Continue working to support build 38 - Githubissues

broadinstitute / regional_missense_constraint

Code to calculate regional missense constraint

BSD 3-Clause "New" or "Revised" License

13 stars 1 forks source link

Continue working to support build 38 #306

Closed ch-kr closed 3 months ago

ch-kr commented 3 months ago

This PR updates rmc/utils/constraint.py to support GRCh38.

Major changes:

Updated code in create_filtered_context_ht and calculate_exp_from_mu to use code from gnomad_methods or gnomad_constraint where possible

Minor changes:

Removed redundant code from add_obs_annotation
Updated file_exists to check_file_exists_raise_error where appropriate
Update GRCh37 > GRCh38 import for vep_context
Updated path for all_loci_chisq_ht (for more permanent storage, also consistency with upcoming PR updating pipeline script)