pair.rb now working correctly

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1930 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_ruby/lib/maasha/align/pair.rb b/code_ruby/lib/maasha/align/pair.rb
index c17dba60036bb8442e00d8d56e9bfbabfb3395c4..0969fe724852f9c52536ad90a7d54abec6cf5355 100644 (file)
--- a/code_ruby/lib/maasha/align/pair.rb
+++ b/code_ruby/lib/maasha/align/pair.rb
@@ -46,8 +46,8 @@ module PairAlign
       @q_entry.seq.downcase!
       @s_entry.seq.downcase!
 
-      space = Space.new( 0, 0, @q_entry.length - 1, @s_entry.length - 1)
-      kmer  = 64
+      space = Space.new(0, 0, @q_entry.length - 1, @s_entry.length - 1)
+      kmer  = 32
 
       align_recurse(@q_entry.seq, @s_entry.seq, space, kmer)
       matches_upcase
@@ -76,7 +76,6 @@ module PairAlign
           matches = matches_select_by_score(matches, space)
         end
 
-#      $stderr.puts "#{kmer}   #{matches.size}   #{space.q_dim} x #{space.s_dim}"
         kmer /= 2
       end
 
@@ -116,10 +115,6 @@ module PairAlign
         score_diag   = match_score_diag(match, space)
 
         match.score = score_length + score_diag
-
-
-#        $stderr.puts "score_length: #{score_length}   score_diag: #{score_diag}   score: #{match.score}"   # DEBUG
-#        $stderr.puts match
       end
 
       matches.sort_by! { |match| match.score }