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/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