Examples with OptionalInt java.util.OptionalInt used on opensource projects

Example 36 with OptionalInt

use of java.util.OptionalInt in project jetcache by alibaba.

the class StatInfoLogger method logStatSummary.

private StringBuilder logStatSummary(StatInfo statInfo) {
    StringBuilder sb = logTitle(2048, statInfo);
    List<CacheStat> stats = statInfo.getStats();
    OptionalInt maxCacheNameLength = stats.stream().mapToInt((s) -> getName(s.getCacheName()).length()).max();
    int len = Math.max(5, maxCacheNameLength.orElse(0));
    String title = String.format("%-" + len + "s|%10s|%7s|%14s|%14s|%14s|%14s|%11s|%11s", "cache", "qps", "rate", "get", "hit", "fail", "expire", "avgLoadTime", "maxLoadTime");
    sb.append(title).append('\n');
    printSepLine(sb, title);
    for (CacheStat s : stats) {
        sb.append(String.format("%-" + len + "s", getName(s.getCacheName()))).append('|');
        sb.append(String.format("%,10.2f", s.qps())).append('|');
        sb.append(String.format("%6.2f%%", s.hitRate() * 100)).append('|');
        sb.append(String.format("%,14d", s.getGetCount())).append('|');
        sb.append(String.format("%,14d", s.getGetHitCount())).append('|');
        sb.append(String.format("%,14d", s.getGetFailCount())).append('|');
        sb.append(String.format("%,14d", s.getGetExpireCount())).append('|');
        sb.append(String.format("%,11.1f", s.avgLoadTime())).append('|');
        sb.append(String.format("%,11d", s.getMaxLoadTime())).append('\n');
    }
    printSepLine(sb, title);
    return sb;
}

Example 37 with OptionalInt

use of java.util.OptionalInt in project gatk-protected by broadinstitute.

the class CreatePanelOfNormals method runPipeline.

@Override
protected void runPipeline(final JavaSparkContext ctx) {
    if (!new HDF5Library().load(null)) {
        //Note: passing null means using the default temp dir.
        throw new UserException.HardwareFeatureException("Cannot load the required HDF5 library. " + "HDF5 is currently supported on x86-64 architecture and Linux or OSX systems.");
    }
    if (blacklistOutFile == null) {
        blacklistOutFile = new File(outFile + BLACKLIST_FILE_APPEND);
    }
    if (targetWeightsOutFile == null) {
        targetWeightsOutFile = new File(outFile + TARGET_WEIGHTS_FILE_APPEND);
    }
    // Check parameters and load values to meet the backend PoN creation interface
    validateArguments();
    final TargetCollection<Target> targets = targetArguments.readTargetCollection(true);
    final OptionalInt numberOfEigensamples = parseNumberOfEigensamples(numberOfEigensamplesString);
    // Create the PoN, including QC, if specified.
    if (!isNoQc && !dryRun) {
        logger.info("QC:  Beginning creation of QC PoN...");
        final File outputQCFile = IOUtils.createTempFile("qc-pon-", ".hd5");
        HDF5PCACoveragePoNCreationUtils.create(ctx, outputQCFile, HDF5File.OpenMode.READ_WRITE, inputFile, targets, new ArrayList<>(), targetFactorThreshold, maximumPercentZerosInColumn, maximumPercentZerosInTarget, columnExtremeThresholdPercentile, outlierTruncatePercentileThresh, OptionalInt.of(NUM_QC_EIGENSAMPLES), dryRun);
        logger.info("QC:  QC PoN created...");
        logger.info("QC:  Collecting suspicious samples...");
        try (final HDF5File ponReader = new HDF5File(outputQCFile, HDF5File.OpenMode.READ_ONLY)) {
            final PCACoveragePoN qcPoN = new HDF5PCACoveragePoN(ponReader);
            final List<String> failingSampleNames = CoveragePoNQCUtils.retrieveSamplesWithArmLevelEvents(qcPoN, ctx);
            ParamUtils.writeStringListToFile(failingSampleNames, blacklistOutFile);
            // If no suspicious samples were found, just redo the PoN reduction to save time.
            if (failingSampleNames.size() != 0) {
                logger.info("QC:  Suspicious sample list created...");
                logger.info("Creating final PoN with " + failingSampleNames.size() + " suspicious samples removed...");
                HDF5PCACoveragePoNCreationUtils.create(ctx, outFile, HDF5File.OpenMode.CREATE, inputFile, targets, failingSampleNames, targetFactorThreshold, maximumPercentZerosInColumn, maximumPercentZerosInTarget, columnExtremeThresholdPercentile, outlierTruncatePercentileThresh, numberOfEigensamples, dryRun);
            } else {
                logger.info("QC:  No suspicious samples found ...");
                logger.info("Creating final PoN only redo'ing the reduction step ...");
                HDF5PCACoveragePoNCreationUtils.redoReduction(ctx, numberOfEigensamples, outputQCFile, outFile, HDF5File.OpenMode.CREATE);
            }
        }
    } else {
        logger.info("Creating PoN directly (skipping QC)...");
        HDF5PCACoveragePoNCreationUtils.create(ctx, outFile, HDF5File.OpenMode.CREATE, inputFile, targets, new ArrayList<>(), targetFactorThreshold, maximumPercentZerosInColumn, maximumPercentZerosInTarget, columnExtremeThresholdPercentile, outlierTruncatePercentileThresh, numberOfEigensamples, dryRun);
    }
    if (!dryRun) {
        logger.info("Writing target weights file to " + targetWeightsOutFile + "...");
        writeTargetWeightsFile(outFile, targetWeightsOutFile);
    }
    logger.info("Done...");
}

Example 38 with OptionalInt

use of java.util.OptionalInt in project gatk by broadinstitute.

the class CreatePanelOfNormals method runPipeline.

@Override
protected void runPipeline(final JavaSparkContext ctx) {
    if (!new HDF5Library().load(null)) {
        //Note: passing null means using the default temp dir.
        throw new UserException.HardwareFeatureException("Cannot load the required HDF5 library. " + "HDF5 is currently supported on x86-64 architecture and Linux or OSX systems.");
    }
    if (blacklistOutFile == null) {
        blacklistOutFile = new File(outFile + BLACKLIST_FILE_APPEND);
    }
    if (targetWeightsOutFile == null) {
        targetWeightsOutFile = new File(outFile + TARGET_WEIGHTS_FILE_APPEND);
    }
    // Check parameters and load values to meet the backend PoN creation interface
    validateArguments();
    final TargetCollection<Target> targets = targetArguments.readTargetCollection(true);
    final OptionalInt numberOfEigensamples = parseNumberOfEigensamples(numberOfEigensamplesString);
    // Create the PoN, including QC, if specified.
    if (!isNoQc && !dryRun) {
        logger.info("QC:  Beginning creation of QC PoN...");
        final File outputQCFile = IOUtils.createTempFile("qc-pon-", ".hd5");
        HDF5PCACoveragePoNCreationUtils.create(ctx, outputQCFile, HDF5File.OpenMode.READ_WRITE, inputFile, targets, new ArrayList<>(), targetFactorThreshold, maximumPercentZerosInColumn, maximumPercentZerosInTarget, columnExtremeThresholdPercentile, outlierTruncatePercentileThresh, OptionalInt.of(NUM_QC_EIGENSAMPLES), dryRun);
        logger.info("QC:  QC PoN created...");
        logger.info("QC:  Collecting suspicious samples...");
        try (final HDF5File ponReader = new HDF5File(outputQCFile, HDF5File.OpenMode.READ_ONLY)) {
            final PCACoveragePoN qcPoN = new HDF5PCACoveragePoN(ponReader);
            final List<String> failingSampleNames = CoveragePoNQCUtils.retrieveSamplesWithArmLevelEvents(qcPoN, ctx);
            ParamUtils.writeStringListToFile(failingSampleNames, blacklistOutFile);
            // If no suspicious samples were found, just redo the PoN reduction to save time.
            if (failingSampleNames.size() != 0) {
                logger.info("QC:  Suspicious sample list created...");
                logger.info("Creating final PoN with " + failingSampleNames.size() + " suspicious samples removed...");
                HDF5PCACoveragePoNCreationUtils.create(ctx, outFile, HDF5File.OpenMode.CREATE, inputFile, targets, failingSampleNames, targetFactorThreshold, maximumPercentZerosInColumn, maximumPercentZerosInTarget, columnExtremeThresholdPercentile, outlierTruncatePercentileThresh, numberOfEigensamples, dryRun);
            } else {
                logger.info("QC:  No suspicious samples found ...");
                logger.info("Creating final PoN only redo'ing the reduction step ...");
                HDF5PCACoveragePoNCreationUtils.redoReduction(ctx, numberOfEigensamples, outputQCFile, outFile, HDF5File.OpenMode.CREATE);
            }
        }
    } else {
        logger.info("Creating PoN directly (skipping QC)...");
        HDF5PCACoveragePoNCreationUtils.create(ctx, outFile, HDF5File.OpenMode.CREATE, inputFile, targets, new ArrayList<>(), targetFactorThreshold, maximumPercentZerosInColumn, maximumPercentZerosInTarget, columnExtremeThresholdPercentile, outlierTruncatePercentileThresh, numberOfEigensamples, dryRun);
    }
    if (!dryRun) {
        logger.info("Writing target weights file to " + targetWeightsOutFile + "...");
        writeTargetWeightsFile(outFile, targetWeightsOutFile);
    }
    logger.info("Done...");
}