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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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Rearrange RMC and generic code #282

Closed lw453 closed 1 year ago

lw453 commented 1 year ago

This PR moves the code to generate the OE-annotated VEP context table into the RMC utils file and moves the code calling it into the finalize section of the RMC pipeline file (originally located in the MPC pipeline file). It also moves a few other functions out of the missense badness and MPC utils files and into the RMC or generic utils files where they more appropriately belong.

lw453 commented 1 year ago

Also a fix was added to make the context table-generating code responsive to RMC freeze selection.

lw453 commented 1 year ago

Additional major change made: Freeze arguments added for missense badness and MPC functions. Additional minor change made: Moved some temp misbad and MPC resources from TEMP_PATH to TEMP_PATH_WITH_FAST_DEL.