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

Version 1.3.21

This is a minor release containing an GATK update a improvement to VariantQC and -maxContigs.

Version 1.3.20

This release includes minor improvements to VcfComparison and AnnotateNovelSites.

What's Changed

• Bump docker/setup-qemu-action from 2.0.0 to 2.1.0 by @dependabot in #197
• Bump docker/build-push-action from 3.1.1 to 3.2.0 by @dependabot in #194
• Bump docker/login-action from 2.0.0 to 2.1.0 by @dependabot in #193
• Bump docker/setup-buildx-action from 2.0.0 to 2.1.0 by @dependabot in #196
• Bump crazy-max/ghaction-docker-meta from 4.0.1 to 4.1.0 by @dependabot in #195
• Bump docker/setup-buildx-action from 2.1.0 to 2.2.0 by @dependabot in #198
• Bump docker/setup-buildx-action from 2.2.0 to 2.2.1 by @dependabot in #200
• Bump crazy-max/ghaction-docker-meta from 4.1.0 to 4.1.1 by @dependabot in #201
• Misc improvements to VcfComparison and AnnotateNovelSites by @bbimber in #202
• Bump peaceiris/actions-gh-pages from 3.8.0 to 3.9.0 by @dependabot in #203
• Preserve original header for AnnotateNovelSites by @bbimber in #204

Full Changelog: 1.3.19...1.3.20

Version 1.3.19

Add SplitVcfBySamples, a tool to subset a VCF into batches based on sample.

Version 1.3.18

This version adds a feature to MergeVcfsAndGenotypes to optionally tag each variant with the source VCF from which is was derived.