v2.15.5

2.15.5 (2024-11-13)

Bug Fixes

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

v2.15.4

2.15.4 (2024-10-15)

Bug Fixes

• bump version for Dockerhub fix (3ab49f3)

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

2.15.2 (2024-08-20)

Bug Fixes

• data: fill in DPYD lookupkeys for DPWG (90d587b)
• tools: gene regions for F5, CYP2D6, VKORC1, IFNL4 for research purposes (5f0e6dd)
• tools: show the name of the sample whose result files are being processed (8d6d1c8)

v2.15.1

2.15.1 (2024-08-17)

Bug Fixes

• do not require any base filename before the sample IDs (7250db4)
• validate outside call diplotypes (9c49fbc)
• data: include missing CPIC metoprolol guidance (b117835)
• subsetter: fix bugs in subsetter (683a361)

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

2.11.0 (2024-3-26)

Features

• data: remove F5 (0c6123b)

Bug Fixes

• datamanager: make sure we remove obsolete data files (da21f6e)