From 72bdee400078921c708370e9b9e101df4c5ebbe1 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Thu, 5 Dec 2013 13:45:19 +0000
Subject: [PATCH] fixed encoding bug in bowtie_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2273 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/bowtie_seq | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bp_bin/bowtie_seq b/bp_bin/bowtie_seq
index 19368f8..0737421 100755
--- a/bp_bin/bowtie_seq
+++ b/bp_bin/bowtie_seq
@@ -103,7 +103,7 @@ push @args, "-n $options->{ 'mismatches' }";
 push @args, "-v $options->{ 'mismatches' }";  # DANGER: using seed mismatches as alignment mismatches - may work, may not!
 push @args, "-f" if $type eq "FASTA";
 push @args, "-p $options->{ 'cpus' }";
-push @args, "--phred64-quals" unless $type eq "FASTA";
+push @args, "--phred33-quals" unless $type eq "FASTA";
 
 if ( defined $options->{ 'max_hits' } ) {
     push @args, "-k $options->{ 'max_hits' }";
-- 
2.39.2