Merge pull request #444 from sanger-pathogens/farm5_snps

Added some missing scripts to bin for snps pipeline

bin/make_indel_mask.pl

@@ -0,0 +1,48 @@
+#!/usr/bin/env perl
+#
+# usage: make_indel_mask.pl indel.calls.bed mask_size indels.mask.bed
+#
+# Author: Sendu Bala <[email protected]>
+# PODNAME: bobby_tables.pl at /usr/local/share/perl/5.14.2/Pod/Weaver.pm line 73.
+
+use strict;
+use warnings;
+
+use File::Spec;
+use File::Basename;
+
+# get user input
+my ($in_bed, $mask_size, $out_bed) = @ARGV;
+chomp($out_bed);
+
+($in_bed && -e $in_bed && $mask_size && $out_bed) or die <<USAGE;
+Creates a mask version of a bed file.
+
+Usage: $0 indel.calls.bed mask_size indels.mask.bed
+
+where indel.calls.bed is the input bed file, mask_size is the size in bases
+(eg. 10), and indels.mask.bed is the output file
+
+USAGE
+
+open(my $ifh, $in_bed) || die "Could not open $in_bed\n";
+open(my $ofh, '>', $out_bed) || die "Could not write to $out_bed\n";
+$mask_size = int($mask_size);
+$mask_size >= 1 || die "Invalid mask_size '$mask_size' (should be int >= 1)\n";
+
+
+# covert to mask
+while (<$ifh>) {
+    # chr1    71996   72005   -AAAAAAAAA:4/6
+    my ($chr, $start, $stop, $notes) = split;
+
+    $start -= $mask_size;
+    $stop += $mask_size;
+    $notes .= ":+/-$mask_size" ;
+
+    print $ofh join("\t", $chr, $start, $stop, $notes), "\n";
+}
+close($ifh);
+close($ofh);
+
+exit;