Refactor Natural Sorting to be a Comparator<String> in StringUtils
Reworked Pileup interfaces... kept NGSUtils Pileup, but renamed it
DenovoPileup. It probably shouldn't be used much. Added an interface to
a forked samtools mpileup call. This is going to be more standard and
easier to support in the future.

Migrated these classes from cgsutils
Updated annotation interfaces to provide an explicit way to get the
GenomeRegion for an annotation
Made NGSUtilsException a RuntimeException to let it get called from
Pileup
Added a --unique flag to bam-count
Added a fastq prefix qual filter