Add gatk test file and rename test script

tests/test_dummy.py

-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

tests/test_evaluate.py

+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