Releases: PharmGKB/PharmCAT
Releases · PharmGKB/PharmCAT
v2.15.3
2.15.3 (2024-08-28)
Bug Fixes
- data: track singular variants (fb1ebbd)
- data: update data (c8100ec)
- namedallelematcher: fix permutation generation with mix of phased/unphased data (2146db0)
- phenotyper: improve support for combinations in outside calls (b1a6deb)
- reporter: fix limiting reports by source (ac0c52e)
- reporter: fix matching diplotype-specific recommendations (11fc7b4)
- reporter: take subsetting into account when calculating total genes (6ef47cc)
v2.15.2
v2.15.1
v2.15.0
2.15.0 (2024-08-06)
Features
- json2tsv: report error when no allele definition json can be found (03a8b1f)
- phenotyper: generate diplotype data (ed4d03f)
Bug Fixes
- fix haplotype name sorting (f9888b0)
- improve Subsetter (971ba16)
- reduce data size (5bdcc49)
- data: update data (a57b955)
- json2tsv: allow the script to find the allele definition jsons from wherever it is run (03151ba)
- namedallelematcher: avoid exceptions (f4fe35a)
- namedallelematcher: fix handling of phased DPYD HapB3 alleles (286b76d)
- namedallelematcher: make NamedAllele.structuralVariant a private property (df68105)
- namedallelematcher: make sure cached properties are updated correctly (ab1e194)
- phenotyper: fix typo in CYP2D6 activity value assignment and drug count (36cc688)
- phenotyper: fix typo in two specific CYP2D6 diplotype activity score assignment (cae0f8c)
- phenotyper: use correct comparator (4cf8cb2)
- preprocessor: resolve errors caused by similar sample names (905b2c3)
- subsetter: fix how numeric cells are handled in Excel (bbaa135)
v2.14.0
2.14.0 (2024-07-19)
Features
- data: make all allele definitions import from PharmGKB (47da939)
- data: update to PharmVar v6.1.3 (e4b8fc2)
Bug Fixes
- data: fix downloading new guidance data (a1007c0)
- diplotype-comparator: update string delimiter (e10a2ea)
- namedallelematcher: fix exception thrown while sorting diplotype matches (093f5b2)
- namedallelematcher: handle CYP2D6 and HLA outside calls with sub-alleles gracefully (dcaa055)
- reporter: fix how allele presence phenotypes are shown in final report (2f00c6c)
- reporter: fix missing PMID in report citation data (81a0df2), closes #187
- reporter: fix multiple version check logic (3af2726)
- reporter: fix phenotype check by querying only phenotype-related genes in an annotation (b666953), closes #180
- reporter: warn if multiple versions found (9bb2a55)
v2.13.0
2.13.0 (2024-06-11)
Features
- diplotype-comparator: find equivalent phased alleles (a8a786c)
- pharmcat: add FDA drug guidance (ae6ea63)
- preprocessor: retain genomic regions specified in a bed file (d017be5)
Bug Fixes
- remove non-existent test class (1a91885)
- data: delete obsolete files before exporting positions (8acb549)
- datamanager: add support for subsetting allele definitions (79fb6ea)
- datamanager: handle all allele/position removal during data ingestion phase (85a770f)
- datamanager: remove populationFrequency from named allele (never used) (5ecaa74)
- preprocessor: ploidy at multiallelic positions (8805275)
- preprocessor: ploidy in X chromosomes for -0/--missing-to-ref (9f83767)
v2.12.0
2.12.0 (2024-4-23)
The primary goal for this release is to fix issue #180, that happens when multiple diplotypes are matched for genes related to warfarin.
Beginning with this release, we will also be releasing Docker images that run on the linux/arm64 architecture. This means those running PharmCAT on Macs with Apple silicon will see a dramatic performance improvement.
Features
- pharmcat: support more than one outside call file (154ac49)
- pipeline: add the feature of bypassing the gVCF check to the pipeline (d38005e)
Bug Fixes
- add json2tsv script (dfabdc1)
- namedallelematcher: improve VCF warnings (1659e21)
- pharmcat: add to path in docker container to fix running scripts (57a956b)
- phenotyper: strip gene symbol prefix from outside call diplotype alleles (940f6cf)
- reporter: add "Activity Value" prefix to formatted function (8735554)
- reporter: avoid exception for multiple phenotypes or activity scores for warfarin (da65834), closes #180
- reporter: fix display of function/activity in variant position section (2181f31)
- reporter: no tags for CPIC warfarin report (3842c1f)
v2.11.0
v2.10.0
2.10.0 (2024-3-25)
Features
- data: update to CPIC v1.38 and latest PharmVar (560bdb8)
- pharmcat: report RYR1 using lowest-function gene algorithm (596058a)
- preprocessor: an option to not perform a gVCF check (209f68f), closes #174
Bug Fixes
- data: update data (984c73a)
- namedallelematcher: update DPYD HapB3 support for HapB3 intronic allele (b32b4ae)
- preprocessor: improve message for gVCF (2d4da7d), closes #174
- reporter: add check for multiple conflicting phenotype/activity values (b9b1cd1)
- reporter: fix edge-case for outside calls of AS genes that only specify phenotype and not score (1321518)
- reporter: fix genotype display when no genotype is provided in outside call (1be5c6d)
- reporter: fix missing phenotype and activity score in drug section of HTML report (e3f1029)
- reporter: standardize naming (29e3900)
Performance Improvements
- diplotype-comparator: reduce runtime (d17ca4a)
Reverts
- revert message annotation update (6cf0e3b)
v2.9.0
2.9.0 (2024-1-17)
Features
- data: update to CPIC version v1.35 (5cb6717)
- data: update to PharmGKB version 2023-12-19 (66c49f9)
- reporter: add new "non-match" type of message (f5df05a)
Bug Fixes
- namedallelematcher: DPYD matching should ignore find-combinations mode (153853a)
- namedallelematcher: improve AD number warning (9d9a0b9), closes #168
- phenotyper: fix bug with stripping gene symbol from outside call diplotypes (cb97898), closes #161
Performance Improvements
- improve runtime of diplotype comparison (406930c)