private long fileStart, virtualStart, virtualEnd;
private boolean isInitialized = false;
private boolean keepReadPairsTogether;
private boolean readPair;
private boolean lastOfPair;
<BUG>private List<Locatable> intervals;

public static long getKey(final SAMRecord rec) {</BUG>
final int refIdx = rec.getReferenceIndex();
final int start  = rec.getAlignmentStart();

private long fileStart, virtualStart, virtualEnd;
private boolean isInitialized = false;
private boolean keepReadPairsTogether;
private boolean readPair;
private boolean lastOfPair;
private List<Interval> intervals;
private OverlapDetector<Interval> overlapDetector;
public static long getKey(final SAMRecord rec) {
final int refIdx = rec.getReferenceIndex();
final int start  = rec.getAlignmentStart();
