if (alignmentStart >= start && alignmentEnd <= end)
countContained ++;
if (alignmentStart < start && alignmentEnd > end)
countSpan ++;
}//while
<BUG>iter.close();
if (contained)</BUG>
os.print(sep + countContained);
<BUG>if (overlap)
os.print(sep + countOverlap);</BUG>
if (span)

if (alignmentStart >= start && alignmentEnd <= end)
countContained ++;
if (alignmentStart < start && alignmentEnd > end)
countSpan ++;
}//while
iter.close();
if (overlap)
os.print(sep + countOverlap);
if (contained)
os.print(sep + countContained);
if (span)
