diff --git a/CHANGELOG.md b/CHANGELOG.md index 538458a..6715a68 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,11 @@ +# v0.12.0 +## Changes +- Hard-coded coordinates (GRCh38) for HLA-A, HLA-B, and CYP2D6 calling have been moved into the database file. Prior database versions without this new config information will automatically load the previously hard-coded values. This configuration is provided for transparency and experimentation in other reference coordinate systems, we do not recommend or support changing the provided default values. +- Released an updated database with the updated config format and name pattern change: `data/v0.12.0/pbstarphase_20240716.json.gz` +- Changed CYP2D6 consensus merging component to merge on sub-alleles instead of core alleles. + - To support the this change, consensuses with ambiguous CYP2D6 assignments (e.g. equal matches to "*4.001" and "*4.015") are labeled as unknown for the purpose of merging with similar consensus alleles prior to generating a final consensus set. + - Internal tests showed this combination of changes led to increased sensitivity for sub-allele identification without injecting errors at the core allele or diplotype level. + # v0.11.3 ## Fixed - Updated the `build` mode to account for IMGT-HLA's new database format that was released with `v3.57.0-alpha` diff --git a/data/README.md b/data/README.md index 6664fc9..113d68c 100644 --- a/data/README.md +++ b/data/README.md @@ -2,14 +2,14 @@ ## Database files Databases were pre-generated for ease-of-use, sharing, and backwards compatibility when using older versions of pb-StarPhase. Though we will do our best to avoid breaking changes, database files are **not** guaranteed to work on versions that do not match. -Additionally, these databases represent a snapshot in time of upstream data sources (e.g., CPIC and IMGTHLA). +Additionally, these databases represent a snapshot in time of upstream data sources (e.g., CPIC, IMGTHLA, and PharmVar). Running the same command at a later date may produce a different database with updated annotations. -Each file is labeled as `{version}/cpic_{YYYYMMDD}.json` and represents a run of the following command using the specified `{version}` of pb-StarPhase on the corresponding date (`{YYYYMMDD}`): +As of v0.12.0, each file is labeled as `{version}/pbstarphase_{YYYYMMDD}.json.gz` and represents a run of the following command using the specified `{version}` of pb-StarPhase on the corresponding date (`{YYYYMMDD}`): ```bash pbstarphase build \ - --output-db {version}/cpic_{YYYYMMDD}.json + --output-db {version}/pbstarphase_{YYYYMMDD}.json.gz ``` # Data sources and citations diff --git a/data/v0.12.0/pbstarphase_20240716.json.gz b/data/v0.12.0/pbstarphase_20240716.json.gz new file mode 100644 index 0000000..e11a377 Binary files /dev/null and b/data/v0.12.0/pbstarphase_20240716.json.gz differ