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# Copyright 2018 Google LLC.
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from "deepvariant/protos/realigner_pyclif.h" import *
from "third_party/nucleus/protos/reads_pyclif.h" import *

from "deepvariant/realigner/fast_pass_aligner.h":
  namespace `learning::genomics::deepvariant`:
    class FastPassAligner:
      def `set_reference` as set_reference(self, ref: bytes)
      def `set_ref_start` as set_ref_start(self, chr: bytes, pos: int)
      def `set_haplotypes` as set_haplotypes(self, hyplotypes:list<bytes>)
      def `set_options` as set_options(self, options:AlignerOptions)
      def `set_is_debug` as set_is_debug(self, isDebug: bool)
      def `set_normalize_reads` as set_normalize_reads(self,
                                                       normalizeReads: bool)
      def `set_debug_read_id` as set_debug_read_id(self, readId: int)
      def `set_ref_prefix_len` as set_ref_prefix_len(self, ref_prefix_len: int)
      def `set_ref_suffix_len` as set_ref_suffix_len(self, set_ref_suffix_len: int)
      def `AlignReads` as realign_reads(self, reads:list<Read>) -> list<Read>