From 6562310687801d888c0afbfd1dc90cef4aee9006 Mon Sep 17 00:00:00 2001
From: Redmar van den Berg <RedmarvandenBerg@lumc.nl>
Date: Tue, 27 Aug 2019 11:30:00 +0200
Subject: [PATCH] Add real test for site_concordancy
---
tests/test_dummy.py | 18 ++++++++++++++----
tox.ini | 3 +--
2 files changed, 15 insertions(+), 6 deletions(-)
diff --git a/tests/test_dummy.py b/tests/test_dummy.py
index 60b9ef7..11b4eaa 100644
--- a/tests/test_dummy.py
+++ b/tests/test_dummy.py
@@ -1,6 +1,16 @@
-def func(x):
- return x + 1
+import pytest
+from vtools.evaluate import site_concordancy
-def test_answer():
- assert func(41) == 42
+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/tox.ini b/tox.ini
index 772d67c..8b42584 100644
--- a/tox.ini
+++ b/tox.ini
@@ -2,8 +2,7 @@
envlist = py36
[testenv]
-deps =
- -rrequirements.txt
+deps =
pytest
commands = pytest
--
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