def test_should_filter_variant_when_all_reads_have_quality_below_threshold(
self):
svc = SVCDriver(self)
threshold = 50
svc.with_var_filters("MQ")
svc.with_min_root_mean_square_mapping_q(threshold)
svc.with_read_mapping_filter_q(0)
svc\
.with_ref_sequence(
"AAAGCGTACAACCGGGTTAGTCACAAACCCGTTACGTATGCATG")\
.with_read(
"................G...........................", n_fwd=10, n_rev=10, mapping_quality=threshold - 1)
expect = svc.call()
vcf_expectation = expect.with_output_vcf()
vcf_expectation.record_count(1)
vcf_expectation\
.has_record_for_variant(Variant(DEFAULT_CHROM, 16, "T", "G"))\
.with_filters({"MQ"})
def test_should_take_max_mq_over_all_the_samples_which_support_the_variant(
self):
svc = SVCDriver(self)
threshold = 50
svc.with_var_filters("MQ")
svc.with_min_root_mean_square_mapping_q(threshold)
svc.with_read_mapping_filter_q(0)
svc\
.with_ref_sequence(
# 1234567890123456789
"AAAGCGTACAACCGGGTTAGTCACAAACCCGTTACGTATGCATG")\
.with_read(
"................G......................... ",
n_fwd=10, n_rev=10, mapping_quality=threshold - 1, sample_name="Ugly")\
.with_read(
"................G...........................",
n_fwd=10, n_rev=10, mapping_quality=threshold, sample_name="Good")
expect = svc.call()
vcf_expectation = expect.with_output_vcf()
vcf_expectation.record_count(1)
vcf_expectation\
.has_record_for_variant(Variant(DEFAULT_CHROM, 16, "T", "G"))\
.with_no_filters()