# HG changeset patch
# User mcharles
# Date 1410942008 14400
# Node ID 9074a5104cdd1af5d62e6f4aba0109fe5602b157
# Parent  9332b9da749136e5383715387f6c2fc0044342db
Uploaded

diff -r 9332b9da7491 -r 9074a5104cdd rapsodyn/PrepareFastqLight.pl
--- a/rapsodyn/PrepareFastqLight.pl	Thu Sep 11 07:31:20 2014 -0400
+++ b/rapsodyn/PrepareFastqLight.pl	Wed Sep 17 04:20:08 2014 -0400
@@ -279,7 +279,8 @@
 	my $startnoN = 0;
 	my $stopnoN = length($quality)-1;
 	
-	#print "SEQ :\n$seq\n";
+#print "HEAD:\t$header";	
+#print "SEQ:\t$seq\n";
 	
 	my $chercheN = $seq;
 	my @bad_position;
@@ -306,14 +307,18 @@
 	}
 	my $lengthnoN = $stopnoN - $startnoN + 1;
 	my $seqnoN = substr($seq,$startnoN,$lengthnoN);
-	#print "$seqnoN\n";
+#	print "SEQnoN\t:$seqnoN\n";
+#	for (my $i=0;$i<=$#bad_position;$i++){
+#		print $bad_position[$i]."\t";
+#	}
+#	print "\n";
 	
 	if ($lengthnoN >= $MIN_LENGTH){
 		my $startTrim = $startnoN;
 		my $stopTrim = $stopnoN;
 		
 		my $quality_converted="";
-		my @bad_position;
+		#my @bad_position;
 		
 		my @q = split(//,$quality);
 		#print "QUALITY\n";
@@ -336,10 +341,11 @@
 		
 		
 		if ($#bad_position>=0){
-			# for (my $i=0;$i<=$#bad_position;$i++){
-				# print $bad_position[$i]."\t";
-			# }
-			# print "\n";
+			@bad_position = sort {$a <=> $b} @bad_position;
+#			for (my $i=0;$i<=$#bad_position;$i++){
+#				print $bad_position[$i]."\t";
+#			}
+#			print "\n";
 			my %coord=%{&extract_longer_string_coordinates_from_bad_position($startnoN,$stopnoN,\@bad_position)};
 			$startTrim = $coord{"start"};
 			$stopTrim = $coord{"stop"};
@@ -356,7 +362,9 @@
 			$fastq_lines .= substr($seq,$startTrim,$lengthTrim)."\n";
 			$fastq_lines .= "+\n";
 			$fastq_lines .= substr($quality,$startTrim,$lengthTrim)."\n";
+#			print $fastq_lines;
 			return $fastq_lines;
+			
 		}
 		else {
 			return "";