X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=code_ruby%2Ftest%2Fmaasha%2Ftest_seq.rb;h=171e6b1ae9157205527a0613ef68fe65686bf4e7;hb=d4b9c1bec954d5ff3e6eb2f7dc6c1aaa1f7f810f;hp=d177d311467901296a0d2d0aa90f01dce29ffd86;hpb=162aeddb3605c07e27906be021786e2db3ce0664;p=biopieces.git

diff --git a/code_ruby/test/maasha/test_seq.rb b/code_ruby/test/maasha/test_seq.rb
index d177d31..171e6b1 100755
--- a/code_ruby/test/maasha/test_seq.rb
+++ b/code_ruby/test/maasha/test_seq.rb
@@ -488,6 +488,55 @@ class TestSeq < Test::Unit::TestCase
     assert_equal("-atCG", @entry.mask_seq_soft!(20).seq)
   end
 
+  # qual score detection
+
+  def test_Seq_qual_base33_returns_correctly
+    # self.qual.match(/[!-:]/)
+    @entry.qual = '!"#$%&\'()*+,-./0123456789:'
+    assert_equal(true,  @entry.qual_base33? )
+    @entry.qual = 32.chr
+    assert_equal(false, @entry.qual_base33? )
+    @entry.qual = 59.chr
+    assert_equal(false, @entry.qual_base33? )
+  end
+
+  def test_Seq_qual_base64_returns_correctly
+    # self.qual.match(/[K-h]/)
+    @entry.qual = 'KLMNOPQRSTUVWXYZ[\]^_`abcdefgh'
+    assert_equal(true,  @entry.qual_base64? )
+    @entry.qual = 74.chr
+    assert_equal(false, @entry.qual_base64? )
+    @entry.qual = 105.chr
+    assert_equal(false, @entry.qual_base64? )
+  end
+
+  def test_Seq_qual_valid_with_nil_qual_raises
+    assert_raise(SeqError) { @entry.qual_valid?("illumina1.8") }
+  end
+
+  def test_Seq_qual_valid_with_bad_encoding_raises
+    @entry.qual = "abc"
+    assert_raise(SeqError) { @entry.qual_valid?("foobar") }
+  end
+
+  def test_Seq_qual_valid_returns_correctly
+    tests = [["sanger",      0, 40, 33],
+             ["454",         0, 40, 64],
+             ["solexa",     -5, 40, 64],
+             ["illumina13",  0, 40, 64],
+             ["illumina15",  0, 40, 64],
+             ["illumina18",  0, 41, 33]]
+
+    tests.each do |test|
+      @entry.qual = (test[1] + test[-1]).chr + (test[2] + test[-1]).chr
+      assert_equal(true, @entry.qual_valid?(test[0]))
+      @entry.qual = (test[1] + test[-1] - 1).chr
+      assert_equal(false, @entry.qual_valid?(test[0]))
+      @entry.qual = (test[2] + test[-1] + 1).chr
+      assert_equal(false, @entry.qual_valid?(test[0]))
+    end
+  end
+
   # convert sanger to ...
 
   def test_Seq_convert_scores_bang_from_sanger_to_sanger_returns_OK