* `roh`: Fixed malfunctioning options `-m, --genetic-map` and `-M, --rec-rate`,
  and newly allowed their combination. Added a convenience wrapper `misc/run-roh.pl`
  and an interactive script for visualizing the calls `misc/plot-roh.py`.

* `csq`: More control over warning messages (#585).

* Portability improvements (#587). Still work to be done on this front.

* Add support for breakends to `view`, `norm`, `query` and filtering (#592).

* `plot-vcfstats`: Fix for python 2/3 compatibility (#593).

* New `-l, --list` option for `+af-dist` plugin.

* New `-i, --use-id` option for `+fix-ref` plugin.

* Add `--include/--exclude` options to `+guess-ploidy` plugin.

* New `+check-sparsity` plugin.

* Miscellaneous bugfixes for #575, #584, #588, #599, #535.