v2.4.0

What's Changed

• Update dependencies and the Exomiser DB adapter by @ielis in #692

Full Changelog: v2.3.0...v2.4.0

v2.3.0

What's Changed

• BREAKING Remove support for UCSC transcripts by @ielis in #690

Full Changelog: v2.2.1...v2.3.0

v2.2.1

What's Changed

• Fix the order of D and B parameters in genotype LR by @chrisxu2016 in #684

New Contributors

• @chrisxu2016 made their first contribution in #684

-- EDIT --

The distribution file was updated with a hotfix, which corrected the LIRICAL version, such that java -jar lirical.jar --version outputs lirical v2.2.1 instead of lirical v2.2.1-SNAPSHOT.

Full Changelog: v2.2.0...v2.2.1

v2.2.0

What's Changed

• Allow running in phenotype only mode by @ielis in #680

Full Changelog: v2.1.0...v2.2.0

v2.1.0

Changes

Migrate to 2.1.0

We made several changes that require user's attention.

Added support for latest Exomiser database format

LIRICAL 2.1.0 supports the most recent Exomiser database format (2402 or newer) and the previous format is not supported anymore.

To migrate to the latest Exomiser databases, download the release ZIP (see Exomiser discussion), unpack the ZIP and use -ed19 or -ed38 CLI options to point to the unpacked data directory.

Added Ensembl and RefSeq curated transcripts

We added support for Ensembl and RefSeq curated transcript databases. To use these in the analysis, please redownload the LIRICAL data using the download CLI command with the --overwrite option enabled. This will ensure you have the latest data available.

What's Changed

• Support Exomiser resources 2402 or newer by @ielis in #661
• Fix ORPHA parsing by @ielis in #671
• Use Jannovar caches deployed to Zenovo by @ielis in #672
• Update dependencies by @ielis in #673

Full Changelog: v2.0.4...v2.1.0

v2.0.4

What's Changed

• Allow focusing the prioritization on a subset of diseases by @ielis in #668

Full Changelog: v2.0.3...v2.0.4

v2.0.3

What's Changed

• Bump biodownload dependency by @ielis in #666

Full Changelog: v2.0.2...v2.0.3

v2.0.2

A patch release with bug fixes and no novel functionality.

What's Changed

• Remove extra \t from the TSV template by @ielis in #657
• Use en_US to run tests by @ielis in #658

Full Changelog: v2.0.1...v2.0.2

v2.0.1

The v2.0.1 includes one bug fix and no new functionality.

The bug fix rectifies the behavior of the --sdwndv CLI flag which is used to report the diseases with no mutations in the associated gene. Prior v2.0.1, the option was considered only in HTML report, and the TSV output included all diseases all the time. Since v2.0.1, the TSV report will only include a disease with no mutation found in the associated gene if the --sdwndv is used, and the diseases will not be shown by default.

What's Changed

• Do not show the candidate disease unless there is a (predicted) pathogenic variant(s) in the associated gene by @ielis in #651
• Add docs section to describe building LIRICAL to use as a library by @ielis in #649
• Remove misplaced dependency from lirical-configuration POM by @ielis in #648

Full Changelog: v2.0.0...v2.0.1

v2.0.0

What's Changed

• Add prioritize command for running LIRICAL entirely from CLI
• Support running analysis starting from both v1 and v2 phenopacket versions
• Simplify the YAML input format
• Enhance HTML report, add JSON output format
• Split the codebase into several modules
• Require Java 17 or better
• Host documentation and API docs on github.io

New Contributors

• @mabeckwith made their first contribution in #595

Full Changelog: v1.3.4...v2.0.0