--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/countDiff.pl	Wed Feb 08 16:59:24 2012 -0500
@@ -0,0 +1,74 @@
+#!/nfs_exports/apps/64-bit/gnu-apps/perl5.8.9/bin/perl -w
+use strict;
+use Carp;
+use Getopt::Long;
+use English;
+use Pod::Usage;
+use Data::Dumper;
+use Bio::DB::Sam;
+use Bio::DB::Sam::Constants;
+use Bio::SearchIO;
+use Bio::SeqIO;
+use File::Temp qw/ tempfile tempdir /;
+use File::Spec;
+use File::Path;
+use File::Copy;
+use File::Basename;
+use Cwd;
+
+# bam related variables
+# input/output
+my($file_d, $file_g);
+
+my ( $help, $man, $version, $usage );
+my $optionOK = GetOptions(
+	'd|diagnostic=s'	=> \$file_d,
+	'g|germline=s'		=> \$file_g,
+	'h|help|?'			=> \$help,
+	'man'				=> \$man,
+	'usage'				=> \$usage,
+	'v|version'			=> \$version,
+);
+
+pod2usage(-verbose=>2) if($man or $usage);
+pod2usage(1) if($help or $version );
+
+my $start_dir = getcwd;
+
+# figure out input file
+if(!$file_d or !$file_g ) {
+	croak "you need specify diagnostic and germline input file";
+}
+my ( @cover_D, @cover_diff);
+for( my $i = 1; $i < 1000; $i++) {
+	$cover_D[$i] = 0;
+	$cover_diff[$i] = 0;
+}
+my($prefix, $path, $suffix) = fileparse($file_d);
+my $diff_file = $prefix . ".somatic.cover";
+$diff_file = File::Spec->catfile($path, $diff_file);
+open my $SOMATIC, ">$diff_file" or croak "can't open $diff_file:$OS_ERROR";
+open my $IN_D, "<$file_d" or croak "can't open $file_d:$OS_ERROR";
+open my $IN_G, "<$file_g" or croak "can't open $file_g:$OS_ERROR";
+my %g_sclip;
+while( my $line = <$IN_G> ) {
+	chomp $line;
+	my ($chr, $pos, $ort, $cover) = split /\t/, $line;
+	$g_sclip{$chr} = {} if(!exists($g_sclip{$chr}));
+	$g_sclip{$chr}->{$pos} = $ort;
+}
+close($IN_G);
+while( my $line = <$IN_D> ) {
+	chomp $line;
+	my ($chr, $pos, $ort, $cover) = split /\t/, $line;
+	$cover_D[$cover]++;
+	next if(exists ($g_sclip{$chr}->{$pos}) && $g_sclip{$chr}->{$pos} eq $ort);
+	$cover_diff[$cover]++;
+	print $SOMATIC $line, "\n";
+}
+close($IN_D);
+close $SOMATIC;
+for( my $i = 1; $i < 1000; $i++) {
+	print join("\t", $i, $cover_D[$i], $cover_diff[$i]), "\n";
+}
+