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 2eb9c93ff1749ff40853640844683bf35daf7e7e..b0ec7386ef18530e063cf8ed84be150110317a9d 100644 (file)
--- 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