Bug fix for #49
Added try/catch block to samtools BAM reader in WigMath/pileup

1. More complete comparator for tagnode sorting to address issue #29
2. Added threshold option to limit output to only those peaks equal to or greater than --threshold. Fixes for issue #30 #26

add cpm normalization.

Shuffle training region candidates before choosing to address Issue #22, reduce log output for viterbi status, add option to print training regions or excluded regions to additional files rather than to standard output. Add user specified seed for shuffling training regions.

Bug fix for issue #18

Bug fix for issue #13

Bug fix for issue #12

Bug fixes for scoring and summit reporting. Bug fix for issue #11