/**
* The main method to check the mappabilities of the given read file names.
*
* @param btOutputFileName BowTie output file name
* @param fileTileLength Tile length
* @param outputFileName Output file name which the result will be saved into
* @param readFileName Reads file name
* @param chr1FileLines chromosome file name
* @throws IOException
*/
public void checkMappability(
String btOutputFileName,
int fileTileLength,
String outputFileName,
String readFileName,
List<String> chr1FileLines)
throws IOException {
System.out.println("Creating [" + outputFileName + "]...");
StopWatch stopWatch = new StopWatch();
stopWatch.start();
System.out.println("Reading [" + btOutputFileName + "]");
List<String> btOutputFileLines = FileUtils.getInstance().readFile(btOutputFileName);
System.out.println("Done reading [" + btOutputFileName + "]");
System.out.println("Reading [" + readFileName + "]");
List<String> readFileLines = FileUtils.getInstance().readFile(readFileName);
System.out.println("Done reading [" + readFileName + "]");
Map<String, Mappability> result =
createMappability(btOutputFileLines, readFileLines, chr1FileLines);
FileUtils.getInstance().writeFile(result, outputFileName, fileTileLength);
stopWatch.stop();
System.out.println(
"["
+ outputFileName
+ "] is done in ["
+ TimeUnit.MILLISECONDS.convert(stopWatch.getNanoTime(), TimeUnit.NANOSECONDS)
+ "] MILLISECONDS");
}
@Test
public void testTimeFor_FiftyThousand() {
Choir testChoir = new Choir();
Address choirAddress = new Address();
choirAddress.setCity("Omaha");
choirAddress.setState("NE");
testChoir.setChoirName("Omaha Children's Choir");
testChoir.setAddress(choirAddress);
StopWatch timer = new StopWatch();
String result = null;
timer.start();
for (int i = 0; i < 50000; i++) {
result = TestUtility.post(timeTestBase + "names", testChoir.toJson(false));
}
timer.stop();
assertNotNull(result);
say("\n\nTime taken = " + timer.getTime());
say("Time taken (nano) = " + timer.getNanoTime());
}