From 7c18441aa7cd1049632fffc6b70256c0f1f64999 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 16 Nov 2011 13:31:52 +0000
Subject: [PATCH] fixed FLAG bug in sam.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1654 74ccb610-7750-0410-82ae-013aeee3265d
---
 code_ruby/lib/maasha/sam.rb | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/code_ruby/lib/maasha/sam.rb b/code_ruby/lib/maasha/sam.rb
index 3bd71ac..d718627 100644
--- a/code_ruby/lib/maasha/sam.rb
+++ b/code_ruby/lib/maasha/sam.rb
@@ -475,58 +475,58 @@ class Sam < Filesys
     # Method to test if template have
     # multiple fragments in sequencing.
     def multi?
-      flag & FLAG_MULTI
+      (flag & FLAG_MULTI) == 0
     end
 
     # Method to test if each fragment
     # properly aligned according to the aligner.
     def aligned?
-      flag & FLAG_ALIGNED 
+      (flag & FLAG_ALIGNED) == 0
     end
     
     # Method to test if the fragment was unmapped.
     def unmapped?
-      flag & FLAG_UNMAPPED
+      (flag & FLAG_UNMAPPED) == 0
     end
 
     # Method to test if the next fragment was unmapped.
     def next_unmapped?
-      flag & FLAG_NEXT_UNMAPPED
+      (flag & FLAG_NEXT_UNMAPPED) == 0
     end
 
     # Method to test if the fragment was reverse complemented.
     def revcomp?
-      flag & FLAG_REVCOMP
+      (flag & FLAG_REVCOMP) == 0
     end
 
     # Method to test if the next fragment was reverse complemented.
     def next_revcomp?
-      flag & FLAG_NEXT_REVCOMP
+      (flag & FLAG_NEXT_REVCOMP) == 0
     end
 
     # Method to test if the fragment was first in the template.
     def first?
-      flag & FLAG_FIRST
+      (flag & FLAG_FIRST) == 0
     end
 
     # Method to test if the fragment was last in the template.
     def last?
-      flag & FLAG_LAST
+      (flag & FLAG_LAST) == 0
     end
 
     # Method to test for secondary alignment.
     def secondary_alignment?
-      flag & FLAG_SECONDARY_ALIGNMENT
+      (flag & FLAG_SECONDARY_ALIGNMENT) == 0
     end
 
     # Method to test for quality fail.
     def quality_fail?
-      flag & FLAG_QUALITY_FAIL
+      (flag & FLAG_QUALITY_FAIL) == 0
     end
 
     # Method to test for PCR or optical duplicates.
     def duplicates?
-      flag & FLAG_DUPLICATES
+      (flag & FLAG_DUPLICATES) == 0
     end
   end
 end
-- 
2.39.2