Package org.broadinstitute.gatk.utils

Examples of org.broadinstitute.gatk.utils.GenomeLocParser

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public class ProgressMeterDaemonUnitTest extends BaseTest {
    private GenomeLocParser genomeLocParser;

    @BeforeClass
    public void init() throws FileNotFoundException {
        genomeLocParser = new GenomeLocParser(new CachingIndexedFastaSequenceFile(new File(b37KGReference)));
    }
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    @BeforeClass
    private void init() throws IOException {
        reference = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        dictionary = reference.getSequenceDictionary();
        genomeLocParser = new GenomeLocParser(dictionary);
        header = ArtificialSAMUtils.createDefaultReadGroup(new SAMFileHeader(), "test", "test");
        header.setSequenceDictionary(dictionary);
        header.setSortOrder(SAMFileHeader.SortOrder.coordinate);
        readGroup = new GATKSAMReadGroupRecord(header.getReadGroup("test"));
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     */
    @BeforeMethod
    public void doForEachTest() throws FileNotFoundException {
        // sequence
        seq = new CachingIndexedFastaSequenceFile(new File(hg18Reference));
        genomeLocParser = new GenomeLocParser(seq.getSequenceDictionary());
    }
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    public void doForEachTest() throws FileNotFoundException {
        readers = new ArrayList<SAMReaderID>();

        // sequence
        seq = new CachingIndexedFastaSequenceFile(new File(b36KGReference));
        genomeLocParser = new GenomeLocParser(seq.getSequenceDictionary());
    }
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        final DownsamplingMethod downsamplingMethod = DownsamplingMethod.NONE;
        final ValidationExclusion exclusionList = composeValidationExclusion();
        final Collection<ReadFilter> supplementalFilters = Collections.EMPTY_SET;
        final boolean includeReadsWithDeletionAtLoci = true;

        final GenomeLocParser glp = new GenomeLocParser(header.getSequenceDictionary());
        final SAMDataSource res = new SAMDataSource(
                readerIDs,
                ta,
                numFileHandles,
                glp,
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        testEngine.checkForDuplicateSamFiles();
    }

    @Test
    public void testEmptyIntervalSetHandling() throws Exception {
        GenomeLocParser genomeLocParser = new GenomeLocParser(ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000).getSequenceDictionary());

        GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();

        testEngine.setWalker(new PrintReads());
        testEngine.setIntervals(new GenomeLocSortedSet(genomeLocParser));
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    @BeforeMethod
    public void setup() {
        File referenceFile = new File(b36KGReference);
        try {
            IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(referenceFile);
            genomeLocParser = new GenomeLocParser(seq);
            manager = new FeatureManager();
        }
        catch(FileNotFoundException ex) {
            throw new UserException.CouldNotReadInputFile(referenceFile,ex);
        }
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    @Test
    @SuppressWarnings("unchecked")
    public void testCloseFilePointers() throws IOException {
        final String chr = "20";
        IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(BaseTest.hg19Reference));
        GenomeLocParser parser = new GenomeLocParser(seq);
        File file = new File(privateTestDir + "NA12878.hg19.example1.vcf");
        VCFCodec codec = new VCFCodec();
        TestFeatureReader reader = new TestFeatureReader(file.getAbsolutePath(), codec);
        CheckableCloseableTribbleIterator<Feature> tribbleIterator = reader.query(chr, 1, 100000);
        FeatureToGATKFeatureIterator gatkIterator = new FeatureToGATKFeatureIterator(parser, tribbleIterator, "test");
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            seq = new CachingIndexedFastaSequenceFile(referenceFile);
        }
        catch(FileNotFoundException ex) {
            throw new UserException.CouldNotReadInputFile(referenceFile,ex);
        }
        genomeLocParser = new GenomeLocParser(seq);

        // We have to disable auto-index creation/locking in the RMDTrackBuilder for tests,
        // as the lock acquisition calls were intermittently hanging on our farm. This unfortunately
        // means that we can't include tests for the auto-index creation feature.
        builder = new RMDTrackBuilder(seq.getSequenceDictionary(),genomeLocParser,null,true,null);
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    @BeforeClass
    public void init() throws FileNotFoundException {
        // sequence
        seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        genomeLocParser = new GenomeLocParser(seq);
        contig = "1";
        contigLength = genomeLocParser.getContigInfo(contig).getSequenceLength();
    }
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Related Classes of org.broadinstitute.gatk.utils.GenomeLocParser

  • htsjdk.samtools.SAMSequenceRecord
  • org.broad.igv.plugin.mongovariant.VariantReviewSource
  • org.broadinstitute.gatk.engine.datasources.providers.IntervalReferenceOrderedViewUnitTest
  • org.broadinstitute.gatk.engine.datasources.providers.LocusViewTemplate
  • org.broadinstitute.gatk.engine.datasources.providers.ReferenceOrderedViewUnitTest
  • org.broadinstitute.gatk.engine.datasources.providers.ReferenceViewTemplate
  • org.broadinstitute.gatk.engine.datasources.reads.ActiveRegionShardBalancerUnitTest
  • org.broadinstitute.gatk.engine.datasources.reads.FilePointerUnitTest
  • org.broadinstitute.gatk.engine.datasources.reads.IntervalOverlapFilteringIteratorUnitTest
  • org.broadinstitute.gatk.engine.datasources.reads.ReadShardBalancerUnitTest$ReadShardBalancerTest
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