text: /*
   * 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.
   *
   */
  
  #ifndef THIRD_PARTY_NUCLEUS_IO_HTS_PATH_H_
  #define THIRD_PARTY_NUCLEUS_IO_HTS_PATH_H_
  
  #include <string>
  
  #include "htslib/faidx.h"
  #include "htslib/hts.h"
  #include "htslib/tbx.h"
  
  namespace nucleus {
  
  // This is a wrapper for hts_open that lets us select a default
  // protocol, like "file:" or just plain "".
  htsFile *hts_open_x(const std::string &fn, const char *mode);
  
  htsFile *hts_open_format_x(const std::string &fn, const char *mode,
                             htsFormat *fmt);
  
  faidx_t *fai_load3_x(const std::string &fa_path, const std::string &fai_path,
                       const std::string &gzi_path, int flags);
  
  int tbx_index_build_x(const std::string &fn, int min_shift,
                        const tbx_conf_t *conf);
  
  }  // namespace nucleus
  
  #endif  // THIRD_PARTY_NUCLEUS_IO_HTS_PATH_H_
  