Release 2.2.0

[diekhans]

[2.2.0] 2025-05-06

• Returned diffexp and diffsplice as standard modules. The BioConda
  environment does not include the dependencies for these modules
  and required software does not run on Apple Silicon (ARM64) systems.
• The flair combine functionality is now to a module. The
  flair_combine program is run with flair combine.
• Changed default MAPQ minimum quality score to 0. This allows more reads to
  be used in identifying isoforms, which tends to improve the overall models
  with out adversely affecting the accuracy.
• GitHub releases include the Conda YAML files for building FLAIR
  environments. Useful if the BioConda release has not been manually
  reviewed.
• The FLAIR Docker now includes all dependencies to run diffexp and diffsplice.
• Reorganized the installation documentation.
• Fixed flair_quantify --output_bam crash
• Other bug fixes

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This discussion was created from the release Release 2.2.0.