boolean isChromosomeMissing(Marker marker) {
		// Missing chromosome in marker?
		if (marker.getChromosome() == null) return true;

		// Missing chromosome in genome?
		String chrName = marker.getChromosomeName();
		Chromosome chr = genome.getChromosome(chrName);
		if (chr == null) return true;

		// Chromosome length is 1 or less?
		if (chr.size() < 1) return true;

		// Tree not found in interval forest?
		if (!intervalForest.hasTree(chrName)) return true;

		// OK, we have the chromosome
		return false;
	}