/usr/lib/R/site-library/Rsamtools/unitTests/test_compression.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 | test_bgzip_openclose <- function()
{
## trying to determine that file handle has been cleaned up
checkIdentical(TRUE, dir.create(d <- tempfile()))
fin <- file.path(d, "in")
fout <- file.path(d, "out")
writeLines("123", con=fin)
bgzip(fin, fout)
checkIdentical(TRUE, file.remove(fin))
checkIdentical(TRUE, file.remove(fout))
checkIdentical(0L, unlink(d, recursive=TRUE))
}
test_razip_small_files <- function()
{
src <- system.file("extdata", "ce2dict1.fa", package="Rsamtools")
file.copy(src, dest <- tempfile())
checkIdentical(readLines(src), readLines(dest))
}
test_razip_gzcompressed <- function()
{
file.copy(system.file("extdata", "ce2dict1.fa", package="Rsamtools"),
src <- tempfile())
con <- gzfile(gzdest <- tempfile(), "wb")
writeLines(readLines(src), con, sep="\n")
close(con)
rzdest <- razip(gzdest)
checkIdentical(src, indexFa(src))
checkIdentical(gzdest, indexFa(gzdest))
checkIdentical(rzdest, indexFa(rzdest))
src <- scanFa(src, param=as(seqinfo(FaFile(rzdest)), "GRanges"))
rz <- scanFa(rzdest, param=as(seqinfo(FaFile(rzdest)), "GRanges"))
gz <- scanFa(rzdest, param=as(seqinfo(FaFile(rzdest)), "GRanges"))
checkIdentical(as.character(src), as.character(rz))
checkIdentical(as.character(src), as.character(gz))
}
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