Java Code Examples for htsjdk.samtools.util.Log

The following examples show how to use htsjdk.samtools.util.Log. These examples are extracted from open source projects. You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may check out the related API usage on the sidebar.
Example 1
Source Project: Drop-seq   Source File: FilterProgramUtils.java    License: MIT License 6 votes vote down vote up
public static void reportAndCheckFilterResults(
        final String elementType, final long elementsAccepted, final long elementsRejected,
        final Double passingThreshold, final Log log) {
    final long totalElements = elementsAccepted + elementsRejected;
    log.info(String.format("Total %d %s processed.  %d %s accepted; %d %s rejected.",
            totalElements, elementType, elementsAccepted, elementType, elementsRejected, elementType));
    if (passingThreshold != null) {
        if (passingThreshold >= 1) {
            if (elementsAccepted < passingThreshold) {
                throw new RuntimeException(String.format("Fewer than %d %s passed filters",
                        passingThreshold.intValue(), elementType));
            }
        } else if (elementsAccepted/((double)totalElements) < passingThreshold) {
            throw new RuntimeException(String.format("A smaller fraction than %f %s passed filters",
                    passingThreshold, elementType));
        }
    }
    
}
 
Example 2
Source Project: Drop-seq   Source File: PolyATrimmerTest.java    License: MIT License 6 votes vote down vote up
@Test(dataProvider = "testClpDataProvider")
public void testClp(final boolean newTrimmer) throws IOException {
    final File tempDir = Files.createTempDirectory("PolyATrimmerTest.").toFile();
    final Log.LogLevel saveLogLevel = Log.getGlobalLogLevel();
    Log.setGlobalLogLevel(Log.LogLevel.DEBUG);
    try {
        final PolyATrimmer clp = new PolyATrimmer();
        clp.INPUT = INPUT;
        clp.OUTPUT = File.createTempFile("PolyATrimmerTest.", ".sam");
        clp.OUTPUT.deleteOnExit();
        clp.OUTPUT_SUMMARY = File.createTempFile("PolyATrimmerTest.", ".summary");
        clp.OUTPUT_SUMMARY.deleteOnExit();
        clp.TMP_DIR = Arrays.asList(tempDir);
        tempDir.deleteOnExit();
        clp.MISMATCHES = 0;
        clp.NUM_BASES = 6;
        clp.VALIDATION_STRINGENCY = ValidationStringency.STRICT;
        clp.USE_NEW_TRIMMER = newTrimmer;
        Assert.assertEquals(clp.doWork(), 0);
        final File expectedResult = new File(TESTDATA_DIR, String.format("N701.%s_trimmer.sam", newTrimmer? "new": "old"));
        TestUtils.assertSamFilesSame(clp.OUTPUT, expectedResult);
    } finally {
        Log.setGlobalLogLevel(saveLogLevel);
        IOUtil.recursiveDelete(tempDir.toPath());
    }
}
 
Example 3
@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}
    };
}
 
Example 4
@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);
}
 
Example 5
Source Project: rtg-tools   Source File: Diagnostic.java    License: BSD 2-Clause "Simplified" License 6 votes vote down vote up
/**
 * Set the stream to which logging messages are sent.  It is permissible,
 * but unadvisable to set this to null, as setting it to null causes all
 * logging information to be discarded.
 *
 * @param logStream stream to use for logging
 */
public static synchronized void setLogStream(final LogStream logStream) {
  sLogRedirect = false;
  if (sLogStream == logStream) {
    return;
  }
  if (sLogStream != null && logStream != null && logStream.stream() == sLogStream.stream()) {
    return;
  }
  if (sLogStream != null) {
    closeLog();
  }
  sLogStream = logStream;
  Log.setGlobalPrintStream(sLogStream == null ? NullStreamUtils.getNullPrintStream() : sLogStream.stream());
  sLogClosed = false;
  sProgressClosed = false;
}
 
Example 6
Source Project: picard   Source File: SamFormatConverter.java    License: MIT License 6 votes vote down vote up
/**
 * Convert a file from one of sam/bam/cram format to another based on the extension of output.
 *
 * @param input             input file in one of sam/bam/cram format
 * @param output            output to write converted file to, the conversion is based on the extension of this filename
 * @param referenceSequence the reference sequence to use, necessary when reading/writing cram
 * @param createIndex       whether or not an index should be written alongside the output file
 */
public static void convert(final File input, final File output, final File referenceSequence, final Boolean createIndex) {
    IOUtil.assertFileIsReadable(input);
    IOUtil.assertFileIsWritable(output);
    final SamReader reader = SamReaderFactory.makeDefault().referenceSequence(referenceSequence).open(input);
    final SAMFileWriter writer = new SAMFileWriterFactory().makeWriter(reader.getFileHeader(), true, output, referenceSequence);
    if (createIndex && 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();
}
 
Example 7
Source Project: picard   Source File: ReplaceSamHeader.java    License: MIT License 6 votes vote down vote up
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);
}
 
Example 8
Source Project: picard   Source File: RnaSeqMetricsCollector.java    License: MIT License 6 votes vote down vote up
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;
    }
 
Example 9
Source Project: picard   Source File: DbSnpBitSetUtil.java    License: MIT License 6 votes vote down vote up
/** 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;
}
 
Example 10
Source Project: picard   Source File: OpticalDuplicateFinderTest.java    License: MIT License 6 votes vote down vote up
@Test
public void testKeeperOrderDependence() {
    final Log log = Log.getInstance(OpticalDuplicateFinderTest.class);
    final OpticalDuplicateFinder finder = new OpticalDuplicateFinder(OpticalDuplicateFinder.DEFAULT_READ_NAME_REGEX, 100, log);
    final List<PhysicalLocation> locs = Arrays.asList(
            loc(1, 100, 190),
            loc(1, 100, 280),
            loc(1,  100, 370),
            loc(1,  100, 460)
    );
    final List<PhysicalLocation> locsReordered = Arrays.asList(
            loc(1, 100, 190),
            loc(1, 100, 460),
            loc(1,  100, 370),
            loc(1,  100, 280)
    );

    Assert.assertEquals(countTrue(finder.findOpticalDuplicates(locs, locs.get(0))), 3);
    Assert.assertEquals(countTrue(finder.findOpticalDuplicates(locsReordered, locsReordered.get(0))), 3);
}
 
Example 11
/**
 * Returns the Spark log level for the argument set. This is simply sparkVerbosity
 * if it was specified. Otherwise, it returns the log level corresponding to the
 * provided tool (htsjdk) verbosity.
 *
 * @param  toolVerbosity  Current tool's htsjdk log level
 * @return      Spark log level String
 */
public String getSparkVerbosity(final Log.LogLevel toolVerbosity) {
    Utils.nonNull(toolVerbosity, "Tool verbosity cannot be null");
    if (sparkVerbosity != null) return sparkVerbosity;
    if (toolVerbosity.equals(Log.LogLevel.DEBUG)) {
        return Level.DEBUG.name();
    }
    if (toolVerbosity.equals(Log.LogLevel.INFO)) {
        return Level.INFO.name();
    }
    if (toolVerbosity.equals(Log.LogLevel.WARNING)) {
        return Level.WARN.name();
    }
    if (toolVerbosity.equals(Log.LogLevel.ERROR)) {
        return Level.ERROR.name();
    }
    throw new IllegalStateException("Unknown tool verbosity: " + toolVerbosity.name());
}
 
Example 12
Source Project: gatk   Source File: ConfigFactory.java    License: BSD 3-Clause "New" or "Revised" License 6 votes vote down vote up
/**
 * 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());
    }
}
 
Example 13
/**
 * 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;
}
 
Example 14
Source Project: cramtools   Source File: CRAMFileWriter.java    License: Apache License 2.0 6 votes vote down vote up
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();
	}
 
Example 15
Source Project: cramtools   Source File: QualityScoreStats.java    License: Apache License 2.0 6 votes vote down vote up
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));
}
 
Example 16
@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);
}
 
Example 17
Source Project: picard   Source File: CleanSam.java    License: MIT License 5 votes vote down vote up
/**
 * Do the work after command line has been parsed.
 * RuntimeException may be thrown by this method, and are reported appropriately.
 *
 * @return program exit status.
 */
@Override
protected int doWork() {
    IOUtil.assertFileIsReadable(INPUT);
    IOUtil.assertFileIsWritable(OUTPUT);
    final SamReaderFactory factory = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE);
    if (VALIDATION_STRINGENCY == ValidationStringency.STRICT) {
        factory.validationStringency(ValidationStringency.LENIENT);
    }
    final SamReader reader = factory.open(INPUT);
    final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(reader.getFileHeader(), true, OUTPUT);
    final CloseableIterator<SAMRecord> it = reader.iterator();
    final ProgressLogger progress = new ProgressLogger(Log.getInstance(CleanSam.class));

    // If the read (or its mate) maps off the end of the alignment, clip it
    while (it.hasNext()) {
        final SAMRecord rec = it.next();

        // If the read (or its mate) maps off the end of the alignment, clip it
        AbstractAlignmentMerger.createNewCigarsIfMapsOffEndOfReference(rec);

        // check the read's mapping quality
        if (rec.getReadUnmappedFlag() && 0 != rec.getMappingQuality()) {
            rec.setMappingQuality(0);
        }

        writer.addAlignment(rec);
        progress.record(rec);
    }

    writer.close();
    it.close();
    CloserUtil.close(reader);
    return 0;
}
 
Example 18
Source Project: picard   Source File: MarkDuplicatesWithMateCigarIterator.java    License: MIT License 5 votes vote down vote up
public void logMemoryStats(final Log log) {
    System.gc();
    final Runtime runtime = Runtime.getRuntime();
    log.info("freeMemory: " + runtime.freeMemory() +
            "; totalMemory: " + runtime.totalMemory() +
            "; maxMemory: " + runtime.maxMemory() +
            "; output buffer size: " + outputBuffer.size() +
            "; duplicate queue size: " + toMarkQueue.size()
    );
}
 
Example 19
Source Project: picard   Source File: OpticalDuplicateFinderTest.java    License: MIT License 5 votes vote down vote up
@Test
public void testKeeper() {
    final Log log = Log.getInstance(OpticalDuplicateFinderTest.class);
    final OpticalDuplicateFinder finder = new OpticalDuplicateFinder(OpticalDuplicateFinder.DEFAULT_READ_NAME_REGEX, 100, log);
    final List<PhysicalLocation> locs = Arrays.asList(
            loc(7, 1500, 1500),
            loc(7, 1501, 1501),
            loc(5, 1500, 1500),
            loc(7, 1490, 1502),
            loc(7, 2500, 2500),
            loc(7,   10,   10)
    );

    assertEquals(finder.findOpticalDuplicates(locs, null       ), new boolean[] {true, true,  false, false, false, false});
    assertEquals(finder.findOpticalDuplicates(locs, locs.get(0)), new boolean[] {false, true,  false, true, false, false});
    assertEquals(finder.findOpticalDuplicates(locs, locs.get(1)), new boolean[] {true,  false, false, true, false, false});
    assertEquals(finder.findOpticalDuplicates(locs, locs.get(3)), new boolean[] {true,  true,  false, false, false, false});

    for (int i=0; i<100; ++i) {
        final Random random = new Random(i);
        final List<PhysicalLocation> shuffled = new ArrayList<>(locs);
        final List<PhysicalLocation> keepers  = Arrays.asList(locs.get(0), locs.get(1), locs.get(3));
        final PhysicalLocation keeper = keepers.get(random.nextInt(keepers.size()));
        Collections.shuffle(shuffled);

        int opticalDupeCount = countTrue(finder.findOpticalDuplicates(shuffled, keeper));
        Assert.assertEquals(opticalDupeCount, 2);
    }
}
 
Example 20
Source Project: picard   Source File: OpticalDuplicateFinderTest.java    License: MIT License 5 votes vote down vote up
/**
 * Tests the case where the "keeper" record is not in the list that is passed to the OpticalDuplicateFinder. This can happen
 * when there are, e.g. FR and RF reads, which can all be molecular duplicates of one another, but cannot be duplicates of one
 * another and are thus partitioned into two sets for optical duplicate checking.
 */
@Test
public void testKeeperNotInList() {
    final Log log = Log.getInstance(OpticalDuplicateFinderTest.class);
    final OpticalDuplicateFinder finder = new OpticalDuplicateFinder(OpticalDuplicateFinder.DEFAULT_READ_NAME_REGEX, 100, log);
    final List<PhysicalLocation> locs = Arrays.asList(
            loc(1, 100, 100),
            loc(1, 101, 101),
            loc(1,  99, 99),
            loc(1,  99, 102)
    );

    Assert.assertEquals(countTrue(finder.findOpticalDuplicates(locs, loc(7, 5000, 5000))), 3);
}
 
Example 21
Source Project: picard   Source File: OpticalDuplicateFinderTest.java    License: MIT License 5 votes vote down vote up
@Test
public void testKeeperAtEndWithinCliqueOfAllOpticalDuplicates() {
    final Log log = Log.getInstance(OpticalDuplicateFinderTest.class);
    final OpticalDuplicateFinder finder = new OpticalDuplicateFinder(OpticalDuplicateFinder.DEFAULT_READ_NAME_REGEX, 15, log);
    final List<PhysicalLocation> locs = Arrays.asList(
            loc(1, 10, 0),
            loc(1, 20, 0),
            loc(1, 30, 0)
    );

    assertEquals(finder.findOpticalDuplicates(locs, locs.get(2)), new boolean[] {true, true, false});
}
 
Example 22
Source Project: gatk   Source File: LoggingUtils.java    License: BSD 3-Clause "New" or "Revised" License 5 votes vote down vote up
/**
 * Propagate the verbosity level to Picard, log4j, the java built in logger, and Kryo's MinLog
 */
public static void setLoggingLevel(final Log.LogLevel verbosity) {

    // Call the Picard API to establish the logging level used by Picard
    Log.setGlobalLogLevel(verbosity);

    // set the Log4JLoggingLevel
    setLog4JLoggingLevel(verbosity);

    // set the java.util.logging Level
    setJavaUtilLoggingLevel(verbosity);

    // set the esotericsoft MinLog level, this is used by kryo
    setMinLogLoggingLevel(verbosity);
}
 
Example 23
Source Project: gatk   Source File: LoggingUtils.java    License: BSD 3-Clause "New" or "Revised" License 5 votes vote down vote up
private static void setLog4JLoggingLevel(Log.LogLevel verbosity) {
    // Now establish the logging level used by log4j by propagating the requested
    // logging level to all loggers associated with our logging configuration.
    final LoggerContext loggerContext = (LoggerContext) LogManager.getContext(false);
    final Configuration loggerContextConfig = loggerContext.getConfiguration();
    final String contextClassName = LoggingUtils.class.getName();
    final LoggerConfig loggerConfig = loggerContextConfig.getLoggerConfig(contextClassName);

    loggerConfig.setLevel(levelToLog4jLevel(verbosity));
    loggerContext.updateLoggers();
}
 
Example 24
Source Project: gatk   Source File: LoggingUtils.java    License: BSD 3-Clause "New" or "Revised" License 5 votes vote down vote up
/**
 * set the logging level for {@link com.esotericsoftware.minlog.Log}, the logger used by Kryo
 */
private static void setMinLogLoggingLevel(Log.LogLevel verbosity) {
    switch (verbosity) {
        case DEBUG: com.esotericsoftware.minlog.Log.DEBUG(); break;
        case INFO: com.esotericsoftware.minlog.Log.INFO(); break;
        case WARNING: com.esotericsoftware.minlog.Log.WARN(); break;
        case ERROR: com.esotericsoftware.minlog.Log.ERROR(); break;
        default:
            throw new GATKException("This log level is not implemented properly: " + verbosity);
    }
}
 
Example 25
/**
 * 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()
                .forEach((key, value) -> logger.info("HTSJDK " + Defaults.class.getSimpleName() + "." + key + " : " + value));
    }

    // 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());
    if (Strings.isNullOrEmpty(NIO_PROJECT_FOR_REQUESTER_PAYS)) {
        logger.info("Requester pays: disabled");
    } else {
        logger.info("Requester pays: enabled. Billed to: " + NIO_PROJECT_FOR_REQUESTER_PAYS);
    }
}
 
Example 26
@DataProvider(name="toolLogLevels")
public Object[][] toolLogLevels(){
    return new Object[][] {
            {Log.LogLevel.DEBUG, Level.DEBUG.name()},
            {Log.LogLevel.INFO, Level.INFO.name()},
            {Log.LogLevel.WARNING, Level.WARN.name()},
            {Log.LogLevel.ERROR, Level.ERROR.name()},
    };
}
 
Example 27
@Test(dataProvider = "sparkLogLevels")
public void test(String sparkLevel){
    final SparkCommandLineArgumentCollection sparkArgumentCollection = new SparkCommandLineArgumentCollection();
    sparkArgumentCollection.setSparkVerbosity(sparkLevel);
    final String level = sparkArgumentCollection.getSparkVerbosity(Log.LogLevel.INFO);
    Assert.assertEquals(level, sparkLevel);
}
 
Example 28
@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));
}
 
Example 29
Source Project: cramtools   Source File: DetectFeatureB.java    License: Apache License 2.0 5 votes vote down vote up
public static void main(String[] args) throws IOException, IllegalArgumentException, IllegalAccessException {
	Log.setGlobalLogLevel(LogLevel.INFO);
	File cramFile = new File(args[0]);
	InputStream is = new BufferedInputStream(new FileInputStream(cramFile));
	CramHeader header = CramIO.readCramHeader(is);
	Container c = null;
	while ((c = ContainerIO.readContainer(header.getVersion(), is)) != null && !c.isEOF()) {
		for (Slice slice : c.slices) {
			final DataReaderFactory dataReaderFactory = new DataReaderFactory();
			final Map<Integer, InputStream> inputMap = new HashMap<Integer, InputStream>();
			for (final Integer exId : slice.external.keySet()) {
				inputMap.put(exId, new ByteArrayInputStream(slice.external.get(exId).getRawContent()));
			}

			final CramRecordReader reader = new CramRecordReader(ValidationStringency.SILENT);
			dataReaderFactory.buildReader(reader, new DefaultBitInputStream(new ByteArrayInputStream(
					slice.coreBlock.getRawContent())), inputMap, c.header, slice.sequenceId);

			for (int i = 0; i < slice.nofRecords; i++) {
				CramCompressionRecord record = new CramCompressionRecord();
				reader.read(record);
				if (record.isSegmentUnmapped() || record.readFeatures == null || record.readFeatures.isEmpty())
					continue;
				for (ReadFeature rf : record.readFeatures) {
					if (rf.getOperator() == ReadBase.operator) {
						System.out.println("Read feature B detected.");
						System.exit(1);
					}
				}
			}
		}
	}
}
 
Example 30
Source Project: cramtools   Source File: DetectMultiref.java    License: Apache License 2.0 5 votes vote down vote up
public static void main(String[] args) throws IOException, IllegalArgumentException, IllegalAccessException {
	Log.setGlobalLogLevel(LogLevel.INFO);
	File cramFile = new File(args[0]);
	InputStream is = new BufferedInputStream(new FileInputStream(cramFile));
	CramHeader header = CramIO.readCramHeader(is);
	Container c = null;
	while ((c = ContainerIO.readContainer(header.getVersion(), is)) != null && !c.isEOF()) {
		for (Slice slice : c.slices) {
			if (slice.sequenceId == Slice.MULTI_REFERENCE) {
				System.out.println("Read feature B detected.");
				System.exit(1);
			}
		}
	}
}