--- a/rapsodyn/filtersam_mapped_and_unique.pl	Mon Sep 29 03:02:16 2014 -0400
+++ b/rapsodyn/filtersam_mapped_and_unique.pl	Tue Oct 07 10:34:34 2014 -0400
@@ -1,23 +1,83 @@
 #!/usr/bin/perl
+#V1.0.1 added log, option parameters
 use strict;
 use warnings;
+use Getopt::Long;
 
-open(IN, $ARGV[0]) or die ("Can't open $ARGV[0]\n");
+my $input_sam_file;
+my $output_sam_file;
+my $log_file;
+
+my %bitscore_all;
+my %bitscore_selected;
+
+GetOptions (
+"input_sam_file=s" => \$input_sam_file,
+"output_sam_file=s" => \$output_sam_file,
+"log_file=s" => \$log_file
+) or die("Error in command line arguments\n");
+
+open(IN, $input_sam_file) or die ("Can't open $input_sam_file\n");
 while (my $line=<IN>){
-	if ($line =~ /^\@/){
+	if (($line =~ /^\@SQ/)||($line =~ /^\@PG/)){
 		#Header conservation
 		print $line;
 	}
 	else {
 		#Optionnal flag verification
+		my @fields_all = split (/\s+/,$line);
+		my $bit = $fields_all[1];
+		if ($bitscore_all{$bit}){
+			$bitscore_all{$bit}++;
+		}
+		else {
+			$bitscore_all{$bit}=1;
+		}
 		if (($line =~ /XT\:A\:U/)&&($line =~ /X0\:i\:1/)&&($line =~ /X1\:i\:0\s/)){
-			my @fields = split (/\s+/,$line);
-			if (($fields[1]==83)||($fields[1]==163)||($fields[1]==147)||($fields[1]==99)){
+			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;
+				my $bit = $fields_selected[1];
+				if ($bitscore_selected{$bit}){
+					$bitscore_selected{$bit}++;
+				}
+				else {
+					$bitscore_selected{$bit}=1;
+				}
 			}
 		}
 	}
 }
 
+close (IN);
 
-close (IN);
\ No newline at end of file
+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";
+}
+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);
+
+
+
+
+
+
+