1. Added a new -C option to the intersect tool that separately reports the count of intersections observed for each database (-b) file given. Formerly, the -c option reported to sum of all intersections observed across all database files.
2. Fixed an important bug in intersect that prevented some split reads from being counted properly with using the -split option with the -f option.
3. Fixed a bug in shuffle such that shuffled regions should have the same strand as the chose -incl region.
4. Added a new -L option to Limit the output of the `complement tool to solely the chromosomes that are represented in the -i file.
5. Fixed a regression in the multicov tool introduced in 2.28 that caused incorrect counts.
6. Added support for multi-mapping reads in the bamtofastq tool.
7. Fixed a bug that prevented the “window” tool from properly adding interval “slop” to BAM records.
8. Fixed a bug that caused the slop tool to not truncate an interval’s end coordinate when it overlapped the end of a chromosome.
9. Added support for the “=” and “X” CIGAR operations to bamtobed.
10. Various other minor bug fixes and improvements to documentation.