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

Example 96 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 97 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 98 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";
}

Example 99 with UserException

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

the class ApplyVQSR method doAlleleSpecificFiltering.

/**
     * Calculate the allele-specific filter status of vc
     * @param vc
     * @param recals
     * @param builder   is modified by adding attributes
     * @return a String with the filter status for this site
     */
private String doAlleleSpecificFiltering(final VariantContext vc, final List<VariantContext> recals, final VariantContextBuilder builder) {
    double bestLod = VariantRecalibratorEngine.MIN_ACCEPTABLE_LOD_SCORE;
    final List<String> culpritStrings = new ArrayList<>();
    final List<String> lodStrings = new ArrayList<>();
    final List<String> AS_filterStrings = new ArrayList<>();
    String[] prevCulpritList = null;
    String[] prevLodList = null;
    String[] prevASfiltersList = null;
    //get VQSR annotations from previous run of ApplyRecalibration, if applicable
    if (foundINDELTranches || foundSNPTranches) {
        final String prevCulprits = vc.getAttributeAsString(GATKVCFConstants.AS_CULPRIT_KEY, "");
        prevCulpritList = prevCulprits.isEmpty() ? new String[0] : prevCulprits.split(listPrintSeparator);
        final String prevLodString = vc.getAttributeAsString(GATKVCFConstants.AS_VQS_LOD_KEY, "");
        prevLodList = prevLodString.isEmpty() ? new String[0] : prevLodString.split(listPrintSeparator);
        final String prevASfilters = vc.getAttributeAsString(GATKVCFConstants.AS_FILTER_STATUS_KEY, "");
        prevASfiltersList = prevASfilters.isEmpty() ? new String[0] : prevASfilters.split(listPrintSeparator);
    }
    //for each allele in the current VariantContext
    for (int altIndex = 0; altIndex < vc.getNAlleles() - 1; altIndex++) {
        final Allele allele = vc.getAlternateAllele(altIndex);
        //if the current allele is not part of this recalibration mode, add its annotations to the list and go to the next allele
        if (!VariantDataManager.checkVariationClass(vc, allele, MODE)) {
            updateAnnotationsWithoutRecalibrating(altIndex, prevCulpritList, prevLodList, prevASfiltersList, culpritStrings, lodStrings, AS_filterStrings);
            continue;
        }
        //if the current allele does need to have recalibration applied...
        //initialize allele-specific VQSR annotation data with values for spanning deletion
        String alleleLodString = emptyFloatValue;
        String alleleFilterString = emptyStringValue;
        String alleleCulpritString = emptyStringValue;
        //if it's not a spanning deletion, replace those allele strings with the real values
        if (!GATKVCFConstants.isSpanningDeletion(allele)) {
            VariantContext recalDatum = getMatchingRecalVC(vc, recals, allele);
            if (recalDatum == null) {
                throw new UserException("Encountered input allele which isn't found in the input recal file. Please make sure VariantRecalibrator and ApplyRecalibration were run on the same set of input variants with flag -AS. First seen at: " + vc);
            }
            //compare VQSLODs for all alleles in the current mode for filtering later
            final double lod = recalDatum.getAttributeAsDouble(GATKVCFConstants.VQS_LOD_KEY, VariantRecalibratorEngine.MIN_ACCEPTABLE_LOD_SCORE);
            if (lod > bestLod)
                bestLod = lod;
            alleleLodString = String.format("%.4f", lod);
            alleleFilterString = generateFilterString(lod);
            alleleCulpritString = recalDatum.getAttributeAsString(GATKVCFConstants.CULPRIT_KEY, ".");
            if (recalDatum != null) {
                if (recalDatum.hasAttribute(GATKVCFConstants.POSITIVE_LABEL_KEY))
                    builder.attribute(GATKVCFConstants.POSITIVE_LABEL_KEY, true);
                if (recalDatum.hasAttribute(GATKVCFConstants.NEGATIVE_LABEL_KEY))
                    builder.attribute(GATKVCFConstants.NEGATIVE_LABEL_KEY, true);
            }
        }
        //append per-allele VQSR annotations
        lodStrings.add(alleleLodString);
        AS_filterStrings.add(alleleFilterString);
        culpritStrings.add(alleleCulpritString);
    }
    // Annotate the new record with its VQSLOD, AS_FilterStatus, and the worst performing annotation
    if (!AS_filterStrings.isEmpty())
        builder.attribute(GATKVCFConstants.AS_FILTER_STATUS_KEY, AnnotationUtils.encodeStringList(AS_filterStrings));
    if (!lodStrings.isEmpty())
        builder.attribute(GATKVCFConstants.AS_VQS_LOD_KEY, AnnotationUtils.encodeStringList(lodStrings));
    if (!culpritStrings.isEmpty())
        builder.attribute(GATKVCFConstants.AS_CULPRIT_KEY, AnnotationUtils.encodeStringList(culpritStrings));
    return generateFilterStringFromAlleles(vc, bestLod);
}

Example 100 with UserException

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

the class ASEReadCounter method filterPileup.

private ReadPileup filterPileup(final ReadPileup originalPileup, final CountPileupType countType) {
    SAMFileHeader header = getHeaderForReads();
    final ReadPileup pileupWithDeletions;
    switch(countType) {
        case COUNT_FRAGMENTS_REQUIRE_SAME_BASE:
            pileupWithDeletions = originalPileup.getOverlappingFragmentFilteredPileup(true, ReadPileup.baseQualTieBreaker, header);
            break;
        case COUNT_READS:
            pileupWithDeletions = originalPileup;
            break;
        case COUNT_FRAGMENTS:
            pileupWithDeletions = originalPileup.getOverlappingFragmentFilteredPileup(false, ReadPileup.baseQualTieBreaker, header);
            break;
        default:
            throw new UserException("Must use valid CountPileupType");
    }
    return pileupWithDeletions.makeFilteredPileup(p -> !p.isDeletion());
}