def test_should_not_call_variant_with_duplicate_reads_and_duplicate_reads_not_allowed(self):
svc = SVCDriver(self)
svc.with_duplicates_filter(True)
svc.with_ref_sequence(
# 1234567890123456789
"AAAGCGTACAACCGGGTTAGTCACAAACCCGTTACGTATGCATG",
).with_read(
"................G...........................",
n_rev=10, n_fwd=10, read_flags=FORWARD_GOOD_READ | DUPLICATE
)
expect = svc.call()
expect.with_output_vcf() \
.record_count(0)
def test_should_call_variant_if_reads_are_not_duplicates(self):
svc = SVCDriver(self)
svc.with_duplicates_filter(True)
svc.with_ref_sequence(
# 1234567890123456789
"AAAGCGTACAACCGGGTTAGTCACAAACCCGTTACGTATGCATG",
).with_read(
"................G...........................",
n_rev=10, n_fwd=10, read_flags=FORWARD_GOOD_READ & ~DUPLICATE
)
expect = svc.call()
expect.with_output_vcf() \
.record_count(1) \
.has_record_for_variant(Variant(DEFAULT_CHROM, 16, "T", "G"))