def genotypes(self):
"""
Extracts the genotypes from a VCF record
"""
alleles = vcf_allele_parser(self.data, self.field_format)
return alleles
def test_vcf_allele_parser():
format = 'GT:DP:SOMETHING:SOMETHINGELSE'
a = "0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,."
expected = list(reversed([(2,1), (4,1), (5, 1)])) # stacks are FILO
observed = vcf_allele_parser(a, format)
assert observed.tolist() == expected
def test_vcf_allele_parser():
format = 'GT:DP:SOMETHING:SOMETHINGELSE'
a = "0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,."
expected = list(reversed([(2, 1), (4, 1), (5, 1)])) # stacks are FILO
observed = vcf_allele_parser(a, format)
assert observed.tolist() == expected
def genotypes(self):
''' Extract the genotypes from a VCF record '''
alleles = vcf_allele_parser(self.data, self.format)
return alleles