List of seekForward() Examples

Examples of seekForward()

org.apache.hadoop.io.simpleseekableformat.SimpleSeekableFormatInputStream.seekForward()
This function seeks forward using all "available" bytes. It returns the offset after the seek. This function throws EOFException if there are no available complete metaDataBlock or the metaDataBlock points to a position after the file end (e.g. truncated files).
org.broadinstitute.gatk.engine.refdata.utils.LocationAwareSeekableRODIterator.seekForward()

Examples of org.apache.hadoop.io.simpleseekableformat.SimpleSeekableFormatInputStream.seekForward()

      }


      SimpleSeekableFormatInputStream in = new SimpleSeekableFormatInputStream(fileForRead);
      DataInputStream dataIn = new DataInputStream(in);


      long seekedPosition = in.seekForward();
      {
        // We should not be at the beginning of the stream any more.
        InterleavedInputStream interleavedIn = in.getInterleavedIn();
        long blocks = interleavedIn.getRawOffset() / interleavedIn.getCompleteBlockSize();
        long blocksAvailable = (availableBytes - interleavedIn.getMetaDataBlockSize()) / interleavedIn.getCompleteBlockSize();

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Examples of org.broadinstitute.gatk.engine.refdata.utils.LocationAwareSeekableRODIterator.seekForward()


            // grab the ROD iterator from the data source, and compute the first location in this shard, forwarding
            // the iterator to immediately before it, so that it can be added to the merging iterator primed for
            // next() to return the first real ROD in this shard
            LocationAwareSeekableRODIterator it = dataSource.seek(provider.getLocus());
            it.seekForward(genomeLocParser.createGenomeLoc(loc.getContig(), loc.getStart()-1));


            states.add(new ReferenceOrderedDataState(dataSource,it));            


            // we need to special case the interval so we don't always think there's a rod at the first location
            if ( dataSource.getName().equals(INTERVAL_ROD_NAME) ) {

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Examples of org.broadinstitute.gatk.engine.refdata.utils.LocationAwareSeekableRODIterator.seekForward()

        Assert.assertEquals(iteratorPool.numIterators(), 2, "Number of iterators in the pool is incorrect");
        Assert.assertEquals(iteratorPool.numAvailableIterators(), 0, "Number of available iterators in the pool is incorrect");


        // Test out-of-order access: first iterator2, then iterator1.
        // Ugh...first call to a region needs to be a seek.
        TableFeature datum = (TableFeature)iterator2.seekForward(testSite2).get(0).getUnderlyingObject();
        assertTrue(datum.getLocation().equals(testSite2));
        assertTrue(datum.get("COL1").equals("C"));
        assertTrue(datum.get("COL2").equals("D"));
        assertTrue(datum.get("COL3").equals("E"));

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Examples of org.broadinstitute.gatk.engine.refdata.utils.LocationAwareSeekableRODIterator.seekForward()


        // Make sure that the previously acquired iterator was reused.
        Assert.assertEquals(iteratorPool.numIterators(), 1, "Number of iterators in the pool is incorrect");
        Assert.assertEquals(iteratorPool.numAvailableIterators(), 0, "Number of available iterators in the pool is incorrect");


        datum = (TableFeature)iterator.seekForward(testSite3).get(0).getUnderlyingObject();
        assertTrue(datum.getLocation().equals(testSite3));
        assertTrue(datum.get("COL1").equals("F"));
        assertTrue(datum.get("COL2").equals("G"));
        assertTrue(datum.get("COL3").equals("H"));

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