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# Copyright 2018 Google LLC.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
#    this list of conditions and the following disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright
#    notice, this list of conditions and the following disclaimer in the
#    documentation and/or other materials provided with the distribution.
#
# 3. Neither the name of the copyright holder nor the names of its
#    contributors may be used to endorse or promote products derived from this
#    software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.

from "third_party/nucleus/protos/range_pyclif.h" import *
from "third_party/nucleus/protos/reference_pyclif.h" import *
from "third_party/nucleus/protos/variants_pyclif.h" import *
from "third_party/nucleus/util/proto_clif_converter.h" import *
from "third_party/nucleus/core/statusor_clif_converters.h" import *

from third_party.nucleus.io.clif_postproc import ValueErrorOnFalse
from third_party.nucleus.io.clif_postproc import WrappedVariantIterable


from "third_party/nucleus/io/vcf_reader.h":
  namespace `nucleus`:

    class VariantIterable:
      def PythonNext(self, variant: EmptyProtoPtr<Variant>) -> StatusOr<bool>
      def Release(self) -> Status
      @__enter__
      def PythonEnter(self) -> Status
      @__exit__
      def PythonExit(self) -> Status

    class VcfReader:
      @classmethod
      def `FromFile` as from_file(cls, variantsPath: str, options: VcfReaderOptions)
        -> StatusOr<VcfReader>

      @classmethod
      def `FromFileWithHeader` as from_file_with_header(cls, variantsPath: str, options: VcfReaderOptions, header: VcfHeader)
        -> StatusOr<VcfReader>

      def `Iterate` as iterate(self) -> StatusOr<VariantIterable>:
        return WrappedVariantIterable(...)
      def `Query` as query(self, region: Range) -> StatusOr<VariantIterable>:
        return WrappedVariantIterable(...)

      def `FromStringPython` as from_string(self, vcf_line: str) -> (status: StatusOr<bool>, variant: Variant):
        # If status is an error object, the statusor_clif_converters
        # will have already converted it into a Python error message.
        # We call ValueErrorOnFalse here so that users only see a single
        # return object (the Variant).
        return ValueErrorOnFalse(...)

      @__enter__
      def PythonEnter(self) -> Status
      @__exit__
      def Close(self) -> Status
      header: VcfHeader = property(`Header`)