Adding config creation features (#138)

* improve efficiency, modularization of create_main_config function * bug-fix updating min_common_af based on user MAF threshold input * change dtype to float * fix list operation * update handle_pretrained_models function logic for readability & efficiency * issue 131 fixed - allow update of base_configurations via input_config * Update docs for configuration file udpates * merge in deterministic flag , optional input keys, and clobber from main * fixup! Format Python code with psf/black pull_request * move logging setup command * update base-config default MAF, add optional 'sample_files' config key, add resolve for pretrained_model_path * Add pytests for configuration file generation * fixup! Format Python code with psf/black pull_request --------- Co-authored-by: PMBio <[email protected]>
PMBio · Sep 27, 2024 · 4dd101f · 4dd101f
1 parent d9b11b2
commit 4dd101f
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diff --git a/deeprvat/deeprvat/base_configurations.yaml b/deeprvat/deeprvat/base_configurations.yaml
@@ -73,7 +73,7 @@ training_data:
 association_testing_data:
     dataset_config:
         min_common_af:
-            MAF: 0.01
+            MAF: 0.001
         use_common_variants: False
         use_rare_variants: True
         rare_embedding: