diff PsiCLASS-1.0.2/samtools-0.1.19/misc/soap2sam.pl @ 0:903fc43d6227 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PsiCLASS-1.0.2/samtools-0.1.19/misc/soap2sam.pl	Fri Mar 26 16:52:45 2021 +0000
@@ -0,0 +1,109 @@
+#!/usr/bin/perl -w
+
+# Contact: lh3
+# Version: 0.1.1
+
+use strict;
+use warnings;
+use Getopt::Std;
+
+&soap2sam;
+exit;
+
+sub mating {
+  my ($s1, $s2) = @_;
+  my $isize = 0;
+  if ($s1->[2] ne '*' && $s1->[2] eq $s2->[2]) { # then calculate $isize
+	my $x1 = ($s1->[1] & 0x10)? $s1->[3] + length($s1->[9]) : $s1->[3];
+	my $x2 = ($s2->[1] & 0x10)? $s2->[3] + length($s2->[9]) : $s2->[3];
+	$isize = $x2 - $x1;
+  }
+  # update mate coordinate
+  if ($s2->[2] ne '*') {
+	@$s1[6..8] = (($s2->[2] eq $s1->[2])? "=" : $s2->[2], $s2->[3], $isize);
+	$s1->[1] |= 0x20 if ($s2->[1] & 0x10);
+  } else {
+	$s1->[1] |= 0x8;
+  }
+  if ($s1->[2] ne '*') {
+	@$s2[6..8] = (($s1->[2] eq $s2->[2])? "=" : $s1->[2], $s1->[3], -$isize);
+	$s2->[1] |= 0x20 if ($s1->[1] & 0x10);
+  } else {
+	$s2->[1] |= 0x8;
+  }
+}
+
+sub soap2sam {
+  my %opts = ();
+  getopts("p", \%opts);
+  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, $s_curr);
+	  print join("\t", @$s_last), "\n";
+	  print join("\t", @$s_curr), "\n";
+	  @$s_last = (); @$s_curr = ();
+	} else {
+	  print join("\t", @$s_last), "\n" if (@$s_last != 0);
+	  my $s = $s_last; $s_last = $s_curr; $s_curr = $s;
+	}
+  }
+  print join("\t", @$s_last), "\n" if (@$s_last != 0);
+}
+
+sub soap2sam_aux {
+  my ($line, $s, $is_paired) = @_;
+  chomp($line);
+  my @t = split(/\s+/, $line);
+  return -1 if (@t < 9 || $line =~ /^\s/ || !$t[0]);
+  @$s = ();
+  # fix SOAP-2.1.x bugs
+  @t = @t[0..2,4..$#t] unless ($t[3] =~ /^\d+$/);
+  # read name
+  $s->[0] = $t[0];
+  $s->[0] =~ s/\/[12]$//g;
+  # initial flag (will be updated later)
+  $s->[1] = 0;
+  $s->[1] |= 1 | 1<<($t[4] eq 'a'? 6 : 7);
+  $s->[1] |= 2 if ($is_paired);
+  # read & quality
+  $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
+  $s->[2] = $t[7]; $s->[3] = $t[8];
+  $s->[1] |= 0x10 if ($t[6] eq '-');
+  # mapQ
+  $s->[4] = $t[3] == 1? 30 : 0;
+  # mate coordinate
+  $s->[6] = '*'; $s->[7] = $s->[8] = 0;
+  # aux
+  push(@$s, "NM:i:$t[9]");
+  my $md = '';
+  if ($t[9]) {
+	my @x;
+	for (10 .. $#t) {
+	  push(@x, sprintf("%.3d,$1", $2)) if ($t[$_] =~ /^([ACGT])->(\d+)/i);
+	}
+	@x = sort(@x);
+	my $a = 0;
+	for (@x) {
+	  my ($y, $z) = split(",");
+	  $md .= (int($y)-$a) . $z;
+	  $a += $y - $a + 1;
+	}
+	$md .= length($t[1]) - $a;
+  } else {
+	$md = length($t[1]);
+  }
+  push(@$s, "MD:Z:$md");
+  return 0;
+}