From 891aa087b1b4eaf52767051d841c8bb12949d087 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 13 Oct 2010 10:19:37 +0000
Subject: [PATCH] fixed SAM.pm qual scores from phred-33 to phred-64

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1127 74ccb610-7750-0410-82ae-013aeee3265d
---
 code_perl/Maasha/SAM.pm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/code_perl/Maasha/SAM.pm b/code_perl/Maasha/SAM.pm
index 197a957..ff8cb66 100644
--- a/code_perl/Maasha/SAM.pm
+++ b/code_perl/Maasha/SAM.pm
@@ -118,6 +118,7 @@ sub sam2biopiece
     $record->{ 'ISIZE' }    = $entry->[ ISIZE ];
     $record->{ 'SEQ' }      = $entry->[ SEQ ];
     $record->{ 'SCORES' }   = $entry->[ QUAL ];
+    $record->{ 'SCORES' }   =~ s/(.)/chr( ( ord( $1 ) - 33 ) + 64 )/ge; # convert phred-33 to phred-64 scores
     $record->{ 'SCORE' }    = sprintf( "%.2f", Maasha::Fastq::phred_str_mean( $entry->[ QUAL ] ) );
 
     $record->{ 'S_BEG' } -= 1 if $record->{ 'S_BEG' }  != 0;
-- 
2.39.5