Compare allele genotypes directly

Previously we used cyvcf2 gt_types, which indicate whether a site is
hom_ref, heterozygous, hom_alt or unknown. A limitation of this approach
is that it only makes sense when the two vcf files have the same REF and
ALT alleles for a given position.

If this was not the case, vtools would silently skip the variant.
However, even when the ALT alleles are different between two vcf files,
the actual genotypes can still be compared. This was implemented in this
commit, which also fixes issue #8.

vtools/evaluate.py

@@ -11,6 +11,33 @@ from typing import List, Dict
 from cyvcf2 import VCF
 
 
+def parse_variants(call: List[any], pos: List[any], results: Dict[str, int]):
+    """ Parse the variants and add to results """
+
+    call_variant = sorted(call[0:2])
+    pos_variant = sorted(pos[0:2])
+
+    # The types of concordant calls are counted separately
+    if call_variant == pos_variant:
+        # These variants are homozygous reference
+        if call_variant == [0, 0]:
+            results['alleles_hom_ref_concordant'] += 2
+        # These variants are heterozygous, since they have different calls
+        elif call_variant[0] != call_variant[1]:
+            results['alleles_het_concordant'] += 2
+        # If they are not homozygous reference, and not heterozygous, they must
+        # be homozygous alternative, for whichever alt allele they have
+        else:
+            results['alleles_hom_alt_concordant'] += 2
+
+    # Here we count all alleles independently, also for the concordant calls
+    for i, j in zip(call_variant, pos_variant):
+        if i == j:
+            results['alleles_concordant'] += 1
+        else:
+            results['alleles_discordant'] += 1
+
+
 def site_concordancy(call_vcf: VCF,
                      positive_vcf: VCF,
                      call_samples: List[str],
@@ -98,6 +125,7 @@ def site_concordancy(call_vcf: VCF,
             continue
 
         call_record = same[0]
+
         d['sites_considered'] += 1
         d['alleles_considered'] += (2 * len(positive_samples))
 
@@ -133,44 +161,12 @@ def site_concordancy(call_vcf: VCF,
             if failed_quality_check:
                 continue
 
-            # If the site passed the quality requirements
-            if p_gt == 0 and c_gt == 0:
-                # both homozygous reference
-                d['alleles_concordant'] += 2
-                d['alleles_hom_ref_concordant'] += 2
-            elif p_gt == 0 and c_gt == 1:
-                # heterozygous when homozygous reference
-                d['alleles_concordant'] += 1
-                d['alleles_discordant'] += 1
-            elif p_gt == 0 and c_gt == 2:
-                # homozygous alt when homozygous ref
-                d['alleles_discordant'] += 2
-            elif p_gt == 1 and c_gt == 0:
-                # homozygous ref when heterozygous
-                d['alleles_concordant'] += 1
-                d['alleles_discordant'] += 1
-            elif p_gt == 1 and c_gt == 1:
-                # both heterozygous
-                d['alleles_concordant'] += 2
-                d['alleles_het_concordant'] += 2
-            elif p_gt == 1 and c_gt == 2:
-                # homozygous alt when heterozygous
-                d['alleles_concordant'] += 1
-                d['alleles_discordant'] += 1
-            elif p_gt == 2 and c_gt == 0:
-                # homozygous ref when homozygous alt
-                d['alleles_discordant'] += 2
-            elif p_gt == 2 and c_gt == 1:
-                # heterozygous when homozygous alt
-                d['alleles_concordant'] += 1
-                d['alleles_discordant'] += 1
-            elif p_gt == 2 and c_gt == 2:
-                # both homozygous alt
-                d['alleles_concordant'] += 2
-                d['alleles_hom_alt_concordant'] += 2
-            else:
-                # This should not be reached
-                raise RuntimeError('Unhandled genotype call')
+            # Get the genotypes
+            pos = pos_record.genotypes[p_s]
+            cal = call_record.genotypes[c_s]
+
+            # Parse the genotypes and add the results into d
+            parse_variants(pos, cal, d)
 
             # The current variant is discordant
             if d['alleles_discordant'] > discordant_count: