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Issue #298: boundary checks when columns in FORMAT != samples #299

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Issue #298: boundary checks when columns in FORMAT != samples #299

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2 changes: 1 addition & 1 deletion vcf/model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -683,7 +683,7 @@ def __repr__(self):
def make_calldata_tuple(fields):
""" Return a namedtuple for a given call format """

class CallData(collections.namedtuple('calldata', fields)):
class CallData(collections.namedtuple('calldata', fields, rename=True)):
__slots__ = ()

_types = []
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2 changes: 2 additions & 0 deletions vcf/parser.py
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Expand Up @@ -474,6 +474,8 @@ def _parse_samples(self, samples, samp_fmt, site):
sampdat = [None] * nfields

for i, vals in enumerate(sample.split(':')):
if i >= nfields:
break

# short circuit the most common
if samp_fmt._fields[i] == 'GT':
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7 changes: 7 additions & 0 deletions vcf/test/issue_298.vcf
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@@ -0,0 +1,7 @@
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1
chr1 123123123 . A C . . . . 1:2
chr1 123123123 . A C . . . A 1:2
chr1 123123123 . A C . . . A:B 1:2
chr1 123123123 . A C . . . A:B:C 1:2
chr1 123123123 . A C . . . :: 1:2
chr1 123123123 . A C . . . -invalid!:B:C 1:2
12 changes: 12 additions & 0 deletions vcf/test/test_vcf.py
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Expand Up @@ -1716,6 +1716,17 @@ def test_strelka(self):
n = next(reader)
assert n is not None

class TestIssue298(unittest.TestCase):
def test_issue_298(self):
records = list(vcf.Reader(fh('issue_298.vcf')))
assert len(records) == 6

assert not records[0].samples
assert records[1].samples and tuple(records[1].samples[0].data) == (['1'],), records[1].samples
assert records[2].samples and tuple(records[2].samples[0].data) == (['1'], ['2']), records[2].samples
assert records[3].samples and tuple(records[3].samples[0].data) == (['1'], ['2'], None), records[3].samples
assert records[4].samples and tuple(records[4].samples[0].data) == (['1'], ['2'], None), records[4].samples
assert records[5].samples and tuple(records[5].samples[0].data) == (['1'], ['2'], None), records[5].samples

suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestVcfSpecs))
suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestGatkOutput))
Expand Down Expand Up @@ -1753,3 +1764,4 @@ def test_strelka(self):
suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestUncalledGenotypes))
suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestStrelka))
suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestBadInfoFields))
suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestIssue298))