R/bam2DNAStringSet.R

In GuangchuangYu/seqmagick: Sequence Manipulation Utilities

##' convert bam file to aligned fasta file
##'
##'
##' @title bam2DNAStringSet
##' @param bamfile bam file
##' @param refseq refseq, DNAStringSet object
##' @return DNAStringSet object
##' @export
##' @author Guangchuang Yu
bam2DNAStringSet <- function(bamfile, refseq) {
    w <- width(refseq)
    if (length(refseq) > 1) {
        stop("please use bam2DNAStringSet2...")
    }
    pm <- GenomicRanges::GRanges(names(refseq), IRanges::IRanges(1, w))

    GenomicAlignments::stackStringsFromBam(Rsamtools::BamFile(bamfile),
                                          param=pm,
                                          Lpadding.letter='-',
                                          Rpadding.letter='-',
                                          use.names=TRUE)

}

##' convert bam file to aligned fasta file
##'
##'
##' @title bam2DNAStringSet2
##' @param bamfile bam file
##' @param refseq refseq, DNAStringSet object
##' @return DNAStringSet object
##' @export
##' @author Guangchuang Yu
bam2DNAStringSet2 <- function(bamfile, refseq) {
    lapply(seq_along(refseq), function(i) {
        bam2DNAStringSet(bamfile, refseq[i])
    })
}