HMM for X chr: separate all_true_geno for X chr
simple versions of calc_geno_prob and estmap
First stab at BC/F2 functions for HMM for X chr
a few missing semi-colons
Fix template business for estmap and calc_geno_prob
Add a bunch of overrides in cross.d
A few typos and missing autos
Revised HMM code making cross_direction a fixed type