Add check for decomposed calls

Before, we would iterate over decomposed called variants until we found
the variant where the REF and ALT matched the one in the positive vcf.
However, this meant that sites where the called vcf had different ALTs
could not be processed.

To resolve this, we had to drop support for decomposed variants.

tests/test_evaluate.py

@@ -132,3 +132,29 @@ def test_phased_call_file():
                        match='Phased variants are not supported'):
         site_concordancy(call, positive, call_samples=['BLANK'],
                          positive_samples=['NA12878'])
+
+
+def test_decomposed_positive_file():
+    """ Test error message when the positive vcf contains decomposed variants
+    """
+    filename = 'tests/cases/gatk.vcf.gz'
+    decomposed = 'tests/cases/dummy_decomposed.vcf.gz'
+    call = VCF(filename, gts012=True)
+    positive = VCF(decomposed, gts012=True)
+    with pytest.raises(NotImplementedError,
+                       match='Decomposed variants are not supported'):
+        site_concordancy(call, positive, call_samples=['BLANK'],
+                         positive_samples=['NA12878'])
+
+
+def test_decomposed_call_file():
+    """ Test error message when the positive vcf contains decomposed variants
+    """
+    filename = 'tests/cases/gatk.vcf.gz'
+    decomposed = 'tests/cases/dummy_decomposed.vcf.gz'
+    call = VCF(decomposed, gts012=True)
+    positive = VCF(filename, gts012=True)
+    with pytest.raises(NotImplementedError,
+                       match='Decomposed variants are not supported'):
+        site_concordancy(call, positive, call_samples=['BLANK'],
+                         positive_samples=['NA12878'])

vtools/evaluate.py

@@ -7,6 +7,7 @@ vtools.evaluate
 :license: MIT
 """
 from typing import List, Dict
+from types import SimpleNamespace
 
 from cyvcf2 import VCF
 
@@ -91,40 +92,48 @@ def site_concordancy(call_vcf: VCF,
         "alleles_low_qual": 0,
         "alleles_low_depth": 0
     }
+
+    # Keep track of the discordant sites
     discordant_count = 0
     discordant_records = list()
 
+    # Keep track of the previous record, to make sure the positive vcf file
+    # does not contain decomposed records
+    prev_record = SimpleNamespace()
+    prev_record.POS = -1
+    prev_record.CHROM = -1
+
     for pos_record in positive_vcf:
+        # Check to make sure the POS and CHROM are different from the previous
+        # variant
+        if (prev_record.POS == pos_record.POS and
+                prev_record.CHROM == pos_record.CHROM):
+            raise NotImplementedError('Decomposed variants are not supported')
+        else:
+            prev_record.POS = pos_record.POS
+            prev_record.CHROM = pos_record.CHROM
+
         d['total_sites'] += 1
         query_str = "{0}:{1}-{2}".format(
             pos_record.CHROM,
-            pos_record.start,
+            pos_record.start+1,
             pos_record.end
         )
 
-        it = call_vcf(query_str)
-        same = []
-        # If the vcf file has been decomposed, there can be multiple sites with
-        # the same CHROM and POS, which is why we have to iterate over all the
-        # sites that are returned
-        for it_record in it:
-            # We only want to consider sites that have the same CHROM, POS, REF
-            # and ALT as the positive vcf, since otherwise we might consider
-            # A/T and A/G as identical since they are both heterozygous
-            if (it_record.CHROM == pos_record.CHROM
-                    and it_record.POS == pos_record.POS
-                    and it_record.REF == pos_record.REF
-                    and it_record.ALT == pos_record.ALT):
-                same.append(it_record)
+        call_records = list(call_vcf(query_str))
 
         # If the variant is not present in the call vcf
-        if len(same) == 0:
+        if len(call_records) == 0:
             d['alleles_no_call'] += 2
-
-        if len(same) != 1:
             continue
 
-        call_record = same[0]
+        # If there are multiple variants with the same CHROM and POS, the
+        # variant in the call vcf file must have been decomposted
+        if len(call_records) > 1:
+            raise NotImplementedError('Decomposed variants are not supported')
+
+        # Now we know there is only one call record
+        call_record = call_records[0]
 
         d['sites_considered'] += 1
         d['alleles_considered'] += (2 * len(positive_samples))