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/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
bio-tradis-1.4.5+dfsg2/bin/tradis_merge_plots-76- my $cmd = join(" ", ("tradis_gene_insert_sites", '-o', $outputfilename.'.csv', $path_to_annotation, $joined_plots ));
bio-tradis-1.4.5+dfsg2/bin/tradis_merge_plots:77: `bsub -M1000 -R 'select[mem>1000] rusage[mem=1000]' '$cmd'`;
bio-tradis-1.4.5+dfsg2/bin/tradis_merge_plots-78- print "Output from bsub will be in: ".$outputfilename.'.csv'."\n";
##############################################
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Map.pm-36- }
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Map.pm:37: system($cmd);
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Map.pm-38- return $cmd;
##############################################
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Map.pm-102-
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Map.pm:103: system($align);
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Map.pm-104- unlink('align.stderr');
##############################################
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RunTradis.pm-100- if ( !-e "$temporary_directory/$newfq" ) {
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RunTradis.pm:101: `gunzip -c $fq > $temporary_directory/$newfq`;
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RunTradis.pm-102- }
##############################################
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RunTradis.pm-202- my $output_directory = $self->output_directory;
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RunTradis.pm:203: system("mv $temporary_directory/$outfile* $output_directory");
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RunTradis.pm:204: system("mv $temporary_directory/mapped.sort.bam $output_directory/$outfile.mapped.bam");
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RunTradis.pm:205: system("mv $temporary_directory/mapped.sort.bam.bai $output_directory/$outfile.mapped.bam.bai");
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RunTradis.pm:206: system("mv $temporary_directory/mapped.bamcheck $output_directory/$outfile.mapped.bamcheck");
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RunTradis.pm-207-
##############################################
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RunTradis.pm-358- #my $plotname = $self->_plotname($sn);
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RunTradis.pm:359: system("gunzip -c $plotname > $temporary_directory/tmp.plot");
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RunTradis.pm-360- system(
##############################################
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RunTradis.pm-362- );
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RunTradis.pm:363: system("gzip -c rv_plot > $plotname");
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RunTradis.pm-364- }
##############################################
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RunTradis.pm-381- my $stats = "$fql[-1],";
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RunTradis.pm:382: my $total_reads = `wc $fq | awk '{print \$1/4}'`;
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RunTradis.pm-383- chomp($total_reads);
##############################################
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RunTradis.pm-388- if (defined($self->tag)) {
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RunTradis.pm:389: $matching = `wc $temporary_directory/filter.fastq | awk '{print \$1/4}' `;
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RunTradis.pm-390- chomp($matching);
##############################################
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RunTradis.pm-406- );
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RunTradis.pm:407: my $uis = `grep -c -v "0 0" $temporary_directory/tmp.plot`;
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RunTradis.pm-408- chomp($uis);
##############################################
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/FilterTags.pm-52- if ( !-e $newfq ) {
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/FilterTags.pm:53: `gunzip -c $fq > $newfq`;
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/FilterTags.pm-54- }
##############################################
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/AddTagsToSeq.pm-52- print STDERR "Reading ".uc($self->_file_extension)." header\n" if($self->verbose);
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/AddTagsToSeq.pm:53: system($self->samtools_exec." view -H $filename > $tmp_sam");
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/AddTagsToSeq.pm-54- open( TMPFILE, ">>$tmp_sam" );
##############################################
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/AddTagsToSeq.pm-131-
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/AddTagsToSeq.pm:132: system($self->samtools_exec." view -h -S ".$self->_output_switch." -o $outfile $tmp_sam");
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/AddTagsToSeq.pm-133-
##############################################
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CombinePlots.pm-71-
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CombinePlots.pm:72: my @id_order = `awk '{print \$1}' $filelist`;
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CombinePlots.pm-73- foreach my $id (@id_order) {
##############################################
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CombinePlots.pm-87-
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CombinePlots.pm:88: system("mkdir $combined_dir") unless ( -d "$combined_dir" );
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CombinePlots.pm-89- my @tabix_plot;
##############################################
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CombinePlots.pm-128- $self->_write_stats($id, $filelen);
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CombinePlots.pm:129: system("gzip -f $comb_plot_name");
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CombinePlots.pm-130- }
##############################################
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CombinePlots.pm-153-
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CombinePlots.pm:154: `cat $tabix_plot_name | gunzip - | sort -k1,1 -k2,2n | bgzip > $sorted_tabix_plot_name && tabix -b 2 -e 2 $sorted_tabix_plot_name`;
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CombinePlots.pm-155- unlink($tabix_plot_name);
##############################################
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CombinePlots.pm-185- for my $f ( @{$files} ) {
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CombinePlots.pm:186: my $wc = `wc $f | awk '{print \$1}'`;
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CombinePlots.pm-187- chomp $wc;
##############################################
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CombinePlots.pm-226-
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CombinePlots.pm:227: #my $seq_len = `wc $comb_plot | awk '{print \$1}'`;
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CombinePlots.pm-228- #chomp($seq_len);
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CombinePlots.pm:229: my $uis = `grep -c -v "0 0" $comb_plot`;
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CombinePlots.pm-230- chomp($uis);
##############################################
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CombinePlots.pm-285- my $unzip_cmd = "gunzip -c $plotname > $destination_directory/$unz";
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CombinePlots.pm:286: system($unzip_cmd);
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CombinePlots.pm-287- push(@unz_plots, "$destination_directory/$unz");
##############################################
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/AddTags.pm-37- $self->verbose($verbose) if ( defined($verbose) );
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/AddTags.pm:38: $self->samtools_exec($samtools_exec) if ( defined($samtools_exec) );
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/AddTags.pm-39-
##############################################
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/TradisBam.pm-49- $self->verbose($verbose) if ( defined($verbose) );
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/TradisBam.pm:50: $self->samtools_exec($samtools_exec) if ( defined($samtools_exec) );
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/TradisBam.pm-51-
##############################################
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/CheckTags.pm-32- $self->help($help) if ( defined($help) );
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/CheckTags.pm:33: $self->samtools_exec($samtools_exec) if ( defined($samtools_exec) );
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/CheckTags.pm-34-
##############################################
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/TradisAnalysis.pm-102- $self->verbose($verbose) if ( defined($verbose));
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/TradisAnalysis.pm:103: $self->samtools_exec($samtools_exec) if ( defined($samtools_exec) );
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/TradisAnalysis.pm-104-
##############################################
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/TradisAnalysis.pm-225- close(STATS);
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/TradisAnalysis.pm:226: system("mv $output_directory/tmp.stats $stats_filename");
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/TradisAnalysis.pm-227-}
##############################################
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Samtools.pm-26- $cmd = join( ' ', ( $self->exec, 'sort', '-@', $self->threads, '-O', 'bam', '-T', $input_file.'.tmp', '-o', $output_file, $input_file ) );
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Samtools.pm:27: system($cmd);
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Samtools.pm-28-}
##############################################
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Samtools.pm-31- my ( $self, $input_file ) = @_;
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Samtools.pm:32: system( $self->exec . " index $input_file" );
bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Samtools.pm-33-}
##############################################
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/AddTagsToSeq.t-34-ok( -e 't/data/output.bam', 'checking file existence' );
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/AddTagsToSeq.t:35:`$samtools_exec view -h -o t/data/output.sam t/data/output.bam`;
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/AddTagsToSeq.t:36:`$samtools_exec view -h -o t/data/AddTags/expected_tradis.sam t/data/AddTags/expected_tradis.bam`;
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/AddTagsToSeq.t-37-compare_ok(
##############################################
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/AddTagsToSeq.t-53-ok( -e 't/data/output.bam', 'checking file existence' );
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/AddTagsToSeq.t:54:`$samtools_exec view -h -o t/data/output.sam t/data/output.bam`;
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/AddTagsToSeq.t:55:`$samtools_exec view -h -o t/data/AddTags/sample_sm_no_tr.sam t/data/AddTags/sample_sm_no_tr.bam`;
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/AddTagsToSeq.t-56-
##############################################
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/AddTagsToSeq.t-83-ok( -e 't/data/output.cram', 'checking file existence' );
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/AddTagsToSeq.t:84:`$samtools_exec view -h -o t/data/output.sam t/data/output.cram`;
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/AddTagsToSeq.t:85:`$samtools_exec view -h -o t/data/AddTags/expected_tradis.sam t/data/AddTags/expected_tradis.cram`;
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/AddTagsToSeq.t-86-compare_ok(
##############################################
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t-64-ok( $obj->_check_filter, 'testing check filtering step' );
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t:65:system("mv $temp_directory/filter.fastq $temp_directory/filter.fastq.bak");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t-66-throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if no filtered reads';
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t:67:system("touch $temp_directory/filter.fastq");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t-68-throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if filtered reads are empty';
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t:69:system("echo foo > $temp_directory/filter.fastq");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t-70-throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if filtered reads has less than 4 lines';
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t:71:system("echo 'foo\nbar\nbaz\nquux' > $temp_directory/filter.fastq");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t-72-throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if filtered reads do not look like a fastq';
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t:73:system("echo 'foo\nbar\n+' > $temp_directory/filter.fastq");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t-74-throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if filtered reads are too short';
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t:75:system("echo 'foo\nbar\n+\nquux' > $temp_directory/filter.fastq");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t-76-ok( $obj->_check_filter, 'check very basic filtered reads validation');
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t:77:system("mv $temp_directory/filter.fastq.bak $temp_directory/filter.fastq");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t-78-
##############################################
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t-91-ok( -e "$temp_directory/mapped.sam", 'checking SAM existence' );
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t:92:`grep -v "\@PG" $temp_directory/mapped.sam > $output_directory/tmp1.sam`;
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t:93:`grep -v "\@PG" t/data/RunTradisBWA/mapped.sam > $output_directory/tmp2.sam`;
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t-94-compare_ok(
##############################################
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t-122-);
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t:123:system("gunzip -c t/data/RunTradisBWA/expected.plot.gz > $output_directory/expected.plot.unzipped");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t-124-compare_ok(
##############################################
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t-134- 'checking plot file existence - Normal files, no mismatch' );
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t:135:system("gunzip -c $output_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t:136:system("gunzip -c t/data/RunTradisBWA/expected.plot.gz > $output_directory/expected.plot.unzipped");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t-137-compare_ok(
##############################################
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t-173- 'checking plot file existence - Normal files one mismatch' );
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t:174:system("gunzip -c $output_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t-175-
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t-176-
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t:177:system("gunzip -c t/data/RunTradisBWA/expected.1mm.plot.gz > $output_directory/expected.plot.unzipped");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t-178-compare_ok(
##############################################
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t-217-
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t:218:system("gunzip -c $output_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t:219:system("gunzip -c t/data/RunTradisBWA/expected.plot.gz > $output_directory/expected.plot.unzipped");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t-220-compare_ok(
##############################################
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t-64-ok( $obj->_check_filter, 'testing check filtering step' );
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t:65:system("mv $temp_directory/filter.fastq $temp_directory/filter.fastq.bak");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t-66-throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if no filtered reads';
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t:67:system("touch $temp_directory/filter.fastq");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t-68-throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if filtered reads are empty';
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t:69:system("echo foo > $temp_directory/filter.fastq");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t-70-throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if filtered reads has less than 4 lines';
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t:71:system("echo 'foo\nbar\nbaz\nquux' > $temp_directory/filter.fastq");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t-72-throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if filtered reads do not look like a fastq';
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t:73:system("echo 'foo\nbar\n+' > $temp_directory/filter.fastq");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t-74-throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if filtered reads are too short';
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t:75:system("echo 'foo\nbar\n+\nquux' > $temp_directory/filter.fastq");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t-76-ok( $obj->_check_filter, 'check very basic filtered reads validation');
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t:77:system("mv $temp_directory/filter.fastq.bak $temp_directory/filter.fastq");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t-78-
##############################################
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t-91-ok( -e "$temp_directory/mapped.sam", 'checking SAM existence' );
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t:92:`grep -v "\@PG" $temp_directory/mapped.sam > $output_directory/tmp1.sam`;
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t:93:`grep -v "\@PG" t/data/RunTradisSmalt/mapped.sam > $output_directory/tmp2.sam`;
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t-94-compare_ok(
##############################################
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t-122-);
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t:123:system("gunzip -c t/data/RunTradisSmalt/expected.plot.gz > $output_directory/expected.plot.unzipped");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t-124-compare_ok(
##############################################
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t-134- 'checking plot file existence - Normal files, no mismatch' );
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t:135:system("gunzip -c $output_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t:136:system("gunzip -c t/data/RunTradisSmalt/expected.plot.gz > $output_directory/expected.plot.unzipped");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t-137-compare_ok(
##############################################
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t-173- 'checking plot file existence - Normal files one mismatch' );
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t:174:system("gunzip -c $output_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t-175-system(
##############################################
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t-215-
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t:216:system("gunzip -c $output_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t:217:system("gunzip -c t/data/RunTradisSmalt/expected.plot.gz > $output_directory/expected.plot.unzipped");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t-218-compare_ok(
##############################################
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisTaglessBwa.t-53-ok( -e "$temp_directory/mapped.sam", 'checking SAM existence' );
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisTaglessBwa.t:54:`grep -v "\@PG" $temp_directory/mapped.sam > $output_directory/tmp1.sam`;
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisTaglessBwa.t:55:`grep -v "\@PG" t/data/RunTradisTaglessBWA/mapped.sam > $output_directory/tmp2.sam`;
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisTaglessBwa.t-56-compare_ok(
##############################################
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisTaglessBwa.t-84-);
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisTaglessBwa.t:85:system("gunzip -c t/data/RunTradisTaglessBWA/expected.plot.gz > $output_directory/expected.plot.unzipped");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisTaglessBwa.t-86-compare_ok(
##############################################
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisTaglessBwa.t-96- 'checking plot file existence - Normal files, no mismatch' );
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisTaglessBwa.t:97:system("gunzip -c $output_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisTaglessBwa.t:98:system("gunzip -c t/data/RunTradisTaglessBWA/expected.plot.gz > $output_directory/expected.plot.unzipped");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisTaglessBwa.t-99-compare_ok(
##############################################
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisTaglessSmalt.t-53-ok( -e "$temp_directory/mapped.sam", 'checking SAM existence' );
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisTaglessSmalt.t:54:`grep -v "\@PG" $temp_directory/mapped.sam > $output_directory/tmp1.sam`;
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisTaglessSmalt.t:55:`grep -v "\@PG" t/data/RunTradisTaglessSmalt/mapped.sam > $output_directory/tmp2.sam`;
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisTaglessSmalt.t-56-compare_ok(
##############################################
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisTaglessSmalt.t-84-);
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisTaglessSmalt.t:85:system("gunzip -c t/data/RunTradisTaglessSmalt/expected.plot.gz > $output_directory/expected.plot.unzipped");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisTaglessSmalt.t-86-compare_ok(
##############################################
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisTaglessSmalt.t-96- 'checking plot file existence - Normal files, no mismatch' );
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisTaglessSmalt.t:97:system("gunzip -c $output_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisTaglessSmalt.t:98:system("gunzip -c t/data/RunTradisTaglessSmalt/expected.plot.gz > $output_directory/expected.plot.unzipped");
bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisTaglessSmalt.t-99-compare_ok(
##############################################
bio-tradis-1.4.5+dfsg2/debian/createmanpages-4-
bio-tradis-1.4.5+dfsg2/debian/createmanpages:5:VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
bio-tradis-1.4.5+dfsg2/debian/createmanpages-6-
##############################################
bio-tradis-1.4.5+dfsg2/debian/patches/samtools1.10-73-+ $cmd = join( ' ', ( $self->exec, 'sort', '-@', $self->threads, '-O', 'bam', '-T', $input_file.'.tmp', '-o', $output_file, $input_file ) );
bio-tradis-1.4.5+dfsg2/debian/patches/samtools1.10:74: system($cmd);
bio-tradis-1.4.5+dfsg2/debian/patches/samtools1.10-75- }
##############################################
bio-tradis-1.4.5+dfsg2/.pc/samtools1.10/lib/Bio/Tradis/Samtools.pm-77- }
bio-tradis-1.4.5+dfsg2/.pc/samtools1.10/lib/Bio/Tradis/Samtools.pm:78: system($cmd);
bio-tradis-1.4.5+dfsg2/.pc/samtools1.10/lib/Bio/Tradis/Samtools.pm-79-}
##############################################
bio-tradis-1.4.5+dfsg2/.pc/samtools1.10/lib/Bio/Tradis/Samtools.pm-82- my ( $self, $input_file ) = @_;
bio-tradis-1.4.5+dfsg2/.pc/samtools1.10/lib/Bio/Tradis/Samtools.pm:83: system( $self->exec . " index $input_file" );
bio-tradis-1.4.5+dfsg2/.pc/samtools1.10/lib/Bio/Tradis/Samtools.pm-84-}