diff rapsodyn/mpileupfilterandstat.pl @ 29:7b8646f46010 draft

Uploaded

--- a/rapsodyn/mpileupfilterandstat.pl	Wed Sep 10 08:10:38 2014 -0400
+++ b/rapsodyn/mpileupfilterandstat.pl	Wed Oct 08 09:06:53 2014 -0400
@@ -1,4 +1,5 @@
 #!/usr/bin/perl
+#V1.0.0
 use strict;
 use Getopt::Long;
 
@@ -29,6 +30,9 @@
 my $ONLY_UNFILTERED_VARIANT="OFF";
 my $DO_STAT="NO";
 
+my $nb_variant_checked=0;
+my $nb_variant_selected=0;
+
 
 my $STAT_MIN_DEPTH_MIN = 2;
 my $STAT_MIN_DEPTH_MAX = 10;
@@ -83,6 +87,7 @@
 #Extraction des variants
 my $nb_line=0;
 while (my $line=<IF>){
+	$nb_variant_checked++;
 	$nb_line++;
 	if (($nb_line % 1000000 == 0)&&($VERBOSE==1)){
 		print "$nb_line\n";
@@ -151,6 +156,7 @@
 	my $error_code = check_error($tbl_line[$i],$before,$after,\%USR_PARAM);
 	if ($error_code == 0){
 		print $line{"line"};
+		$nb_variant_selected++;
 	}
 	else {
 		push(@error,$error_code,"\t",$line{"line"});
@@ -159,8 +165,12 @@
 
 ### LOG
 open(LF,">$logfile") or die ("Can't open $logfile\n");
-
-if ($DO_STAT eq "YES"){
+print LF "\n####\t MPileup filtering \n";
+print LF "Variant checked  :\t$nb_variant_checked\n";
+if ($DO_STAT eq "NO"){
+	print LF "Variant selected :\t$nb_variant_selected\n";
+}
+elsif ($DO_STAT eq "YES"){
 	for (my $idx_min_depth=$STAT_MIN_DEPTH_MIN;$idx_min_depth<=$STAT_MIN_DEPTH_MAX;$idx_min_depth = $idx_min_depth + $STAT_MIN_DEPTH_STEP ){
 		for (my $idx_max_depth=$STAT_MAX_DEPTH_MIN;$idx_max_depth<=$STAT_MAX_DEPTH_MAX;$idx_max_depth = $idx_max_depth + $STAT_MAX_DEPTH_STEP ){
 			for (my $idx_freq = $STAT_FREQ_MIN;$idx_freq<=$STAT_FREQ_MAX;$idx_freq= $idx_freq+$STAT_FREQ_STEP){ 
@@ -183,9 +193,9 @@
 }
 
 
-for (my $i=0;$i<=$#error;$i++){
-	print LF $error[$i];
-}
+#for (my $i=0;$i<=$#error;$i++){
+#	print LF $error[$i];
+#}
 close (LF);