## [3.1.0](v3.0.1...v3.1.0) (2025-11-11) ### Features * add square icon to fetch file ([a8c9fef](a8c9fef)) * adjust DPYD recommendations for DPWG guidelines ([3d7c4a8](3d7c4a8)) * removal of DPWG-specific phenotypes and functions ([bd22137](bd22137)) * **namedAlleleMatcher:** support suballeles to work around ambiguous core alleles ([6d6f272](6d6f272)) ### Bug Fixes * fix class import ([e3b0f04](e3b0f04)) * fix failing tests ([3843d8d](3843d8d)) * fix unit test for checking DPWG phenotype assignment ([dfdfc3e](dfdfc3e)) * update DPYD unit tests for new DPWG function assignment ([3a99eb5](3a99eb5)) * update for ClinPGx ([652a5b8](652a5b8)) * update for ClinPGx ([5c9e65a](5c9e65a)) * **data:** update data ([8c85b47](8c85b47)) * **data:** update data from PharmVar and ClinPGx ([27bceed](27bceed)) * **data:** update to latest CPIC data ([7767b0a](7767b0a)) * **namedAlleleMatcher:** add flag (-g) to only call specified genes ([3e8f042](3e8f042)) * **namedAlleleMatcher:** fix bug with calling combinations related to removing subsets ([bf70e9f](bf70e9f)) * **namedAlleleMatcher:** fix DPYD calling when data is effectively phased or has phase sets ([cf75f24](cf75f24)), closes [#209](#209) * **namedAlleleMatcher:** fix handling of -bf in BatchPharmCAT ([f082289](f082289)) * **namedAlleleMatcher:** fix how partials are added to combinations ([fe927f2](fe927f2)) * **namedAlleleMatcher:** fix partials handling in DPYD ([15dd9f1](15dd9f1)) * **namedAlleleMatcher:** fixed regression in scoring ([0c6d59e](0c6d59e)) * **preprocessor:** add back accidentally deleted function ([74c4098](74c4098)) * **preprocessor:** add support for BCF ([abebc39](abebc39)), closes [#212](#212) * **preprocessor:** BCF files cannot be gVCF ([628a964](628a964)) * **preprocessor:** improve error message ([cc117c6](cc117c6)) * **reporter:** add "Section IV" label to disclaimer section ([d6b3e5b](d6b3e5b)) * **reporter:** add drug tags to Section I ([881b416](881b416)), closes [#213](#213) * **reporter:** correctly print allele ([d3c48b9](d3c48b9)) * **reporter:** expose inferredSourceDiplotypes ([aea6cd9](aea6cd9)) * **reporter:** fix wrapping in section 2 to keep table within bounds ([f21fc78](f21fc78)) * **reporter:** more fine grained controls for what metadata to export ([a97375a](a97375a)) * **reporter:** tweak report title to include sample id ([39db498](39db498)) * **tools:** add pivot column hint ([2d563a1](2d563a1)) * **tools:** add support for calculating phenotype stats ([989f420](989f420)) * **tools:** add tool to merge reports ([8c3e25a](8c3e25a)) * **tools:** handle blank lines gracefully ([c09c811](c09c811)) * **tools:** improve support for compressed files ([1f0c693](1f0c693)) * **tools:** support mixing results with and without sample id ([7b36957](7b36957))

Support BCF #212

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