def test_iter_qname_sorted(self):
reads = Reads(self.sam1_file)
previous = 0
for read in reads.reads(sort_by_qname_ix=True):
assert read.qname_ix > previous
previous = read.qname_ix
assert previous != 0
reads.close()
def test_iterate_exclude_filters(self):
reads = Reads(self.sam1_file)
reads.filter_unmapped(queue=True)
reads.filter_quality(35, queue=True)
reads.filter_non_unique(strict=True, queue=True)
reads.run_queued_filters()
assert len(
list(
reads.reads(
excluded_filters=['unmapped', 'mapq', 'uniqueness'
]))) == 271
assert len(
list(reads.reads(
excluded_filters=['unmapped', 'uniqueness']))) == 246
assert len(list(
reads.reads(excluded_filters=['unmapped', 'mapq']))) == 153
assert len(list(
reads.reads(excluded_filters=['mapq', 'uniqueness']))) == 271
assert len(list(reads.reads(excluded_filters=['unmapped']))) == 153
assert len(list(reads.reads(excluded_filters=['mapq']))) == 153
assert len(list(reads.reads(excluded_filters=['uniqueness']))) == 246
reads.close()
