Java Code Examples for htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder#unsetOption()

The following examples show how to use htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder#unsetOption() . You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may check out the related API usage on the sidebar.
Example 1
Source File: VcfFormatConverter.java    From picard with MIT License 5 votes vote down vote up 
@Override
protected int doWork() {
    final ProgressLogger progress = new ProgressLogger(LOG, 10000);
    
    IOUtil.assertFileIsReadable(INPUT);
    IOUtil.assertFileIsWritable(OUTPUT);

    final VCFFileReader reader = new VCFFileReader(INPUT, REQUIRE_INDEX);
    final VCFHeader header = new VCFHeader(reader.getFileHeader());
    final SAMSequenceDictionary sequenceDictionary = header.getSequenceDictionary();
    if (CREATE_INDEX && sequenceDictionary == null) {
        throw new PicardException("A sequence dictionary must be available in the input file when creating indexed output.");
    }

    final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
            .setOutputFile(OUTPUT)
            .setReferenceDictionary(sequenceDictionary);
    if (CREATE_INDEX)
        builder.setOption(Options.INDEX_ON_THE_FLY);
    else
        builder.unsetOption(Options.INDEX_ON_THE_FLY);
    final VariantContextWriter writer = builder.build();
    writer.writeHeader(header);
    final CloseableIterator<VariantContext> iterator = reader.iterator();

    while (iterator.hasNext()) {
        final VariantContext context = iterator.next();
        writer.add(context);
        progress.record(context.getContig(), context.getStart());
    }

    CloserUtil.close(iterator);
    CloserUtil.close(reader);
    writer.close();

    return 0;
}
Example 2
Source File: MakeSitesOnlyVcf.java    From picard with MIT License 4 votes vote down vote up 
@Override
protected int doWork() {
    IOUtil.assertFileIsReadable(INPUT);
    IOUtil.assertFileIsWritable(OUTPUT);

    final VCFFileReader reader = new VCFFileReader(INPUT, false);
    final VCFHeader inputVcfHeader = new VCFHeader(reader.getFileHeader().getMetaDataInInputOrder());
    final SAMSequenceDictionary sequenceDictionary = inputVcfHeader.getSequenceDictionary();

    if (CREATE_INDEX && sequenceDictionary == null) {
        throw new PicardException("A sequence dictionary must be available (either through the input file or by setting it explicitly) when creating indexed output.");
    }

    final ProgressLogger progress = new ProgressLogger(Log.getInstance(MakeSitesOnlyVcf.class), 10000);

    // Setup the site-only file writer
    final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
            .setOutputFile(OUTPUT)
            .setReferenceDictionary(sequenceDictionary);
    if (CREATE_INDEX)
        builder.setOption(Options.INDEX_ON_THE_FLY);
    else
        builder.unsetOption(Options.INDEX_ON_THE_FLY);
    final VariantContextWriter writer = builder.build();

    final VCFHeader header = new VCFHeader(inputVcfHeader.getMetaDataInInputOrder(), SAMPLE);
    writer.writeHeader(header);

    // Go through the input, strip the records and write them to the output
    final CloseableIterator<VariantContext> iterator = reader.iterator();
    while (iterator.hasNext()) {
        final VariantContext full = iterator.next();
        final VariantContext site = subsetToSamplesWithOriginalAnnotations(full, SAMPLE);
        writer.add(site);
        progress.record(site.getContig(), site.getStart());
    }

    CloserUtil.close(iterator);
    CloserUtil.close(reader);
    writer.close();

    return 0;
}
Example 3
Source File: MergeVcfs.java    From picard with MIT License 4 votes vote down vote up 
@Override
protected int doWork() {
    final ProgressLogger progress = new ProgressLogger(log, 10000);
    final List<String> sampleList = new ArrayList<String>();
    INPUT = IOUtil.unrollFiles(INPUT, IOUtil.VCF_EXTENSIONS);
    final Collection<CloseableIterator<VariantContext>> iteratorCollection = new ArrayList<CloseableIterator<VariantContext>>(INPUT.size());
    final Collection<VCFHeader> headers = new HashSet<VCFHeader>(INPUT.size());
    VariantContextComparator variantContextComparator = null;
    SAMSequenceDictionary sequenceDictionary = null;

    if (SEQUENCE_DICTIONARY != null) {
        sequenceDictionary = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(SEQUENCE_DICTIONARY).getFileHeader().getSequenceDictionary();
    }

    for (final File file : INPUT) {
        IOUtil.assertFileIsReadable(file);
        final VCFFileReader fileReader = new VCFFileReader(file, false);
        final VCFHeader fileHeader = fileReader.getFileHeader();
        if (fileHeader.getContigLines().isEmpty()) {
            if (sequenceDictionary == null) {
                throw new IllegalArgumentException(SEQ_DICT_REQUIRED);
            } else {
                fileHeader.setSequenceDictionary(sequenceDictionary);
            }
        }

        if (variantContextComparator == null) {
            variantContextComparator = fileHeader.getVCFRecordComparator();
        } else {
            if (!variantContextComparator.isCompatible(fileHeader.getContigLines())) {
                throw new IllegalArgumentException(
                        "The contig entries in input file " + file.getAbsolutePath() + " are not compatible with the others.");
            }
        }

        if (sequenceDictionary == null) sequenceDictionary = fileHeader.getSequenceDictionary();

        if (sampleList.isEmpty()) {
            sampleList.addAll(fileHeader.getSampleNamesInOrder());
        } else {
            if (!sampleList.equals(fileHeader.getSampleNamesInOrder())) {
                throw new IllegalArgumentException("Input file " + file.getAbsolutePath() + " has sample entries that don't match the other files.");
            }
        }
        
        // add comments in the first header
        if (headers.isEmpty()) {
            COMMENT.stream().forEach(C -> fileHeader.addMetaDataLine(new VCFHeaderLine("MergeVcfs.comment", C)));
        }

        headers.add(fileHeader);
        iteratorCollection.add(fileReader.iterator());
    }

    if (CREATE_INDEX && sequenceDictionary == null) {
        throw new PicardException(String.format("Index creation failed. %s", SEQ_DICT_REQUIRED));
    }

    final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
            .setOutputFile(OUTPUT)
            .setReferenceDictionary(sequenceDictionary);

    if (CREATE_INDEX) {
        builder.setOption(Options.INDEX_ON_THE_FLY);
    } else {
        builder.unsetOption(Options.INDEX_ON_THE_FLY);
    }
    final VariantContextWriter writer = builder.build();

    writer.writeHeader(new VCFHeader(VCFUtils.smartMergeHeaders(headers, false), sampleList));

    final MergingIterator<VariantContext> mergingIterator = new MergingIterator<VariantContext>(variantContextComparator, iteratorCollection);
    while (mergingIterator.hasNext()) {
        final VariantContext context = mergingIterator.next();
        writer.add(context);
        progress.record(context.getContig(), context.getStart());
    }

    CloserUtil.close(mergingIterator);
    writer.close();
    return 0;
}