From: Heng Li <lh3@live.co.uk>
Date: Wed, 8 Apr 2009 09:57:08 +0000 (+0000)
Subject: make the script robust to the bugs in SOAP-2.1.7
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=7c8e419216b32789afc3ee7a6dadfad6010c97de;p=samtools.git

make the script robust to the bugs in SOAP-2.1.7
---

diff --git a/misc/bowtie2sam.pl b/misc/bowtie2sam.pl
index 4ead839..5dff88d 100755
--- a/misc/bowtie2sam.pl
+++ b/misc/bowtie2sam.pl
@@ -12,7 +12,7 @@ exit;
 
 sub bowtie2sam {
   my %opts = ();
-  die("Usage: bowtie2sam.pl <aln.bowtie>\n") if (@ARGV == 0);
+  die("Usage: bowtie2sam.pl <aln.bowtie>\n") if (@ARGV == 0 && -t STDIN);
   # core loop
   my (@s, $last, @staging, $k, $best_s, $subbest_s, $best_k);
   $last = '';
diff --git a/misc/soap2sam.pl b/misc/soap2sam.pl
index 5e721f9..1628c0f 100755
--- a/misc/soap2sam.pl
+++ b/misc/soap2sam.pl
@@ -36,13 +36,14 @@ sub mating {
 sub soap2sam {
   my %opts = ();
   getopts("p", \%opts);
-  die("Usage: soap2sam.pl [-p] <aln.soap>\n") if (@ARGV == 0);
+  die("Usage: soap2sam.pl [-p] <aln.soap>\n") if (@ARGV == 0 && -t STDIN);
   my $is_paired = defined($opts{p});
   # core loop
   my @s1 = ();
   my @s2 = ();
   my ($s_last, $s_curr) = (\@s1, \@s2);
   while (<>) {
+	s/[\177-\377]|[\000-\010]|[\012-\040]//g;
 	next if (&soap2sam_aux($_, $s_curr, $is_paired) < 0);
 	if (@$s_last != 0 && $s_last->[0] eq $s_curr->[0]) {
 	  &mating($s_last, $s_curr);
@@ -60,8 +61,8 @@ sub soap2sam {
 sub soap2sam_aux {
   my ($line, $s, $is_paired) = @_;
   chomp($line);
-  my @t = split("\t", $line);
-  return -1 if (@t < 9);
+  my @t = split(/\s+/, $line);
+  return -1 if (@t < 9 || $line =~ /^\s/ || !$t[0]);
   @$s = ();
   # read name
   $s->[0] = $t[0];
@@ -71,7 +72,8 @@ sub soap2sam_aux {
   $s->[1] |= 1 | 1<<($t[4] eq 'a'? 6 : 7);
   $s->[1] |= 2 if ($is_paired);
   # read & quality
-  $s->[9] = $t[1]; $s->[10] = $t[2];
+  $s->[9] = $t[1];
+  $s->[10] = (length($t[2]) > length($t[1]))? substr($t[2], 0, length($t[1])) : $t[2];
   # cigar
   $s->[5] = length($s->[9]) . "M";
   # coor
diff --git a/misc/wgsim_eval.pl b/misc/wgsim_eval.pl
index ecc53cc..99e2ac9 100755
--- a/misc/wgsim_eval.pl
+++ b/misc/wgsim_eval.pl
@@ -33,7 +33,6 @@ sub wgsim_eval {
 	# skip unmapped reads
 	next if (($t[1]&0x4) || $chr eq '*');
 	# parse read name and check
-	++$c0[$q];
 	if ($t[0] =~ /^(\S+)_(\d+)_(\d+)_/) {
 	  if ($1 ne $chr) { # different chr
 		$is_correct = 0;
@@ -57,8 +56,10 @@ sub wgsim_eval {
 		}
 	  }
 	} else {
-	  die("[wgsim_eval] read '$t[0]' was not generated by wgsim?\n");
+	  warn("[wgsim_eval] read '$t[0]' was not generated by wgsim?\n");
+	  next;
 	}
+	++$c0[$q];
 	++$c1[$q] unless ($is_correct);
 	print STDERR $line if (($flag&1) && !$is_correct && $q > 0);
   }