Ejemplo n.º 1
0
  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;
  }