Truvari

* The default `--align` method for `phab` and `bench` switched to POA. See [discussion](https://github.com/ACEnglish/truvari/discussions/261) for details.
* Fix bug in `--pick ac` where FN/FP variants were not being counted/output.
* Fix `--dup-to-ins` Ticket [258](https://github.com/ACEnglish/truvari/issues/258)
* `ga4gh` now also writes a variant count summary json

**Full Changelog**: https://github.com/ACEnglish/truvari/compare/v5.1.1...v5.2.0

* Decomposition into BNDs strand/direction fixed
* More exhaustive checks of sequence similarity
* New `refine` variant counting strategy for more representative performance metrics and UI refactor for easier whole-genome commands

See [Updates](https://github.com/ACEnglish/truvari/wiki/Updates#truvari-511) for details.

**Full Changelog**: https://github.com/ACEnglish/truvari/compare/v5.0.0...v5.1.1

Improved Symbolic Variant and BND handling. Revamped API. Cleaned UI.

This version has several command-line parameters removed or renamed and a completely different package structure. Furthermore, the sets of matches reported by v5 is likely to be more sensitive than v4. For example, symbolic ALTs which were previously filtered when `--pctseq != 0` and BNDs which were always filtered are now analyzed. Additionally, the default `--sizemax` is unlimited. For these reasons, we've made the major-version bump.

See [Updates](https://github.com/ACEnglish/truvari/wiki/Updates#truvari-50) for full list of changes.

**Full Changelog**: https://github.com/ACEnglish/truvari/compare/v4.3.1...v5.0.0

Minor bug fixes and slight speed increase for collapse.

**Full Updates**: https://github.com/ACEnglish/truvari/wiki/Updates
**Full Changelog**: https://github.com/ACEnglish/truvari/compare/v4.3.0...v4.3.1

Minor bug fixes for `collapse` and accuracy/speed improvements for `refine`.

**Full Updates**: https://github.com/ACEnglish/truvari/wiki/Updates
**Full Changelog**: https://github.com/ACEnglish/truvari/compare/v4.2.1...v4.2.2

- Faster collapse handling of genotype information
- Fix of off-by-one error for variant's inclusion in region
- New `ga4gh` command

What's Changed
* Update Dockerfile by ctsa in https://github.com/ACEnglish/truvari/pull/191
* Update Dockerfile to install dependent python packages. by ctsa in https://github.com/ACEnglish/truvari/pull/192

New Contributors
* ctsa made their first contribution in https://github.com/ACEnglish/truvari/pull/191

**Full Changelog**: https://github.com/ACEnglish/truvari/compare/v4.2.0...v4.2.1