From 49b2f9e5aae65a2c4e7457488433a15267ae15d4 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Thu, 13 Sep 2012 13:19:26 +0000 Subject: [PATCH] pair.rb now working correctly git-svn-id: http://biopieces.googlecode.com/svn/trunk@1930 74ccb610-7750-0410-82ae-013aeee3265d --- code_ruby/lib/maasha/align/pair.rb | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/code_ruby/lib/maasha/align/pair.rb b/code_ruby/lib/maasha/align/pair.rb index c17dba6..0969fe7 100644 --- 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 } -- 2.39.5