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

Example 26 with UserException

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

the class FeatureDataSource method getFeatureReader.

@SuppressWarnings("unchecked")
private static <T extends Feature> FeatureReader<T> getFeatureReader(final FeatureInput<T> featureInput, final Class<? extends Feature> targetFeatureType, final Function<SeekableByteChannel, SeekableByteChannel> cloudWrapper, final Function<SeekableByteChannel, SeekableByteChannel> cloudIndexWrapper, final Path reference) {
    if (isGenomicsDBPath(featureInput.getFeaturePath())) {
        try {
            if (reference == null) {
                throw new UserException.MissingReference("You must provide a reference if you want to load from GenomicsDB");
            }
            try {
                final File referenceAsFile = reference.toFile();
                return (FeatureReader<T>) getGenomicsDBFeatureReader(featureInput.getFeaturePath(), referenceAsFile);
            } catch (final UnsupportedOperationException e) {
                throw new UserException.BadInput("GenomicsDB requires that the reference be a local file.", e);
            }
        } catch (final ClassCastException e) {
            throw new UserException("GenomicsDB inputs can only be used to provide VariantContexts.", e);
        }
    } else {
        final Path featurePath = IOUtils.getPath(featureInput.getFeaturePath());
        IOUtils.assertFileIsReadable(featurePath);
        final FeatureCodec<T, ?> codec = (FeatureCodec<T, ?>) FeatureManager.getCodecForFile(featurePath, targetFeatureType);
        return getTribbleFeatureReader(featureInput, codec, cloudWrapper, cloudIndexWrapper);
    }
}

Example 27 with UserException

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

the class FeatureWalker method initializeDrivingFeatures.

@SuppressWarnings("unchecked")
private void initializeDrivingFeatures() {
    final File drivingFile = getDrivingFeatureFile();
    final FeatureCodec<? extends Feature, ?> codec = FeatureManager.getCodecForFile(drivingFile);
    if (isAcceptableFeatureType(codec.getFeatureType())) {
        drivingFeatures = new FeatureDataSource<>(new FeatureInput<>(drivingFile.getAbsolutePath()), FeatureDataSource.DEFAULT_QUERY_LOOKAHEAD_BASES, null, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, referenceArguments.getReferencePath());
        final FeatureInput<F> drivingFeaturesInput = new FeatureInput<>(drivingFile.getAbsolutePath(), "drivingFeatureFile");
        features.addToFeatureSources(0, drivingFeaturesInput, codec.getFeatureType(), cloudPrefetchBuffer, cloudIndexPrefetchBuffer, referenceArguments.getReferencePath());
    } else {
        throw new UserException("File " + drivingFile + " contains features of the wrong type.");
    }
}

Example 28 with UserException

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

the class SinglePassSamProgram method makeItSo.

public static void makeItSo(final File input, final File referenceSequence, final boolean assumeSorted, final long stopAfter, final Collection<SinglePassSamProgram> programs) {
    // Setup the standard inputs
    IOUtil.assertFileIsReadable(input);
    final SamReader in = SamReaderFactory.makeDefault().referenceSequence(referenceSequence).open(input);
    // Optionally load up the reference sequence and double check sequence dictionaries
    final ReferenceSequenceFileWalker walker;
    if (referenceSequence == null) {
        walker = null;
    } else {
        IOUtil.assertFileIsReadable(referenceSequence);
        walker = new ReferenceSequenceFileWalker(referenceSequence);
        if (!in.getFileHeader().getSequenceDictionary().isEmpty()) {
            SequenceUtil.assertSequenceDictionariesEqual(in.getFileHeader().getSequenceDictionary(), walker.getSequenceDictionary());
        }
    }
    // Check on the sort order of the BAM file
    {
        final SortOrder sort = in.getFileHeader().getSortOrder();
        if (sort != SortOrder.coordinate) {
            if (assumeSorted) {
                logger.warn("File reports sort order '" + sort + "', assuming it's coordinate sorted anyway.");
            } else {
                throw new UserException("File " + input.getAbsolutePath() + " should be coordinate sorted but " + "the header says the sort order is " + sort + ". If you believe the file " + "to be coordinate sorted you may pass ASSUME_SORTED=true");
            }
        }
    }
    // Call the abstract setup method!
    boolean anyUseNoRefReads = false;
    for (final SinglePassSamProgram program : programs) {
        program.setup(in.getFileHeader(), input);
        anyUseNoRefReads = anyUseNoRefReads || program.usesNoRefReads();
    }
    final ProgressLogger progress = new ProgressLogger(logger);
    for (final SAMRecord rec : in) {
        final ReferenceSequence ref;
        if (walker == null || rec.getReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
            ref = null;
        } else {
            ref = walker.get(rec.getReferenceIndex());
        }
        for (final SinglePassSamProgram program : programs) {
            program.acceptRead(rec, ref);
        }
        progress.record(rec);
        // See if we need to terminate early?
        if (stopAfter > 0 && progress.getCount() >= stopAfter) {
            break;
        }
        // And see if we're into the unmapped reads at the end
        if (!anyUseNoRefReads && rec.getReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
            break;
        }
    }
    CloserUtil.close(in);
    for (final SinglePassSamProgram program : programs) {
        program.finish();
    }
}

Example 29 with UserException

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

the class CollectSequencingArtifactMetrics method acceptRead.

@Override
protected void acceptRead(final SAMRecord rec, final ReferenceSequence ref) {
    // see if the whole read should be skipped
    if (recordFilter.filterOut(rec))
        return;
    // check read group + library
    final String library = (rec.getReadGroup() == null) ? UNKNOWN_LIBRARY : getOrElse(rec.getReadGroup().getLibrary(), UNKNOWN_LIBRARY);
    if (!libraries.contains(library)) {
        // should never happen if SAM is valid
        throw new UserException("Record contains library that is missing from header: " + library);
    }
    // iterate over aligned positions
    for (final AlignmentBlock block : rec.getAlignmentBlocks()) {
        for (int offset = 0; offset < block.getLength(); offset++) {
            // remember, these are 1-based!
            final int readPos = block.getReadStart() + offset;
            final int refPos = block.getReferenceStart() + offset;
            /**
                 * Skip regions outside of intervals.
                 *
                 * NB: IntervalListReferenceSequenceMask.get() has side-effects which assume
                 * that successive ReferenceSequence's passed to this method will be in-order
                 * (e.g. it will break if you call acceptRead() with chr1, then chr2, then chr1
                 * again). So this only works if the underlying iteration is coordinate-sorted.
                 */
            if (intervalMask != null && !intervalMask.get(ref.getContigIndex(), refPos))
                continue;
            // skip dbSNP sites
            if (dbSnpMask != null && dbSnpMask.isDbSnpSite(ref.getName(), refPos))
                continue;
            // skip the ends of the reference
            final int contextStartIndex = refPos - CONTEXT_SIZE - 1;
            final int contextFullLength = 2 * CONTEXT_SIZE + 1;
            if (contextStartIndex < 0 || contextStartIndex + contextFullLength > ref.length())
                continue;
            // skip contexts with N bases
            final String context = StringUtil.bytesToString(ref.getBases(), contextStartIndex, contextFullLength).toUpperCase();
            if (context.contains("N"))
                continue;
            // skip low BQ sites
            if (failsBaseQualityCutoff(readPos, rec))
                continue;
            // skip N bases in read
            final char readBase = Character.toUpperCase((char) rec.getReadBases()[readPos - 1]);
            if (readBase == 'N')
                continue;
            // count the base!
            artifactCounters.get(library).countRecord(context, readBase, rec);
        }
    }
}

Example 30 with UserException

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

the class CollectJumpingLibraryMetrics method doWork.

/**
     * Calculates the detailed statistics about the jumping library and then generates the results.
     */
@Override
protected Object doWork() {
    for (File f : INPUT) {
        IOUtil.assertFileIsReadable(f);
    }
    IOUtil.assertFileIsWritable(OUTPUT);
    Histogram<Integer> innieHistogram = new Histogram<>();
    Histogram<Integer> outieHistogram = new Histogram<>();
    int fragments = 0;
    int innies = 0;
    int outies = 0;
    int innieDupes = 0;
    int outieDupes = 0;
    int crossChromPairs = 0;
    int superSized = 0;
    int tandemPairs = 0;
    double chimeraSizeMinimum = Math.max(getOutieMode(), (double) CHIMERA_KB_MIN);
    for (File f : INPUT) {
        SamReader reader = SamReaderFactory.makeDefault().open(f);
        if (reader.getFileHeader().getSortOrder() != SAMFileHeader.SortOrder.coordinate) {
            throw new UserException("SAM file must " + f.getName() + " must be sorted in coordinate order");
        }
        for (SAMRecord sam : reader) {
            // We're getting all our info from the first of each pair.
            if (!sam.getFirstOfPairFlag()) {
                continue;
            }
            // Ignore unmapped read pairs
            if (sam.getReadUnmappedFlag()) {
                if (!sam.getMateUnmappedFlag()) {
                    fragments++;
                    continue;
                }
                // If both ends are unmapped and we've hit unaligned reads we're done
                if (sam.getReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
                    break;
                }
                continue;
            }
            if (sam.getMateUnmappedFlag()) {
                fragments++;
                continue;
            }
            // Ignore low-quality reads.  If we don't have the mate mapping quality, assume it's OK
            if ((sam.getAttribute(SAMTag.MQ.name()) != null && sam.getIntegerAttribute(SAMTag.MQ.name()) < MINIMUM_MAPPING_QUALITY) || sam.getMappingQuality() < MINIMUM_MAPPING_QUALITY) {
                continue;
            }
            final int absInsertSize = Math.abs(sam.getInferredInsertSize());
            if (absInsertSize > chimeraSizeMinimum) {
                superSized++;
            } else if (sam.getMateNegativeStrandFlag() == sam.getReadNegativeStrandFlag()) {
                tandemPairs++;
            } else if (!sam.getMateReferenceIndex().equals(sam.getReferenceIndex())) {
                crossChromPairs++;
            } else {
                final PairOrientation pairOrientation = SamPairUtil.getPairOrientation(sam);
                if (pairOrientation == PairOrientation.RF) {
                    outieHistogram.increment(absInsertSize);
                    outies++;
                    if (sam.getDuplicateReadFlag()) {
                        outieDupes++;
                    }
                } else if (pairOrientation == PairOrientation.FR) {
                    innieHistogram.increment(absInsertSize);
                    innies++;
                    if (sam.getDuplicateReadFlag()) {
                        innieDupes++;
                    }
                } else {
                    throw new IllegalStateException("This should never happen");
                }
            }
        }
        CloserUtil.close(reader);
    }
    MetricsFile<JumpingLibraryMetrics, Integer> metricsFile = getMetricsFile();
    JumpingLibraryMetrics metrics = new JumpingLibraryMetrics();
    metrics.JUMP_PAIRS = outies;
    metrics.JUMP_DUPLICATE_PAIRS = outieDupes;
    metrics.JUMP_DUPLICATE_PCT = outies != 0 ? outieDupes / (double) outies : 0;
    metrics.JUMP_LIBRARY_SIZE = (outies > 0 && outieDupes > 0) ? DuplicationMetrics.estimateLibrarySize(outies, outies - outieDupes) : 0;
    outieHistogram.trimByTailLimit(TAIL_LIMIT);
    metrics.JUMP_MEAN_INSERT_SIZE = outieHistogram.getMean();
    metrics.JUMP_STDEV_INSERT_SIZE = outieHistogram.getStandardDeviation();
    metrics.NONJUMP_PAIRS = innies;
    metrics.NONJUMP_DUPLICATE_PAIRS = innieDupes;
    metrics.NONJUMP_DUPLICATE_PCT = innies != 0 ? innieDupes / (double) innies : 0;
    metrics.NONJUMP_LIBRARY_SIZE = (innies > 0 && innieDupes > 0) ? DuplicationMetrics.estimateLibrarySize(innies, innies - innieDupes) : 0;
    innieHistogram.trimByTailLimit(TAIL_LIMIT);
    metrics.NONJUMP_MEAN_INSERT_SIZE = innieHistogram.getMean();
    metrics.NONJUMP_STDEV_INSERT_SIZE = innieHistogram.getStandardDeviation();
    metrics.CHIMERIC_PAIRS = crossChromPairs + superSized + tandemPairs;
    metrics.FRAGMENTS = fragments;
    double totalPairs = outies + innies + metrics.CHIMERIC_PAIRS;
    metrics.PCT_JUMPS = totalPairs != 0 ? outies / totalPairs : 0;
    metrics.PCT_NONJUMPS = totalPairs != 0 ? innies / totalPairs : 0;
    metrics.PCT_CHIMERAS = totalPairs != 0 ? metrics.CHIMERIC_PAIRS / totalPairs : 0;
    metricsFile.addMetric(metrics);
    metricsFile.write(OUTPUT);
    return null;
}