faidx.h

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/* faidx.h -- FASTA random access.

   Copyright (C) 2008, 2009, 2013, 2014 Genome Research Ltd.

   Author: Heng Li <lh3@sanger.ac.uk>

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

#ifndef HTSLIB_FAIDX_H
#define HTSLIB_FAIDX_H

struct __faidx_t;
typedef struct __faidx_t faidx_t;

#ifdef __cplusplus
extern "C" {
#endif

    int fai_build(const char *fn);

    void fai_destroy(faidx_t *fai);

    faidx_t *fai_load(const char *fn);

    char *fai_fetch(const faidx_t *fai, const char *reg, int *len);

    int faidx_fetch_nseq(const faidx_t *fai);

    char *faidx_fetch_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len);

    int faidx_has_seq(const faidx_t *fai, const char *seq);

    int faidx_nseq(const faidx_t *fai);

    const char *faidx_iseq(const faidx_t *fai, int i);

    int faidx_seq_len(const faidx_t *fai, const char *seq);

#ifdef __cplusplus
}
#endif

#endif