Cacher is the code snippet organizer for pro developers

rs123 chr1 300 AB
-> no rsid -> rsid = "."
-> AA =~ /-*/  -> next
-> [D,I]B -> next

-> if not find chr1:300 in ref -> log error
-> if find chr1:300 in ref -> stre $ref
-> if $ref == PASS -> next

-> processAltAndGenotype (AB, $ref)
-> if only "A" and A == $ref -> $alt = '.'
-> else
	-> if A != B
		-> if ref == A or B
			-> alt=A or B, GT=0/1
		else
			-> alt=A,B, GT= 1/2
	else
		-> if a == ref
			-> alt=., GT=0/0
		else
			-> alt=A, GT=1/1