# Copyright (c) 2015. Mount Sinai School of Medicine
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

from __future__ import absolute_import

from collections import namedtuple, defaultdict, OrderedDict
import logging
import itertools
import re

import pandas
from pysam import Samfile
import typechecks
import pyensembl

from ..locus import Locus
from . import Pileup, PileupElement, alignment_key, read_key

MatchingEvidence = namedtuple("MatchingEvidence", "ref alt other")

class PileupCollection(object):