/// @file htslib/faidx.h
/// FASTA random access.
/*
   Copyright (C) 2008, 2009, 2013, 2014, 2016, 2017 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

/** @file

  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`
 */

struct __faidx_t;
/// Opaque structure representing FASTA index
typedef struct __faidx_t faidx_t;

/// Build index for a FASTA or bgzip-compressed FASTA file.
/**  @param  fn  FASTA file name
     @param  fnfai Name of .fai file to build.
     @param  fngzi Name of .gzi file to build (if fn is bgzip-compressed).
     @return     0 on success; or -1 on failure

If fnfai is NULL, ".fai" will be appended to fn to make the FAI file name.
If fngzi is NULL, ".gzi" will be appended to fn for the GZI file.  The GZI
file will only be built if fn is bgzip-compressed.
*/
int fai_build3(const char *fn, const char *fnfai, const char *fngzi) HTS_RESULT_USED;

/// Build index for a FASTA or bgzip-compressed FASTA file.
/** @param  fn  FASTA file name
    @return     0 on success; or -1 on failure

File "fn.fai" will be generated.  This function is equivalent to
fai_build3(fn, NULL, NULL);
*/
int fai_build(const char *fn) HTS_RESULT_USED;

/// Destroy a faidx_t struct
void fai_destroy(faidx_t *fai);

enum fai_load_options {
    FAI_CREATE = 0x01,
};

/// Load FASTA indexes.
/** @param  fn  File name of the FASTA file (can be compressed with bgzip).
    @param  fnfai File name of the FASTA index.
    @param  fngzi File name of the bgzip index.
    @param  flags Option flags to control index file caching and creation.
    @return Pointer to a faidx_t struct on success, NULL on failure.

If fnfai is NULL, ".fai" will be appended to fn to make the FAI file name.
If fngzi is NULL, ".gzi" will be appended to fn for the bgzip index name.
The bgzip index is only needed if fn is compressed.

If (flags & FAI_CREATE) is true, the index files will be built using
fai_build3() if they are not already present.
*/
faidx_t *fai_load3(const char *fn, const char *fnfai, const char *fngzi,
                   int flags);

/// Load index from "fn.fai".
/** @param  fn  File name of the FASTA file
    @return Pointer to a faidx_t struct on success, NULL on failure.

This function is equivalent to fai_load3(fn, NULL, NULL, FAI_CREATE|FAI_CACHE);
*/
faidx_t *fai_load(const char *fn);

/// 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

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);

/// 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");

/// 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

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);

/// Alternative to faidx_fetch_seq() -- by H.P.
/** @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  out  User-supplied output buffer
    @return      Number of bytes written; -1 on failure

Differences with faidx_fetch_seq(): (1) writes the incoming sequence to
user-supplied output buffer, (2) doesn't write the terminating null byte
('\0'), (3) properly handles 0-length sequences, (4) returns the number of
bytes written; -1 on failure.
*/
int faidx_fetch_seq2(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, char *out);

/// Alternative to faidx_fetch_seq() -- originally by Daniel Jones (author of
/// the seqbias package), moved to Rhtslib and ported to htslib-1.7 by H.P.
/** @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

The returned sequence is allocated by `malloc()` family and should be destroyed
by end users by calling `free()` on it.
Difference with faidx_fetch_seq(): if coordinates are outside the actual
sequence, write N's, rather than adjusting the start,end.
*/
char *faidx_fetch_seq_forced_lower(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i);

/// 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);

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

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

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

#ifdef __cplusplus
}
#endif

#endif