=========================================================== .___ __ __ _________________ __ __ __| _/|__|/ |_ / ___\_` __ \__ \ | | \/ __ | | \\_ __\ / /_/ > | \// __ \| | / /_/ | | || | \___ /|__| (____ /____/\____ | |__||__| /_____/ \/ \/ 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;