From 26922303b9850fc52a1062bca7bed22983f5da5a Mon Sep 17 00:00:00 2001
From: Redmar van den Berg <RedmarvandenBerg@lumc.nl>
Date: Tue, 27 Aug 2019 16:19:49 +0200
Subject: [PATCH] Add testcase for every field in the output
---
tests/test_evaluate.py | 39 ++++++++++++++++++++++++++++++++++++++-
1 file changed, 38 insertions(+), 1 deletion(-)
diff --git a/tests/test_evaluate.py b/tests/test_evaluate.py
index df922e7..717ef87 100644
--- a/tests/test_evaluate.py
+++ b/tests/test_evaluate.py
@@ -7,7 +7,7 @@ from cyvcf2 import VCF
@pytest.fixture
def known_concordant():
- known = '/home/rrvandenberg/devel/vtools/tests/cases/gatk.vcf.gz'
+ known = 'tests/cases/gatk.vcf.gz'
d, disc = site_concordancy(VCF(known, gts012=True), VCF(known,
gts012=True),
['NA12878'], ['NA12878'], min_gq=0,
@@ -15,6 +15,15 @@ def known_concordant():
return d
+@pytest.fixture
+def blank_NA12878():
+ filename = 'tests/cases/gatk.vcf.gz'
+ d, disc = site_concordancy(VCF(filename, gts012=True), VCF(filename,
+ gts012=True),
+ ['NA12878'], ['BLANK'], min_gq=0, min_dp=0)
+ return d
+
+
def test_total_sites(known_concordant):
assert known_concordant['total_sites'] == 37
@@ -29,3 +38,31 @@ def test_alleles_considered(known_concordant):
def test_alleles_het_concordant(known_concordant):
assert known_concordant['alleles_het_concordant'] == 42
+
+
+def test_alleles_hom_alt_concordant(known_concordant):
+ assert known_concordant['alleles_hom_alt_concordant'] == 18
+
+
+def test_alleles_hom_ref_concordant(known_concordant):
+ assert known_concordant['alleles_hom_ref_concordant'] == 14
+
+
+def test_alleles_concordant(known_concordant):
+ assert known_concordant['alleles_concordant'] == 74
+
+
+def test_alleles_discordant(known_concordant):
+ assert known_concordant['alleles_discordant'] == 0
+
+
+def test_alleles_no_call(blank_NA12878):
+ assert blank_NA12878['alleles_no_call'] == 8
+
+
+def test_alleles_low_qual(known_concordant):
+ assert known_concordant['alleles_low_qual'] == 0
+
+
+def test_alleles_low_depth(known_concordant):
+ assert known_concordant['alleles_low_depth'] == 0
--
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