--- a/rapsodyn/filtersam_mapped_and_unique.pl	Mon Oct 20 05:58:31 2014 -0400
+++ b/rapsodyn/filtersam_mapped_and_unique.pl	Mon Jan 19 04:33:21 2015 -0500
@@ -1,4 +1,5 @@
 #!/usr/bin/perl
+#V1.1.0 manage empty files
 #V1.0.1 added log, option parameters
 use strict;
 use warnings;
@@ -7,6 +8,7 @@
 my $input_sam_file;
 my $output_sam_file;
 my $log_file;
+my $empty_file=1;
 
 my %bitscore_all;
 my %bitscore_selected;
@@ -37,6 +39,7 @@
 			my @fields_selected = split (/\s+/,$line);
 			if (($fields_selected[1]==83)||($fields_selected[1]==163)||($fields_selected[1]==147)||($fields_selected[1]==99)){
 				print $line;
+				$empty_file=0;
 				my $bit = $fields_selected[1];
 				if ($bitscore_selected{$bit}){
 					$bitscore_selected{$bit}++;
@@ -50,29 +53,30 @@
 }
 
 close (IN);
-
 open (LF,">$log_file") or die("Can't open $log_file\n");
-print LF "\n####\t Sam filtering \n";
-print LF "## Before filtering\n";
-print LF "bitscore\t:\t";
-foreach my $key (sort {$bitscore_all{$b} <=> $bitscore_all{$a}} keys %bitscore_all) {
-	print LF $key,"\t*\t";
-}
-print LF "\n number \t:\t";
-foreach my $key (sort {$bitscore_all{$b} <=> $bitscore_all{$a}} keys %bitscore_all) {
-	print LF $bitscore_all{$key},"\t*\t";
+if ($empty_file==0){
+	print LF "\n####\t Sam filtering \n";
+	print LF "## Before filtering\n";
+	print LF "bitscore\t:\t";
+	foreach my $key (sort {$bitscore_all{$b} <=> $bitscore_all{$a}} keys %bitscore_all) {
+		print LF $key,"\t*\t";
+	}
+	print LF "\n number \t:\t";
+	foreach my $key (sort {$bitscore_all{$b} <=> $bitscore_all{$a}} keys %bitscore_all) {
+		print LF $bitscore_all{$key},"\t*\t";
+	}
+	print LF "\n";
+	print LF "## After filtering\n";
+	print LF "bitscore\t:\t";
+	foreach my $key (sort {$bitscore_selected{$b} <=> $bitscore_selected{$a}} keys %bitscore_selected) {
+		print LF $key,"\t*\t";
+	}
+	print LF "\n number \t:\t";
+	foreach my $key (sort {$bitscore_selected{$b} <=> $bitscore_selected{$a}} keys %bitscore_selected) {
+		print LF $bitscore_selected{$key},"\t*\t";
+	}
+	print LF "\n";
 }
-print LF "\n";
-print LF "## After filtering\n";
-print LF "bitscore\t:\t";
-foreach my $key (sort {$bitscore_selected{$b} <=> $bitscore_selected{$a}} keys %bitscore_selected) {
-	print LF $key,"\t*\t";
-}
-print LF "\n number \t:\t";
-foreach my $key (sort {$bitscore_selected{$b} <=> $bitscore_selected{$a}} keys %bitscore_selected) {
-	print LF $bitscore_selected{$key},"\t*\t";
-}
-print LF "\n";
 close (LF);