v3.3.0

3.3.0 (2026-07-10)

This update is highly recommended. It fixes an issue with pharmcat_pipeline where it uses the original input VCF instead of the preprocessed VCF if it is given a directory instead of a file.

Data Highlights

PharmVar

• new alleles were released for CYP2C9, CYP2D6, CYP3A4, CYP3A5, NUDT15

ClinPGx

• updates released/published for the CPIC Guideline for RYR1, CACNA1S and Volatile anesthetic agents and Succinylcholine and the CPIC Guideline for CYP2D6 and Ondansetron and Tropisetron
• updates to the DPWG guideline for CYP2D6 gefitinib and the addition of the DPWG guideline for UGT1A1 sacituzumab govitecan

Features:

• data: update data from ClinPGx (af8b4577)

Bug Fixes

• preprocessor: handle unquoted Java version string from Bioconda (#230) (0b1d0fe2). Thanks, @rkmishra3893!
• preprocessor: correct _is_phased() early return and prevent KeyError on duplicate variants (#222) (67e36690). Thanks, @haoyu-haoyu!
• preprocessor: quick fix to not crash due to unordered symbolic structural variants (#225) (76360022)
• preprocessor: fix bug when running pipeline on a directory (#229) (b67ebb0a)
• preprocessor: don't display ambiguity warning if gene is effectively phased (#219) (1767da4e)
• preprocessor: use long form for bcftools -W to support v1.18 (7b075811)
• preprocessor: update versions of htslib/bcftools dependencies (bf2ab5b4)