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 cd0aeb2eddc5790a7e4dadca38476e06878115c3..cf25188e6e42019ae131ee23fbd10837b3adf9af 100755 (executable)
--- 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' }";