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_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
bedops-2.4.39+dfsg/Makefile-70-symlink_typical:
bedops-2.4.39+dfsg/Makefile:71: $(eval SRCNAMES=`find $(BINDIR)/ -maxdepth 1 -mindepth 1 -type f -name '*$(TYPICAL)' -print0 | xargs -L1 -0 -I{} sh -c 'basename {}'`)
bedops-2.4.39+dfsg/Makefile-72- for SRCNAME in ${SRCNAMES}; do \
bedops-2.4.39+dfsg/Makefile:73: DESTNAME=`echo $$SRCNAME | sed 's/-$(TYPICAL)//'`; \
bedops-2.4.39+dfsg/Makefile-74- ln -sf $$SRCNAME $(BINDIR)/$${DESTNAME}; \
##############################################
bedops-2.4.39+dfsg/Makefile-77-symlink_megarow:
bedops-2.4.39+dfsg/Makefile:78: $(eval SRCNAMES=`find $(BINDIR)/ -maxdepth 1 -mindepth 1 -type f -name '*$(MEGAROW)' -print0 | xargs -L1 -0 -I{} sh -c 'basename {}'`)
bedops-2.4.39+dfsg/Makefile-79- for SRCNAME in ${SRCNAMES}; do \
bedops-2.4.39+dfsg/Makefile:80: DESTNAME=`echo $$SRCNAME | sed 's/-$(MEGAROW)//'`; \
bedops-2.4.39+dfsg/Makefile-81- ln -sf $$SRCNAME $(BINDIR)/$${DESTNAME}; \
##############################################
bedops-2.4.39+dfsg/Makefile-84-symlink_float128:
bedops-2.4.39+dfsg/Makefile:85: $(eval SRCNAMES=`find $(BINDIR)/ -maxdepth 1 -mindepth 1 -type f -name '*$(FLOAT128)' -print0 | xargs -L1 -0 -I{} sh -c 'basename {}'`)
bedops-2.4.39+dfsg/Makefile-86- for SRCNAME in ${SRCNAMES}; do \
bedops-2.4.39+dfsg/Makefile:87: DESTNAME=`echo $$SRCNAME | sed 's/-$(FLOAT128)//'`; \
bedops-2.4.39+dfsg/Makefile-88- ln -sf $$SRCNAME $(BINDIR)/$${DESTNAME}; \
##############################################
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_gnuParallel-39-@ clean = 0
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_gnuParallel:40:foreach argc (`seq 1 $#argv`)
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_gnuParallel-41- if ( "$argv[$argc]" == "--help" ) then
##############################################
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_gnuParallel-102- set output = $here/$output
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_gnuParallel:103:else if ( `echo $output | awk '{ print substr($0, 1, 1); }'` == "/" ) then
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_gnuParallel-104- # $output includes absolute path
##############################################
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_gnuParallel-113-
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_gnuParallel:114:@ chrom_count = (`samtools idxstats $input | awk '$1!~"^*"' | awk 'END { print NR }'`)
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_gnuParallel-115-
##############################################
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_gnuParallel-117-
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_gnuParallel:118:@ converted_file_count = `find $here/$nm -name '*.bed' | wc -l`
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_gnuParallel-119-if ( $chrom_count != $converted_file_count ) then
##############################################
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_sge-51-@ clean = 0
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_sge:52:foreach argc (`seq 1 $#argv`)
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_sge-53- if ( "$argv[$argc]" == "--help" ) then
##############################################
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_sge-114- set output = $here/$output
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_sge:115:else if ( `echo $output | awk '{ print substr($0, 1, 1); }'` == "/" ) then
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_sge-116- # $output includes absolute path
##############################################
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_sge-128-@ cntr = 0
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_sge:129:foreach chrom (`samtools idxstats $input | awk '$1!~"^*"'`)
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_sge-130- qsub $sge_opts -N $nm.$cntr > /dev/stderr << __EXTRACTION__
##############################################
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_sge-147-
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_sge:148:qsub $sge_opts -N $nm.union -hold_jid `echo $jids | tr ' ' ','` > /dev/stderr << __CATTED__
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_sge-149- bedops --everything $files > $output
##############################################
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_slurm-46-@ clean = 0
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_slurm:47:foreach argc (`seq 1 $#argv`)
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_slurm-48- if ( "$argv[$argc]" == "--help" ) then
##############################################
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_slurm-109- set output = $here/$output
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_slurm:110:else if ( `echo $output | awk '{ print substr($0, 1, 1); }'` == "/" ) then
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_slurm-111- # $output includes absolute path
##############################################
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_slurm-123-@ cntr = 0
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_slurm:124:foreach chrom (`samtools idxstats $input | awk '$1!~"^*"'`)
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_slurm:125: set res = `sbatch $slurm_opts -J "$nm.$cntr" --wrap="module add samtools; module add bedops; samtools view -b $input $chrom | bam2bed - > $here/$nm/$cntr"`
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_slurm:126: set slurm_jid = `echo $res | sed 's|^Submitted batch job ||'`
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_slurm-127- set jids = ($jids $slurm_jid)
##############################################
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_slurm-141-
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_slurm:142:set dependencies = `echo $jids | tr ' ' ':'`
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2bed_slurm-143-sbatch $slurm_opts -J $nm.union --dependency=afterok:$dependencies --wrap="module add bedops; bedops --everything $files > $output; cd $here; rm -rf $nm; if [ $clean != 0 ]; then rm -f $originput; fi;"
##############################################
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_gnuParallel-39-@ clean = 0
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_gnuParallel:40:foreach argc (`seq 1 $#argv`)
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_gnuParallel-41- if ( "$argv[$argc]" == "--help" ) then
##############################################
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_gnuParallel-102- set output = $here/$output
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_gnuParallel:103:else if ( `echo $output | awk '{ print substr($0, 1, 1); }'` == "/" ) then
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_gnuParallel-104- # $output includes absolute path
##############################################
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_gnuParallel-113-
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_gnuParallel:114:@ chrom_count = (`samtools idxstats $input | awk '$1!~"^*"' | awk 'END { print NR }'`)
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_gnuParallel-115-
##############################################
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_gnuParallel-117-
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_gnuParallel:118:@ converted_file_count = `find $here/$nm -name '*.starch' | wc -l`
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_gnuParallel-119-if ( $chrom_count != $converted_file_count ) then
##############################################
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_sge-51-@ clean = 0
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_sge:52:foreach argc (`seq 1 $#argv`)
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_sge-53- if ( "$argv[$argc]" == "--help" ) then
##############################################
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_sge-114- set output = $here/$output
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_sge:115:else if ( `echo $output | awk '{ print substr($0, 1, 1); }'` == "/" ) then
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_sge-116- # $output includes absolute path
##############################################
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_sge-128-@ cntr = 0
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_sge:129:foreach chrom (`samtools idxstats $input | awk '$1!~"^*"'`)
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_sge-130- qsub $sge_opts -N $nm.$cntr > /dev/stderr << __EXTRACTION__
##############################################
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_sge-147-
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_sge:148:qsub $sge_opts -N $nm.union -hold_jid `echo $jids | tr ' ' ','` > /dev/stderr << __CATTED__
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_sge-149- starchcat $files > $output
##############################################
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_slurm-46-@ clean = 0
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_slurm:47:foreach argc (`seq 1 $#argv`)
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_slurm-48- if ( "$argv[$argc]" == "--help" ) then
##############################################
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_slurm-109- set output = $here/$output
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_slurm:110:else if ( `echo $output | awk '{ print substr($0, 1, 1); }'` == "/" ) then
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_slurm-111- # $output includes absolute path
##############################################
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_slurm-123-@ cntr = 0
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_slurm:124:foreach chrom (`samtools idxstats $input | awk '$1!~"^*"'`)
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_slurm:125: set res = `sbatch $slurm_opts -J "$nm.$cntr" --wrap="module add samtools; module add bedops; samtools view -b $input $chrom | bam2starch - > $here/$nm/$cntr"`
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_slurm:126: set slurm_jid = `echo $res | sed 's|^Submitted batch job ||'`
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_slurm-127- set jids = ($jids $slurm_jid)
##############################################
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_slurm-141-
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_slurm:142:set dependencies = `echo $jids | tr ' ' ':'`
bedops-2.4.39+dfsg/applications/bed/conversion/src/wrappers/bam2starch_slurm-143-sbatch $slurm_opts -J $nm.union --dependency=afterok:$dependencies --wrap="module add bedops; starchcat $files > $output; cd $here; rm -rf $nm; if [ $clean != 0 ]; then rm -f $originput; fi;"
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_gnuParallel.tcsh-44-@ clean = 0
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_gnuParallel.tcsh:45:foreach argc (`seq 1 $#argv`)
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_gnuParallel.tcsh-46- if ( "$argv[$argc]" == "--help" ) then
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_gnuParallel.tcsh-101- set output = $here/$output
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_gnuParallel.tcsh:102:else if ( `echo $output | awk '{ print substr($0, 1, 1); }'` == "/" ) then
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_gnuParallel.tcsh-103- # $output includes absolute path
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_gnuParallel.tcsh-112-
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_gnuParallel.tcsh:113:@ chrom_count = `bedextract --list-chr $input | awk 'END { print NR }'`
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_gnuParallel.tcsh-114-
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_gnuParallel.tcsh-116-
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_gnuParallel.tcsh:117:@ extracted_file_count = `find $here/$nm -name '*.starch' | wc -l`
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_gnuParallel.tcsh-118-if ( $chrom_count != $extracted_file_count ) then
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_sge.tcsh-56-@ clean = 0
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_sge.tcsh:57:foreach argc (`seq 1 $#argv`)
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_sge.tcsh-58- if ( "$argv[$argc]" == "--help" ) then
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_sge.tcsh-113- set output = $here/$output
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_sge.tcsh:114:else if ( `echo $output | awk '{ print substr($0, 1, 1); }'` == "/" ) then
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_sge.tcsh-115- # $output includes absolute path
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_sge.tcsh-127-@ cntr = 0
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_sge.tcsh:128:foreach chrom (`bedextract --list-chr $input`)
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_sge.tcsh-129-
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_sge.tcsh-147-
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_sge.tcsh:148:qsub $sge_opts -N $nm.union -hold_jid `echo $jids | tr ' ' ','` > /dev/stderr << __CATTED__
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_sge.tcsh-149- starchcat $files > $output
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_slurm.tcsh-51-@ clean = 0
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_slurm.tcsh:52:foreach argc (`seq 1 $#argv`)
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_slurm.tcsh-53- if ( "$argv[$argc]" == "--help" ) then
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_slurm.tcsh-108- set output = $here/$output
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_slurm.tcsh:109:else if ( `echo $output | awk '{ print substr($0, 1, 1); }'` == "/" ) then
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_slurm.tcsh-110- # $output includes absolute path
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_slurm.tcsh-122-@ cntr = 0
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_slurm.tcsh:123:foreach chrom (`bedextract --list-chr $input`)
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_slurm.tcsh:124: set res = `sbatch $slurm_opts -J "$nm.$cntr" --wrap="module add bedops; bedextract $chrom $input | starch - > $nm/$cntr"`
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_slurm.tcsh:125: set slurm_jid = `echo $res | sed 's|^Submitted batch job ||'`
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_slurm.tcsh-126- set jids = ($jids $slurm_jid)
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_slurm.tcsh-139-
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_slurm.tcsh:140:set dependencies = `echo $jids | tr ' ' ':'`
bedops-2.4.39+dfsg/applications/bed/starch/src/starchcluster_slurm.tcsh-141-sbatch $slurm_opts -J $nm.union --dependency=afterok:$dependencies --wrap="module add bedops; starchcat $files > $output; cd $here; rm -rf $nm; if [ $clean != 0 ]; then rm -f $originput; fi;"
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/compare_disjoint_element_counts_with_merged_archive.pl-10-
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/compare_disjoint_element_counts_with_merged_archive.pl:11:my $mergedElementCount = `$unstarchBin --elements $mergedFn`; chomp $mergedElementCount;
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/compare_disjoint_element_counts_with_merged_archive.pl-12-my $disjointElementCount = 0;
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/compare_disjoint_element_counts_with_merged_archive.pl-14- # we do not assume that the disjoint archives are starch v2 (i.e. that they support --elements operator)
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/compare_disjoint_element_counts_with_merged_archive.pl:15: my $disjointFnElementCount = `$unstarchBin $disjointFn | wc -l`; chomp $disjointFnElementCount;
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/compare_disjoint_element_counts_with_merged_archive.pl-16- $disjointElementCount += $disjointFnElementCount;
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_archives_with_merged_archive.pl-16-#print STDERR "CMD -> $observedElementsCmd\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_archives_with_merged_archive.pl:17:system("$unstarchBin $mergedFn > $observedElementsFn") == 0 or die "ERROR: could not extract merged archive data\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_archives_with_merged_archive.pl-18-foreach my $disjointFn (@disjointFns) {
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_archives_with_merged_archive.pl-21- #print STDERR "CMD -> $tempDisjointCmd\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_archives_with_merged_archive.pl:22: system("$tempDisjointCmd") == 0 or die "ERROR: could not extract disjoint archive data\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_archives_with_merged_archive.pl-23-}
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_archives_with_merged_archive.pl-26-#print STDERR "CMD -> $expectedElementsCmd\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_archives_with_merged_archive.pl:27:system("sort-bed $tempDir/disjoint.*.bed > $expectedElementsFn") == 0 or die "ERROR: could not sort extracted disjoint data\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_archives_with_merged_archive.pl-28-
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_archives_with_merged_archive.pl:29:system("diff --brief $observedElementsFn $expectedElementsFn") == 0 or die "ERROR: could not diff observed and expected archive data\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_archives_with_merged_archive.pl-30-
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_by_chromosome_archives_with_merged_archive.pl-14-
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_by_chromosome_archives_with_merged_archive.pl:15:system("$unstarchBin $mergedFn > $observedElementsFn") == 0 or die "ERROR: could not extract merged archive data\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_by_chromosome_archives_with_merged_archive.pl-16-my @fns = ();
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_by_chromosome_archives_with_merged_archive.pl-18- my $tempDisjointFn = "$tempDir/disjoint.".basename($disjointFn).".bed";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_by_chromosome_archives_with_merged_archive.pl:19: system("$unstarchBin $disjointFn > $tempDisjointFn") == 0 or die "ERROR: could not extract disjoint archive data\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_by_chromosome_archives_with_merged_archive.pl-20- push @fns, $tempDisjointFn;
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_by_chromosome_archives_with_merged_archive.pl-23-my $bedToSort = join(" ", @fns);
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_by_chromosome_archives_with_merged_archive.pl:24:system("sort-bed $bedToSort > $expectedElementsFn") == 0 or die "ERROR: could not sort extracted disjoint data\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_by_chromosome_archives_with_merged_archive.pl-25-
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_by_chromosome_archives_with_merged_archive.pl:26:system("diff --brief $observedElementsFn $expectedElementsFn") == 0 or die "ERROR: could not diff observed and expected archive data\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_by_chromosome_archives_with_merged_archive.pl-27-
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_by_fixed_size_archives_with_merged_archive.pl-17-#print STDERR "CMD -> $observedCmd\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_by_fixed_size_archives_with_merged_archive.pl:18:system("$observedCmd") == 0 or die "ERROR: could not extract merged archive data\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_by_fixed_size_archives_with_merged_archive.pl-19-my @fns = ();
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_by_fixed_size_archives_with_merged_archive.pl-23- #print STDERR "CMD -> $tempDisjointCmd\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_by_fixed_size_archives_with_merged_archive.pl:24: system("$tempDisjointCmd") == 0 or die "ERROR: could not extract disjoint archive data\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_by_fixed_size_archives_with_merged_archive.pl-25- push @fns, $tempDisjointFn;
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_by_fixed_size_archives_with_merged_archive.pl-31-#print STDERR "CMD -> $expectedCmd\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_by_fixed_size_archives_with_merged_archive.pl:32:system("$expectedCmd") == 0 or die "ERROR: could not sort extracted disjoint data\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_by_fixed_size_archives_with_merged_archive.pl-33-
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_by_fixed_size_archives_with_merged_archive.pl-35-#print STDERR "CMD -> $diffCmd\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_by_fixed_size_archives_with_merged_archive.pl:36:system("$diffCmd") == 0 or die "ERROR: could not diff observed and expected archive data\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/diff_disjoint_by_fixed_size_archives_with_merged_archive.pl-37-
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives.pl-92- my $final_out_fn = "$intermediate_out_fn.starch";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives.pl:93: system ("$starch_binary --$archive_type $intermediate_out_fn > $final_out_fn") == 0 or die "could not create final starch output!\n$?\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives.pl-94- # cleanup
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives.pl:95: system ("rm $intermediate_out_fn") == 0 or die "could not delete intermediate file: $intermediate_out_fn\n$?\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives.pl-96- }
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_chromosome.pl-44- foreach my $bzip2_fn (@bzip2_fns) {
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_chromosome.pl:45: my $chr_list = `$binaries_dir/$version/bin/unstarch --list-chr $compr_extr_results_dir/$bzip2_fn`; chomp $chr_list;
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_chromosome.pl-46- my @chrs = split("\n", $chr_list);
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_chromosome.pl-50- my $cmd = "$binaries_dir/$version/bin/unstarch $chr $compr_extr_results_dir/$bzip2_fn | $binaries_dir/$version/bin/starch --bzip2 - > $result_fn";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_chromosome.pl:51: system ("$cmd") == 0 or die "could not extract $chr from $bzip2_fn\nCMD: $cmd\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_chromosome.pl-52- push (@result_fns, $result_fn);
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_chromosome.pl-55- my $fn_list = join(" ", @result_fns);
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_chromosome.pl:56: system ("$binaries_dir/$version/bin/starchcat $fn_list > $concat_results_dir/$bzip2_fn.merge_test") == 0 or die "could not merge chr's from split $bzip2_fn\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_chromosome.pl-57- }
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_chromosome.pl-60- foreach my $gzip_fn (@gzip_fns) {
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_chromosome.pl:61: my $chr_list = `$binaries_dir/$version/bin/unstarch --list-chr $compr_extr_results_dir/$gzip_fn`; chomp $chr_list;
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_chromosome.pl-62- my @chrs = split("\n", $chr_list);
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_chromosome.pl-66- my $cmd = "$binaries_dir/$version/bin/unstarch $chr $compr_extr_results_dir/$gzip_fn | $binaries_dir/$version/bin/starch --gzip - > $result_fn";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_chromosome.pl:67: system ("$cmd") == 0 or die "could not extract $chr from $gzip_fn\nCMD: $cmd\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_chromosome.pl-68- push (@result_fns, $result_fn);
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_chromosome.pl-70- my $fn_list = join(" ", @result_fns);
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_chromosome.pl:71: system ("$binaries_dir/$version/bin/starchcat $fn_list > $concat_results_dir/$gzip_fn.merge_test") == 0 or die "could not merge chr's from split $gzip_fn\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_chromosome.pl-72- }
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_fixed_size.pl-57- #print STDERR "CMD -> $cmd\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_fixed_size.pl:58: system ("$cmd") == 0 or die "could not split $bzip2_fn at boundaries [$start, $stop]\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_fixed_size.pl-59- push @out_fns, $out_fn;
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_fixed_size.pl-64- my $concat_cmd = "$binaries_dir/$version_str/bin/starchcat $out_str > $out_final_fn";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_fixed_size.pl:65: `$concat_cmd`;
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_fixed_size.pl:66: system ("mv $out_final_fn $concat_results_dir/fixed_merged_".basename($out_final_fn));
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_fixed_size.pl-67- #print STDERR "BZIP - $concat_results_dir/fixed_merged_".basename($out_final_fn)."\n";
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_fixed_size.pl-80- #print STDERR "CMD -> $cmd\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_fixed_size.pl:81: system ("$cmd") == 0 or die "could not split $gzip_fn at boundaries [$start, $stop]\n";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_fixed_size.pl-82- push @out_fns, $out_fn;
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_fixed_size.pl-86- my $concat_cmd = "$binaries_dir/$version_str/bin/starchcat $out_str > $out_final_fn";
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_fixed_size.pl:87: `$concat_cmd`;
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_fixed_size.pl:88: system ("mv $out_final_fn $concat_results_dir/fixed_merged_".basename($out_final_fn));
bedops-2.4.39+dfsg/applications/bed/starch/test/concatenation/src/split_random_inputs_into_disjoint_archives_by_fixed_size.pl-89- #print STDERR "GZIP - $concat_results_dir/fixed_merged_".basename($out_final_fn)."\n";
##############################################
bedops-2.4.39+dfsg/applications/bed/starch/test/original_data/src/make_unsorted_random_bed_file.sh-6- -e=*|--elements=*)
bedops-2.4.39+dfsg/applications/bed/starch/test/original_data/src/make_unsorted_random_bed_file.sh:7: ELEMENTS=`echo $i | sed 's/[-a-zA-Z0-9]*=//'`
bedops-2.4.39+dfsg/applications/bed/starch/test/original_data/src/make_unsorted_random_bed_file.sh-8- ;;
##############################################
bedops-2.4.39+dfsg/applications/other/switch-BEDOPS-binary-type-86-echo $BINDIR
bedops-2.4.39+dfsg/applications/other/switch-BEDOPS-binary-type:87:for SRCNAME in `find ${BINDIR} -maxdepth 1 -mindepth 1 -type f -name "*${TYPE}" -print0 | xargs -L1 -0 -I{} sh -c 'basename {}'`
bedops-2.4.39+dfsg/applications/other/switch-BEDOPS-binary-type-88-do
bedops-2.4.39+dfsg/applications/other/switch-BEDOPS-binary-type:89: DESTNAME=`echo ${SRCNAME} | perl -Tpe 's/-'${TYPE}'//'`
bedops-2.4.39+dfsg/applications/other/switch-BEDOPS-binary-type-90- ln -sf ${BINDIR}/${SRCNAME} ${BINDIR}/${DESTNAME}
##############################################
bedops-2.4.39+dfsg/docs/content/reference/file-management/sorting/sort-bed.rst-74-
bedops-2.4.39+dfsg/docs/content/reference/file-management/sorting/sort-bed.rst:75:For example, to use the current working directory to store temporary data, one could use the ``$PWD`` environment variable:
bedops-2.4.39+dfsg/docs/content/reference/file-management/sorting/sort-bed.rst-76-
##############################################
bedops-2.4.39+dfsg/docs/content/reference/set-operations/bedextract.rst-224-
bedops-2.4.39+dfsg/docs/content/reference/set-operations/bedextract.rst:225: ``$ bedextract query.bed target.bed | bedops -e 50% - target.bed``
bedops-2.4.39+dfsg/docs/content/reference/set-operations/bedextract.rst-226-
##############################################
bedops-2.4.39+dfsg/docs/content/reference/statistics/bedmap.rst-24-
bedops-2.4.39+dfsg/docs/content/reference/statistics/bedmap.rst:25: An :code:`awk` script can help with translating ID spaces to another non-whitespace delimiter, *e.g.*, :code:`bedmap (--options...) reference.bed <(awk -vOFS="\t" -vFS="\t" '{gsub(" ", "%%", $4); print;}' map.bed)` and then `awk -vOFS="\t" -vFS="\t" '{gsub("%%", " "); print;}' result.bed` to convert delimiters back to spaces.
bedops-2.4.39+dfsg/docs/content/reference/statistics/bedmap.rst-26-
##############################################
bedops-2.4.39+dfsg/docs/content/reference/statistics/bedmap.rst-292-
bedops-2.4.39+dfsg/docs/content/reference/statistics/bedmap.rst:293: An :code:`awk` script can help with translating ID spaces to another non-whitespace delimiter, *e.g.*, :code:`bedmap (--options...) reference.bed <(awk -vOFS="\t" -vFS="\t" '{gsub(" ", "%%", $4); print;}' map.bed)` and then `awk -vOFS="\t" -vFS="\t" '{gsub("%%", " "); print;}' result.bed` to convert delimiters back to spaces.
bedops-2.4.39+dfsg/docs/content/reference/statistics/bedmap.rst-294-
##############################################
bedops-2.4.39+dfsg/docs/content/reference/statistics/bedmap.rst-484-
bedops-2.4.39+dfsg/docs/content/reference/statistics/bedmap.rst:485: An :code:`awk` script can help with translating ID spaces to another non-whitespace delimiter, *e.g.*, :code:`bedmap (--options...) reference.bed <(awk -vOFS="\t" -vFS="\t" '{gsub(" ", "%%", $4); print;}' map.bed)` and then `awk -vOFS="\t" -vFS="\t" '{gsub("%%", " "); print;}' result.bed` to convert delimiters back to spaces.
bedops-2.4.39+dfsg/docs/content/reference/statistics/bedmap.rst-486-
##############################################
bedops-2.4.39+dfsg/docs/content/revision-history.rst-95-
bedops-2.4.39+dfsg/docs/content/revision-history.rst:96: * Begun work on a comprehensive test suite for BEDOPS applications. Tests are available via source distribution in :code:`${root}/tests` and can be run by entering :code:`make` in this directory.
bedops-2.4.39+dfsg/docs/content/revision-history.rst-97-
##############################################
bedops-2.4.39+dfsg/docs/content/revision-history.rst-521-
bedops-2.4.39+dfsg/docs/content/revision-history.rst:522: If the sort order of the input data is unknown or uncertain, simply use :code:`sort-bed` to generate the correct ordering and pipe the output from that to :code:`starch`, *e.g.* :code:`$ cat elements.bed | sort-bed - | starch - > elements.starch`.
bedops-2.4.39+dfsg/docs/content/revision-history.rst-523-
##############################################
bedops-2.4.39+dfsg/docs/content/usage-examples/master-list.rst-71- solns="$solns $tmpd/$iters.bed"
bedops-2.4.39+dfsg/docs/content/usage-examples/master-list.rst:72: echo "Adding `awk 'END { print NR }' $tmpd/$iters.bed` elements"
bedops-2.4.39+dfsg/docs/content/usage-examples/master-list.rst-73-
##############################################
bedops-2.4.39+dfsg/tests/starch/generate_random_intervals.sh-11-while IFS='' read -r line || [[ -n "$line" ]]; do
bedops-2.4.39+dfsg/tests/starch/generate_random_intervals.sh:12: chr=`printf "$line" | awk '{ print $1 }'`
bedops-2.4.39+dfsg/tests/starch/generate_random_intervals.sh:13: chrN=`printf "$chr" | awk '{ sub(/chr/, "", $1); print $1; }'`
bedops-2.4.39+dfsg/tests/starch/generate_random_intervals.sh:14: bound=`printf "$line" | awk '{ print $3 }'`
bedops-2.4.39+dfsg/tests/starch/generate_random_intervals.sh-15- adjustedBound=$((${bound} - ${maxLength} - 1))
bedops-2.4.39+dfsg/tests/starch/generate_random_intervals.sh:16: for sample in `seq 1 ${samples}`; do
bedops-2.4.39+dfsg/tests/starch/generate_random_intervals.sh-17- # start=$(od -N 4 -t uL -An /dev/urandom | tr -d " ") && start=$(($start % $adjustedBound))
##############################################
bedops-2.4.39+dfsg/debian/patches/2to3.patch-292- while IFS='' read -r line || [[ -n "$line" ]]; do
bedops-2.4.39+dfsg/debian/patches/2to3.patch:293: chr=`printf "$line" | awk '{ print $1 }'`
bedops-2.4.39+dfsg/debian/patches/2to3.patch-294-@@ -18,10 +18,10 @@ while IFS='' read -r line || [[ -n "$lin
##############################################
bedops-2.4.39+dfsg/.pc/2to3.patch/tests/starch/generate_random_intervals.sh-11-while IFS='' read -r line || [[ -n "$line" ]]; do
bedops-2.4.39+dfsg/.pc/2to3.patch/tests/starch/generate_random_intervals.sh:12: chr=`printf "$line" | awk '{ print $1 }'`
bedops-2.4.39+dfsg/.pc/2to3.patch/tests/starch/generate_random_intervals.sh:13: chrN=`printf "$chr" | awk '{ sub(/chr/, "", $1); print $1; }'`
bedops-2.4.39+dfsg/.pc/2to3.patch/tests/starch/generate_random_intervals.sh:14: bound=`printf "$line" | awk '{ print $3 }'`
bedops-2.4.39+dfsg/.pc/2to3.patch/tests/starch/generate_random_intervals.sh-15- adjustedBound=$((${bound} - ${maxLength} - 1))
bedops-2.4.39+dfsg/.pc/2to3.patch/tests/starch/generate_random_intervals.sh:16: for sample in `seq 1 ${samples}`; do
bedops-2.4.39+dfsg/.pc/2to3.patch/tests/starch/generate_random_intervals.sh-17- # start=$(od -N 4 -t uL -An /dev/urandom | tr -d " ") && start=$(($start % $adjustedBound))