update crlmmDownstream vignette
update import from methods package in namespace
Process all chromosomes at once.  Parallelization:  store ocSamples() of LRRs and BAFs in RAM; use iterators to send columns of LRR and BAF matrix to workers.

Timing:  15 samples using 10 CPUs: 45 minutes / 79G.
Parellization:  pass ff objects to workers.  Workers read from file.
15 samples, ocSamples()=1, 10 workers:  27 minutes, 40G.
add anyNP argument to viterbi2Wrapper
updates to vignette
updates
Add generator-functions.R
update to viterbi2Wrapper.  Handles nupdates=1.  Does not convert to granges when returnEmission is TRUE (not necessary for minimumdistane)
updates to hmm functions
update hmm function documentation
updates