--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/MergeSamFiles.pl	Tue Oct 07 10:34:34 2014 -0400
@@ -0,0 +1,32 @@
+#!/usr/bin/perl
+#V1.0.0
+use strict;
+use warnings;
+
+my $header_done = 0;
+my @files = split(/,/,$ARGV[0]);
+for (my $i=0;$i<=$#files;$i++){
+	open(IN, $files[$i]) or die ("Can't open ",$files[$i],"\n");
+	while (my $line = <IN>){
+		if ($line =~ /^\@PG\s/){
+			if ($header_done == 0){
+				$header_done = 1;
+				print $line;
+			}
+			else {
+			}
+		}
+		elsif ($line =~ /^\@SQ\s/){
+			if ($header_done == 0){
+				print $line;
+			}
+			else {
+			}
+		}
+		else{
+			print $line;
+		}
+	}
+	close (IN);
+}
+