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CHANGELOG.md

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2024-08-05

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

2024-08-02

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

2024-07-29

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

2024-06-19

Patch release pgscatalog-match-0.2.2

  • Fixes pgscatalog-intersect with bim target input #25

2024-06-14

Patch releases to downgrade minimum Python version to 3.10:

2024-06-13

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

2024-06-12

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

2024-05-23

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

2024-04-09

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

2024-03-22

Initial release of new python packages:

Also pgscatalog-utils migrated to using these tools on the backend (v1.0.0)