JaneliaSciComp/msg — pull request #35 by shackett (2012-09-17 16:34:26+00:00)
Title: Viterbi HMM

I've made changes to fit-hmm.R and hmmlib.R:

added viterbi paramters passing:

added the ability to run to either or both HMMs
changes plotting to make a haplotype plot for each HMM and to label
breakpoints and mismatch frequency for each HMM

This changes the output files slightly:
2 plots stacked if both HMMs are selected
breakpoints and mismatch frequency (within homozygous regions) are outputted for each HMM and labeled accordingly.