Mercurial > repos > romaingred > pirna_pipeline

changeset 44:bd4b30bff219 draft

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Uploaded
author romaingred
date Fri, 01 Dec 2017 08:02:00 -0500
parents 0be8011b3d98
children ffc66227835f
files bin/align.pm
diffstat 1 files changed, 4 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/bin/align.pm	Fri Dec 01 08:01:45 2017 -0500
+++ b/bin/align.pm	Fri Dec 01 08:02:00 2017 -0500
@@ -40,11 +40,11 @@
 
 sub get_unique
 {
-	my ( $sam, $s_uni, $prefix, $details, $report ) = @_;
+	my ( $sam, $s_uni, $out_prefix, $col_prefix, $details, $report ) = @_;
 
-	my $fout = $prefix.'all.fastq'; 
-	my $funi = $prefix.'unique.fastq';
-	my $frej = $prefix.'rejected.fastq';
+	my $fout = $col_prefix.'all_mappers.fastq'; 
+	my $funi = $col_prefix.'unique_mappers.fastq';
+	my $frej = $col_prefix.'unmapped.fastq';
 	
   my $repartition = $prefix.'distribution.txt';
 	my $png_rep = $prefix.'distribution.png';