From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 30 May 2012 11:41:17 +0000 (+0000)
Subject: fixed bug in sff.rb clip and mask methods
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=5e4f217771644a45d3f866fafb1c21b0568a8ed8;p=biopieces.git

fixed bug in sff.rb clip and mask methods

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1834 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_ruby/lib/maasha/sff.rb b/code_ruby/lib/maasha/sff.rb
index 2eb9c93..b0ec738 100644
--- a/code_ruby/lib/maasha/sff.rb
+++ b/code_ruby/lib/maasha/sff.rb
@@ -226,6 +226,8 @@ class Read
     right  = self.bases[self.clip_qual_right ... self.bases.length].downcase
 
     self.bases = left + middle + right
+
+    self
   end
 
   # Method that clips sequence (i.e. trims) according to
@@ -233,6 +235,8 @@ class Read
   def clip
     self.bases          = self.bases[self.clip_qual_left - 1 ... self.clip_qual_right]
     self.quality_scores = self.quality_scores[self.clip_qual_left - 1 ... self.clip_qual_right]
+
+    self
   end
 
   private