Nothing
test.findTemplate <- function() {
checkTrue(file.exists(HTSeqGenie:::findTemplate("default-config.txt")), "findTemplate() finds template in package")
tfile <- "template_test_config.txt"
file(file.path(tempdir(), tfile), "w")
## make sure we can find files in absolute paths
abs.path <- file.path(tempdir(), tfile)
checkTrue(file.exists(HTSeqGenie:::findTemplate(abs.path)), "findTemplate() finds template in absolute path")
## test finding in current dir
cwd <- getwd()
setwd(tempdir())
checkTrue(file.exists(HTSeqGenie:::findTemplate(tfile)), "findTemplate() finds template in current dir")
setwd(cwd)
Sys.setenv(HTSEQGENIE_CONFIG=tempdir())
checkTrue(file.exists(HTSeqGenie:::findTemplate(tfile)), "findTemplate() finds template from HTSEQGENIE_CONFIG env")
## create env with multiple values
Sys.setenv(HTSEQGENIE_CONFIG=paste(c("bla",tempdir()), collapse=":"))
checkTrue(file.exists(HTSeqGenie:::findTemplate(tfile)), "findTemplate() finds template from HTSEQGENIE_CONFIG env with multiple entries")
## clean up
unlink(file.path(tempdir(), tfile))
}
test.checkConfig.analyzeVariants <- function() {
setupTestFramework(config.filename="test-data/test_config.txt",
config.update=list(),
testname="test.checkConfig.analyzeVariants")
checkTrue(HTSeqGenie:::checkConfig.analyzeVariants(),
"checkConfig.analyzeVariants() passes valid config")
updateConfig(list(analyzeVariants.method = "bogus"))
checkException(HTSeqGenie:::checkConfig.analyzeVariants(),
"checkConfig.analyzeVariants() detects bogus method", silent=TRUE)
updateConfig(list(analyzeVariants.method = 'VariantTools',
analyzeVariants.callingFilters='nonRef, nonNRef'))
checkTrue(HTSeqGenie:::checkConfig.analyzeVariants(),
"checkConfig.analyzeVariants() checks callingFilter config")
updateConfig(list(analyzeVariants.callingFilters='nonRef, XRef'))
checkException(HTSeqGenie:::checkConfig.analyzeVariants(),
"checkConfig.analyzeVariants() detects filters not provided by VT",
silent=TRUE)
updateConfig(list(analyzeVariants.callingFilters=''))
checkTrue(HTSeqGenie:::checkConfig.analyzeVariants(),
"checkConfig.analyzeVariants() handles empty vector configs")
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.