Merge pull request #22 from PacificBiosciences/db_updates

changes and DB update

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`

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