def test_extract_sample_name_from_reads_single_sample(self):
mock_sample_reader = mock.Mock()
mock_sample_reader.header = reads_pb2.SamHeader(
read_groups=[reads_pb2.ReadGroup(sample_id='sample_name')])
self.assertEqual(
make_examples_core.extract_sample_name_from_sam_reader(
mock_sample_reader), 'sample_name')
def test_extract_sample_name_from_reads_uses_default_when_necessary(
self, samples, expected_sample_name):
mock_sample_reader = mock.Mock()
mock_sample_reader.header = reads_pb2.SamHeader(read_groups=[
reads_pb2.ReadGroup(sample_id=sample) for sample in samples
])
self.assertEqual(
expected_sample_name,
make_examples_core.extract_sample_name_from_sam_reader(
mock_sample_reader))
def setUp(self):
self.read1 = test_utils.make_read(bases='ACCGT',
chrom='chr1',
start=10,
cigar='5M',
mapq=50,
quals=range(30, 35),
name='read1')
self.read2 = test_utils.make_read(bases='AACCTT',
chrom='chr2',
start=15,
cigar='7M',
mapq=40,
quals=range(20, 26),
name='read2')
self.contigs = [
reference_pb2.ContigInfo(name='chr1'),
reference_pb2.ContigInfo(name='chr2'),
]
self.header = reads_pb2.SamHeader()