diff SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/misc/bowtie2sam.pl @ 0:74f5ea818cea

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/misc/bowtie2sam.pl	Wed Oct 12 19:50:38 2011 -0400
@@ -0,0 +1,92 @@
+#!/usr/bin/perl -w
+
+# Contact: lh3
+# Version: 0.1.1
+
+use strict;
+use warnings;
+use Getopt::Std;
+
+&bowtie2sam;
+exit;
+
+sub bowtie2sam {
+  my %opts = ();
+  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);
+  $last = '';
+  while (<>) {
+	my ($name, $nm) = &bowtie2sam_aux($_, \@s); # read_name, number of mismatches
+	if ($name eq $last) {
+	  # I do not know whether the multiple hits are ordered on the
+	  # number of mismatches. I assume they are not and so I have to
+	  # keep all these multiple hits in memory.
+	  @{$staging[$k]} = @s;
+	  if ($best_s > $nm) {
+		$subbest_s = $best_s;
+		$best_s = $nm;
+		$best_k = $k;
+	  } elsif ($subbest_s > $nm) {
+		$subbest_s = $nm;
+	  }
+	  ++$k;
+	} else {
+	  if ($last) {
+		if ($best_s == $subbest_s) {
+		  $staging[$best_k][4] = 0;
+		} elsif ($subbest_s - $best_s == 1) {
+		  $staging[$best_k][4] = 15 if ($staging[$best_k][4] > 15);
+		}
+		print join("\t", @{$staging[$best_k]}), "\n";
+	  }
+	  $k = 1; $best_s = $nm; $subbest_s = 1000; $best_k = 0;
+	  @{$staging[0]} = @s;
+	  $last = $name;
+	}
+  }
+  print join("\t", @{$staging[$best_k]}), "\n" if ($best_k >= 0);
+}
+
+sub bowtie2sam_aux {
+  my ($line, $s) = @_;
+  chomp($line);
+  my @t = split("\t", $line);
+  my $ret;
+  @$s = ();
+  # read name
+  $s->[0] = $ret = $t[0];
+  $s->[0] =~ s/\/[12]$//g;
+  # initial flag (will be updated later)
+  $s->[1] = 0;
+  # read & quality
+  $s->[9] = $t[4]; $s->[10] = $t[5];
+  # cigar
+  $s->[5] = length($s->[9]) . "M";
+  # coor
+  $s->[2] = $t[2]; $s->[3] = $t[3] + 1;
+  $s->[1] |= 0x10 if ($t[1] eq '-');
+  # mapQ
+  $s->[4] = $t[6] == 0? 25 : 0;
+  # mate coordinate
+  $s->[6] = '*'; $s->[7] = $s->[8] = 0;
+  # aux
+  my $nm = @t - 7;
+  push(@$s, "NM:i:" . (@t-7));
+  push(@$s, "X$nm:i:" . ($t[6]+1));
+  my $md = '';
+  if ($t[7]) {
+	$_ = $t[7];
+	my $a = 0;
+	while (/(\d+):[ACGTN]>([ACGTN])/gi) {
+	  my ($y, $z) = ($1, $2);
+	  $md .= (int($y)-$a) . $z;
+	  $a += $y - $a + 1;
+	}
+	$md .= length($s->[9]) - $a;
+  } else {
+	$md = length($s->[9]);
+  }
+  push(@$s, "MD:Z:$md");
+  return ($ret, $nm);
+}