add option to get score column
fix offset bug when writing states intervals
first draft of simple bed comparison
remove print
add test for comparision.  more detailed view of stats
lower default em iteration from 1000 to 10
make teHmmView output more verbose and hopefully easier to read
add some logging to teHmmEval
fix loggign option
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fix logging
add timing info to logging.  seems if statement with singleLogProb is a huge slowdown