3dd1925e6551df4388e13d50c556b37fa92206ea,src/main/java/org/seqdoop/hadoop_bam/BAMRecordReader.java,BAMRecordReader,overlaps,#SAMRecord#List#,225

Before Change


					// the purpose of sorting that is in the query region".
					return true;
				}
			} else if (r.getContig().equals(interval.getContig()) &&
					CoordMath.overlaps(r.getStart(), r.getEnd(),
						interval.getStart(), interval.getEnd())) {
				return true;

After Change


				}
			}
		}
		final Interval interval = new Interval(r.getContig(), r.getStart(), r.getEnd());
		Collection<Interval> overlaps = overlapDetector.getOverlaps(interval);
		return !overlaps.isEmpty();
	}