pgsc_calc v1.1.0

The first public release of the pgsc_calc pipeline. This release adds compatibility
for every score published in the PGS Catalog. Each scoring file in the PGS Catalog
has been processed to provide consistent genomic coordinates in builds GRCh37 and GRCh38.
The pipeline has been updated to take advantage of the harmonised scoring files (see
PGS Catalog downloads for additional details).

Features

• Many of the underlying software tools are now implemented within a pgscatalog_utils
  package (v0.1.2, https://github.com/PGScatalog/pgscatalog_utils and
  https://pypi.org/project/pgscatalog-utils/). The packaging allows for independent
  testing and development of tools for downloading and working with the scoring files.

• The output report has been improved to have more detailed metadata describing
  the scoring files and how well the variants match the target sampleset(s).

• Improvements to variant matching:

  • More precise control of variant matching parameters is now possible, like
    ignoring strand flips
  • match_variants should now use less RAM by default:
    • A laptop with 16GB of RAM should be able to comfortably calculate scores on
      the 1000 genomes dataset
    • Fast matching mode (--fast_match) is available if ~32GB of RAM is
      available and you'd like to calculate scores for larger datasets

• Groups of scores from the PGS Catalog can be calculated by specifying a specific
  --trait (EFO ID) or --publication (PGP ID), in addition to using individual
  scoring files --pgs_id (PGS ID).

• Score validation has been integrated with the test suite

• Support for M1 Macs with --platform parameter (docker executor only)

Bug fixes

• Implemented a more robust prioritisation procedure if a variant has multiple
  candidate matches or duplicated IDs

• Fixed processing multiple samplesets in parallel (e.g. 1000 Genomes + UK
  Biobank)

• When combining multiple scoring files, all variants are now kept to reflect the
  correct denominator for % matching statistics.

• When trying to correct for strand flips the matched effect allele wasn't being
  correctly complemented