Java LoggingUtils类代码示例

import org.broadinstitute.hellbender.utils.LoggingUtils; //导入依赖的package包/类
@DataProvider(name = "biasCorrection")
public Object[][] dataBiasCorrection() {
    LoggingUtils.setLoggingLevel(Log.LogLevel.INFO);
    final AllelicCountCollection sampleNormal = new AllelicCountCollection(SAMPLE_NORMAL_FILE);
    final AllelicCountCollection sampleWithBadSNPs = new AllelicCountCollection(SAMPLE_WITH_BAD_SNPS_FILE);
    final AllelicCountCollection sampleWithEvent = new AllelicCountCollection(SAMPLE_WITH_EVENT_FILE);

    final AllelicPanelOfNormals allelicPoNNormal = new AllelicPanelOfNormals(new AllelicCountCollection(ALLELIC_PON_NORMAL_COUNTS_FILE));
    final AllelicPanelOfNormals allelicPoNWithBadSNPs = new AllelicPanelOfNormals(new AllelicCountCollection(ALLELIC_PON_WITH_BAD_SNPS_COUNTS_FILE));

    final double minorFractionExpectedInMiddleSegmentNormal = 0.5;
    final double minorFractionExpectedInMiddleSegmentWithBadSNPsAndNormalPoN = 0.4;
    final double minorFractionExpectedInMiddleSegmentWithEvent = 0.33;

    return new Object[][]{
            {sampleNormal, allelicPoNNormal, minorFractionExpectedInMiddleSegmentNormal},
            {sampleWithBadSNPs, allelicPoNNormal, minorFractionExpectedInMiddleSegmentWithBadSNPsAndNormalPoN},
            {sampleWithEvent, allelicPoNNormal, minorFractionExpectedInMiddleSegmentWithEvent},
            {sampleWithBadSNPs, allelicPoNWithBadSNPs, minorFractionExpectedInMiddleSegmentNormal}
    };
}
 

import org.broadinstitute.hellbender.utils.LoggingUtils; //导入依赖的package包/类
@Test
public void testPoNHyperparameterInitialization() {
    LoggingUtils.setLoggingLevel(Log.LogLevel.INFO);
    final AllelicPanelOfNormals allelicPoN = new AllelicPanelOfNormals(new AllelicCountCollection(ALLELIC_PON_NORMAL_COUNTS_FILE));

    final SimpleInterval firstSite = new SimpleInterval("1", 1, 1);
    final SimpleInterval siteNotInPoN = new SimpleInterval("2", 1, 1);  //all sites in PoN are from chr1

    // test initialization of hyperparameters for first site in PoN (a = 1218, r = 1317)
    final double alphaAtFirstSite = allelicPoN.getAlpha(firstSite);
    final double betaAtFirstSite = allelicPoN.getBeta(firstSite);

    Assert.assertEquals(alphaAtFirstSite, ALPHA_EXPECTED_AT_FIRST_SITE, DELTA);
    Assert.assertEquals(betaAtFirstSite, BETA_EXPECTED_AT_FIRST_SITE, DELTA);

    // test initialization of MLE hyperparameters (which are default values for sites not in PoN)
    final double alphaNotInPoN = allelicPoN.getAlpha(siteNotInPoN);
    final double betaNotInPoN = allelicPoN.getBeta(siteNotInPoN);
    final double meanBias = allelicPoN.getGlobalMeanBias();
    final double biasVariance = allelicPoN.getGlobalBiasVariance();

    Assert.assertEquals(alphaNotInPoN, MLE_ALPHA_EXPECTED, DELTA);
    Assert.assertEquals(betaNotInPoN, MLE_BETA_EXPECTED, DELTA);
    Assert.assertEquals(meanBias, MLE_MEAN_BIAS_EXPECTED, DELTA);
    Assert.assertEquals(biasVariance, MLE_BIAS_VARIANCE_EXPECTED, DELTA);
}
 

import org.broadinstitute.hellbender.utils.LoggingUtils; //导入依赖的package包/类
@Test(singleThreaded = true)
public void testPrintStackTrace() throws Exception {
    try (final ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
            final PrintStream printStream = new PrintStream(outputStream)) {
        // set the main class with the custom exception output
        final Main main = new Main();
        main.exceptionOutput = printStream;

        // set to debug mode an try to print the stack-trace
        LoggingUtils.setLoggingLevel(Log.LogLevel.DEBUG);
        main.printStackTrace(new RuntimeException());
        // assert non-empty stack-trace message
        Assert.assertFalse(main.exceptionOutput.toString().isEmpty());
    } finally {
        // set back to normal verbosity
        setTestVerbosity();
    }
}
 

import org.broadinstitute.hellbender.utils.LoggingUtils; //导入依赖的package包/类
/**
 * Logs all the parameters in the given {@link Config} object at the given {@link Log.LogLevel}
 * @param config A {@link Config} object from which to log all parameters and values.
 * @param logLevel The log {@link htsjdk.samtools.util.Log.LogLevel} at which to log the data in {@code config}
 * @param <T> any {@link Config} type to use to log all configuration information.
 */
public static <T extends Config> void logConfigFields(final T config, final Log.LogLevel logLevel) {

    Utils.nonNull(config);
    Utils.nonNull(logLevel);

    final Level level = LoggingUtils.levelToLog4jLevel(logLevel);

    // Only continue in this method here if we would log the given level:
    if ( !logger.isEnabled(level) ) {
        return;
    }

    logger.log(level, "Configuration file values: ");
    for ( final Map.Entry<String, Object> entry : getConfigMap(config, false).entrySet() ) {
        logger.log(level, "\t" + entry.getKey() + " = " + entry.getValue());
    }
}
 

import org.broadinstitute.hellbender.utils.LoggingUtils; //导入依赖的package包/类
@Test(dataProvider = "dataCreate")
public void testCreate(final double siteFrequencyThreshold, final AllelicPanelOfNormals expected) {
    LoggingUtils.setLoggingLevel(Log.LogLevel.INFO);
    final AllelicPanelOfNormalsCreator allelicPoNCreator = new AllelicPanelOfNormalsCreator(PULLDOWN_FILES);
    final AllelicPanelOfNormals result = allelicPoNCreator.create(siteFrequencyThreshold);
    AllelicPoNTestUtils.assertAllelicPoNsEqual(result, expected);
}
 

import org.broadinstitute.hellbender.utils.LoggingUtils; //导入依赖的package包/类
@Test
void addTest() {
    LoggingUtils.setLoggingLevel(Log.LogLevel.DEBUG);
    final LongBloomFilter bloomFilter = new LongBloomFilter(testVals.length, FPP);
    for (final long val : testVals) {
        bloomFilter.add(val);
    }
    Assert.assertTrue(bloomFilter.containsAll(testVals));
}
 

import org.broadinstitute.hellbender.utils.LoggingUtils; //导入依赖的package包/类
@BeforeSuite @Override
public void setTestVerbosity() {
    LoggingUtils.setLoggingLevel(Log.LogLevel.INFO);
}
 

import org.broadinstitute.hellbender.utils.LoggingUtils; //导入依赖的package包/类
@BeforeTest
private void doBeforeTest() {
    LoggingUtils.setLoggingLevel(Log.LogLevel.INFO);
}
 

import org.broadinstitute.hellbender.utils.LoggingUtils; //导入依赖的package包/类
/** All the tests will have only the error verbosity. */
@BeforeSuite
public void setTestVerbosity() {
    LoggingUtils.setLoggingLevel(Log.LogLevel.ERROR);
}
 

import org.broadinstitute.hellbender.utils.LoggingUtils; //导入依赖的package包/类
@BeforeSuite
public void setTestVerbosity(){
    LoggingUtils.setLoggingLevel(Log.LogLevel.WARNING);
}
 

import org.broadinstitute.hellbender.utils.LoggingUtils; //导入依赖的package包/类
public Object instanceMainPostParseArgs() {
    // Provide one temp directory if the caller didn't
    if (this.TMP_DIR == null) this.TMP_DIR = new ArrayList<>();
    if (this.TMP_DIR.isEmpty()) TMP_DIR.add(IOUtil.getDefaultTmpDir());

    // Build the default headers
    final ZonedDateTime startDateTime = ZonedDateTime.now();
    this.defaultHeaders.add(new StringHeader(commandLine));
    this.defaultHeaders.add(new StringHeader("Started on: " + Utils.getDateTimeForDisplay(startDateTime)));

    LoggingUtils.setLoggingLevel(VERBOSITY);  // propagate the VERBOSITY level to logging frameworks

    for (final File f : TMP_DIR) {
        // Intentionally not checking the return values, because it may be that the program does not
        // need a tmp_dir. If this fails, the problem will be discovered downstream.
        if (!f.exists()) f.mkdirs();
        f.setReadable(true, false);
        f.setWritable(true, false);
        System.setProperty("java.io.tmpdir", f.getAbsolutePath()); // in loop so that last one takes effect
    }

    //Set defaults (note: setting them here means they are not controllable by the user)
    if (! useJdkDeflater) {
        BlockCompressedOutputStream.setDefaultDeflaterFactory(new IntelDeflaterFactory());
    }
    if (! useJdkInflater) {
        BlockGunzipper.setDefaultInflaterFactory(new IntelInflaterFactory());
    }

    BucketUtils.setGlobalNIODefaultOptions(NIO_MAX_REOPENS);

    if (!QUIET) {
        printStartupMessage(startDateTime);
    }

    try {
        return runTool();
    } finally {
        // Emit the time even if program throws
        if (!QUIET) {
            final ZonedDateTime endDateTime = ZonedDateTime.now();
            final double elapsedMinutes = (Duration.between(startDateTime, endDateTime).toMillis()) / (1000d * 60d);
            final String elapsedString  = new DecimalFormat("#,##0.00").format(elapsedMinutes);
            System.err.println("[" + Utils.getDateTimeForDisplay(endDateTime) + "] " +
                    getClass().getName() + " done. Elapsed time: " + elapsedString + " minutes.");
            System.err.println("Runtime.totalMemory()=" + Runtime.getRuntime().totalMemory());
        }
    }
}
 

import org.broadinstitute.hellbender.utils.LoggingUtils; //导入依赖的package包/类
/**
 * Tests that the allelic PoN is appropriately used to correct reference bias.  The basic set up for the test data is
 * simulated hets at 1000 sites (1:1-1000) across 3 segments.  The outer two segments are balanced with
 * minor-allele fraction = 0.5; however, in the middle segment consisting of 100 sites (1:451-550), all of the sites
 *
 * <p>
 *     1) are balanced and have biases identical to the sites in the other two segments,
 *     which are drawn from a gamma distribution with alpha = 65, beta = 60 -> mean bias = 1.083 ("SAMPLE_NORMAL")
 * </p>
 *
 * <p>
 *     2) are balanced and have relatively high biases,
 *     which are drawn from a gamma distribution with alpha = 9, beta = 6 -> mean bias = 1.5 ("SAMPLE_WITH_BAD_SNPS")
 * </p>
 *
 * <p>
 *     3) have minor-allele fraction = 0.33, copy ratio = 1.5, and biases identical to the sites in the other two segments,
 *     which are drawn from a gamma distribution with alpha = 65, beta = 60 -> mean bias = 1.083 ("SAMPLE_EVENT").
 * </p>
 *
 * In this segment, using a PoN that doesn't know about the high reference bias of these sites ("ALLELIC_PON_NORMAL")
 * we should infer a minor-allele fraction of 6 / (6 + 9) = 0.40 in scenario 2; however, with a PoN that does know
 * about the high bias at these sites ("ALLELIC_PON_WITH_BAD_SNPS") we correctly infer that all of the segments are balanced.
 *
 * <p>
 *     Note that alpha and beta are not actually correctly recovered in this PoN via MLE because the biases are
 *     drawn from a mixture of gamma distributions (as opposed to a single gamma distribution as assumed in the model).
 *     TODO https://github.com/broadinstitute/gatk-protected/issues/421
 * </p>
 */
@Test(dataProvider = "biasCorrection")
public void testBiasCorrection(final AllelicCountCollection sample,
                               final AllelicPanelOfNormals allelicPoN,
                               final double minorFractionExpectedInMiddleSegment) {
    LoggingUtils.setLoggingLevel(Log.LogLevel.INFO);
    final JavaSparkContext ctx = SparkContextFactory.getTestSparkContext();

    final double minorFractionTolerance = 0.025;

    final Genome genome = new Genome(AlleleFractionSimulatedData.TRIVIAL_TARGETS, sample.getCounts());
    final List<SimpleInterval> segments = SegmentUtils.readIntervalsFromSegmentFile(SEGMENTS_FILE);
    final SegmentedGenome segmentedGenome = new SegmentedGenome(segments, genome);

    final int numSamples = 150;
    final int numBurnIn = 50;
    final AlleleFractionModeller modeller = new AlleleFractionModeller(segmentedGenome, allelicPoN);
    modeller.fitMCMC(numSamples, numBurnIn);

    final List<PosteriorSummary> minorAlleleFractionPosteriorSummaries =
            modeller.getMinorAlleleFractionsPosteriorSummaries(CREDIBLE_INTERVAL_ALPHA, ctx);
    final List<Double> minorFractionsResult = minorAlleleFractionPosteriorSummaries.stream().map(PosteriorSummary::getCenter).collect(Collectors.toList());

    final double minorFractionBalanced = 0.5;
    final List<Double> minorFractionsExpected = Arrays.asList(minorFractionBalanced, minorFractionExpectedInMiddleSegment, minorFractionBalanced);
    for (int segment = 0; segment < 3; segment++) {
        Assert.assertEquals(minorFractionsResult.get(segment), minorFractionsExpected.get(segment), minorFractionTolerance);
    }
}