Commit c76505da authored by van den Berg's avatar van den Berg

Merge branch 'testing' of git.lumc.nl:klinische-genetica/capture-lumc/vtools into testing

parents d37115cc 955802ec
Pipeline #2786 failed with stage
in 23 seconds
......@@ -393,3 +393,51 @@ def test_known_concordant_RGQ_min_qc_100():
positive_samples=['NA12878'],
min_gq=100, min_dp=0)
assert d['alleles_hom_ref_concordant'] == 0
@pytest.fixture(scope='module')
def gatk_no_alt_in_call():
""" Test statistics when the ALT allele is missing from the called vcf
The ALT allele has been set to '.' for each variant, and the corresponding
GT has been set to 0/0 to generate valid variants.
"""
filename = 'tests/cases/gatk.vcf.gz'
no_alt = 'tests/cases/gatk_no_alt.vcf.gz'
positive = VCF(filename, gts012=True)
call = VCF(no_alt, gts012=True)
d, disc = site_concordancy(call, positive, call_samples=['BLANK'],
positive_samples=['BLANK'], min_dp=0, min_gq=0)
return d
def test_no_alt_call_total_sites(gatk_no_alt_in_call):
assert gatk_no_alt_in_call['total_sites'] == 37
def test_no_alt_call_sites_considered(gatk_no_alt_in_call):
assert gatk_no_alt_in_call['sites_considered'] == 37
def test_no_alt_call_het_concordant(gatk_no_alt_in_call):
assert gatk_no_alt_in_call['alleles_het_concordant'] == 0
def test_no_alt_call_hom_alt_concordant(gatk_no_alt_in_call):
assert gatk_no_alt_in_call['alleles_hom_alt_concordant'] == 0
def test_no_alt_call_hom_ref_concordant(gatk_no_alt_in_call):
assert gatk_no_alt_in_call['alleles_hom_ref_concordant'] == 32
def test_no_alt_call_alleles_concordant(gatk_no_alt_in_call):
assert gatk_no_alt_in_call['alleles_concordant'] == 46
def test_no_alt_call_alleles_discordant(gatk_no_alt_in_call):
assert gatk_no_alt_in_call['alleles_discordant'] == 20
def test_no_alt_call_alleles_no_call(gatk_no_alt_in_call):
assert gatk_no_alt_in_call['alleles_no_call'] == 8
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