public CloseableIterator<PicardAlignment> query(
String sequence, int start, int end, boolean contained) {
try {
if (reader == null) {
reader = getSamReader(locator, true);
}
CloseableIterator<SAMRecord> iter = reader.query(sequence, start + 1, end, contained);
return new WrappedIterator(iter);
} catch (IOException e) {
log.error("Error opening SAM reader", e);
throw new RuntimeException("Error opening SAM reader", e);
}
}