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.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
lagan-2.0/slagan-mfa.pl-28-my $args = join(" ", @ARGV);
lagan-2.0/slagan-mfa.pl:29:system($LAGAN_DIR."/slagan.pl $args > slagan.pl.out");
lagan-2.0/slagan-mfa.pl-30-die("$0: slagan.pl returned error $?. Stopped") if $?;
lagan-2.0/slagan-mfa.pl-31-
lagan-2.0/slagan-mfa.pl:32:system($LAGAN_DIR."/xmfa2mfa.pl ".($base eq "2" ? "2" : "1")." < slagan.pl.out ".($outfile ? "> $outfile" : ""));
lagan-2.0/slagan-mfa.pl-33-die("$0: xmfa2mfa.pl returned error $?. Stopped") if $?;
##############################################
lagan-2.0/slagan.pl-52- $outfile = $ARGV[++$i];
lagan-2.0/slagan.pl:53: if (-e "$outfile") { system("rm $outfile") and exit(1); }
lagan-2.0/slagan.pl-54- } elsif ($ARGV[$i] =~ /-order/) {
##############################################
lagan-2.0/slagan.pl-78-
lagan-2.0/slagan.pl:79:my $seq1len = `$lagandir/utils/getlength $firstName`;
lagan-2.0/slagan.pl:80:my $seq2len = `$lagandir/utils/getlength $secondName`;
lagan-2.0/slagan.pl-81-chomp $seq1len;
##############################################
lagan-2.0/slagan.pl-84-if ($lazy && -e "${outName1}_$outName2.chaos") {
lagan-2.0/slagan.pl:85: `cp ${outName1}_$outName2.chaos chaos.$$`;
lagan-2.0/slagan.pl-86-}
lagan-2.0/slagan.pl-87-else {
lagan-2.0/slagan.pl:88: `$lagandir/chaos $seq1 $seq2 $chaos_fl > chaos.$$`;
lagan-2.0/slagan.pl-89- if ($?) { exit(1); }
lagan-2.0/slagan.pl:90: `cat chaos.$$ > ${outName1}_$outName2.chaos`;
lagan-2.0/slagan.pl-91-}
##############################################
lagan-2.0/slagan.pl-97-#print $supermap_inv."\n";
lagan-2.0/slagan.pl:98:system($supermap_inv);
lagan-2.0/slagan.pl-99-
##############################################
lagan-2.0/slagan.pl-119-#print "$lagandir/utils/fa2xfa $firstName $startreg1 $endreg1 1 > seq1$k.$$\n";
lagan-2.0/slagan.pl:120: `$lagandir/utils/fa2xfa $firstName $startreg1 $endreg1 1 > seq1$k.$$\n`;
lagan-2.0/slagan.pl-121-#print "$lagandir/utils/fa2xfa $secondName $startreg2 $endreg2 2 $rcf > seq2$k.$$\n";
lagan-2.0/slagan.pl:122: `$lagandir/utils/fa2xfa $secondName $startreg2 $endreg2 2 $rcf > seq2$k.$$\n`;
lagan-2.0/slagan.pl:123: if ($extra1) { `$lagandir/utils/fa2xfa $seq1 $startreg1 $endreg1 1 > seq1$k.$$.masked\n`; }
lagan-2.0/slagan.pl:124: if ($extra2) { `$lagandir/utils/fa2xfa $seq2 $startreg2 $endreg2 2 $rcf > seq2$k.$$.masked\n`; }
lagan-2.0/slagan.pl-125-
lagan-2.0/slagan.pl-126-#print "$lagandir/lagan.pl seq1$k.$$ seq2$k.$$ $arglist $lagan_fl -mfa -out lagan.$k.$$\n";
lagan-2.0/slagan.pl:127: `$lagandir/lagan.pl seq1$k.$$ seq2$k.$$ $arglist $lagan_fl -mfa -out lagan.$k.$$\n`;
lagan-2.0/slagan.pl-128-
##############################################
lagan-2.0/slagan.pl-133-#print "$lagandir/utils/scorealign lagan.$k.$$ 45 -cropxmfa -ibounds $suff\n";
lagan-2.0/slagan.pl:134: print `$lagandir/utils/scorealign lagan.$k.$$ 45 -cropxmfa -ibounds $suff`;
lagan-2.0/slagan.pl-135- } else {
lagan-2.0/slagan.pl-136-#print "$lagandir/utils/scorealign lagan.$k.$$ 45 -ibounds\n";
lagan-2.0/slagan.pl:137: my $sc = `$lagandir/utils/scorealign lagan.$k.$$ 45 -ibounds`;
lagan-2.0/slagan.pl-138- chomp($sc);
lagan-2.0/slagan.pl-139- if ($sc) {
lagan-2.0/slagan.pl:140: print `cat lagan.$k.$$ $suff`;
lagan-2.0/slagan.pl:141: print `echo \"=$sc $type\n\" $suff`;
lagan-2.0/slagan.pl-142- }
##############################################
lagan-2.0/slagan.pl-146-
lagan-2.0/slagan.pl:147:####`cat out.$$ > ${outName1}_$outName2.mon`;
lagan-2.0/slagan.pl-148-unlink(glob("*.$$"));
lagan-2.0/slagan.pl:149:if ($extra1 || $extra2) { `rm *.$$.masked`; }
lagan-2.0/slagan.pl-150-exit(0);
##############################################
lagan-2.0/src/lagan.pl-93- elsif ($ARGV[$i] =~ /-rc/) {
lagan-2.0/src/lagan.pl:94: `$lagandir/utils/rc < $ARGV[1] > $ARGV[1].rc`;
lagan-2.0/src/lagan.pl-95- if ($?) { exit(1); }
##############################################
lagan-2.0/src/lagan.pl-97- if (-e "$ARGV[1].masked") {
lagan-2.0/src/lagan.pl:98: `$lagandir/utils/rc < $ARGV[1].masked > $ARGV[1].rc.masked`;
lagan-2.0/src/lagan.pl-99- if ($?) { exit(1);}
##############################################
lagan-2.0/src/lagan.pl-125-if ($rundraft){
lagan-2.0/src/lagan.pl:126: `$lagandir/draft.pl $firstName $secondName $draftparams`;
lagan-2.0/src/lagan.pl-127- if ($?) { exit(1);}
##############################################
lagan-2.0/src/lagan.pl-131-# print STDERR "perl $lagandir/rechaos.pl $firstName $secondName $gfc $arglist > $$.anchs.final\n";
lagan-2.0/src/lagan.pl:132:`perl $lagandir/rechaos.pl $firstName $secondName $gfc $arglist > $$.anchs.final`;
lagan-2.0/src/lagan.pl-133-
##############################################
lagan-2.0/src/lagan.pl-138-if ($contigflag){
lagan-2.0/src/lagan.pl:139: @bounds = `$lagandir/utils/getbounds $$.anchs.final $firstName $secondName`;
lagan-2.0/src/lagan.pl-140- if ($?) { exit(1); }
##############################################
lagan-2.0/src/lagan.pl-142- print STDERR ("Aligning with bounds: $bounds[0]\n");
lagan-2.0/src/lagan.pl:143: print `$lagandir/order $firstName $secondName $bounds[0] $orderfl -anc $$.anchs.final`;
lagan-2.0/src/lagan.pl-144- if ($?) { exit(1); }
##############################################
lagan-2.0/src/lagan.pl-170-
lagan-2.0/src/lagan.pl:171: `$lagandir/order $firstName $secondName $format -out $$.align $orderfl -anc $$.anchs.final`;
lagan-2.0/src/lagan.pl-172- if ($?) { exit(1); }
##############################################
lagan-2.0/src/lagan.pl-175- if ($filename) {
lagan-2.0/src/lagan.pl:176: `$lagandir/utils/bin2bl $$.align > $filename`;
lagan-2.0/src/lagan.pl-177- }
lagan-2.0/src/lagan.pl-178- else {
lagan-2.0/src/lagan.pl:179: print `$lagandir/utils/bin2bl $$.align`;
lagan-2.0/src/lagan.pl-180- }
##############################################
lagan-2.0/src/lagan.pl-183- if ($filename) {
lagan-2.0/src/lagan.pl:184: `cat $$.align > $filename`;
lagan-2.0/src/lagan.pl-185- }
lagan-2.0/src/lagan.pl-186- else {
lagan-2.0/src/lagan.pl:187: print `cat $$.align`;
lagan-2.0/src/lagan.pl-188- }
##############################################
lagan-2.0/src/lagan.pl-190- if ($dofastreject){
lagan-2.0/src/lagan.pl:191: `$lagandir/utils/scorealign $filename $consrate -ibounds -cropxmfa > $$.temp`;
lagan-2.0/src/lagan.pl-192- if ($?) { exit(1); }
lagan-2.0/src/lagan.pl:193: `mv $$.temp $filename`;
lagan-2.0/src/lagan.pl-194- }
##############################################
lagan-2.0/src/lagan.pl-200- if ($binfile){
lagan-2.0/src/lagan.pl:201: `$lagandir/utils/bin2mf $infofilename > $infofilename.mfa`;
lagan-2.0/src/lagan.pl-202- if ($?) { exit(1); }
##############################################
lagan-2.0/src/lagan.pl-204- }
lagan-2.0/src/lagan.pl:205: @temp = `head $secondName`;
lagan-2.0/src/lagan.pl-206- if ($?) { exit(1); }
##############################################
lagan-2.0/src/lagan.pl-209-
lagan-2.0/src/lagan.pl:210: $len = `$lagandir/utils/getlength $secondName`; chomp $len;
lagan-2.0/src/lagan.pl-211- if ($?) { exit(2); }
##############################################
lagan-2.0/src/lagan.pl-213-
lagan-2.0/src/lagan.pl:214: $score = `$lagandir/utils/scorealign $infofilename $consupperrate`; chomp $score;
lagan-2.0/src/lagan.pl-215- if ($?) { exit(3); }
lagan-2.0/src/lagan.pl-216- if ($score > 0){
lagan-2.0/src/lagan.pl:217: $score = `$lagandir/utils/scorealign $infofilename $consrate`; chomp $score;
lagan-2.0/src/lagan.pl-218- if ($?) { exit(4); }
lagan-2.0/src/lagan.pl:219: @temp = `$lagandir/utils/scorealign $infofilename $consrate -bounds 0`;
lagan-2.0/src/lagan.pl-220- if ($?) { exit(5); }
##############################################
lagan-2.0/src/lagan.pl-223-
lagan-2.0/src/lagan.pl:224: @temp = `$lagandir/utils/scorealign $infofilename $consrate -bounds 1`;
lagan-2.0/src/lagan.pl-225- if ($?) { exit(6); }
##############################################
lagan-2.0/src/lagan.pl-232- close (INFOFILE);
lagan-2.0/src/lagan.pl:233:# `$lagandir/utils/rm $infofilename` if ($binfile);
lagan-2.0/src/lagan.pl-234-}
lagan-2.0/src/lagan.pl-235-
lagan-2.0/src/lagan.pl:236:`rm $secondName` if ($rcflag);
lagan-2.0/src/lagan.pl:237:`rm $$.*`;
lagan-2.0/src/lagan.pl-238-if ($?) { exit(1); }
##############################################
lagan-2.0/src/rechaos.pl-124-
lagan-2.0/src/rechaos.pl:125:$seq1len = `$lagandir/utils/getlength $seq1`; chomp $seq1len;
lagan-2.0/src/rechaos.pl:126:$seq2len = `$lagandir/utils/getlength $seq2`; chomp $seq2len;
lagan-2.0/src/rechaos.pl-127-
##############################################
lagan-2.0/src/rechaos.pl-180-# print STDERR "PAIRS hits\n";
lagan-2.0/src/rechaos.pl:181:# print STDERR `cat $$.anchs.pairs`;
lagan-2.0/src/rechaos.pl-182-# print STDERR "-----------------\n";
lagan-2.0/src/rechaos.pl:183:# print STDERR `cat $$.anchs.pairs`;
lagan-2.0/src/rechaos.pl-184-# print STDERR "-----------------\n";
##############################################
lagan-2.0/src/rechaos.pl-189- $saver = "$lagandir/chaos $seq1 $seq2 $extraparams -wl $wordlen -nd $degeneracy -co $cutoff $gfc $chaosfl -pairs $$.anchs.pairs > $$.anchtemp";
lagan-2.0/src/rechaos.pl:190: `$lagandir/chaos $seq1 $seq2 $extraparams -wl $wordlen -nd $degeneracy -co $cutoff $gfc $chaosfl -pairs $$.anchs.pairs > $$.anchtemp`;
lagan-2.0/src/rechaos.pl-191- if ($?) {
##############################################
lagan-2.0/src/rechaos.pl-211-
lagan-2.0/src/rechaos.pl:212:# `wc $$.anchtemp` =~ /(\d+)/x;
lagan-2.0/src/rechaos.pl-213-# $totalanchs = $totalanchs + $1;
lagan-2.0/src/rechaos.pl-214-# print STDERR "CHAOS hits\n";
lagan-2.0/src/rechaos.pl:215:# print STDERR `cat $$.anchtemp`;
lagan-2.0/src/rechaos.pl-216-
##############################################
lagan-2.0/src/rechaos.pl-218-
lagan-2.0/src/rechaos.pl:219: `$lagandir/anchors $$.anchtemp $gfc $anchparams | sort -n +1 > $$.anchs.sorted`;
lagan-2.0/src/rechaos.pl-220- if ($?) { exit(1); }
##############################################
lagan-2.0/src/rechaos.pl-228-
lagan-2.0/src/rechaos.pl:229:# `wc $$.anchs` =~ /(\d+)/x;
lagan-2.0/src/rechaos.pl-230-# print STDERR "ANCHS hits\n";
lagan-2.0/src/rechaos.pl:231:# print STDERR `cat $$.anchs.sorted`;
lagan-2.0/src/rechaos.pl-232-# $goodanchs = $goodanchs + $1;
##############################################
lagan-2.0/src/rechaos.pl-359-
lagan-2.0/src/rechaos.pl:360:$res = `sort -nr +1 $$.anchs.sorted`;
lagan-2.0/src/rechaos.pl-361-if ($?) { exit(1); }
lagan-2.0/src/rechaos.pl-362-
lagan-2.0/src/rechaos.pl:363:`rm $$.*`;
lagan-2.0/src/rechaos.pl-364-
##############################################
lagan-2.0/src/slagan-mfa.pl-28-my $args = join(" ", @ARGV);
lagan-2.0/src/slagan-mfa.pl:29:system($LAGAN_DIR."/slagan.pl $args > slagan.pl.out");
lagan-2.0/src/slagan-mfa.pl-30-die("$0: slagan.pl returned error $?. Stopped") if $?;
lagan-2.0/src/slagan-mfa.pl-31-
lagan-2.0/src/slagan-mfa.pl:32:system($LAGAN_DIR."/xmfa2mfa.pl ".($base eq "2" ? "2" : "1")." < slagan.pl.out ".($outfile ? "> $outfile" : ""));
lagan-2.0/src/slagan-mfa.pl-33-die("$0: xmfa2mfa.pl returned error $?. Stopped") if $?;
##############################################
lagan-2.0/src/slagan.pl-43- $outfile = $ARGV[++$i];
lagan-2.0/src/slagan.pl:44: if (-e "$outfile") { system("rm $outfile") and exit(1); }
lagan-2.0/src/slagan.pl-45- } elsif ($ARGV[$i] =~ /-order/) {
##############################################
lagan-2.0/src/slagan.pl-67-
lagan-2.0/src/slagan.pl:68:my $seq1len = `$lagandir/utils/getlength $firstName`;
lagan-2.0/src/slagan.pl:69:my $seq2len = `$lagandir/utils/getlength $secondName`;
lagan-2.0/src/slagan.pl-70-chomp $seq1len;
##############################################
lagan-2.0/src/slagan.pl-72-
lagan-2.0/src/slagan.pl:73:`$lagandir/chaos $seq1 $seq2 $chaos_fl > chaos.$$`;
lagan-2.0/src/slagan.pl-74-if ($?) { exit(1); }
lagan-2.0/src/slagan.pl-75-
lagan-2.0/src/slagan.pl:76:#`$lagandir/glocal chaos.$$ $glocal_fl > out.$$`;
lagan-2.0/src/slagan.pl:77:#@regs = `$lagandir/anal_gloc.pl < out.$$`;
lagan-2.0/src/slagan.pl-78-#print @regs;
##############################################
lagan-2.0/src/slagan.pl-84-#print $supermap_inv."\n";
lagan-2.0/src/slagan.pl:85:system($supermap_inv);
lagan-2.0/src/slagan.pl-86-
##############################################
lagan-2.0/src/slagan.pl-132-#print "$lagandir/utils/fa2xfa $firstName $startreg1 $endreg1 1 > seq1$k.$$\n";
lagan-2.0/src/slagan.pl:133: `$lagandir/utils/fa2xfa $firstName $startreg1 $endreg1 1 > seq1$k.$$\n`;
lagan-2.0/src/slagan.pl-134-#print "$lagandir/utils/fa2xfa $secondName $startreg2 $endreg2 2 $rcf > seq2$k.$$\n";
lagan-2.0/src/slagan.pl:135: `$lagandir/utils/fa2xfa $secondName $startreg2 $endreg2 2 $rcf > seq2$k.$$\n`;
lagan-2.0/src/slagan.pl:136:# if ($extra1) { `$lagandir/utils/fa2xfa $seq1 $startreg1 $endreg1 1 > seq1$k.$$.masked\n`; }
lagan-2.0/src/slagan.pl:137:# if ($extra2) { `$lagandir/utils/fa2xfa $seq2 $startreg2 $endreg2 2 $rcf > seq2$k.$$.masked\n`; }
lagan-2.0/src/slagan.pl-138-#print "$lagandir/lagan.pl seq1$k.$$ seq2$k.$$ $arglist $lagan_fl -mfa -out lagan.$k.$$\n";
lagan-2.0/src/slagan.pl:139: `$lagandir/lagan.pl seq1$k.$$ seq2$k.$$ $arglist $lagan_fl -mfa -out lagan.$k.$$\n`;
lagan-2.0/src/slagan.pl-140-
##############################################
lagan-2.0/src/slagan.pl-145-#print "$lagandir/utils/scorealign lagan.$k.$$ 45 -cropxmfa -ibounds $suff\n";
lagan-2.0/src/slagan.pl:146: print `$lagandir/utils/scorealign lagan.$k.$$ 45 -cropxmfa -ibounds $suff`;
lagan-2.0/src/slagan.pl-147- } else {
lagan-2.0/src/slagan.pl-148-#print "$lagandir/utils/scorealign lagan.$k.$$ 45 -ibounds\n";
lagan-2.0/src/slagan.pl:149: my $sc = `$lagandir/utils/scorealign lagan.$k.$$ 45 -ibounds`;
lagan-2.0/src/slagan.pl-150- chomp($sc);
lagan-2.0/src/slagan.pl-151- if ($sc) {
lagan-2.0/src/slagan.pl:152: print `cat lagan.$k.$$ $suff`;
lagan-2.0/src/slagan.pl:153: print `echo \"=$sc $type\n\" $suff`;
lagan-2.0/src/slagan.pl-154- }
##############################################
lagan-2.0/src/slagan.pl-164-
lagan-2.0/src/slagan.pl:165:`cat chaos.$$ > ${outName1}_$outName2.chaos`;
lagan-2.0/src/slagan.pl:166:####`cat out.$$ > ${outName1}_$outName2.mon`;
lagan-2.0/src/slagan.pl-167-unlink(glob("*.$$"));
lagan-2.0/src/slagan.pl:168:if ($extra1 || $extra2) { `rm *.$$.masked`; }
lagan-2.0/src/slagan.pl-169-exit(0);
##############################################
lagan-2.0/src/supermap.pl-349- foreach my $file (@input_files) {
lagan-2.0/src/supermap.pl:350: system('awk \'{$13=($13+$15)?$13:1; print $1,$2,$3";",$5,$6,$7"; '.
lagan-2.0/src/supermap.pl-351- 'score = "' . $c1 . '*$8-' . $c2 . '*$9-' . $c3 . '*($12+$14)-' . $c4 .
##############################################
lagan-2.0/src/supermap.pl-356- foreach my $file (@input_files) {
lagan-2.0/src/supermap.pl:357: system('ln -s "'.$input_dir.$file.'" "'.$tmp_dir.$file.'.chaos"');
lagan-2.0/src/supermap.pl-358- }
##############################################
lagan-2.0/src/supermap.pl-539- print("Job $.: \"$0 $_\"\n") if $debug;
lagan-2.0/src/supermap.pl:540: system("cd $tmp_dir; $supermapexec ".$_);
lagan-2.0/src/supermap.pl-541- }
##############################################
lagan-2.0/src/supermap.pl-552- } else { # I am the child
lagan-2.0/src/supermap.pl:553: die("$0: Could not exec \"$clust_run_invoke\"") unless exec($clust_run_invoke);
lagan-2.0/src/supermap.pl-554- }
##############################################
lagan-2.0/src/supermap.pl-558- foreach my $i (1..$num_jobs-1) {
lagan-2.0/src/supermap.pl:559: system("cd $tmp_dir; tar -xf ".$tmp_dir."JOB".$i.".results.tar");
lagan-2.0/src/supermap.pl-560- unlink $tmp_dir."JOB".$i.".tar" unless $nodelete;
##############################################
lagan-2.0/src/supermap.pl-1400- move($io_dir."/".$tar_file, $tmp_dir);
lagan-2.0/src/supermap.pl:1401: my @files = `cd $tmp_dir; tar -xvf $tar_file` or warn("$0 (worker): Error extracting $tar_file");
lagan-2.0/src/supermap.pl-1402- foreach my $file (@files) {
##############################################
lagan-2.0/src/utils/cmerge2.pl-51-close (OFILE);
lagan-2.0/src/utils/cmerge2.pl:52:`cp $ARGV[3] $ARGV[3].masked`;
lagan-2.0/src/utils/cmerge2.pl-53-
##############################################
lagan-2.0/src/utils/cmerge2.pl-58-close (OFILE);
lagan-2.0/src/utils/cmerge2.pl:59:$padlength = `$lagandir/utils/getlength $newdir/padding`; chomp $padlength;
lagan-2.0/src/utils/cmerge2.pl-60-
lagan-2.0/src/utils/cmerge2.pl-61-# other initialization
lagan-2.0/src/utils/cmerge2.pl:62:$totlength = `$lagandir/utils/getlength $ARGV[0]`;
lagan-2.0/src/utils/cmerge2.pl-63-chomp $totlength;
##############################################
lagan-2.0/src/utils/cmerge2.pl-67-$numContigs = 0;
lagan-2.0/src/utils/cmerge2.pl:68:@list = `cat $ARGV[2]`;
lagan-2.0/src/utils/cmerge2.pl-69-
##############################################
lagan-2.0/src/utils/cmerge2.pl-81- $temp = $seq1Begin[$i-3] - $s1shifts[$i-3];
lagan-2.0/src/utils/cmerge2.pl:82: $seq2Begin[$i-3] = `$lagandir/utils/getcontigpos $filenames[$i-3].mfa $temp`; chomp $seq2Begin[$i-3];
lagan-2.0/src/utils/cmerge2.pl-83- $seq2Begin[$i-3] += $s2shifts[$i-3];
##############################################
lagan-2.0/src/utils/cmerge2.pl-85- $temp = $seq1End[$i-3] - $s1shifts[$i-3];
lagan-2.0/src/utils/cmerge2.pl:86: $seq2End[$i-3] = `$lagandir/utils/getcontigpos $filenames[$i-3].mfa $temp`; chomp $seq2End[$i-3];
lagan-2.0/src/utils/cmerge2.pl-87- $seq2End[$i-3] += $s2shifts[$i-3];
##############################################
lagan-2.0/src/utils/cmerge2.pl-101-# start out merged file with only padding
lagan-2.0/src/utils/cmerge2.pl:102:`mv $ARGV[3] $ARGV[3].new`;
lagan-2.0/src/utils/cmerge2.pl:103:`$lagandir/utils/seqmerge $ARGV[3].new $newdir/padding > $ARGV[3]`;
lagan-2.0/src/utils/cmerge2.pl:104:`mv $ARGV[3].masked $ARGV[3].masked.new`;
lagan-2.0/src/utils/cmerge2.pl:105:`$lagandir/utils/seqmerge $ARGV[3].masked.new $newdir/padding > $ARGV[3].masked`;
lagan-2.0/src/utils/cmerge2.pl-106-$contigStart[0] = 1;
##############################################
lagan-2.0/src/utils/cmerge2.pl-108-
lagan-2.0/src/utils/cmerge2.pl:109:`cp $filenames[0] $newdir/current`;
lagan-2.0/src/utils/cmerge2.pl:110:`cp $filenames[0].masked $newdir/current.masked`;
lagan-2.0/src/utils/cmerge2.pl-111-
##############################################
lagan-2.0/src/utils/cmerge2.pl-113-for ($i = 1; $i < $numContigs; $i++){
lagan-2.0/src/utils/cmerge2.pl:114: `$lagandir/rechaos.pl $newdir/current $filenames[$i] -recurse \"(12,0,40,0)x\" -maskedonly > $newdir/currentanchs`;
lagan-2.0/src/utils/cmerge2.pl-115- # find the overlap
lagan-2.0/src/utils/cmerge2.pl-116-
lagan-2.0/src/utils/cmerge2.pl:117: `$lagandir/utils/getoverlap $newdir/currentanchs` =~ /(-?\d+) (-?\d+) (-?\d+) (-?\d+)/;
lagan-2.0/src/utils/cmerge2.pl-118- $rangebegin1 = $1;
##############################################
lagan-2.0/src/utils/cmerge2.pl-127-
lagan-2.0/src/utils/cmerge2.pl:128: $thislength = `$lagandir/utils/getlength $filenames[$i-1]`; chomp $thislength;
lagan-2.0/src/utils/cmerge2.pl:129: $nextlength = `$lagandir/utils/getlength $filenames[$i]`; chomp $nextlength;
lagan-2.0/src/utils/cmerge2.pl-130-
##############################################
lagan-2.0/src/utils/cmerge2.pl-135-
lagan-2.0/src/utils/cmerge2.pl:136: `mv $ARGV[3] $ARGV[3].new`;
lagan-2.0/src/utils/cmerge2.pl:137: `$lagandir/utils/seqmerge $ARGV[3].new $newdir/current $newdir/padding > $ARGV[3]`;
lagan-2.0/src/utils/cmerge2.pl:138: `cp $filenames[$i] $newdir/current`;
lagan-2.0/src/utils/cmerge2.pl-139-
lagan-2.0/src/utils/cmerge2.pl:140: `mv $ARGV[3].masked $ARGV[3].masked.new`;
lagan-2.0/src/utils/cmerge2.pl:141: `$lagandir/utils/seqmerge $ARGV[3].masked.new $newdir/current.masked $newdir/padding > $ARGV[3].masked`;
lagan-2.0/src/utils/cmerge2.pl:142: `cp $filenames[$i].masked $newdir/current.masked`;
lagan-2.0/src/utils/cmerge2.pl-143-
##############################################
lagan-2.0/src/utils/cmerge2.pl-155- if ($j > 0){
lagan-2.0/src/utils/cmerge2.pl:156: `$lagandir/utils/cextract $newdir/current 1 $j 0 0 > $newdir/overlap`;
lagan-2.0/src/utils/cmerge2.pl:157: `$lagandir/utils/cextract $newdir/current.masked 1 $j 0 0 > $newdir/overlap.masked`;
lagan-2.0/src/utils/cmerge2.pl:158: $overlaplength = `$lagandir/utils/getlength $newdir/overlap`; chomp $overlaplength;
lagan-2.0/src/utils/cmerge2.pl-159-
lagan-2.0/src/utils/cmerge2.pl:160: `mv $ARGV[3] $ARGV[3].new`;
lagan-2.0/src/utils/cmerge2.pl:161: `$lagandir/utils/seqmerge $ARGV[3].new $newdir/overlap > $ARGV[3]`;
lagan-2.0/src/utils/cmerge2.pl:162: `mv $ARGV[3].masked $ARGV[3].masked.new`;
lagan-2.0/src/utils/cmerge2.pl:163: `$lagandir/utils/seqmerge $ARGV[3].masked.new $newdir/overlap.masked > $ARGV[3].masked`;
lagan-2.0/src/utils/cmerge2.pl-164- }
##############################################
lagan-2.0/src/utils/cmerge2.pl-166- # extract the nonoverlapped region > current
lagan-2.0/src/utils/cmerge2.pl:167: `$lagandir/utils/cextract $filenames[$i] $rangebegin2 $nextlength 0 0 > $newdir/current`;
lagan-2.0/src/utils/cmerge2.pl:168: `$lagandir/utils/cextract $filenames[$i].masked $rangebegin2 $nextlength 0 0 > $newdir/current.masked`;
lagan-2.0/src/utils/cmerge2.pl-169-
##############################################
lagan-2.0/src/utils/cmerge2.pl-176- if (index ($filenames[$i-1], ".rc") == -1) { $direction = "+"; } else { $direction = "-"; }
lagan-2.0/src/utils/cmerge2.pl:177: @temp = `head $filenames[$i-1]`;
lagan-2.0/src/utils/cmerge2.pl-178- chomp $temp[0]; $temp[0] = substr $temp[0], 1;
##############################################
lagan-2.0/src/utils/cmerge2.pl-184-
lagan-2.0/src/utils/cmerge2.pl:185:$thislength = `$lagandir/utils/getlength $filenames[$numContigs - 1]`; chomp $thislength;
lagan-2.0/src/utils/cmerge2.pl-186-$contigEnd[$numContigs - 1] = $contigStart[$numContigs - 1] + $thislength - 1;
##############################################
lagan-2.0/src/utils/cmerge2.pl-188-
lagan-2.0/src/utils/cmerge2.pl:189:`mv $ARGV[3] $ARGV[3].new`;
lagan-2.0/src/utils/cmerge2.pl:190:`$lagandir/utils/seqmerge $ARGV[3].new $newdir/current $newdir/padding > $ARGV[3]`;
lagan-2.0/src/utils/cmerge2.pl:191:`mv $ARGV[3].masked $ARGV[3].masked.new`;
lagan-2.0/src/utils/cmerge2.pl:192:`$lagandir/utils/seqmerge $ARGV[3].masked.new $newdir/current.masked $newdir/padding > $ARGV[3].masked`;
lagan-2.0/src/utils/cmerge2.pl-193-
lagan-2.0/src/utils/cmerge2.pl-194-if (index ($filenames[$numContigs - 1], ".rc") == -1) { $direction = "+"; } else { $direction = "-"; }
lagan-2.0/src/utils/cmerge2.pl:195:@temp = `head $filenames[$numContigs - 1]`;
lagan-2.0/src/utils/cmerge2.pl-196-chomp $temp[0]; $temp[0] = substr $temp[0], 1;
##############################################
lagan-2.0/src/utils/draft.pl-62-$newdir = "$newdir/$pid";
lagan-2.0/src/utils/draft.pl:63:`mkdir $newdir` if (!(-e $newdir));
lagan-2.0/src/utils/draft.pl-64-
##############################################
lagan-2.0/src/utils/draft.pl-78-
lagan-2.0/src/utils/draft.pl:79:`cp $ARGV[1] $newdir`;
lagan-2.0/src/utils/draft.pl:80:@contigs = `perl $lagandir/mextract.pl $newdir/$contigfile`;
lagan-2.0/src/utils/draft.pl-81-if ($?) { exit(1);}
##############################################
lagan-2.0/src/utils/draft.pl-83- chomp $contigs[$i];
lagan-2.0/src/utils/draft.pl:84: `$lagandir/utils/rc < $contigs[$i] > $contigs[$i].rc`;
lagan-2.0/src/utils/draft.pl-85- if ($?) { exit(1); }
##############################################
lagan-2.0/src/utils/draft.pl-92- $maskedcontigfile = basename ($maskedname);
lagan-2.0/src/utils/draft.pl:93: `cp $maskedname $newdir`;
lagan-2.0/src/utils/draft.pl:94: @maskedcontigs = `perl $lagandir/mextract.pl $newdir/$maskedcontigfile -masked`;
lagan-2.0/src/utils/draft.pl-95- if ($?) { exit(1);}
##############################################
lagan-2.0/src/utils/draft.pl-97- chomp $maskedcontigs[$i];
lagan-2.0/src/utils/draft.pl:98: `$lagandir/utils/rc < $maskedcontigs[$i] > $contigs[$i].rc.masked`;
lagan-2.0/src/utils/draft.pl-99- if ($?) { exit(1); }
##############################################
lagan-2.0/src/utils/draft.pl-113- $execute = $execute." -gap $anchgapstart $anchgapcont" if ($usebounds);
lagan-2.0/src/utils/draft.pl:114: `$execute`;
lagan-2.0/src/utils/draft.pl-115- $ex_val = $? >> 8;
##############################################
lagan-2.0/src/utils/draft.pl-120- # compute bounds
lagan-2.0/src/utils/draft.pl:121: @bounds = `$lagandir/utils/getbounds anchs.final $ARGV[0] $contigs[$i]`;
lagan-2.0/src/utils/draft.pl-122- if ($?) { exit(1);}
##############################################
lagan-2.0/src/utils/draft.pl-132- $execute = $execute." -gap $anchgapstart $anchgapcont" if ($usebounds);
lagan-2.0/src/utils/draft.pl:133: `$execute`;
lagan-2.0/src/utils/draft.pl-134- $ex_val = $? >> 8;
##############################################
lagan-2.0/src/utils/draft.pl-138- # compute bounds
lagan-2.0/src/utils/draft.pl:139: @bounds = `$lagandir/utils/getbounds anchs.final $ARGV[0] $contigs[$i].rc`;
lagan-2.0/src/utils/draft.pl-140- if ($?) { exit(1);}
##############################################
lagan-2.0/src/utils/draft.pl-151- else {
lagan-2.0/src/utils/draft.pl:152: $fscore = `$lagandir/utils/scorealign $contigs[$i].mfa $startingrate`; chomp $fscore;
lagan-2.0/src/utils/draft.pl-153- if ($?) { exit(1);}
##############################################
lagan-2.0/src/utils/draft.pl-158- else {
lagan-2.0/src/utils/draft.pl:159: $bscore = `$lagandir/utils/scorealign $contigs[$i].rc.mfa $startingrate`; chomp $bscore;
lagan-2.0/src/utils/draft.pl-160- if ($?) { exit(1);}
##############################################
lagan-2.0/src/utils/draft.pl-201-for ($cutoff = $startingrate; !$foundorder && ($cutoff < 100); $cutoff += $rateinc){
lagan-2.0/src/utils/draft.pl:202: `$lagandir/utils/scorecontigs /$newdir/filenames $ARGV[0] $newdir/contignames $cutoff > $newdir/ranges`;
lagan-2.0/src/utils/draft.pl-203- if ($?) { exit(1);}
lagan-2.0/src/utils/draft.pl:204: @list = `cat $newdir/ranges`;
lagan-2.0/src/utils/draft.pl-205- $list[0] =~ /numContigs = (\d+)/;
##############################################
lagan-2.0/src/utils/draft.pl-207-
lagan-2.0/src/utils/draft.pl:208: `$lagandir/utils/contigorder $newdir/ranges > $newdir/corder`;
lagan-2.0/src/utils/draft.pl-209- if ($?) { exit(1);}
lagan-2.0/src/utils/draft.pl:210: @list = `cat $newdir/corder`;
lagan-2.0/src/utils/draft.pl-211- chomp $list[0];
##############################################
lagan-2.0/src/utils/draft.pl-219-
lagan-2.0/src/utils/draft.pl:220: @contignames = `cat $newdir/contignames`;
lagan-2.0/src/utils/draft.pl-221- for ($i = 0; $i < @contignames; $i++){
##############################################
lagan-2.0/src/utils/draft.pl-228-
lagan-2.0/src/utils/draft.pl:229: @list = `cat $newdir/corder`;
lagan-2.0/src/utils/draft.pl-230- for ($i = 0; $i < @list; $i++){
##############################################
lagan-2.0/src/utils/draft.pl-236-
lagan-2.0/src/utils/draft.pl:237: print STDERR `cat $newdir/draft`;
lagan-2.0/src/utils/draft.pl:238: print LOGFILE `cat $newdir/draft`;
lagan-2.0/src/utils/draft.pl-239- close (LOGFILE);
##############################################
lagan-2.0/src/utils/draft.pl-250-
lagan-2.0/src/utils/draft.pl:251:`$lagandir/cmerge2.pl $filename1 $filename2 $newdir/draft $filename2.merged -skipfr $pid`;
lagan-2.0/src/utils/draft.pl-252-if ($?) { exit(1); }
##############################################
lagan-2.0/src/utils/draft.pl-255-
lagan-2.0/src/utils/draft.pl:256:`cp $filename2.merged merged_seq.fa`;
lagan-2.0/src/utils/draft.pl:257:`cp $filename2.merged.masked merged_seq.fa.masked`;
lagan-2.0/src/utils/draft.pl:258:`cp $newdir/minfo minfo`;
lagan-2.0/src/utils/draft.pl:259:`cp $newdir/ranges ranges`;
lagan-2.0/src/utils/draft.pl:260:`cp $newdir/log log`;
lagan-2.0/src/utils/draft.pl-261-
##############################################
lagan-2.0/src/utils/draft.pl-265-
lagan-2.0/src/utils/draft.pl:266:# `rm -rf $newdir`;
lagan-2.0/src/utils/draft.pl-267-
##############################################
lagan-2.0/src/utils/mrun.pl-96-print "$mextstr\n";
lagan-2.0/src/utils/mrun.pl:97:if(!`$mextstr`) { print "\nMulti-FASTA extraction failure...\n"; exit(1); }
lagan-2.0/src/utils/mrun.pl-98-
##############################################
lagan-2.0/src/utils/mrun.pl-101- print "$mextstr\n";
lagan-2.0/src/utils/mrun.pl:102: if(!`$mextstr`) {
lagan-2.0/src/utils/mrun.pl-103- print "\nMasked Multi-FASTA extraction failure...\n";
##############################################
lagan-2.0/src/utils/mrun.pl-173-print STDERR "\n$mlagan\n\n";
lagan-2.0/src/utils/mrun.pl:174:if(`$mlagan`) { print "\n\n"; exit(1); }
lagan-2.0/src/utils/mrun.pl-175-
##############################################
lagan-2.0/src/utils/mrun.pl-194- print "$pstr\n";
lagan-2.0/src/utils/mrun.pl:195: if(`$pstr`) { print "\nprojection failure...\n"; exit(1); }
lagan-2.0/src/utils/mrun.pl-196- $bstr = "$binhead $outprefix.prj -out $outprefix.bin";
lagan-2.0/src/utils/mrun.pl-197- print "$bstr\n";
lagan-2.0/src/utils/mrun.pl:198: if(`$bstr`) { print "\npacking failure...\n"; exit(1); }
lagan-2.0/src/utils/mrun.pl-199- @bins[$j++] = "$outprefix.bin";
##############################################
lagan-2.0/src/utils/mrun.pl-232-print "touch $prefix.ann\n\n";
lagan-2.0/src/utils/mrun.pl:233:`touch $prefix.ann`;
lagan-2.0/src/utils/mrun.pl-234-
##############################################
lagan-2.0/src/utils/mrun.pl-244-
lagan-2.0/src/utils/mrun.pl:245:#$vistadir = `echo \$VISTA_DIR`;
lagan-2.0/src/utils/mrun.pl-246-#chomp $vistadir;
##############################################
lagan-2.0/src/utils/mrun.pl-254-#print "$vistastr\n";
lagan-2.0/src/utils/mrun.pl:255:#if (!`$vistastr`) { print "\nVISTA failure...\n"; exit(1); }
lagan-2.0/src/utils/mrun.pl-256-
##############################################
lagan-2.0/src/utils/mrunfile.pl-76-print "$mstr\n";
lagan-2.0/src/utils/mrunfile.pl:77:`$mstr`;
lagan-2.0/src/utils/mrunfile.pl-78-
##############################################
lagan-2.0/src/utils/mrunfile.pl-93- print "$vistastr\n";
lagan-2.0/src/utils/mrunfile.pl:94: if (!`$vistastr`) { print "\nVISTA failure...\n"; exit(1); }
lagan-2.0/src/utils/mrunfile.pl-95-
##############################################
lagan-2.0/src/utils/mrunpairs.pl-96-print "$mextstr\n";
lagan-2.0/src/utils/mrunpairs.pl:97:if(!`$mextstr`) { print "\nMulti-FASTA extraction failure...\n"; exit(1); }
lagan-2.0/src/utils/mrunpairs.pl-98-
##############################################
lagan-2.0/src/utils/mrunpairs.pl-101- print "$mextstr\n";
lagan-2.0/src/utils/mrunpairs.pl:102: if(!`$mextstr`) {
lagan-2.0/src/utils/mrunpairs.pl-103- print "\nMasked Multi-FASTA extraction failure...\n";
##############################################
lagan-2.0/src/utils/mrunpairs.pl-193- print "\n$mlagan\n\n";
lagan-2.0/src/utils/mrunpairs.pl:194: if(`$mlagan`) { print "\n\n"; exit(1); }
lagan-2.0/src/utils/mrunpairs.pl-195-
##############################################
lagan-2.0/src/utils/mrunpairs.pl-198- print "$bstr\n";
lagan-2.0/src/utils/mrunpairs.pl:199: if(`$bstr`) { print "\npacking failure...\n"; exit(1); }
lagan-2.0/src/utils/mrunpairs.pl-200- @bins[$j++] = "$outprefix.bin";
##############################################
lagan-2.0/src/utils/mrunpairs.pl-236-print "touch $prefix.ann\n\n";
lagan-2.0/src/utils/mrunpairs.pl:237:`touch $prefix.ann`;
lagan-2.0/src/utils/mrunpairs.pl-238-
##############################################
lagan-2.0/src/utils/mrunpairs.pl-248-
lagan-2.0/src/utils/mrunpairs.pl:249:#$vistadir = `echo \$VISTA_DIR`;
lagan-2.0/src/utils/mrunpairs.pl-250-#chomp $vistadir;
##############################################
lagan-2.0/src/utils/mrunpairs.pl-258-#print "$vistastr\n";
lagan-2.0/src/utils/mrunpairs.pl:259:#if (!`$vistastr`) { print "\nVISTA failure...\n"; exit(1); }
lagan-2.0/src/utils/mrunpairs.pl-260-
##############################################
lagan-2.0/src/utils/mviz.pl-159- print "$pstr\n";
lagan-2.0/src/utils/mviz.pl:160: if(`$pstr`) { print "\nprojection failure...\n"; exit(1); }
lagan-2.0/src/utils/mviz.pl-161- $bstr = "$binhead $outprefix.prj -out $outprefix.bin";
lagan-2.0/src/utils/mviz.pl-162- print "$bstr\n";
lagan-2.0/src/utils/mviz.pl:163: if(`$bstr`) { print "\npacking failure...\n"; exit(1); }
lagan-2.0/src/utils/mviz.pl-164- @bins[$j++] = "$outprefix.bin";
##############################################
lagan-2.0/src/utils/mviz.pl-199- print "touch $prefix.ann\n\n";
lagan-2.0/src/utils/mviz.pl:200: `touch $prefix.ann`;
lagan-2.0/src/utils/mviz.pl-201-
##############################################
lagan-2.0/src/utils/mviz.pl-217-print "$vistastr\n";
lagan-2.0/src/utils/mviz.pl:218:if (!`$vistastr`) { print "\nVISTA failure...\n"; exit(1); }
lagan-2.0/src/utils/mviz.pl-219-
##############################################
lagan-2.0/src/Utils.pm-117- }
lagan-2.0/src/Utils.pm:118: my $Host = $Uname ? `$Uname -n` : 'localhost';
lagan-2.0/src/Utils.pm-119- chomp($Host);
##############################################
lagan-2.0/src/xmfa2mfa.pl-49-
lagan-2.0/src/xmfa2mfa.pl:50:system($ENV{"LAGAN_DIR"}."/utils/Glue tmp.xmfa > glue.out 2> glue.err");
lagan-2.0/src/xmfa2mfa.pl-51-
##############################################
lagan-2.0/supermap.pl-349- foreach my $file (@input_files) {
lagan-2.0/supermap.pl:350: system('awk \'{$13=($13+$15)?$13:1; print $1,$2,$3";",$5,$6,$7"; '.
lagan-2.0/supermap.pl-351- 'score = "' . $c1 . '*$8-' . $c2 . '*$9-' . $c3 . '*($12+$14)-' . $c4 .
##############################################
lagan-2.0/supermap.pl-356- foreach my $file (@input_files) {
lagan-2.0/supermap.pl:357: system('ln -s "'.$input_dir.$file.'" "'.$tmp_dir.$file.'.chaos"');
lagan-2.0/supermap.pl-358- }
##############################################
lagan-2.0/supermap.pl-539- print("Job $.: \"$0 $_\"\n") if $debug;
lagan-2.0/supermap.pl:540: system("cd $tmp_dir; $supermapexec ".$_);
lagan-2.0/supermap.pl-541- }
##############################################
lagan-2.0/supermap.pl-552- } else { # I am the child
lagan-2.0/supermap.pl:553: die("$0: Could not exec \"$clust_run_invoke\"") unless exec($clust_run_invoke);
lagan-2.0/supermap.pl-554- }
##############################################
lagan-2.0/supermap.pl-558- foreach my $i (1..$num_jobs-1) {
lagan-2.0/supermap.pl:559: system("cd $tmp_dir; tar -xf ".$tmp_dir."JOB".$i.".results.tar");
lagan-2.0/supermap.pl-560- unlink $tmp_dir."JOB".$i.".tar" unless $nodelete;
##############################################
lagan-2.0/supermap.pl-1400- move($io_dir."/".$tar_file, $tmp_dir);
lagan-2.0/supermap.pl:1401: my @files = `cd $tmp_dir; tar -xvf $tar_file` or warn("$0 (worker): Error extracting $tar_file");
lagan-2.0/supermap.pl-1402- foreach my $file (@files) {
##############################################
lagan-2.0/utils/cmerge2.pl-51-close (OFILE);
lagan-2.0/utils/cmerge2.pl:52:`cp $ARGV[3] $ARGV[3].masked`;
lagan-2.0/utils/cmerge2.pl-53-
##############################################
lagan-2.0/utils/cmerge2.pl-58-close (OFILE);
lagan-2.0/utils/cmerge2.pl:59:$padlength = `$lagandir/utils/getlength $newdir/padding`; chomp $padlength;
lagan-2.0/utils/cmerge2.pl-60-
lagan-2.0/utils/cmerge2.pl-61-# other initialization
lagan-2.0/utils/cmerge2.pl:62:$totlength = `$lagandir/utils/getlength $ARGV[0]`;
lagan-2.0/utils/cmerge2.pl-63-chomp $totlength;
##############################################
lagan-2.0/utils/cmerge2.pl-67-$numContigs = 0;
lagan-2.0/utils/cmerge2.pl:68:@list = `cat $ARGV[2]`;
lagan-2.0/utils/cmerge2.pl-69-
##############################################
lagan-2.0/utils/cmerge2.pl-81- $temp = $seq1Begin[$i-3] - $s1shifts[$i-3];
lagan-2.0/utils/cmerge2.pl:82: $seq2Begin[$i-3] = `$lagandir/utils/getcontigpos $filenames[$i-3].mfa $temp`; chomp $seq2Begin[$i-3];
lagan-2.0/utils/cmerge2.pl-83- $seq2Begin[$i-3] += $s2shifts[$i-3];
##############################################
lagan-2.0/utils/cmerge2.pl-85- $temp = $seq1End[$i-3] - $s1shifts[$i-3];
lagan-2.0/utils/cmerge2.pl:86: $seq2End[$i-3] = `$lagandir/utils/getcontigpos $filenames[$i-3].mfa $temp`; chomp $seq2End[$i-3];
lagan-2.0/utils/cmerge2.pl-87- $seq2End[$i-3] += $s2shifts[$i-3];
##############################################
lagan-2.0/utils/cmerge2.pl-101-# start out merged file with only padding
lagan-2.0/utils/cmerge2.pl:102:`mv $ARGV[3] $ARGV[3].new`;
lagan-2.0/utils/cmerge2.pl:103:`$lagandir/utils/seqmerge $ARGV[3].new $newdir/padding > $ARGV[3]`;
lagan-2.0/utils/cmerge2.pl:104:`mv $ARGV[3].masked $ARGV[3].masked.new`;
lagan-2.0/utils/cmerge2.pl:105:`$lagandir/utils/seqmerge $ARGV[3].masked.new $newdir/padding > $ARGV[3].masked`;
lagan-2.0/utils/cmerge2.pl-106-$contigStart[0] = 1;
##############################################
lagan-2.0/utils/cmerge2.pl-108-
lagan-2.0/utils/cmerge2.pl:109:`cp $filenames[0] $newdir/current`;
lagan-2.0/utils/cmerge2.pl:110:`cp $filenames[0].masked $newdir/current.masked`;
lagan-2.0/utils/cmerge2.pl-111-
##############################################
lagan-2.0/utils/cmerge2.pl-113-for ($i = 1; $i < $numContigs; $i++){
lagan-2.0/utils/cmerge2.pl:114: `$lagandir/rechaos.pl $newdir/current $filenames[$i] -recurse \"(12,0,40,0)x\" -maskedonly > $newdir/currentanchs`;
lagan-2.0/utils/cmerge2.pl-115- # find the overlap
lagan-2.0/utils/cmerge2.pl-116-
lagan-2.0/utils/cmerge2.pl:117: `$lagandir/utils/getoverlap $newdir/currentanchs` =~ /(-?\d+) (-?\d+) (-?\d+) (-?\d+)/;
lagan-2.0/utils/cmerge2.pl-118- $rangebegin1 = $1;
##############################################
lagan-2.0/utils/cmerge2.pl-127-
lagan-2.0/utils/cmerge2.pl:128: $thislength = `$lagandir/utils/getlength $filenames[$i-1]`; chomp $thislength;
lagan-2.0/utils/cmerge2.pl:129: $nextlength = `$lagandir/utils/getlength $filenames[$i]`; chomp $nextlength;
lagan-2.0/utils/cmerge2.pl-130-
##############################################
lagan-2.0/utils/cmerge2.pl-135-
lagan-2.0/utils/cmerge2.pl:136: `mv $ARGV[3] $ARGV[3].new`;
lagan-2.0/utils/cmerge2.pl:137: `$lagandir/utils/seqmerge $ARGV[3].new $newdir/current $newdir/padding > $ARGV[3]`;
lagan-2.0/utils/cmerge2.pl:138: `cp $filenames[$i] $newdir/current`;
lagan-2.0/utils/cmerge2.pl-139-
lagan-2.0/utils/cmerge2.pl:140: `mv $ARGV[3].masked $ARGV[3].masked.new`;
lagan-2.0/utils/cmerge2.pl:141: `$lagandir/utils/seqmerge $ARGV[3].masked.new $newdir/current.masked $newdir/padding > $ARGV[3].masked`;
lagan-2.0/utils/cmerge2.pl:142: `cp $filenames[$i].masked $newdir/current.masked`;
lagan-2.0/utils/cmerge2.pl-143-
##############################################
lagan-2.0/utils/cmerge2.pl-155- if ($j > 0){
lagan-2.0/utils/cmerge2.pl:156: `$lagandir/utils/cextract $newdir/current 1 $j 0 0 > $newdir/overlap`;
lagan-2.0/utils/cmerge2.pl:157: `$lagandir/utils/cextract $newdir/current.masked 1 $j 0 0 > $newdir/overlap.masked`;
lagan-2.0/utils/cmerge2.pl:158: $overlaplength = `$lagandir/utils/getlength $newdir/overlap`; chomp $overlaplength;
lagan-2.0/utils/cmerge2.pl-159-
lagan-2.0/utils/cmerge2.pl:160: `mv $ARGV[3] $ARGV[3].new`;
lagan-2.0/utils/cmerge2.pl:161: `$lagandir/utils/seqmerge $ARGV[3].new $newdir/overlap > $ARGV[3]`;
lagan-2.0/utils/cmerge2.pl:162: `mv $ARGV[3].masked $ARGV[3].masked.new`;
lagan-2.0/utils/cmerge2.pl:163: `$lagandir/utils/seqmerge $ARGV[3].masked.new $newdir/overlap.masked > $ARGV[3].masked`;
lagan-2.0/utils/cmerge2.pl-164- }
##############################################
lagan-2.0/utils/cmerge2.pl-166- # extract the nonoverlapped region > current
lagan-2.0/utils/cmerge2.pl:167: `$lagandir/utils/cextract $filenames[$i] $rangebegin2 $nextlength 0 0 > $newdir/current`;
lagan-2.0/utils/cmerge2.pl:168: `$lagandir/utils/cextract $filenames[$i].masked $rangebegin2 $nextlength 0 0 > $newdir/current.masked`;
lagan-2.0/utils/cmerge2.pl-169-
##############################################
lagan-2.0/utils/cmerge2.pl-176- if (index ($filenames[$i-1], ".rc") == -1) { $direction = "+"; } else { $direction = "-"; }
lagan-2.0/utils/cmerge2.pl:177: @temp = `head $filenames[$i-1]`;
lagan-2.0/utils/cmerge2.pl-178- chomp $temp[0]; $temp[0] = substr $temp[0], 1;
##############################################
lagan-2.0/utils/cmerge2.pl-184-
lagan-2.0/utils/cmerge2.pl:185:$thislength = `$lagandir/utils/getlength $filenames[$numContigs - 1]`; chomp $thislength;
lagan-2.0/utils/cmerge2.pl-186-$contigEnd[$numContigs - 1] = $contigStart[$numContigs - 1] + $thislength - 1;
##############################################
lagan-2.0/utils/cmerge2.pl-188-
lagan-2.0/utils/cmerge2.pl:189:`mv $ARGV[3] $ARGV[3].new`;
lagan-2.0/utils/cmerge2.pl:190:`$lagandir/utils/seqmerge $ARGV[3].new $newdir/current $newdir/padding > $ARGV[3]`;
lagan-2.0/utils/cmerge2.pl:191:`mv $ARGV[3].masked $ARGV[3].masked.new`;
lagan-2.0/utils/cmerge2.pl:192:`$lagandir/utils/seqmerge $ARGV[3].masked.new $newdir/current.masked $newdir/padding > $ARGV[3].masked`;
lagan-2.0/utils/cmerge2.pl-193-
lagan-2.0/utils/cmerge2.pl-194-if (index ($filenames[$numContigs - 1], ".rc") == -1) { $direction = "+"; } else { $direction = "-"; }
lagan-2.0/utils/cmerge2.pl:195:@temp = `head $filenames[$numContigs - 1]`;
lagan-2.0/utils/cmerge2.pl-196-chomp $temp[0]; $temp[0] = substr $temp[0], 1;
##############################################
lagan-2.0/utils/draft.pl-62-$newdir = "$newdir/$pid";
lagan-2.0/utils/draft.pl:63:`mkdir $newdir` if (!(-e $newdir));
lagan-2.0/utils/draft.pl-64-
##############################################
lagan-2.0/utils/draft.pl-78-
lagan-2.0/utils/draft.pl:79:`cp $ARGV[1] $newdir`;
lagan-2.0/utils/draft.pl:80:@contigs = `perl $lagandir/mextract.pl $newdir/$contigfile`;
lagan-2.0/utils/draft.pl-81-if ($?) { exit(1);}
##############################################
lagan-2.0/utils/draft.pl-83- chomp $contigs[$i];
lagan-2.0/utils/draft.pl:84: `$lagandir/utils/rc < $contigs[$i] > $contigs[$i].rc`;
lagan-2.0/utils/draft.pl-85- if ($?) { exit(1); }
##############################################
lagan-2.0/utils/draft.pl-92- $maskedcontigfile = basename ($maskedname);
lagan-2.0/utils/draft.pl:93: `cp $maskedname $newdir`;
lagan-2.0/utils/draft.pl:94: @maskedcontigs = `perl $lagandir/mextract.pl $newdir/$maskedcontigfile -masked`;
lagan-2.0/utils/draft.pl-95- if ($?) { exit(1);}
##############################################
lagan-2.0/utils/draft.pl-97- chomp $maskedcontigs[$i];
lagan-2.0/utils/draft.pl:98: `$lagandir/utils/rc < $maskedcontigs[$i] > $contigs[$i].rc.masked`;
lagan-2.0/utils/draft.pl-99- if ($?) { exit(1); }
##############################################
lagan-2.0/utils/draft.pl-113- $execute = $execute." -gap $anchgapstart $anchgapcont" if ($usebounds);
lagan-2.0/utils/draft.pl:114: `$execute`;
lagan-2.0/utils/draft.pl-115- $ex_val = $? >> 8;
##############################################
lagan-2.0/utils/draft.pl-120- # compute bounds
lagan-2.0/utils/draft.pl:121: @bounds = `$lagandir/utils/getbounds anchs.final $ARGV[0] $contigs[$i]`;
lagan-2.0/utils/draft.pl-122- if ($?) { exit(1);}
##############################################
lagan-2.0/utils/draft.pl-132- $execute = $execute." -gap $anchgapstart $anchgapcont" if ($usebounds);
lagan-2.0/utils/draft.pl:133: `$execute`;
lagan-2.0/utils/draft.pl-134- $ex_val = $? >> 8;
##############################################
lagan-2.0/utils/draft.pl-138- # compute bounds
lagan-2.0/utils/draft.pl:139: @bounds = `$lagandir/utils/getbounds anchs.final $ARGV[0] $contigs[$i].rc`;
lagan-2.0/utils/draft.pl-140- if ($?) { exit(1);}
##############################################
lagan-2.0/utils/draft.pl-151- else {
lagan-2.0/utils/draft.pl:152: $fscore = `$lagandir/utils/scorealign $contigs[$i].mfa $startingrate`; chomp $fscore;
lagan-2.0/utils/draft.pl-153- if ($?) { exit(1);}
##############################################
lagan-2.0/utils/draft.pl-158- else {
lagan-2.0/utils/draft.pl:159: $bscore = `$lagandir/utils/scorealign $contigs[$i].rc.mfa $startingrate`; chomp $bscore;
lagan-2.0/utils/draft.pl-160- if ($?) { exit(1);}
##############################################
lagan-2.0/utils/draft.pl-201-for ($cutoff = $startingrate; !$foundorder && ($cutoff < 100); $cutoff += $rateinc){
lagan-2.0/utils/draft.pl:202: `$lagandir/utils/scorecontigs /$newdir/filenames $ARGV[0] $newdir/contignames $cutoff > $newdir/ranges`;
lagan-2.0/utils/draft.pl-203- if ($?) { exit(1);}
lagan-2.0/utils/draft.pl:204: @list = `cat $newdir/ranges`;
lagan-2.0/utils/draft.pl-205- $list[0] =~ /numContigs = (\d+)/;
##############################################
lagan-2.0/utils/draft.pl-207-
lagan-2.0/utils/draft.pl:208: `$lagandir/utils/contigorder $newdir/ranges > $newdir/corder`;
lagan-2.0/utils/draft.pl-209- if ($?) { exit(1);}
lagan-2.0/utils/draft.pl:210: @list = `cat $newdir/corder`;
lagan-2.0/utils/draft.pl-211- chomp $list[0];
##############################################
lagan-2.0/utils/draft.pl-219-
lagan-2.0/utils/draft.pl:220: @contignames = `cat $newdir/contignames`;
lagan-2.0/utils/draft.pl-221- for ($i = 0; $i < @contignames; $i++){
##############################################
lagan-2.0/utils/draft.pl-228-
lagan-2.0/utils/draft.pl:229: @list = `cat $newdir/corder`;
lagan-2.0/utils/draft.pl-230- for ($i = 0; $i < @list; $i++){
##############################################
lagan-2.0/utils/draft.pl-236-
lagan-2.0/utils/draft.pl:237: print STDERR `cat $newdir/draft`;
lagan-2.0/utils/draft.pl:238: print LOGFILE `cat $newdir/draft`;
lagan-2.0/utils/draft.pl-239- close (LOGFILE);
##############################################
lagan-2.0/utils/draft.pl-250-
lagan-2.0/utils/draft.pl:251:`$lagandir/cmerge2.pl $filename1 $filename2 $newdir/draft $filename2.merged -skipfr $pid`;
lagan-2.0/utils/draft.pl-252-if ($?) { exit(1); }
##############################################
lagan-2.0/utils/draft.pl-255-
lagan-2.0/utils/draft.pl:256:`cp $filename2.merged merged_seq.fa`;
lagan-2.0/utils/draft.pl:257:`cp $filename2.merged.masked merged_seq.fa.masked`;
lagan-2.0/utils/draft.pl:258:`cp $newdir/minfo minfo`;
lagan-2.0/utils/draft.pl:259:`cp $newdir/ranges ranges`;
lagan-2.0/utils/draft.pl:260:`cp $newdir/log log`;
lagan-2.0/utils/draft.pl-261-
##############################################
lagan-2.0/utils/draft.pl-265-
lagan-2.0/utils/draft.pl:266:# `rm -rf $newdir`;
lagan-2.0/utils/draft.pl-267-
##############################################
lagan-2.0/utils/mrun.pl-96-print "$mextstr\n";
lagan-2.0/utils/mrun.pl:97:if(!`$mextstr`) { print "\nMulti-FASTA extraction failure...\n"; exit(1); }
lagan-2.0/utils/mrun.pl-98-
##############################################
lagan-2.0/utils/mrun.pl-101- print "$mextstr\n";
lagan-2.0/utils/mrun.pl:102: if(!`$mextstr`) {
lagan-2.0/utils/mrun.pl-103- print "\nMasked Multi-FASTA extraction failure...\n";
##############################################
lagan-2.0/utils/mrun.pl-173-print STDERR "\n$mlagan\n\n";
lagan-2.0/utils/mrun.pl:174:if(`$mlagan`) { print "\n\n"; exit(1); }
lagan-2.0/utils/mrun.pl-175-
##############################################
lagan-2.0/utils/mrun.pl-194- print "$pstr\n";
lagan-2.0/utils/mrun.pl:195: if(`$pstr`) { print "\nprojection failure...\n"; exit(1); }
lagan-2.0/utils/mrun.pl-196- $bstr = "$binhead $outprefix.prj -out $outprefix.bin";
lagan-2.0/utils/mrun.pl-197- print "$bstr\n";
lagan-2.0/utils/mrun.pl:198: if(`$bstr`) { print "\npacking failure...\n"; exit(1); }
lagan-2.0/utils/mrun.pl-199- @bins[$j++] = "$outprefix.bin";
##############################################
lagan-2.0/utils/mrun.pl-232-print "touch $prefix.ann\n\n";
lagan-2.0/utils/mrun.pl:233:`touch $prefix.ann`;
lagan-2.0/utils/mrun.pl-234-
##############################################
lagan-2.0/utils/mrun.pl-244-
lagan-2.0/utils/mrun.pl:245:#$vistadir = `echo \$VISTA_DIR`;
lagan-2.0/utils/mrun.pl-246-#chomp $vistadir;
##############################################
lagan-2.0/utils/mrun.pl-254-#print "$vistastr\n";
lagan-2.0/utils/mrun.pl:255:#if (!`$vistastr`) { print "\nVISTA failure...\n"; exit(1); }
lagan-2.0/utils/mrun.pl-256-
##############################################
lagan-2.0/utils/mrunfile.pl-76-print "$mstr\n";
lagan-2.0/utils/mrunfile.pl:77:`$mstr`;
lagan-2.0/utils/mrunfile.pl-78-
##############################################
lagan-2.0/utils/mrunfile.pl-93- print "$vistastr\n";
lagan-2.0/utils/mrunfile.pl:94: if (!`$vistastr`) { print "\nVISTA failure...\n"; exit(1); }
lagan-2.0/utils/mrunfile.pl-95-
##############################################
lagan-2.0/utils/mrunpairs.pl-96-print "$mextstr\n";
lagan-2.0/utils/mrunpairs.pl:97:if(!`$mextstr`) { print "\nMulti-FASTA extraction failure...\n"; exit(1); }
lagan-2.0/utils/mrunpairs.pl-98-
##############################################
lagan-2.0/utils/mrunpairs.pl-101- print "$mextstr\n";
lagan-2.0/utils/mrunpairs.pl:102: if(!`$mextstr`) {
lagan-2.0/utils/mrunpairs.pl-103- print "\nMasked Multi-FASTA extraction failure...\n";
##############################################
lagan-2.0/utils/mrunpairs.pl-193- print "\n$mlagan\n\n";
lagan-2.0/utils/mrunpairs.pl:194: if(`$mlagan`) { print "\n\n"; exit(1); }
lagan-2.0/utils/mrunpairs.pl-195-
##############################################
lagan-2.0/utils/mrunpairs.pl-198- print "$bstr\n";
lagan-2.0/utils/mrunpairs.pl:199: if(`$bstr`) { print "\npacking failure...\n"; exit(1); }
lagan-2.0/utils/mrunpairs.pl-200- @bins[$j++] = "$outprefix.bin";
##############################################
lagan-2.0/utils/mrunpairs.pl-236-print "touch $prefix.ann\n\n";
lagan-2.0/utils/mrunpairs.pl:237:`touch $prefix.ann`;
lagan-2.0/utils/mrunpairs.pl-238-
##############################################
lagan-2.0/utils/mrunpairs.pl-248-
lagan-2.0/utils/mrunpairs.pl:249:#$vistadir = `echo \$VISTA_DIR`;
lagan-2.0/utils/mrunpairs.pl-250-#chomp $vistadir;
##############################################
lagan-2.0/utils/mrunpairs.pl-258-#print "$vistastr\n";
lagan-2.0/utils/mrunpairs.pl:259:#if (!`$vistastr`) { print "\nVISTA failure...\n"; exit(1); }
lagan-2.0/utils/mrunpairs.pl-260-
##############################################
lagan-2.0/utils/mviz.pl-159- print "$pstr\n";
lagan-2.0/utils/mviz.pl:160: if(`$pstr`) { print "\nprojection failure...\n"; exit(1); }
lagan-2.0/utils/mviz.pl-161- $bstr = "$binhead $outprefix.prj -out $outprefix.bin";
lagan-2.0/utils/mviz.pl-162- print "$bstr\n";
lagan-2.0/utils/mviz.pl:163: if(`$bstr`) { print "\npacking failure...\n"; exit(1); }
lagan-2.0/utils/mviz.pl-164- @bins[$j++] = "$outprefix.bin";
##############################################
lagan-2.0/utils/mviz.pl-199- print "touch $prefix.ann\n\n";
lagan-2.0/utils/mviz.pl:200: `touch $prefix.ann`;
lagan-2.0/utils/mviz.pl-201-
##############################################
lagan-2.0/utils/mviz.pl-217-print "$vistastr\n";
lagan-2.0/utils/mviz.pl:218:if (!`$vistastr`) { print "\nVISTA failure...\n"; exit(1); }
lagan-2.0/utils/mviz.pl-219-
##############################################
lagan-2.0/utils/Utils.pm-115- }
lagan-2.0/utils/Utils.pm:116: my $Host = $Uname ? `$Uname -n` : 'localhost';
lagan-2.0/utils/Utils.pm-117- chomp($Host);
##############################################
lagan-2.0/Utils.pm-117- }
lagan-2.0/Utils.pm:118: my $Host = $Uname ? `$Uname -n` : 'localhost';
lagan-2.0/Utils.pm-119- chomp($Host);
##############################################
lagan-2.0/xmfa2mfa.pl-49-
lagan-2.0/xmfa2mfa.pl:50:system($ENV{"LAGAN_DIR"}."/utils/Glue tmp.xmfa > glue.out 2> glue.err");
lagan-2.0/xmfa2mfa.pl-51-
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-93- elsif ($ARGV[$i] =~ /-rc/) {
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl:94: `$lagandir/utils/rc < $ARGV[1] > $ARGV[1].rc`;
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-95- if ($?) { exit(1); }
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-97- if (-e "$ARGV[1].masked") {
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl:98: `$lagandir/utils/rc < $ARGV[1].masked > $ARGV[1].rc.masked`;
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-99- if ($?) { exit(1);}
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-125-if ($rundraft){
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl:126: `$lagandir/draft.pl $firstName $secondName $draftparams`;
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-127- if ($?) { exit(1);}
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-131-# print STDERR "perl $lagandir/rechaos.pl $firstName $secondName $gfc $arglist > $$.anchs.final\n";
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl:132:`perl $lagandir/rechaos.pl $firstName $secondName $gfc $arglist > $$.anchs.final`;
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-133-
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-138-if ($contigflag){
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl:139: @bounds = `$lagandir/utils/getbounds $$.anchs.final $firstName $secondName`;
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-140- if ($?) { exit(1); }
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-142- print STDERR ("Aligning with bounds: $bounds[0]\n");
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl:143: print `$lagandir/order $firstName $secondName $bounds[0] $orderfl -anc $$.anchs.final`;
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-144- if ($?) { exit(1); }
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-170-
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl:171: `$lagandir/order $firstName $secondName $format -out $$.align $orderfl -anc $$.anchs.final`;
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-172- if ($?) { exit(1); }
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-175- if ($filename) {
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl:176: `$lagandir/utils/bin2bl $$.align > $filename`;
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-177- }
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-178- else {
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl:179: print `$lagandir/utils/bin2bl $$.align`;
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-180- }
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-183- if ($filename) {
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl:184: `cat $$.align > $filename`;
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-185- }
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-186- else {
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl:187: print `cat $$.align`;
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-188- }
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-190- if ($dofastreject){
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl:191: `$lagandir/utils/scorealign $filename $consrate -ibounds -cropxmfa > $$.temp`;
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-192- if ($?) { exit(1); }
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl:193: `mv $$.temp $filename`;
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-194- }
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-200- if ($binfile){
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl:201: `$lagandir/utils/bin2mf $infofilename > $infofilename.mfa`;
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-202- if ($?) { exit(1); }
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-204- }
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl:205: @temp = `head $secondName`;
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-206- if ($?) { exit(1); }
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-209-
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl:210: $len = `$lagandir/utils/getlength $secondName`; chomp $len;
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-211- if ($?) { exit(2); }
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-213-
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl:214: $score = `$lagandir/utils/scorealign $infofilename $consupperrate`; chomp $score;
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-215- if ($?) { exit(3); }
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-216- if ($score > 0){
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl:217: $score = `$lagandir/utils/scorealign $infofilename $consrate`; chomp $score;
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-218- if ($?) { exit(4); }
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl:219: @temp = `$lagandir/utils/scorealign $infofilename $consrate -bounds 0`;
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-220- if ($?) { exit(5); }
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-223-
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl:224: @temp = `$lagandir/utils/scorealign $infofilename $consrate -bounds 1`;
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-225- if ($?) { exit(6); }
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-232- close (INFOFILE);
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl:233:# `$lagandir/utils/rm $infofilename` if ($binfile);
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-234-}
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-235-
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl:236:`rm $secondName` if ($rcflag);
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl:237:`rm $$.*`;
lagan-2.0/.pc/adjustPerlPaths.patch/lagan.pl-238-if ($?) { exit(1); }
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl-124-
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl:125:$seq1len = `$lagandir/utils/getlength $seq1`; chomp $seq1len;
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl:126:$seq2len = `$lagandir/utils/getlength $seq2`; chomp $seq2len;
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl-127-
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl-180-# print STDERR "PAIRS hits\n";
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl:181:# print STDERR `cat $$.anchs.pairs`;
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl-182-# print STDERR "-----------------\n";
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl:183:# print STDERR `cat $$.anchs.pairs`;
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl-184-# print STDERR "-----------------\n";
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl-189- $saver = "$lagandir/chaos $seq1 $seq2 $extraparams -wl $wordlen -nd $degeneracy -co $cutoff $gfc $chaosfl -pairs $$.anchs.pairs > $$.anchtemp";
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl:190: `$lagandir/chaos $seq1 $seq2 $extraparams -wl $wordlen -nd $degeneracy -co $cutoff $gfc $chaosfl -pairs $$.anchs.pairs > $$.anchtemp`;
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl-191- if ($?) {
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl-211-
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl:212:# `wc $$.anchtemp` =~ /(\d+)/x;
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl-213-# $totalanchs = $totalanchs + $1;
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl-214-# print STDERR "CHAOS hits\n";
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl:215:# print STDERR `cat $$.anchtemp`;
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl-216-
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl-218-
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl:219: `$lagandir/anchors $$.anchtemp $gfc $anchparams | sort -n +1 > $$.anchs.sorted`;
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl-220- if ($?) { exit(1); }
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl-228-
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl:229:# `wc $$.anchs` =~ /(\d+)/x;
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl-230-# print STDERR "ANCHS hits\n";
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl:231:# print STDERR `cat $$.anchs.sorted`;
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl-232-# $goodanchs = $goodanchs + $1;
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl-359-
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl:360:$res = `sort -nr +1 $$.anchs.sorted`;
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl-361-if ($?) { exit(1); }
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl-362-
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl:363:`rm $$.*`;
lagan-2.0/.pc/adjustPerlPaths.patch/rechaos.pl-364-
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-51-close (OFILE);
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:52:`cp $ARGV[3] $ARGV[3].masked`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-53-
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-58-close (OFILE);
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:59:$padlength = `$lagandir/utils/getlength $newdir/padding`; chomp $padlength;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-60-
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-61-# other initialization
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:62:$totlength = `$lagandir/utils/getlength $ARGV[0]`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-63-chomp $totlength;
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-67-$numContigs = 0;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:68:@list = `cat $ARGV[2]`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-69-
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-81- $temp = $seq1Begin[$i-3] - $s1shifts[$i-3];
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:82: $seq2Begin[$i-3] = `$lagandir/utils/getcontigpos $filenames[$i-3].mfa $temp`; chomp $seq2Begin[$i-3];
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-83- $seq2Begin[$i-3] += $s2shifts[$i-3];
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-85- $temp = $seq1End[$i-3] - $s1shifts[$i-3];
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:86: $seq2End[$i-3] = `$lagandir/utils/getcontigpos $filenames[$i-3].mfa $temp`; chomp $seq2End[$i-3];
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-87- $seq2End[$i-3] += $s2shifts[$i-3];
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-101-# start out merged file with only padding
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:102:`mv $ARGV[3] $ARGV[3].new`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:103:`$lagandir/utils/seqmerge $ARGV[3].new $newdir/padding > $ARGV[3]`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:104:`mv $ARGV[3].masked $ARGV[3].masked.new`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:105:`$lagandir/utils/seqmerge $ARGV[3].masked.new $newdir/padding > $ARGV[3].masked`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-106-$contigStart[0] = 1;
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-108-
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:109:`cp $filenames[0] $newdir/current`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:110:`cp $filenames[0].masked $newdir/current.masked`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-111-
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-113-for ($i = 1; $i < $numContigs; $i++){
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:114: `$lagandir/rechaos.pl $newdir/current $filenames[$i] -recurse \"(12,0,40,0)x\" -maskedonly > $newdir/currentanchs`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-115- # find the overlap
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-116-
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:117: `$lagandir/utils/getoverlap $newdir/currentanchs` =~ /(-?\d+) (-?\d+) (-?\d+) (-?\d+)/;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-118- $rangebegin1 = $1;
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-127-
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:128: $thislength = `$lagandir/utils/getlength $filenames[$i-1]`; chomp $thislength;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:129: $nextlength = `$lagandir/utils/getlength $filenames[$i]`; chomp $nextlength;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-130-
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-135-
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:136: `mv $ARGV[3] $ARGV[3].new`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:137: `$lagandir/utils/seqmerge $ARGV[3].new $newdir/current $newdir/padding > $ARGV[3]`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:138: `cp $filenames[$i] $newdir/current`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-139-
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:140: `mv $ARGV[3].masked $ARGV[3].masked.new`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:141: `$lagandir/utils/seqmerge $ARGV[3].masked.new $newdir/current.masked $newdir/padding > $ARGV[3].masked`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:142: `cp $filenames[$i].masked $newdir/current.masked`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-143-
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-155- if ($j > 0){
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:156: `$lagandir/utils/cextract $newdir/current 1 $j 0 0 > $newdir/overlap`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:157: `$lagandir/utils/cextract $newdir/current.masked 1 $j 0 0 > $newdir/overlap.masked`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:158: $overlaplength = `$lagandir/utils/getlength $newdir/overlap`; chomp $overlaplength;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-159-
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:160: `mv $ARGV[3] $ARGV[3].new`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:161: `$lagandir/utils/seqmerge $ARGV[3].new $newdir/overlap > $ARGV[3]`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:162: `mv $ARGV[3].masked $ARGV[3].masked.new`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:163: `$lagandir/utils/seqmerge $ARGV[3].masked.new $newdir/overlap.masked > $ARGV[3].masked`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-164- }
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-166- # extract the nonoverlapped region > current
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:167: `$lagandir/utils/cextract $filenames[$i] $rangebegin2 $nextlength 0 0 > $newdir/current`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:168: `$lagandir/utils/cextract $filenames[$i].masked $rangebegin2 $nextlength 0 0 > $newdir/current.masked`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-169-
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-176- if (index ($filenames[$i-1], ".rc") == -1) { $direction = "+"; } else { $direction = "-"; }
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:177: @temp = `head $filenames[$i-1]`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-178- chomp $temp[0]; $temp[0] = substr $temp[0], 1;
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-184-
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:185:$thislength = `$lagandir/utils/getlength $filenames[$numContigs - 1]`; chomp $thislength;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-186-$contigEnd[$numContigs - 1] = $contigStart[$numContigs - 1] + $thislength - 1;
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-188-
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:189:`mv $ARGV[3] $ARGV[3].new`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:190:`$lagandir/utils/seqmerge $ARGV[3].new $newdir/current $newdir/padding > $ARGV[3]`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:191:`mv $ARGV[3].masked $ARGV[3].masked.new`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:192:`$lagandir/utils/seqmerge $ARGV[3].masked.new $newdir/current.masked $newdir/padding > $ARGV[3].masked`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-193-
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-194-if (index ($filenames[$numContigs - 1], ".rc") == -1) { $direction = "+"; } else { $direction = "-"; }
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl:195:@temp = `head $filenames[$numContigs - 1]`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/cmerge2.pl-196-chomp $temp[0]; $temp[0] = substr $temp[0], 1;
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-62-$newdir = "$newdir/$pid";
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:63:`mkdir $newdir` if (!(-e $newdir));
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-64-
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-78-
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:79:`cp $ARGV[1] $newdir`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:80:@contigs = `perl $lagandir/mextract.pl $newdir/$contigfile`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-81-if ($?) { exit(1);}
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-83- chomp $contigs[$i];
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:84: `$lagandir/utils/rc < $contigs[$i] > $contigs[$i].rc`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-85- if ($?) { exit(1); }
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-92- $maskedcontigfile = basename ($maskedname);
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:93: `cp $maskedname $newdir`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:94: @maskedcontigs = `perl $lagandir/mextract.pl $newdir/$maskedcontigfile -masked`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-95- if ($?) { exit(1);}
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-97- chomp $maskedcontigs[$i];
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:98: `$lagandir/utils/rc < $maskedcontigs[$i] > $contigs[$i].rc.masked`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-99- if ($?) { exit(1); }
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-113- $execute = $execute." -gap $anchgapstart $anchgapcont" if ($usebounds);
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:114: `$execute`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-115- $ex_val = $? >> 8;
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-120- # compute bounds
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:121: @bounds = `$lagandir/utils/getbounds anchs.final $ARGV[0] $contigs[$i]`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-122- if ($?) { exit(1);}
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-132- $execute = $execute." -gap $anchgapstart $anchgapcont" if ($usebounds);
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:133: `$execute`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-134- $ex_val = $? >> 8;
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-138- # compute bounds
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:139: @bounds = `$lagandir/utils/getbounds anchs.final $ARGV[0] $contigs[$i].rc`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-140- if ($?) { exit(1);}
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-151- else {
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:152: $fscore = `$lagandir/utils/scorealign $contigs[$i].mfa $startingrate`; chomp $fscore;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-153- if ($?) { exit(1);}
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-158- else {
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:159: $bscore = `$lagandir/utils/scorealign $contigs[$i].rc.mfa $startingrate`; chomp $bscore;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-160- if ($?) { exit(1);}
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-201-for ($cutoff = $startingrate; !$foundorder && ($cutoff < 100); $cutoff += $rateinc){
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:202: `$lagandir/utils/scorecontigs /$newdir/filenames $ARGV[0] $newdir/contignames $cutoff > $newdir/ranges`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-203- if ($?) { exit(1);}
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:204: @list = `cat $newdir/ranges`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-205- $list[0] =~ /numContigs = (\d+)/;
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-207-
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:208: `$lagandir/utils/contigorder $newdir/ranges > $newdir/corder`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-209- if ($?) { exit(1);}
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:210: @list = `cat $newdir/corder`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-211- chomp $list[0];
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-219-
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:220: @contignames = `cat $newdir/contignames`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-221- for ($i = 0; $i < @contignames; $i++){
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-228-
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:229: @list = `cat $newdir/corder`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-230- for ($i = 0; $i < @list; $i++){
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-236-
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:237: print STDERR `cat $newdir/draft`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:238: print LOGFILE `cat $newdir/draft`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-239- close (LOGFILE);
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-250-
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:251:`$lagandir/cmerge2.pl $filename1 $filename2 $newdir/draft $filename2.merged -skipfr $pid`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-252-if ($?) { exit(1); }
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-255-
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:256:`cp $filename2.merged merged_seq.fa`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:257:`cp $filename2.merged.masked merged_seq.fa.masked`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:258:`cp $newdir/minfo minfo`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:259:`cp $newdir/ranges ranges`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:260:`cp $newdir/log log`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-261-
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-265-
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl:266:# `rm -rf $newdir`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/draft.pl-267-
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrun.pl-96-print "$mextstr\n";
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrun.pl:97:if(!`$mextstr`) { print "\nMulti-FASTA extraction failure...\n"; exit(1); }
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrun.pl-98-
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrun.pl-101- print "$mextstr\n";
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrun.pl:102: if(!`$mextstr`) {
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrun.pl-103- print "\nMasked Multi-FASTA extraction failure...\n";
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrun.pl-173-print STDERR "\n$mlagan\n\n";
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrun.pl:174:if(`$mlagan`) { print "\n\n"; exit(1); }
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrun.pl-175-
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrun.pl-194- print "$pstr\n";
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrun.pl:195: if(`$pstr`) { print "\nprojection failure...\n"; exit(1); }
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrun.pl-196- $bstr = "$binhead $outprefix.prj -out $outprefix.bin";
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrun.pl-197- print "$bstr\n";
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrun.pl:198: if(`$bstr`) { print "\npacking failure...\n"; exit(1); }
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrun.pl-199- @bins[$j++] = "$outprefix.bin";
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrun.pl-232-print "touch $prefix.ann\n\n";
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrun.pl:233:`touch $prefix.ann`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrun.pl-234-
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrun.pl-244-
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrun.pl:245:#$vistadir = `echo \$VISTA_DIR`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrun.pl-246-#chomp $vistadir;
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrun.pl-254-#print "$vistastr\n";
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrun.pl:255:#if (!`$vistastr`) { print "\nVISTA failure...\n"; exit(1); }
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrun.pl-256-
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrunfile.pl-76-print "$mstr\n";
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrunfile.pl:77:`$mstr`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrunfile.pl-78-
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrunfile.pl-93- print "$vistastr\n";
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrunfile.pl:94: if (!`$vistastr`) { print "\nVISTA failure...\n"; exit(1); }
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrunfile.pl-95-
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrunpairs.pl-96-print "$mextstr\n";
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrunpairs.pl:97:if(!`$mextstr`) { print "\nMulti-FASTA extraction failure...\n"; exit(1); }
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrunpairs.pl-98-
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrunpairs.pl-101- print "$mextstr\n";
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrunpairs.pl:102: if(!`$mextstr`) {
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrunpairs.pl-103- print "\nMasked Multi-FASTA extraction failure...\n";
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrunpairs.pl-193- print "\n$mlagan\n\n";
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrunpairs.pl:194: if(`$mlagan`) { print "\n\n"; exit(1); }
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrunpairs.pl-195-
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrunpairs.pl-198- print "$bstr\n";
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrunpairs.pl:199: if(`$bstr`) { print "\npacking failure...\n"; exit(1); }
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrunpairs.pl-200- @bins[$j++] = "$outprefix.bin";
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrunpairs.pl-236-print "touch $prefix.ann\n\n";
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrunpairs.pl:237:`touch $prefix.ann`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrunpairs.pl-238-
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrunpairs.pl-248-
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrunpairs.pl:249:#$vistadir = `echo \$VISTA_DIR`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrunpairs.pl-250-#chomp $vistadir;
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrunpairs.pl-258-#print "$vistastr\n";
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrunpairs.pl:259:#if (!`$vistastr`) { print "\nVISTA failure...\n"; exit(1); }
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mrunpairs.pl-260-
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mviz.pl-159- print "$pstr\n";
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mviz.pl:160: if(`$pstr`) { print "\nprojection failure...\n"; exit(1); }
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mviz.pl-161- $bstr = "$binhead $outprefix.prj -out $outprefix.bin";
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mviz.pl-162- print "$bstr\n";
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mviz.pl:163: if(`$bstr`) { print "\npacking failure...\n"; exit(1); }
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mviz.pl-164- @bins[$j++] = "$outprefix.bin";
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mviz.pl-199- print "touch $prefix.ann\n\n";
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mviz.pl:200: `touch $prefix.ann`;
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mviz.pl-201-
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mviz.pl-217-print "$vistastr\n";
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mviz.pl:218:if (!`$vistastr`) { print "\nVISTA failure...\n"; exit(1); }
lagan-2.0/.pc/adjustPerlPaths.patch/utils/mviz.pl-219-
##############################################
lagan-2.0/.pc/adjustPerlPaths.patch/utils/Utils.pm-117- }
lagan-2.0/.pc/adjustPerlPaths.patch/utils/Utils.pm:118: my $Host = $Uname ? `$Uname -n` : 'localhost';
lagan-2.0/.pc/adjustPerlPaths.patch/utils/Utils.pm-119- chomp($Host);
##############################################
lagan-2.0/lagan.pl-93- elsif ($ARGV[$i] =~ /-rc/) {
lagan-2.0/lagan.pl:94: `$lagandir/utils/rc < $ARGV[1] > $ARGV[1].rc`;
lagan-2.0/lagan.pl-95- if ($?) { exit(1); }
##############################################
lagan-2.0/lagan.pl-97- if (-e "$ARGV[1].masked") {
lagan-2.0/lagan.pl:98: `$lagandir/utils/rc < $ARGV[1].masked > $ARGV[1].rc.masked`;
lagan-2.0/lagan.pl-99- if ($?) { exit(1);}
##############################################
lagan-2.0/lagan.pl-125-if ($rundraft){
lagan-2.0/lagan.pl:126: `$lagandir/draft.pl $firstName $secondName $draftparams`;
lagan-2.0/lagan.pl-127- if ($?) { exit(1);}
##############################################
lagan-2.0/lagan.pl-131-# print STDERR "perl $lagandir/rechaos.pl $firstName $secondName $gfc $arglist > $$.anchs.final\n";
lagan-2.0/lagan.pl:132:`perl $lagandir/rechaos.pl $firstName $secondName $gfc $arglist > $$.anchs.final`;
lagan-2.0/lagan.pl-133-
##############################################
lagan-2.0/lagan.pl-138-if ($contigflag){
lagan-2.0/lagan.pl:139: @bounds = `$lagandir/utils/getbounds $$.anchs.final $firstName $secondName`;
lagan-2.0/lagan.pl-140- if ($?) { exit(1); }
##############################################
lagan-2.0/lagan.pl-142- print STDERR ("Aligning with bounds: $bounds[0]\n");
lagan-2.0/lagan.pl:143: print `$lagandir/order $firstName $secondName $bounds[0] $orderfl -anc $$.anchs.final`;
lagan-2.0/lagan.pl-144- if ($?) { exit(1); }
##############################################
lagan-2.0/lagan.pl-170-
lagan-2.0/lagan.pl:171: `$lagandir/order $firstName $secondName $format -out $$.align $orderfl -anc $$.anchs.final`;
lagan-2.0/lagan.pl-172- if ($?) { exit(1); }
##############################################
lagan-2.0/lagan.pl-175- if ($filename) {
lagan-2.0/lagan.pl:176: `$lagandir/utils/bin2bl $$.align > $filename`;
lagan-2.0/lagan.pl-177- }
lagan-2.0/lagan.pl-178- else {
lagan-2.0/lagan.pl:179: print `$lagandir/utils/bin2bl $$.align`;
lagan-2.0/lagan.pl-180- }
##############################################
lagan-2.0/lagan.pl-183- if ($filename) {
lagan-2.0/lagan.pl:184: `cat $$.align > $filename`;
lagan-2.0/lagan.pl-185- }
lagan-2.0/lagan.pl-186- else {
lagan-2.0/lagan.pl:187: print `cat $$.align`;
lagan-2.0/lagan.pl-188- }
##############################################
lagan-2.0/lagan.pl-190- if ($dofastreject){
lagan-2.0/lagan.pl:191: `$lagandir/utils/scorealign $filename $consrate -ibounds -cropxmfa > $$.temp`;
lagan-2.0/lagan.pl-192- if ($?) { exit(1); }
lagan-2.0/lagan.pl:193: `mv $$.temp $filename`;
lagan-2.0/lagan.pl-194- }
##############################################
lagan-2.0/lagan.pl-200- if ($binfile){
lagan-2.0/lagan.pl:201: `$lagandir/utils/bin2mf $infofilename > $infofilename.mfa`;
lagan-2.0/lagan.pl-202- if ($?) { exit(1); }
##############################################
lagan-2.0/lagan.pl-204- }
lagan-2.0/lagan.pl:205: @temp = `head $secondName`;
lagan-2.0/lagan.pl-206- if ($?) { exit(1); }
##############################################
lagan-2.0/lagan.pl-209-
lagan-2.0/lagan.pl:210: $len = `$lagandir/utils/getlength $secondName`; chomp $len;
lagan-2.0/lagan.pl-211- if ($?) { exit(2); }
##############################################
lagan-2.0/lagan.pl-213-
lagan-2.0/lagan.pl:214: $score = `$lagandir/utils/scorealign $infofilename $consupperrate`; chomp $score;
lagan-2.0/lagan.pl-215- if ($?) { exit(3); }
lagan-2.0/lagan.pl-216- if ($score > 0){
lagan-2.0/lagan.pl:217: $score = `$lagandir/utils/scorealign $infofilename $consrate`; chomp $score;
lagan-2.0/lagan.pl-218- if ($?) { exit(4); }
lagan-2.0/lagan.pl:219: @temp = `$lagandir/utils/scorealign $infofilename $consrate -bounds 0`;
lagan-2.0/lagan.pl-220- if ($?) { exit(5); }
##############################################
lagan-2.0/lagan.pl-223-
lagan-2.0/lagan.pl:224: @temp = `$lagandir/utils/scorealign $infofilename $consrate -bounds 1`;
lagan-2.0/lagan.pl-225- if ($?) { exit(6); }
##############################################
lagan-2.0/lagan.pl-232- close (INFOFILE);
lagan-2.0/lagan.pl:233:# `$lagandir/utils/rm $infofilename` if ($binfile);
lagan-2.0/lagan.pl-234-}
lagan-2.0/lagan.pl-235-
lagan-2.0/lagan.pl:236:`rm $secondName` if ($rcflag);
lagan-2.0/lagan.pl:237:`rm $$.*`;
lagan-2.0/lagan.pl-238-if ($?) { exit(1); }
##############################################
lagan-2.0/rechaos.pl-124-
lagan-2.0/rechaos.pl:125:$seq1len = `$lagandir/utils/getlength $seq1`; chomp $seq1len;
lagan-2.0/rechaos.pl:126:$seq2len = `$lagandir/utils/getlength $seq2`; chomp $seq2len;
lagan-2.0/rechaos.pl-127-
##############################################
lagan-2.0/rechaos.pl-180-# print STDERR "PAIRS hits\n";
lagan-2.0/rechaos.pl:181:# print STDERR `cat $$.anchs.pairs`;
lagan-2.0/rechaos.pl-182-# print STDERR "-----------------\n";
lagan-2.0/rechaos.pl:183:# print STDERR `cat $$.anchs.pairs`;
lagan-2.0/rechaos.pl-184-# print STDERR "-----------------\n";
##############################################
lagan-2.0/rechaos.pl-189- $saver = "$lagandir/chaos $seq1 $seq2 $extraparams -wl $wordlen -nd $degeneracy -co $cutoff $gfc $chaosfl -pairs $$.anchs.pairs > $$.anchtemp";
lagan-2.0/rechaos.pl:190: `$lagandir/chaos $seq1 $seq2 $extraparams -wl $wordlen -nd $degeneracy -co $cutoff $gfc $chaosfl -pairs $$.anchs.pairs > $$.anchtemp`;
lagan-2.0/rechaos.pl-191- if ($?) {
##############################################
lagan-2.0/rechaos.pl-211-
lagan-2.0/rechaos.pl:212:# `wc $$.anchtemp` =~ /(\d+)/x;
lagan-2.0/rechaos.pl-213-# $totalanchs = $totalanchs + $1;
lagan-2.0/rechaos.pl-214-# print STDERR "CHAOS hits\n";
lagan-2.0/rechaos.pl:215:# print STDERR `cat $$.anchtemp`;
lagan-2.0/rechaos.pl-216-
##############################################
lagan-2.0/rechaos.pl-218-
lagan-2.0/rechaos.pl:219: `$lagandir/anchors $$.anchtemp $gfc $anchparams | sort -n +1 > $$.anchs.sorted`;
lagan-2.0/rechaos.pl-220- if ($?) { exit(1); }
##############################################
lagan-2.0/rechaos.pl-228-
lagan-2.0/rechaos.pl:229:# `wc $$.anchs` =~ /(\d+)/x;
lagan-2.0/rechaos.pl-230-# print STDERR "ANCHS hits\n";
lagan-2.0/rechaos.pl:231:# print STDERR `cat $$.anchs.sorted`;
lagan-2.0/rechaos.pl-232-# $goodanchs = $goodanchs + $1;
##############################################
lagan-2.0/rechaos.pl-359-
lagan-2.0/rechaos.pl:360:$res = `sort -nr +1 $$.anchs.sorted`;
lagan-2.0/rechaos.pl-361-if ($?) { exit(1); }
lagan-2.0/rechaos.pl-362-
lagan-2.0/rechaos.pl:363:`rm $$.*`;
lagan-2.0/rechaos.pl-364-