Examples with UserException org.broadinstitute.hellbender.exceptions.UserException used on opensource projects

Example 91 with UserException

use of org.broadinstitute.hellbender.exceptions.UserException in project gatk by broadinstitute.

the class Main method extractCommandLineProgram.

/**
     * Returns the command line program specified, or prints the usage and exits with exit code 1 *
     */
private static CommandLineProgram extractCommandLineProgram(final String[] args, final List<String> packageList, final List<Class<? extends CommandLineProgram>> classList, final String commandLineName) {
    /** Get the set of classes that are our command line programs **/
    final ClassFinder classFinder = new ClassFinder();
    for (final String pkg : packageList) {
        classFinder.find(pkg, CommandLineProgram.class);
    }
    String missingAnnotationClasses = "";
    final Set<Class<?>> toCheck = classFinder.getClasses();
    toCheck.addAll(classList);
    final Map<String, Class<?>> simpleNameToClass = new LinkedHashMap<>();
    for (final Class<?> clazz : toCheck) {
        // No interfaces, synthetic, primitive, local, or abstract classes.
        if (ClassUtils.canMakeInstances(clazz)) {
            final CommandLineProgramProperties property = getProgramProperty(clazz);
            // Check for missing annotations
            if (null == property) {
                if (missingAnnotationClasses.isEmpty())
                    missingAnnotationClasses += clazz.getSimpleName();
                else
                    missingAnnotationClasses += ", " + clazz.getSimpleName();
            } else if (!property.omitFromCommandLine()) {
                /** We should check for missing annotations later **/
                if (simpleNameToClass.containsKey(clazz.getSimpleName())) {
                    throw new RuntimeException("Simple class name collision: " + clazz.getSimpleName());
                }
                simpleNameToClass.put(clazz.getSimpleName(), clazz);
            }
        }
    }
    if (!missingAnnotationClasses.isEmpty()) {
        throw new RuntimeException("The following classes are missing the required CommandLineProgramProperties annotation: " + missingAnnotationClasses);
    }
    final Set<Class<?>> classes = new LinkedHashSet<>();
    classes.addAll(simpleNameToClass.values());
    if (args.length < 1) {
        printUsage(classes, commandLineName);
    } else {
        if (args[0].equals("-h") || args[0].equals("--help")) {
            printUsage(classes, commandLineName);
        } else {
            if (simpleNameToClass.containsKey(args[0])) {
                final Class<?> clazz = simpleNameToClass.get(args[0]);
                try {
                    return (CommandLineProgram) clazz.newInstance();
                } catch (final InstantiationException | IllegalAccessException e) {
                    throw new RuntimeException(e);
                }
            }
            printUsage(classes, commandLineName);
            throw new UserException(getUnknownCommandMessage(classes, args[0]));
        }
    }
    return null;
}

Example 92 with UserException

use of org.broadinstitute.hellbender.exceptions.UserException in project gatk by broadinstitute.

the class CreateHadoopBamSplittingIndex method createBaiAndSplittingIndex.

private static void createBaiAndSplittingIndex(final File inputBam, final File index, final int granularity, final ValidationStringency readValidationStringency) {
    assertIsBam(inputBam);
    try (SamReader reader = SamReaderFactory.makeDefault().validationStringency(readValidationStringency).setOption(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS, true).open(inputBam);
        BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(index))) {
        final SAMFileHeader header = reader.getFileHeader();
        assertBamIsCoordinateSorted(header);
        final SplittingBAMIndexer indexer = new SplittingBAMIndexer(out, granularity);
        final BAMIndexer bamIndexer = new BAMIndexer(IOUtils.replaceExtension(index, BAMIndex.BAMIndexSuffix), header);
        for (final SAMRecord read : reader) {
            indexer.processAlignment(read);
            bamIndexer.processAlignment(read);
        }
        indexer.finish(inputBam.length());
        bamIndexer.finish();
    } catch (final IOException e) {
        throw new UserException("Couldn't create splitting index", e);
    }
}

Example 93 with UserException

use of org.broadinstitute.hellbender.exceptions.UserException in project gatk-protected by broadinstitute.

the class ConvertACNVResults method runPipeline.

@Override
protected void runPipeline(final JavaSparkContext ctx) {
    final String originalLogLevel = (ctx.getLocalProperty("logLevel") != null) ? ctx.getLocalProperty("logLevel") : "INFO";
    ctx.setLogLevel("WARN");
    final CNLOHCaller cnlohCaller = new CNLOHCaller();
    cnlohCaller.setRhoThreshold(rhoThreshold);
    final List<ACNVModeledSegment> segments = SegmentUtils.readACNVModeledSegmentFile(new File(segmentsFile));
    String sampleName = determineSampleName(new File(segmentsFile));
    // Create the outputdir
    try {
        FileUtils.forceMkdir(outputDir);
    } catch (final IOException ioe) {
        throw new UserException("Cannot create " + outputDir + ".  Does a file (not directory) exist with the same name?  Do you have access to create?", ioe);
    }
    final Genome genome = new Genome(targetCoveragesFile, snpCountsFile);
    // Make the calls
    logger.info("Making the balanced-segment (and CNLoH) calls...");
    final List<AllelicCalls> calls = cnlohCaller.makeCalls(segments, numIterations, ctx);
    // Write updated ACNV file with calls
    logger.info("Writing updated ACNV file with calls ...");
    final File finalACNVModeledSegmentsFile = new File(outputDir, getSegmentsBaseFilename() + "." + BALANCED_SEG_FILE_TAG + ".seg");
    SegmentUtils.writeCnLoHACNVModeledSegmentFile(finalACNVModeledSegmentsFile, calls, genome);
    // write file for GATK CNV formatted seg file
    logger.info("Writing file with same output format as GATK CNV...");
    final File finalModeledSegmentsFileAsGatkCNV = new File(outputDir, getSegmentsBaseFilename() + "." + GATK_SEG_FILE_TAG + ".seg");
    SegmentUtils.writeModeledSegmentFile(finalModeledSegmentsFileAsGatkCNV, ACNVModeledSegmentConversionUtils.convertACNVModeledSegmentsToModeledSegments(segments, genome), sampleName);
    //write file for ACS-compatible output to help Broad CGA
    logger.info("Writing file with same output format as Broad CGA Allelic CapSeg ...");
    final File finalACSModeledSegmentsFile = new File(outputDir, getSegmentsBaseFilename() + "." + CGA_ACS_SEG_FILE_TAG + ".seg");
    ACSModeledSegmentUtils.writeACNVModeledSegmentFileAsAllelicCapSegFile(finalACSModeledSegmentsFile, calls, genome);
    //write files for TITAN-compatible output to help Broad CGA
    logger.info("Writing het file with input format for TITAN ...");
    final File finalTitanHetFile = new File(outputDir, getSegmentsBaseFilename() + "." + TITAN_HET_FILE_TAG + ".tsv");
    TitanFileConverter.convertHetPulldownToTitanHetFile(snpCountsFile, finalTitanHetFile);
    logger.info("Writing tangent-normalized target CR estimates with input format for TITAN ...");
    final File finalTitanTNFile = new File(outputDir, getSegmentsBaseFilename() + "." + TITAN_TN_FILE_TAG + ".tsv");
    TitanFileConverter.convertCRToTitanCovFile(targetCoveragesFile, finalTitanTNFile);
    ctx.setLogLevel(originalLogLevel);
    logger.info("SUCCESS: CNLoH and splits called for sample " + sampleName + ".");
}

Example 94 with UserException

use of org.broadinstitute.hellbender.exceptions.UserException in project gatk-protected by broadinstitute.

the class FilterByOrientationBias method onTraversalStart.

@Override
public void onTraversalStart() {
    // Gets around issue 2274 in gatk public
    if (transitions.size() == 0) {
        transitions.add(DEFAULT_ARTIFACT_MODE);
    }
    // Sort the input artifacts argument
    transitions.sort(null);
    final MetricsFile<SequencingArtifactMetrics.PreAdapterDetailMetrics, Comparable<?>> mf = new MetricsFile<>();
    try {
        mf.read(new FileReader(preAdapterMetricsFile));
    } catch (final FileNotFoundException fnfe) {
        throw new UserException("Could not find file: " + preAdapterMetricsFile.getAbsolutePath());
    }
    // Collect all of the transitions that were specified in the parameters.
    relevantTransitions.addAll(transitions.stream().map(s -> convertParameterToTransition(s)).collect(Collectors.toSet()));
    // Get the PreAdapterQ score from the picard metrics tool, which gives an indication of how badly infested the bam file is.
    transitionToPreAdapterScoreMap = PreAdapterOrientationScorer.scoreOrientationBiasMetricsOverContext(mf.getMetrics());
    logger.info("preAdapter scores:");
    transitionToPreAdapterScoreMap.keySet().stream().forEach(k -> logger.info(k + ": " + transitionToPreAdapterScoreMap.get(k)));
    setupVCFWriter();
}

Example 95 with UserException

use of org.broadinstitute.hellbender.exceptions.UserException in project gatk by broadinstitute.

the class GATKSparkTool method initializeIntervals.

/**
     * Loads our intervals using the best available sequence dictionary (as returned by {@link #getBestAvailableSequenceDictionary})
     * to parse/verify them. Does nothing if no intervals were specified.
     */
private void initializeIntervals() {
    if (intervalArgumentCollection.intervalsSpecified()) {
        final SAMSequenceDictionary intervalDictionary = getBestAvailableSequenceDictionary();
        if (intervalDictionary == null) {
            throw new UserException("We require at least one input source that has a sequence dictionary (reference or reads) when intervals are specified");
        }
        intervals = intervalArgumentCollection.getIntervals(intervalDictionary);
    }
    intervals = editIntervals(intervals);
}