From 955802ec1aa07a576df4e07be03382a00b649f83 Mon Sep 17 00:00:00 2001
From: Redmar van den Berg <RedmarvandenBerg@lumc.nl>
Date: Mon, 4 Nov 2019 11:27:32 +0100
Subject: [PATCH] Add test cases for missing ALT in call vcf
When a vcf file contains calls for all specified positions, the ALT field will
be empty if there is only a reference call in that position. This commits adds
tests for this case.
---
tests/cases/gatk_no_alt.vcf.gz | Bin 0 -> 3364 bytes
tests/cases/gatk_no_alt.vcf.gz.tbi | Bin 0 -> 171 bytes
tests/test_evaluate.py | 48 +++++++++++++++++++++++++++++
3 files changed, 48 insertions(+)
create mode 100644 tests/cases/gatk_no_alt.vcf.gz
create mode 100644 tests/cases/gatk_no_alt.vcf.gz.tbi
diff --git a/tests/cases/gatk_no_alt.vcf.gz b/tests/cases/gatk_no_alt.vcf.gz
new file mode 100644
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diff --git a/tests/cases/gatk_no_alt.vcf.gz.tbi b/tests/cases/gatk_no_alt.vcf.gz.tbi
new file mode 100644
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diff --git a/tests/test_evaluate.py b/tests/test_evaluate.py
index 26e142d..999c72f 100644
--- a/tests/test_evaluate.py
+++ b/tests/test_evaluate.py
@@ -362,3 +362,51 @@ def test_parse_variants_concordant():
parse_variants('A', call, pos, results)
assert results['alleles_concordant'] == 1
+
+
+@pytest.fixture(scope='module')
+def gatk_no_alt_in_call():
+ """ Test statistics when the ALT allele is missing from the called vcf
+
+ The ALT allele has been set to '.' for each variant, and the corresponding
+ GT has been set to 0/0 to generate valid variants.
+ """
+ filename = 'tests/cases/gatk.vcf.gz'
+ no_alt = 'tests/cases/gatk_no_alt.vcf.gz'
+ positive = VCF(filename, gts012=True)
+ call = VCF(no_alt, gts012=True)
+ d, disc = site_concordancy(call, positive, call_samples=['BLANK'],
+ positive_samples=['BLANK'], min_dp=0, min_gq=0)
+ return d
+
+
+def test_no_alt_call_total_sites(gatk_no_alt_in_call):
+ assert gatk_no_alt_in_call['total_sites'] == 37
+
+
+def test_no_alt_call_sites_considered(gatk_no_alt_in_call):
+ assert gatk_no_alt_in_call['sites_considered'] == 37
+
+
+def test_no_alt_call_het_concordant(gatk_no_alt_in_call):
+ assert gatk_no_alt_in_call['alleles_het_concordant'] == 0
+
+
+def test_no_alt_call_hom_alt_concordant(gatk_no_alt_in_call):
+ assert gatk_no_alt_in_call['alleles_hom_alt_concordant'] == 0
+
+
+def test_no_alt_call_hom_ref_concordant(gatk_no_alt_in_call):
+ assert gatk_no_alt_in_call['alleles_hom_ref_concordant'] == 32
+
+
+def test_no_alt_call_alleles_concordant(gatk_no_alt_in_call):
+ assert gatk_no_alt_in_call['alleles_concordant'] == 46
+
+
+def test_no_alt_call_alleles_discordant(gatk_no_alt_in_call):
+ assert gatk_no_alt_in_call['alleles_discordant'] == 20
+
+
+def test_no_alt_call_alleles_no_call(gatk_no_alt_in_call):
+ assert gatk_no_alt_in_call['alleles_no_call'] == 8
--
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