Package org.broadinstitute.gatk.engine.datasources.reads

Examples of org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource$SAMReaders

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        IndexedFastaSequenceFile refReader = new IndexedFastaSequenceFile(referenceFile);
        GenomeLocParser genomeLocParser = new GenomeLocParser(refReader);       

        // initialize reads
        List<SAMReaderID> bamReaders = ListFileUtils.unpackBAMFileList(samFiles,parser);
        SAMDataSource dataSource = new SAMDataSource(bamReaders,new ThreadAllocation(),null,genomeLocParser);

        // intervals
        final GenomeLocSortedSet intervalSortedSet;
        if ( intervals != null )
            intervalSortedSet = IntervalUtils.sortAndMergeIntervals(genomeLocParser, IntervalUtils.parseIntervalArguments(genomeLocParser, intervals), IntervalMergingRule.ALL);
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        final ValidationExclusion ve = new ValidationExclusion(Arrays.asList(excl));

        final MalformedReadFilter filter = new MalformedReadFilter();

        final SAMFileHeader h = getHeader();
        final SAMDataSource ds =  getDataSource();

        final GenomeAnalysisEngine gae = new GenomeAnalysisEngine() {
            @Override
            public SAMFileHeader getSAMFileHeader() {
                return h;
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        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,
                useOriginalBaseQualities,
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    @Override
    public void initialize(final GenomeAnalysisEngine engine) {
        header = engine.getSAMFileHeader();
        ValidationExclusion validationExclusions = null;
        final SAMDataSource rds = engine.getReadsDataSource();
        if (rds != null) {
          final ReadProperties rps = rds.getReadsInfo();
          if (rps != null) {
            validationExclusions = rps.getValidationExclusionList();
          }
        }
        if (validationExclusions == null) {
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    @Test
    public void emptyAlignmentContextTest() {
        SAMRecordIterator iterator = new SAMRecordIterator();

        GenomeLoc shardBounds = genomeLocParser.createGenomeLoc("chr1", 1, 5);
        Shard shard = new LocusShard(genomeLocParser, new SAMDataSource(Collections.<SAMReaderID>emptyList(),new ThreadAllocation(),null,genomeLocParser),Collections.singletonList(shardBounds),Collections.<SAMReaderID,SAMFileSpan>emptyMap());
        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
        WindowMaker.WindowMakerIterator window = windowMaker.next();
        LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, null, genomeLocParser, window.getLocus(), window, null, null);

        LocusView view = createView(dataProvider);
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* @version 0.1
*/
public class MockLocusShard extends LocusShard {
    public MockLocusShard(final GenomeLocParser genomeLocParser,final List<GenomeLoc> intervals) {
        super(  genomeLocParser,
                new SAMDataSource(Collections.<SAMReaderID>emptyList(),new ThreadAllocation(),null,genomeLocParser),
                intervals,
                null);
    }
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Related Classes of org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource$SAMReaders

  • htsjdk.samtools.MergingSamRecordIterator
  • htsjdk.samtools.SamFileHeaderMerger
  • org.broadinstitute.gatk.engine.arguments.ValidationExclusion
  • org.broadinstitute.gatk.engine.datasources.providers.LocusViewTemplate
  • org.broadinstitute.gatk.engine.datasources.reads.MockLocusShard
  • org.broadinstitute.gatk.engine.datasources.reads.utilities.FindLargeShards
  • org.broadinstitute.gatk.engine.filters.CountingFilteringIterator
  • org.broadinstitute.gatk.engine.filters.MalformedReadFilter
  • org.broadinstitute.gatk.engine.filters.MalformedReadFilterUnitTest
  • org.broadinstitute.gatk.engine.filters.ReadFilterTest
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