When reducing multiple samples it is possible to try to close a region that for a given sample has no reads.  Currently we'd NPE.  Fixed.
Forgot an include
Another RR bug: off by one error led to ArrayIndexOutOfBoundsException when working with multiple samples and the variant region ended 1 base after the end of the last read for a given sample.
Merge branch 'master' of https://github.com/broadgsa/gatk into vcf-to-glstring