change indexing of the patient_hla to lanl_hla to autoincrement integers
change indexing of list_scores_to_compute to autoincrement integers
update documentation
Merge branch 'feature/better-list-indices' into develop
breaking things
make score_sequence_epitopes work with Scoring_Jobs
design notes for error logging
Add error logging to scoring_list building
update logging features of shiny app
change compute_epitope_scores to use a Scoring_Job
compute epitope scores only on relevant query sequences
clean up error logging in score_sequence_epitopes
rename score_sequence_epitopes to score_all_epitopes
renaming functions
update installation instructions
adds the match_epitopes function
refactor match_epitopes by splitting out score_all_epitopes
rename alignment_successful to epitope_found
Merge branch 'feature/scoring-with-proper-data-structures' into develop
update NEWS file