final GenomeLoc loc = getWalker().getToolkit().getGenomeLocParser().createGenomeLoc(cnv);
IntervalTree<GenomeLoc> intervalTree = knownCNVs.get(loc.getContig());
final Iterator<IntervalTree.Node<GenomeLoc>> nodeIt = intervalTree.overlappers(loc.getStart(), loc.getStop());
while ( nodeIt.hasNext() ) {
final double overlapP = loc.reciprocialOverlapFraction(nodeIt.next().getValue());
if ( overlapP > MIN_CNV_OVERLAP )
return true;
}
}