private boolean overlapsKnownCNV(VariantContext cnv) {
if (knownCNVs != null) {
final GenomeLoc loc =
getWalker().getToolkit().getGenomeLocParser().createGenomeLoc(cnv, true);
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;
}
}
return false;
}
