changed bowtie_seq to use phred64

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1126 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/bowtie_seq b/bp_bin/bowtie_seq
index 8ccd201499f8e8039be64eb3e08d3868aa5d450d..cd0aeb2eddc5790a7e4dadca38476e06878115c3 100755 (executable)
--- a/bp_bin/bowtie_seq
+++ b/bp_bin/bowtie_seq
@@ -96,6 +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";
 
 if ( defined $options->{ 'max_hits' } ) {
     push @args, "-k $options->{ 'max_hits' }";
@@ -164,8 +165,7 @@ sub bowtie2biopiece
     $record->{ 'S_LEN' }      = length $entry->[ 4 ];
     $record->{ 'SEQ_LEN' }    = length $entry->[ 4 ];
     $record->{ 'S_END' }      = $record->{ 'S_BEG' } + $record->{ 'SEQ_LEN' } - 1;
-    $record->{ 'SCORES' }     =~ s/(.)/ord( $1 ) - 33 . ";"/ge; # http://maq.sourceforge.net/fastq.shtml
-    $record->{ 'SCORE_MEAN' } = sprintf( "%.2f", Maasha::Calc::mean( [ split /;/, $record->{ 'SCORES' } ] ) );
+    $record->{ 'SCORES' }     =~ s/(.)/chr( ( ord( $1 ) - 33 ) + 64 )/ge; # convert phred scores to illumina scores
 
     $record->{ 'HITS' }       = '.';
     $record->{ 'REC_TYPE' } = "BOWTIE";