else bufferedStream = IOUtil.toBufferedStream(stream);
if (isCRAMFile(bufferedStream)) {
mIsBinary = true;
if (file != null && file.isFile())
bufferedStream.close();
ReferenceSequenceFile referenceSequenceFile = ReferenceDiscovery
.findReferenceSequenceFileOrFail(stream, file,
indexFile);
if (indexFile != null && file != null)
mReader = new CRAMFileReader (file, indexFile, referenceSequenceFile) ;
else