@Override
public void testEquals() throws IOException {
final File dir = FileHelper.createTempDirectory(mDir);
final File otherDir = FileHelper.createTempDirectory(mDir);
ReaderTestUtils.getReaderDNAFastq("", dir, false).close();
ReaderTestUtils.getReaderDNAFastq("", otherDir, false).close();
final CompressedMemorySequencesReader cmsr =
new CompressedMemorySequencesReader(
dir, new IndexFile(dir), 5, true, false, new LongRange(0, 0));
final CompressedMemorySequencesReader other =
new CompressedMemorySequencesReader(
otherDir, new IndexFile(dir), 5, true, false, new LongRange(0, 0));
assertTrue(cmsr.equals(cmsr));
assertFalse(cmsr.equals(null));
assertFalse(cmsr.equals(other));
assertFalse(cmsr.equals("FDSA"));
}
@Override
public void setUp() throws IOException {
Diagnostic.setLogStream();
mDir = FileHelper.createTempDirectory();
}
public void testValidator() throws IOException {
Diagnostic.setLogStream();
final MemoryPrintStream err = new MemoryPrintStream();
final CliDiagnosticListener listener = new CliDiagnosticListener(err.printStream());
Diagnostic.addListener(listener);
final File tempDir = FileHelper.createTempDirectory();
try {
final CFlags flags =
new CFlags("PhyloTest", TestUtils.getNullPrintStream(), err.printStream());
SimilarityCli.initFlags(flags);
checkErrorMessage(
flags,
new String[] {"-o", "blah", "-I", "ba", "-i", "humbug"},
err,
"Only set one of --input or --input-list-file");
checkErrorMessage(
flags,
new String[] {"-o", "blah", "-i", "humbug"},
err,
"The specified SDF, \"humbug\", does not exist.");
final File fakePaired = new File(tempDir, "fakePaired");
assertTrue(fakePaired.mkdir());
final File left = new File(fakePaired, "left");
assertTrue(left.mkdir());
assertTrue(new File(fakePaired, "right").mkdir());
checkErrorMessage(
flags,
new String[] {"-o", "blah", "-i", fakePaired.getPath()},
err,
"The specified SDF, \"" + fakePaired.getPath() + "\", is a paired end SDF.");
checkErrorMessage(
flags, new String[] {"-o", "blah"}, err, "Must set one of --input or --input-list-file");
checkErrorMessage(
flags,
new String[] {"-o", "blah", "-I", "ba"},
err,
"The specified list file, \"ba\", does not exist.");
checkErrorMessage(
flags,
new String[] {"-o", "blah", "-I", fakePaired.getPath()},
err,
"The specified list file,",
"\"" + fakePaired.getPath() + "\",",
"directory.");
final File fakeList = new File(tempDir, "fakeList.txt");
assertTrue(fakeList.createNewFile());
checkErrorMessage(
flags,
new String[] {"-o", fakePaired.getPath(), "-I", fakeList.getPath()},
err,
"The directory",
"\"" + fakePaired.getPath() + "\"",
"already exists.");
checkErrorMessage(
flags,
new String[] {"-o", "blah", "-I", fakeList.getPath(), "-w", "-1"},
err,
"The specified flag \"--word\" has invalid value \"-1\". It should be greater than or equal to \"1\".");
checkErrorMessage(
flags,
new String[] {"-o", "blah", "-I", fakeList.getPath(), "-w", "0"},
err,
"The specified flag \"--word\" has invalid value \"0\". It should be greater than or equal to \"1\".");
checkErrorMessage(
flags,
new String[] {"-o", "blah", "-I", fakeList.getPath(), "-w", "33"},
err,
"The specified flag \"--word\" has invalid value \"33\". It should be less than or equal to \"32\".");
checkErrorMessage(
flags,
new String[] {"-o", "blah", "-I", fakeList.getPath(), "--max-reads", "0"},
err,
"The --max-reads must be greater than 0");
checkErrorMessage(
flags,
new String[] {"-o", "blah", "-I", fakeList.getPath(), "-w", "20", "-s", "20"},
err);
checkErrorMessage(
flags,
new String[] {"-o", "blah", "-i", left.getPath(), "--max-reads", "1"},
err,
"Only set --max-reads when using --input-list-file");
checkErrorMessage(flags, new String[] {"-o", "blah", "-i", left.getPath()}, err);
} finally {
Diagnostic.removeListener(listener);
err.close();
assertTrue(FileHelper.deleteAll(tempDir));
}
}