From 65baf77435b97f755b1cf0b3220173eff1f63b83 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Wed, 28 Jan 2009 12:54:08 +0000
Subject: [PATCH] Script for filtering indel results

---
 misc/indel_filter.pl | 42 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100755 misc/indel_filter.pl

diff --git a/misc/indel_filter.pl b/misc/indel_filter.pl
new file mode 100755
index 0000000..7427f06
--- /dev/null
+++ b/misc/indel_filter.pl
@@ -0,0 +1,42 @@
+#!/usr/bin/perl -w
+
+# Contact: lh3
+
+use strict;
+use warnings;
+use Getopt::Std;
+
+my %opts = (D=>100, m=>10, r=>undef);
+getopts('D:m:r', \%opts);
+
+die(qq/
+Usage:   indel_filter.pl [options] <in.indel>\n
+Options: -D INT    maximum read depth [$opts{D}]
+         -m INT    minimum distance between two adjacent indels [$opts{m}]
+\n/) if (@ARGV == 0 && -t STDIN);
+
+my (@arr1, @arr2);
+my ($curr, $last) = (\@arr1, \@arr2);
+my $is_ref = defined($opts{r})? 1 : 0;
+while (<>) {
+  my @t = split;
+  next if ($t[2] ne '*');
+  if (!$is_ref) {
+	next if ($t[3] eq '*/*');
+	next if ($t[5] == 0);
+  }
+  next if ($t[8] + $t[9] + $t[10] + $t[11] > $opts{D});
+  @$curr = ($t[0], $t[1], $t[5], $_);
+  my $do_swap = 1;
+  if (defined $last->[0]) {
+	if ($curr->[0] eq $last->[0] && $last->[1] + $opts{m} > $curr->[1]) {
+	  $do_swap = 0 if ($last->[2] > $curr->[2]);
+	} else { # then print
+	  print $last->[3];
+	}
+  }
+  if ($do_swap) {
+	my $tmp = $curr; $curr = $last; $last = $tmp;
+  }
+}
+print $last->[3] if (defined $last->[0]);
-- 
2.39.2