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Releases: TheJacksonLaboratory/LIRICAL

v2.0.2

01 May 19:29
@ielis ielis
v2.0.2
22bf5f2
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v2.0.2 Latest
Latest

A patch release with bug fixes and no novel functionality.

What's Changed

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

Contributors

ielis
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v2.0.1

16 Apr 14:37
@ielis ielis
v2.0.1
d95d3fb
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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

Contributors

ielis
Assets 3
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v2.0.0

29 Dec 15:49
@ielis ielis
v2.0.0
a3323e4
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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

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

Contributors

mabeckwith
Assets 3
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v2.0.0-RC3

28 Dec 20:34
@ielis ielis
v2.0.0-RC3
d871901
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v2.0.0-RC3 Pre-release
Pre-release

The last release candidate RC before LIRICAL v2.

Full Changelog: v2.0.0-RC2...v2.0.0-RC3

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v2.0.0-RC2

07 Apr 18:30
@ielis ielis
v2.0.0-RC2
2cf43b1
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v2.0.0-RC2 Pre-release
Pre-release

Release candidate (2)

The last release candidate before v2.0.0. The v2 will introduce many breaking changes most of which are @Deprecated in this release.

What's Changed

  • Rework configuration and analysis options by @ielis in #594
  • Update documentation by @iimpulse in #598 @ielis in #602 #605
  • Rework logging by @ielis in #603
  • Implement JSON output format by @ielis in #588
  • Fix Exomiser file locked error when running LIRICAL multiple times by @mabeckwith in #595
  • Shrink poisson API, improve javadoc, use selected disease databases to calculate pretest probability by @ielis in #604

New Contributors

Full Changelog: v2.0.0-RC1...v2.0.0-RC2

Contributors

iimpulse, ielis, and mabeckwith
Assets 3
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v2.0.0-RC1

14 Jul 18:34
@ielis ielis
v2.0.0-RC1
3335669
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v2.0.0-RC1 Pre-release
Pre-release

What's Changed

  • Require Java 17
  • Prune and split codebase into several Maven modules
  • Enhance HTML report (by @iimpulse )
  • Add prioritize command for running LIRICAL entirely from CLI
  • Add support for phenopacket schema v2

Full Changelog: v1.3.4...v2.0.0-RC1

Contributors

iimpulse
Assets 3
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v1.3.4

26 Sep 19:54
@pnrobinson pnrobinson
v1.3.4
71ff360
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v1.3.4

Fixes an issue with the output template, updates some dependencies

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v1.3.3

14 May 18:34
@pnrobinson pnrobinson
v1.3.3
425e9c3
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v1.3.3 
Merge pull request #547 from TheJacksonLaboratory/develop

Develop
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v1.3.2

10 Apr 12:15
@pnrobinson pnrobinson
v1.3.2
425e9c3
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v1.3.2 
Merge pull request #547 from TheJacksonLaboratory/develop

Develop
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v1.3.1

03 Mar 15:26
@pnrobinson pnrobinson
v1.3.1
b4b2b98
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v1.3.1

Fixes download bug after move of phenotype.hpoa file

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