def test_build_target_index(self, seq, expected_kmers_or_none):
"""Test Aligner.set_targets()."""
target = aligner.Target(seq)
result = target.build_target_index(k=3)
self.assertEqual(result, bool(expected_kmers_or_none))
if expected_kmers_or_none is None:
self.assertEqual(len(target.kmer_index), 0)
else:
self.assertEqual(expected_kmers_or_none, target.kmer_index)
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))