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        / /_/  >  | \// __ \|  |  / /_/ | |  ||  |  
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              grep rough audit - static analysis tool
                  v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
nanook-1.33+dfsg/bin/nanook_get_read_stats.pl-39-print "Merging template reads\n";
nanook-1.33+dfsg/bin/nanook_get_read_stats.pl:40:system("find ${basedir}/${sample}/fasta/Template -name '*BaseCalled_Template.fasta' | xargs cat > ${basedir}/${sample}/fasta/all_Template.fasta");
nanook-1.33+dfsg/bin/nanook_get_read_stats.pl-41-print "Merging complement reads\n";
nanook-1.33+dfsg/bin/nanook_get_read_stats.pl:42:system("find ${basedir}/${sample}/fasta/Complement -name '*BaseCalled_Complement.fasta' | xargs cat > ${basedir}/${sample}/fasta/all_Complement.fasta");
nanook-1.33+dfsg/bin/nanook_get_read_stats.pl-43-print "Merging 2D reads\n";
nanook-1.33+dfsg/bin/nanook_get_read_stats.pl:44:system("find ${basedir}/${sample}/fasta/2D -name '*BaseCalled_2D.fasta' | xargs cat > ${basedir}/${sample}/fasta/all_2D.fasta");
nanook-1.33+dfsg/bin/nanook_get_read_stats.pl-45-
nanook-1.33+dfsg/bin/nanook_get_read_stats.pl-46-print "Generating stats for template reads\n";
nanook-1.33+dfsg/bin/nanook_get_read_stats.pl:47:system("get_contig_stats.pl -i ${basedir}/${sample}/fasta/all_Template.fasta -a -g ${basedir}/${sample}/analysis/all_Template_fasta_hist.txt -r ${basedir}/${sample}/analysis/all_Template_lengths.txt -l 500,1000,1500,2000,2500,3000,3500,4000,4500,5000 > ${basedir}/${sample}/analysis/all_Template_stats.txt");
nanook-1.33+dfsg/bin/nanook_get_read_stats.pl-48-print "Generating stats for complement reads\n";
nanook-1.33+dfsg/bin/nanook_get_read_stats.pl:49:system("get_contig_stats.pl -i ${basedir}/${sample}/fasta/all_Complement.fasta -a -g ${basedir}/${sample}/analysis/all_Complement_fasta_hist.txt -r ${basedir}/${sample}/analysis/all_Complement_lengths.txt -l 500,1000,1500,2000,2500,3000,3500,4000,4500,5000 > ${basedir}/${sample}/analysis/all_Complement_stats.txt");
nanook-1.33+dfsg/bin/nanook_get_read_stats.pl-50-print "Generating stats for 2D reads\n";
nanook-1.33+dfsg/bin/nanook_get_read_stats.pl:51:system("get_contig_stats.pl -i ${basedir}/${sample}/fasta/all_2D.fasta -a -g ${basedir}/${sample}/analysis/all_2D_fasta_hist.txt -r ${basedir}/${sample}/analysis/all_2D_lengths.txt -l 500,1000,1500,2000,2500,3000,3500,4000,4500,5000 > ${basedir}/${sample}/analysis/all_2D_stats.txt");
nanook-1.33+dfsg/bin/nanook_get_read_stats.pl-52-
nanook-1.33+dfsg/bin/nanook_get_read_stats.pl:53:system("echo \"\" >> ${basedir}/${sample}/summary.txt");
nanook-1.33+dfsg/bin/nanook_get_read_stats.pl:54:system("cat ${basedir}/${sample}/all_Template_stats.txt | grep 'Headings:' | sed 's/Headings:/  ReadType/' >> ${basedir}/${sample}/summary.txt");
nanook-1.33+dfsg/bin/nanook_get_read_stats.pl:55:system("cat ${basedir}/${sample}/all_Template_stats.txt | grep 'AllFields:' | sed 's/AllFields:/  Template/' >> ${basedir}/${sample}/summary.txt");
nanook-1.33+dfsg/bin/nanook_get_read_stats.pl:56:system("cat ${basedir}/${sample}/all_Complement_stats.txt | grep 'AllFields:' | sed 's/AllFields:/Complement/' >> ${basedir}/${sample}/summary.txt");
nanook-1.33+dfsg/bin/nanook_get_read_stats.pl:57:system("cat ${basedir}/${sample}/all_2D_stats.txt | grep 'AllFields:' | sed 's/AllFields:/        2D/' >> ${basedir}/${sample}/summary.txt");
nanook-1.33+dfsg/bin/nanook_get_read_stats.pl-58-
##############################################
nanook-1.33+dfsg/bin/nanook_get_tracking.pl-86-        my $pathname = "${input_dir}/${file}";
nanook-1.33+dfsg/bin/nanook_get_tracking.pl:87:        my @dump = `h5dump -a /Analyses/Basecall_2D_000/BaseCalled_template/Events/start_time ${pathname}`;
nanook-1.33+dfsg/bin/nanook_get_tracking.pl-88-        for (my $i=0; $i<@dump; $i++) {
##############################################
nanook-1.33+dfsg/bin/nanook_get_tracking.pl-93-        
nanook-1.33+dfsg/bin/nanook_get_tracking.pl:94:        #@dump = `h5dump -a /Analyses/Basecall_2D_000/BaseCalled_complement/Events/start_time ${pathname}`;
nanook-1.33+dfsg/bin/nanook_get_tracking.pl-95-        #for (my $i=0; $i<@dump; $i++) {