; ------------------------------------------
; example input file for NullHap application
; ------------------------------------------

; semicolon starts comment (it ends at the next newline)

; example genotype: two loci A and B,
; locus A: two variants, A0 and A1, it has a null allele
; locus B: two variants, B1 and B2, it has not a null allele
;----------------------------------------------------------------------------------------
;   GENOTYPE      |     HAPLOTYPE PHASE                        | NUMBER OF PHASES
;----------------------------------------------------------------------------------------
;  A1.B1          | A1.B1./A1.B1., A1.B1./A0.B1.               |   2
;  A1.B1.B2.      | A1.B1./A1.B2., A1.B1./A0.B2. A1.B2./A0.B1. |   3
;  A1.B2.         | A1.B2./A1.B2., A1.B2./A0.B2.               |   2
;  A0.B1.         | A0.B1./A0.B1.                              |   1
;  A0.B1.B2.      | A0.B1./A0.B2.                              |   1
;  A0.B2.         | A0.B2./A0.B2.                              |   1
;----------------------------------------------------------------------------------------

;assume that p(A1.B1.) = 0.2, p(A1.B2) = 0.2, p(A0.B1) = 0.2, p(A1.B2.) = 0.4
;thus observations are as below.

Locus("A" 2 true)
Locus("B" 2 false)

O("A1.B1." 3)
O("A1.B1.B2." 8)
O("A1.B2." 5)
O("A0.B1." 1)
O("A0.B1.B2." 4)
O("A0.B2." 4)