def getCounts(ref, countLs, key, altLs, oneKPopInfo, effField):
"""Rm indels, non-rare 1kg, and non-func vars."""
finalCountLs = []
effectVars = parseEffectVars(effField)
for count, alt in zip(countLs, altLs):
isRare = filterExac1kg.checkRare(oneKPopInfo, (alt,), ref, key)
if isRare and len(alt) == 1 and len(ref) == 1 and alt in effectVars:
finalCountLs.append(count)
return finalCountLs
def getCounts(ref, countLs, key, altLs, oneKPopInfo, effField, gene, inGoodPos):
"""Rm indels, non-rare 1kg, and non-func vars.
Indles are filtered by kaviar and cg.
"""
finalCountLs = []
effectVars = parseEffectVars(effField, gene)
for count, alt in zip(countLs, altLs):
if inGoodPos:
isRare = filterExac1kg.checkRare(oneKPopInfo, (alt,), ref, key)
if isRare and alt in effectVars:
finalCountLs.append(count)
return finalCountLs