def test_should_not_filter_similar_reads_with_different_sequences(self): svc = SVCDriver(self) svc.with_min_reads_per_var(6) svc.with_no_similar_reads_filter(True) svc.with_allow_MNP_calls(False) svc.with_ref_sequence( # 1234567890123456789 "TTAATGCATGCATGCATGCATGCATGCATGCATGCCCCG", ).with_read( " ....G...G...G........... ", n_fwd=1, n_rev=1).with_read( " G.......G...G........... ", n_fwd=1, n_rev=1).with_read( " G...G.......G........... ", n_fwd=1, n_rev=1).with_read( ".......G...G...G...G...................", n_fwd=1, n_rev=1) expect = svc.call() expect.with_output_vcf() \ .record_count(4)
def test_should_filter_similar_reads(self): svc = SVCDriver(self) svc.with_no_similar_reads_filter(True) svc.with_min_reads_per_var(2) svc.with_ref_sequence( # 1234567890123456789 "AAAGCGTACAACCGGGTTAGTCACAAACCCGTTACGTATGCATG", ).with_read( "................G...........................", n_rev=10, n_fwd=0) expect = svc.call() expect.with_output_vcf() \ .record_count(0)