output comparison and allow for tolerance if desired

    * -1 if junc comes before self
    * 1 if junc comes after self
    * 0 if overlaps
    * 2 if else

    :param junc:
    :param tolerance: optional search space (default=0, no tolerance)
    :type junc: Junction
    :type tolerance: int
    :return: value of comparison
    :rtype: int

def cmp(self,junc,tolerance=0):
    """ output comparison and allow for tolerance if desired

    * -1 if junc comes before self
    * 1 if junc comes after self
    * 0 if overlaps
    * 2 if else

    :param junc:
    :param tolerance: optional search space (default=0, no tolerance)
    :type junc: Junction
    :type tolerance: int
    :return: value of comparison
    :rtype: int
    """
    if self.overlaps(junc,tolerance):
      return 0 #equal
    if self.left.chr == junc.right.chr:
      if self.left.start > junc.right.start:
        return -1 #comes before
    if self.right.chr == junc.left.chr:
      if self.right.start < junc.right.start:
        return 1 #comes after
    return 2