From 28d3a1726ca4adb648287d3e98fd58d3e0903efe Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 29 Sep 2009 08:44:46 +0000
Subject: [PATCH] fixed STRAND in SAM format

git-svn-id: http://biopieces.googlecode.com/svn/trunk@687 74ccb610-7750-0410-82ae-013aeee3265d
---
 code_perl/Maasha/SAM.pm | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/code_perl/Maasha/SAM.pm b/code_perl/Maasha/SAM.pm
index c900867..79f697d 100644
--- a/code_perl/Maasha/SAM.pm
+++ b/code_perl/Maasha/SAM.pm
@@ -116,6 +116,12 @@ sub sam2biopiece
     $record->{ 'S_BEG' } -= 1 if $record->{ 'S_BEG' }  != 0;
     $record->{ 'S_BEG' } -= 1 if $record->{ 'S_BEG2' } != 0;
 
+    if ( $record->{ 'FLAG' } & 0x0010 ) {
+        $record->{ 'STRAND' } = '+';
+    } else {
+        $record->{ 'STRAND' } = '-';
+    }
+
     return wantarray ? %{ $record } : $record;
 }
 
-- 
2.39.5