Need to update documentation BatchMutationCalling

[massonix]

I installed the development branch, and noticed that some of the parameters have been updated in the function BatchMutationCalling but the documentation is not updated. This is the function in the tutorial

BatchMutationCalling(
  out  = path_out,
  barcodes.file.path = barcodes.file.path,
  wt.max.mismatch = 0,
  mut.max.mismatch = 0,
  keep.raw.reads = F,
  reverse.complement = T,
  testing = F,
  which.read = which.read,
  primer.sequence = primer.sequence,
  primed.max.mismatch = 3,
  wt.sequence = wt.sequence,
  mut.sequence = mut.sequence,
  mutation.start = mutation.start,
  mutation.end = mutation.end,
  soptions = list(output=paste0('GoT_','%x_%j.log'),mem = '10g', 'cpus-per-task' = 5) 
)

And this is the function in the documentation ?BatchMutationCalling:

BatchMutationCalling(out = "/path_to_filtered_fastqs/",
                  whitelist.file.path = "/path_to_whitelist/whitelist.txt",
                  wt.max.mismatch = 0,
                  mut.max.mismatch = 0,
                  keep.raw.reads = F,
                  ncores = 1,
                  reverse.complement = T,
                  testing = F,
                  which.read = "R1",
                  atac.barcodes = T,
                  primer.sequence = "CCTCATCATCCTCCTTGTC",
                  primed.max.mismatch = 3,
                  atac.barcodes.file.path = "/path_to_singlecell.csv",
                  wt.sequence =  "CGG",
                  mut.sequence = "CAG",
                  mutation.start = 31,
                  mutation.end = 34,
                  soptions = list(mem = '20g', 'cpus-per-task' = 10))

I think this applies to the whitelist.file.path / barcodes.file.path and atac.barcodes.file.path. Thanks for looking into it:)!