/usr/include/htslib/faidx.h is in libhts-dev 1.7-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 | /// @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);
/// 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
|