===========================================================
                                      .___ __  __   
          _________________  __ __  __| _/|__|/  |_ 
         / ___\_` __ \__  \ |  |  \/ __ | | \\_  __\
        / /_/  >  | \// __ \|  |  / /_/ | |  ||  |  
        \___  /|__|  (____  /____/\____ | |__||__|  
       /_____/            \/           \/           
              grep rough audit - static analysis tool
                  v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
bcftools-1.11/.appveyor.yml-39-  - "sh -lc \"git show-branch --sha1-name HEAD"
bcftools-1.11/.appveyor.yml:40:  - "sh -lc \"git clone --branch=$APPVEYOR_REPO_BRANCH https://github.com/`echo $APPVEYOR_REPO_NAME|sed 's#/bcftools#/htslib#'`.git $APPVEYOR_BUILD_FOLDER/htslib || git clone https://github.com/samtools/htslib.git $APPVEYOR_BUILD_FOLDER/htslib \""
bcftools-1.11/.appveyor.yml-41-  - "sh -lc \"cd $APPVEYOR_BUILD_FOLDER/htslib && git show-branch --sha1-name HEAD\""
##############################################
bcftools-1.11/install-sh-234-      fi
bcftools-1.11/install-sh:235:      cp_umask=`expr '(' 777 - $mode % 1000 ')' $u_plus_rw`;;
bcftools-1.11/install-sh-236-    *)
##############################################
bcftools-1.11/install-sh-281-      dstdir=$dst
bcftools-1.11/install-sh:282:      dst=$dstdir/`basename "$src"`
bcftools-1.11/install-sh-283-      dstdir_status=0
bcftools-1.11/install-sh-284-    else
bcftools-1.11/install-sh:285:      dstdir=`dirname "$dst"`
bcftools-1.11/install-sh-286-      test -d "$dstdir"
##############################################
bcftools-1.11/install-sh-337-                   # FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
bcftools-1.11/install-sh:338:                   ls_ld_tmpdir=`ls -ld "$tmpdir"`
bcftools-1.11/install-sh-339-                   case $ls_ld_tmpdir in
##############################################
bcftools-1.11/install-sh-344-                   $mkdirprog -m$different_mode -p -- "$tmpdir" && {
bcftools-1.11/install-sh:345:                     ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
bcftools-1.11/install-sh-346-                     test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
##############################################
bcftools-1.11/install-sh-402-            case $prefix in
bcftools-1.11/install-sh:403:              *\'*) qprefix=`echo "$prefix" | sed "s/'/'\\\\\\\\''/g"`;;
bcftools-1.11/install-sh-404-              *) qprefix=$prefix;;
##############################################
bcftools-1.11/install-sh-451-    if $copy_on_change &&
bcftools-1.11/install-sh:452:       old=`LC_ALL=C ls -dlL "$dst"     2>/dev/null` &&
bcftools-1.11/install-sh:453:       new=`LC_ALL=C ls -dlL "$dsttmp"  2>/dev/null` &&
bcftools-1.11/install-sh-454-       set -f &&
##############################################
bcftools-1.11/m4/hts_prog_cc_warnings.m4-141-dnl Print result, with underscores as spaces
bcftools-1.11/m4/hts_prog_cc_warnings.m4:142:ac_arg_result=`echo "$hts_cv_prog_cc_warnings" | tr '#' ' '`
bcftools-1.11/m4/hts_prog_cc_warnings.m4-143-AC_MSG_RESULT($ac_arg_result)
##############################################
bcftools-1.11/m4/hts_prog_cc_warnings.m4-148-do
bcftools-1.11/m4/hts_prog_cc_warnings.m4:149:  ac_arg_sp=`echo "$ac_arg" | tr '#' ' '`
bcftools-1.11/m4/hts_prog_cc_warnings.m4-150-  AS_CASE([" $CFLAGS "],
##############################################
bcftools-1.11/misc/plot-vcfstats-285-    $$opts{logfile} = "plot-vcfstats.log";
bcftools-1.11/misc/plot-vcfstats:286:    if ( !-d $$opts{dir} ) { `mkdir -p $$opts{dir}`; }
bcftools-1.11/misc/plot-vcfstats:287:    `> $$opts{dir}/$$opts{logfile}` unless $$opts{merge};
bcftools-1.11/misc/plot-vcfstats-288-    return $opts;
##############################################
bcftools-1.11/misc/plot-vcfstats-298-    print STDERR "Plotting graphs: $cmd\n" unless !$$opts{verbose};
bcftools-1.11/misc/plot-vcfstats:299:    system($cmd);
bcftools-1.11/misc/plot-vcfstats-300-    if ( $? ) { error("The command exited with non-zero status $?:\n\t$cmd\n\n"); }
##############################################
bcftools-1.11/misc/plot-vcfstats-2121-    print STDERR "Creating PDF: $cmd\n" unless !$$opts{verbose};
bcftools-1.11/misc/plot-vcfstats:2122:    system($cmd);
bcftools-1.11/misc/plot-vcfstats-2123-    if ( $? ) { error("The command exited with non-zero status, please consult the output of $engine: $$opts{dir}$$opts{logfile}\n\n"); }
##############################################
bcftools-1.11/misc/run-roh.pl-129-        # child
bcftools-1.11/misc/run-roh.pl:130:        exec('bash', '-o','pipefail','-c', $cmd) or error("Failed to run the command [bash -o pipefail -c $cmd]: $!");
bcftools-1.11/misc/run-roh.pl-131-    }
##############################################
bcftools-1.11/test/create-bam-test-101-
bcftools-1.11/test/create-bam-test:102:    `samtools view -b $$opts{out}.sam -o $$opts{out}.bam`;
bcftools-1.11/test/create-bam-test:103:    `samtools index $$opts{out}.bam`;
bcftools-1.11/test/create-bam-test:104:    `samtools faidx $$opts{ref} $chr:$beg-$end | sed 's,:, ,' > $$opts{out}.fa`;
bcftools-1.11/test/create-bam-test:105:    `samtools faidx $$opts{out}.fa`;
bcftools-1.11/test/create-bam-test-106-
##############################################
bcftools-1.11/test/csq/make-csq-test-172-    $$opts{refseq} = $ref;
bcftools-1.11/test/csq/make-csq-test:173:    `rm -f $$opts{out}.fai; samtools faidx $$opts{out}.fa`;
bcftools-1.11/test/csq/make-csq-test-174-}
##############################################
bcftools-1.11/test/test.pl-688-    my ($path) = @_;
bcftools-1.11/test/test.pl:689:    $path = `cygpath -m $path`;
bcftools-1.11/test/test.pl-690-    $path =~ s/\r?\n//;
##############################################
bcftools-1.11/test/test.pl-750-        # child
bcftools-1.11/test/test.pl:751:        exec('bash', '-o','pipefail','-c', $cmd) or error("Cannot execute the command [bash -o pipefail -c $cmd]: $!");
bcftools-1.11/test/test.pl-752-    }
##############################################
bcftools-1.11/test/test.pl-762-    {
bcftools-1.11/test/test.pl:763:        exec('bash', '-o','pipefail','-c', "($cmd) 2>$tmp.e >$tmp.o");
bcftools-1.11/test/test.pl-764-    }
##############################################
bcftools-1.11/test/test.pl-862-            }
bcftools-1.11/test/test.pl:863:            my @diff = `diff $$opts{path}/$args{out} $$opts{path}/$args{out}.new | head -20`;
bcftools-1.11/test/test.pl-864-            if ( @diff==20 ) { push @diff,"etc.\n"; }
##############################################
bcftools-1.11/test/test.pl-1349-    if ($^O =~ /^msys/) {
bcftools-1.11/test/test.pl:1350:        $wpath = `cygpath -w $$opts{path}`;
bcftools-1.11/test/test.pl-1351-        $wpath =~ s/\r?\n//;
##############################################
bcftools-1.11/test/test.pl-1576-
bcftools-1.11/test/test.pl:1577:                my @nsmpl = `$$opts{bin}/bcftools query -l $vcf`;
bcftools-1.11/test/test.pl-1578-                if ( !@nsmpl )
##############################################
bcftools-1.11/test/test.pl-1597-            {
bcftools-1.11/test/test.pl:1598:                chomp(my $cmd = (`cat $dirname/$dir/$file`)[0]);
bcftools-1.11/test/test.pl-1599-                $cmd =~ s/{bin}/$$opts{bin}/g;
##############################################
bcftools-1.11/.pc/tests-pluginpath.patch/test/test.pl-688-    my ($path) = @_;
bcftools-1.11/.pc/tests-pluginpath.patch/test/test.pl:689:    $path = `cygpath -m $path`;
bcftools-1.11/.pc/tests-pluginpath.patch/test/test.pl-690-    $path =~ s/\r?\n//;
##############################################
bcftools-1.11/.pc/tests-pluginpath.patch/test/test.pl-750-        # child
bcftools-1.11/.pc/tests-pluginpath.patch/test/test.pl:751:        exec('bash', '-o','pipefail','-c', $cmd) or error("Cannot execute the command [bash -o pipefail -c $cmd]: $!");
bcftools-1.11/.pc/tests-pluginpath.patch/test/test.pl-752-    }
##############################################
bcftools-1.11/.pc/tests-pluginpath.patch/test/test.pl-762-    {
bcftools-1.11/.pc/tests-pluginpath.patch/test/test.pl:763:        exec('bash', '-o','pipefail','-c', "($cmd) 2>$tmp.e >$tmp.o");
bcftools-1.11/.pc/tests-pluginpath.patch/test/test.pl-764-    }
##############################################
bcftools-1.11/.pc/tests-pluginpath.patch/test/test.pl-862-            }
bcftools-1.11/.pc/tests-pluginpath.patch/test/test.pl:863:            my @diff = `diff $$opts{path}/$args{out} $$opts{path}/$args{out}.new | head -20`;
bcftools-1.11/.pc/tests-pluginpath.patch/test/test.pl-864-            if ( @diff==20 ) { push @diff,"etc.\n"; }
##############################################
bcftools-1.11/.pc/tests-pluginpath.patch/test/test.pl-1349-    if ($^O =~ /^msys/) {
bcftools-1.11/.pc/tests-pluginpath.patch/test/test.pl:1350:        $wpath = `cygpath -w $$opts{path}`;
bcftools-1.11/.pc/tests-pluginpath.patch/test/test.pl-1351-        $wpath =~ s/\r?\n//;
##############################################
bcftools-1.11/.pc/tests-pluginpath.patch/test/test.pl-1576-
bcftools-1.11/.pc/tests-pluginpath.patch/test/test.pl:1577:                my @nsmpl = `$$opts{bin}/bcftools query -l $vcf`;
bcftools-1.11/.pc/tests-pluginpath.patch/test/test.pl-1578-                if ( !@nsmpl )
##############################################
bcftools-1.11/.pc/tests-pluginpath.patch/test/test.pl-1597-            {
bcftools-1.11/.pc/tests-pluginpath.patch/test/test.pl:1598:                chomp(my $cmd = (`cat $dirname/$dir/$file`)[0]);
bcftools-1.11/.pc/tests-pluginpath.patch/test/test.pl-1599-                $cmd =~ s/{bin}/$$opts{bin}/g;
##############################################
bcftools-1.11/.pc/skip_new_test_failing_on_32bit.patch/test/test.pl-688-    my ($path) = @_;
bcftools-1.11/.pc/skip_new_test_failing_on_32bit.patch/test/test.pl:689:    $path = `cygpath -m $path`;
bcftools-1.11/.pc/skip_new_test_failing_on_32bit.patch/test/test.pl-690-    $path =~ s/\r?\n//;
##############################################
bcftools-1.11/.pc/skip_new_test_failing_on_32bit.patch/test/test.pl-750-        # child
bcftools-1.11/.pc/skip_new_test_failing_on_32bit.patch/test/test.pl:751:        exec('bash', '-o','pipefail','-c', $cmd) or error("Cannot execute the command [bash -o pipefail -c $cmd]: $!");
bcftools-1.11/.pc/skip_new_test_failing_on_32bit.patch/test/test.pl-752-    }
##############################################
bcftools-1.11/.pc/skip_new_test_failing_on_32bit.patch/test/test.pl-762-    {
bcftools-1.11/.pc/skip_new_test_failing_on_32bit.patch/test/test.pl:763:        exec('bash', '-o','pipefail','-c', "($cmd) 2>$tmp.e >$tmp.o");
bcftools-1.11/.pc/skip_new_test_failing_on_32bit.patch/test/test.pl-764-    }
##############################################
bcftools-1.11/.pc/skip_new_test_failing_on_32bit.patch/test/test.pl-862-            }
bcftools-1.11/.pc/skip_new_test_failing_on_32bit.patch/test/test.pl:863:            my @diff = `diff $$opts{path}/$args{out} $$opts{path}/$args{out}.new | head -20`;
bcftools-1.11/.pc/skip_new_test_failing_on_32bit.patch/test/test.pl-864-            if ( @diff==20 ) { push @diff,"etc.\n"; }
##############################################
bcftools-1.11/.pc/skip_new_test_failing_on_32bit.patch/test/test.pl-1349-    if ($^O =~ /^msys/) {
bcftools-1.11/.pc/skip_new_test_failing_on_32bit.patch/test/test.pl:1350:        $wpath = `cygpath -w $$opts{path}`;
bcftools-1.11/.pc/skip_new_test_failing_on_32bit.patch/test/test.pl-1351-        $wpath =~ s/\r?\n//;
##############################################
bcftools-1.11/.pc/skip_new_test_failing_on_32bit.patch/test/test.pl-1576-
bcftools-1.11/.pc/skip_new_test_failing_on_32bit.patch/test/test.pl:1577:                my @nsmpl = `$$opts{bin}/bcftools query -l $vcf`;
bcftools-1.11/.pc/skip_new_test_failing_on_32bit.patch/test/test.pl-1578-                if ( !@nsmpl )
##############################################
bcftools-1.11/.pc/skip_new_test_failing_on_32bit.patch/test/test.pl-1597-            {
bcftools-1.11/.pc/skip_new_test_failing_on_32bit.patch/test/test.pl:1598:                chomp(my $cmd = (`cat $dirname/$dir/$file`)[0]);
bcftools-1.11/.pc/skip_new_test_failing_on_32bit.patch/test/test.pl-1599-                $cmd =~ s/{bin}/$$opts{bin}/g;