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* Copyright (c) 2012 The Broad Institute
*
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* Software is furnished to do so, subject to the following
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*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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package org.broadinstitute.gatk.engine.refdata.utils;
import htsjdk.samtools.reference.IndexedFastaSequenceFile;
import htsjdk.tribble.Feature;
import org.broadinstitute.gatk.utils.BaseTest;
import org.broadinstitute.gatk.utils.GenomeLoc;
import org.broadinstitute.gatk.utils.GenomeLocParser;
import htsjdk.variant.vcf.VCFCodec;
import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
import org.testng.Assert;
import org.testng.annotations.Test;
import java.io.File;
import java.io.IOException;
public class FeatureToGATKFeatureIteratorUnitTest extends BaseTest {
@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");
Assert.assertTrue(gatkIterator.hasNext(), "GATK feature iterator does not have a next value.");
GenomeLoc gatkLocation = gatkIterator.next().getLocation();
Assert.assertEquals(gatkLocation.getContig(), chr, "Instead of chr 20 rod iterator was at location " + gatkLocation);
Assert.assertFalse(tribbleIterator.isClosed(), "Tribble iterator is closed but should be still open.");
gatkIterator.close();
Assert.assertTrue(tribbleIterator.isClosed(), "Tribble iterator is open but should be now closed.");
reader.close();
}
}