library(immuneSIM)
library(Biostrings)

generate_repertoires <- function(number_of_sequences) {
  a_chain <- immuneSIM(
    number_of_seqs = number_of_sequences,
    species = "hs",
    receptor = "tr",
    chain = "a",
    verbose = TRUE
  )
  b_chain <- immuneSIM(
    number_of_seqs = number_of_sequences,
    species = "hs",
    receptor = "tr",
    chain = "b",
    verbose = TRUE
  )
  return(list("a_chain" = a_chain, "b_chain" = b_chain))
}

process_chain <- function(repertoire) {
  sequences <- as.character(repertoire$sequence)
  counts <- as.integer(repertoire$counts)
  reads <- Biostrings::DNAStringSet(rep(sequences, counts))
  names(reads) <- seq_len(length(reads))
  reverse_complement <- Biostrings::reverseComplement(reads)
  return(reverse_complement)
}

preprocess_data <- function(repertoires) {
  filtered_repertoires <- lapply(repertoires, process_chain)
  names(filtered_repertoires) <- names(repertoires)
  return(filtered_repertoires)
}


parse_cli_arguments <- function(args) {
  if (length(args) != 1) {
    stop("usage: repertoire.r <number of sequences>")
  }
  return(as.integer(args[1]))
}

args <- commandArgs(trailingOnly = TRUE)
number_of_sequences <- parse_cli_arguments(args)
sim_repertoire <- generate_repertoires(number_of_sequences)
processed_data <- preprocess_data(sim_repertoire)