From 168ab8c7b46e3438765c9364e670f780489a1863 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 19 Jan 2010 08:16:09 +0000
Subject: [PATCH] fixed strand bug in SAM.pm

git-svn-id: http://biopieces.googlecode.com/svn/trunk@836 74ccb610-7750-0410-82ae-013aeee3265d
---
 code_perl/Maasha/SAM.pm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/code_perl/Maasha/SAM.pm b/code_perl/Maasha/SAM.pm
index be1002a..197a957 100644
--- a/code_perl/Maasha/SAM.pm
+++ b/code_perl/Maasha/SAM.pm
@@ -130,10 +130,10 @@ sub sam2biopiece
     $record->{ 'Q_SEQ_UNMAPPED' } = $record->{ 'FLAG' } & 0x0004;
     $record->{ 'MATE_UNMAPPED' }  = $record->{ 'FLAG' } & 0x0008;
 
-    if ( $record->{ 'FLAG' } & 0x0010 ) {
-        $record->{ 'STRAND' } = '+';
-    } else {
+    if ( $record->{ 'FLAG' } & 0x0010 ) {   # 0 for forward, 1 for reverse
         $record->{ 'STRAND' } = '-';
+    } else {
+        $record->{ 'STRAND' } = '+';
     }
 
     $record->{ 'MATE_STRAND' }    = $record->{ 'FLAG' } & 0x0020;
-- 
2.39.2