simple script to make gathering readcounts slightly more user friendly

src/scripts/prepare_for_readcount.pl

@@ -0,0 +1,71 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+
+use IO::File;
+use Getopt::Long;
+
+my $snp_file;
+my $out_file;
+my $help;
+
+my $opt_result;
+
+$opt_result = GetOptions(
+    'snp-file=s' => \$snp_file,
+    'out-file=s' => \$out_file,
+    'help' => \$help,
+);
+
+unless($opt_result) {
+    die help_text();
+}
+
+if($help) {
+    print STDOUT help_text();
+    exit 0;
+}
+
+unless($snp_file) {
+    warn "You must provide a file to be converted\n";
+    die help_text();
+}
+
+unless(-s $snp_file) {
+    die "Can not find valid bam-somaticsniper output file: $snp_file\n";
+}
+
+$out_file ||= $snp_file . '.pos';
+my $out_fh = IO::File->new($out_file,"w") or die "Unable to open $out_file for writing: $!\n";
+my $snp_fh = IO::File->new($snp_file) or die "Unable to open $snp_file for reading: $1\n";
+
+while (my $snp = $snp_fh->getline) {
+    chomp $snp;
+    my @fields = split /\t/, $snp;
+    print $out_fh join("\t",@fields[0,1,1]),"\n";
+}
+
+
+sub help_text {
+    return <<HELP;
+prepare_for_readcount - Convert bam-somaticsniper output to an appropriate list of positions for bam-readcount's -l option
+
+SYNOPSIS
+prepare_for_readcount [options]
+
+OPTIONS
+--snp-file              the input bam-somaticsniper output file (requires v1.0.0 or greater output)
+--out-file              snp output file after filter
+--help                  this message
+
+DESCRIPTION
+This program extracts positions for use with bam-readcount's -l option.
+
+AUTHORS
+Dave Larson     Extraction from standard TGI framework and modification specifically for bam-somaticsniper
+
+SUPPORT
+For user support please mail genome-dev\@genome.wustl.edu.
+HELP
+}