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()