library(Biostrings)
library(parallel)

construct_dataframe <- function(data) {
  vdj_string_set <- lapply(data, FUN = Biostrings::DNAStringSet)
  vdj_dataframe <- as.data.frame(vdj_string_set)
  vdj_dataframe$hvr_region <- paste(vdj_dataframe$v_sequence,
    vdj_dataframe$d_sequence, vdj_dataframe$j_sequence,
    sep = ""
  )
  return(vdj_dataframe)
}

parse_data <- function(files) {
  reversed_sequences <- Biostrings::readQualityScaledDNAStringSet(files[1])
  sequences <- Biostrings::reverseComplement(reversed_sequences)
  vdj_alignment <- read.csv(files[2])
  vdj_dataframe <- construct_dataframe(vdj_alignment)
  return(list(sequences, vdj_dataframe))
}

align_sequence <- function(sequence, vdj_segment) {
  return(Biostrings::pairwiseAlignment(
    pattern = sequence,
    subject = vdj_segment,
    type = "global-local",
    gapOpening = 1
  ))
}


perform_alignment <- function(sequences, vdj_segments) {
  sequence_alignment <- mcmapply(sequences,
    vdj_segments$hvr_region,
    FUN = align_sequence,
    mc.cores = 4
  )
  return(sequence_alignment)
}

input_files <- c("data/curesim_sequence.fastq", "data/vdj_alignment.csv")
data <- parse_data(input_files)
alignment <- perform_alignment(sequences = data[[1]], vdj_segments = data[[2]])
print(alignment)