/usr/lib/R/site-library/Rsamtools/unitTests/test_RsamtoolsFile.R is in r-bioc-rsamtools 1.30.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 | 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
}
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