Nothing
test.markDuplicates_w_outfile<- function(){
if (checkPicardJar('MarkDuplicates')){
tmp <- tempfile()
bam.file <- getPackageFile("test-data/test_picard_dups.bam")
markDuplicates(bam.file, tmp)
checkTrue(file.exists(tmp), 'markDuplicates() creates file')
reads <- scanBam(tmp, param=ScanBamParam(what=c("flag")))[[1]]
checkEqualsNumeric(sum(reads$flag > 1024), 2, "markDuplicates() finds one pair of dups.")
} else {
DEACTIVATED("Skipped markDuplicates() test")
}
}
test.markDuplicates <- function(){
## check without passing outfile
## copy test file to tmp dir so we don't write next to the original test file
if (checkPicardJar('MarkDuplicates')){
bam.file <- getPackageFile("test-data/test_picard_dups.bam")
tmpdir <- HTSeqGenie:::createTmpDir(prefix="test_markDuplicates")
inp <- file.path(tmpdir, "pic_md.bam")
file.copy(bam.file, inp)
outfile <- markDuplicates(inp)
checkTrue(file.exists(outfile), 'markDuplicates() creates file')
reads <- scanBam(outfile, param=ScanBamParam(what=c("flag")))[[1]]
checkEqualsNumeric(sum(reads$flag > 1024), 2, "markDuplicates finds one pair of dups.")
} else {
DEACTIVATED("Skipped markDuplicates() test")
}
}
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