===========================================================
.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
vcftools-0.1.16/README.md-58-A manual page is also available. If prefix is set to `/usr` or if `MANPATH` points to
vcftools-0.1.16/README.md:59:`$prefix/share/man`, you can access the manual page via:
vcftools-0.1.16/README.md-60-
##############################################
vcftools-0.1.16/build-aux/git-version-gen-140-then
vcftools-0.1.16/build-aux/git-version-gen:141: v=`cat $tarball_version_file` || v=
vcftools-0.1.16/build-aux/git-version-gen-142- case $v in
##############################################
vcftools-0.1.16/build-aux/git-version-gen-159- || git describe --abbrev=4 HEAD 2>/dev/null` \
vcftools-0.1.16/build-aux/git-version-gen:160: && v=`printf '%s\n' "$v" | sed "$tag_sed_script"` \
vcftools-0.1.16/build-aux/git-version-gen-161- && case $v in
##############################################
vcftools-0.1.16/build-aux/git-version-gen-176- # of git describe.
vcftools-0.1.16/build-aux/git-version-gen:177: vtag=`echo "$v" | sed 's/-.*//'`
vcftools-0.1.16/build-aux/git-version-gen:178: commit_list=`git rev-list "$vtag"..HEAD 2>/dev/null` \
vcftools-0.1.16/build-aux/git-version-gen-179- || { commit_list=failed;
vcftools-0.1.16/build-aux/git-version-gen-180- echo "$0: WARNING: git rev-list failed" 1>&2; }
vcftools-0.1.16/build-aux/git-version-gen:181: numcommits=`echo "$commit_list" | wc -l`
vcftools-0.1.16/build-aux/git-version-gen:182: v=`echo "$v" | sed "s/\(.*\)-\(.*\)/\1-$numcommits-\2/"`;
vcftools-0.1.16/build-aux/git-version-gen-183- test "$commit_list" = failed && v=UNKNOWN
##############################################
vcftools-0.1.16/build-aux/git-version-gen-188- # Remove the "g" in git describe's output string, to save a byte.
vcftools-0.1.16/build-aux/git-version-gen:189: v=`echo "$v" | sed 's/-/./;s/\(.*\)-g/\1-/'`;
vcftools-0.1.16/build-aux/git-version-gen-190- v_from_git=1
##############################################
vcftools-0.1.16/build-aux/git-version-gen-196-
vcftools-0.1.16/build-aux/git-version-gen:197:v=`echo "$v" |sed "s/^$prefix//"`
vcftools-0.1.16/build-aux/git-version-gen-198-
##############################################
vcftools-0.1.16/src/cpp/knetfile.c-167- struct in_addr addr;
vcftools-0.1.16/src/cpp/knetfile.c:168: addr.s_addr = inet_addr(host);
vcftools-0.1.16/src/cpp/knetfile.c:169: hp = gethostbyaddr((char*)&addr, 4, AF_INET);
vcftools-0.1.16/src/cpp/knetfile.c-170- }
##############################################
vcftools-0.1.16/src/perl/FaSlice.pm-61- my ($self,$cmd) = @_;
vcftools-0.1.16/src/perl/FaSlice.pm:62: my @out = `$cmd`;
vcftools-0.1.16/src/perl/FaSlice.pm-63- if ( $? )
##############################################
vcftools-0.1.16/src/perl/Vcf.pm-2669- if ( !$$self{file} ) { $self->throw(qq[The parameter "file" not set.\n]); }
vcftools-0.1.16/src/perl/Vcf.pm:2670: my (@out) = `tabix -l '$$self{file}'`;
vcftools-0.1.16/src/perl/Vcf.pm-2671- if ( $? )
##############################################
vcftools-0.1.16/src/perl/VcfStats.pm-605- elsif ( $prefix=~m{([^/]+)/?$} ) { $dir=$1; $prefix=$dir.'/'.$1; }
vcftools-0.1.16/src/perl/VcfStats.pm:606: if ( $dir ) { `mkdir -p $dir`; }
vcftools-0.1.16/src/perl/VcfStats.pm-607- }
##############################################
vcftools-0.1.16/src/perl/fill-aa-48- " ls human_ancestor_*.fa.bz2 | while read IN; do\n",
vcftools-0.1.16/src/perl/fill-aa:49: " OUT=`echo \$IN | sed 's,bz2\$,gz,'`\n",
vcftools-0.1.16/src/perl/fill-aa:50: " CHR=`echo \$IN | sed 's,human_ancestor_,, ; s,.fa.bz2,,'`\n",
vcftools-0.1.16/src/perl/fill-aa-51- " bzcat \$IN | sed \"s,^>.*,>\$CHR,\" | gzip -c > \$OUT\n",
##############################################
vcftools-0.1.16/src/perl/fill-ref-md5-188- # List chromosomes
vcftools-0.1.16/src/perl/fill-ref-md5:189: my @chroms = `tabix -l $$opts{file}`;
vcftools-0.1.16/src/perl/fill-ref-md5-190- if ( $? ) { error("The command failed: tabix -l $$opts{file}\n"); }
##############################################
vcftools-0.1.16/src/perl/fill-ref-md5-201-
vcftools-0.1.16/src/perl/fill-ref-md5:202: `tabix -r $$opts{outfile}.header $$opts{file} > $$opts{outfile}`;
vcftools-0.1.16/src/perl/fill-ref-md5-203-}
##############################################
vcftools-0.1.16/src/perl/vcf-compare-479- print
vcftools-0.1.16/src/perl/vcf-compare:480: "#INFO/".$infoTag." Number of matching and mismatching genotypes vs INFO/". $infoTag. (exists($$opts{INFOgroupIdx}{$infoTag}) ? "[".$$opts{INFOgroupIdx}{$infoTag}."]" : ""). ". Use `^INFO/".$infoTag." | cut -f 2-` to extract this part.\n",
vcftools-0.1.16/src/perl/vcf-compare-481- "#INFO/".$infoTag." The columns are:\n",
##############################################
vcftools-0.1.16/src/perl/vcf-compare-664- elsif ( $prefix=~m{([^/]+)/?$} ) { $dir=$1; $prefix=$dir.'/'.$1; }
vcftools-0.1.16/src/perl/vcf-compare:665: if ( $dir ) { `mkdir -p $dir`; }
vcftools-0.1.16/src/perl/vcf-compare-666- }
##############################################
vcftools-0.1.16/src/perl/vcf-compare-690- my ($file) = @_;
vcftools-0.1.16/src/perl/vcf-compare:691: system("GDFONTPATH=/usr/share/fonts/truetype/ttf-dejavu/ gnuplot $file");
vcftools-0.1.16/src/perl/vcf-compare-692-}
##############################################
vcftools-0.1.16/src/perl/vcf-isec-109- elsif ( $prefix=~m{([^/]+)/?$} ) { $dir=$1; $prefix=$dir.'/'.$1; }
vcftools-0.1.16/src/perl/vcf-isec:110: if ( $dir ) { `mkdir -p $dir`; }
vcftools-0.1.16/src/perl/vcf-isec-111- }
##############################################
vcftools-0.1.16/src/perl/vcf-isec-671- if ( !$$self{file} ) { $self->throw(qq[The parameter "file" not set.\n]); }
vcftools-0.1.16/src/perl/vcf-isec:672: my (@out) = `tabix -l $$self{file}`;
vcftools-0.1.16/src/perl/vcf-isec-673- if ( $? )
##############################################
vcftools-0.1.16/src/perl/vcf-phased-join-289- {
vcftools-0.1.16/src/perl/vcf-phased-join:290: my @chroms = `tabix -l $vcf`;
vcftools-0.1.16/src/perl/vcf-phased-join-291- if ( $? )
##############################################
vcftools-0.1.16/src/perl/vcf-phased-join-418- {
vcftools-0.1.16/src/perl/vcf-phased-join:419: error("ERROR\tThe lines out of sync: $$rec1[0]:$$rec1[1] in (1) vs $$rec2[0]:$$rec2[1] in (2), where (1)=$$opts{file1} (2)=$$opts{file2}\n");
vcftools-0.1.16/src/perl/vcf-phased-join-420- }
##############################################
vcftools-0.1.16/src/perl/vcf-phased-join-466- {
vcftools-0.1.16/src/perl/vcf-phased-join:467: log_msg($opts,"WARNING\tThe lines out of sync: $$rec1[0]:$$rec1[1] in (1) vs $$rec2[0]:$$rec2[1] in (2), where (1)=$$opts{file1} (2)=$$opts{file2}\n");
vcftools-0.1.16/src/perl/vcf-phased-join-468- return 1;
##############################################
vcftools-0.1.16/src/perl/test.t-64- $cmd = "cat $file | bgzip -c > $file.gz";
vcftools-0.1.16/src/perl/test.t:65: system($cmd);
vcftools-0.1.16/src/perl/test.t-66- is($?,0,"Is bgzip OK? .. $cmd");
##############################################
vcftools-0.1.16/src/perl/test.t-68- $cmd = "tabix $file.gz";
vcftools-0.1.16/src/perl/test.t:69: system($cmd);
vcftools-0.1.16/src/perl/test.t-70- is($?,0,"Is tabix OK? .. $cmd");
##############################################
vcftools-0.1.16/src/perl/test.t-77- my $cmd = "perl -I$path -MVcf -e validate $fname";
vcftools-0.1.16/src/perl/test.t:78: my @out = `$cmd 2>&1`;
vcftools-0.1.16/src/perl/test.t-79- my @exp = ();
##############################################
vcftools-0.1.16/src/perl/test.t-159- my $cmd = "perl -I$path -MVcf $path/vcf-stats $file";
vcftools-0.1.16/src/perl/test.t:160: my @out = `$cmd 2>&1`;
vcftools-0.1.16/src/perl/test.t-161- open(my $fh,'<',"$file.stats") or confess("$file.stats: $!");
##############################################
vcftools-0.1.16/src/perl/test.t-216- {
vcftools-0.1.16/src/perl/test.t:217: `cat $file | bgzip -c > $file.gz`;
vcftools-0.1.16/src/perl/test.t:218: `tabix -p vcf -f $file.gz`;
vcftools-0.1.16/src/perl/test.t-219- }
##############################################
vcftools-0.1.16/src/perl/test.t-221- my $cmd = "perl -I../perl/ -MVcf ../perl/vcf-compare -g $a.gz $b.gz | grep -v '^# The command'";
vcftools-0.1.16/src/perl/test.t:222: my @out = `$cmd 2>&1`;
vcftools-0.1.16/src/perl/test.t-223- open(my $fh,'<',"$expected") or confess("$expected: $!");
##############################################
vcftools-0.1.16/src/perl/test.t-242- {
vcftools-0.1.16/src/perl/test.t:243: `cat $file | bgzip -c > $file.gz; tabix -f -p vcf $file.gz`;
vcftools-0.1.16/src/perl/test.t-244- $cmd .= " $file.gz";
vcftools-0.1.16/src/perl/test.t-245- }
vcftools-0.1.16/src/perl/test.t:246: my @out = `$cmd 2>/dev/null | grep -v ^##source`;
vcftools-0.1.16/src/perl/test.t-247- open(my $fh,'<',$expected) or confess("$expected: $!");
##############################################
vcftools-0.1.16/src/perl/test.t-265- {
vcftools-0.1.16/src/perl/test.t:266: `cat $file | bgzip -c > $file.gz; tabix -f -p vcf $file.gz`;
vcftools-0.1.16/src/perl/test.t-267- $cmd .= " $file.gz";
vcftools-0.1.16/src/perl/test.t-268- }
vcftools-0.1.16/src/perl/test.t:269: my @out = `$cmd 2>&1 | grep -v ^##source`;
vcftools-0.1.16/src/perl/test.t-270- open(my $fh,'<',$expected) or confess("$expected: $!");
##############################################
vcftools-0.1.16/src/perl/test.t-287- my $cmd = "perl -I../perl/ -MVcf ../perl/vcf-query -f '$query' $file";
vcftools-0.1.16/src/perl/test.t:288: my @out = `$cmd 2>&1`;
vcftools-0.1.16/src/perl/test.t-289- open(my $fh,'<',$expected) or confess("$expected: $!");
##############################################
vcftools-0.1.16/src/perl/test.t-306- my $cmd = "perl -I../perl/ -MVcf ../perl/vcf-shuffle-cols -t $template $file";
vcftools-0.1.16/src/perl/test.t:307: my @out = `$cmd 2>&1`;
vcftools-0.1.16/src/perl/test.t-308- open(my $fh,'<',$template) or confess("$template: $!");
##############################################
vcftools-0.1.16/src/perl/test.t-326- {
vcftools-0.1.16/src/perl/test.t:327: `cat $file | bgzip -c > $file.gz`;
vcftools-0.1.16/src/perl/test.t:328: `tabix -p vcf -f $file.gz`;
vcftools-0.1.16/src/perl/test.t-329- $cmd .= " $file.gz";
##############################################
vcftools-0.1.16/src/perl/test.t-331-
vcftools-0.1.16/src/perl/test.t:332: my @out = `$cmd 2>&1`;
vcftools-0.1.16/src/perl/test.t-333- open(my $fh,'<',$out) or confess("$out: $!");
##############################################
vcftools-0.1.16/src/perl/test.t-353- {
vcftools-0.1.16/src/perl/test.t:354: `cat $annot | bgzip -c > $annot.gz`;
vcftools-0.1.16/src/perl/test.t:355: `tabix -s 3 -b 1 -e 2 -f $annot.gz`;
vcftools-0.1.16/src/perl/test.t-356- $cmd .= " -a $annot.gz";
##############################################
vcftools-0.1.16/src/perl/test.t-358-
vcftools-0.1.16/src/perl/test.t:359: my @out = `$cmd 2>&1 | grep -v ^##source`;
vcftools-0.1.16/src/perl/test.t-360- open(my $fh,'<',$out) or confess("$out: $!");
##############################################
vcftools-0.1.16/src/perl/test.t-376- my $cmd = "perl -I../perl/ -MVcf ../perl/fill-an-ac $vcf";
vcftools-0.1.16/src/perl/test.t:377: my @out = `$cmd 2>&1`;
vcftools-0.1.16/src/perl/test.t-378- open(my $fh,'<',$out) or confess("$out: $!");
##############################################
vcftools-0.1.16/src/perl/test.t-394- my $cmd = "perl -I../perl/ -MVcf ../perl/vcf-indel-stats -e $tab < $vcf";
vcftools-0.1.16/src/perl/test.t:395: my @out = `$cmd 2>&1`;
vcftools-0.1.16/src/perl/test.t-396- open(my $fh,'<',$out) or confess("$out: $!");
##############################################
vcftools-0.1.16/src/perl/test.t-410- chdir("$path/../examples");
vcftools-0.1.16/src/perl/test.t:411: `cat $vcf | bgzip -c > $vcf.gz`;
vcftools-0.1.16/src/perl/test.t:412: `tabix -p vcf -f $vcf.gz`;
vcftools-0.1.16/src/perl/test.t-413- my $cmd = "perl -I../perl/ -MVcf ../perl/vcf-consensus $args $vcf.gz < $fa";
vcftools-0.1.16/src/perl/test.t:414: my @out = `$cmd`;
vcftools-0.1.16/src/perl/test.t-415- open(my $fh,'<',$out) or confess("$out: $!");
##############################################
vcftools-0.1.16/src/perl/test.t-429- my $cmd = "perl -I../perl/ -MVcf ../perl/vcf-contrast $args $vcf | grep -v ^##source";
vcftools-0.1.16/src/perl/test.t:430: my @out = `$cmd 2>&1`;
vcftools-0.1.16/src/perl/test.t-431- open(my $fh,'<',$out) or confess("$out: $!");
##############################################
vcftools-0.1.16/src/perl/test.t-445- my $cmd = "cat $prefix.vcf | perl -I../perl/ -MVcf ../perl/vcf-fix-ploidy -s $prefix.samples -p $prefix.txt 2>/dev/null | vcf-query -f '\%POS[\\t\%SAMPLE \%GTR \%PL]\\n'";
vcftools-0.1.16/src/perl/test.t:446: my @out = `$cmd 2>&1`;
vcftools-0.1.16/src/perl/test.t-447- open(my $fh,'<',"$prefix.out") or confess("$prefix.out: $!");
##############################################
vcftools-0.1.16/src/perl/fill-fs-193- {
vcftools-0.1.16/src/perl/fill-fs:194: my @tabix = `tabix $file $chr:$from-$to`;
vcftools-0.1.16/src/perl/fill-fs-195- for my $ret (@tabix)
##############################################
vcftools-0.1.16/src/perl/fill-fs-206- {
vcftools-0.1.16/src/perl/fill-fs:207: my @tabix = `tabix $file $chr:$from-$to`;
vcftools-0.1.16/src/perl/fill-fs-208- for my $ret (@tabix)
##############################################
vcftools-0.1.16/debian/makeman-4-MANDIR=mans
vcftools-0.1.16/debian/makeman:5:VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
vcftools-0.1.16/debian/makeman-6-
##############################################
vcftools-0.1.16/debian/tests/run-unit-test-6-if [ "$AUTOPKGTEST_TMP" = "" ] ; then
vcftools-0.1.16/debian/tests/run-unit-test:7: AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
vcftools-0.1.16/debian/tests/run-unit-test-8-fi
##############################################
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-64- $cmd = "cat $file | bgzip -c > $file.gz";
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t:65: system($cmd);
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-66- is($?,0,"Is bgzip OK? .. $cmd");
##############################################
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-68- $cmd = "tabix $file.gz";
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t:69: system($cmd);
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-70- is($?,0,"Is tabix OK? .. $cmd");
##############################################
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-77- my $cmd = "perl -I$path -MVcf -e validate $fname";
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t:78: my @out = `$cmd 2>&1`;
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-79- my @exp = ();
##############################################
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-159- my $cmd = "perl -I$path -MVcf $path/vcf-stats $file";
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t:160: my @out = `$cmd 2>&1`;
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-161- open(my $fh,'<',"$file.stats") or confess("$file.stats: $!");
##############################################
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-216- {
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t:217: `cat $file | bgzip -c > $file.gz`;
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t:218: `tabix -p vcf -f $file.gz`;
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-219- }
##############################################
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-221- my $cmd = "perl -I../perl/ -MVcf ../perl/vcf-compare -g $a.gz $b.gz | grep -v '^# The command'";
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t:222: my @out = `$cmd 2>&1`;
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-223- open(my $fh,'<',"$expected") or confess("$expected: $!");
##############################################
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-242- {
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t:243: `cat $file | bgzip -c > $file.gz; tabix -f -p vcf $file.gz`;
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-244- $cmd .= " $file.gz";
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-245- }
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t:246: my @out = `$cmd 2>/dev/null | grep -v ^##source`;
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-247- open(my $fh,'<',$expected) or confess("$expected: $!");
##############################################
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-265- {
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t:266: `cat $file | bgzip -c > $file.gz; tabix -f -p vcf $file.gz`;
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-267- $cmd .= " $file.gz";
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-268- }
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t:269: my @out = `$cmd 2>&1 | grep -v ^##source`;
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-270- open(my $fh,'<',$expected) or confess("$expected: $!");
##############################################
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-287- my $cmd = "perl -I../perl/ -MVcf ../perl/vcf-query -f '$query' $file";
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t:288: my @out = `$cmd 2>&1`;
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-289- open(my $fh,'<',$expected) or confess("$expected: $!");
##############################################
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-306- my $cmd = "perl -I../perl/ -MVcf ../perl/vcf-shuffle-cols -t $template $file";
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t:307: my @out = `$cmd 2>&1`;
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-308- open(my $fh,'<',$template) or confess("$template: $!");
##############################################
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-326- {
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t:327: `cat $file | bgzip -c > $file.gz`;
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t:328: `tabix -p vcf -f $file.gz`;
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-329- $cmd .= " $file.gz";
##############################################
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-331-
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t:332: my @out = `$cmd 2>&1`;
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-333- open(my $fh,'<',$out) or confess("$out: $!");
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vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-353- {
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t:354: `cat $annot | bgzip -c > $annot.gz`;
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t:355: `tabix -s 3 -b 1 -e 2 -f $annot.gz`;
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-356- $cmd .= " -a $annot.gz";
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vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-358-
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t:359: my @out = `$cmd 2>&1 | grep -v ^##source`;
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-360- open(my $fh,'<',$out) or confess("$out: $!");
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vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-376- my $cmd = "perl -I../perl/ -MVcf ../perl/fill-an-ac $vcf";
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t:377: my @out = `$cmd 2>&1`;
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-378- open(my $fh,'<',$out) or confess("$out: $!");
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vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-394- my $cmd = "perl -I../perl/ -MVcf ../perl/vcf-indel-stats -e $tab < $vcf";
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t:395: my @out = `$cmd 2>&1`;
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-396- open(my $fh,'<',$out) or confess("$out: $!");
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vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-410- chdir("$path/../examples");
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t:411: `cat $vcf | bgzip -c > $vcf.gz`;
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t:412: `tabix -p vcf -f $vcf.gz`;
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-413- my $cmd = "perl -I../perl/ -MVcf ../perl/vcf-consensus $args $vcf.gz < $fa";
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t:414: my @out = `$cmd`;
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-415- open(my $fh,'<',$out) or confess("$out: $!");
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vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-429- my $cmd = "perl -I../perl/ -MVcf ../perl/vcf-contrast $args $vcf | grep -v ^##source";
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t:430: my @out = `$cmd 2>&1`;
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-431- open(my $fh,'<',$out) or confess("$out: $!");
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vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-445- my $cmd = "cat $prefix.vcf | perl -I../perl/ -MVcf ../perl/vcf-fix-ploidy -s $prefix.samples -p $prefix.txt 2>/dev/null | vcf-query -f '\%POS[\\t\%SAMPLE \%GTR \%PL]\\n'";
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t:446: my @out = `$cmd 2>&1`;
vcftools-0.1.16/.pc/temporary_test_fix.patch/src/perl/test.t-447- open(my $fh,'<',"$prefix.out") or confess("$prefix.out: $!");
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vcftools-0.1.16/.pc/spelling.patch/src/perl/fill-fs-193- {
vcftools-0.1.16/.pc/spelling.patch/src/perl/fill-fs:194: my @tabix = `tabix $file $chr:$from-$to`;
vcftools-0.1.16/.pc/spelling.patch/src/perl/fill-fs-195- for my $ret (@tabix)
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vcftools-0.1.16/.pc/spelling.patch/src/perl/fill-fs-206- {
vcftools-0.1.16/.pc/spelling.patch/src/perl/fill-fs:207: my @tabix = `tabix $file $chr:$from-$to`;
vcftools-0.1.16/.pc/spelling.patch/src/perl/fill-fs-208- for my $ret (@tabix)