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();