unit_addr (state, base_address, a, error_callback, data,
canu-2.0+dfsg/src/utility/libbacktrace/dwarf.c-1317- addrs))
##############################################
canu-2.0+dfsg/src/utility/libbacktrace/dwarf.c-1456-
canu-2.0+dfsg/src/utility/libbacktrace/dwarf.c:1457: if (!add_unit_addr (state, base_address, a, error_callback, data,
canu-2.0+dfsg/src/utility/libbacktrace/dwarf.c-1458- addrs))
##############################################
canu-2.0+dfsg/src/Makefile-493-
canu-2.0+dfsg/src/Makefile:494: ifneq ($(shell echo `$(CXX) --version 2>&1 | grep -c clang`), 0)
canu-2.0+dfsg/src/Makefile:495: CPATH := $(shell echo `which $(CXX)`)
canu-2.0+dfsg/src/Makefile:496: CLANG := $(shell echo `$(CXX) --version 2>&1 | grep clang`)
canu-2.0+dfsg/src/Makefile-497- space :=
##############################################
canu-2.0+dfsg/src/Makefile-632-
canu-2.0+dfsg/src/Makefile:633:GXX_45 := $(shell expr `${CXX} -dumpversion | sed -e 's/\.\([0-9][0-9]\)/\1/g' -e 's/\.\([0-9]\)/0\1/g' -e 's/^[0-9]\{3,4\}$$/&00/'` \>= 40500)
canu-2.0+dfsg/src/Makefile-634-GXX_VV := $(shell ${CXX} -dumpversion)
##############################################
canu-2.0+dfsg/src/Makefile-636-ifeq (${GXX_VV}, 7)
canu-2.0+dfsg/src/Makefile:637:GXX_45 := $(shell expr `${CXX} -dumpfullversion | sed -e 's/\.\([0-9][0-9]\)/\1/g' -e 's/\.\([0-9]\)/0\1/g' -e 's/^[0-9]\{3,4\}$$/&00/'` \>= 40500)
canu-2.0+dfsg/src/Makefile-638-GXX_VV := $(shell ${CXX} -dumpfullversion)
##############################################
canu-2.0+dfsg/.pc/use-debian-mhap-at-runtime.patch/src/pipelines/canu/OverlapMhap.pm-68-sub mhapConfigure ($$$) {
canu-2.0+dfsg/.pc/use-debian-mhap-at-runtime.patch/src/pipelines/canu/OverlapMhap.pm:69: my $asm = shift @_;
canu-2.0+dfsg/.pc/use-debian-mhap-at-runtime.patch/src/pipelines/canu/OverlapMhap.pm-70- my $tag = shift @_;
##############################################
canu-2.0+dfsg/.pc/use-debian-mhap-at-runtime.patch/src/pipelines/canu/OverlapMhap.pm-463-
canu-2.0+dfsg/.pc/use-debian-mhap-at-runtime.patch/src/pipelines/canu/OverlapMhap.pm:464: print F "for ii in `ls ./queries/\$qry` ; do\n";
canu-2.0+dfsg/.pc/use-debian-mhap-at-runtime.patch/src/pipelines/canu/OverlapMhap.pm-465- print F " echo Fetch blocks/\$ii\n";
##############################################
canu-2.0+dfsg/.pc/use-debian-mhap-at-runtime.patch/src/pipelines/canu/OverlapMhap.pm-593-sub mhapPrecomputeCheck ($$$) {
canu-2.0+dfsg/.pc/use-debian-mhap-at-runtime.patch/src/pipelines/canu/OverlapMhap.pm:594: my $asm = shift @_;
canu-2.0+dfsg/.pc/use-debian-mhap-at-runtime.patch/src/pipelines/canu/OverlapMhap.pm-595- my $tag = shift @_;
##############################################
canu-2.0+dfsg/.pc/use-debian-mhap-at-runtime.patch/src/pipelines/canu/OverlapMhap.pm-685-sub mhapCheck ($$$) {
canu-2.0+dfsg/.pc/use-debian-mhap-at-runtime.patch/src/pipelines/canu/OverlapMhap.pm:686: my $asm = shift @_;
canu-2.0+dfsg/.pc/use-debian-mhap-at-runtime.patch/src/pipelines/canu/OverlapMhap.pm-687- my $tag = shift @_;
##############################################
canu-2.0+dfsg/.pc/external-mhap.patch/src/Makefile-493-
canu-2.0+dfsg/.pc/external-mhap.patch/src/Makefile:494: ifneq ($(shell echo `$(CXX) --version 2>&1 | grep -c clang`), 0)
canu-2.0+dfsg/.pc/external-mhap.patch/src/Makefile:495: CPATH := $(shell echo `which $(CXX)`)
canu-2.0+dfsg/.pc/external-mhap.patch/src/Makefile:496: CLANG := $(shell echo `$(CXX) --version 2>&1 | grep clang`)
canu-2.0+dfsg/.pc/external-mhap.patch/src/Makefile-497- space :=
##############################################
canu-2.0+dfsg/.pc/external-mhap.patch/src/Makefile-632-
canu-2.0+dfsg/.pc/external-mhap.patch/src/Makefile:633:GXX_45 := $(shell expr `${CXX} -dumpversion | sed -e 's/\.\([0-9][0-9]\)/\1/g' -e 's/\.\([0-9]\)/0\1/g' -e 's/^[0-9]\{3,4\}$$/&00/'` \>= 40500)
canu-2.0+dfsg/.pc/external-mhap.patch/src/Makefile-634-GXX_VV := $(shell ${CXX} -dumpversion)
##############################################
canu-2.0+dfsg/.pc/external-mhap.patch/src/Makefile-636-ifeq (${GXX_VV}, 7)
canu-2.0+dfsg/.pc/external-mhap.patch/src/Makefile:637:GXX_45 := $(shell expr `${CXX} -dumpfullversion | sed -e 's/\.\([0-9][0-9]\)/\1/g' -e 's/\.\([0-9]\)/0\1/g' -e 's/^[0-9]\{3,4\}$$/&00/'` \>= 40500)
canu-2.0+dfsg/.pc/external-mhap.patch/src/Makefile-638-GXX_VV := $(shell ${CXX} -dumpfullversion)