Version 1.3.90

What's Changed

• Improve reporting for ImmunoGenotyper by @bbimber in #391

Full Changelog: 1.3.89...1.3.90

Version 1.3.89

What's Changed

• Bump docker/setup-qemu-action from 3.6.0 to 3.7.0 by @dependabot[bot] in #389
• Add IntegrationSiteMapper definition for BxbI by @bbimber in #390

Full Changelog: 1.3.88...1.3.89

Version 1.3.88

What's Changed

• Bump actions/checkout from 4 to 5 by @dependabot[bot] in #383
• Bump actions/setup-java from 4 to 5 by @dependabot[bot] in #384
• Bump docker/login-action from 3.4.0 to 3.5.0 by @dependabot[bot] in #382
• Update Save10xBarcodes to write to single file with CB+UB by @bbimber in #386
• Bump docker/login-action from 3.5.0 to 3.6.0 by @dependabot[bot] in #385
• Update Save10xBarcodes to write to single file with CB alone by @bbimber in #387
• Minor cleanup to Save10xBarcodes by @bbimber in #388

Full Changelog: 1.3.87...1.3.88

Version 1.3.87

What's Changed

• Bump docker/build-push-action from 6.15.0 to 6.16.0 by @dependabot[bot] in #374
• Bump docker/build-push-action from 6.16.0 to 6.17.0 by @dependabot[bot] in #375
• Bump docker/setup-buildx-action from 3.10.0 to 3.11.1 by @dependabot[bot] in #378
• Bump docker/build-push-action from 6.17.0 to 6.18.0 by @dependabot[bot] in #376
• Support both picard and bcftools labels for ORIGINAL_CONTIG by @bbimber in #379
• Improve error message by @bbimber in #380
• Allow more lenient handling of mismatched alleles in BackportLiftedVcf by @bbimber in #381

Full Changelog: 1.3.86...1.3.87

Version 1.3.86

What's Changed

• Update GATK version and support --retainAllSources in MergeVcfsAndGenotypes by @bbimber in #373

Full Changelog: 1.3.85...1.3.86

Version 1.3.85

What's Changed

• Do not re-compute the offset for each contig in VcfToLuceneIndexer by @bbimber in #372
• Bump docker/login-action from 3.3.0 to 3.4.0 by @dependabot in #371

Full Changelog: 1.3.84...1.3.85

Version 1.3.84

What's Changed

• Improve SVType annotation and add testing by @bbimber in #369
• Reduce logging in Save10xBarcodes by @bbimber in #370

Full Changelog: 1.3.83...1.3.84

Version 1.3.83

What's Changed

• Add SVType annotation by @bbimber in #368

Full Changelog: 1.3.82...1.3.83

Version 1.3.82

What's Changed

• Bump docker/setup-buildx-action from 3.9.0 to 3.10.0 by @dependabot in #365
• Bump docker/setup-qemu-action from 3.4.0 to 3.5.0 by @dependabot in #364
• Bump docker/build-push-action from 6.13.0 to 6.15.0 by @dependabot in #363
• Bump docker/setup-qemu-action from 3.5.0 to 3.6.0 by @dependabot in #366
• Add Save10xBarcodes to store CB/UB combinations by @bbimber in #367

Full Changelog: 1.3.81...1.3.82

Version 1.3.81

What's Changed

• Update VariantConcordanceScore to exclude the input VCF from driving variants by @bbimber in #361
• Bump docker/setup-qemu-action from 3.3.0 to 3.4.0 by @dependabot in #360
• Bump docker/setup-buildx-action from 3.8.0 to 3.9.0 by @dependabot in #359

Full Changelog: 1.3.80...1.3.81