inst/unitTests/test_asBam.R

In Rsamtools: Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

test_asBam <- function()
{
    src <- system.file("unitTests", "cases", package="Rsamtools")
    fl <- file.path(src, "ex1.sam.gz")
    ofl <- tempfile()
    on.exit(unlink(ofl))
    bam <- asBam(fl, ofl)
    checkIdentical(bam, paste(ofl, "bam", sep="."))

    which <- GRanges("seq2", IRanges(1000, 2000))
    res <- scanBam(bam, param=ScanBamParam(which=which, what="rname"))[[1]]
    checkIdentical(642L, length(res[["rname"]]))
    checkIdentical("seq2", as.character(unique(res[["rname"]])))

    checkException(asBam(fl, ofl), silent=TRUE)

    ## asBam destination construction
    tmp_sam <- file.path(tempdir(), "ex1.sam.gz")
    file.copy(fl, tmp_sam)
    tmp_bam <- asBam(tmp_sam)
    tmp_bai <- paste0(tmp_bam, ".bai")
    checkTrue(file.exists(tmp_sam))
    checkTrue(file.exists(tmp_bai))
    file.remove(tmp_bam)
    file.remove(tmp_bai)
    file.remove(tmp_sam)
}