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         / ___\_` __ \__  \ |  |  \/ __ | | \\_  __\
        / /_/  >  | \// __ \|  |  / /_/ | |  ||  |  
        \___  /|__|  (____  /____/\____ | |__||__|  
       /_____/            \/           \/           
              grep rough audit - static analysis tool
                  v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
stacks-2.54+dfsg/tests/kmer_filter.t-3-# Preamble
stacks-2.54+dfsg/tests/kmer_filter.t:4:test_path=$(cd `dirname "${BASH_SOURCE[0]}"` && pwd)
stacks-2.54+dfsg/tests/kmer_filter.t-5-test_data_path="$test_path/"$(basename "${BASH_SOURCE[0]}" | sed -e 's@\.t$@@')
##############################################
stacks-2.54+dfsg/tests/process_radtags.t-3-# Preamble
stacks-2.54+dfsg/tests/process_radtags.t:4:test_path=$(cd `dirname "${BASH_SOURCE[0]}"` && pwd)
stacks-2.54+dfsg/tests/process_radtags.t-5-test_data_path="$test_path/"$(basename "${BASH_SOURCE[0]}" | sed -e 's@\.t$@@')
##############################################
stacks-2.54+dfsg/tests/ustacks.t-3-# Preamble
stacks-2.54+dfsg/tests/ustacks.t:4:test_path=$(cd `dirname "${BASH_SOURCE[0]}"` && pwd)
stacks-2.54+dfsg/tests/ustacks.t-5-test_data_path="$test_path/"$(basename "${BASH_SOURCE[0]}" | sed -e 's@\.t$@@')
##############################################
stacks-2.54+dfsg/tests/pstacks.t-3-# Preamble
stacks-2.54+dfsg/tests/pstacks.t:4:test_path=$(cd `dirname "${BASH_SOURCE[0]}"` && pwd)
stacks-2.54+dfsg/tests/pstacks.t-5-test_data_path="$test_path/"$(basename "${BASH_SOURCE[0]}" | sed -e 's@\.t$@@')
##############################################
stacks-2.54+dfsg/autogen.sh-2-
stacks-2.54+dfsg/autogen.sh:3:test -n "$srcdir" || srcdir=`dirname "$0"`
stacks-2.54+dfsg/autogen.sh-4-test -n "$srcdir" || srcdir=.
##############################################
stacks-2.54+dfsg/scripts/ref_map.pl-80-sub check_return_value {
stacks-2.54+dfsg/scripts/ref_map.pl:81:    # $? is a 16 bit int. Exit code is given by `$? & 255` if the process was
stacks-2.54+dfsg/scripts/ref_map.pl:82:    # terminated by a signal, and by `$? >> 8` if it exited normally.
stacks-2.54+dfsg/scripts/ref_map.pl-83-    my ($rv, $log_fh) = @_;
##############################################
stacks-2.54+dfsg/scripts/denovo_map.pl-100-sub check_return_value {
stacks-2.54+dfsg/scripts/denovo_map.pl:101:    # $? is a 16 bit int. Exit code is given by `$? & 255` if the process was
stacks-2.54+dfsg/scripts/denovo_map.pl:102:    # terminated by a signal, and by `$? >> 8` if it exited normally.
stacks-2.54+dfsg/scripts/denovo_map.pl-103-    my ($rv, $log_fh) = @_;
##############################################
stacks-2.54+dfsg/scripts/convert_stacks.pl-57-    if ($gzipped == true) {
stacks-2.54+dfsg/scripts/convert_stacks.pl:58: 	`cp $in_path/${file}.catalog.alleles.tsv.gz $out_path/.`;
stacks-2.54+dfsg/scripts/convert_stacks.pl-59-    } else {
stacks-2.54+dfsg/scripts/convert_stacks.pl:60: 	`cp $in_path/${file}.catalog.alleles.tsv $out_path/.`;
stacks-2.54+dfsg/scripts/convert_stacks.pl-61-    }
##############################################
stacks-2.54+dfsg/scripts/convert_stacks.pl-80-    if ($gzipped == true) {
stacks-2.54+dfsg/scripts/convert_stacks.pl:81: 	`cp $in_path/${file}.alleles.tsv.gz $out_path/.`;
stacks-2.54+dfsg/scripts/convert_stacks.pl-82-    } else {
stacks-2.54+dfsg/scripts/convert_stacks.pl:83: 	`cp $in_path/${file}.alleles.tsv $out_path/.`;
stacks-2.54+dfsg/scripts/convert_stacks.pl-84-    }
##############################################
stacks-2.54+dfsg/scripts/convert_stacks.pl-116-
stacks-2.54+dfsg/scripts/convert_stacks.pl:117:    `gzip -f $path` if ($gzipped);
stacks-2.54+dfsg/scripts/convert_stacks.pl-118-}
##############################################
stacks-2.54+dfsg/scripts/convert_stacks.pl-152-
stacks-2.54+dfsg/scripts/convert_stacks.pl:153:    `gzip -f $path` if ($gzipped);
stacks-2.54+dfsg/scripts/convert_stacks.pl-154-}
##############################################
stacks-2.54+dfsg/scripts/convert_stacks.pl-184-
stacks-2.54+dfsg/scripts/convert_stacks.pl:185:    `gzip -f $path` if ($gzipped);
stacks-2.54+dfsg/scripts/convert_stacks.pl-186-}
##############################################
stacks-2.54+dfsg/scripts/convert_stacks.pl-192-
stacks-2.54+dfsg/scripts/convert_stacks.pl:193:    @ls = `ls -1 $in_path/*.tags.tsv* 2> /dev/null`;
stacks-2.54+dfsg/scripts/convert_stacks.pl-194-
##############################################
stacks-2.54+dfsg/scripts/convert_stacks.pl-214-
stacks-2.54+dfsg/scripts/convert_stacks.pl:215:    @ls = `ls -1 $in_path/*.catalog.tags.tsv* 2> /dev/null`;
stacks-2.54+dfsg/scripts/convert_stacks.pl-216-
##############################################
stacks-2.54+dfsg/src/process_radtags.cc-894-    if (!in_path_1.empty()) {
stacks-2.54+dfsg/src/process_radtags.cc:895:        // In directory mode, use `$out_path/process_radtags.$(basename $in_path).log`.
stacks-2.54+dfsg/src/process_radtags.cc-896-        // For consistency we always use realpath().
##############################################
stacks-2.54+dfsg/debian/bin/stacks-13-    echo "Stacks - a pipeline for building loci from short-read sequences"
stacks-2.54+dfsg/debian/bin/stacks:14:    echo "         v"`dpkg-query -f'${Version}' -W stacks | cut -d- -f1` 'http://creskolab.uoregon.edu/stacks/'
stacks-2.54+dfsg/debian/bin/stacks-15-    echo
##############################################
stacks-2.54+dfsg/debian/rules-25-	  for f in *.pl ; do \
stacks-2.54+dfsg/debian/rules:26:	    ln -s "$$f" "`basename $$f .pl`" ; \
stacks-2.54+dfsg/debian/rules-27-	    sed -i '1s?^#!/usr/bin/env.*perl?#!/usr/bin/perl?' $$f ; \
##############################################
stacks-2.54+dfsg/debian/rules-34-	cd debian/$(DEB_SOURCE)/usr/lib/debian-med/bin && \
stacks-2.54+dfsg/debian/rules:35:	for f in `ls $(CURDIR)/debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/bin` ; do \
stacks-2.54+dfsg/debian/rules-36-	    ln -s ../../$(DEB_SOURCE)/bin/$$f ; \