From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 30 May 2012 11:37:01 +0000 (+0000)
Subject: added to_seq method to sff.rb
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=1b969d23f52856a45f9e0b4ab52b64a32121f2b9;p=biopieces.git

added to_seq method to sff.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1832 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_ruby/lib/maasha/sff.rb b/code_ruby/lib/maasha/sff.rb
index f4c3931..c5243ad 100644
--- a/code_ruby/lib/maasha/sff.rb
+++ b/code_ruby/lib/maasha/sff.rb
@@ -23,6 +23,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 require 'maasha/base36'
+require 'maasha/seq'
 
 # Error class for all exceptions to do with SFF.
 class SFFError < StandardError; end
@@ -212,6 +213,11 @@ class Read
     hash
   end
 
+  # Method that converts a Read object's data to a Seq object.
+  def to_seq
+    Seq.new(self.name, self.bases, nil, self.quality_scores.map { |i| (i += 64).chr }.join "")
+  end
+
   # Method that soft masks the sequence (i.e. lowercases sequence) according to
   # clip_qual_left and clip_qual_right information.
   def mask