Noteworthy changes in release 1.4.1 (8th May 2017) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This is primarily a security bug fix update.

HTSLib

• Fixed SECURITY issue with buffer overruns with malicious data. (#514).

• S3 support for non Amazon AWS endpoints. (#506)

• Support for variant breakpoints in bcftools. (#516)

• Improved handling of BCF NaNs. (#485)

• Compilation / portability improvements. (#255, #423, #498, #488)

• Miscellaneous bug fixes (#482, #521, #522, #523, #524).

• Sanitise headers (#509)

Samtools

• Added options to fastq to create fastq files from BC (or other) tags.

• Samtools view has gained a -G <flags> option to exclude on all bits set. For example to discard reads where neither end has been mapped use "-G 12".

• Samtools cat has a -b <fofn> option to ease concatenation of many files.

• Added misc/samtools_tab_completion for bash auto-completion of samtools sub-commands. (#560)

• Samtools tview now has J and K keys for verticale movement by 20 lines. (#257)

• Various compilation / portability improvements.

• Fixed issue with more than 65536 CIGAR operations and SAM/CRAM files. (#667)

Bcftools

• 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.