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)