/usr/include/htslib/faidx.h is in libhts-dev 1.1-1.
This file is owned by root:root, with mode 0o644.
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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 | /* 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
/*!
@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;
#ifdef __cplusplus
extern "C" {
#endif
/*!
@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);
/*!
@abstract Distroy 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);
/*!
@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
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