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#
# Copyright (C) 2010-2017 Institute for Computational Biomedicine,
# Weill Medical College of Cornell University
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
""" Contains classes that can parse binary sequence data
stored in the Goby "compact" format.
"""
import struct
from collections import ByteString
import goby.MessageChunks
import goby.Reads_pb2
def CompactReads(basename):
if not basename.endswith(".compact-reads"):
basename += ".compact-reads"
collection = goby.Reads_pb2.ReadCollection()
for reads in MessageChunks.MessageChunksGenerator(
basename, collectionContainer=collection):
for read in reads.reads:
yield read
def decodeSequence(sequence):
return str(sequence, "utf-8")
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