/*
 * Copyright 2018 Google LLC.
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 * 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
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#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_