match_epitopes: Computes similarities between certain epitopes and sequences
In philliplab/EpitopeMatcher: Epitope Matcher

A query alignment and a file specifying which hla_genotypes should be checked for different patients are first compared to construct a list of scores that must be computed. This list is then passed to the score_all_epitopes function which computes the scores. The results and error logs are then returned as output.

match_epitopes(
  query_alignment,
  patient_hla,
  lanl_hla_data,
  range_expansion = 5,
  update_progress_bar = NULL,
  substitutionMatrix = "BLOSUM50"
)

`query_alignment`	The query alignment
`patient_hla`	The data.frame (of class Patient_HLA) that contain lists all the HLA genotypes each patient has.
`lanl_hla_data`	The data.frame (of class LANL_HLA_data) that contains the descriptions of the different HLA genotypes
`range_expansion`	After the epitope is found in the reference seqeuence, search in each of the query sequences for the same epitope, but expand the range with this number of amino acids
`update_progress_bar`	A closure passed in from a reactive shiny expression that allows a progress bar to be updated when using the shiny web ui.
`substitutionMatrix`	substitution matrix representing the fixed substitution scores for an alignment. It cannot be used in conjunction with ‘patternQuality’ and ‘subjectQuality’ arguments.