1.4.1

This is primarily a security bug fix update.

• 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.

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The bcftools-1.4.1.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.