R/samtoolsIndex.R

In dvera/gyro: gyro: Genomic utility wrappers in R

#' Index bam files
#'
#' \code{samtools.index} is a simple wrapper for \code{samtools index} for indexing position-sorted bam files.
#'
#' @param bamFiles A character vector of paths to bam files.
#' @param threads A positive integer specifying how many bams to process simultaneously.

samtoolsIndex <-
function( bamFiles , threads=getOption("threads",1L) ){

	cmdString <- paste("samtools index",bamFiles)

	res <- cmdRun(cmdString,threads)
        return(bamFiles)
}