Version 1.3.31

This adds a variant annotation to summarize SnpEff ANN into a simpler IMPAC field.

What's Changed

• Bump docker/build-push-action from 4.0.0 to 4.1.0 by @dependabot in #243
• Bump docker/setup-buildx-action from 2.6.0 to 2.7.0 by @dependabot in #246
• Bump docker/build-push-action from 4.1.0 to 4.1.1 by @dependabot in #245
• Add IMPACT annotation by @bbimber in #247
• Allow SampleSpecificGenotypeFiltration to run when the filter express… by @bbimber in #248

Full Changelog: 1.3.30...1.3.31

Version 1.3.30

This release includes minor updates to IntegrationSiteMapper to more precisely report the border of piggyBac-mediated insertions, and improvements to VCF annotation tools

What's Changed

• Allow transgene definitions to supply an offset value to adjust junction by @bbimber in #237
• Initial work to extend funcotator output by @bbimber in #233
• Add new test cases for genotype filter by @bbimber in #241
• Bump docker/login-action from 2.1.0 to 2.2.0 by @dependabot in #240
• Bump docker/setup-buildx-action from 2.5.0 to 2.6.0 by @dependabot in #238
• Bump docker/setup-qemu-action from 2.1.0 to 2.2.0 by @dependabot in #239
• Support more data sources in MultiSourceAnnotator by @bbimber in #242

Full Changelog: 1.3.29...1.3.30

Version 1.3.29

This is minor release, which updates the Apache Lucene version.

What's Changed

• Update lucene version by @hextraza in #234
• Increment lucene version by @bbimber in #235

Full Changelog: 1.3.28...1.3.29

Version 1.3.28

The primary enhancement in this version is updating the underlying GATK version, which allows DISCVR-seq to run against modern versions of java.

What's Changed

• Bump docker/setup-buildx-action from 2.4.1 to 2.5.0 by @dependabot in #229
• Update GATK version and support new java versions by @bbimber in #224
• Update java distributions by @bbimber in #231
• Bump peaceiris/actions-gh-pages from 3.9.2 to 3.9.3 by @dependabot in #232

Full Changelog: 1.3.27...1.3.28

Version 1.3.27

This version includes enhancements to VcfToLuceneIndexer, a tool that generates an Apache Lucene index from a VCF file.

What's Changed

• Bump docker/setup-buildx-action from 2.2.1 to 2.4.0 by @dependabot in #222
• Bump docker/build-push-action from 3.3.0 to 4.0.0 by @dependabot in #223
• Bump docker/setup-buildx-action from 2.4.0 to 2.4.1 by @dependabot in #225
• Improve VcfToLuceneIndexer and add more tests by @bbimber in #226

Full Changelog: 1.3.26...1.3.27

Version 1.3.26

What's Changed

• Add VariantQC test case to exercise VCF without dictionary in header by @bbimber in #219
• Add validation to Contig VariantStratifier by @bbimber in #220

Full Changelog: 1.3.25...1.3.26

Version 1.3.25

This release adds a performance improvement to PrintReadBackedHaplotypes.

What's Changed

• Update PrintReadBackedHaplotypes to use SortingCollection by @bbimber in #218

Full Changelog: 1.3.24...1.3.25

Version 1.3.24

This version improves the error message for VariantQC when the tool cannot find a sequence dictionary.

What's Changed

• Bump docker/build-push-action from 3.2.0 to 3.3.0 by @dependabot in #214
• Bump peaceiris/actions-gh-pages from 3.9.1 to 3.9.2 by @dependabot in #215
• Add clearer error message when dictionary is missing for VariantQC by @bbimber in #217

Full Changelog: 1.3.23...1.3.24

Version 1.3.23

This version adds a new insert template for esTag-PCR PREDICT plasmids for IntegrationSiteMapper

Version 1.3.22

This release adds the tool VcfToLuceneIndexer, which can create an Apache Lucene index from a VCF.

What's Changed

• Vcf index by @hextraza in #205
• Add better test coverage and bugfixes to VcfToLuceneIndexer by @bbimber in #209

New Contributors

• @hextraza made their first contribution in #205

Full Changelog: 1.3.21...1.3.22