From 1dfd0a46cba3492791f7dcd0ddbaee3abfb4ed9f Mon Sep 17 00:00:00 2001 From: Jules Jacobsen Date: Wed, 28 Feb 2024 17:55:36 +0000 Subject: [PATCH] Update CHANGELOG.md --- exomiser-cli/CHANGELOG.md | 17 ++++++++++++----- exomiser-core/CHANGELOG.md | 22 ++++++++++++++++++---- 2 files changed, 30 insertions(+), 9 deletions(-) diff --git a/exomiser-cli/CHANGELOG.md b/exomiser-cli/CHANGELOG.md index 724a8a0d0..15659a4e8 100644 --- a/exomiser-cli/CHANGELOG.md +++ b/exomiser-cli/CHANGELOG.md @@ -1,12 +1,19 @@ # The Exomiser Command Line Executable - Changelog -## 14.0.0 2023-MM-dd - -- Minimum Java version is now set to __Java 17__ -- Enabled independent update of ClinVar data [#501](https://github.com/exomiser/Exomiser/issues/501) +## 14.0.0 2024-02-29 + +- Minimum Java version is now **Java 17** +- Update database format **REQUIRES DATABASE VERSION 2402** - these are significantly smaller than the previous versions (~50-60% of previous size) +- Added new GeneBlacklistFilter [#457](https://github.com/exomiser/Exomiser/issues/457) +- Add new ClinVar conflicting evidence counts in HTML output [#535](https://github.com/exomiser/Exomiser/issues/535) +- Added PS1, PM1, PM5 categories to ACMG assignments +- Altered reporting of InheritanceModeFilter to state that the number shown refers to variants rather than genes. +- Updated gene constraints to use gnomad v4.0 data. +- TSV genes, TSV variants and VCF outputs will only write to a single file where the possible modes of inheritances are now shown together rather than split across separate files. - Fix for issue [#531](https://github.com/exomiser/Exomiser/issues/531) where the `priorityScoreFilter` and `regulatoryFeatureFilter` pass/fail counts were not displayed in the HTML. - Fix for issue [#534](https://github.com/exomiser/Exomiser/issues/534) where variant frequency and/or pathogenicity annotations are missing in certain run configurations. - +- Fix for issue [#541](https://github.com/exomiser/Exomiser/issues/541) where logging to /tmp/spring.log causes clashes in shared user environments. +- TSV output column `CLINVAR_ALLELE_ID` has been changed to `CLINVAR_VARIANT_ID` to allow easier reference to ClinVar variants. ## 13.3.0 2023-10-17 diff --git a/exomiser-core/CHANGELOG.md b/exomiser-core/CHANGELOG.md index 8539843bf..a528ffc25 100644 --- a/exomiser-core/CHANGELOG.md +++ b/exomiser-core/CHANGELOG.md @@ -1,11 +1,16 @@ # The Exomiser - Core Library Changelog -## 14.0.0 2023-MM-dd +## 14.0.0 2024-02-29 -This release **requires data version >= 2210** and **Java version >= 17** (the most recent LTS release). +This release **requires data version >= 2402** and **Java version >= 17** (the previous LTS release). - Added new GeneBlacklistFilter [#457](https://github.com/exomiser/Exomiser/issues/457) - Enabled independent update of ClinVar data [#501](https://github.com/exomiser/Exomiser/issues/501) +- Add new ClinVar conflicting evidence counts in HTML output [#535](https://github.com/exomiser/Exomiser/issues/535) +- Added PS1, PM1, PM5 categories to ACMG assignments +- Updated gene constraints to use gnomad v4.0 data +- TSV genes, TSV variants and VCF outputs will only write to a single file where the possible modes of inheritances are now shown together rather than split across separate files. +- Altered reporting of InheritanceModeFilter to state that the number shown refers to variants rather than genes. - Added new `ClinVarDao` and `ClinVarWhiteListReader` to take advantage of the independently upgradeable ClinVar data files. - The `VariantWhiteList` is now dynamically loaded from the ClinVar data provided in the clinvar.mv.db file - `VariantDataServiceImpl` now requires a `ClinVarDao` @@ -21,12 +26,21 @@ New APIs: - New `Filterable.failedFilter()` method - New `AlleleData` class to encapsulate building AlleleProto.Frequency and AlleleProto.PathogenicityScore instances - Added new `ClinVarDao` and `ClinVarWhiteListReader` to take advantage of the independently upgradeable ClinVar data files. -- +- `Frequency` can either be constructed from a percentage frequency or a set of AC, AN, HOM counts. +- Added `AlleleProto.AlleleKey alleleKey()` method to `Variant` to memoise +- Add PathogenicitySource `ALPHA_MISSENSE`, `EVE`, `SPLICE_AI` +- Add new `Frequency`, `FrequencySource`, `PathogenicityScore`, `PathogenicitySource`, `VariantEffect` and `ClinVar.ReviewStatus` to proto schema. + API breaking changes: +- `PathogenicityData` and `FrequencyData` now follow a 'record' rather than 'java bean' pattern for field accessors e.g. `PathogenicityData.clinVarData()` rather than `PathogenicityData.getClinVarData()` +- Deleted deprecated `TsvGeneAllMoiResultsWriter`, `TsvVariantAllMoiResultsWriter` and `VcfAllMoiResultsWriter` classes +- Delete PathogenicitySource `M_CAP`, `MPC`, `PRIMATE_AI` +- Alter ESP FrequencySource long forms to short e.g. `ESP_AFRICAN_AMERICAN` to `ESP_AA` +- TSV output column `CLINVAR_ALLELE_ID` has been changed to `CLINVAR_VARIANT_ID` to allow easier reference to ClinVar variants. Other changes: -- Updated Spring Boot to version 3.1.0 +- Updated Spring Boot to version 3.2.3 ## 13.3.0 2023-10-17