public void buildForest() {
		intervalForest = new IntervalForest();

		// Add all chromosomes to forest
		if (useChromosomes) {
			for (Chromosome chr : genome)
				intervalForest.add(chr);
		}

		// Add all genes to forest
		for (Gene gene : genome.getGenes())
			intervalForest.add(gene);

		//---
		// Create (and add) up-down stream, splice sites, intergenic, etc
		//---
		markers.add(createGenomicRegions());

		// Add all 'markers' to forest (includes custom intervals)
		intervalForest.add(markers);

		// Build interval forest
		intervalForest.build();
	}