Examples of org.broadinstitute.gatk.utils.codecs.table.TableFeature

Package org.broadinstitute.gatk.utils.codecs.table

Examples of org.broadinstitute.gatk.utils.codecs.table.TableFeature

org.broadinstitute.gatk.utils.codecs.table.TableFeature
A feature representing a single row out of a text table

            return n;
        }
    }


    private final TableFeature makeSpan(int start, int stop) {
        return new TableFeature(genomeLocParser.createGenomeLoc("chr1", start, stop),
                Collections.<String>emptyList(), Collections.<String>emptyList());
    }

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        LocusShardDataProvider provider = new LocusShardDataProvider(shard, null, genomeLocParser, shard.getGenomeLocs().get(0), null, seq, Collections.singletonList(dataSource));
        ReferenceOrderedView view = new ManagingReferenceOrderedView( provider );


        RefMetaDataTracker tracker = view.getReferenceOrderedDataAtLocus(genomeLocParser.createGenomeLoc("chrM",20));
        TableFeature datum = tracker.getFirstValue(new RodBinding<TableFeature>(TableFeature.class, "tableTest"));


        Assert.assertEquals(datum.get("COL1"),"C","datum parameter for COL1 is incorrect");
        Assert.assertEquals(datum.get("COL2"),"D","datum parameter for COL2 is incorrect");
        Assert.assertEquals(datum.get("COL3"),"E","datum parameter for COL3 is incorrect");
    }

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        LocusShardDataProvider provider = new LocusShardDataProvider(shard, null, genomeLocParser, shard.getGenomeLocs().get(0), null, seq, Arrays.asList(dataSource1,dataSource2));
        ReferenceOrderedView view = new ManagingReferenceOrderedView( provider );


        RefMetaDataTracker tracker = view.getReferenceOrderedDataAtLocus(genomeLocParser.createGenomeLoc("chrM",20));
        TableFeature datum1 = tracker.getFirstValue(new RodBinding<TableFeature>(TableFeature.class, "tableTest1"));


        Assert.assertEquals(datum1.get("COL1"),"C","datum1 parameter for COL1 is incorrect");
        Assert.assertEquals(datum1.get("COL2"),"D","datum1 parameter for COL2 is incorrect");
        Assert.assertEquals(datum1.get("COL3"),"E","datum1 parameter for COL3 is incorrect");


        TableFeature datum2 = tracker.getFirstValue(new RodBinding<TableFeature>(TableFeature.class, "tableTest2"));


        Assert.assertEquals(datum2.get("COL1"),"C","datum2 parameter for COL1 is incorrect");
        Assert.assertEquals(datum2.get("COL2"),"D","datum2 parameter for COL2 is incorrect");
        Assert.assertEquals(datum2.get("COL3"),"E","datum2 parameter for COL3 is incorrect");
    }

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        LocationAwareSeekableRODIterator iterator = (LocationAwareSeekableRODIterator)iteratorPool.iterator( new MappedStreamSegment(testSite1) );


        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");


        TableFeature datum = (TableFeature)iterator.next().get(0).getUnderlyingObject();


        assertTrue(datum.getLocation().equals(testSite1));
        assertTrue(datum.get("COL1").equals("A"));
        assertTrue(datum.get("COL2").equals("B"));
        assertTrue(datum.get("COL3").equals("C"));


        iteratorPool.release(iterator);


        Assert.assertEquals(iteratorPool.numIterators(), 1, "Number of iterators in the pool is incorrect");
        Assert.assertEquals(iteratorPool.numAvailableIterators(), 1, "Number of available iterators in the pool is incorrect");

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        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"));


        datum = (TableFeature)iterator1.next().get(0).getUnderlyingObject();
        assertTrue(datum.getLocation().equals(testSite1));
        assertTrue(datum.get("COL1").equals("A"));
        assertTrue(datum.get("COL2").equals("B"));
        assertTrue(datum.get("COL3").equals("C"));


        // Advance iterator2, and make sure both iterator's contents are still correct.
        datum = (TableFeature)iterator2.next().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"));


        datum = (TableFeature)iterator1.next().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"));


        // Cleanup, and make sure the number of iterators dies appropriately.
        iteratorPool.release(iterator1);


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

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        LocationAwareSeekableRODIterator iterator = iteratorPool.iterator( new MappedStreamSegment(testSite1) );


        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");


        TableFeature datum = (TableFeature)iterator.next().get(0).getUnderlyingObject();
        assertTrue(datum.getLocation().equals(testSite1));
        assertTrue(datum.get("COL1").equals("A"));
        assertTrue(datum.get("COL2").equals("B"));
        assertTrue(datum.get("COL3").equals("C"));


        iteratorPool.release(iterator);


        // Create another iterator after the current iterator.
        iterator = iteratorPool.iterator( new MappedStreamSegment(testSite3) );


        // 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"));


        iteratorPool.release(iterator);


        Assert.assertEquals(iteratorPool.numIterators(), 1, "Number of iterators in the pool is incorrect");
        Assert.assertEquals(iteratorPool.numAvailableIterators(), 1, "Number of available iterators in the pool is incorrect");

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Related Classes of org.broadinstitute.gatk.utils.codecs.table.TableFeature

org.broadinstitute.gatk.engine.datasources.providers.ReferenceOrderedViewUnitTest

org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataPoolUnitTest

org.broadinstitute.gatk.engine.refdata.RefMetaDataTrackerUnitTest

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