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

Example 6 with UserException

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

the class AbstractMarkDuplicatesCommandLineProgram method trackOpticalDuplicates.

/**
     * Looks through the set of reads and identifies how many of the duplicates are
     * in fact optical duplicates, and stores the data in the instance level histogram.
     */
public static void trackOpticalDuplicates(List<? extends ReadEnds> ends, final OpticalDuplicateFinder opticalDuplicateFinder, final LibraryIdGenerator libraryIdGenerator) {
    boolean hasFR = false, hasRF = false;
    // Check to see if we have a mixture of FR/RF
    for (final ReadEnds end : ends) {
        if (ReadEnds.FR == end.orientationForOpticalDuplicates) {
            hasFR = true;
        } else if (ReadEnds.RF == end.orientationForOpticalDuplicates) {
            hasRF = true;
        }
    }
    // Check if we need to partition since the orientations could have changed
    if (hasFR && hasRF) {
        // need to track them independently
        // Variables used for optical duplicate detection and tracking
        final List<ReadEnds> trackOpticalDuplicatesF = new ArrayList<>();
        final List<ReadEnds> trackOpticalDuplicatesR = new ArrayList<>();
        // Split into two lists: first of pairs and second of pairs, since they must have orientation and same starting end
        for (final ReadEnds end : ends) {
            if (ReadEnds.FR == end.orientationForOpticalDuplicates) {
                trackOpticalDuplicatesF.add(end);
            } else if (ReadEnds.RF == end.orientationForOpticalDuplicates) {
                trackOpticalDuplicatesR.add(end);
            } else {
                throw new UserException("Found an unexpected orientation: " + end.orientation);
            }
        }
        // track the duplicates
        trackOpticalDuplicates(trackOpticalDuplicatesF, opticalDuplicateFinder, libraryIdGenerator.getOpticalDuplicatesByLibraryIdMap());
        trackOpticalDuplicates(trackOpticalDuplicatesR, opticalDuplicateFinder, libraryIdGenerator.getOpticalDuplicatesByLibraryIdMap());
    } else {
        // No need to partition
        AbstractMarkDuplicatesCommandLineProgram.trackOpticalDuplicates(ends, opticalDuplicateFinder, libraryIdGenerator.getOpticalDuplicatesByLibraryIdMap());
    }
}

Example 7 with UserException

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

the class GATKReport method loadReport.

/**
     * Load a GATKReport from a {@link Reader}
     *
     * @param in the reader to load from
     */
private void loadReport(Reader in) {
    BufferedReader reader = new BufferedReader(in);
    String reportHeader;
    try {
        reportHeader = reader.readLine();
    } catch (IOException e) {
        throw new UserException("Could not read " + RECAL_FILE, e);
    }
    if (reportHeader == null) {
        throw new UserException(RECAL_FILE + " is empty.");
    }
    // Read the first line for the version and number of tables.
    version = GATKReportVersion.fromHeader(reportHeader);
    if (version.equals(GATKReportVersion.V0_1) || version.equals(GATKReportVersion.V0_2))
        throw new UserException("The GATK no longer supports reading legacy GATK Reports. Please use v1.0 or newer.");
    int nTables = Integer.parseInt(reportHeader.split(":")[2]);
    // Read each table according ot the number of tables
    for (int i = 0; i < nTables; i++) {
        addTable(new GATKReportTable(reader, version));
    }
}

Example 8 with UserException

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

the class ReadCountCollectionUtils method writeReadCountsFromSimpleInterval.

/**
     * Write a read counts file of targets with coverage to file with dummy names
     * @param outWriter Writer to write targets with coverage. Never {@code null}
     * @param outName Name of the output writer. Never {@code null}
     * @param sampleName Name of sample being written. Never {@code null}
     * @param byKeySorted Map of simple-intervals to their copy-ratio. Never {@code null}
     * @param comments Comments to add to header of coverage file.
     */
public static <N extends Number> void writeReadCountsFromSimpleInterval(final Writer outWriter, final String outName, final String sampleName, final SortedMap<SimpleInterval, N> byKeySorted, final String[] comments) {
    Utils.nonNull(outWriter, "Output writer cannot be null.");
    Utils.nonNull(sampleName, "Sample name cannot be null.");
    Utils.nonNull(byKeySorted, "Targets cannot be null.");
    Utils.nonNull(comments, "Comments cannot be null.");
    final boolean areTargetIntervalsAllPopulated = byKeySorted.keySet().stream().allMatch(t -> t != null);
    if (!areTargetIntervalsAllPopulated) {
        throw new UserException("Cannot write target coverage file with any null intervals.");
    }
    try (final TableWriter<ReadCountRecord> writer = writerWithIntervals(outWriter, Collections.singletonList(sampleName))) {
        for (String comment : comments) {
            writer.writeComment(comment);
        }
        for (final Locatable locatable : byKeySorted.keySet()) {
            final SimpleInterval interval = new SimpleInterval(locatable);
            final double coverage = byKeySorted.get(locatable).doubleValue();
            writer.writeRecord(new ReadCountRecord.SingleSampleRecord(new Target(interval), coverage));
        }
    } catch (final IOException e) {
        throw new UserException.CouldNotCreateOutputFile(outName, e);
    }
}

Example 9 with UserException

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

the class ConvertHeaderlessHadoopBamShardToBam method doWork.

@Override
protected Object doWork() {
    SAMFileHeader header = null;
    try (final SamReader headerReader = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT).open(bamWithHeader)) {
        header = headerReader.getFileHeader();
    } catch (IOException e) {
        throw new UserException("Error reading header from " + bamWithHeader.getAbsolutePath(), e);
    }
    SparkUtils.convertHeaderlessHadoopBamShardToBam(bamShard, header, outputBam);
    return null;
}

Example 10 with UserException

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

the class IntervalArgumentCollection method parseIntervals.

private void parseIntervals(final GenomeLocParser genomeLocParser) {
    // return if no interval arguments at all
    if (!intervalsSpecified()) {
        throw new GATKException("Cannot call parseIntervals() without specifying either intervals to include or exclude.");
    }
    GenomeLocSortedSet includeSortedSet;
    if (getIntervalStrings().isEmpty()) {
        // the -L argument isn't specified, which means that -XL was, since we checked intervalsSpecified()
        // therefore we set the include set to be the entire reference territory
        includeSortedSet = GenomeLocSortedSet.createSetFromSequenceDictionary(genomeLocParser.getSequenceDictionary());
    } else {
        try {
            includeSortedSet = IntervalUtils.loadIntervals(getIntervalStrings(), intervalSetRule, intervalMerging, intervalPadding, genomeLocParser);
        } catch (UserException.EmptyIntersection e) {
            throw new CommandLineException.BadArgumentValue("-L, --interval_set_rule", getIntervalStrings() + "," + intervalSetRule, "The specified intervals had an empty intersection");
        }
    }
    final GenomeLocSortedSet excludeSortedSet = IntervalUtils.loadIntervals(excludeIntervalStrings, IntervalSetRule.UNION, intervalMerging, intervalExclusionPadding, genomeLocParser);
    if (excludeSortedSet.contains(GenomeLoc.UNMAPPED)) {
        throw new UserException("-XL unmapped is not currently supported");
    }
    GenomeLocSortedSet intervals;
    // if no exclude arguments, can return the included set directly
    if (excludeSortedSet.isEmpty()) {
        intervals = includeSortedSet;
    } else // otherwise there are exclude arguments => must merge include and exclude GenomeLocSortedSets
    {
        intervals = includeSortedSet.subtractRegions(excludeSortedSet);
        if (intervals.isEmpty()) {
            throw new CommandLineException.BadArgumentValue("-L,-XL", getIntervalStrings().toString() + ", " + excludeIntervalStrings.toString(), "The intervals specified for exclusion with -XL removed all territory specified by -L.");
        }
        // logging messages only printed when exclude (-XL) arguments are given
        final long toPruneSize = includeSortedSet.coveredSize();
        final long toExcludeSize = excludeSortedSet.coveredSize();
        final long intervalSize = intervals.coveredSize();
        logger.info(String.format("Initial include intervals span %d loci; exclude intervals span %d loci", toPruneSize, toExcludeSize));
        logger.info(String.format("Excluding %d loci from original intervals (%.2f%% reduction)", toPruneSize - intervalSize, (toPruneSize - intervalSize) / (0.01 * toPruneSize)));
    }
    logger.info(String.format("Processing %d bp from intervals", intervals.coveredSize()));
    // Separate out requests for unmapped records from the rest of the intervals.
    boolean traverseUnmapped = false;
    if (intervals.contains(GenomeLoc.UNMAPPED)) {
        traverseUnmapped = true;
        intervals.remove(GenomeLoc.UNMAPPED);
    }
    traversalParameters = new TraversalParameters(IntervalUtils.convertGenomeLocsToSimpleIntervals(intervals.toList()), traverseUnmapped);
}