===========================================================
.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
gmap-2020-11-20+ds/util/psl_splicesites.pl.in-108- $command = sprintf "$GET_GENOME %s:%u..%u",$chr,$ {$ends}[$i]+1,$ {$ends}[$i]+2;
gmap-2020-11-20+ds/util/psl_splicesites.pl.in:109: $donor_dinucl = `$command | tail -1`;
gmap-2020-11-20+ds/util/psl_splicesites.pl.in-110- chop $donor_dinucl;
##############################################
gmap-2020-11-20+ds/util/psl_splicesites.pl.in-112- $command = sprintf "$GET_GENOME %s:%u..%u",$chr,$ {$starts}[$i]-1,$ {$starts}[$i];
gmap-2020-11-20+ds/util/psl_splicesites.pl.in:113: $acceptor_dinucl = `$command | tail -1`;
gmap-2020-11-20+ds/util/psl_splicesites.pl.in-114- chop $acceptor_dinucl;
##############################################
gmap-2020-11-20+ds/util/psl_splicesites.pl.in-162- $command = sprintf "$GET_GENOME %s:%u..%u",$chr,$ {$starts}[$i],$ {$starts}[$i]-1;
gmap-2020-11-20+ds/util/psl_splicesites.pl.in:163: $donor_dinucl = `$command | tail -1`;
gmap-2020-11-20+ds/util/psl_splicesites.pl.in-164- chop $donor_dinucl;
##############################################
gmap-2020-11-20+ds/util/psl_splicesites.pl.in-166- $command = sprintf "$GET_GENOME %s:%u..%u",$chr,$ {$ends}[$i]+2,$ {$ends}[$i]+1;
gmap-2020-11-20+ds/util/psl_splicesites.pl.in:167: $acceptor_dinucl = `$command | tail -1`;
gmap-2020-11-20+ds/util/psl_splicesites.pl.in-168- chop $acceptor_dinucl;
##############################################
gmap-2020-11-20+ds/util/gmap_cat.pl.in-164-print STDERR "Running $cmd\n";
gmap-2020-11-20+ds/util/gmap_cat.pl.in:165:if (($rc = system($cmd)) != 0) {
gmap-2020-11-20+ds/util/gmap_cat.pl.in-166- die "$cmd failed with return code $rc";
##############################################
gmap-2020-11-20+ds/util/gmap_cat.pl.in-177-print STDERR "Running $cmd\n";
gmap-2020-11-20+ds/util/gmap_cat.pl.in:178:if (($rc = system($cmd)) != 0) {
gmap-2020-11-20+ds/util/gmap_cat.pl.in-179- die "$cmd failed with return code $rc";
##############################################
gmap-2020-11-20+ds/util/gmap_cat.pl.in-186-print STDERR "Running $cmd\n";
gmap-2020-11-20+ds/util/gmap_cat.pl.in:187:if (($rc = system($cmd)) != 0) {
gmap-2020-11-20+ds/util/gmap_cat.pl.in-188- die "$cmd failed with return code $rc";
##############################################
gmap-2020-11-20+ds/util/gmap_cat.pl.in-202-sub check_compiler_assumptions {
gmap-2020-11-20+ds/util/gmap_cat.pl.in:203: if (system("\"$bindir/gmapindex\" -9") != 0) {
gmap-2020-11-20+ds/util/gmap_cat.pl.in-204- print STDERR "There is a mismatch between this computer system and the one where gmapindex was compiled. Exiting.\n";
##############################################
gmap-2020-11-20+ds/util/gmap_cat.pl.in-213- print STDERR "Creating files in directory $destdir/$dbname\n";
gmap-2020-11-20+ds/util/gmap_cat.pl.in:214: system("mkdir -p \"$destdir\"");
gmap-2020-11-20+ds/util/gmap_cat.pl.in:215: system("mkdir -p \"$destdir/$dbname\"");
gmap-2020-11-20+ds/util/gmap_cat.pl.in:216: system("mkdir -p \"$destdir/$dbname/$dbname.maps\"");
gmap-2020-11-20+ds/util/gmap_cat.pl.in:217: system("chmod 755 \"$destdir/$dbname/$dbname.maps\"");
gmap-2020-11-20+ds/util/gmap_cat.pl.in-218-
##############################################
gmap-2020-11-20+ds/util/gmap_cat.pl.in-240- print STDERR "Running $cmd\n";
gmap-2020-11-20+ds/util/gmap_cat.pl.in:241: if (($rc = system($cmd)) != 0) {
gmap-2020-11-20+ds/util/gmap_cat.pl.in-242- die "$cmd failed with return code $rc";
##############################################
gmap-2020-11-20+ds/util/gmap_build.pl.in-269-
gmap-2020-11-20+ds/util/gmap_build.pl.in:270: system("rm -f \"$fasta_sources\"");
gmap-2020-11-20+ds/util/gmap_build.pl.in:271: system("rm -f \"$coordsfile\"");
gmap-2020-11-20+ds/util/gmap_build.pl.in-272-}
##############################################
gmap-2020-11-20+ds/util/gmap_build.pl.in-293-sub check_compiler_assumptions {
gmap-2020-11-20+ds/util/gmap_build.pl.in:294: if (system("\"$bindir/gmapindex\" -9") != 0) {
gmap-2020-11-20+ds/util/gmap_build.pl.in-295- print STDERR "There is a mismatch between this computer system and the one where gmapindex was compiled. Exiting.\n";
##############################################
gmap-2020-11-20+ds/util/gmap_build.pl.in-304- print STDERR "Creating files in directory $gmapdb/$genomename\n";
gmap-2020-11-20+ds/util/gmap_build.pl.in:305: system("mkdir -p \"$gmapdb\"");
gmap-2020-11-20+ds/util/gmap_build.pl.in:306: system("mkdir -p \"$gmapdb/$genomename\"");
gmap-2020-11-20+ds/util/gmap_build.pl.in:307: system("mkdir -p \"$gmapdb/$genomename/$genomename.maps\"");
gmap-2020-11-20+ds/util/gmap_build.pl.in:308: system("chmod 755 \"$gmapdb/$genomename/$genomename.maps\"");
gmap-2020-11-20+ds/util/gmap_build.pl.in-309- if (defined($transcriptomename)) {
gmap-2020-11-20+ds/util/gmap_build.pl.in:310: system("mkdir -p \"$gmapdb/$genomename/$genomename.transcripts\"");
gmap-2020-11-20+ds/util/gmap_build.pl.in:311: system("chmod 755 \"$gmapdb/$genomename/$genomename.transcripts\"");
gmap-2020-11-20+ds/util/gmap_build.pl.in-312- }
##############################################
gmap-2020-11-20+ds/util/gmap_build.pl.in-417- print STDERR "Running $cmd\n";
gmap-2020-11-20+ds/util/gmap_build.pl.in:418: ($noffsets,$npositions) = `$cmd` =~ /(\d+) (\d+)/;
gmap-2020-11-20+ds/util/gmap_build.pl.in-419- if ($npositions <= 4294967295) {
##############################################
gmap-2020-11-20+ds/util/gmap_build.pl.in-488-
gmap-2020-11-20+ds/util/gmap_build.pl.in:489: system("rm -f \"$transcript_fasta.align.iit\"");
gmap-2020-11-20+ds/util/gmap_build.pl.in:490: system("rm -f \"$transcript_fasta.gmap\"");
gmap-2020-11-20+ds/util/gmap_build.pl.in-491-
##############################################
gmap-2020-11-20+ds/util/gmap_build.pl.in-519-
gmap-2020-11-20+ds/util/gmap_build.pl.in:520: system("rm -f \"$transcript_fasta.align.iit\"");
gmap-2020-11-20+ds/util/gmap_build.pl.in:521: system("rm -f \"$transcript_fasta\"");
gmap-2020-11-20+ds/util/gmap_build.pl.in:522: # system("rm -f \"$transcript_genes\""); --Keep given input file
gmap-2020-11-20+ds/util/gmap_build.pl.in-523-
##############################################
gmap-2020-11-20+ds/util/gmap_build.pl.in-531- print STDERR "Running $cmd\n";
gmap-2020-11-20+ds/util/gmap_build.pl.in:532: if (($rc = system($cmd)) != 0) {
gmap-2020-11-20+ds/util/gmap_build.pl.in-533- die "$cmd failed with return code $rc";
##############################################
gmap-2020-11-20+ds/util/psl_introns.pl.in-109- $command = sprintf "$GET_GENOME %s:%u..%u",$chr,$ {$ends}[$i]+1,$ {$ends}[$i]+2;
gmap-2020-11-20+ds/util/psl_introns.pl.in:110: $donor_dinucl = `$command | tail -1`;
gmap-2020-11-20+ds/util/psl_introns.pl.in-111- chop $donor_dinucl;
##############################################
gmap-2020-11-20+ds/util/psl_introns.pl.in-113- $command = sprintf "$GET_GENOME %s:%u..%u",$chr,$ {$starts}[$i]-1,$ {$starts}[$i];
gmap-2020-11-20+ds/util/psl_introns.pl.in:114: $acceptor_dinucl = `$command | tail -1`;
gmap-2020-11-20+ds/util/psl_introns.pl.in-115- chop $acceptor_dinucl;
##############################################
gmap-2020-11-20+ds/util/psl_introns.pl.in-149- $command = sprintf "$GET_GENOME %s:%u..%u",$chr,$ {$starts}[$i],$ {$starts}[$i]-1;
gmap-2020-11-20+ds/util/psl_introns.pl.in:150: $donor_dinucl = `$command | tail -1`;
gmap-2020-11-20+ds/util/psl_introns.pl.in-151- chop $donor_dinucl;
##############################################
gmap-2020-11-20+ds/util/psl_introns.pl.in-153- $command = sprintf "$GET_GENOME %s:%u..%u",$chr,$ {$ends}[$i]+2,$ {$ends}[$i]+1;
gmap-2020-11-20+ds/util/psl_introns.pl.in:154: $acceptor_dinucl = `$command | tail -1`;
gmap-2020-11-20+ds/util/psl_introns.pl.in-155- chop $acceptor_dinucl;
##############################################
gmap-2020-11-20+ds/tests/defs-10- /* | [A-Za-z]:\\*) ;;
gmap-2020-11-20+ds/tests/defs:11: *) srcdir=`\cd $srcdir && pwd` ;;
gmap-2020-11-20+ds/tests/defs-12-esac
##############################################
gmap-2020-11-20+ds/tests/defs-15- /* | [A-Za-z]:\\*) ;;
gmap-2020-11-20+ds/tests/defs:16: *) top_builddir=`\cd ${top_builddir-..} && pwd` ;;
gmap-2020-11-20+ds/tests/defs-17-esac
##############################################
gmap-2020-11-20+ds/config/ax_compiler_vendor.m4-76- *:) vendor=$ventest; continue ;;
gmap-2020-11-20+ds/config/ax_compiler_vendor.m4:77: *) vencpp="defined("`echo $ventest | sed 's/,/) || defined(/g'`")" ;;
gmap-2020-11-20+ds/config/ax_compiler_vendor.m4-78- esac
##############################################
gmap-2020-11-20+ds/config/ax_compiler_vendor.m4-84- done
gmap-2020-11-20+ds/config/ax_compiler_vendor.m4:85: ax_cv_[]_AC_LANG_ABBREV[]_compiler_vendor=`echo $vendor | cut -d: -f1`
gmap-2020-11-20+ds/config/ax_compiler_vendor.m4-86- ])
##############################################
gmap-2020-11-20+ds/config/expand.m4-19- while true; do
gmap-2020-11-20+ds/config/expand.m4:20: new_full_var="`eval echo $full_var`"
gmap-2020-11-20+ds/config/expand.m4-21- if test "x$new_full_var" = "x$full_var"; then break; fi
##############################################
gmap-2020-11-20+ds/configure.ac-476- passed=0;
gmap-2020-11-20+ds/configure.ac:477: AC_CHECK_HEADER(zlib.h,passed=`expr $passed + 1`,failed=`expr $failed + 1`)
gmap-2020-11-20+ds/configure.ac:478: AC_CHECK_LIB(z,gzopen,passed=`expr $passed + 1`,failed=`expr $failed + 1`)
gmap-2020-11-20+ds/configure.ac:479: AC_CHECK_LIB(z,gzeof,passed=`expr $passed + 1`,failed=`expr $failed + 1`)
gmap-2020-11-20+ds/configure.ac:480: AC_CHECK_LIB(z,gzgetc,passed=`expr $passed + 1`,failed=`expr $failed + 1`)
gmap-2020-11-20+ds/configure.ac:481: AC_CHECK_LIB(z,gzgets,passed=`expr $passed + 1`,failed=`expr $failed + 1`)
gmap-2020-11-20+ds/configure.ac:482: AC_CHECK_LIB(z,gzclose,passed=`expr $passed + 1`,failed=`expr $failed + 1`)
gmap-2020-11-20+ds/configure.ac-483- AC_MSG_CHECKING(if zlib package is complete)
##############################################
gmap-2020-11-20+ds/configure.ac-525- passed=0;
gmap-2020-11-20+ds/configure.ac:526: AC_CHECK_HEADER(bzlib.h,passed=`expr $passed + 1`,failed=`expr $failed + 1`)
gmap-2020-11-20+ds/configure.ac:527: AC_CHECK_LIB(bz2,BZ2_bzReadOpen,passed=`expr $passed + 1`,failed=`expr $failed + 1`)
gmap-2020-11-20+ds/configure.ac:528: AC_CHECK_LIB(bz2,BZ2_bzRead,passed=`expr $passed + 1`,failed=`expr $failed + 1`)
gmap-2020-11-20+ds/configure.ac:529: AC_CHECK_LIB(bz2,BZ2_bzReadClose,passed=`expr $passed + 1`,failed=`expr $failed + 1`)
gmap-2020-11-20+ds/configure.ac-530- AC_MSG_CHECKING(if bzlib package is complete)