upgraded assemble.rb to chose proper residue when mismatch

[biopieces.git] / code_ruby / test / maasha / seq / test_assemble.rb

diff --git a/code_ruby/test/maasha/seq/test_assemble.rb b/code_ruby/test/maasha/seq/test_assemble.rb
index bdc759c3297a269493509a21419a27a249a29d32..cf05ca839fca4fb8bcdb0521b0d62b4e9eea6b83 100755 (executable)
--- a/code_ruby/test/maasha/seq/test_assemble.rb
+++ b/code_ruby/test/maasha/seq/test_assemble.rb
@@ -33,4 +33,9 @@ class TestAssemble < Test::Unit::TestCase
     assert_equal("GH??43", Assemble.pair(Seq.new("test1", "atcg", :dna, "GHII"), Seq.new("test2", "cgat", :dna, "5543")).qual)
     assert_equal("I???5", Assemble.pair(Seq.new("test1", "atcg", :dna, "IIII"), Seq.new("test2", "tcga", :dna, "5555")).qual)
   end
+
+  test "Assemble.pair with mismatch returns the highest scoring" do
+    assert_equal("atcga", Assemble.pair(Seq.new("t1", "atcga", :dna, "IIIII"), Seq.new("t2", "attga", :dna, "55555"), :mismatches_max => 20).seq)
+    assert_equal("attga", Assemble.pair(Seq.new("t1", "atcga", :dna, "55555"), Seq.new("t2", "attga", :dna, "IIIII"), :mismatches_max => 20).seq)
+  end
 end