From d48e4293174ba475f6d10ccca07f36761b15b464 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 13 Oct 2010 12:11:28 +0000
Subject: [PATCH] fixed scores in bwa_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1130 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/bwa_seq | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/bp_bin/bwa_seq b/bp_bin/bwa_seq
index ff18185..ed46c20 100755
--- 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 );
     }
 
-- 
2.39.2