closes #236

CHANGES.md

@@ -1,3 +1,6 @@
+# v0.30.15
++ fix num_unknown when gts012=True (#236)
+
 # v0.30.14
 + use warnings instead of sys.stderr (#229 from @grahamgower)
 + use libdeflate in wheel build (#231 from @grahamgower)

cyvcf2/__init__.py

@@ -2,4 +2,4 @@
                      par_het)
 Reader = VCFReader = VCF
 
-__version__ = "0.30.14"
+__version__ = "0.30.15"

cyvcf2/cyvcf2.pyx

@@ -1274,9 +1274,9 @@ cdef class Variant(object):
             if self._gt_types == NULL:
                 self.gt_types
             cdef int n = 0, i = 0
+            cdef int unknown = 3 if self.vcf.gts012 else 2
             for i in range(self.vcf.n_samples):
-                if self._gt_types[i] == 2:
-                    n+=1
+                n += (self._gt_types[i] == unknown)
             return n
 
     property FORMAT:

cyvcf2/tests/test_reader.py

@@ -1302,3 +1302,17 @@ def test_genotypes():
             a = v.genotype.array()[0] # only 0'th item
             print("i:", i, " a:", v.genotype.array()[0], " exp:", exp_array[i])
             assert (a == exp_array[i]).all(), " error with array"
+
+def test_issue236():
+
+
+    for strict_gt in (False, True):
+        res = [[], []]
+
+        for gts in (False, True):
+            vcf = VCF(os.path.join(HERE, "test-genotypes.vcf"), gts012=gts, strict_gt=strict_gt)
+            for v in vcf:
+                res[int(gts)].append(v.num_unknown)
+
+        assert res[0] == res[1]
+        assert len(res[0]) > 0