From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 31 Aug 2011 14:27:37 +0000 (+0000)
Subject: corrected bug in sam.rb
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=83e8f66ea7575f16392e3288b6d6b0dc722ce1e0;p=biopieces.git

corrected bug in sam.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1506 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_ruby/lib/maasha/sam.rb b/code_ruby/lib/maasha/sam.rb
index 272d8fc..a122cc7 100644
--- a/code_ruby/lib/maasha/sam.rb
+++ b/code_ruby/lib/maasha/sam.rb
@@ -111,7 +111,9 @@ class Sam < Filesys
       if m =~ /\d+/      # Matches
         offset += m.to_i
       elsif m[0] == '^'  # Deletions
-        m[1 .. -1].each_char do |nt|
+        1.upto(m.size - 1).each do
+          nt = sam[:SEQ].seq[offset]
+
           align << [offset, "#{nt}>-"]
 
           deletions += 1