R/bt.bamtofastq.R

In PhanstielLab/bedtoolsr: Bedtools Wrapper

#' Convert BAM alignments to FASTQ files. 
#' 
#' @param i <BAM>
#' @param fq <FQ>
#' @param fq2 FASTQ for second end.  Used if BAM contains paired-end data.
#'   BAM should be sorted by query name is creating paired FASTQ.
#' 
#' @param tags Create FASTQ based on the mate info
#'   in the BAM R2 and Q2 tags.
#' 
#' @param output Output filepath instead of returning output in R.
#' 
bt.bamtofastq <- function(i, fq, fq2 = NULL, tags = NULL, output = NULL)
{
	# Required Inputs
	i <- establishPaths(input=i, name="i", allowRobjects=FALSE)
	fq <- establishPaths(input=fq, name="fq", allowRobjects=FALSE)

	options <- ""

	# Options
	options <- createOptions(names=c("fq2", "tags"), values=list(fq2, tags))

	# establish output file 
	tempfile <- tempfile("bedtoolsr", fileext=".txt")
	tempfile <- gsub("\\", "/", tempfile, fixed=TRUE)
	bedtools.path <- getOption("bedtools.path")
	if(!is.null(bedtools.path)) bedtools.path <- paste0(bedtools.path, "/")
	cmd <- paste0(bedtools.path, "bedtools bamtofastq ", options, " -i ", i[[1]], " -fq ", fq[[1]], " > ", tempfile)
	if(.Platform$OS.type == "windows") shell(cmd) else system(cmd)
	if(!is.null(output)) {
		if(file.info(tempfile)$size > 0)
			file.copy(tempfile, output)
	} else {
		if(file.info(tempfile)$size > 0)
			results <- utils::read.table(tempfile, header=FALSE, sep="\t", quote='')
		else
			results <- data.frame()
	}

	# Delete temp files
	temp.files <- c(tempfile, i[[2]], fq[[2]])
	deleteTempFiles(temp.files)

	if(is.null(output))
		return(results)
}