samtools/samtools 1.6

on GitHub

• Added new markdup sub-command and -m option for fixmate. Used together,they allow duplicates to be marked and optionally removed. This fixes a number of problems with the old rmdup sub-command, for
  example issue #497. rmdup is kept for backwards compatibility but markdup should be used in preference.

• Sort is now much better at keeping within the requested memory limit. It should also be slightly faster and need fewer temporary files when the file to be sorted does not fit in memory. (#593; thanks to Nathan Weeks.)

• Sort no longer rewrites the header when merging from files. It can also now merge from memory, so fewer temporary files need to be written and it is better at sorting in parallel when everything fits in memory.

• Both sort and merge now resolve ties when merging based on the position in the input file(s). This makes them fully stable for all ordering options. (Previously position sort was stable, but name and by tag
  sorts were not).

• New --output-qname option for mpileup.

• Support for building on Windows using msys2/mingw64 or cygwin has been improved.

The samtools-1.6.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.