1. The coverage tool now takes advantage of pre-sorted intervals via the -sorted option. This allows the coverage tool to be much faster,
   use far less memory, and report coverage for intervals in their original order in the input file.
2. We have changed the behavior of the coverage tool such that it is consistent with the other tools. Specifically, coverage is now
   computed for the intervals in the A file based on the overlaps with the B file, rather than vice versa.
3. The subtract tool now supports pre-sorted data via the -sorted option and is therefore much faster and scalable.
4. The -nonamecheck option provides greater tolerance for chromosome labeling when using the -sorted option.
5. Support for multiple SVLEN tags in VCF format, and fixed a bug that failed to process SVLEN tags coming at the end of a VCF INFO field.
6. Support for reverse complementing IUPAC codes in the getfasta tool.
7. Provided greater flexibility for "BED+" files, where the first 3 columns are chrom, start, and end, and the remaining columns are free-form.
8. We now detect stale FAI files and recreate an index thanks to a fix from @gtamazian.
9. New feature from Pierre Lindenbaum allowing the sort tool to sort files based on the chromosome order in a faidx file.
10. Eliminated multiple compilation warnings thanks to John Marshall.
11. Fixed bug in handling INS variants in VCF files.