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();
}