Commit d6a8d0e5 authored by van den Berg's avatar van den Berg
Browse files

Extract genotypes to support conflicting ALT calls

parent 8786b514
......@@ -12,16 +12,17 @@ from types import SimpleNamespace
from cyvcf2 import VCF
def parse_variants(call: List[any], pos: List[any], results: Dict[str, int]):
def parse_variants(ref: str, call: List[str], pos: List[str],
results: Dict[str, int]):
""" Parse the variants and add to results """
call_variant = sorted(call[0:2])
pos_variant = sorted(pos[0:2])
call_variant = sorted(call)
pos_variant = sorted(pos)
# The types of concordant calls are counted separately
if call_variant == pos_variant:
# These variants are homozygous reference
if call_variant == [0, 0]:
if call_variant[0] == call_variant[1] and call_variant[0] == ref:
results['alleles_hom_ref_concordant'] += 2
# These variants are heterozygous, since they have different calls
elif call_variant[0] != call_variant[1]:
......@@ -182,8 +183,20 @@ def site_concordancy(call_vcf: VCF,
if pos[2] or cal[2]:
raise NotImplementedError('Phased variants are not supported')
# Get the genotyped bases. There is a deprecationWarning when using
# gt_bases directly so we go via the alleles and the gt call
pos_alleles = [pos_record.REF] + pos_record.ALT
cal_alleles = [call_record.REF] + call_record.ALT
# The third item in pos is a boolean indicating phasing
pos_gt = [pos_alleles[x] for x in pos[:2]]
cal_gt = [cal_alleles[x] for x in cal[:2]]
# Parse the genotypes and add the results into d
parse_variants(pos, cal, d)
# We also need to know the reference call to determine if variants
# are hom ref. For this, we take the positive vcf REF call to be
# the truth
parse_variants(pos_record.REF, pos_gt, cal_gt, d)
# The current variant is discordant
if d['alleles_discordant'] > discordant_count:
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