s.seek(0);
si = new SAMIterator(s, referenceSequenceFile);
si.setValidationStringency(validationStringency);
it = si;
} catch (IOException e) {
throw new RuntimeEOFException(e);
}
Container c = null;
for (int i = 0; i < filePointers.length; i += 2) {
long containerOffset = filePointers[i] >>> 16;