Add option to dump PairHMM debugging outputs to a file in a standard format

[jamesemery]

There has been a request to do some more work on the HMM again and its become clear that there is not an efficient way to rapidly generate large amounts of test data based on the old HMM results. It would be helpful to add an option to dump the hmm scores out to the command line in an easily machine parseable format. Here is an example of how it has been done in the past (and probably how we should do it this time): https://github.com/Intel-HLS/GKL/blob/master/src/test/resources/pairhmm-testdata.txt