diff --git a/tests/cases/gatk.vcf.gz b/tests/cases/gatk.vcf.gz new file mode 100644 index 0000000000000000000000000000000000000000..df6722dd81a3e3c9425a9fadf40e965ff288fd60 Binary files /dev/null and b/tests/cases/gatk.vcf.gz differ diff --git a/tests/cases/gatk.vcf.gz.tbi b/tests/cases/gatk.vcf.gz.tbi new file mode 100644 index 0000000000000000000000000000000000000000..26f3289b70db11b8b83bdb80424688968852fba5 Binary files /dev/null and b/tests/cases/gatk.vcf.gz.tbi differ diff --git a/tests/test_dummy.py b/tests/test_dummy.py deleted file mode 100644 index 11b4eaac431169d56ddb5ff829a727a54c3aab7e..0000000000000000000000000000000000000000 --- a/tests/test_dummy.py +++ /dev/null @@ -1,16 +0,0 @@ -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 diff --git a/tests/test_evaluate.py b/tests/test_evaluate.py new file mode 100644 index 0000000000000000000000000000000000000000..df922e7311e689a0240099fece489ec41a52af95 --- /dev/null +++ b/tests/test_evaluate.py @@ -0,0 +1,31 @@ +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