To do list for filterHD/cloneHD

Bugs/issues to be fixed

filterHD

cloneHD

print full if --*jump is (also) given, only events if --*jumps
check memory leaks

Features to be added in future releases

filterHD

filter loci incompatible with emission model via 2-state HMM
do Baum-Welch
--filter-shortSeg [int] via posterior jump-prob (not via pmean)
Use diffusion constant that scales with size in mode 3/4.
Implement jump subtraction

cloneHD

bias field as distribution
re-think update_snp_fixed (hashing)
different nLevels per chr via max-tcn (for memory efficiency only)

both

string chromosome ids
re-factor emission class