Andreas Tille pushed to branch upstream at Debian Med / cyvcf2
Commits:
90ed00e3 by Andreas Tille at 2022-05-02T12:02:51+02:00
New upstream version 0.30.15
- - - - -
4 changed files:
- CHANGES.md
- cyvcf2/__init__.py
- cyvcf2/cyvcf2.pyx
- cyvcf2/tests/test_reader.py
Changes:
=====================================
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 @@ from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased,
par_relatedness,
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
View it on GitLab:
https://salsa.debian.org/med-team/cyvcf2/-/commit/90ed00e3b986178d008be642b1ea8ff357e2af1d
--
View it on GitLab:
https://salsa.debian.org/med-team/cyvcf2/-/commit/90ed00e3b986178d008be642b1ea8ff357e2af1d
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