/* 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

#include "hts_defs.h"

#ifdef __cplusplus
extern "C" {
#endif

/*!
  @header

  Index FASTA files and extract subsequence.

  The fai file index columns are:
    - chromosome name
    - chromosome length: number of bases
    - offset: number of bytes to skip to get to the first base
        from the beginning of the file, including the length
        of the sequence description string (">chr ..\n")
    - line length: number of bases per line (excluding \n)
    - binary line length: number of bytes, including \n

  @copyright The Wellcome Trust Sanger Institute.
 */

struct __faidx_t;
typedef struct __faidx_t faidx_t;

    /*!
      @abstract   Build index for a FASTA or bgzip-compressed FASTA file.
      @param  fn  FASTA file name
      @return     0 on success; or -1 on failure
      @discussion File "fn.fai" will be generated.
     */
    int fai_build(const char *fn) HTS_RESULT_USED;

    /*!
      @abstract    Destroy a faidx_t struct.
      @param  fai  Pointer to the struct to be destroyed
     */
    void fai_destroy(faidx_t *fai);

    /*!
      @abstract   Load index from "fn.fai".
      @param  fn  File name of the FASTA file
     */
    faidx_t *fai_load(const char *fn);

    /*!
      @abstract    Fetch the sequence in a region.
      @param  fai  Pointer to the faidx_t struct
      @param  reg  Region in the format "chr2:20,000-30,000"
      @param  len  Length of the region; -2 if seq not present, -1 general error
      @return      Pointer to the sequence; null on failure

      @discussion The returned sequence is allocated by malloc family
      and should be destroyed by end users by calling free() on it.
     */
    char *fai_fetch(const faidx_t *fai, const char *reg, int *len);

    /*!
      @abstract    Fetch the number of sequences.
      @param  fai  Pointer to the faidx_t struct
      @return      The number of sequences
     */
    int faidx_fetch_nseq(const faidx_t *fai) HTS_DEPRECATED("Please use faidx_nseq instead");

    /*!
      @abstract    Fetch the sequence in a region.
      @param  fai  Pointer to the faidx_t struct
      @param  c_name Region name
      @param  p_beg_i  Beginning position number (zero-based)
      @param  p_end_i  End position number (zero-based)
      @param  len  Length of the region; -2 if c_name not present, -1 general error
      @return      Pointer to the sequence; null on failure

      @discussion The returned sequence is allocated by malloc family
      and should be destroyed by end users by calling free() on it.
     */
    char *faidx_fetch_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len);

    /*!
      @abstract    Query if sequence is present
      @param  fai  Pointer to the faidx_t struct
      @param  seq  Sequence name
      @return      1 if present or 0 if absent
     */
    int faidx_has_seq(const faidx_t *fai, const char *seq);

    /*!
      @abstract    Return number of sequences in fai index
     */
    int faidx_nseq(const faidx_t *fai);

    /*!
      @abstract    Return name of i-th sequence
     */
    const char *faidx_iseq(const faidx_t *fai, int i);

    /*!
      @abstract    Return sequence length, -1 if not present
     */
    int faidx_seq_len(const faidx_t *fai, const char *seq);

#ifdef __cplusplus
}
#endif

#endif
