From bbb226bcc2c4bb6ba3ebc019df76f49271c8fff1 Mon Sep 17 00:00:00 2001
From: Redmar van den Berg <RedmarvandenBerg@lumc.nl>
Date: Fri, 25 Oct 2019 09:25:14 +0200
Subject: [PATCH] Add test for a rare bug with partial variants
---
tests/test_evaluate.py | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)
diff --git a/tests/test_evaluate.py b/tests/test_evaluate.py
index 0ae13a2..e62dda0 100644
--- a/tests/test_evaluate.py
+++ b/tests/test_evaluate.py
@@ -1,6 +1,8 @@
import pytest
+from collections import defaultdict
from vtools.evaluate import site_concordancy
+from vtools.evaluate import parse_variants
from cyvcf2 import VCF
@@ -340,3 +342,23 @@ def test_ref_alt_changed_call_concordant(ref_alt_changed_call):
def test_ref_alt_changed_call_no_call(ref_alt_changed_call):
assert ref_alt_changed_call['alleles_no_call'] == 54
+
+
+def test_parse_variants_no_call():
+ """ This should be counted as a single no call """
+ results = defaultdict(int)
+ call = ['.', 'A']
+ pos = ['A', 'G']
+
+ parse_variants('A', call, pos, results)
+ assert results['alleles_no_call'] == 1
+
+
+def test_parse_variants_concordant():
+ """ This should be counted as a single concordant allele """
+ results = defaultdict(int)
+ call = ['.', 'A']
+ pos = ['A', 'G']
+
+ parse_variants('A', call, pos, results)
+ assert results['alleles_concordant'] == 1
--
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