@Override void applyTo(final BAMFileReader underlyingReader, final SamReader reader) { underlyingReader.enableIndexCaching(true); }
@Override void applyTo(final BAMFileReader underlyingReader, final SamReader reader) { underlyingReader.enableIndexCaching(true); }
@Override void applyTo(final BAMFileReader underlyingReader, final SamReader reader) { underlyingReader.enableIndexCaching(true); }
@Test public void exhaustivelyTestIndexTest () throws IOException { BAMFileReader bamFileReader1 = new BAMFileReader(BAM_FILE, BAI_FILE, true, false, ValidationStringency.DEFAULT_STRINGENCY, new DefaultSAMRecordFactory()); bamFileReader1.enableIndexCaching(true); BAMFileReader bamFileReader2 = new BAMFileReader(BAM_FILE, CSI_FILE, true, false, ValidationStringency.DEFAULT_STRINGENCY, new DefaultSAMRecordFactory()); final SamReader samFileReader1 = new SamReader.PrimitiveSamReaderToSamReaderAdapter(bamFileReader1, null); final SamReader samFileReader2 = new SamReader.PrimitiveSamReaderToSamReaderAdapter(bamFileReader2, null); int baiCount = BamIndexValidator.exhaustivelyTestIndex(samFileReader1); int csiCount = BamIndexValidator.exhaustivelyTestIndex(samFileReader2); Assert.assertEquals(baiCount, csiCount); }