Package htsjdk.samtools

Examples of htsjdk.samtools.SAMSequenceDictionary

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    final ProgressLogger progress = new ProgressLogger(log, 10000);

    final VCFFileReader fileReader = new VCFFileReader(INPUT);
    final VCFHeader fileHeader = fileReader.getFileHeader();

    final SAMSequenceDictionary sequenceDictionary =
        SEQUENCE_DICTIONARY != null
            ? SAMFileReader.getSequenceDictionary(SEQUENCE_DICTIONARY)
            : fileHeader.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.");
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        for (final File input : INPUT) IOUtil.assertFileIsReadable(input);

        if (SEQUENCE_DICTIONARY != null) IOUtil.assertFileIsReadable(SEQUENCE_DICTIONARY);

        SAMSequenceDictionary samSequenceDictionary = null;
        if (SEQUENCE_DICTIONARY != null) {
            samSequenceDictionary = SamReaderFactory.makeDefault().open(SEQUENCE_DICTIONARY).getFileHeader().getSequenceDictionary();
            CloserUtil.close(SEQUENCE_DICTIONARY);
        }
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    private void collectFileReadersAndHeaders(final List<String> sampleList, SAMSequenceDictionary samSequenceDictionary) {
        for (final File input : INPUT) {
            final VCFFileReader in = new VCFFileReader(input, false);
            final VCFHeader header = in.getFileHeader();
            final SAMSequenceDictionary dict = in.getFileHeader().getSequenceDictionary();
            if (dict == null || dict.isEmpty()) {
                if (null == samSequenceDictionary) {
                    throw new IllegalArgumentException("Sequence dictionary was missing or empty for the VCF: " + input.getAbsolutePath() + " Please add a sequence dictionary to this VCF or specify SEQUENCE_DICTIONARY.");
                }
                header.setSequenceDictionary(samSequenceDictionary);
            } else {
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    final List<String> sampleList = new ArrayList<String>();
    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 = SAMFileReader.getSequenceDictionary(SEQUENCE_DICTIONARY);

    for (final File file : INPUT) {
      IOUtil.assertFileIsReadable(file);
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        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()
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    protected int doWork() {
        IOUtil.assertFileIsReadable(INPUT);
        IOUtil.assertFileIsReadable(SEQUENCE_DICTIONARY);
        IOUtil.assertFileIsWritable(OUTPUT);

        final SAMSequenceDictionary samSequenceDictionary = SAMSequenceDictionaryExtractor.extractDictionary(SEQUENCE_DICTIONARY);

        final VCFFileReader fileReader = new VCFFileReader(INPUT, false);
        final VCFHeader fileHeader = fileReader.getFileHeader();

        final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
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        // Open the files for reading and writing
        final List<SAMFileReader> readers = new ArrayList<SAMFileReader>();
        final List<SAMFileHeader> headers = new ArrayList<SAMFileHeader>();
        {
            SAMSequenceDictionary dict = null; // Used to try and reduce redundant SDs in memory

            for (final File inFile : INPUT) {
                IOUtil.assertFileIsReadable(inFile);
                final SAMFileReader in = new SAMFileReader(inFile);
                readers.add(in);
                headers.add(in.getFileHeader());

                // A slightly hackish attempt to keep memory consumption down when merging multiple files with
                // large sequence dictionaries (10,000s of sequences). If the dictionaries are identical, then
                // replace the duplicate copies with a single dictionary to reduce the memory footprint.
                if (dict == null) {
                    dict = in.getFileHeader().getSequenceDictionary();
                }
                else if (dict.equals(in.getFileHeader().getSequenceDictionary())) {
                    in.getFileHeader().setSequenceDictionary(dict);
                }

                matchedSortOrders = matchedSortOrders && in.getFileHeader().getSortOrder() == SORT_ORDER;
            }
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    @Test(dataProvider = "testSegregate")
    public void testSegregateReference(final String referenceString, final int maxNmerToMerge, final List<Interval> result) throws Exception {

        final SAMSequenceRecord record = new SAMSequenceRecord("fake1", referenceString.length());
        final SAMSequenceDictionary dictionary = new SAMSequenceDictionary();
        dictionary.addSequence(record);

        final ReferenceSequenceFile reference = new ReferenceSequenceFile() {

            boolean done = false;
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Related Classes of htsjdk.samtools.SAMSequenceDictionary

  • org.broad.igv.cli_plugin.VCFEncoder
  • org.broad.igv.plugin.mongovariant.VariantReviewSource
  • org.broad.igv.variant.vcf.VCFWriterTest
  • org.broadinstitute.gatk.engine.alignment.bwa.BWTFiles
  • org.broadinstitute.gatk.engine.alignment.reference.bwt.BWTSupplementaryFileGenerator
  • org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndexUnitTest
  • org.broadinstitute.gatk.engine.GenomeAnalysisEngine
  • org.broadinstitute.gatk.engine.iterators.VerifyingSamIteratorUnitTest
  • org.broadinstitute.gatk.engine.refdata.tracks.IndexDictionaryUtils
  • org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder
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