A new version of samtools, as well as htslib and bcftools is out. According to the release notes, notable changes are:
flagstatnow works on SAM, BAM, or CRAM files (rather than BAM only)
statscalculates mismatches per cycle for unclipped length
mergecan now merge SAM input files
- CRAM reference files are now cached by default (see HTSlib release notes and samtools(1) man page)
- Tested against Intel-optimised zlib (https://github.com/jtkukunas/zlib; see README for details)
- Fixed bugs #302, #309, #318, and #327 and many other improvements and bugs fixed in HTSlib—see the HTSlib release notes
Edit: In the off chance that others are using htslib, you can find the release notes for it here.