1. The merge tool now supports BAM input.
   • The -n, -nms, and -scores options are deprecated in favor of the new, substantially more flexible, -c and -o options. See the docs: http://bedtools.readthedocs.org/en/latest/content/tools/merge.html
   • It now supports the -header option.
   • It now supports the -S option.
2. The map tool now supports BAM input.
3. The jaccard tool is now ~3 times faster.
   • It now supports the -split option.
   • It now supports the -s option.
   • It now supports the -S option.
4. We have fixed several CLANG compiler issues.Thanks to John Marshall for the thorough report.
5. We added support for “X” and “=” CIGAR operators. Thanks to Pierre Lindenbaum.
6. Fixed bugs for empty files.
7. Improved the -incl option in the shuffle tool such that the distibution is much more random.
8. Fixed a bug in slop when very large slop values are used.