fixed scores in bwa_seq

[biopieces.git] / bp_bin / bwa_seq

diff --git a/bp_bin/bwa_seq b/bp_bin/bwa_seq
index ff1818516c69cf58f7833a4bfb41b6555d7ad8aa..ed46c201524fa58a0832ecf7c763780b1c69e602 100755 (executable)
--- a/bp_bin/bwa_seq
+++ b/bp_bin/bwa_seq
@@ -71,7 +71,9 @@ $fh_out = Maasha::Filesys::file_write_open( $tmp_fq );
 
 while ( $record = Maasha::Biopieces::get_record( $in ) ) 
 {
-    if ( $entry = Maasha::Fastq::biopiece2fastq( $record ) ) {
+    if ( $entry = Maasha::Fastq::biopiece2fastq( $record ) )
+    {
+        $entry->[ 2 ] =~ s/(.)/chr( ( ord( $1 ) - 64 ) + 33 )/ge; # convert scores from phred-64 to phred-33
         Maasha::Fastq::put_entry( $entry, $fh_out );
     }