Method getOverlapContainer

src/rnabloom/util/PafUtils.java:249–256

(Overlap q, Collection<Overlap> list)

    }
    
    private static Overlap getOverlapContainer(Overlap q, Collection<Overlap> list) {
        for (Overlap m : list) {
            if (q.qStart >= m.qStart && q.qEnd <= m.qEnd) {
                return m;
            }
        }
        return null;
    }
    
    private static Overlap getOverlapContainer(Overlap q, Collection<Overlap> list, float maxProportion) {
        int maxOverlapLen = 0;