inst/unitTests/test_RsamtoolsFile.R

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

test_RsamtoolsFile_constructor <- function() {
    fl <- system.file("extdata", "example.gtf.gz", package="Rsamtools")
    checkException(TabixFile(c(fl, fl)), silent=TRUE)

    checkTrue(validObject(tbx <- TabixFile(fl, character())))
    checkIdentical(character(0), index(tbx, asNA=FALSE))

    checkTrue(validObject(tbx <- TabixFile(fl, NA)))
    checkIdentical(character(0), index(tbx, asNA=FALSE))

    tbx <- TabixFile(fl)
    checkIdentical(tbx, TabixFile(tbx))
    checkTrue(validObject(TabixFile(tbx))) # idempotent
}

test_RsamtoolsFileList_constructor <- function() {
    fl <- system.file("extdata", "example.gtf.gz", package="Rsamtools")
    fls <- c(fl, fl)

    checkTrue(validObject(TabixFileList())) # 0-length

    checkTrue(validObject(tbx <- TabixFileList(fls)))
    checkIdentical(setNames(fls, basename(fls)), path(tbx))
    checkIdentical(setNames(paste(fls, "tbi", sep="."), basename(fls)),
                   index(tbx))

    checkTrue(validObject(tbx <- TabixFileList(fls, character())))
    checkIdentical(setNames(fls, basename(fls)), path(tbx))
    checkIdentical(setNames(rep(NA_character_, 2), basename(fls)),
                   index(tbx))
    
    checkTrue(validObject(tbx <- TabixFileList(fls, NA)))
    checkIdentical(setNames(fls, basename(fls)), path(tbx))
    checkIdentical(setNames(rep(NA_character_, 2), basename(fls)),
                   index(tbx))

    tbx <- TabixFile(fl)
    checkTrue(validObject(TabixFileList(tbx)))
    checkTrue(validObject(TabixFileList(tbx, tbx)))
    checkTrue(validObject(TabixFileList(list(tbx, tbx))))

    tbx <- TabixFileList(TabixFile(fl))
    checkIdentical(TabixFileList(tbx), tbx) # idempotent
}