Make utility functions to simplify repeated code

[karissawhiting]

• [ ] Check reference genome

• [ ] Perhaps for checking variant class allowed levels?

  
  # Clean Variant Class -----------------------------------------------------
  
  levels_in_data <- names(table(sv$structural_variant_type))
  
  allowed_chr_levels <- c("DELETION",
                        "TRANSLOCATION",
                        "DUPLICATION",
                        "INSERTION",
                        "INVERSION",
                        "FUSION",
                        "UNKNOWN")
  
  all_allowed <- c(allowed_chr_levels, names(allowed_chr_levels))
  not_allowed <- levels_in_data[!levels_in_data %in% all_allowed]
  
  if(length(not_allowed) > 0) {
  cli::cli_abort(c("Unknown values in {.field variant_class} field: {.val {not_allowed}}",
                   "Must be one of the following: {.val {all_allowed}}"))
  }

- [ ] consequence map function/checking should be separated out