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1.6

Release 1.6: New markdup command; sort improvements
@daviesrob daviesrob tagged this 28 Sep 13:09 
* 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 samtools 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.
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