Truvari

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

As part of the GIAB TR effort, we have made many changes to Truvari's tooling to enable comparison of variants in TR regions down to 5bp. Additionally, in order to keep Truvari user friendly we have made changes to the UI. Namely, we've updated some default parameters, some command-line arguments, and some outputs. There are also a few new tools and how a couple of tools work has changed. Therefore, we decided to bump to a new major release. If you're using Truvari in any kind of production capacity, be sure to test your pipeline before moving to v4.0.

Highlighted Changes
* New refine command for improving benchmarking results. [Details](https://github.com/ACEnglish/truvari/wiki/refine)
* Simplified UI for bench command along with improved output organization
* Faster collapse command
* Improved re-usability of Truvari's code. [Details](https://truvari.readthedocs.io/)

[All Updates](https://github.com/ACEnglish/truvari/wiki/Updates#truvari-40)

**Full Changelog**: https://github.com/ACEnglish/truvari/compare/v3.5.1...v4.0.0

This should be the last minor revision of v3. We're freezing this in order to preserve the SV >=50bp focused functionality.

Notable changes
------------------
* `bench --dup-to-ins` flag automatically treats SVTYPE==DUP as INS, which helps compare some programs/benchmarks
* New `anno grpaf` annotates vcf with allele frequency info for groups of samples
* Fixed user issues
* Monomorphic reference ALT alleles no longer throw an error in `bench` ([131](https://github.com/ACEnglish/truvari/issues/131))
* `SVLEN Number=A` fix ([132](../issues/132))

See [Wiki](https://github.com/ACEnglish/truvari/wiki/Updates#truvari-35) for full description of changes.
**Full Changelog**: https://github.com/ACEnglish/truvari/compare/v3.4.0...v3.5.0