From 351549b36ba20cf06daf9cf0e14273d84ae1f83e Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 12 Mar 2013 10:44:52 +0000
Subject: [PATCH] fixed score base bug in sff.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2132 74ccb610-7750-0410-82ae-013aeee3265d
---
 code_ruby/lib/maasha/seq.rb      | 9 +++++++++
 code_ruby/lib/maasha/seq/trim.rb | 1 +
 code_ruby/lib/maasha/sff.rb      | 4 ++--
 3 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index 91e7929..d8a73d3 100644
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -416,6 +416,15 @@ class Seq
     self
   end
 
+  # Method to add two Seq objects.
+  def +(entry)
+    new_entry = Seq.new()
+    new_entry.seq  = self.seq  + entry.seq
+    new_entry.type = self.type              if self.type == entry.type
+    new_entry.qual = self.qual + entry.qual if self.qual and entry.qual
+    new_entry
+  end
+
   # Method to concatenate sequence entries.
   def <<(entry)
     raise SeqError, "sequences of different types" unless self.type == entry.type
diff --git a/code_ruby/lib/maasha/seq/trim.rb b/code_ruby/lib/maasha/seq/trim.rb
index 8efabf9..e7e9bb1 100644
--- a/code_ruby/lib/maasha/seq/trim.rb
+++ b/code_ruby/lib/maasha/seq/trim.rb
@@ -1,3 +1,4 @@
+# Copyright (C) 2007-2013 Martin A. Hansen.
 
 # This program is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
diff --git a/code_ruby/lib/maasha/sff.rb b/code_ruby/lib/maasha/sff.rb
index 7111f64..6b277e3 100644
--- a/code_ruby/lib/maasha/sff.rb
+++ b/code_ruby/lib/maasha/sff.rb
@@ -210,7 +210,7 @@ class Read
     hash[:CLIP_QUAL_RIGHT]    = self.clip_qual_right    - 1
     hash[:CLIP_ADAPTOR_LEFT]  = self.clip_adapter_left  - 1
     hash[:CLIP_ADAPTOR_RIGHT] = self.clip_adaptor_right - 1
-    hash[:SCORES]             = self.quality_scores.map { |i| (i += 64).chr }.join ""
+    hash[:SCORES]             = self.quality_scores.map { |i| (i += Seq::SCORE_BASE).chr }.join ""
     hash[:X_POS]              = self.x_pos
     hash[:Y_POS]              = self.y_pos
 
@@ -219,7 +219,7 @@ class Read
 
   # 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("") )
+    Seq.new(self.name, self.bases, nil, self.quality_scores.map { |i| (i += Seq::SCORE_BASE).chr }.join("") )
   end
 
   # Method that soft masks the sequence (i.e. lowercases sequence) according to
-- 
2.39.2