R/fun_load_bam.R

In MANO-B/MicroSEC: Sequence Error Filter for Formalin-Fixed and Paraffin-Embedded Samples

#' BAM file loader
#'
#' This function attempts to load the BAM file.
#'
#' @param bam_file Path of the BAM file.
#' @return df_bam
#' @importFrom Rsamtools BamFile
#' @importFrom Rsamtools scanBam
#' @importFrom Biostrings DNAStringSet
#' @examples
#' fun_load_bam(
#'   system.file("extdata", "sample.bam", package = "MicroSEC")
#' )
#' @export
fun_load_bam <- function(bam_file) {
  file_bam <- BamFile(bam_file)
  df_bam <- scanBam(file_bam)[[1]]
  df_bam <- df_bam[c("qname", "rname", "strand", "cigar",
                      "seq", "qual", "pos", "isize")]
  df_bam$strand <- as.character(df_bam$strand)
  df_bam$strand[which(is.na(df_bam$strand))] <- "NA"
  df_bam$pos[which(is.na(df_bam$pos))] <- 0
  df_bam$cigar[which(is.na(df_bam$cigar))] <- "150H"
  df_bam$isize[which(is.na(df_bam$isize))] <- 10000
  return(df_bam)
}

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