# Copyright 2023 WHERE TRUE Technologies.
#
# 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.

"""Main biobear package."""

from biobear.fasta_reader import FastaReader
from biobear.fastq_reader import FastqReader
from biobear.vcf_reader import VCFReader, VCFIndexedReader
from biobear.bam_reader import BamReader, BamIndexedReader
from biobear.gtf_reader import GTFReader
from biobear.gff_reader import GFFReader
from biobear.mzml_reader import MzMLReader
from biobear.genbank_reader import GenbankReader
from biobear.bcf_reader import BCFReader, BCFIndexedReader

from biobear import compression
from biobear.compression import Compression

from .biobear import __runtime
from .biobear import connect

from .biobear import FileCompressionType
from .biobear import FASTQReadOptions
from .biobear import FASTAReadOptions

__version__ = "0.18.0"

__all__ = [
    "FastaReader",
    "FastqReader",
    "VCFReader",
    "VCFIndexedReader",
    "BamReader",
    "BamIndexedReader",
    "BCFReader",
    "BCFIndexedReader",
    "GFFReader",
    "GTFReader",
    "GenbankReader",
    "MzMLReader",
    "compression",
    "Compression",
    "FileCompressionType",
    "FASTQReadOptions",
    "FASTAReadOptions",
    "__version__",
    "connect",
    "__runtime",
]
