v5.4.0

• Added stratp command for automated benchmark performance evaluation across stratifications.
• Improved performance: lazy imports for faster startup and cached allele frequency annotations in VariantRecord.
• Enhanced collapse:
  • --sizemax -1 now supports all large SVs.
  • New --fast-cluster option greatly speeds up processing of large (>100 kbp) SVs.
• bwapy is now optional by default (simplifies macOS setup).
• vcf2df --parquet outputs stable, cross-environment Parquet files.
• Various bug fixes and stability improvements

Full Changelog: v5.3.0...v5.4.0

v5.3.0

Refactor of phab to increase speed / decrease memory. Minor bug fixes across tools.

Full Updates: https://github.com/ACEnglish/truvari/wiki/Updates#truvari-53
Full Changelog: v5.2.0...v5.3.0

v5.2.0

• The default --align method for phab and bench switched to POA. See discussion for details.
• Fix bug in --pick ac where FN/FP variants were not being counted/output.
• Fix --dup-to-ins Ticket #258
• ga4gh now also writes a variant count summary json

Full Changelog: v5.1.1...v5.2.0

v5.1.1

• 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 for details.

Full Changelog: v5.0.0...v5.1.1

v5.0.0

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 for full list of changes.

Full Changelog: v4.3.1...v5.0.0

v4.3.1

Minor bug fixes and slight speed increase for collapse.

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

v4.2.2

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

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

v4.2.1

• 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 #191
• Update Dockerfile to install dependent python packages. by @ctsa in #192

New Contributors

• @ctsa made their first contribution in #191

Full Changelog: v4.2.0...v4.2.1

v4.2.0

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: v4.1.0...v4.2.0

v4.1.0

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: v4.0.0...v4.1.0