Fixed: Bug where lower-case 'n' was not treated (skipped) like upper case 'N'
Added: SOFT_MASKED option: Treat all lower-case letters like 'N'
Added: INTERVAL_LIST option: Interval list file specifiying regions to include in metrics comutation
Added: INTERVAL_LIST_STRING option: String of whitespace separated chrom:[start[-end]] (like samtools regions) specifying regions to include in metrics computation.  Can be used with or without the INTERVAL_LIST file option.