data-raw/old-code/oldCreateBAMSliceFileSamtools.R

In steverozen/DBSverify: Analyze Next Generation Sequencing Data to Verify Somatic Double-BaseSubstituion (DBS) Calls

#' Create a BAM slice as a SAM file using the samtools executable.
#'
#' @param BAM.name The input BAM file name.
#'
#' @param CHROM The chromosome from which to slice.
#'
#' @param POS The position in \code{CHROM} from which to slice.
#'
#' @param padding The number of base pairs on each side of \code{POS} to take.
#'
#' @param save.file.path Where to save the sam file.
#'
#' @return The path of the SAM file that contains the BAM slice.
#'
#' @keywords internal

xCreateBAMSliceFileSamtools <-
  function(BAM.name, CHROM, POS, padding = 10, save.file.path) {
    POS <- as.numeric(POS) # In case it was a character string.
    BAM.coord <- paste0(CHROM, ":", POS - padding, "-", POS + padding)
    if (is.null(save.file.path)) {
      save.file.path <- tempfile(pattern = "")
    }
    status <- system2("samtools",
                      c("view", "-h", BAM.name, BAM.coord),
                      stdout = save.file.path,
                      wait = TRUE)
    if (status == 127) stop("samtools: command not found")
    if (status != 0) stop("samtools returned error status ", status)

    return(save.file.path)
  }