Add check for non-diploid calls

Since it is not clear how we should handle non-diploid calls, we check
if variants are haploid/polyploid and error out if this is the case.

tests/test_evaluate.py

@@ -158,3 +158,29 @@ def test_decomposed_call_file():
                        match='Decomposed variants are not supported'):
         site_concordancy(call, positive, call_samples=['BLANK'],
                          positive_samples=['NA12878'])
+
+
+def test_haploid_positive_file():
+    """ Test error message when the positive vcf contains non-diploid variants
+    """
+    filename = 'tests/cases/gatk.vcf.gz'
+    haploid = 'tests/cases/dummy_haploid.vcf.gz'
+    call = VCF(filename, gts012=True)
+    positive = VCF(haploid, gts012=True)
+    with pytest.raises(NotImplementedError,
+                       match='Non-diploid variants are not supported'):
+        site_concordancy(call, positive, call_samples=['NA12878'],
+                         positive_samples=['BLANK'])
+
+
+def test_haploid_call_file():
+    """ Test error message when the call vcf contains non-diploid variants
+    """
+    filename = 'tests/cases/gatk.vcf.gz'
+    haploid = 'tests/cases/dummy_haploid.vcf.gz'
+    call = VCF(haploid, gts012=True)
+    positive = VCF(filename, gts012=True)
+    with pytest.raises(NotImplementedError,
+                       match='Non-diploid variants are not supported'):
+        site_concordancy(call, positive, call_samples=['BLANK'],
+                         positive_samples=['NA12878'])

vtools/evaluate.py

@@ -174,6 +174,10 @@ def site_concordancy(call_vcf: VCF,
             pos = pos_record.genotypes[p_s]
             cal = call_record.genotypes[c_s]
 
+            # If the genotypes are not diploid
+            if len(pos) != 3 or len(cal) != 3:
+                raise NotImplementedError('Non-diploid variants are not '
+                                          'supported')
             # If the genotypes are phased
             if pos[2] or cal[2]:
                 raise NotImplementedError('Phased variants are not supported')