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

Example 36 with GATKException

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

the class TargetMetricsCollector method reflectiveCopy.

/**
     * Since the targeted metrics (HsMetrics, TargetedPcrMetrics,...) share many of the same values as TargetMetrics, this copy will copy all public attributes in targetMetrics
     * to the outputMetrics' attributes of the same name.  If no matching attribute exists in the outputMetrics or the attribute of the target metrics class also is found
     * in targetKeys then it's value is not copied.  Further more, targetKeys and outputKeys are attribute name arrays synchronized by the index.
     * For each target key, targetMetrics.<targetKeys[i]> is assigned to outputMetrics.<outputKeys[i]>
     *
     * @param targetMetrics A metric with values to be copied
     * @param outputMetrics A metrics intended to receive values from targetMetrics
     * @param targetKeys Specific names of attributes of targetMetrics to copy to outputMetrics, each key has a corresponding one in outputKeys
     * @param outputKeys Specific names of the destination attributes of outputMetrics that will be filled with values of outputMetrics, each key has a corresponding one in targetKeys
     * @param <MT> The type of metric of outputMetrics
     */
protected static <MT extends MetricBase> void reflectiveCopy(final TargetMetrics targetMetrics, final MT outputMetrics, final String[] targetKeys, final String[] outputKeys) {
    if (targetKeys == null || outputKeys == null) {
        if (outputKeys != null) {
            throw new GATKException("Target keys is null but output keys == " + StringUtil.join(",", outputKeys));
        }
        if (targetKeys != null) {
            throw new GATKException("Output keys is null but target keys == " + StringUtil.join(",", targetKeys));
        }
    } else {
        if (targetKeys.length != outputKeys.length) {
            throw new GATKException("Target keys and output keys do not have the same length: " + "targetKeys == (" + StringUtil.join(",", targetKeys) + ") " + "outputKeys == (" + StringUtil.join(",", outputKeys) + ")");
        }
    }
    final Class<?> mtClass = outputMetrics.getClass();
    final Set<Field> targetSet = CollectionUtil.makeSet(TargetMetrics.class.getFields());
    for (final String targetKey : targetKeys) {
        if (targetSet.contains(targetKey)) {
            targetSet.remove(targetKey);
        }
    }
    final Set<String> outputSet = new HashSet<>();
    for (final Field field : outputMetrics.getClass().getFields()) {
        outputSet.add(field.getName());
    }
    for (final Field field : targetSet) {
        if (outputSet.contains(field.getName())) {
            try {
                final Field outputField = mtClass.getField(field.getName());
                outputField.set(outputMetrics, field.get(targetMetrics));
            } catch (Exception e) {
                throw new GATKException("Exception while copying targetMetrics to " + outputMetrics.getClass().getName(), e);
            }
        }
    }
    for (int i = 0; i < targetKeys.length; i++) {
        try {
            Field targetMetricField = TargetMetrics.class.getField(targetKeys[i]);
            Field outputMetricField = mtClass.getField(outputKeys[i]);
            outputMetricField.set(outputMetrics, targetMetricField.get(targetMetrics));
        } catch (final Exception exc) {
            throw new GATKException("Exception while copying TargetMetrics." + targetKeys[i] + " to " + mtClass.getName() + "." + outputKeys[i], exc);
        }
    }
}

Example 37 with GATKException

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

the class BedToIntervalList method doWork.

@Override
protected Object doWork() {
    IOUtil.assertFileIsReadable(INPUT);
    IOUtil.assertFileIsReadable(SEQUENCE_DICTIONARY);
    IOUtil.assertFileIsWritable(OUTPUT);
    try {
        final SAMFileHeader header = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).getFileHeader(SEQUENCE_DICTIONARY);
        final IntervalList intervalList = new IntervalList(header);
        /**
             * NB: BED is zero-based, but a BEDCodec by default (since it is returns tribble Features) has an offset of one,
             * so it returns 1-based starts.  Ugh.  Set to zero.
             */
        final FeatureReader<BEDFeature> bedReader = AbstractFeatureReader.getFeatureReader(INPUT.getAbsolutePath(), new BEDCodec(BEDCodec.StartOffset.ZERO), false);
        final CloseableTribbleIterator<BEDFeature> iterator = bedReader.iterator();
        final ProgressLogger progressLogger = new ProgressLogger(logger, (int) 1e6);
        while (iterator.hasNext()) {
            final BEDFeature bedFeature = iterator.next();
            final String sequenceName = bedFeature.getContig();
            /**
                 * NB: BED is zero-based, so we need to add one here to make it one-based.  Please observe we set the start
                 * offset to zero when creating the BEDCodec.
                 */
            final int start = bedFeature.getStart() + 1;
            /**
                 * NB: BED is 0-based OPEN (which, for the end is equivalent to 1-based closed).
                 */
            final int end = bedFeature.getEnd();
            // NB: do not use an empty name within an interval
            String name = bedFeature.getName();
            if (name.isEmpty())
                name = null;
            final SAMSequenceRecord sequenceRecord = header.getSequenceDictionary().getSequence(sequenceName);
            // Do some validation
            if (null == sequenceRecord) {
                throw new GATKException(String.format("Sequence '%s' was not found in the sequence dictionary", sequenceName));
            } else if (start < 1) {
                throw new GATKException(String.format("Start on sequence '%s' was less than one: %d", sequenceName, start));
            } else if (sequenceRecord.getSequenceLength() < start) {
                throw new GATKException(String.format("Start on sequence '%s' was past the end: %d < %d", sequenceName, sequenceRecord.getSequenceLength(), start));
            } else if (end < 1) {
                throw new GATKException(String.format("End on sequence '%s' was less than one: %d", sequenceName, end));
            } else if (sequenceRecord.getSequenceLength() < end) {
                throw new GATKException(String.format("End on sequence '%s' was past the end: %d < %d", sequenceName, sequenceRecord.getSequenceLength(), end));
            } else if (end < start - 1) {
                throw new GATKException(String.format("On sequence '%s', end < start-1: %d <= %d", sequenceName, end, start));
            }
            final Interval interval = new Interval(sequenceName, start, end, bedFeature.getStrand() == Strand.POSITIVE, name);
            intervalList.add(interval);
            progressLogger.record(sequenceName, start);
        }
        CloserUtil.close(bedReader);
        // Sort and write the output
        intervalList.uniqued().write(OUTPUT);
    } catch (final IOException e) {
        throw new RuntimeException(e);
    }
    return null;
}

Example 38 with GATKException

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

the class FindBadGenomicKmersSparkUnitTest method miniRefTest.

@Test(groups = "spark")
public void miniRefTest() throws IOException {
    final JavaSparkContext ctx = SparkContextFactory.getTestSparkContext();
    final ReferenceMultiSource ref = new ReferenceMultiSource((PipelineOptions) null, REFERENCE_FILE_NAME, ReferenceWindowFunctions.IDENTITY_FUNCTION);
    final SAMSequenceDictionary dict = ref.getReferenceSequenceDictionary(null);
    if (dict == null)
        throw new GATKException("No reference dictionary available.");
    final Map<SVKmer, Long> kmerMap = new LinkedHashMap<>();
    for (final SAMSequenceRecord rec : dict.getSequences()) {
        final SimpleInterval interval = new SimpleInterval(rec.getSequenceName(), 1, rec.getSequenceLength());
        final byte[] bases = ref.getReferenceBases(null, interval).getBases();
        final SVKmerizer kmerizer = new SVKmerizer(bases, KMER_SIZE, new SVKmerLong());
        while (kmerizer.hasNext()) {
            final SVKmer kmer = kmerizer.next().canonical(KMER_SIZE);
            final Long currentCount = kmerMap.getOrDefault(kmer, 0L);
            kmerMap.put(kmer, currentCount + 1);
        }
    }
    final Iterator<Map.Entry<SVKmer, Long>> kmerIterator = kmerMap.entrySet().iterator();
    while (kmerIterator.hasNext()) {
        if (kmerIterator.next().getValue() <= FindBadGenomicKmersSpark.MAX_KMER_FREQ)
            kmerIterator.remove();
    }
    final List<SVKmer> badKmers = FindBadGenomicKmersSpark.findBadGenomicKmers(ctx, KMER_SIZE, Integer.MAX_VALUE, ref, null, null);
    final Set<SVKmer> badKmerSet = new HashSet<>(badKmers);
    Assert.assertEquals(badKmers.size(), badKmerSet.size());
    Assert.assertEquals(badKmerSet, kmerMap.keySet());
}

Example 39 with GATKException

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

the class HDF5PCACoveragePoN method readMatrixAndCheckDimensions.

/**
     * Reads a matrix from the underlying PoN file and check its dimensions.
     * @param fullPath the target data-set full path within the HDF5 file.
     * @param expectedRowCount a predicate that returns true iff its argument is an expected number of rows.
     * @param expectedColumnCount a predicate that returns true iff its argument is an expected number of columns.
     * @return GATKException if the result matrix dimensions do not match the expectations or
     *  any other cause as described in {@link #readMatrix(String)}.
     */
private RealMatrix readMatrixAndCheckDimensions(final String fullPath, final IntPredicate expectedRowCount, final IntPredicate expectedColumnCount) {
    final RealMatrix result = readMatrix(fullPath);
    if (expectedRowCount.test(result.getRowDimension()) && expectedColumnCount.test(result.getColumnDimension())) {
        return result;
    }
    final RealMatrix transpose = result.transpose();
    if (!expectedRowCount.test(transpose.getRowDimension())) {
        throw new GATKException(String.format("wrong number of rows in '%s' matrix from file '%s': %d", fullPath, file.getFile(), result.getRowDimension()));
    }
    if (!expectedColumnCount.test(transpose.getColumnDimension())) {
        throw new GATKException(String.format("wrong number of columns in '%s' from file '%s': %d", fullPath, file.getFile(), result.getColumnDimension()));
    }
    return transpose;
}

Example 40 with GATKException

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

the class HDF5PCACoveragePoN method renderPoNTargets.

private static List<Target> renderPoNTargets(final String[][] values, final List<String> targetNamesToRender, final HDF5File reader) {
    if (values.length != targetNamesToRender.size()) {
        throw new GATKException(String.format("Wrong number of elements in the targets recovered " + "from file '%s': number of targets found in file (%d) != number of target names (%d)", reader.getFile(), values.length, targetNamesToRender.size()));
    }
    final int numTargetCols = (int) reader.readDouble(NUM_TARGET_COLUMNS_PATH);
    final List<Target> result = new ArrayList<>(values.length);
    for (int i = 0; i < values.length; i++) {
        if (values[i].length != numTargetCols) {
            throw new GATKException(String.format("Wrong number of column elements in the targets recovered " + "from file '%s': number of columns found in file (%d) != number of target columns (%d)", reader.getFile(), values[i].length, numTargetCols));
        }
        result.add(new Target(targetNamesToRender.get(i), new SimpleInterval(values[i][0], Integer.parseInt(values[i][1]), Integer.parseInt(values[i][2]))));
    }
    return result;
}