/**
* Is the chromosome missing in this marker?
*
* @param marker
* @return
*/
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;
}