From 983dc04f11e51471172c810bd04a87a8f9fb32eb Mon Sep 17 00:00:00 2001 From: semantic-release-bot Date: Wed, 13 Nov 2024 07:46:20 +0000 Subject: [PATCH] chore(release): 2.15.5 ## [2.15.5](https://github.com/PharmGKB/PharmCAT/compare/v2.15.4...v2.15.5) (2024-11-13) ### Bug Fixes * update pharmcat_regions.bed on data update ([8911fa1](https://github.com/PharmGKB/PharmCAT/commit/8911fa1c4eb5dc1a295464483b492b28f12ed076)) * **data:** update data ([f429762](https://github.com/PharmGKB/PharmCAT/commit/f429762f69641546dcc5842bacd972e7e30d64c8)) * **preprocessor:** add a check and test on the GVCFBlock comment in the gVCF header lines ([76b31dd](https://github.com/PharmGKB/PharmCAT/commit/76b31dd4e075f5abdc82dc5883d45fc4bc08a684)) * **preprocessor:** add a function to fill up homozygous reference genotypes ([f302af6](https://github.com/PharmGKB/PharmCAT/commit/f302af65bc956922b310dca344df0fa9e2cf7738)) * **preprocessor:** add back --missing-to-ref ([fad76c9](https://github.com/PharmGKB/PharmCAT/commit/fad76c9776411a6bb735c910f8d5ab8d94a4ebd0)) * **preprocessor:** check whether the index file exists before indexing the uniallelic position VCF ([d2078f0](https://github.com/PharmGKB/PharmCAT/commit/d2078f0062bc6f18d81a362f72ac17a5e19fbc00)) * **preprocessor:** improve the check on the gVCF END block ([6854ec3](https://github.com/PharmGKB/PharmCAT/commit/6854ec3d7cd51982cfa8b712ed1286f3381d4472)), closes [#199](https://github.com/PharmGKB/PharmCAT/issues/199) * **preprocessor:** make search path precedence count ([1b5754d](https://github.com/PharmGKB/PharmCAT/commit/1b5754d02095e80558b672fc3cacc4854c84f8f2)) * **preprocessor:** matching pattern for GVCFBlock in the header ([6509882](https://github.com/PharmGKB/PharmCAT/commit/6509882af82ff2225445ea54a216aeedb1b455fb)) * **preprocessor:** only retrieve regions to extract once ([3964b13](https://github.com/PharmGKB/PharmCAT/commit/3964b1384e5439827afdb920e4b4a82556c36a0c)) * **preprocessor:** remove -refRegion argument from preprocessor ([5331c2b](https://github.com/PharmGKB/PharmCAT/commit/5331c2b0dd1f2538763dc7fb5fd598698b58fe89)) * **preprocessor:** replace the "--missing-to-ref" functionality with two separate functions, --absent-to-ref and --unspecified-to-ref. ([98f7559](https://github.com/PharmGKB/PharmCAT/commit/98f7559fac37d0260b6309701544c2c70366fdd5)) * **preprocessor:** simplifies the check on sex chromosome haploidy ([90a0306](https://github.com/PharmGKB/PharmCAT/commit/90a030656b8c110beb399786af90b8987b8f17b0)) --- CHANGELOG.md | 18 ++++++++++++++++++ dockstore/pipeline/PharmCAT_Pipeline.wdl | 2 +- dockstore/pipeline/README.md | 2 +- docs/index.md | 2 +- package.json | 2 +- preprocessor/preprocessor/common.py | 2 +- 6 files changed, 23 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 31937942..ce96af2e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,21 @@ +## [2.15.5](https://github.com/PharmGKB/PharmCAT/compare/v2.15.4...v2.15.5) (2024-11-13) + +### Bug Fixes + +* update pharmcat_regions.bed on data update ([8911fa1](https://github.com/PharmGKB/PharmCAT/commit/8911fa1c4eb5dc1a295464483b492b28f12ed076)) +* **data:** update data ([f429762](https://github.com/PharmGKB/PharmCAT/commit/f429762f69641546dcc5842bacd972e7e30d64c8)) +* **preprocessor:** add a check and test on the GVCFBlock comment in the gVCF header lines ([76b31dd](https://github.com/PharmGKB/PharmCAT/commit/76b31dd4e075f5abdc82dc5883d45fc4bc08a684)) +* **preprocessor:** add a function to fill up homozygous reference genotypes ([f302af6](https://github.com/PharmGKB/PharmCAT/commit/f302af65bc956922b310dca344df0fa9e2cf7738)) +* **preprocessor:** add back --missing-to-ref ([fad76c9](https://github.com/PharmGKB/PharmCAT/commit/fad76c9776411a6bb735c910f8d5ab8d94a4ebd0)) +* **preprocessor:** check whether the index file exists before indexing the uniallelic position VCF ([d2078f0](https://github.com/PharmGKB/PharmCAT/commit/d2078f0062bc6f18d81a362f72ac17a5e19fbc00)) +* **preprocessor:** improve the check on the gVCF END block ([6854ec3](https://github.com/PharmGKB/PharmCAT/commit/6854ec3d7cd51982cfa8b712ed1286f3381d4472)), closes [#199](https://github.com/PharmGKB/PharmCAT/issues/199) +* **preprocessor:** make search path precedence count ([1b5754d](https://github.com/PharmGKB/PharmCAT/commit/1b5754d02095e80558b672fc3cacc4854c84f8f2)) +* **preprocessor:** matching pattern for GVCFBlock in the header ([6509882](https://github.com/PharmGKB/PharmCAT/commit/6509882af82ff2225445ea54a216aeedb1b455fb)) +* **preprocessor:** only retrieve regions to extract once ([3964b13](https://github.com/PharmGKB/PharmCAT/commit/3964b1384e5439827afdb920e4b4a82556c36a0c)) +* **preprocessor:** remove -refRegion argument from preprocessor ([5331c2b](https://github.com/PharmGKB/PharmCAT/commit/5331c2b0dd1f2538763dc7fb5fd598698b58fe89)) +* **preprocessor:** replace the "--missing-to-ref" functionality with two separate functions, --absent-to-ref and --unspecified-to-ref. ([98f7559](https://github.com/PharmGKB/PharmCAT/commit/98f7559fac37d0260b6309701544c2c70366fdd5)) +* **preprocessor:** simplifies the check on sex chromosome haploidy ([90a0306](https://github.com/PharmGKB/PharmCAT/commit/90a030656b8c110beb399786af90b8987b8f17b0)) + ## [2.15.4](https://github.com/PharmGKB/PharmCAT/compare/v2.15.3...v2.15.4) (2024-10-15) ### Bug Fixes diff --git a/dockstore/pipeline/PharmCAT_Pipeline.wdl b/dockstore/pipeline/PharmCAT_Pipeline.wdl index f58d2343..f7569b77 100644 --- a/dockstore/pipeline/PharmCAT_Pipeline.wdl +++ b/dockstore/pipeline/PharmCAT_Pipeline.wdl @@ -144,7 +144,7 @@ task pharmcat_pipeline_task { } runtime { - docker: "pgkb/pharmcat:2.15.4" + docker: "pgkb/pharmcat:2.15.5" memory: max_memory cpu: max_concurrent_processes } diff --git a/dockstore/pipeline/README.md b/dockstore/pipeline/README.md index 1d439e5e..8b70317f 100644 --- a/dockstore/pipeline/README.md +++ b/dockstore/pipeline/README.md @@ -127,7 +127,7 @@ Successfully tested on v53 and v87. ### PharmCAT Version -PharmCAT v2.15.4. +PharmCAT v2.15.5. ## Contact diff --git a/docs/index.md b/docs/index.md index c4320fe9..b340ca7c 100644 --- a/docs/index.md +++ b/docs/index.md @@ -3,7 +3,7 @@ title: Home permalink: / nav_order: 1 # version is dynamically updated - DO NOT MODIFY MANUALLY -pharmcat_version: 2.15.4 +pharmcat_version: 2.15.5 --- # PharmCAT:
Pharmacogenomics Clinical Annotation Tool diff --git a/package.json b/package.json index 1bdda993..500f71c1 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "pharmcat", - "version": "2.15.4", + "version": "2.15.5", "repository": { "type": "git", "url": "https://github.com/PharmGKB/PharmCAT.git" diff --git a/preprocessor/preprocessor/common.py b/preprocessor/preprocessor/common.py index ed5fb065..a43eda7a 100644 --- a/preprocessor/preprocessor/common.py +++ b/preprocessor/preprocessor/common.py @@ -2,7 +2,7 @@ # version is dynamically updated - DO NOT MODIFY MANUALLY -PHARMCAT_VERSION = '2.15.4' +PHARMCAT_VERSION = '2.15.5' # expected tool versions MIN_BCFTOOLS_VERSION = '1.18'