From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 2 Nov 2011 09:31:08 +0000 (+0000)
Subject: fixed qual argument for bowtie on fasta only
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=acd65310e4cf43ad3fb8af7810cbc246301b3b87;p=biopieces.git

fixed qual argument for bowtie on fasta only

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1609 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/bowtie_seq b/bp_bin/bowtie_seq
index cd0aeb2..cf25188 100755
--- a/bp_bin/bowtie_seq
+++ b/bp_bin/bowtie_seq
@@ -96,7 +96,7 @@ 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";
+push @args, "--phred64-quals" unless $type eq "FASTA";
 
 if ( defined $options->{ 'max_hits' } ) {
     push @args, "-k $options->{ 'max_hits' }";