Package htsjdk.samtools.reference

Examples of htsjdk.samtools.reference.IndexedFastaSequenceFile

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    @DataProvider(name="invalidIntervalTestData")
    public Object[][] invalidIntervalDataProvider() throws Exception {
        GATKArgumentCollection argCollection = new GATKArgumentCollection();
        File fastaFile = new File(publicTestDir + "exampleFASTA.fasta");
        GenomeLocParser genomeLocParser = new GenomeLocParser(new IndexedFastaSequenceFile(fastaFile));

        return new Object[][] {
                new Object[] {argCollection, genomeLocParser, "chr1", 10000000, 20000000},
                new Object[] {argCollection, genomeLocParser, "chr2", 1, 2},
                new Object[] {argCollection, genomeLocParser, "chr1", -1, 50}
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    }

    @Test (enabled = true)
    public void testReadWithNsRefIndexInDeletion() throws FileNotFoundException {

        final IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
        final int readLength = 76;

        final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 8975, readLength);
        read.setReadBases(Utils.dupBytes((byte) 'A', readLength));
        read.setBaseQualities(Utils.dupBytes((byte)30, readLength));
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    }

    @Test (enabled = true)
    public void testReadWithNsRefAfterDeletion() throws FileNotFoundException {

        final IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
        final int readLength = 76;

        final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 8975, readLength);
        read.setReadBases(Utils.dupBytes((byte) 'A', readLength));
        read.setBaseQualities(Utils.dupBytes((byte)30, readLength));
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    }

    private void testSequential(final CachingIndexedFastaSequenceFile caching, final File fasta, final int querySize) throws FileNotFoundException {
        Assert.assertTrue(caching.isPreservingCase(), "testSequential only works for case preserving CachingIndexedFastaSequenceFile readers");

        final IndexedFastaSequenceFile uncached = new IndexedFastaSequenceFile(fasta);

        SAMSequenceRecord contig = uncached.getSequenceDictionary().getSequence(0);
        for ( int i = 0; i < contig.getSequenceLength(); i += STEP_SIZE ) {
            int start = i;
            int stop = start + querySize;
            if ( stop <= contig.getSequenceLength() ) {
                ReferenceSequence cachedVal = caching.getSubsequenceAt(contig.getSequenceName(), start, stop);
                ReferenceSequence uncachedVal = uncached.getSubsequenceAt(contig.getSequenceName(), start, stop);

                Assert.assertEquals(cachedVal.getName(), uncachedVal.getName());
                Assert.assertEquals(cachedVal.getContigIndex(), uncachedVal.getContigIndex());
                Assert.assertEquals(cachedVal.getBases(), uncachedVal.getBases());
            }
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    }

    // Tests grabbing sequences around a middle cached value.
    @Test(dataProvider = "fastas", enabled = true && ! DEBUG)
    public void testCachingIndexedFastaReaderTwoStage(File fasta, int cacheSize, int querySize) throws FileNotFoundException {
        final IndexedFastaSequenceFile uncached = new IndexedFastaSequenceFile(fasta);
        final CachingIndexedFastaSequenceFile caching = new CachingIndexedFastaSequenceFile(fasta, getCacheSize(cacheSize), true, false);

        SAMSequenceRecord contig = uncached.getSequenceDictionary().getSequence(0);

        int middleStart = (contig.getSequenceLength() - querySize) / 2;
        int middleStop = middleStart + querySize;

        logger.warn(String.format("Checking contig %s length %d with cache size %d and query size %d with intermediate query",
                contig.getSequenceName(), contig.getSequenceLength(), cacheSize, querySize));

        for ( int i = 0; i < contig.getSequenceLength(); i += 10 ) {
            int start = i;
            int stop = start + querySize;
            if ( stop <= contig.getSequenceLength() ) {
                ReferenceSequence grabMiddle = caching.getSubsequenceAt(contig.getSequenceName(), middleStart, middleStop);
                ReferenceSequence cachedVal = caching.getSubsequenceAt(contig.getSequenceName(), start, stop);
                ReferenceSequence uncachedVal = uncached.getSubsequenceAt(contig.getSequenceName(), start, stop);

                Assert.assertEquals(cachedVal.getName(), uncachedVal.getName());
                Assert.assertEquals(cachedVal.getContigIndex(), uncachedVal.getContigIndex());
                Assert.assertEquals(cachedVal.getBases(), uncachedVal.getBases());
            }
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    }

    // make sure some bases are lower case and some are upper case
    @Test(enabled = true)
    public void testMixedCasesInExample() throws FileNotFoundException, InterruptedException {
        final IndexedFastaSequenceFile original = new IndexedFastaSequenceFile(new File(exampleFASTA));
        final CachingIndexedFastaSequenceFile casePreserving = new CachingIndexedFastaSequenceFile(new File(exampleFASTA), true);
        final CachingIndexedFastaSequenceFile allUpper = new CachingIndexedFastaSequenceFile(new File(exampleFASTA));

        int nMixedCase = 0;
        for ( SAMSequenceRecord contig : original.getSequenceDictionary().getSequences() ) {
            nMixedCase += testCases(original, casePreserving, allUpper, contig.getSequenceName(), -1, -1);

            final int step = 100;
            for ( int lastPos = step; lastPos < contig.getSequenceLength(); lastPos += step ) {
                testCases(original, casePreserving, allUpper, contig.getSequenceName(), lastPos - step, lastPos);
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        createStratificationStates(stratificationObjects, evaluationClasses);

        // Load ancestral alignments
        if (ancestralAlignmentsFile != null) {
            try {
                ancestralAlignments = new IndexedFastaSequenceFile(ancestralAlignmentsFile);
            } catch (FileNotFoundException e) {
                throw new ReviewedGATKException(String.format("The ancestral alignments file, '%s', could not be found", ancestralAlignmentsFile.getAbsolutePath()));
            }
        }
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    @Test
    public void testCloseFilePointers() throws IOException {
        // Build up query parameters
        File file = new File(BaseTest.privateTestDir + "NA12878.hg19.example1.vcf");
        RMDTriplet triplet = new RMDTriplet("test", "VCF", file.getAbsolutePath(), RMDTriplet.RMDStorageType.FILE, new Tags());
        IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(BaseTest.hg19Reference));
        GenomeLocParser parser = new GenomeLocParser(seq);
        GenomeLoc loc = parser.createGenomeLoc("20", 1, 100000);
        TestRMDTrackBuilder builder = new TestRMDTrackBuilder(seq.getSequenceDictionary(), parser);

        // Create the query data pool
        ReferenceOrderedQueryDataPool pool = new ReferenceOrderedQueryDataPool(triplet, builder, seq.getSequenceDictionary(), parser);

        for (int i = 0; i < 3; i++) {
            // Ensure our tribble iterators are closed.
            CheckableCloseableTribbleIterator.clearThreadIterators();
            Assert.assertTrue(CheckableCloseableTribbleIterator.getThreadIterators().isEmpty(), "Tribble iterators list was not cleared.");
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    @Argument(fullName = "dt", shortName = "dt", doc = "Enable downsampling", required = false)
    public boolean downsample = false;

    @Override
    public int execute() throws IOException {
        final IndexedFastaSequenceFile reference = new CachingIndexedFastaSequenceFile(referenceFile);
        final GenomeLocParser genomeLocParser = new GenomeLocParser(reference);

        final SAMFileReader reader = new SAMFileReader(samFile);
        reader.setSAMRecordFactory(new GATKSamRecordFactory());
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Related Classes of htsjdk.samtools.reference.IndexedFastaSequenceFile

  • org.broadinstitute.gatk.engine.alignment.bwa.java.AlignerTestHarness
  • org.broadinstitute.gatk.engine.datasources.reads.utilities.FindLargeShards
  • org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPoolUnitTest
  • org.broadinstitute.gatk.engine.refdata.tracks.FeatureManagerUnitTest
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  • org.broadinstitute.gatk.tools.walkers.indels.PairHMMIndelErrorModelUnitTest
  • org.broadinstitute.gatk.tools.walkers.varianteval.VariantEval
  • org.broadinstitute.gatk.utils.baq.BAQUnitTest
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