Examples with SAMSequenceDictionary htsjdk.samtools.SAMSequenceDictionary used on opensource projects

Example 26 with SAMSequenceDictionary

use of htsjdk.samtools.SAMSequenceDictionary in project gatk by broadinstitute.

the class GenomicsDBImport method initializeIntervals.

/**
     * Loads our intervals using the best available sequence
     * dictionary (as returned by {@link #getBestAvailableSequenceDictionary})
     * to parse/verify them. Does nothing if no intervals were specified.
     */
private void initializeIntervals() {
    if (intervalArgumentCollection.intervalsSpecified()) {
        final SAMSequenceDictionary intervalDictionary = getBestAvailableSequenceDictionary();
        if (intervalDictionary == null) {
            throw new UserException("We require at least one input source that " + "has a sequence dictionary (reference or reads) when intervals are specified");
        }
        intervals = new ArrayList<>();
        final List<SimpleInterval> simpleIntervalList = intervalArgumentCollection.getIntervals(intervalDictionary);
        if (simpleIntervalList.size() > 1) {
            throw new UserException("More than one interval specified. The tool takes only one");
        }
        for (final SimpleInterval simpleInterval : simpleIntervalList) {
            intervals.add(new ChromosomeInterval(simpleInterval.getContig(), simpleInterval.getStart(), simpleInterval.getEnd()));
        }
    } else {
        throw new UserException("No intervals specified");
    }
}

Example 27 with SAMSequenceDictionary

use of htsjdk.samtools.SAMSequenceDictionary in project gatk 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 28 with SAMSequenceDictionary

use of htsjdk.samtools.SAMSequenceDictionary in project gatk by broadinstitute.

the class Mutect2 method onTraversalStart.

@Override
public void onTraversalStart() {
    m2Engine = new Mutect2Engine(MTAC, getHeaderForReads(), referenceArguments.getReferenceFileName());
    final SAMSequenceDictionary sequenceDictionary = getHeaderForReads().getSequenceDictionary();
    vcfWriter = createVCFWriter(outputVCF);
    m2Engine.writeHeader(vcfWriter, sequenceDictionary, getDefaultToolVCFHeaderLines());
}

Example 29 with SAMSequenceDictionary

use of htsjdk.samtools.SAMSequenceDictionary in project gatk by broadinstitute.

the class FeatureDataSourceUnitTest method testGetSequenceDictionary.

@Test
public void testGetSequenceDictionary() {
    try (FeatureDataSource<VariantContext> featureSource = new FeatureDataSource<>(QUERY_TEST_VCF, "CustomName")) {
        final SAMSequenceDictionary dict = featureSource.getSequenceDictionary();
        Assert.assertEquals(dict.size(), 4);
        Assert.assertEquals(dict.getSequences().stream().map(s -> s.getSequenceName()).collect(Collectors.toList()), Arrays.asList("1", "2", "3", "4"));
    }
}

Example 30 with SAMSequenceDictionary

use of htsjdk.samtools.SAMSequenceDictionary in project gatk by broadinstitute.

the class GATKToolUnitTest method testBestSequenceDictionary_fromReads.

@Test
public void testBestSequenceDictionary_fromReads() throws Exception {
    final GATKTool tool = new TestGATKToolWithReads();
    final CommandLineParser clp = new CommandLineArgumentParser(tool);
    final File bamFile = new File(publicTestDir + "org/broadinstitute/hellbender/engine/reads_data_source_test1.bam");
    final String[] args = { "-I", bamFile.getCanonicalPath() };
    clp.parseArguments(System.out, args);
    tool.onStartup();
    //read the dict back in and compare to bam dict
    final SAMSequenceDictionary toolDict = tool.getBestAvailableSequenceDictionary();
    try (final SamReader open = SamReaderFactory.makeDefault().open(bamFile)) {
        final SAMSequenceDictionary bamDict = open.getFileHeader().getSequenceDictionary();
        toolDict.assertSameDictionary(bamDict);
        bamDict.assertSameDictionary(toolDict);
        Assert.assertEquals(toolDict, bamDict);
    }
}