corrected bug in sam.rb

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

diff --git a/code_ruby/lib/maasha/sam.rb b/code_ruby/lib/maasha/sam.rb
index 272d8fc977f859141f2f9b3100f24013099a4fae..a122cc7486205cc0105e755e3efacc1c5a0df176 100644 (file)
--- 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