Examples with VariantContextWriter htsjdk.variant.variantcontext.writer.VariantContextWriter used on opensource projects

Example 66 with VariantContextWriter

use of htsjdk.variant.variantcontext.writer.VariantContextWriter in project jvarkit by lindenb.

the class VcfSetSequenceDictionary method doVcfToVcf.

@Override
protected int doVcfToVcf(final String inputName, final VcfIterator in, final VariantContextWriter delegate) {
    final VariantContextWriter out = this.component.open(delegate);
    out.writeHeader(in.getHeader());
    final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(in.getHeader()).logger(LOG);
    while (in.hasNext()) {
        out.add(progress.watch(in.next()));
    }
    progress.finish();
    return 0;
}

Example 67 with VariantContextWriter

use of htsjdk.variant.variantcontext.writer.VariantContextWriter in project jvarkit by lindenb.

the class SortVcfOnRef2 method sortvcf.

protected int sortvcf(BufferedReader in) throws IOException {
    if (this.refdict != null) {
        LOG.info("load dict from " + this.refdict);
        this.dict = SAMSequenceDictionaryExtractor.extractDictionary(this.refdict);
        if (this.dict == null) {
            LOG.error("cannot find sam sequence dictionary from " + refdict);
        }
    }
    final VCFUtils.CodecAndHeader cah = VCFUtils.parseHeader(in);
    final VCFHeader h2 = new VCFHeader(cah.header);
    if (this.dict != null) {
        h2.setSequenceDictionary(this.dict);
    } else {
        this.dict = h2.getSequenceDictionary();
        if (this.dict == null) {
            LOG.error("No internal sequence dictionay found in input");
            return -1;
        }
    }
    addMetaData(h2);
    if (this.dict.isEmpty()) {
        LOG.warn("SEQUENCE DICTIONARY IS EMPTY/NULL");
    }
    CloseableIterator<ChromPosLine> iter = null;
    SortingCollection<ChromPosLine> array = null;
    VariantContextWriter w = null;
    try {
        array = SortingCollection.newInstance(ChromPosLine.class, new VariantCodec(), new VariantComparator(), this.writingSortingCollection.getMaxRecordsInRam(), this.writingSortingCollection.getTmpPaths());
        array.setDestructiveIteration(true);
        final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(this.dict);
        String line;
        while ((line = in.readLine()) != null) {
            final ChromPosLine cpl = new ChromPosLine(line);
            progress.watch(cpl.tid, cpl.pos);
            array.add(cpl);
        }
        array.doneAdding();
        progress.finish();
        w = super.openVariantContextWriter(outputFile);
        w.writeHeader(h2);
        iter = array.iterator();
        while (iter.hasNext()) {
            w.add(cah.codec.decode(iter.next().line));
            if (w.checkError())
                break;
        }
        return RETURN_OK;
    } catch (Exception e) {
        LOG.error(e);
        return -1;
    } finally {
        CloserUtil.close(w);
        CloserUtil.close(iter);
        if (array != null)
            array.cleanup();
    }
}

Example 68 with VariantContextWriter

use of htsjdk.variant.variantcontext.writer.VariantContextWriter in project gatk-protected by broadinstitute.

the class HaplotypeCallerEngine method makeVCFWriter.

/**
     * Create a VCF or GVCF writer as appropriate, given our arguments
     *
     * @param outputVCF location to which the vcf should be written
     * @param readsDictionary sequence dictionary for the reads
     * @return a VCF or GVCF writer as appropriate, ready to use
     */
public VariantContextWriter makeVCFWriter(final String outputVCF, final SAMSequenceDictionary readsDictionary) {
    Utils.nonNull(outputVCF);
    Utils.nonNull(readsDictionary);
    VariantContextWriter writer = GATKVariantContextUtils.createVCFWriter(new File(outputVCF), readsDictionary, false);
    if (hcArgs.emitReferenceConfidence == ReferenceConfidenceMode.GVCF) {
        try {
            writer = new GVCFWriter(writer, hcArgs.GVCFGQBands, hcArgs.genotypeArgs.samplePloidy);
        } catch (IllegalArgumentException e) {
            throw new CommandLineException.BadArgumentValue("GQBands", "are malformed: " + e.getMessage());
        }
    }
    return writer;
}

Example 69 with VariantContextWriter

use of htsjdk.variant.variantcontext.writer.VariantContextWriter in project gatk-protected by broadinstitute.

the class CreateSomaticPanelOfNormals method doWork.

public Object doWork() {
    final List<File> inputVcfs = new ArrayList<>(vcfs);
    final Collection<CloseableIterator<VariantContext>> iterators = new ArrayList<>(inputVcfs.size());
    final Collection<VCFHeader> headers = new HashSet<>(inputVcfs.size());
    final VCFHeader headerOfFirstVcf = new VCFFileReader(inputVcfs.get(0), false).getFileHeader();
    final SAMSequenceDictionary sequenceDictionary = headerOfFirstVcf.getSequenceDictionary();
    final VariantContextComparator comparator = headerOfFirstVcf.getVCFRecordComparator();
    for (final File vcf : inputVcfs) {
        final VCFFileReader reader = new VCFFileReader(vcf, false);
        iterators.add(reader.iterator());
        final VCFHeader header = reader.getFileHeader();
        Utils.validateArg(comparator.isCompatible(header.getContigLines()), () -> vcf.getAbsolutePath() + " has incompatible contigs.");
        headers.add(header);
    }
    final VariantContextWriter writer = GATKVariantContextUtils.createVCFWriter(outputVcf, sequenceDictionary, false, Options.INDEX_ON_THE_FLY);
    writer.writeHeader(new VCFHeader(VCFUtils.smartMergeHeaders(headers, false)));
    final MergingIterator<VariantContext> mergingIterator = new MergingIterator<>(comparator, iterators);
    SimpleInterval currentPosition = new SimpleInterval("FAKE", 1, 1);
    final List<VariantContext> variantsAtThisPosition = new ArrayList<>(20);
    while (mergingIterator.hasNext()) {
        final VariantContext vc = mergingIterator.next();
        if (!currentPosition.overlaps(vc)) {
            processVariantsAtSamePosition(variantsAtThisPosition, writer);
            variantsAtThisPosition.clear();
            currentPosition = new SimpleInterval(vc.getContig(), vc.getStart(), vc.getStart());
        }
        variantsAtThisPosition.add(vc);
    }
    mergingIterator.close();
    writer.close();
    return "SUCCESS";
}

Example 70 with VariantContextWriter

use of htsjdk.variant.variantcontext.writer.VariantContextWriter in project gatk-protected by broadinstitute.

the class EvaluateCopyNumberTriStateCalls method openVCFWriter.

private VariantContextWriter openVCFWriter(final File outputFile, final Set<String> samples) {
    final VariantContextWriterBuilder builder = new VariantContextWriterBuilder();
    builder.setOutputFile(outputFile);
    builder.clearOptions();
    final VariantContextWriter result = builder.build();
    final VCFHeader header = new VCFHeader(Collections.emptySet(), samples);
    CopyNumberTriStateAllele.addHeaderLinesTo(header);
    EvaluationClass.addHeaderLinesTo(header);
    // Format annotations.
    header.addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.Character, "Called genotype"));
    header.addMetaDataLine(new VCFFormatHeaderLine(VariantEvaluationContext.CALL_QUALITY_KEY, 1, VCFHeaderLineType.Float, "Quality of the call"));
    header.addMetaDataLine(new VCFFormatHeaderLine(VariantEvaluationContext.CALLED_SEGMENTS_COUNT_KEY, 1, VCFHeaderLineType.Integer, "Number of called segments that overlap with the truth"));
    header.addMetaDataLine(new VCFFormatHeaderLine(VariantEvaluationContext.CALLED_ALLELE_COUNTS_KEY, VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "Called allele count for mixed calls"));
    header.addMetaDataLine(new VCFFormatHeaderLine(VariantEvaluationContext.TRUTH_COPY_FRACTION_KEY, 1, VCFHeaderLineType.Float, "Truth copy fraction estimated"));
    header.addMetaDataLine(new VCFFormatHeaderLine(VariantEvaluationContext.TRUTH_QUALITY_KEY, 1, VCFHeaderLineType.Float, "Truth call quality"));
    header.addMetaDataLine(new VCFFormatHeaderLine(VariantEvaluationContext.EVALUATION_CLASS_KEY, 1, VCFHeaderLineType.Character, "The evaluation class for the call or lack of call. It the values of the header key '" + EvaluationClass.VCF_HEADER_KEY + "'"));
    header.addMetaDataLine(new VCFFormatHeaderLine(VariantEvaluationContext.TRUTH_GENOTYPE_KEY, 1, VCFHeaderLineType.Character, "The truth genotype"));
    header.addMetaDataLine(new VCFFormatHeaderLine(VariantEvaluationContext.CALLED_TARGET_COUNT_KEY, 1, VCFHeaderLineType.Integer, "Number of targets covered by called segments"));
    header.addMetaDataLine(new VCFFormatHeaderLine(VariantEvaluationContext.CALL_QUALITY_KEY, 1, VCFHeaderLineType.Float, "1 - The probability of th event in Phred scale (the maximum if ther are more than one segment"));
    header.addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_QUALITY_KEY, 1, VCFHeaderLineType.Integer, "The quality of the call (the maximum if there are more than one segment"));
    header.addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_FILTER_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Character, "Genotype filters"));
    // Info annotations.
    header.addMetaDataLine(new VCFInfoHeaderLine(VariantEvaluationContext.TRUTH_ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "The frequency of the alternative alleles in the truth callset"));
    header.addMetaDataLine(new VCFInfoHeaderLine(VariantEvaluationContext.TRUTH_ALLELE_NUMBER_KEY, 1, VCFHeaderLineType.Integer, "Total number of called alleles in the truth callset"));
    header.addMetaDataLine(new VCFInfoHeaderLine(VariantEvaluationContext.CALLS_ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "The frequency of the alternative alleles in the actual callset"));
    header.addMetaDataLine(new VCFInfoHeaderLine(VariantEvaluationContext.CALLS_ALLELE_NUMBER_KEY, 1, VCFHeaderLineType.Integer, "Total number of called alleles in the actual callset"));
    header.addMetaDataLine(new VCFInfoHeaderLine(VariantEvaluationContext.TRUTH_TARGET_COUNT_KEY, 1, VCFHeaderLineType.Integer, "Number of targets overlapped by this variant"));
    header.addMetaDataLine(new VCFInfoHeaderLine(VCFConstants.END_KEY, 1, VCFHeaderLineType.Integer, "Stop position for the variant"));
    // Filter annotations.
    for (final EvaluationFilter filter : EvaluationFilter.values()) {
        header.addMetaDataLine(new VCFFilterHeaderLine(filter.name(), filter.description));
        header.addMetaDataLine(new VCFFilterHeaderLine(filter.acronym, filter.description));
    }
    header.addMetaDataLine(new VCFFilterHeaderLine(EvaluationFilter.PASS, "Indicates that it passes all filters"));
    result.writeHeader(header);
    return result;
}