def test_fetch_invalid_read(self, log_patcher):
bad_read = mock.Mock(is_unmapped=False, reference_start=0, reference_end=0, query_name='BAD_READ')
fh = mock.Mock(references=['chr'], spec=['references', 'fetch'])
fh.configure_mock(**{'fetch.return_value': [bad_read]})
cache = BamCache(fh)
cache.fetch('chr', 1, 10)
self.assertEqual(0, len(cache.cache))
log_patcher.assert_called_with('ignoring invalid read', 'BAD_READ', level=logging.DEBUG)
def setUpModule():
global REFERENCE_GENOME
REFERENCE_GENOME = load_reference_genome(get_data('mock_reference_genome.fa'))
if 'CTCCAAAGAAATTGTAGTTTTCTTCTGGCTTAGAGGTAGATCATCTTGGT' != REFERENCE_GENOME['fake'].seq[0:50].upper():
raise AssertionError('fake genome file does not have the expected contents')
global BAM_CACHE
BAM_CACHE = BamCache(get_data('mini_mock_reads_for_events.sorted.bam'))
global FULL_BAM_CACHE
FULL_BAM_CACHE = BamCache(get_data('mock_reads_for_events.sorted.bam'))
global READS
READS = {}
for read in BAM_CACHE.fetch('reference3', 1, 8000):
if read.qname not in READS:
READS[read.qname] = [None, None]
if read.is_supplementary:
continue
if read.is_read1:
READS[read.qname][0] = read
else:
READS[read.qname][1] = read