def test_bad_reads_filter_not_applied_if_one_sample_is_not_naughty(self):
svc = SVCDriver(self)
svc.with_var_filters("BR")
svc.with_bad_reads_window_size(7)
svc.with_min_bad_reads_score(13)
svc.with_ref_sequence(
# 1234567890123456789
"AAAGCGTACAACCGGGTTAGTCACAAACCCGTTACGTATGCATG").with_read(
"................G...........................",
" 3333333 3333333 ",
sample_name="GOOD",
n_rev=2,
n_fwd=2).with_read(
"................G...........................",
" 0000000 0000000 ",
sample_name="BAD",
n_rev=10,
n_fwd=10).with_read(
"................G...........................",
" 00000 0000 ",
sample_name="UGLY",
n_rev=10,
n_fwd=10)
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()
def test_bad_reads_filter_not_applied_when_snp_has_high_quality_bases_nearby(
self):
svc = SVCDriver(self)
svc.with_var_filters("BR")
svc.with_bad_reads_window_size(7)
svc.with_min_bad_reads_score(15)
svc.with_ref_sequence(
# 1234567890123456789
"AAAGCGTACAACCGGGTTAGTCACAAACCCGTTACGTATGCATG").with_read(
"................G...........................",
" 4444444 4444444 ",
n_rev=10,
n_fwd=10)
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()