public void testOk1() throws Exception {
final File map = File.createTempFile("testok1", "coverageParams");
try {
FileUtils.stringToFile(SharedSamConstants.SAM9, map);
assertTrue(map.isFile());
final CoverageParams ccp;
final File outFile = new File(mDir, TEST_OUTPUT);
assertTrue(outFile.mkdir());
final List<File> mapped = new ArrayList<>();
mapped.add(map);
ccp = getCoverageParams(outFile, mapped);
assertFalse(ccp.errorRates());
assertNotNull(ccp.filterParams());
assertEquals(1, ccp.ioThreads());
assertEquals(3, ccp.minimumCoverageForBreadth());
final String ccs = ccp.toString();
// System.err.println(ccs);
TestUtils.containsAll(ccs, BASE_PARAMS);
ccp.close();
} finally {
assertTrue(map.delete());
}
}
/**
* Creates test serialized form for current serial version
*
* @param args directory in which test data should be saved
* @throws IOException it happens
*/
public static void main(String[] args) throws IOException {
final File dir = new File(args[0]);
final File output =
new File(dir, "testZeroRVersion_" + ZeroRBuilder.ZeroRClassifier.SERIAL_VERSION);
try (DataOutputStream dos = new DataOutputStream(FileUtils.createOutputStream(output))) {
createTestZeroR().save(dos, null);
}
}
/**
* Creates a GZIP file copying the string <code>content</code> to it.
*
* @param content a <code>String</code>
* @param file a non-null <code>File</code> to write to
* @return a <code>File</code> containing the string content (same as <code>file</code>).
* @exception IOException if an error occurs.
* @exception NullPointerException if the content is null
*/
public static File stringToGzFile(final String content, final File file) throws IOException {
if (content == null) {
throw new NullPointerException("null string given");
}
try (OutputStream out = FileUtils.createOutputStream(file, true, false, true)) {
out.write(content.getBytes());
}
return file;
}
/**
* Gets the contents of the given resource as a string.
*
* @param resource name (classpath) of the resource.
* @return a String containing the contents of the stream
* @exception IOException if an error occurs.
*/
public static String resourceToString(final String resource) throws IOException {
final InputStream str = Resources.getResourceAsStream(resource);
if (str == null) {
throw new RuntimeException("Unable to find resource:" + resource);
}
final String res = FileUtils.streamToString(str);
str.close();
return res;
}
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 writeTempFile(File out) throws IOException {
final TempRecordWriter trw =
new TempRecordWriterNio(FileUtils.createOutputStream(out, true, false));
try {
final BinaryTempFileRecord bar = new BinaryTempFileRecord(false, false, false, false);
// + "3\t16\t0\t28734\t30\t35M\t=\t0\t0\tACCT\t<<<<\tAS:i:0\tNM:i:1\n"
bar.setAlignmentScore(0);
bar.setCigarString("35M".getBytes());
bar.setMdString(new byte[0]);
bar.setNumberMismatches(0);
bar.setReadId(3);
bar.setReferenceId(0);
bar.setSamFlags((byte) 16);
bar.setStartPosition(28734);
trw.writeRecord(bar);
// + "1\t0\t0\t28833\t20\t4M5M\t=\t0\t0\tAGCT\t<<<<\tNM:i:1\tAS:i:3\n"
bar.setAlignmentScore(3);
bar.setCigarString("4M5M".getBytes());
bar.setNumberMismatches(1);
bar.setReadId(1);
bar.setSamFlags((byte) 0);
bar.setStartPosition(28833);
trw.writeRecord(bar);
// + "3\t16\t0\t28834\t30\t35M\t=\t0\t0\tACCT\t<<<<\tMF:i:18\tAS:i:1\n"
bar.setAlignmentScore(1);
bar.setCigarString("35M".getBytes());
bar.setNumberMismatches(0);
bar.setReadId(3);
bar.setSamFlags((byte) 16);
bar.setStartPosition(28834);
trw.writeRecord(bar);
// + "20\t0\t0\t28934\t30\t35M\t=\t0\t0\tACCT\t<<<<\tMF:i:18\tAS:i:4\n"
bar.setAlignmentScore(4);
bar.setReadId(20);
bar.setSamFlags((byte) 0);
bar.setStartPosition(28934);
trw.writeRecord(bar);
// + "66\t0\t0\t28934\t30\t35M\t=\t0\t0\tACCT\t<<<<\tMF:i:18\tAS:i:4\n";
bar.setReadId(66);
trw.writeRecord(bar);
bar.setSentinelRecord();
trw.writeRecord(bar);
} finally {
trw.close();
}
}
/**
* Read the contents of a reader and turn it into a string.
*
* @param fileReader where to get the string.
* @return the contents of the file.
* @throws IOException if an I/O error occurs.
*/
public static String readerToString(final Reader fileReader) throws IOException {
final StringBuilder sb = new StringBuilder();
try (BufferedReader br = new BufferedReader(fileReader)) {
final char[] buffer = FileUtils.makeBuffer();
final int eof = -1;
for (int len = br.read(buffer); len > eof; len = br.read(buffer)) {
for (int i = 0; i < len; i++) {
sb.append(buffer[i]);
}
}
}
return sb.toString();
}
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 testDefaultParams() throws IOException {
final File outDir = new File(mDir, "output");
final CoverageParams cp =
CoverageParams.builder()
.outputParams(new OutputParams(outDir, false, false))
.genome(makeGenome())
.create();
assertFalse(cp.tsvOutput());
assertTrue(cp.bedOutput());
assertFalse(cp.blockCompressed());
assertFalse(cp.onlyMappedRegions());
assertFalse(cp.errorRates());
assertEquals(0, cp.smoothing());
assertEquals(1, cp.minimumCoverageForBreadth());
assertEquals(outDir, cp.directory());
assertEquals(cp.outFile(), cp.file("coverage.bed"));
assertEquals("coverage.bed", cp.outFile().getName());
final OutputStream out = cp.bedStream();
out.write("test".getBytes());
out.close();
assertTrue(cp.outFile().exists());
assertEquals("test", FileUtils.fileToString(cp.outFile()));
}
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);
}
/**
* Constructor
*
* @param outputFile compressed file to write
* @param bits number of bits used per entry
* @throws IOException If an IO error occurs
*/
public FileBitwiseOutputStream(File outputFile, int bits) throws IOException {
mStream = new DataOutputStream(FileUtils.createOutputStream(outputFile, false));
mBits = bits;
// mRawBuffer = new byte[1024 * 1024];
mBuffer = new long[1024 * 1024 / 8];
}
private void compareToFile(final String str, final File f) throws IOException {
final String main = FileUtils.fileToString(f);
assertEquals(str, main);
}