Initial commit: digital-patients pipeline (clean, no large files)

Large reference/model files excluded from repo - to be staged to S3 or baked into Docker images.

Notes.txt

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+add rna splice step
+
+fix borzoi - muatation step (main_borzoi;PREDICT_EXPRESSION;create_mut()) onyl POINT MUTATIONS add INDEL MUATAIONS
+
+Borzoi can have alternativ chromosoms and chrUn_* as well, VCF2PROT CAN NOT have them. This will cause discrepancies in the code.
+
+Name output files from borzoi ==> need to have patients name/id