Examples with VariantContext htsjdk.variant.variantcontext.VariantContext used on opensource projects

Example 81 with VariantContext

use of htsjdk.variant.variantcontext.VariantContext in project gatk by broadinstitute.

the class RenameSampleInVcf method doWork.

@Override
protected Object doWork() {
    IOUtil.assertFileIsReadable(INPUT);
    IOUtil.assertFileIsWritable(OUTPUT);
    try (final VCFFileReader in = new VCFFileReader(INPUT)) {
        final VCFHeader header = in.getFileHeader();
        Utils.validateArg(header.getGenotypeSamples().size() == 1, "Input VCF must be single-sample.");
        Utils.validateArg(OLD_SAMPLE_NAME == null || OLD_SAMPLE_NAME.equals(header.getGenotypeSamples().get(0)), () -> "Input VCF did not contain expected sample. Contained: " + header.getGenotypeSamples().get(0));
        final EnumSet<Options> options = EnumSet.copyOf(VariantContextWriterBuilder.DEFAULT_OPTIONS);
        if (CREATE_INDEX)
            options.add(Options.INDEX_ON_THE_FLY);
        else
            options.remove(Options.INDEX_ON_THE_FLY);
        final VCFHeader outHeader = new VCFHeader(header.getMetaDataInInputOrder(), CollectionUtil.makeList(NEW_SAMPLE_NAME));
        try (final VariantContextWriter out = new VariantContextWriterBuilder().setOutputFile(OUTPUT).setReferenceDictionary(outHeader.getSequenceDictionary()).setOptions(options).build()) {
            out.writeHeader(outHeader);
            for (final VariantContext ctx : in) {
                out.add(ctx);
            }
        }
    }
    return null;
}

Example 82 with VariantContext

use of htsjdk.variant.variantcontext.VariantContext in project gatk by broadinstitute.

the class SortVcf method sortInputs.

/**
     * Merge the inputs and sort them by adding each input's content to a single SortingCollection.
     * <p/>
     * NB: It would be better to have a merging iterator as in MergeSamFiles, as this would perform better for pre-sorted inputs.
     * Here, we are assuming inputs are unsorted, and so adding their VariantContexts iteratively is fine for now.
     * MergeVcfs exists for simple merging of presorted inputs.
     *
     * @param readers      - a list of VCFFileReaders, one for each input VCF
     * @param outputHeader - The merged header whose information we intend to use in the final output file
     */
private SortingCollection<VariantContext> sortInputs(final List<VCFFileReader> readers, final VCFHeader outputHeader) {
    final ProgressLogger readProgress = new ProgressLogger(logger, 25000, "read", "records");
    // NB: The default MAX_RECORDS_IN_RAM may not be appropriate here. VariantContexts are smaller than SamRecords
    // We would have to play around empirically to find an appropriate value. We are not performing this optimization at this time.
    final SortingCollection<VariantContext> sorter = SortingCollection.newInstance(VariantContext.class, new VCFRecordCodec(outputHeader), outputHeader.getVCFRecordComparator(), MAX_RECORDS_IN_RAM, TMP_DIR);
    int readerCount = 1;
    for (final VCFFileReader reader : readers) {
        logger.info("Reading entries from input file " + readerCount);
        for (final VariantContext variantContext : reader) {
            sorter.add(variantContext);
            readProgress.record(variantContext.getContig(), variantContext.getStart());
        }
        reader.close();
        readerCount++;
    }
    return sorter;
}

Example 83 with VariantContext

use of htsjdk.variant.variantcontext.VariantContext in project gatk by broadinstitute.

the class SortVcf method writeSortedOutput.

private void writeSortedOutput(final VCFHeader outputHeader, final SortingCollection<VariantContext> sortedOutput) {
    final ProgressLogger writeProgress = new ProgressLogger(logger, 25000, "wrote", "records");
    final EnumSet<Options> options = CREATE_INDEX ? EnumSet.of(Options.INDEX_ON_THE_FLY) : EnumSet.noneOf(Options.class);
    final VariantContextWriter out = new VariantContextWriterBuilder().setReferenceDictionary(outputHeader.getSequenceDictionary()).setOptions(options).setOutputFile(OUTPUT).build();
    out.writeHeader(outputHeader);
    for (final VariantContext variantContext : sortedOutput) {
        out.add(variantContext);
        writeProgress.record(variantContext.getContig(), variantContext.getStart());
    }
    out.close();
}

Example 84 with VariantContext

use of htsjdk.variant.variantcontext.VariantContext in project gatk by broadinstitute.

the class PairedVariantSubContextIterator method next.

@Override
public VcTuple next() {
    Utils.validate(hasNext(), "next() called while hasNext() is false.");
    final VariantContext truthVariantContext = this.truthIterator.hasNext() ? this.truthIterator.peek() : null;
    final VariantContext callVariantContext = this.callIterator.hasNext() ? this.callIterator.peek() : null;
    // If one or the other is null because there is no next, just return a one-sided tuple
    if (truthVariantContext == null) {
        return new VcTuple(null, this.callIterator.next().subContextFromSample(callSample));
    } else if (callVariantContext == null) {
        return new VcTuple(this.truthIterator.next().subContextFromSample(truthSample), null);
    }
    // Otherwise check the ordering and do the right thing
    final int ordering = this.comparator.compare(truthVariantContext, callVariantContext);
    if (ordering == 0) {
        return new VcTuple(this.truthIterator.next().subContextFromSample(truthSample), this.callIterator.next().subContextFromSample(callSample));
    } else if (ordering < 0) {
        return new VcTuple(this.truthIterator.next().subContextFromSample(truthSample), null);
    } else {
        return new VcTuple(null, this.callIterator.next().subContextFromSample(callSample));
    }
}

Example 85 with VariantContext

use of htsjdk.variant.variantcontext.VariantContext in project gatk by broadinstitute.

the class VariantRecalibrator method onTraversalStart.

//---------------------------------------------------------------------------------------------------------------
//
// onTraversalStart
//
//---------------------------------------------------------------------------------------------------------------
@Override
public void onTraversalStart() {
    if (gatk3Compatibility) {
        // Temporary argument for validation of GATK4 implementation against GATK3 results:
        // Reset the RNG and draw a single int to align the RNG initial state with that used
        // by GATK3 to allow comparison of results with GATK3
        Utils.resetRandomGenerator();
        Utils.getRandomGenerator().nextInt();
    }
    dataManager = new VariantDataManager(new ArrayList<>(USE_ANNOTATIONS), VRAC);
    if (RSCRIPT_FILE != null && !RScriptExecutor.RSCRIPT_EXISTS)
        Utils.warnUser(logger, String.format("Rscript not found in environment path. %s will be generated but PDF plots will not.", RSCRIPT_FILE));
    if (IGNORE_INPUT_FILTERS != null) {
        ignoreInputFilterSet.addAll(IGNORE_INPUT_FILTERS);
    }
    try {
        tranchesStream = new PrintStream(TRANCHES_FILE);
    } catch (FileNotFoundException e) {
        throw new UserException.CouldNotCreateOutputFile(TRANCHES_FILE, e);
    }
    for (FeatureInput<VariantContext> variantFeature : resource) {
        dataManager.addTrainingSet(new TrainingSet(variantFeature));
    }
    if (!dataManager.checkHasTrainingSet()) {
        throw new CommandLineException("No training set found! Please provide sets of known polymorphic loci marked with the training=true feature input tag. For example, -resource hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmapFile.vcf");
    }
    if (!dataManager.checkHasTruthSet()) {
        throw new CommandLineException("No truth set found! Please provide sets of known polymorphic loci marked with the truth=true feature input tag. For example, -resource hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmapFile.vcf");
    }
    //TODO: this should be refactored/consolidated as part of
    // https://github.com/broadinstitute/gatk/issues/2112
    // https://github.com/broadinstitute/gatk/issues/121,
    // https://github.com/broadinstitute/gatk/issues/1116 and
    // Initialize VCF header lines
    Set<VCFHeaderLine> hInfo = getDefaultToolVCFHeaderLines();
    VariantRecalibrationUtils.addVQSRStandardHeaderLines(hInfo);
    SAMSequenceDictionary sequenceDictionary = getBestAvailableSequenceDictionary();
    if (hasReference()) {
        hInfo = VcfUtils.updateHeaderContigLines(hInfo, referenceArguments.getReferenceFile(), sequenceDictionary, true);
    } else if (null != sequenceDictionary) {
        hInfo = VcfUtils.updateHeaderContigLines(hInfo, null, sequenceDictionary, true);
    }
    recalWriter = createVCFWriter(new File(output));
    recalWriter.writeHeader(new VCFHeader(hInfo));
    for (int iii = 0; iii < REPLICATE * 2; iii++) {
        replicate.add(Utils.getRandomGenerator().nextDouble());
    }
}