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

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: v3.5.1...v4.0.0

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: v3.4.0...v3.5.0

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 #126
• Refactor consistency_report.py by @pwwang in #127

New Contributors

• @pwwang made their first contribution in #126

Full Changelog: v3.3.0...v3.4.0

Truvari v3.3.0

• New utilities vcf_ranges and make_temp_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 #121

New Contributors

• @bnoyvert made their first contribution in #121

Full Changelog: v3.2.0...v3.3.0

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

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 #69
• Create CODE_OF_CONDUCT.md by @ACEnglish in #73
• Fix if condition by @wwliao in #79
• Remove redundant code by @wwliao in #81
• See wiki for full details

New Contributors

• @scalavision made their first contribution in #69
• @wwliao made their first contribution in #79

Full Changelog: v3.0.1...v3.1.0