--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/2.4/src/Merge_Soft.pl	Mon Jun 02 07:35:53 2014 -0400
@@ -0,0 +1,39 @@
+#!/usr/bin/perl -s
+#Merge Softsearch results by chrom
+if(!$ARGV[0]){die "Usage: <Sample.1.vcf>\n";}
+my ($sample,$cmd);
+
+#Get basename
+$sample="$ARGV[0]";
+$sample=~s/.[0-9(+)].out.vcf//;
+$sample=~s/.[0-9(+)].pe.vcf//;
+
+my $outfile=$sample;
+$outfile.="out.vcf";
+if( -e $outfile ){unlink($outfile)}
+$cmd="ls $sample\*vcf";
+my @samples=`$cmd`;
+print "there are " .scalar(@samples)." samples\n";
+
+open (OUT,">$outfile");
+my $i=1;
+my $tmp=@samples[$i];
+open(TMP,"$tmp");
+while (<TMP>){
+	print OUT if ($_=~/^#/);
+}
+
+open (OUT,">>$outfile");
+my $chr;
+for (my $i=0;$i<@samples;$i++){
+	my $tmp=@samples[$i];
+	open(TMP,"$tmp");
+	while (<TMP>){
+		unless (($_=~/^chrGL/)||($_=~/^#/)){print OUT $_;}
+	}
+	print "Done with $tmp";
+        unlink($tmp);
+	system("rm $tmp");
+	close TMP;
+}
+close OUT;