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/ /_/ > | \// __ \| | / /_/ | | || |
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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
rtax-0.984/greengenes/prepare-greengenes-16-then
rtax-0.984/greengenes/prepare-greengenes:17: echo "Usage: `basename $0` (in a directory containing greengenes16SrRNAgenes.txt.gz)"
rtax-0.984/greengenes/prepare-greengenes-18- exit 1
##############################################
rtax-0.984/scripts/rtaxSearch.pl-494- my $dir = tempdir(CLEANUP => 1);
rtax-0.984/scripts/rtaxSearch.pl:495: if ( system( 'mknod', "$dir/a", 'p' ) && system( 'mkfifo', "$dir/a" ) ) { die "mk{nod,fifo} $dir/a failed"; }
rtax-0.984/scripts/rtaxSearch.pl-496- if ( !fork() ) {
##############################################
rtax-0.984/scripts/rtaxSearch.pl-649- my $dir = tempdir(CLEANUP => 1);
rtax-0.984/scripts/rtaxSearch.pl:650: if ( system( 'mknod', "$dir/a", 'p' ) && system( 'mkfifo', "$dir/a" ) ) { die "mk{nod,fifo} $dir/a failed"; }
rtax-0.984/scripts/rtaxSearch.pl:651: if ( system( 'mknod', "$dir/b", 'p' ) && system( 'mkfifo', "$dir/b" ) ) { die "mk{nod,fifo} $dir/b failed"; }
rtax-0.984/scripts/rtaxSearch.pl-652-
##############################################
rtax-0.984/scripts/splitDelimitedFasta.pl-9-
rtax-0.984/scripts/splitDelimitedFasta.pl:10:my $infilename = `basename $infile`;
rtax-0.984/scripts/splitDelimitedFasta.pl-11-chomp $infilename;
##############################################
rtax-0.984/.pc/fix-bash-syntax-error.patch/greengenes/prepare-greengenes-16-then
rtax-0.984/.pc/fix-bash-syntax-error.patch/greengenes/prepare-greengenes:17: echo "Usage: `basename $0` (in a directory containing greengenes16SrRNAgenes.txt.gz)"
rtax-0.984/.pc/fix-bash-syntax-error.patch/greengenes/prepare-greengenes-18- exit 1
##############################################
rtax-0.984/.pc/find_script_path.patch/rtax-173-h) printHelpAndExit 0;;
rtax-0.984/.pc/find_script_path.patch/rtax:174:r) refdb=`abspath "$OPTARG"`;;
rtax-0.984/.pc/find_script_path.patch/rtax:175:t) taxonomy=`abspath "$OPTARG"`;;
rtax-0.984/.pc/find_script_path.patch/rtax:176:a) queryA=`abspath "$OPTARG"`;;
rtax-0.984/.pc/find_script_path.patch/rtax:177:b) queryB=`abspath "$OPTARG"`;;
rtax-0.984/.pc/find_script_path.patch/rtax-178-x) revcompA="--revcompA";;
##############################################
rtax-0.984/.pc/find_script_path.patch/rtax-181-i) idRegex="$OPTARG";;
rtax-0.984/.pc/find_script_path.patch/rtax:182:l) idList=`abspath "$OPTARG"`;;
rtax-0.984/.pc/find_script_path.patch/rtax:183:o) outpath=`abspath "$OPTARG"`;;
rtax-0.984/.pc/find_script_path.patch/rtax:184:m) tempdir=`abspath "$OPTARG"`;;
rtax-0.984/.pc/find_script_path.patch/rtax-185-v) verbose="0";;
##############################################
rtax-0.984/.pc/find_script_path.patch/rtax-255- $scripts/splitDelimitedFasta.pl $delimiter $queryA
rtax-0.984/.pc/find_script_path.patch/rtax:256: queryAa=`basename $queryA`.a
rtax-0.984/.pc/find_script_path.patch/rtax:257: queryAb=`basename $queryA`.b
rtax-0.984/.pc/find_script_path.patch/rtax-258- $scripts/rtaxSearch.pl --database $refdb --queryA $queryAa --queryB $queryAb $idList $revcompA $revcompB --usearch $usearch --idRegex "$idRegex" $fallback $noGenericFallback > rawhits
##############################################
rtax-0.984/.pc/fix.perl.path.patch/scripts/rtaxSearch.pl-494- my $dir = tempdir(CLEANUP => 1);
rtax-0.984/.pc/fix.perl.path.patch/scripts/rtaxSearch.pl:495: if ( system( 'mknod', "$dir/a", 'p' ) && system( 'mkfifo', "$dir/a" ) ) { die "mk{nod,fifo} $dir/a failed"; }
rtax-0.984/.pc/fix.perl.path.patch/scripts/rtaxSearch.pl-496- if ( !fork() ) {
##############################################
rtax-0.984/.pc/fix.perl.path.patch/scripts/rtaxSearch.pl-649- my $dir = tempdir(CLEANUP => 1);
rtax-0.984/.pc/fix.perl.path.patch/scripts/rtaxSearch.pl:650: if ( system( 'mknod', "$dir/a", 'p' ) && system( 'mkfifo', "$dir/a" ) ) { die "mk{nod,fifo} $dir/a failed"; }
rtax-0.984/.pc/fix.perl.path.patch/scripts/rtaxSearch.pl:651: if ( system( 'mknod', "$dir/b", 'p' ) && system( 'mkfifo', "$dir/b" ) ) { die "mk{nod,fifo} $dir/b failed"; }
rtax-0.984/.pc/fix.perl.path.patch/scripts/rtaxSearch.pl-652-
##############################################
rtax-0.984/.pc/fix.perl.path.patch/scripts/splitDelimitedFasta.pl-9-
rtax-0.984/.pc/fix.perl.path.patch/scripts/splitDelimitedFasta.pl:10:my $infilename = `basename $infile`;
rtax-0.984/.pc/fix.perl.path.patch/scripts/splitDelimitedFasta.pl-11-chomp $infilename;
##############################################
rtax-0.984/rtax-165-h) printHelpAndExit 0;;
rtax-0.984/rtax:166:r) refdb=`abspath "$OPTARG"`;;
rtax-0.984/rtax:167:t) taxonomy=`abspath "$OPTARG"`;;
rtax-0.984/rtax:168:a) queryA=`abspath "$OPTARG"`;;
rtax-0.984/rtax:169:b) queryB=`abspath "$OPTARG"`;;
rtax-0.984/rtax-170-x) revcompA="--revcompA";;
##############################################
rtax-0.984/rtax-173-i) idRegex="$OPTARG";;
rtax-0.984/rtax:174:l) idList=`abspath "$OPTARG"`;;
rtax-0.984/rtax:175:o) outpath=`abspath "$OPTARG"`;;
rtax-0.984/rtax:176:m) tempdir=`abspath "$OPTARG"`;;
rtax-0.984/rtax-177-v) verbose="0";;
##############################################
rtax-0.984/rtax-247- $scripts/splitDelimitedFasta.pl $delimiter $queryA
rtax-0.984/rtax:248: queryAa=`basename $queryA`.a
rtax-0.984/rtax:249: queryAb=`basename $queryA`.b
rtax-0.984/rtax-250- $scripts/rtaxSearch.pl --database $refdb --queryA $queryAa --queryB $queryAb $idList $revcompA $revcompB --usearch $usearch --idRegex "$idRegex" $fallback $noGenericFallback > rawhits