Python _sw_start_offsets Examples

Example #1

 def test_sw_start_offsets(self):
   """Test Aligner._sw_start_offsets()."""
   k = 3
   read = aligner.Read(
       test_utils.make_read(
           'AaGAt', start=0, cigar=[(5, 'M')], quals=[64] * 5, name='read_1'))
   read.set_read_kmers(k)
   target = aligner.Target('TgATCAGATAAG')
   target.build_target_index(k)
   self.assertEqual([-1, 4, 9],
                    aligner._sw_start_offsets(target.kmer_index, read.kmers))

Example #2

File: aligner_test.py Project: kong75/deepvariant

 def test_sw_start_offsets(self):
   """Test Aligner._sw_start_offsets()."""
   k = 3
   read = aligner.Read(
       test_utils.make_read(
           'AaGAt', start=0, cigar=[(5, 'M')], quals=[64] * 5, name='read_1'))
   read.set_read_kmers(k)
   target = aligner.Target('TgATCAGATAAG')
   target.build_target_index(k)
   self.assertEqual([-1, 4, 9],
                    aligner._sw_start_offsets(target.kmer_index, read.kmers))