def test_realign_read(self, read_seq, target_seq, expected_align_start,
expected_cigar, comment):
"""Test Aligner.test_align_read_to_target()."""
read = aligner.Read(
test_utils.make_read(
read_seq,
chrom='ref',
start=0,
cigar=[(len(read_seq), 'M')],
quals=[64] * len(read_seq),
name='read'))
align_reads = self.make_test_aligner(ref_seq=target_seq)
align_reads.set_targets([target_seq])
align_reads.realign_read(read)
if expected_align_start:
self.assertEqual(align_reads.targets[0], read.target, comment)
self.assertEqual(expected_align_start,
read.target_offset + read.alignment.target_begin,
comment)
self.assertEqual(expected_cigar, read.alignment.cigar, comment)
else:
self.assertIsNone(read.target, comment)
self.assertIsNone(read.target_offset, comment)
self.assertIsNone(read.alignment, comment)
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))
