Commit 368545f7 authored by van den Berg's avatar van den Berg
Browse files

Add gatk test file and rename test script

parent 65623106
import pytest
from vtools.evaluate import site_concordancy
from cyvcf2 import VCF
@pytest.fixture
def known():
bla =VCF('tests/cases/known1.vcf.gz', gts012=True)
return bla
def test_evaluate(known):
d, disc = site_concordancy(known, known, ["known1"], ["known1"])
assert d['total_sites'] == 3
assert not disc
\ No newline at end of file
import pytest
from vtools.evaluate import site_concordancy
from cyvcf2 import VCF
@pytest.fixture
def known_concordant():
known = '/home/rrvandenberg/devel/vtools/tests/cases/gatk.vcf.gz'
d, disc = site_concordancy(VCF(known, gts012=True), VCF(known,
gts012=True),
['NA12878'], ['NA12878'], min_gq=0,
min_dp=0)
return d
def test_total_sites(known_concordant):
assert known_concordant['total_sites'] == 37
def test_sites_considered(known_concordant):
assert known_concordant['sites_considered'] == 37
def test_alleles_considered(known_concordant):
assert known_concordant['alleles_considered'] == 74
def test_alleles_het_concordant(known_concordant):
assert known_concordant['alleles_het_concordant'] == 42
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment