Patch release pgscatalog-utils-1.3.1
- Bump dependencies to latest
Patch release pgscatalog-match-0.3.1
- Fix splitting but revert implementation to original function. v0.3.0 would trigger ValueErrors consistently on larger datasets
- Fix variant match information getting dropped from the log if an accession was filtered from output scoring files
Minor release pgscatalog-utils-1.3.0
- Bump dependencies to latest
Minor release pgscatalog-match-0.3.0
- Important Fix splitting duplicate variant IDs across different scoring files #38
- Fix
--keep_ambiguous
PGScatalog/pgsc_calc#346 - Fix
--ignore_strand_flips
Minor release pgscatalog-utils-1.2.0
- Bump dependencies to latest
Patch release pgscatalog-match-0.2.3
- Update
pgscatalog-intersect
PCA_ELIGIBLE filters #33
Patch release pgscatalog-calc-0.2.2
- Sample IDs now use FIDs if available #31
Patch release pgscatalog-core-0.2.2
- Fixes support for missing other_allele column in custom scoring files #30
Patch release pgscatalog-match-0.2.2
- Fixes
pgscatalog-intersect
with bim target input #25
Patch releases to downgrade minimum Python version to 3.10:
Minor release pgscatalog-utils-1.1.0
- Bump dependencies to latest
Minor release pgscatalog-match-0.2.0
- Improve performance when reading target genomes and scoring files #20
- Fix raising MatchRateError when one or more scores fails matching but at least one score passes #21
- Fix warnings about map_element dtypes during labelling
Minor release pgscatalog-calc-0.2.0
- Improve aggregation to have clearer logic and logging #23
- Fix aggregating scores with different numbers of columns
- Fix adjusting averages during ancestry adjustment #19
Minor release pgscatalog-core-0.2.0
- Drop pyarrow support when reading target genomes or scoring files
- Add natural sorting functions to sort scoring file paths by effect type or chromosome
- Remove pyarrow dependency
Patch release pgscatalog-core-0.1.2 and pgscatalog.calc-0.1.1:
- Bug fixes for PGS Catalog Calculator integration
Patch release pgscatalog.match-0.1.1:
- Bug fixes for PGS Catalog Calculator integration
- New pgscatalog-intersect CLI application
Bump pgscatalog-utils to use patched dependencies
Patch release pgscatalog-core-0.1.1:
- Add NCBI35 to GenomeBuild
- Disable concurrency in
pgscatalog-combine
to prevent memory usage explosion (will be fixed and re-enabled later) - Fix handling scoring file cases when only one optional effect type column is present
- Fix reading pvar files with complex headers (like ones made from a VCF)
Bump pgscatalog-utils to use patched core
Initial release of new python packages:
Also pgscatalog-utils migrated to using these tools on the backend (v1.0.0)