Nothing
test.preprocessReads <- function() {
## setup test framework
setupTestFramework(config.filename="test-data/test_config.txt", testname="test.preprocessReads")
## test preprocessReads
summary_preprocess <- preprocessReads()
## checks
checkEqualsNumeric(summary_preprocess$total_reads, 26,
"preprocessReads() does not return the correct number of reads")
checkEquals(summary_preprocess$highqual_reads, 25,
"preprocessReads() does not return the correct number of highqual reads")
checkEqualsNumeric(summary_preprocess$adapter_contam, 1,
"preprocessReads() does not return the correct number of adapter contam")
checkEqualsNumeric(summary_preprocess$read_length, 75,
"preprocessReads() does not return the correct read length")
## Since rRNA contam check is currently disbaled this will be now 0 instead of 1
checkEquals(summary_preprocess$rRNA_contam_reads, 0,
"preprocessReads() does not return the correct number of rRNA contams")
}
test.preprocessReads_single_end <- function() {
## setup test framework
setupTestFramework(config.filename="test-data/test_config_single_end.txt",
config.update=list(detectAdapterContam.force_paired_end_adapter=TRUE),
testname="test.preprocessReads_single_end")
## test preprocessReads
summary_preprocess <- preprocessReads()
## checks
checkEqualsNumeric(summary_preprocess$total_reads, 26,
"preprocessReads() does not return the correct number of reads")
checkEquals(summary_preprocess$highqual_reads, 25,
"preprocessReads() does not return the correct number of highqual reads")
checkEqualsNumeric(summary_preprocess$adapter_contam, 1,
"preprocessReads() does not return the correct number of adapter contam")
checkEqualsNumeric(summary_preprocess$read_length, 75,
"preprocessReads() does not return the correct read length")
## Since rRNA contam check is currently disbaled this will be now 0 instead of 1
checkEquals(summary_preprocess$rRNA_contam_reads, 0,
"preprocessReads() does not return the correct number of rRNA contams")
}
test.preprocessReads.minichunks <- function() {
## setup test framework
config.update <- list(chunk_size=10, detectRRNA.do=FALSE)
setupTestFramework(config.filename="test-data/test_config.txt", config.update=config.update,
testname="test.preprocessReads.minichunks")
## test preprocessReads
summary_preprocess <- preprocessReads()
## checks
checkEqualsNumeric(summary_preprocess$total_reads, 26,
"preprocessReads() does not return the correct number of reads")
checkEquals(summary_preprocess$highqual_reads, 25,
"preprocessReads() does not return the correct number of highqual reads")
checkEqualsNumeric(summary_preprocess$adapter_contam, 1,
"preprocessReads() does not return the correct number of adapter contam")
checkEqualsNumeric(summary_preprocess$read_length, 75,
"preprocessReads() does not return the correct read length")
checkEquals(summary_preprocess$rRNA_contam_reads, 0,
"preprocessReads() does not return 0 rRNA contams (detectRRNA.do is disabled)")
}
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