The use of --no_probabilities is currently limited by the fact that compute_probs imports tcr_rearrangement_new.py or tcr_rearrangement.py (both directly and also through the importing of tcr_sampler.py). the rearrangement scripts have functions that require the existence of hard-coded probabilities files. Currently, --no_probabilities will successfully assign a probability of 1 in all cases, but the pipeline will fail in cases in which the probabilities files do not exist.
The use of --no_probabilities is currently limited by the fact that compute_probs imports tcr_rearrangement_new.py or tcr_rearrangement.py (both directly and also through the importing of tcr_sampler.py). the rearrangement scripts have functions that require the existence of hard-coded probabilities files. Currently, --no_probabilities will successfully assign a probability of 1 in all cases, but the pipeline will fail in cases in which the probabilities files do not exist.