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

Example 61 with SAMSequenceDictionary

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

the class VariantWalkerIntegrationTest method testBestSequenceDictionary_FromVariantReference.

@Test
public void testBestSequenceDictionary_FromVariantReference() throws Exception {
    final GATKTool tool = new TestGATKToolWithFeatures();
    final CommandLineParser clp = new CommandLineArgumentParser(tool);
    final File vcfFile = new File(publicTestDir + "org/broadinstitute/hellbender/engine/example_variants_noSequenceDict.vcf");
    final String[] args = { "-V", vcfFile.getCanonicalPath(), "-R", hg19MiniReference };
    clp.parseArguments(System.out, args);
    tool.onStartup();
    // make sure we DON'T get the seq dictionary from the VCF index, and instead get the one from
    // the reference when its better
    final SAMSequenceDictionary toolDict = tool.getBestAvailableSequenceDictionary();
    Assert.assertFalse(toolDict.getSequences().stream().allMatch(seqRec -> seqRec.getSequenceLength() == 0));
    SAMSequenceDictionary refDict = new ReferenceFileSource(new File(hg19MiniReference)).getSequenceDictionary();
    toolDict.assertSameDictionary(refDict);
    refDict.assertSameDictionary(toolDict);
    Assert.assertEquals(toolDict, refDict);
}

Example 62 with SAMSequenceDictionary

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

the class ReferenceMemorySourceTest method init.

@BeforeTest
public void init() {
    List<SAMSequenceRecord> l = new ArrayList<>();
    l.add(new SAMSequenceRecord("chr1", 1000000));
    SAMSequenceDictionary seqDir = new SAMSequenceDictionary(l);
    memorySource = new ReferenceMemorySource(ref1, seqDir);
}

Example 63 with SAMSequenceDictionary

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

the class GenomicsDBImportIntegrationTest method testPreserveContigOrderingInHeader.

@Test
public void testPreserveContigOrderingInHeader() throws IOException {
    final String workspace = createTempDir("testPreserveContigOrderingInHeader-").getAbsolutePath() + "/workspace";
    writeToGenomicsDB(Arrays.asList(GENOMICSDB_TEST_DIR + "testHeaderContigLineSorting1.g.vcf", GENOMICSDB_TEST_DIR + "testHeaderContigLineSorting2.g.vcf"), new SimpleInterval("chr20", 17959479, 17959479), workspace, 0, false, 0);
    try (final GenomicsDBFeatureReader<VariantContext, PositionalBufferedStream> genomicsDBFeatureReader = new GenomicsDBFeatureReader<>(new File(workspace, GenomicsDBConstants.DEFAULT_VIDMAP_FILE_NAME).getAbsolutePath(), new File(workspace, GenomicsDBConstants.DEFAULT_CALLSETMAP_FILE_NAME).getAbsolutePath(), workspace, GenomicsDBConstants.DEFAULT_ARRAY_NAME, b38_reference_20_21, null, new BCF2Codec());
        final AbstractFeatureReader<VariantContext, LineIterator> inputGVCFReader = AbstractFeatureReader.getFeatureReader(GENOMICSDB_TEST_DIR + "testHeaderContigLineSorting1.g.vcf", new VCFCodec(), true)) {
        final SAMSequenceDictionary dictionaryFromGenomicsDB = ((VCFHeader) genomicsDBFeatureReader.getHeader()).getSequenceDictionary();
        final SAMSequenceDictionary dictionaryFromInputGVCF = ((VCFHeader) inputGVCFReader.getHeader()).getSequenceDictionary();
        Assert.assertEquals(dictionaryFromGenomicsDB, dictionaryFromInputGVCF, "Sequence dictionary from GenomicsDB does not match original sequence dictionary from input GVCF");
    }
}

Example 64 with SAMSequenceDictionary

use of htsjdk.samtools.SAMSequenceDictionary 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 65 with SAMSequenceDictionary

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

the class MergeSamFiles method doWork.

/** Combines multiple SAM/BAM files into one. */
@Override
protected Object doWork() {
    boolean matchedSortOrders = true;
    // Open the files for reading and writing
    final List<SamReader> readers = new ArrayList<>();
    final List<SAMFileHeader> headers = new ArrayList<>();
    {
        // Used to try and reduce redundant SDs in memory
        SAMSequenceDictionary dict = null;
        for (final File inFile : INPUT) {
            IOUtil.assertFileIsReadable(inFile);
            final SamReader in = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(inFile);
            readers.add(in);
            headers.add(in.getFileHeader());
            // 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;
        }
    }
    // If all the input sort orders match the output sort order then just merge them and
    // write on the fly, otherwise setup to merge and sort before writing out the final file
    IOUtil.assertFileIsWritable(OUTPUT);
    final boolean presorted;
    final SAMFileHeader.SortOrder headerMergerSortOrder;
    final boolean mergingSamRecordIteratorAssumeSorted;
    if (matchedSortOrders || SORT_ORDER == SAMFileHeader.SortOrder.unsorted || ASSUME_SORTED) {
        logger.info("Input files are in same order as output so sorting to temp directory is not needed.");
        headerMergerSortOrder = SORT_ORDER;
        mergingSamRecordIteratorAssumeSorted = ASSUME_SORTED;
        presorted = true;
    } else {
        logger.info("Sorting input files using temp directory " + TMP_DIR);
        headerMergerSortOrder = SAMFileHeader.SortOrder.unsorted;
        mergingSamRecordIteratorAssumeSorted = false;
        presorted = false;
    }
    final SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(headerMergerSortOrder, headers, MERGE_SEQUENCE_DICTIONARIES);
    final MergingSamRecordIterator iterator = new MergingSamRecordIterator(headerMerger, readers, mergingSamRecordIteratorAssumeSorted);
    final SAMFileHeader header = headerMerger.getMergedHeader();
    for (final String comment : COMMENT) {
        header.addComment(comment);
    }
    header.setSortOrder(SORT_ORDER);
    final SAMFileWriterFactory samFileWriterFactory = new SAMFileWriterFactory();
    if (USE_THREADING) {
        samFileWriterFactory.setUseAsyncIo(true);
    }
    try (final SAMFileWriter out = createSAMWriter(OUTPUT, REFERENCE_SEQUENCE, header, presorted)) {
        // Lastly loop through and write out the records
        final ProgressLogger progress = new ProgressLogger(logger, PROGRESS_INTERVAL);
        while (iterator.hasNext()) {
            final SAMRecord record = iterator.next();
            out.addAlignment(record);
            progress.record(record);
        }
        logger.info("Finished reading inputs.");
        CloserUtil.close(readers);
    }
    return null;
}