add option to compare to plot accuracy along genome
change how segment length correction works.  only apply transition correction when segment length is larger than effective length.  new scheme makes (good) sense when effective segment length is 1, so we disable other values for now.  current scheme, as well as old logic, unwittingly, were biased for lengths greater than 1
need to add back self-tran correction in estimation.
make seglen > 1 a warning so i can play around with it
make sure window option run on unmasked arguemnts
speed up track dump
revise bic graph
better segment option support
fix buncha bugs in new bic script
svb script
count 0s in transition matrix initialization to remember for bic
bla
merge
add support for initialization of hand drawn transition probs in statesvs bic
add option to extractSingleBase to allow use to extract arbitrary softmask
doh
Merge branch 'development' of github.com:glennhickey/teHmm into development
start mouse and rice tracks lists
mouse and rice chrom info
Merge remote-tracking branch 'origin/development'