Truvari

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

The main change to Truvari v4.2 is a major improvement to the speed and accuracy of `truvari collapse`.
Other changes include various bug fixes and improvements to the bench, phab, and refine workflow.
Several minor quality of life fixes.

**Full Updates**: https://github.com/ACEnglish/truvari/wiki/Updates
**Full Changelog**: https://github.com/ACEnglish/truvari/compare/v4.1.0...v4.2.0

Highlights:
* Ability to run `truvari refine` on whole-genome benchmarking
* Faster `truvari phab` and `truvari refine`
* Better handling of VCF entries (e.g. Unresolved SV are filtered when sequence similarity is turned on)

**Full updates**: https://github.com/ACEnglish/truvari/wiki/updates#truvari-41
**Full Changelog**: https://github.com/ACEnglish/truvari/compare/v4.0.0...v4.1.0