int reportDistance(Markers closestMarkers, Marker queryMarker) {
		Marker firstMarker = closestMarkers.getMarkers().get(0); // If there is more than one marker, they are at the same distance, so we just report the distance to the first one
		if (tss) {
			Transcript tr = findTranscript(firstMarker);
			Marker trTss = tr.getTss();
			int d = trTss.distance(queryMarker);
			return tr.intersects(queryMarker) ? -d : d; // Negative distance denotes the marker is actually intersecting the transcript's TSS
		}
		return firstMarker.distance(queryMarker);
	}