private ReaderParams makeGenome() throws IOException {
final File subjectsDir = FileUtils.createTempDir("test", "coverageparams", mDir);
ReaderTestUtils.getReaderDNA(">t\nacgt", subjectsDir, null).close();
return SequenceParams.builder()
.directory(subjectsDir)
.mode(SequenceMode.UNIDIRECTIONAL)
.create()
.readerParams();
}
public void testFencePost() throws IOException {
final File dir = FileUtils.createTempDir("cmsrt", "fencepost");
try {
randomSDF(dir, 256, 8200, 2L * 1024 * 1024);
final CompressedMemorySequencesReader reader =
(CompressedMemorySequencesReader)
CompressedMemorySequencesReader.createSequencesReader(
dir, true, false, LongRange.NONE);
assertTrue(reader.checkChecksums());
} finally {
assertTrue(FileHelper.deleteAll(dir));
}
}
public void testFilterUnmated() throws IOException {
final ByteArrayOutputStream log = new ByteArrayOutputStream();
try (PrintStream prLog = new PrintStream(log)) {
Diagnostic.setLogStream(prLog);
final int numReads = 100;
final MapQScoringReadBlocker blocker = new MapQScoringReadBlocker(numReads, 2);
blocker.increment(1, 3);
blocker.increment(20, 4);
blocker.increment(20, 4);
blocker.increment(20, 4); // read 20 is blocked for score=4
blocker.increment(3, 1);
blocker.increment(3, 1);
blocker.increment(3, 1); // read 3 is blocked for score=1
blocker.increment(3, 0);
blocker.increment(3, 0); // read 3 is just not blocked for score=0
final File dir = FileUtils.createTempDir("test", "unmatedSamFilter");
OutputStream out = null;
try {
final File in1 = File.createTempFile("sam", "_1.gz", dir);
writeTempFile(in1);
final File outFile = File.createTempFile("out", ".gz", dir);
out = new GZIPOutputStream(new FileOutputStream(outFile));
final StatusListener listener = new StatusListener(numReads);
final ReadBlocker freqBlocker = new ReadBlocker(numReads, 2);
freqBlocker.increment(66);
freqBlocker.increment(66);
final MockSequencesReader msr =
new MockSequencesReader(SequenceType.DNA) {
@Override
public PrereadType getPrereadType() {
return PrereadType.UNKNOWN;
}
@Override
public boolean hasQualityData() {
return true;
}
@Override
public int read(long sequenceIndex, byte[] dataOut) {
dataOut[0] = 1;
if (sequenceIndex == 3) {
dataOut[1] = 3;
dataOut[2] = 3;
} else {
dataOut[1] = 3;
dataOut[2] = 2;
}
dataOut[3] = 4;
return 4;
}
@Override
public int readQuality(final long sequenceIndex, final byte[] dest) {
dest[0] = dest[1] = dest[2] = dest[3] = '<' - 33;
return 4;
}
};
final SingleEndSamResultsFilter filter =
new SingleEndSamResultsFilter(blocker, freqBlocker, listener, 0, msr, null, false);
assertEquals("Alignment", filter.getName());
filter.filterConcat(makeHeader(), out, null, null, mTemplateReader, false, in1);
out.close();
final String contents = FileHelper.gzFileToString(outFile);
// System.out.println("contents=" + contents);
assertTrue(
TestUtils.sameLines(SAM_UNMATED_EXPECTED, TestUtils.stripSAMHeader(contents), false));
// now check that the listener has been updated correctly.
for (int read = 0; read < numReads; read++) {
final int expect;
switch (read) {
case 1:
case 3:
expect = ReadStatusTracker.UNMATED_FIRST;
break;
default:
expect = 0;
break;
}
assertEquals("readId=" + read, expect, listener.getStatus(read));
}
} finally {
if (out != null) {
out.close();
}
assertTrue(FileHelper.deleteAll(dir));
}
} finally {
Diagnostic.setLogStream();
}
final String logString = log.toString();
// System.err.println(logString);
TestUtils.containsAll(logString, "Alignment SAM filter outputs 2/5 records");
}
/**
* Creates an empty directory in the unit test temporary-file directory, automatically generating
* its name.
*
* @return an empty temporary directory
* @exception IOException if a file could not be created
*/
public static File createTempDirectory() throws IOException {
return FileUtils.createTempDir(PREFIX, SUFFIX);
}