samtools release 1.8:
* samtools calmd now has a quiet mode. This can be enabled by
passing `-Q` to calmd. (Thanks to Colin Davenport)
* In samtools depth `-d 0` will effectively remove the depth limit.
(#764)
* Improvements made to samtools collate's interface and
documentation. It is now possible to specify an output file
name using `-o`, instead of deriving it from the prefix used
for temporary files. The prefix itself is now optional if
`-o` or `-O` (to stdout) is used. (#780)
* Bug-fixes:
- Make samtools addreplacerg choose output format by file
extension. (#767; reported by Argy Megalios)
- Merge tests now work on ungzipped data, allowing tests to be run
against different deflate libraries.
- samtools markdup error messages about missing tags have been
updated with the suggestion that samtools fixmate is run
beforehand. (#765; reported by Yudong Cai)
- Enables the `--reference` option for samtools fastq. Now works
like other programs when a reference sequence is needed for CRAM
files. (#791, reported by Milana Kaljevic)