Add pipeline and input data

.gitignore

HOGVAX/README.md

HOGVAX/__init__.py

HOGVAX/aho_corasick_trie.py

HOGVAX/ba_for_embedded_peptides.py

HOGVAX/draw_hog.py

HOGVAX/example_arguments.txt

HOGVAX/filter_substrings_in_ba_predictions.py

HOGVAX/find_superstrings.py

HOGVAX/get_all_peptides_incl_substrings.py

HOGVAX/hogvax.py

HOGVAX/hogvax_env.yaml

HOGVAX/hogvax_ilp.py

HOGVAX/linear_time_hog.py

OptiVax_Data/Peptides/30_filtered_mhc_peptides.pep

...Peptides/combined_filtered_mhc_peptides_gifford_style.pep

.../optivax_robust_mhc1_haplotype_4519_filtered_peptides.pep

...optivax_robust_mhc2_haplotype_37435_filtered_peptides.pep

...Peptides/optivax_unlinked_mhc1_4512_filtered_peptides.pep

...des/optivax_unlinked_mhc1_639_filtered_peptides_spike.pep