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

Example 66 with UserException

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

the class IOUtils method getPath.

/**
     * Converts the given URI to a {@link Path} object. If the filesystem cannot be found in the usual way, then attempt
     * to load the filesystem provider using the thread context classloader. This is needed when the filesystem
     * provider is loaded using a URL classloader (e.g. in spark-submit).
     *
     * @param uriString the URI to convert
     * @return the resulting {@code Path}
     * @throws UserException if an I/O error occurs when creating the file system
     */
public static Path getPath(String uriString) {
    Utils.nonNull(uriString);
    URI uri = URI.create(uriString);
    try {
        // special case GCS, in case the filesystem provider wasn't installed properly but is available.
        if (CloudStorageFileSystem.URI_SCHEME.equals(uri.getScheme())) {
            return BucketUtils.getPathOnGcs(uriString);
        }
        return uri.getScheme() == null ? Paths.get(uriString) : Paths.get(uri);
    } catch (FileSystemNotFoundException e) {
        try {
            ClassLoader cl = Thread.currentThread().getContextClassLoader();
            if (cl == null) {
                throw e;
            }
            return FileSystems.newFileSystem(uri, new HashMap<>(), cl).provider().getPath(uri);
        } catch (IOException io) {
            throw new UserException(uriString + " is not a supported path", io);
        }
    }
}

Example 67 with UserException

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

the class BayesianHetPulldownCalculator method getTumorHetPulldownFromNormalPulldown.

/**
     * Calculates the Het pulldown from a tumor file, given the tumor BAM file and the pulldown from a matched
     * normal BAM file.
     *
     * Note: this method does not perform any statistical inference. The Het SNP sites are directly carried over
     * from the matched normal pulldown. Here, we only collect statistics (ref count, alt count, read depth) and
     * save to a pulldown. The verbosity level of the pulldown is INTERMEDIATE (see {@link AllelicCountTableColumn}).
     *
     * @param tumorBamFile the tumor BAM file
     * @param normalHetPulldown the matched normal Het pulldown
     * @return tumor Het pulldown
     */
public Pulldown getTumorHetPulldownFromNormalPulldown(final File tumorBamFile, final Pulldown normalHetPulldown) {
    try (final SamReader bamReader = SamReaderFactory.makeDefault().validationStringency(validationStringency).referenceSequence(refFile).open(tumorBamFile)) {
        if (bamReader.getFileHeader().getSortOrder() != SAMFileHeader.SortOrder.coordinate) {
            throw new UserException.BadInput("BAM file " + tumorBamFile.toString() + " must be coordinate sorted.");
        }
        final Pulldown tumorHetPulldown = new Pulldown(bamReader.getFileHeader());
        final SamLocusIterator locusIterator = getSamLocusIteratorWithDefaultFilters(bamReader);
        /* get a map of SimpleIntervals in the pulldown to their index */
        final Map<SimpleInterval, Integer> normalPulldownIndexMap = normalHetPulldown.getSimpleIntervalToIndexMap();
        final int totalNumberOfSNPs = snpIntervals.size();
        logger.info("Examining " + totalNumberOfSNPs + " sites in total...");
        int locusCount = 0;
        for (final SamLocusIterator.LocusInfo locus : locusIterator) {
            if (locusCount % NUMBER_OF_SITES_PER_LOGGED_STATUS_UPDATE == 0) {
                logger.info("Examined " + locusCount + " covered sites.");
            }
            locusCount++;
            final int totalReadCount = locus.getRecordAndOffsets().size();
            if (totalReadCount <= readDepthThreshold) {
                continue;
            }
            /* find the AllelicCount from the normal pulldown */
            int indexInNormalPulldown;
            try {
                indexInNormalPulldown = normalPulldownIndexMap.get(new SimpleInterval(locus.getSequenceName(), locus.getPosition(), locus.getPosition()));
            } catch (NullPointerException e) {
                throw new GATKException.ShouldNeverReachHereException("Can not find the required AllelicCount " + "object in the normal pulldown. Stopping.");
            }
            /* just count the alt and ref nucleotide and add to the tumor pulldown */
            final Nucleotide.Counter baseCounts = getPileupBaseCounts(locus);
            tumorHetPulldown.add(new AllelicCount(new SimpleInterval(locus.getSequenceName(), locus.getPosition(), locus.getPosition()), (int) baseCounts.get(normalHetPulldown.getCounts().get(indexInNormalPulldown).getRefNucleotide()), (int) baseCounts.get(normalHetPulldown.getCounts().get(indexInNormalPulldown).getAltNucleotide()), normalHetPulldown.getCounts().get(indexInNormalPulldown).getRefNucleotide(), normalHetPulldown.getCounts().get(indexInNormalPulldown).getAltNucleotide(), totalReadCount));
        }
        logger.info(locusCount + " covered sites out of " + totalNumberOfSNPs + " total sites were examined.");
        return tumorHetPulldown;
    } catch (final IOException | SAMFormatException e) {
        throw new UserException(e.getMessage());
    }
}

Example 68 with UserException

use of org.broadinstitute.hellbender.exceptions.UserException in project gatk 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 69 with UserException

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

the class SelectVariants method apply.

@Override
public void apply(VariantContext vc, ReadsContext readsContext, ReferenceContext ref, FeatureContext featureContext) {
    if (fullyDecode) {
        vc = vc.fullyDecode(getHeaderForVariants(), lenientVCFProcessing);
    }
    if (mendelianViolations && invertLogic((mv.countFamilyViolations(sampleDB, samples, vc) == 0), invertMendelianViolations)) {
        return;
    }
    if (discordanceOnly && !isDiscordant(vc, featureContext.getValues(discordanceTrack))) {
        return;
    }
    if (concordanceOnly && !isConcordant(vc, featureContext.getValues(concordanceTrack))) {
        return;
    }
    if (alleleRestriction.equals(NumberAlleleRestriction.BIALLELIC) && !vc.isBiallelic()) {
        return;
    }
    if (alleleRestriction.equals(NumberAlleleRestriction.MULTIALLELIC) && vc.isBiallelic()) {
        return;
    }
    if (containsIndelLargerOrSmallerThan(vc, maxIndelSize, minIndelSize)) {
        return;
    }
    if (considerFilteredGenotypes()) {
        final int numFilteredSamples = numFilteredGenotypes(vc);
        final double fractionFilteredGenotypes = samples.isEmpty() ? 0.0 : numFilteredSamples / samples.size();
        if (numFilteredSamples > maxFilteredGenotypes || numFilteredSamples < minFilteredGenotypes || fractionFilteredGenotypes > maxFractionFilteredGenotypes || fractionFilteredGenotypes < minFractionFilteredGenotypes)
            return;
    }
    if (considerNoCallGenotypes()) {
        final int numNoCallSamples = numNoCallGenotypes(vc);
        final double fractionNoCallGenotypes = samples.isEmpty() ? 0.0 : ((double) numNoCallSamples) / samples.size();
        if (numNoCallSamples > maxNOCALLnumber || fractionNoCallGenotypes > maxNOCALLfraction)
            return;
    }
    // Initialize the cache of PL index to a list of alleles for each ploidy.
    initalizeAlleleAnyploidIndicesCache(vc);
    final VariantContext sub = subsetRecord(vc, preserveAlleles, removeUnusedAlternates);
    final VariantContextBuilder builder = new VariantContextBuilder(vc);
    if (setFilteredGenotypesToNocall) {
        GATKVariantContextUtils.setFilteredGenotypeToNocall(builder, sub, setFilteredGenotypesToNocall, this::getGenotypeFilters);
    }
    final VariantContext filteredGenotypeToNocall = setFilteredGenotypesToNocall ? builder.make() : sub;
    // Not excluding non-variants or subsetted polymorphic variants AND including filtered loci or subsetted variant is not filtered
    if ((!XLnonVariants || filteredGenotypeToNocall.isPolymorphicInSamples()) && (!XLfiltered || !filteredGenotypeToNocall.isFiltered())) {
        // Write the subsetted variant if it matches all of the expressions
        boolean failedJexlMatch = false;
        try {
            for (VariantContextUtils.JexlVCMatchExp jexl : jexls) {
                if (invertLogic(!VariantContextUtils.match(filteredGenotypeToNocall, jexl), invertSelect)) {
                    failedJexlMatch = true;
                    break;
                }
            }
        } catch (IllegalArgumentException e) {
            //  expression detected...")
            throw new UserException(e.getMessage() + "\nSee https://www.broadinstitute.org/gatk/guide/article?id=1255 for documentation on using JEXL in GATK", e);
        }
        if (!failedJexlMatch && (!selectRandomFraction || Utils.getRandomGenerator().nextDouble() < fractionRandom)) {
            vcfWriter.add(filteredGenotypeToNocall);
        }
    }
}

Example 70 with UserException

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

the class CountFalsePositives method onTraversalSuccess.

@Override
public Object onTraversalSuccess() {
    final List<SimpleInterval> intervals = intervalArgumentCollection.getIntervals(getReferenceDictionary());
    final long targetTerritory = intervals.stream().mapToInt(i -> i.size()).sum();
    try (FalsePositiveTableWriter writer = new FalsePositiveTableWriter(outputFile)) {
        FalsePositiveRecord falsePositiveRecord = new FalsePositiveRecord(id, snpFalsePositiveCount, indelFalsePositiveCount, targetTerritory);
        writer.writeRecord(falsePositiveRecord);
    } catch (IOException e) {
        throw new UserException(String.format("Encountered an IO exception while opening %s", outputFile));
    }
    return "SUCCESS";
}