truvari - 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: https://github.com/ACEnglish/truvari/compare/v5.2.0...v5.3.0

- Python
Published by ACEnglish 10 months ago

truvari - 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: https://github.com/ACEnglish/truvari/compare/v5.1.1...v5.2.0

- Python
Published by ACEnglish about 1 year ago

truvari - 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: https://github.com/ACEnglish/truvari/compare/v5.0.0...v5.1.1

- Python
Published by ACEnglish about 1 year ago

truvari - 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: https://github.com/ACEnglish/truvari/compare/v4.3.1...v5.0.0

- Python
Published by ACEnglish about 1 year ago

truvari - v4.3.1

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

- Python
Published by ACEnglish over 1 year ago

truvari - 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: https://github.com/ACEnglish/truvari/compare/v4.2.1...v4.2.2

- Python
Published by ACEnglish almost 2 years ago

truvari - 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 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

- Python
Published by ACEnglish about 2 years ago

truvari - 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: https://github.com/ACEnglish/truvari/compare/v4.1.0...v4.2.0

- Python
Published by ACEnglish about 2 years ago

truvari - 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: https://github.com/ACEnglish/truvari/compare/v4.0.0...v4.1.0

- Python
Published by ACEnglish over 2 years ago

truvari - Truvari v4.0.0

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 * Simplified UI for bench command along with improved output organization * Faster collapse command * Improved re-usability of Truvari's code. Details

All Updates

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

- Python
Published by ACEnglish almost 3 years ago

truvari - Truvari v3.5.0

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)
  • SVLEN Number=A fix (#132)

See Wiki for full description of changes. Full Changelog: https://github.com/ACEnglish/truvari/compare/v3.4.0...v3.5.0

- Python
Published by ACEnglish over 3 years ago

truvari - Truvari v3.4.0

Truvari is now officially on conda! Plus a new, faster truvari consistency. And, as always there are minor bug fixes and small, backwards compatible, improvements.

See Updates for full details

What's Changed

• Use generator instead of list in create_file_intersections() to save memory by @pwwang in https://github.com/ACEnglish/truvari/pull/126
• Refactor consistency_report.py by @pwwang in https://github.com/ACEnglish/truvari/pull/127

New Contributors

• @pwwang made their first contribution in https://github.com/ACEnglish/truvari/pull/126

Full Changelog: https://github.com/ACEnglish/truvari/compare/v3.3.0...v3.4.0

- Python
Published by ACEnglish over 3 years ago

truvari - Truvari v3.3.0

• New utilities vcfranges and maketemp_filename
• New annotations dpcnt and lcr
• Fixed a bug in truvari collapse --keep that prevented the maxqual or common options from working
• Increased determinism for truvari collapse so that in cases of tied variant position the longer allele is returned. If the alleles also have the same length, they are sorted alphabetically by the REF
• New truvari bench --extend functionality. See discussion for details

What's Changed

• Soft bed regions v2 by @bnoyvert in https://github.com/ACEnglish/truvari/pull/121

New Contributors

• @bnoyvert made their first contribution in https://github.com/ACEnglish/truvari/pull/121

Full Changelog: https://github.com/ACEnglish/truvari/compare/v3.2.0...v3.3.0

- Python
Published by ACEnglish over 3 years ago

truvari - Truvari v3.2.0

• Removed truvari.copy_entry for pysam.VariantRecord.translate a 10x faster operation
• Faster truvari collapse (@c8b319b)
• When building MatchResult between variants with shared start/end positions, we save processing work by skipping haplotype creation and just compare REFs/ALTs directly.
• Updated documentation to reference the paper https://doi.org/10.1101/2022.02.21.481353
• New truvari anno density for identifying regions with 'sparse' and 'dense' overlapping SVs (details)
• Better bench genotype reporting with summary.txt having a gt_matrix of Base GT x Comp GT for all Base calls' best, TP match.
• New truvari anno bpovl for intersecting against tab-delimited files (details)
• New truvari divide command to split VCFs into independent parts (details)
• Replaced --buffer parameter with --minhaplen for slightly better matching specificity
• Bugfix - truvari anno trf no longer duplicates entries spanning multple parallelization regions
• Bugfix - collapse MatchId/CollapseId annotation wasn't working
• Bugfixes - from wwliao (@4dd9968 @ef2cfb3)
• Bugfixes - Issues #107, #108

- Python
Published by ACEnglish almost 4 years ago

truvari - Truvari v3.1.0

Expanded bench annotation and code re-usability

• Bench annotations are more informative and now placed on false positives/negatives as well.
• A new vcf iteration technique is faster and uses less memory.
• Improvements to the code's readability and expanded developer docs allows Truvari to be used not only as a tool, but as a library.

Full Updates

• https://github.com/spiralgenetics/truvari/wiki/Updates#truvari-31

What's Changed

• python-levenshtein: 0.12.1 -> 0.12.2 by @scalavision in https://github.com/spiralgenetics/truvari/pull/69
• Create CODEOFCONDUCT.md by @ACEnglish in https://github.com/spiralgenetics/truvari/pull/73
• Fix if condition by @wwliao in https://github.com/spiralgenetics/truvari/pull/79
• Remove redundant code by @wwliao in https://github.com/spiralgenetics/truvari/pull/81
• See wiki for full details

New Contributors

• @scalavision made their first contribution in https://github.com/spiralgenetics/truvari/pull/69
• @wwliao made their first contribution in https://github.com/spiralgenetics/truvari/pull/79

Full Changelog: https://github.com/spiralgenetics/truvari/compare/v3.0.1...v3.1.0

- Python
Published by ACEnglish about 4 years ago