samtools/samtools 1.2

on GitHub

Noteworthy changes in samtools:

• flagstat now works on SAM, BAM, or CRAM files (rather than BAM only)
• stats calculates mismatches per cycle for unclipped length
• merge can 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

The samtools-1.2.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.