# HG changeset patch
# User romaingred
# Date 1512134062 18000
# Node ID a034086659040879af12c8bd48bb1748fd7ca235
# Parent  ffc66227835f7569b2d657a42fac8410debc5641
Uploaded

diff -r ffc66227835f -r a03408665904 bin/align.pm
--- a/bin/align.pm	Fri Dec 01 08:06:35 2017 -0500
+++ b/bin/align.pm	Fri Dec 01 08:14:22 2017 -0500
@@ -46,8 +46,8 @@
 	my $funi = $col_prefix.'unique_mappers.fastq';
 	my $frej = $col_prefix.'unmapped.fastq';
 	
-  my $repartition = $prefix.'distribution.txt';
-	my $png_rep = $prefix.'distribution.png';
+  my $repartition = $out_prefix.'distribution.txt';
+	my $png_rep = $out_prefix.'distribution.png';
 	my ( %duplicates, %genome_hits) ;
 
 	#alignement to the first reference
@@ -77,9 +77,9 @@
 		histogram($size_mappedHashR, $png_rep, $total);
 
 
-		my $dup = $prefix.'dup_mapnum.txt';
-		my $dup_u = $prefix .'dup_unique.txt';
-		my $dup_r = $prefix .'dup_nonmapp.txt';
+		my $dup = $out_prefix.'dup_mapnum.txt';
+		my $dup_u = $out_prefix .'dup_unique.txt';
+		my $dup_r = $out_prefix .'dup_nonmapp.txt';
 		open(my $tab,">".$dup) || die "cannot open output txt file\n";
 		open(my $tab_r,">".$dup_r) || die "cannot open output txt file\n";
 		open(my $tab_u,">".$dup_u) || die "cannot open output txt file\n";