MAF thresholds above 0.01 won't work

[bfclarke]

Setting a MAF threshold above 0.01 for *_data_thresholds in deeprvat_input_config.yaml won't work because of the below lines in base_configurations.yaml, which don't get updated when the full config is generated.

training_data:
    dataset_config:
        min_common_af:
            MAF: 0.01

association_testing_data:
    dataset_config:
        min_common_af:
            MAF: 0.01