News:Samtools/htslib v1.2 released

Question

[Devon Ryan]

A new version of samtools, as well as htslib and bcftools is out. According to the release notes, notable changes are:

• 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

Edit: In the off chance that others are using htslib, you can find the release notes for it here.

[Istvan Albert]

I would love if people that release tools would drop notes like this. Otherwise it is way too difficult to keep track of what version is each tool at.

[John Marshall]

We announce new releases on the samtools-announce mailing list and also on Twitter. I'm sure other tools have similar announcement mailing lists that you can subscribe to.