adapt values for TCR

[rodrigarc]

Testing with a TCR dataset using this command

quality_report(
  folder_sequences = "test/sanger/", #use full path
  output_dir = "results/",  #use full path
  folder_path_fcs = "test/fcs/", #use full path
  compensation = FALSE,
  probe1 = "FSC.A", 
  probe2 = "SSC.A",
  posvalue_probe1 = 0, 
  posvalue_probe2 = 0,
  raw_length = 200, trim_start = 20, trim_finish = 250, 
  plot_chromatogram = TRUE
)

• Use TCR data to assign thresholds for TCR. Or create a warning for the user to double-check the thresholds for their dataset.

• Fix the error when a sanger file is currently named "A1.ab1" instead of "A1-NNNN.ab1" or "A1_NNNN.ab1", it does not identify the "." as a separator and generates "A.ab11")

• The quality report should give an error if the sanger folder or fcs sequences files are not organized correctly with matching sequences.

• Give an error when the naming of the fcs file does not match the folder name of the plate.

• Print only one fasta file if it has only one plate, not 3. Right now it prints "combined_sequences.fasta", "ID.fasta", "sanger.fasta"

• If there is no specificity being assigned, do not use it for naming the sequences. So, if the specificity column is NA or empty, just leave the name of the sequence as it is, without pasting the specificity column.

• plot chromatograms should plot the entire chromatogram of all files when TRUE