polished pairwise alignment code

[biopieces.git] / code_ruby / lib / maasha / sff.rb

diff --git a/code_ruby/lib/maasha/sff.rb b/code_ruby/lib/maasha/sff.rb
index 2eb9c93ff1749ff40853640844683bf35daf7e7e..7111f643426469cfe9cbebc32608854c0310584b 100644 (file)
--- a/code_ruby/lib/maasha/sff.rb
+++ b/code_ruby/lib/maasha/sff.rb
@@ -195,7 +195,11 @@ class Read
 
   # Method that converts a Read object's data to a Biopiece record (a hash).
   def to_bp
-    coordinates_get
+    # Simulated SFF files may not have coordinates.
+    begin
+      coordinates_get
+    rescue
+    end
 
     hash = {}
 
@@ -226,6 +230,8 @@ 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 +239,8 @@ 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