def merge_alleles(alleles): from hail.expr.functions import _num_allele_type, _allele_ints return hl.rbind( alleles.map(lambda a: hl.or_else(a[0], '')) .fold(lambda s, t: hl.cond(hl.len(s) > hl.len(t), s, t), ''), lambda ref: hl.rbind( alleles.map( lambda al: hl.rbind( al[0], lambda r: hl.array([ref]).extend( al[1:].map( lambda a: hl.rbind( _num_allele_type(r, a), lambda at: hl.cond( (_allele_ints['SNP'] == at) | (_allele_ints['Insertion'] == at) | (_allele_ints['Deletion'] == at) | (_allele_ints['MNP'] == at) | (_allele_ints['Complex'] == at), a + ref[hl.len(r):], a)))))), lambda lal: hl.struct( globl=hl.array([ref]).extend(hl.array(hl.set(hl.flatten(lal)).remove(ref))), local=lal)))
def allele_type(ref, alt): return hl.bind(lambda at: hl.cond(at == allele_ints['SNP'], hl.cond(hl.is_transition(ref, alt), allele_ints['Transition'], allele_ints['Transversion']), at), _num_allele_type(ref, alt))
def merge_alleles(alleles): from hail.expr.functions import _num_allele_type, _allele_ints return hl.rbind( alleles.map(lambda a: hl.or_else(a[0], '')) .fold(lambda s, t: hl.cond(hl.len(s) > hl.len(t), s, t), ''), lambda ref: hl.rbind( alleles.map( lambda al: hl.rbind( al[0], lambda r: hl.array([ref]).extend( al[1:].map( lambda a: hl.rbind( _num_allele_type(r, a), lambda at: hl.cond( (_allele_ints['SNP'] == at) | (_allele_ints['Insertion'] == at) | (_allele_ints['Deletion'] == at) | (_allele_ints['MNP'] == at) | (_allele_ints['Complex'] == at), a + ref[hl.len(r):], a)))))), lambda lal: hl.struct( globl=hl.array([ref]).extend(hl.array(hl.set(hl.flatten(lal)).remove(ref))), local=lal)))