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broadinstitute / regional_missense_constraint

Code to calculate regional missense constraint
BSD 3-Clause "New" or "Revised" License
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Runtime branch for RMC freeze7 #297

Closed Ruchit10 closed 1 year ago

Ruchit10 commented 1 year ago

This PR includes various bug fixes for running RMC pipeline on freeze 7 including:

  1. Fixing use of prepare_ht_for_constraint_calculations, adding an option to switch to adding annotations in process_context_ht and in process_vep. This was to avoid a bug later which was trying to read a non-existent column in HT.
  2. Move another annotation function into process_vep.
  3. Fix a typo in create_filtered_context.
  4. Add a toggle for building plateau models or use the existing models if available.
  5. Fix model naming to avoid inconsistencies.
  6. Fix a bug in resource path to plateau model.
  7. Update Hail in docker file.
  8. Change number of partitions for performance improvement.
  9. Adding additional checkpoint in process_sections and fix some logic.
  10. Remove gnomad and gnomad_qc from docker and fix python versioning in Dockerfile
  11. Update search_for_two_breaks function to use chisq annotation throughout instead of max_chisq.
  12. Update default docker image path to reflect newer image.
  13. remove wait=False from b.run() in run_batches.py.
  14. Temporary workaround changes due to a hail bug and updating docstring for future to-do in run_batches.py.