chore(release): 2.15.5

## [2.15.5](v2.15.4...v2.15.5) (2024-11-13)

### Bug Fixes

* update pharmcat_regions.bed on data update ([8911fa1](8911fa1))
* **data:** update data ([f429762](f429762))
* **preprocessor:** add a check and test on the GVCFBlock comment in the gVCF header lines ([76b31dd](76b31dd))
* **preprocessor:** add a function to fill up homozygous reference genotypes ([f302af6](f302af6))
* **preprocessor:** add back --missing-to-ref ([fad76c9](fad76c9))
* **preprocessor:** check whether the index file exists before indexing the uniallelic position VCF ([d2078f0](d2078f0))
* **preprocessor:** improve the check on the gVCF END block ([6854ec3](6854ec3)), closes [#199](#199)
* **preprocessor:** make search path precedence count ([1b5754d](1b5754d))
* **preprocessor:** matching pattern for GVCFBlock in the header ([6509882](6509882))
* **preprocessor:** only retrieve regions to extract once ([3964b13](3964b13))
* **preprocessor:** remove -refRegion argument from preprocessor ([5331c2b](5331c2b))
* **preprocessor:** replace the "--missing-to-ref" functionality with two separate functions, --absent-to-ref and --unspecified-to-ref. ([98f7559](98f7559))
* **preprocessor:** simplifies the check on sex chromosome haploidy ([90a0306](90a0306))

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

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
   }

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

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:<br />Pharmacogenomics Clinical Annotation Tool

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"

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'