def test_get_strands_lumpy(lumpy, bnd):
bnd[0]["id"] = "_1"
p = vcf_sv_parser.SV_vcf(lumpy, caller="lumpy")
mate1, mate2 = p._get_mates(bnd)
strand1, strand2 = p._get_strands(mate1, mate2)
assert strand1 == "+"
assert strand2 == "-"
def test_filter_low_qual_calls_lumpy_filtered(lumpy):
p = vcf_sv_parser.SV_vcf(lumpy, caller="lumpy")
records = p._parse_vcf()
record = [list(next(p._group_bnds(records)))]
record[0][0]["filter"] = "LOW_QUAL"
filt_records = list(p._filter_low_qual_calls(record))
assert filt_records == []
def test_filter_low_qual_calls_non_svaba_filtered(svaba):
p = vcf_sv_parser.SV_vcf(svaba, caller="svaba")
records = p._parse_vcf()
record = [list(next(p._group_bnds(records)))]
record[0][0]["filter"] = "LOW_QUAL"
record[0][1]["filter"] = "LOW_QUAL"
filt_records = list(p._filter_low_qual_calls(record))
assert filt_records == []
def test_get_strands_lumpy_unmatched(lumpy, bnd):
bnd[0]["id"] = "_1"
bnd[0]["STRANDS"] = bnd[1]["STRANDS"]
p = vcf_sv_parser.SV_vcf(lumpy, caller="lumpy")
mate1, mate2 = p._get_mates(bnd)
assert _raises_correct_error(p._get_strands,
mate1,
mate2,
expected_error=AssertionError)
def test_filter_low_qual_calls_svaba_unfiltered(svaba):
p = vcf_sv_parser.SV_vcf(svaba, caller="svaba")
records = p._parse_vcf()
record = [list(next(p._group_bnds(records)))]
filt_records = list(p._filter_low_qual_calls(record))
assert record[0][0] == filt_records[0][0]
def test_filter_low_qual_calls_lumpy_unfiltered(lumpy):
p = vcf_sv_parser.SV_vcf(lumpy, caller="lumpy")
records = p._parse_vcf()
record = [list(next(p._group_bnds(records)))]
filt_records = list(p._filter_low_qual_calls(record))
assert record[0][0] == filt_records[0][0]
def test_get_mates_reversed_svaba(svaba, bnd):
bnd[0]["id"] = ":2"
matched = vcf_sv_parser.SV_vcf(svaba, caller="svaba")._get_mates(bnd)
assert bnd[0] == matched[1]
assert bnd[1] == matched[0]
def test_get_mates_reversed_gridss(gridss, bnd):
bnd[0]["id"] = "_2"
matched = vcf_sv_parser.SV_vcf(gridss, caller="gridss")._get_mates(bnd)
assert bnd[0] == matched[1]
assert bnd[1] == matched[0]
def test_get_mates_reversed_lumpy(lumpy, bnd):
bnd[0]["id"] = "_2"
matched = vcf_sv_parser.SV_vcf(lumpy, caller="lumpy")._get_mates(bnd)
assert bnd[0] == matched[1]
assert bnd[1] == matched[0]
def test_bnd_matched(lumpy, bnd):
matched = next(
vcf_sv_parser.SV_vcf(lumpy, caller="lumpy")._group_bnds(bnd))
assert isinstance(matched, tuple)