===========================================================
.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
samtools-1.11/install-sh-234- fi
samtools-1.11/install-sh:235: cp_umask=`expr '(' 777 - $mode % 1000 ')' $u_plus_rw`;;
samtools-1.11/install-sh-236- *)
##############################################
samtools-1.11/install-sh-281- dstdir=$dst
samtools-1.11/install-sh:282: dst=$dstdir/`basename "$src"`
samtools-1.11/install-sh-283- dstdir_status=0
samtools-1.11/install-sh-284- else
samtools-1.11/install-sh:285: dstdir=`dirname "$dst"`
samtools-1.11/install-sh-286- test -d "$dstdir"
##############################################
samtools-1.11/install-sh-337- # FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
samtools-1.11/install-sh:338: ls_ld_tmpdir=`ls -ld "$tmpdir"`
samtools-1.11/install-sh-339- case $ls_ld_tmpdir in
##############################################
samtools-1.11/install-sh-344- $mkdirprog -m$different_mode -p -- "$tmpdir" && {
samtools-1.11/install-sh:345: ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
samtools-1.11/install-sh-346- test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
##############################################
samtools-1.11/install-sh-402- case $prefix in
samtools-1.11/install-sh:403: *\'*) qprefix=`echo "$prefix" | sed "s/'/'\\\\\\\\''/g"`;;
samtools-1.11/install-sh-404- *) qprefix=$prefix;;
##############################################
samtools-1.11/install-sh-451- if $copy_on_change &&
samtools-1.11/install-sh:452: old=`LC_ALL=C ls -dlL "$dst" 2>/dev/null` &&
samtools-1.11/install-sh:453: new=`LC_ALL=C ls -dlL "$dsttmp" 2>/dev/null` &&
samtools-1.11/install-sh-454- set -f &&
##############################################
samtools-1.11/m4/hts_prog_cc_warnings.m4-141-dnl Print result, with underscores as spaces
samtools-1.11/m4/hts_prog_cc_warnings.m4:142:ac_arg_result=`echo "$hts_cv_prog_cc_warnings" | tr '#' ' '`
samtools-1.11/m4/hts_prog_cc_warnings.m4-143-AC_MSG_RESULT($ac_arg_result)
##############################################
samtools-1.11/m4/hts_prog_cc_warnings.m4-148-do
samtools-1.11/m4/hts_prog_cc_warnings.m4:149: ac_arg_sp=`echo "$ac_arg" | tr '#' ' '`
samtools-1.11/m4/hts_prog_cc_warnings.m4-150- AS_CASE([" $CFLAGS "],
##############################################
samtools-1.11/misc/plot-ampliconstats-283- close($fh_reads);
samtools-1.11/misc/plot-ampliconstats:284: system("gnuplot", "$prefix-heat-reads-$fh_reads_page.gp") && die;
samtools-1.11/misc/plot-ampliconstats-285- undef $fh_reads;
##############################################
samtools-1.11/misc/plot-ampliconstats-327- close($fh_depth);
samtools-1.11/misc/plot-ampliconstats:328: system("gnuplot", "$prefix-heat-depth-$fh_depth_page.gp") && die;
samtools-1.11/misc/plot-ampliconstats-329- undef $fh_depth;
##############################################
samtools-1.11/misc/plot-ampliconstats-369- close($fh_amp);
samtools-1.11/misc/plot-ampliconstats:370: system("gnuplot", "$prefix-heat-amp-$fh_amp_page.gp") && die;
samtools-1.11/misc/plot-ampliconstats-371- undef $fh_amp;
##############################################
samtools-1.11/misc/plot-ampliconstats-425- close($fh_rperc);
samtools-1.11/misc/plot-ampliconstats:426: system("gnuplot", "$prefix-heat-read-perc-$fh_rperc_page.gp") && die;
samtools-1.11/misc/plot-ampliconstats-427- undef $fh_rperc;
##############################################
samtools-1.11/misc/plot-ampliconstats-431- close($fh_rperl);
samtools-1.11/misc/plot-ampliconstats:432: system("gnuplot", "$prefix-heat-read-perc-log-$fh_rperc_page.gp") && die;
samtools-1.11/misc/plot-ampliconstats-433- undef $fh_rperl;
##############################################
samtools-1.11/misc/plot-ampliconstats-499- close($fh_cover{$1});
samtools-1.11/misc/plot-ampliconstats:500: system("gnuplot", "$prefix-heat-coverage-$1-$fh_cover_page{$1}.gp") && die;
samtools-1.11/misc/plot-ampliconstats-501- undef $fh_cover{$1};
##############################################
samtools-1.11/misc/plot-ampliconstats-597- close($fh);
samtools-1.11/misc/plot-ampliconstats:598: system("gnuplot", "$prefix-combined-coverage-$1.gp") && die;
samtools-1.11/misc/plot-ampliconstats-599- }
##############################################
samtools-1.11/misc/plot-ampliconstats-641- close($fh_depth);
samtools-1.11/misc/plot-ampliconstats:642: system("gnuplot", "$prefix-heat-depth-$fh_depth_page.gp") && die;
samtools-1.11/misc/plot-ampliconstats-643-}
##############################################
samtools-1.11/misc/plot-ampliconstats-647- close($fh_amp);
samtools-1.11/misc/plot-ampliconstats:648: system("gnuplot", "$prefix-heat-amp-$fh_amp_page.gp") && die;
samtools-1.11/misc/plot-ampliconstats-649-}
##############################################
samtools-1.11/misc/plot-ampliconstats-653- close($fh_reads);
samtools-1.11/misc/plot-ampliconstats:654: system("gnuplot", "$prefix-heat-reads-$fh_reads_page.gp") && die;
samtools-1.11/misc/plot-ampliconstats-655-}
##############################################
samtools-1.11/misc/plot-ampliconstats-659- close($fh_rperc);
samtools-1.11/misc/plot-ampliconstats:660: system("gnuplot", "$prefix-heat-read-perc-$fh_rperc_page.gp") && die;
samtools-1.11/misc/plot-ampliconstats-661-}
##############################################
samtools-1.11/misc/plot-ampliconstats-665- close($fh_rperl);
samtools-1.11/misc/plot-ampliconstats:666: system("gnuplot", "$prefix-heat-read-perc-log-$fh_rperc_page.gp") && die;
samtools-1.11/misc/plot-ampliconstats-667-}
##############################################
samtools-1.11/misc/plot-ampliconstats-671- close($fh_cover{$_});
samtools-1.11/misc/plot-ampliconstats:672: system("gnuplot", "$prefix-heat-coverage-$_-$fh_cover_page{$_}.gp") && die;
samtools-1.11/misc/plot-ampliconstats-673- }
##############################################
samtools-1.11/misc/plot-ampliconstats-733-close($ch_reads);
samtools-1.11/misc/plot-ampliconstats:734:system("gnuplot", "$prefix-combined-reads.gp") && die;
samtools-1.11/misc/plot-ampliconstats-735-
##############################################
samtools-1.11/misc/plot-ampliconstats-781-close($ch_depth);
samtools-1.11/misc/plot-ampliconstats:782:system("gnuplot", "$prefix-combined-depth.gp") && die;
samtools-1.11/misc/plot-ampliconstats-783-
samtools-1.11/misc/plot-ampliconstats-784-close($ch_rperc);
samtools-1.11/misc/plot-ampliconstats:785:system("gnuplot", "$prefix-combined-read-perc.gp") && die;
samtools-1.11/misc/plot-ampliconstats-786-
samtools-1.11/misc/plot-ampliconstats-787-close($ch_amp);
samtools-1.11/misc/plot-ampliconstats:788:system("gnuplot", "$prefix-combined-amp.gp") && die;
samtools-1.11/misc/plot-ampliconstats-789-
##############################################
samtools-1.11/misc/plot-ampliconstats-848- close($fh);
samtools-1.11/misc/plot-ampliconstats:849: system("gnuplot", "$fn.gp") && die;
samtools-1.11/misc/plot-ampliconstats-850-
##############################################
samtools-1.11/misc/plot-ampliconstats-901- close($fh);
samtools-1.11/misc/plot-ampliconstats:902: system("gnuplot", "$fn.gp") && die;
samtools-1.11/misc/plot-ampliconstats-903- skip_coord:
##############################################
samtools-1.11/misc/plot-ampliconstats-951- close($fh);
samtools-1.11/misc/plot-ampliconstats:952: system("gnuplot", "$fn.gp") && die;
samtools-1.11/misc/plot-ampliconstats-953- }
##############################################
samtools-1.11/misc/plot-ampliconstats-1015- close($fh);
samtools-1.11/misc/plot-ampliconstats:1016: system("gnuplot", "$fn.gp") && die;
samtools-1.11/misc/plot-ampliconstats-1017-
##############################################
samtools-1.11/misc/plot-ampliconstats-1079- close($fh);
samtools-1.11/misc/plot-ampliconstats:1080: system("gnuplot", "$fn.gp") && die;
samtools-1.11/misc/plot-ampliconstats-1081- }
##############################################
samtools-1.11/misc/plot-ampliconstats-1132- close($fh);
samtools-1.11/misc/plot-ampliconstats:1133: system("gnuplot", "$fn.gp") && die;
samtools-1.11/misc/plot-ampliconstats-1134-
##############################################
samtools-1.11/misc/plot-ampliconstats-1216- close($fh);
samtools-1.11/misc/plot-ampliconstats:1217: system("gnuplot", "$fn.gp") && die;
samtools-1.11/misc/plot-ampliconstats-1218-
##############################################
samtools-1.11/misc/plot-ampliconstats-1260- close($fh);
samtools-1.11/misc/plot-ampliconstats:1261: system("gnuplot", "$fn.gp") && die;
samtools-1.11/misc/plot-ampliconstats-1262-
##############################################
samtools-1.11/misc/plot-ampliconstats-1331- my $scale = 100*$opts{thumb_size}/[split(",",$opts{size})]->[0],"\n";
samtools-1.11/misc/plot-ampliconstats:1332: system("convert", "-scale", "$scale%", $imgs[$i], "$imgs[$i].thumb.png") && die;
samtools-1.11/misc/plot-ampliconstats-1333- print $fh qq[<td><a class="thumbnail" href="$img"><img src="$img.thumb.png" width="$opts{thumb_size}px"></a></td>\n];
##############################################
samtools-1.11/misc/plot-bamstats-231- if ( !exists($$opts{prefix}) ) { error("Expected -p parameter.\n") }
samtools-1.11/misc/plot-bamstats:232: if ( $$opts{prefix}=~m{/$} ) { `mkdir -p $$opts{prefix}`; }
samtools-1.11/misc/plot-bamstats-233- elsif ( !($$opts{prefix}=~/-$/) ) { $$opts{prefix} .= '-'; }
##############################################
samtools-1.11/misc/plot-bamstats-334- my $cmd = "gnuplot $cmdfile";
samtools-1.11/misc/plot-bamstats:335: system($cmd);
samtools-1.11/misc/plot-bamstats-336- if ( $? ) { error("The command exited with non-zero status $?:\n\t$cmd\n\n"); }
##############################################
samtools-1.11/misc/plot-bamstats-576- $dir =~ s{/[^/]+$}{};
samtools-1.11/misc/plot-bamstats:577: if ( $dir && $dir ne $gp_file ) { `mkdir -p $dir`; }
samtools-1.11/misc/plot-bamstats-578-
##############################################
samtools-1.11/misc/sam2vcf.pl-256- my $cmd = "samtools faidx $$self{file} $chr:$pos-$to";
samtools-1.11/misc/sam2vcf.pl:257: my @out = `$cmd`;
samtools-1.11/misc/sam2vcf.pl-258- if ( $? ) { $self->throw("$cmd: $!"); }
##############################################
samtools-1.11/test/ampliconclip/2_both_clipped.expected.sam-3-@RG ID:12345_1#2
samtools-1.11/test/ampliconclip/2_both_clipped.expected.sam:4:m64097_200403_120115/82116974/ccs 16 vir1 55 60 61S241M1D89M58S * 0 0 GTGGACTGGAGTTCAGACGTGTGCTCTTTCCGATCTTACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT x~[%rZd~k~~~~~~~~r~~~~~z~|~~)~>~uZUT)J~Q~d\C~dh~~pd~~~x~y~C~~~~~~N~~~ny~x~~~dky~pW~~]~~~W~z|~~~x~Ou~p{x~t~d~ly`g~~~~z~m~~~qb~y~\lxdg~|~~~~j~d~t~~Z[~~b~~~q~~~c~~l~~s~~reCqP~t{z~kTqTntC~`nO~eL~z~~~eo~_f~y~}~r~~R|s~~Rv~~~{{|~~~P~~~u~wf~om~~w~z~~~n~~~_x~~F~~X~~~~~~[~~~]~Y~~wS~~~O~j~Q~Ywl`~~~Ct~e~~tl~~zy~]~j$O~|~y~~~f~~`~f~~~~M|~a~~~~~Wx|~~E~IyDrmc]q~~z~~~~~}~~~wz~yX~c~q~y~~h~~~Z~~r~~n~x~x~~~~q~~q[~a~~}~mq_s|~kc~)~p~s~?~oc~S~d~~~}r~~s~t~~~~[~~M~~~~~~ NM:i:2 MD:Z:210C54^A114 AS:i:367 XS:i:0
samtools-1.11/test/ampliconclip/2_both_clipped.expected.sam-5-m64097_200403_120115/39389595/ccs 0 vir1 55 60 59S47M3D281M58S * 0 0 GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCCTACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT ~~~~~~s~~~~~~~~~~~~~~~|~_W~l~~WeZc2o`~z~b~m~~w~~p~~~~~~e~~~~~~~~~~b~~~n~Z~~~~~~~t~~O~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~|k~R{a~~~h~t~~{~~p~I~~~~~~~~+~U}:r~~~~~q~~~~~r~xn{~~~~~~~~~~~~D~~~~{~|z~~~[~Z~~~q~~~~~H~~~~~k~~~~~~~~~~V~~Xw~~~~~~~~~~~~~~h~5~~q~~`~c~~~~~~~M~~R~~~~~~~~~~l~~~~~z~~~~~U~~~~~]~{p~~~~~-.~~~r~y~x~Y8~\~~~~~~o~~~t~~~c~~~~~~~~~~~~~~~~~~~~~~~~x~~~`~~g~~l~~~~y~\~~~~~~~~~~~~~~~oz~~~~~~~~~~~~j~~y}w`r[~~~~k~~~~~xf~f~~~~~~~~~~~~~z~~q~~~~~~~~ NM:i:4 MD:Z:71^GCT136C169 AS:i:363 XS:i:0
##############################################
samtools-1.11/test/ampliconclip/2_both_test_data.sam-3-@RG ID:12345_1#2
samtools-1.11/test/ampliconclip/2_both_test_data.sam:4:m64097_200403_120115/82116974/ccs 16 vir1 31 60 37S265M1D114M33S * 0 0 GTGGACTGGAGTTCAGACGTGTGCTCTTTCCGATCTTACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT x~[%rZd~k~~~~~~~~r~~~~~z~|~~)~>~uZUT)J~Q~d\C~dh~~pd~~~x~y~C~~~~~~N~~~ny~x~~~dky~pW~~]~~~W~z|~~~x~Ou~p{x~t~d~ly`g~~~~z~m~~~qb~y~\lxdg~|~~~~j~d~t~~Z[~~b~~~q~~~c~~l~~s~~reCqP~t{z~kTqTntC~`nO~eL~z~~~eo~_f~y~}~r~~R|s~~Rv~~~{{|~~~P~~~u~wf~om~~w~z~~~n~~~_x~~F~~X~~~~~~[~~~]~Y~~wS~~~O~j~Q~Ywl`~~~Ct~e~~tl~~zy~]~j$O~|~y~~~f~~`~f~~~~M|~a~~~~~Wx|~~E~IyDrmc]q~~z~~~~~}~~~wz~yX~c~q~y~~h~~~Z~~r~~n~x~x~~~~q~~q[~a~~}~mq_s|~kc~)~p~s~?~oc~S~d~~~}r~~s~t~~~~[~~M~~~~~~ NM:i:2 MD:Z:210C54^A114 AS:i:367 XS:i:0
samtools-1.11/test/ampliconclip/2_both_test_data.sam-5-m64097_200403_120115/39389595/ccs 0 vir1 31 60 35S71M3D306M33S * 0 0 GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCCTACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT ~~~~~~s~~~~~~~~~~~~~~~|~_W~l~~WeZc2o`~z~b~m~~w~~p~~~~~~e~~~~~~~~~~b~~~n~Z~~~~~~~t~~O~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~|k~R{a~~~h~t~~{~~p~I~~~~~~~~+~U}:r~~~~~q~~~~~r~xn{~~~~~~~~~~~~D~~~~{~|z~~~[~Z~~~q~~~~~H~~~~~k~~~~~~~~~~V~~Xw~~~~~~~~~~~~~~h~5~~q~~`~c~~~~~~~M~~R~~~~~~~~~~l~~~~~z~~~~~U~~~~~]~{p~~~~~-.~~~r~y~x~Y8~\~~~~~~o~~~t~~~c~~~~~~~~~~~~~~~~~~~~~~~~x~~~`~~g~~l~~~~y~\~~~~~~~~~~~~~~~oz~~~~~~~~~~~~j~~y}w`r[~~~~k~~~~~xf~f~~~~~~~~~~~~~z~~q~~~~~~~~ NM:i:4 MD:Z:71^GCT136C169 AS:i:363 XS:i:0
##############################################
samtools-1.11/test/mpileup/regression.sh-39- e=$1; shift
samtools-1.11/test/mpileup/regression.sh:40: test_iter=`expr $test_iter + 1`
samtools-1.11/test/mpileup/regression.sh-41- #echo "p=$p e=$e cmd=$@"
samtools-1.11/test/mpileup/regression.sh-42- # All output here is text, so blanket and naive removal of cr just about works.
samtools-1.11/test/mpileup/regression.sh:43: result=`eval ${@+"$@"} 2>/dev/null | tr -d '\015' > _out`
samtools-1.11/test/mpileup/regression.sh:44: #result=`eval ${@+"$@"} > _out`
samtools-1.11/test/mpileup/regression.sh:45: #result=`eval valgrind --error-exitcode=1 --leak-check=full ${@+"$@"}`
samtools-1.11/test/mpileup/regression.sh-46- if [ $? != 0 ]
##############################################
samtools-1.11/test/mpileup/regression.sh-49- mv _out FAIL-$e.${test_iter}
samtools-1.11/test/mpileup/regression.sh:50: nufail=`expr $nufail + 1`
samtools-1.11/test/mpileup/regression.sh-51- return 0
##############################################
samtools-1.11/test/mpileup/regression.sh-60- mv _out PASS-$e.${test_iter}
samtools-1.11/test/mpileup/regression.sh:61: nupass=`expr $nupass + 1`
samtools-1.11/test/mpileup/regression.sh-62- return 0
samtools-1.11/test/mpileup/regression.sh-63- else
samtools-1.11/test/mpileup/regression.sh:64: nepass=`expr $nepass + 1`
samtools-1.11/test/mpileup/regression.sh-65- rm _out
##############################################
samtools-1.11/test/mpileup/regression.sh-73- echo "when running $@"
samtools-1.11/test/mpileup/regression.sh:74: nefail=`expr $nefail + 1`
samtools-1.11/test/mpileup/regression.sh-75- rm _out
##############################################
samtools-1.11/test/mpileup/regression.sh-81- mv _out FAIL-$e.${test_iter}
samtools-1.11/test/mpileup/regression.sh:82: nufail=`expr $nufail + 1`
samtools-1.11/test/mpileup/regression.sh-83- return 0
##############################################
samtools-1.11/test/mpileup/regression.sh-114- test_iter=0
samtools-1.11/test/mpileup/regression.sh:115: if [ "`expr \"$cmd\" : '.*\$fmt'`" != 0 -a "$samtools" != "./samtools-0.1.19" ]
samtools-1.11/test/mpileup/regression.sh-116- then
samtools-1.11/test/mpileup/regression.sh:117: _cmd=`printf '%s' "$cmd" | sed 's/\$fmt/bam/'`
samtools-1.11/test/mpileup/regression.sh-118- run_test $p $o $_cmd
samtools-1.11/test/mpileup/regression.sh:119: #_cmd=`printf '%s' "$cmd" | sed 's/\$fmt/sam/'`
samtools-1.11/test/mpileup/regression.sh-120- #run_test $p $o $_cmd
samtools-1.11/test/mpileup/regression.sh:121: _cmd=`printf '%s' "$cmd" | sed 's/\$fmt/cram/'`
samtools-1.11/test/mpileup/regression.sh-122- run_test $p $o $_cmd
samtools-1.11/test/mpileup/regression.sh-123- else
samtools-1.11/test/mpileup/regression.sh:124: _cmd=`printf '%s' "$cmd" | sed 's/\$fmt/bam/'`
samtools-1.11/test/mpileup/regression.sh-125- run_test $p $o $_cmd
##############################################
samtools-1.11/test/test.pl-119- my ($path) = @_;
samtools-1.11/test/test.pl:120: $path = `cygpath -m $path`;
samtools-1.11/test/test.pl-121- $path =~ s/\r?\n//;
##############################################
samtools-1.11/test/test.pl-173- print STDERR "Signal caught, cleaning and exiting...\n";
samtools-1.11/test/test.pl:174: `rm -rf $$opts{tmp}`;
samtools-1.11/test/test.pl-175-}
##############################################
samtools-1.11/test/test.pl-2889- # Sort inputs by PG, then merge
samtools-1.11/test/test.pl:2890: system("$$opts{bin}/samtools sort -o $$opts{tmp}/merge.tag.1.bam -t PG -m 10M $$opts{path}/dat/test_input_1_b.sam") == 0 or die "failed to create sort BAM: $?";
samtools-1.11/test/test.pl:2891: system("$$opts{bin}/samtools sort -o $$opts{tmp}/merge.tag.2.bam -t PG -m 10M $$opts{path}/dat/test_input_1_d.sam") == 0 or die "failed to create sort BAM: $?";
samtools-1.11/test/test.pl-2892- test_cmd($opts,out=>'merge/tag.pg.merge.expected.sam', ignore_pg_header => 1, cmd=>"$$opts{bin}/samtools merge${threads} -s 1 -p -c -t PG -O SAM - $$opts{tmp}/merge.tag.1.bam $$opts{tmp}/merge.tag.2.bam");
##############################################
samtools-1.11/test/test.pl-2894- # Sort inputs by PG, then merge (name sorted)
samtools-1.11/test/test.pl:2895: system("$$opts{bin}/samtools sort -o $$opts{tmp}/merge.tag.3.bam -n -t PG -m 10M $$opts{path}/dat/test_input_1_c.sam") == 0 or die "failed to create sort BAM: $?";
samtools-1.11/test/test.pl:2896: system("$$opts{bin}/samtools sort -o $$opts{tmp}/merge.tag.4.bam -n -t PG -m 10M $$opts{path}/dat/test_input_1_d.sam") == 0 or die "failed to create sort BAM: $?";
samtools-1.11/test/test.pl-2897- test_cmd($opts,out=>'merge/tag.pg.n.merge.expected.sam', ignore_pg_header => 1, cmd=>"$$opts{bin}/samtools merge${threads} -s 1 -p -c -n -t PG -O SAM - $$opts{tmp}/merge.tag.3.bam $$opts{tmp}/merge.tag.4.bam");
##############################################
samtools-1.11/test/test.pl-2902-
samtools-1.11/test/test.pl:2903: system("$$opts{bin}/samtools view -ho $$opts{tmp}/merge.bed.1.bam --no-PG $$opts{path}/merge/merge.bed.1.sam") == 0 or die "failed to create merge.bed.1.bam: $?";
samtools-1.11/test/test.pl:2904: system("$$opts{bin}/samtools view -ho $$opts{tmp}/merge.bed.2.bam --no-PG $$opts{path}/merge/merge.bed.2.sam") == 0 or die "failed to create merge.bed.2.bam: $?";
samtools-1.11/test/test.pl:2905: system("$$opts{bin}/samtools index $$opts{tmp}/merge.bed.1.bam") == 0 or die "failed to index merge.bed.1.bam: $?";
samtools-1.11/test/test.pl:2906: system("$$opts{bin}/samtools index $$opts{tmp}/merge.bed.2.bam") == 0 or die "failed to index merge.bed.2.bam: $?";
samtools-1.11/test/test.pl-2907- test_cmd($opts, out=>'merge/merge.bed.expected.sam', cmd => "$$opts{bin}/samtools merge${threads} --no-PG -O SAM -L $$opts{path}/merge/merge.bed - $$opts{tmp}/merge.bed.1.bam $$opts{tmp}/merge.bed.2.bam");
##############################################
samtools-1.11/test/test.pl-3059- # Create local BAM and CRAM inputs
samtools-1.11/test/test.pl:3060: system("$$opts{bin}/samtools view -b --no-PG $fn.sam > $fn.tmp.bam") == 0 or die "failed to create bam: $?";
samtools-1.11/test/test.pl:3061: system("$$opts{bin}/samtools view -C --no-PG --output-fmt-option version=2.1 $fn.sam > $fn.tmp.v21.cram") == 0 or die "failed to create cram: $?";
samtools-1.11/test/test.pl:3062: system("$$opts{bin}/samtools view -C --no-PG --output-fmt-option version=3.0 $fn.sam > $fn.tmp.v30.cram") == 0 or die "failed to create cram: $?";
samtools-1.11/test/test.pl-3063-
##############################################
samtools-legacy-0.1.19+dfsg/Makefile-26-all-recur lib-recur clean-recur cleanlocal-recur install-recur:
samtools-legacy-0.1.19+dfsg/Makefile:27: @target=`echo $@ | sed s/-recur//`; \
samtools-legacy-0.1.19+dfsg/Makefile-28- wdir=`pwd`; \
##############################################
samtools-legacy-0.1.19+dfsg/bcftools/Makefile-16-all-recur lib-recur clean-recur cleanlocal-recur install-recur:
samtools-legacy-0.1.19+dfsg/bcftools/Makefile:17: @target=`echo $@ | sed s/-recur//`; \
samtools-legacy-0.1.19+dfsg/bcftools/Makefile-18- wdir=`pwd`; \
##############################################
samtools-legacy-0.1.19+dfsg/knetfile.c-167- struct in_addr addr;
samtools-legacy-0.1.19+dfsg/knetfile.c:168: addr.s_addr = inet_addr(host);
samtools-legacy-0.1.19+dfsg/knetfile.c:169: hp = gethostbyaddr((char*)&addr, 4, AF_INET);
samtools-legacy-0.1.19+dfsg/knetfile.c-170- }
##############################################
samtools-legacy-0.1.19+dfsg/misc/Makefile-18-lib-recur all-recur clean-recur cleanlocal-recur install-recur:
samtools-legacy-0.1.19+dfsg/misc/Makefile:19: @target=`echo $@ | sed s/-recur//`; \
samtools-legacy-0.1.19+dfsg/misc/Makefile-20- wdir=`pwd`; \
##############################################
samtools-legacy-0.1.19+dfsg/misc/plot-bamcheck-61- if ( !exists($$opts{prefix}) ) { error("Expected -p parameter.\n") }
samtools-legacy-0.1.19+dfsg/misc/plot-bamcheck:62: if ( $$opts{prefix}=~m{/$} ) { `mkdir -p $$opts{prefix}`; }
samtools-legacy-0.1.19+dfsg/misc/plot-bamcheck-63- elsif ( !($$opts{prefix}=~/-$/) ) { $$opts{prefix} .= '-'; }
##############################################
samtools-legacy-0.1.19+dfsg/misc/plot-bamcheck-150- my $cmd = "gnuplot $cmdfile";
samtools-legacy-0.1.19+dfsg/misc/plot-bamcheck:151: system($cmd);
samtools-legacy-0.1.19+dfsg/misc/plot-bamcheck-152- if ( $? ) { error("The command exited with non-zero status $?:\n\t$cmd\n\n"); }
##############################################
samtools-legacy-0.1.19+dfsg/misc/plot-bamcheck-216- $dir =~ s{/[^/]+$}{};
samtools-legacy-0.1.19+dfsg/misc/plot-bamcheck:217: if ( $dir && $dir ne $gp_file ) { `mkdir -p $dir`; }
samtools-legacy-0.1.19+dfsg/misc/plot-bamcheck-218-
##############################################
samtools-legacy-0.1.19+dfsg/misc/plot-bamcheck-833- {
samtools-legacy-0.1.19+dfsg/misc/plot-bamcheck:834: my (@lines) = `cat $$opts{bamcheck} | grep ^$tag | wc -l`;
samtools-legacy-0.1.19+dfsg/misc/plot-bamcheck-835- chomp($lines[0]);
##############################################
samtools-legacy-0.1.19+dfsg/misc/plot-bamcheck-845- my $args = get_defaults($opts,"$$opts{prefix}mism-per-cycle.png");
samtools-legacy-0.1.19+dfsg/misc/plot-bamcheck:846: my ($nquals) = `grep ^MPC $$opts{bamcheck} | awk '\$2==1' | sed 's,\\t,\\n,g' | wc -l`;
samtools-legacy-0.1.19+dfsg/misc/plot-bamcheck:847: my ($ncycles) = `grep ^MPC $$opts{bamcheck} | wc -l`;
samtools-legacy-0.1.19+dfsg/misc/plot-bamcheck-848- chomp($nquals);
##############################################
samtools-legacy-0.1.19+dfsg/misc/sam2vcf.pl-237- my $cmd = "samtools faidx $$self{file} $chr:$pos-$to";
samtools-legacy-0.1.19+dfsg/misc/sam2vcf.pl:238: my @out = `$cmd`;
samtools-legacy-0.1.19+dfsg/misc/sam2vcf.pl-239- if ( $? ) { $self->throw("$cmd: $!"); }