Examples of Shard

com.amazonaws.services.kinesis.model.Shard

A uniquely identified group of data records in an Amazon Kinesis stream.
com.senseidb.indexing.hadoop.keyvalueformat.Shard
This class represents the metadata of a shard. Version is the version number of the entire index. Directory is the directory where this shard resides in. Generation is the Lucene index's generation. Version and generation are reserved for future use. Note: Currently the version number of the entire index is not used and defaults to -1.
com.volantis.mcs.dissection.impl.Shard
This class contains all the shard related information needed by the dissector.
There is one instance of this class for each shard in each dissectable area.
When the shard contents are being selected this object is in the pending state. Once this has been completed it is moved to the ready state.
net.sf.katta.protocol.metadata.IndexMetaData.Shard
org.apache.hadoop.contrib.index.mapred.Shard
This class represents the metadata of a shard. Version is the version number of the entire index. Directory is the directory where this shard resides in. Generation is the Lucene index's generation. Version and generation are reserved for future use. Note: Currently the version number of the entire index is not used and defaults to -1.
org.broadinstitute.gatk.engine.datasources.reads.Shard
@author aaron @version 1.0 @date Apr 10, 2009
Interface Shard
The base abstract class for shards.
org.elasticsearch.hadoop.serialization.dto.Shard
org.elasticsearch.river.mongodb.MongoConfig.Shard
org.makersoft.shards.Shard
每个物理分区为一个Shard

Examples of org.broadinstitute.gatk.engine.datasources.reads.Shard

     */
    protected void queueNextShardTraverse( Walker walker, ReduceTree reduceTree ) {
        if (!traversalTasks.hasNext())
            throw new IllegalStateException("Cannot traverse; no pending traversals exist.");


        final Shard shard = traversalTasks.next();


        // todo -- add ownership claim here


        final ShardTraverser traverser = new ShardTraverser(this, walker, shard, outputTracker);

View Full Code Here

Examples of org.broadinstitute.gatk.engine.datasources.reads.Shard

    @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);


        testReadsInContext(view, shard.getGenomeLocs(), Collections.<GATKSAMRecord>emptyList());
    }

View Full Code Here

Examples of org.broadinstitute.gatk.engine.datasources.reads.Shard

    public void singleReadTest() {
        GATKSAMRecord read = buildSAMRecord("read1","chr1", 1, 5);
        SAMRecordIterator iterator = new SAMRecordIterator(read);


        GenomeLoc shardBounds = genomeLocParser.createGenomeLoc("chr1", 1, 5);
        Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(shardBounds));
        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
        WindowMaker.WindowMakerIterator window = windowMaker.next();
        LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);


        LocusView view = createView(dataProvider);


        testReadsInContext(view, shard.getGenomeLocs(), Collections.singletonList(read));
    }

View Full Code Here

Examples of org.broadinstitute.gatk.engine.datasources.reads.Shard

    @Test
    public void readCoveringFirstPartTest() {
        GATKSAMRecord read = buildSAMRecord("read1","chr1", 1, 5);
        SAMRecordIterator iterator = new SAMRecordIterator(read);


        Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
        WindowMaker.WindowMakerIterator window = windowMaker.next();
        LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
        LocusView view = createView(dataProvider);


        testReadsInContext(view, shard.getGenomeLocs(), Collections.singletonList(read));
    }

View Full Code Here

Examples of org.broadinstitute.gatk.engine.datasources.reads.Shard

    @Test
    public void readCoveringLastPartTest() {
        GATKSAMRecord read = buildSAMRecord("read1","chr1", 6, 10);
        SAMRecordIterator iterator = new SAMRecordIterator(read);


        Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
        WindowMaker.WindowMakerIterator window = windowMaker.next();
        LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
        LocusView view = createView(dataProvider);


        testReadsInContext(view, shard.getGenomeLocs(), Collections.singletonList(read));
    }

View Full Code Here

Examples of org.broadinstitute.gatk.engine.datasources.reads.Shard

    @Test
    public void readCoveringMiddleTest() {
        GATKSAMRecord read = buildSAMRecord("read1","chr1", 3, 7);
        SAMRecordIterator iterator = new SAMRecordIterator(read);


        Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
        WindowMaker.WindowMakerIterator window = windowMaker.next();
        LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
        LocusView view = createView(dataProvider);


        testReadsInContext(view, shard.getGenomeLocs(), Collections.singletonList(read));
    }

View Full Code Here

Examples of org.broadinstitute.gatk.engine.datasources.reads.Shard

    @Test
    public void readAndLocusOverlapAtLastBase() {
        GATKSAMRecord read = buildSAMRecord("read1","chr1", 1, 5);
        SAMRecordIterator iterator = new SAMRecordIterator(read);


        Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 5, 5)));
        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
        WindowMaker.WindowMakerIterator window = windowMaker.next();
        LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
        LocusView view = createView(dataProvider);


        testReadsInContext(view, shard.getGenomeLocs(), Collections.singletonList(read));
    }

View Full Code Here

Examples of org.broadinstitute.gatk.engine.datasources.reads.Shard

    @Test
    public void readOverlappingStartTest() {
        GATKSAMRecord read = buildSAMRecord("read1","chr1", 1, 10);
        SAMRecordIterator iterator = new SAMRecordIterator(read);


        Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 6, 15)));
        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
        WindowMaker.WindowMakerIterator window = windowMaker.next();
        LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
        LocusView view = createView(dataProvider);


        testReadsInContext(view, shard.getGenomeLocs(), Collections.singletonList(read));
    }

View Full Code Here

Examples of org.broadinstitute.gatk.engine.datasources.reads.Shard

    @Test
    public void readOverlappingEndTest() {
        GATKSAMRecord read = buildSAMRecord("read1","chr1", 6, 15);
        SAMRecordIterator iterator = new SAMRecordIterator(read);


        Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
        WindowMaker.WindowMakerIterator window = windowMaker.next();
        LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
        LocusView view = createView(dataProvider);


        testReadsInContext(view, shard.getGenomeLocs(), Collections.singletonList(read));
    }

View Full Code Here

Examples of org.broadinstitute.gatk.engine.datasources.reads.Shard

    public void readsSpanningTest() {
        GATKSAMRecord read1 = buildSAMRecord("read1","chr1", 1, 5);
        GATKSAMRecord read2 = buildSAMRecord("read2","chr1", 6, 10);
        SAMRecordIterator iterator = new SAMRecordIterator(read1, read2);


        Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
        WindowMaker.WindowMakerIterator window = windowMaker.next();
        LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
        LocusView view = createView(dataProvider);


        List<GATKSAMRecord> expectedReads = new ArrayList<GATKSAMRecord>();
        Collections.addAll(expectedReads, read1, read2);
        testReadsInContext(view, shard.getGenomeLocs(), expectedReads);
    }

View Full Code Here

0 1 2 3 4

TOP

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.