## Noteworthy changes for the next release:

## Release 1.4.1 (8 May 2017)

* `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.


## Release 1.4 (13 March 2017)

Two new commands - `mpileup` and `csq`:

* The `mpileup` command has been imported from samtools to bcftools. The
  reasoning behind this is that bcftools calling is intimately tied to mpileup
  and any changes to one, often requires changes to the other. Only the
  genotype likelihood (BCF output) part of mpileup has moved to bcftools,
  while the textual pileup output remains in samtools. The BCF output option
  in `samtools mpileup` will likely be removed in a release or two or when
  changes to `bcftools call` are incompatible with the old mpileup output.

  The basic mpileup functionality remains unchanged as do most of the command
  line options, but there are some differences and new features that one
  should be aware of:

  - The option `samtools mpileup -t, --output-tags` changed to `bcftools
    mpileup -a, --annotate` to avoid conflict with the `-t, --targets`
    option common across other bcftools commands.

  - `-O, --output-BP` and `-s, --output-MQ` are no longer used as they are
    only for textual pipelup output, which is not included in `bcftools
    mpileup`. `-O` short option reassigned to `--output-type` and `-s`
    reassigned to `--samples` for consistency with other bcftools commands.

  - `-g, --BCF`, `-v, --VCF`, and ` -u, --uncompressed` options from
    `samtools mpileup` are no longer used, being replaced by the
    `-O, --output-type` option common to other bcftools commands.

  - The `-f, --fasta-ref` option is now required by default to help avoid user
    errors. Can be diabled using `--no-reference`.

  - The option `-d, --depth .. max per-file depth` now behaves as expected
    and according to the documentation, and prints a meaningful diagnostics.

  - The `-S, --samples-file` can be used to rename samples on the fly. See man
    page for details.

  - The `-G, --read-groups` functionality has been extended to allow
    reassignment, grouping and exclusion of readgroups. See man page for
    details.

  - The `-l, --positions` replaced by the `-t, --targets` and
    `-T, --targets-file` options to be consistent with other bcftools
    commands.

  - gVCF output is supported. Per-sample gVCFs created by mpileup can be
    merged using `bcftools merge --gvcf`.

  - Can generate mpileup output on multiple (indexed) regions using the
    `-r, --regions` and `-R, --regions-file` options. In samtools, one
    was restricted to a single region with the `-r, --region` option.

  - Several speedups thanks to @jkbonfield (cf3a55a).

* `csq`: New command for haplotype-aware variant consequence calling.
  See man page and [paper](https://www.ncbi.nlm.nih.gov/pubmed/28205675).


Updates, improvements and bugfixes for many other commands:

* `annotate`: `--collapse` option added. `--mark-sites` now works with
  VCF files rather than just tab-delimited files. Now possible to annotate
  a subset of samples from tab file, not just VCF file (#469). Bugfixes (#428).

* `call`: New option `-F, --prior-freqs` to take advantage of prior knowledge
    of population allele frequencies. Improved calculation of the QUAL score
    particularly for REF sites (#449, 7c56870). `PLs>=256` allowed in
    `call -m`. Bugfixes (#436).

* `concat --naive` now works with vcf.gz in addition to bcf files.

* `consensus`: handle variants overlapping region boundaries (#400).

* `convert`: gvcf2vcf support for mpileup and GATK. new `--sex` option to
  assign sex to be used in certain output types (#500). Large speedup of
  `--hapsample` and `--haplegendsample` (e8e369b) especially with `--threads`
  option enabled. Bugfixes (#460).

* `cnv`: improvements to output (be8b378).

* `filter`: bugfixes (#406).

* `gtcheck`: improved cross-check mode (#441).

* `index` can now specify the path to the output index file. Also, gains the
   `--threads` option.

* `merge`: Large overhaul of `merge` command including support for merging
  gVCF files created by `bcftools mpileup --gvcf` with the new `-g, --gvcf`
  option. New options `-F` to control filter logic and `-0` to set missing
  data to REF. Resolved a number of longstanding issues (#296, #361, #401,
  #408, #412).

* `norm`: Bugfixes (#385,#452,#439), more informative error messages (#364).

* `query`: `%END` plus `%POS0`, `%END0` (0-indexed) support - allows easy BED
  format output (#479). `%TBCSQ` for use with the new `csq` command. Bugfixes
  (#488,#489).

* `plugin`: A number of new plugins:

  - `GTsubset` (thanks to @dlaehnemann)
  - `ad-bias`
  - `af-dist`
  - `fill-from-fasta`
  - `fixref`
  - `guess-ploidy` (deprecates `vcf2sex` plugin)
  - `isecGT`
  - `trio-switch-rate`

  and changes to existing plugins:

  - `tag2tag`: Added `gp-to-gt`, `pl-to-gl` and `--threshold` options and
    bugfixes (#475).
  - `ad-bias`: New `-d` option for minimum depth.
  - `impute-info`: Bugfix (49a9eaf).
  - `fill-tags`:  Added ability to aggregate tags for sample subgroups, thanks
    to @mh11. (#503). HWE tag added as an option.
  - `mendelian`: Bugfix (#566).

* `reheader`: allow muiltispace delimiters in `--samples` option.

* `roh`: Now possible to process multiple samples at once. This allows
  considerable speedups for files with thousands of samples where the cost of
  HMM is neglibible compared to I/O and decompressing. In order to fit tens of
  thousands samples in memory, a sliding HMM can be used (new `--buffer-size`
  option). Viterbi training now uses Baum-Welch algorithm, and works much
  better. Support for gVCFs or FORMAT/PL tags. Added `-o, output` and
  `-O, --output-type` options to control output of sites or regions
  (compression optional). Many bugs fixed - do not segfault on missing PL
  values anymore, a typo in genetic map calculation resulted in a slowdown and
  incorrect results.

* `stats`: Bugfixes (16414e6), new options `-af-bins` and `-af-tags` to control
  allele frequency binning of output. Per-sample genotype concordance tables
  added (#477).

* `view -a, --trim-alt-alleles` various bugfixes for missing data and more
  informative errors should now be given on failure to pinpoint problems.


General changes:

* Timestamps are now added to header lines summarising the command (#467).

* Use of the `--threads` options should be faster across the board thanks to
  changes in HTSlib meaning meaning threads are now shared by the compression
  and decompression calls.

* Changes to genotype filtering with `-i, --include` and `-e, --exclude` (#454).


## Noteworthy changes in release 1.3.1 (22 April 2016)

* The `concat` command has a new `--naive` option for faster operations on
  large BCFs (PR #359).
* `GTisec`: new plugin courtesy of David Laehnemann (@dlaehnemann) to count
  genotype intersections across all possible sample subsets in a VCF file.
* Numerous VCF parsing fixes.
* Build fix: _peakfit.c_ now builds correctly with GSL v2 (#378).
* Various bug fixes and improvements to the `annotate` (#365), `call` (#366),
  `index` (#367), `norm` (#368, #385), `reheader` (#356), and `roh` (#328)
  commands, and to the `fill-tags` (#345) and `tag2tag` (#394) plugins.
* Clarified documentation of `view` filter options, and of the
  `--regions-file` and `--targets-file` options (#357, #411).


## Noteworthy changes in release 1.3 (15 December 2016)

* `bcftools call` has new options `--ploidy` and `--ploidy-file` to make
  handling sample ploidy easier. See man page for details.
* `stats`: `-i`/`-e` short options changed to `-I`/`-E` to be consistent with
  the filtering `-i`/`-e` (`--include`/`--exclude`) options used in other
  tools.
* general `--threads` option to control the number of output compression
  threads used when outputting compressed VCF or BCF.
* `cnv` and `polysomy`: new commands for detecting CNVs, aneuploidy, and
  contamination from SNP genotyping data.
* various new options, plugins, and bug fixes, including #84, #201, #204,
  #205, #208, #211, #222, #225, #242, #243, #249, #282, #285, #289, #302,
  #311, #318, #336, and #338.


## Noteworthy changes in release 1.2 (2 February 2016)

* new `bcftools consensus` command
* new `bcftools annotate` plugins: fixploidy, vcf2sex, tag2tag
* more features in `bcftools convert` command, amongst others new
  `--hapsample` function (thanks to Warren Kretzschmar @wkretzsch)
* support for complements in `bcftools annotate --remove`
* support for `-i`/`-e` filtering expressions in `bcftools isec`
* improved error reporting
* `bcftools call`
  - the default prior increased from `-P 1e-3` to `-P 1.1e-3`, some clear
    calls were missed with default settings previously
  - support for the new symbolic allele `<*>`
  - support for `-f GQ`
  - bug fixes, such as: proper trimming of DPR tag with `-c`; the `-A` switch
    does not add back records removed by `-v` and the behaviour has been made
    consistent with `-c` and `-m`
* many bug fixes and improvements, such as
  - bug in filtering, FMT & INFO vs INFO & FMT
  - fixes in `bcftools merge`
  - filter update AN/AC with `-S`
  - isec outputs matching records for both VCFs in the Venn mode
  - annotate considers alleles when working with `Number=A,R` tags
  - new `--set-id` feature for annotate
  - `convert` can be used similarly to `view`
