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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
libgenome-model-tools-music-perl-0.04/lib/Genome/Model/Tools/Music/Bmr/CalcWigCovg.pm-133- print "Reference fasta index not found. Creating one at: $ref_seq.fai\n";
libgenome-model-tools-music-perl-0.04/lib/Genome/Model/Tools/Music/Bmr/CalcWigCovg.pm:134: system( "samtools faidx $ref_seq" ) or die "Failed to run samtools! $!\n";
libgenome-model-tools-music-perl-0.04/lib/Genome/Model/Tools/Music/Bmr/CalcWigCovg.pm-135- }
##############################################
libgenome-model-tools-music-perl-0.04/lib/Genome/Model/Tools/Music/Bmr/CalcWigCovg.pm-158- my $merged_roi_bed = Genome::Sys->create_temp_file_path();
libgenome-model-tools-music-perl-0.04/lib/Genome/Model/Tools/Music/Bmr/CalcWigCovg.pm:159: system( "mergeBed -i $roi_bed | joinx sort -s - -o $merged_roi_bed" );# or die "Failed to run mergeBed or joinx!\n$roi_bed\n$merged_roi_bed\n $!\n";
libgenome-model-tools-music-perl-0.04/lib/Genome/Model/Tools/Music/Bmr/CalcWigCovg.pm-160-
##############################################
libgenome-model-tools-music-perl-0.04/lib/Genome/Model/Tools/Music/Bmr/CalcWigCovg.pm-179- # Use joinx to parse the WIG file and return per-ROI coverages of AT, CG (non-CpG), and CpG
libgenome-model-tools-music-perl-0.04/lib/Genome/Model/Tools/Music/Bmr/CalcWigCovg.pm:180: system( "joinx wig2bed -Zc $wig_file | joinx sort -s | joinx intersect -F \"I A3\" $roi_bed - | joinx ref-stats - $ref_seq | cut -f 1-7 > $roi_covg_dir/$sample.covg" );# or die "Failed to run joinx to calculate per-gene coverages in $sample! $!\n";
libgenome-model-tools-music-perl-0.04/lib/Genome/Model/Tools/Music/Bmr/CalcWigCovg.pm-181-
##############################################
libgenome-model-tools-music-perl-0.04/lib/Genome/Model/Tools/Music/Bmr/CalcWigCovg.pm-212- my $merged_roi_bed_covg = Genome::Sys->create_temp_file_path();
libgenome-model-tools-music-perl-0.04/lib/Genome/Model/Tools/Music/Bmr/CalcWigCovg.pm:213: system( "joinx wig2bed -Zc $wig_file | joinx sort -s | joinx intersect $merged_roi_bed - | joinx ref-stats - $ref_seq | cut -f 1-6 > $merged_roi_bed_covg" );# or die "Failed to run joinx to calculate overall coverages in $sample! $!\n";
libgenome-model-tools-music-perl-0.04/lib/Genome/Model/Tools/Music/Bmr/CalcWigCovg.pm-214-
##############################################
libgenome-model-tools-music-perl-0.04/lib/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm-166- my $ref_seq_idx = "$ref_seq.fai";
libgenome-model-tools-music-perl-0.04/lib/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm:167: system( "samtools faidx $ref_seq" ) unless( -e $ref_seq_idx );
libgenome-model-tools-music-perl-0.04/lib/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm-168-
##############################################
libgenome-model-tools-music-perl-0.04/lib/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm-183- # Run the calcRoiCovg command on this tumor-normal pair. This could take a while
libgenome-model-tools-music-perl-0.04/lib/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm:184: elsif( system( "$calcRoiCovg_cmd" ) != 0 )
libgenome-model-tools-music-perl-0.04/lib/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm-185- {
##############################################
libgenome-model-tools-music-perl-0.04/lib/Genome/Model/Tools/Music/Bmr/CalcCovg.pm-239- my $ref_seq_idx = "$ref_seq.fai";
libgenome-model-tools-music-perl-0.04/lib/Genome/Model/Tools/Music/Bmr/CalcCovg.pm:240: system( "samtools faidx $ref_seq" ) unless( -e $ref_seq_idx );
libgenome-model-tools-music-perl-0.04/lib/Genome/Model/Tools/Music/Bmr/CalcCovg.pm-241-
##############################################
libgenome-model-tools-music-perl-0.04/.pc/01-fixpod2man/lib/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm-165- my $ref_seq_idx = "$ref_seq.fai";
libgenome-model-tools-music-perl-0.04/.pc/01-fixpod2man/lib/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm:166: system( "samtools faidx $ref_seq" ) unless( -e $ref_seq_idx );
libgenome-model-tools-music-perl-0.04/.pc/01-fixpod2man/lib/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm-167-
##############################################
libgenome-model-tools-music-perl-0.04/.pc/01-fixpod2man/lib/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm-182- # Run the calcRoiCovg command on this tumor-normal pair. This could take a while
libgenome-model-tools-music-perl-0.04/.pc/01-fixpod2man/lib/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm:183: elsif( system( "$calcRoiCovg_cmd" ) != 0 )
libgenome-model-tools-music-perl-0.04/.pc/01-fixpod2man/lib/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm-184- {
##############################################
libgenome-model-tools-music-perl-0.04/.pc/01-fixpod2man/lib/Genome/Model/Tools/Music/Bmr/CalcCovg.pm-238- my $ref_seq_idx = "$ref_seq.fai";
libgenome-model-tools-music-perl-0.04/.pc/01-fixpod2man/lib/Genome/Model/Tools/Music/Bmr/CalcCovg.pm:239: system( "samtools faidx $ref_seq" ) unless( -e $ref_seq_idx );
libgenome-model-tools-music-perl-0.04/.pc/01-fixpod2man/lib/Genome/Model/Tools/Music/Bmr/CalcCovg.pm-240-