def _hits_hashed_by_query(self, hits):
        '''Input: list of nucmer hits. Output: dictionary, keys are query names, values are lists of hits'''
        d = {}
        for hit in hits:
            if hit.qry_name not in d:
                d[hit.qry_name] = []
            d[hit.qry_name].append(hit)
        return d
Input: list of nucmer hits. Output: dictionary, keys are query names, values are lists of hits