From 368545f795cb313fb2cd895a8f3ab4cd9d101380 Mon Sep 17 00:00:00 2001
From: Redmar van den Berg <RedmarvandenBerg@lumc.nl>
Date: Tue, 27 Aug 2019 16:02:01 +0200
Subject: [PATCH] Add gatk test file and rename test script

---
 tests/cases/gatk.vcf.gz     | Bin 0 -> 7761 bytes
 tests/cases/gatk.vcf.gz.tbi | Bin 0 -> 172 bytes
 tests/test_dummy.py         |  16 ----------------
 tests/test_evaluate.py      |  31 +++++++++++++++++++++++++++++++
 4 files changed, 31 insertions(+), 16 deletions(-)
 create mode 100644 tests/cases/gatk.vcf.gz
 create mode 100644 tests/cases/gatk.vcf.gz.tbi
 delete mode 100644 tests/test_dummy.py
 create mode 100644 tests/test_evaluate.py

diff --git a/tests/cases/gatk.vcf.gz b/tests/cases/gatk.vcf.gz
new file mode 100644
index 0000000000000000000000000000000000000000..df6722dd81a3e3c9425a9fadf40e965ff288fd60
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diff --git a/tests/cases/gatk.vcf.gz.tbi b/tests/cases/gatk.vcf.gz.tbi
new file mode 100644
index 0000000000000000000000000000000000000000..26f3289b70db11b8b83bdb80424688968852fba5
GIT binary patch
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diff --git a/tests/test_dummy.py b/tests/test_dummy.py
deleted file mode 100644
index 11b4eaa..0000000
--- 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 0000000..df922e7
--- /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
-- 
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