--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/samtools-0.1.16/misc/psl2sam.pl	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,65 @@
+#!/usr/bin/perl -w
+
+# Author: lh3
+
+# This script calculates a score using the BLAST scoring
+# system. However, I am not sure how to count gap opens and gap
+# extensions. It seems to me that column 5-8 are not what I am
+# after. This script counts gaps from the last three columns. It does
+# not generate reference skip (N) in the CIGAR as it is not easy to
+# directly tell which gaps correspond to introns.
+
+use strict;
+use warnings;
+use Getopt::Std;
+
+my %opts = (a=>1, b=>3, q=>5, r=>2);
+getopts('a:b:q:r:', \%opts);
+die("Usage: psl2sam.pl [-a $opts{a}] [-b $opts{b}] [-q $opts{q}] [-r $opts{r}] <in.psl>\n") if (@ARGV == 0 && -t STDIN);
+
+my @stack;
+my $last = '';
+my ($a, $b, $q, $r) = ($opts{a}, $opts{b}, $opts{q}, $opts{r});
+while (<>) {
+  next unless (/^\d/);
+  my @t = split;
+  my @s;
+  my $cigar = '';
+  if ($t[8] eq '-') {
+	my $tmp = $t[11];
+	$t[11] = $t[10] - $t[12];
+	$t[12] = $t[10] - $tmp;
+  }
+  @s[0..4] = ($t[9], (($t[8] eq '+')? 0 : 16), $t[13], $t[15]+1, 0);
+  @s[6..10] = ('*', 0, 0, '*', '*');
+  $cigar .= $t[11].'H' if ($t[11]); # 5'-end clipping
+  my @x = split(',', $t[18]);
+  my @y = split(',', $t[19]);
+  my @z = split(',', $t[20]);
+  my ($y0, $z0) = ($y[0], $z[0]);
+  my ($gap_open, $gap_ext) = (0, 0, 0);
+  for (1 .. $t[17]-1) {
+	my $ly = $y[$_] - $y[$_-1] - $x[$_-1];
+	my $lz = $z[$_] - $z[$_-1] - $x[$_-1];
+	if ($ly < $lz) { # del: the reference gap is longer
+	  ++$gap_open;
+	  $gap_ext += $lz - $ly;
+	  $cigar .= ($y[$_] - $y0) . 'M';
+	  $cigar .= ($lz - $ly) . 'D';
+	  ($y0, $z0) = ($y[$_], $z[$_]);
+	} elsif ($lz < $ly) { # ins: the query gap is longer
+	  ++$gap_open;
+	  $gap_ext += $ly - $lz;
+	  $cigar .= ($z[$_] - $z0) . 'M';
+	  $cigar .= ($ly - $lz) . 'I';
+	  ($y0, $z0) = ($y[$_], $z[$_]);
+	}
+  }
+  $cigar .= ($t[12] - $y0) . 'M';
+  $cigar .= ($t[10] - $t[12]).'H' if ($t[10] != $t[12]); # 3'-end clipping
+  $s[5] = $cigar;
+  my $score = $a * $t[0] - $b * $t[1] - $q * $gap_open - $r * $gap_ext;
+  $score = 0 if ($score < 0);
+  $s[11] = "AS:i:$score";
+  print join("\t", @s), "\n";
+}