import htsjdk.samtools.util.Log; //导入依赖的package包/类
public static void mockPrimitiveLoadFromTo(S3InputStreamFactory factory, int dataSize) {
    PowerMockito.mockStatic(S3InputStreamFactory.class);
    PowerMockito.when(factory.loadFromTo(Mockito.any(AmazonS3URI.class), Mockito.anyLong(), Mockito.anyLong()))
            .then((invocation) -> new InputStream() {
                        final Log log = Log.getInstance(InputStream.class);
                        private int size = dataSize;

                        @Override
                        public int read() throws IOException {
                            final int returnByte = (size-- > 0) ? FROM_STREAM_CHAR : -1;
                            log.debug("Stream(", this.hashCode(), " size = ", size, " return: ", returnByte);
                            return returnByte;
                        }
                    }
            );
}
 

import htsjdk.samtools.util.Log; //导入依赖的package包/类
@Override
public RecordReader<LongWritable, SAMRecordWritable> createRecordReader(
		InputSplit inputSplit, TaskAttemptContext context)
		throws IOException, InterruptedException {
	Log.setGlobalLogLevel(LogLevel.ERROR);
	Configuration conf = context.getConfiguration();
	int type = conf.getInt("cram.inputformat.type", 0);
	CramInputFormatType inputType = CramInputFormatType.valueOf(type);
	
	RecordReader<LongWritable, SAMRecordWritable> rr = null;
	if(inputType == CramInputFormatType.ALL)
		rr = new GaeaCramRecordReader();
	else if(inputType == CramInputFormatType.CHROMOSOME)
		rr = new GaeaCramChromosomeRecordReader();
	return rr;
}
 

import htsjdk.samtools.util.Log; //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 htsjdk.samtools.util.Log; //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 htsjdk.samtools.util.Log; //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 htsjdk.samtools.util.Log; //导入依赖的package包/类
protected int doWork() {
    IOUtil.assertFileIsReadable(INPUT);
    IOUtil.assertFileIsWritable(OUTPUT);
    final SamReader reader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(INPUT);
    final SAMFileWriter writer = new SAMFileWriterFactory().makeWriter(reader.getFileHeader(), true, OUTPUT, REFERENCE_SEQUENCE);

    if (CREATE_INDEX && writer.getFileHeader().getSortOrder() != SAMFileHeader.SortOrder.coordinate) {
        throw new PicardException("Can't CREATE_INDEX unless sort order is coordinate");
    }

    final ProgressLogger progress = new ProgressLogger(Log.getInstance(SamFormatConverter.class));
    for (final SAMRecord rec : reader) {
        writer.addAlignment(rec);
        progress.record(rec);
    }
    CloserUtil.close(reader);
    writer.close();
    return 0;
}
 

import htsjdk.samtools.util.Log; //导入依赖的package包/类
private void standardReheader(final SAMFileHeader replacementHeader) {
    final SamReader recordReader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).validationStringency(ValidationStringency.SILENT).open(INPUT);
    if (replacementHeader.getSortOrder() != recordReader.getFileHeader().getSortOrder()) {
        throw new PicardException("Sort orders of INPUT (" + recordReader.getFileHeader().getSortOrder().name() +
                ") and HEADER (" + replacementHeader.getSortOrder().name() + ") do not agree.");
    }
    final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(replacementHeader, true, OUTPUT);

    final ProgressLogger progress = new ProgressLogger(Log.getInstance(ReplaceSamHeader.class));
    for (final SAMRecord rec : recordReader) {
        rec.setHeader(replacementHeader);
        writer.addAlignment(rec);
        progress.record(rec);
    }
    writer.close();
    CloserUtil.close(recordReader);
}
 

import htsjdk.samtools.util.Log; //导入依赖的package包/类
public static OverlapDetector<Interval> makeOverlapDetector(final File samFile, final SAMFileHeader header, final File ribosomalIntervalsFile, final Log log) {

        final OverlapDetector<Interval> ribosomalSequenceOverlapDetector = new OverlapDetector<Interval>(0, 0);
        if (ribosomalIntervalsFile != null) {

            final IntervalList ribosomalIntervals = IntervalList.fromFile(ribosomalIntervalsFile);
            if (ribosomalIntervals.size() == 0) {
                log.warn("The RIBOSOMAL_INTERVALS file, " + ribosomalIntervalsFile.getAbsolutePath() + " does not contain intervals");
            }
            try {
                SequenceUtil.assertSequenceDictionariesEqual(header.getSequenceDictionary(), ribosomalIntervals.getHeader().getSequenceDictionary());
            } catch (SequenceUtil.SequenceListsDifferException e) {
                throw new PicardException("Sequence dictionaries differ in " + samFile.getAbsolutePath() + " and " + ribosomalIntervalsFile.getAbsolutePath(),
                        e);
            }
            final IntervalList uniquedRibosomalIntervals = ribosomalIntervals.uniqued();
            final List<Interval> intervals = uniquedRibosomalIntervals.getIntervals();
            ribosomalSequenceOverlapDetector.addAll(intervals, intervals);
        }
        return ribosomalSequenceOverlapDetector;
    }
 

import htsjdk.samtools.util.Log; //导入依赖的package包/类
/** Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
 * If intervals are given, consider only SNP and indel sites that overlap the intervals.  If log is given,
 * progress loading the variants will be written to the log. */
public static DbSnpBitSets createSnpAndIndelBitSets(final File dbSnpFile,
                                                    final SAMSequenceDictionary sequenceDictionary,
                                                    final IntervalList intervals,
                                                    final Optional<Log> log) {

    final DbSnpBitSets sets = new DbSnpBitSets();
    sets.snps   = new DbSnpBitSetUtil();
    sets.indels = new DbSnpBitSetUtil();

    final Map<DbSnpBitSetUtil, Set<VariantType>> map = new HashMap<>();
    map.put(sets.snps,   EnumSet.of(VariantType.SNP));
    map.put(sets.indels, EnumSet.of(VariantType.insertion, VariantType.deletion));
    loadVcf(dbSnpFile, sequenceDictionary, map, intervals, log);
    return sets;
}
 

import htsjdk.samtools.util.Log; //导入依赖的package包/类
@Test
public void testMaxSetSize() {
    final Log log = Log.getInstance(OpticalDuplicateFinderTest.class);
    List<PhysicalLocation> locs = Arrays.asList(
            loc(7, 1500, 1500),
            loc(7, 1501, 1501),
            loc(7, 1490, 1502));

    // there should be at least 1 optical duplicate
    final OpticalDuplicateFinder normalFinder = new OpticalDuplicateFinder(OpticalDuplicateFinder.DEFAULT_READ_NAME_REGEX, 100, log);
    Assert.assertTrue(countTrue(normalFinder.findOpticalDuplicates(locs, null)) > 0);

    // there should be zero optical duplicates
    final OpticalDuplicateFinder constrainedFinder = new OpticalDuplicateFinder(OpticalDuplicateFinder.DEFAULT_READ_NAME_REGEX, 100, 1, log);
    Assert.assertEquals(countTrue(constrainedFinder.findOpticalDuplicates(locs, null)), 0);
}
 

import htsjdk.samtools.util.Log; //导入依赖的package包/类
/**
 * Set the java.util.logging level since some of our dependencies write messages using it.
 *
 * Taken with modifications from a post by michel.iamit
 * http://stackoverflow.com/users/369060/michel-iamit
 * from http://stackoverflow.com/questions/470430/java-util-logging-logger-doesnt-respect-java-util-logging-level
 */
private static void setJavaUtilLoggingLevel(final Log.LogLevel verbosity) {
    Logger topLogger = java.util.logging.Logger.getLogger("");

    Handler consoleHandler = null;
    for (Handler handler : topLogger.getHandlers()) {
        if (handler instanceof ConsoleHandler) {
            consoleHandler = handler;
            break;
        }
    }

    if (consoleHandler == null) {
        consoleHandler = new ConsoleHandler();
        topLogger.addHandler(consoleHandler);
    }
    consoleHandler.setLevel(levelToJavaUtilLevel(verbosity));
}
 

import htsjdk.samtools.util.Log; //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 htsjdk.samtools.util.Log; //导入依赖的package包/类
/**
 * Inject the verbosity parameter into the list.
 *
 * Default behaviour look for --verbosity argument; if not found, supply a default value that minimizes the amount of logging output.
 */
default List<String> injectDefaultVerbosity(final List<String> args) {

    // global toggle for BunnyLog output.
    BunnyLog.setEnabled(false);

    for (String arg : args) {
        if (arg.equalsIgnoreCase("--" + StandardArgumentDefinitions.VERBOSITY_NAME) || arg.equalsIgnoreCase("-" + StandardArgumentDefinitions.VERBOSITY_NAME)) {
            return args;
        }
    }
    List<String> argsWithVerbosity = new ArrayList<>(args);
    argsWithVerbosity.add("--" + StandardArgumentDefinitions.VERBOSITY_NAME);
    argsWithVerbosity.add(Log.LogLevel.ERROR.name());
    return argsWithVerbosity;
}
 

import htsjdk.samtools.util.Log; //导入依赖的package包/类
/**
 * Output a curated set of important settings to the logger.
 *
 * May be overridden by subclasses to specify a different set of settings to output.
 */
protected void printSettings() {
    if ( VERBOSITY != Log.LogLevel.DEBUG ) {
        logger.info("HTSJDK Defaults.COMPRESSION_LEVEL : " + Defaults.COMPRESSION_LEVEL);
        logger.info("HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : " + Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS);
        logger.info("HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : " + Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS);
        logger.info("HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : " + Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE);
    }
    else {
        // At DEBUG verbosity, print all the HTSJDK defaults:
        Defaults.allDefaults().entrySet().stream().forEach(e->
                logger.info("HTSJDK " + Defaults.class.getSimpleName() + "." + e.getKey() + " : " + e.getValue())
        );
    }

    // Log the configuration options:
    ConfigFactory.logConfigFields(ConfigFactory.getInstance().getGATKConfig(), Log.LogLevel.DEBUG);

    final boolean usingIntelDeflater = (BlockCompressedOutputStream.getDefaultDeflaterFactory() instanceof IntelDeflaterFactory && ((IntelDeflaterFactory)BlockCompressedOutputStream.getDefaultDeflaterFactory()).usingIntelDeflater());
    logger.info("Deflater: " + (usingIntelDeflater ? "IntelDeflater": "JdkDeflater"));
    final boolean usingIntelInflater = (BlockGunzipper.getDefaultInflaterFactory() instanceof IntelInflaterFactory && ((IntelInflaterFactory)BlockGunzipper.getDefaultInflaterFactory()).usingIntelInflater());
    logger.info("Inflater: " + (usingIntelInflater ? "IntelInflater": "JdkInflater"));

    logger.info("GCS max retries/reopens: " + BucketUtils.getCloudStorageConfiguration(NIO_MAX_REOPENS).maxChannelReopens());
    logger.info("Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes");
}
 

import htsjdk.samtools.util.Log; //导入依赖的package包/类
public static void main(String[] args) throws IOException {

		Log.setGlobalLogLevel(LogLevel.INFO);
		File bamFile = new File(args[0]);
		File outCramFile = new File(args[1]);
		ReferenceSource source = new ReferenceSource(new File(args[2]));
		int maxThreads = Integer.valueOf(args[3]);

		BAMFileReader reader = new BAMFileReader(bamFile, null, false, false, ValidationStringency.SILENT,
				new DefaultSAMRecordFactory());
		OutputStream os = new FileOutputStream(outCramFile);
		CRAMFileWriter writer = new CRAMFileWriter(os, source, reader.getFileHeader(), outCramFile.getName(),
				maxThreads);

		CloseableIterator<SAMRecord> iterator = reader.getIterator();

		while (iterator.hasNext()) {
			SAMRecord record = iterator.next();
			writer.addAlignment(record);
		}
		writer.close();
		reader.close();
	}
 

import htsjdk.samtools.util.Log; //导入依赖的package包/类
public static void main(String[] args) throws Exception {
	Params params = new Params();
	JCommander jc = new JCommander(params);
	try {
		jc.parse(args);
	} catch (Exception e) {
		System.out.println("Failed to parse parameteres, detailed message below: ");
		System.out.println(e.getMessage());
		System.out.println();
		System.out.println("See usage: -h");
		System.exit(1);
	}

	if (args.length == 0 || params.help) {
		printUsage(jc);
		System.exit(1);
	}

	Log.setGlobalLogLevel(params.logLevel);

	dist(params.inputFile, (byte) (0xFF & params.defaultQualityScore));
}
 

import htsjdk.samtools.util.Log; //导入依赖的package包/类
@SuppressWarnings({ "rawtypes", "unchecked" })
public RecordWriter<K, SamRecordWritable> getRecordWriter(
		TaskAttemptContext context, Path outputPath) throws IOException {
	Log.setGlobalLogLevel(LogLevel.ERROR);
	return new GaeaKeyIgnoringBamRecordWriter(outputPath,
			Boolean.valueOf(this.writeHeader), context);
}
 

import htsjdk.samtools.util.Log; //导入依赖的package包/类
@SuppressWarnings({ "rawtypes", "unchecked" })
public RecordWriter<K, SAMRecordWritable> getRecordWriter(
		TaskAttemptContext context, Path outputPath) throws IOException {
	Log.setGlobalLogLevel(LogLevel.ERROR);
	return new GaeaKeyIgnoringCramRecordWriter(outputPath,
			Boolean.valueOf(this.writeHeader), context);
}
 

import htsjdk.samtools.util.Log; //导入依赖的package包/类
@Override
public RecordReader<LongWritable, SAMRecordWritable> createRecordReader(
		InputSplit split, TaskAttemptContext context) throws IOException {
	Log.setGlobalLogLevel(Log.LogLevel.ERROR);
	RecordReader<LongWritable, SAMRecordWritable> rr = new GaeaCombineCramFileRecordReader(
			split, context);
	return rr;
}
 

import htsjdk.samtools.util.Log; //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);
}