Nothing
## full tophalf test with 3 chunks in parallel
test.alignReads <- function() {
## setup test framework
setupTestFramework(config.filename="test-data/test_config.txt",
config.update=list(chunk_size=10),
testname="test.alignReads")
preprocessReads()
alignReads()
## correct number of chunks
chunk_dirs <- getChunkDirs()
checkEqualsNumeric(length(chunk_dirs), 3,
"alignReads() produces the expected number of chunks")
## peek into at least one dir to see if it actually computed something
bam_files = dir(file.path(chunk_dirs[1], "bams"), pattern="*.bam$")
checkEqualsNumeric(length(bam_files), 19,
"alignReads() produces 19 bam files")
unlink(getConfig("save_dir"), recursive=TRUE)
}
test.alignReadsOneSingleEnd <- function() {
## setup test framework
setupTestFramework(config.filename="test-data/test_config_single_end.txt",
config.update=list(num_cores=1, prepend_str="test.alignReads",
alignReads.max_mismatches="0"),
testname="test.alignReadsOneSingleEnd")
HTSeqGenie:::alignReadsChunk(getPackageFile("test-data/unit_tests_1.fastq"))
bam_dir <- file.path(getConfig("save_dir"), "bams")
mapping_types= c('unpaired_uniq', 'unpaired_transloc',
'unpaired_mult', 'nomapping')
base <- paste(bam_dir,"test.alignReads", sep='/')
expected_files <- paste(base, mapping_types, "bam", sep=".")
checkTrue(all(file.exists(expected_files)),
"alignReads() creates all expected files for single ends")
expected_files <- paste(base, mapping_types, "bam.bai", sep=".")
checkTrue(all(file.exists(expected_files)),
"alignReads() creates all expected index files for single ends")
unlink(getConfig("save_dir"), recursive=TRUE)
}
test.alignReads.sparsechunks <- function() {
## setup framework, to generate sparse chunks (3 reads out of 26, using chunk_size=8)
save_dir <- setupTestFramework(config.filename="test-data/test_config.txt" ,
config.update=list(chunk_size=8, subsample_nbreads=2),
testname="test.alignReads.sparsechunks")
## run pipeline
preprocessReads()
## check results
summary_preprocess <- getNumericVectorDataFromFile(save_dir, "summary_preprocess")
checkEqualsNumeric(summary_preprocess["total_reads"], 2)
checkEqualsNumeric(sum(is.na(summary_preprocess)), 0, "no NAs were detected in summary_preprocess")
}
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