def QD_impl(test_case, n_fwd, n_rev):
svc = SVCDriver(test_case)
svc.with_var_filters("QD")
svc.with_min_snp_q_over_depth(35)
svc.with_ref_sequence(
# 1234567890123456789
"AAAGCGTACAACCGGGTTAGTCACAAACCCGTTACGTATGCATG").with_read(
"................G...........................",
n_rev=n_rev,
n_fwd=n_fwd)
expect = svc.call()
vcf_expectation = expect.with_output_vcf()
vcf_expectation.record_count(1)
return vcf_expectation.has_record_for_variant(
Variant(DEFAULT_CHROM, 16, "T", "G"))
def test_should_not_apply_soft_filter_to_snp_with_high_quality(self):
svc = SVCDriver(self)
svc.with_var_filters("QD")
svc.with_min_snp_q_over_depth(1.0)
svc.with_ref_sequence(
# 1234567890123456789
"AAAGCGTACAACCGGGTTAGTCACAAACCCGTTACGTATGCATG").with_read(
"................G...........................",
n_rev=10,
n_fwd=10)
expect = svc.call()
vcf_expectation = expect.with_output_vcf()
vcf_expectation.record_count(1)
record_expectation = vcf_expectation.has_record_for_variant(
Variant(DEFAULT_CHROM, 16, "T", "G"))
record_expectation.with_filters(set())