1. When using -sorted with intersect, map, and closest, bedtools can now detect and warn you when your input datasets employ different chromosome sorting orders.
2. Fixed multiple bugs in the new, faster closest tool. Specifically, the -iu, -id, and -D options were not behaving properly with the new "sweeping" algorithm that was implemented for the 2.22.0 release. Many thanks to Sol Katzman for reporting these issues and for providing a detailed analysis and example files.
3. We FINALLY wrote proper documentation for the closest tool.
   http://bedtools.readthedocs.org/en/latest/content/tools/closest.html
4. Fixed bug in the tag tool when using -intervals, -names, or -scores. Thanks to Yarden Katz for reporting this.
5. Fixed issues with chromosome boundaries in the slop tool when using negative distances. Thanks to @acdaugherty!
6. Multiple improvements to the fisher tool. Added a -m option to the fisher tool to merge overlapping intervals prior to comparing overlaps between two input files. Thanks to @brentp
7. Fixed a bug in makewindows tool requiring the use of -b with -s.
8. Fixed a bug in intersect that prevented -split from detecting complete overlaps with -f 1. Thanks to @tleonardi .
9. Restored the default decimal precision to the groupby tool.
10. Added the -prec option to the merge and map tools to specific the decimal precision of the output.