BGI/SOAPdenovo2/standardPregraph/inc/faidx.h

   1 /*
   2  * inc/extvab.h
   3  *
   4  * This file is part of SOAPdenovo.
   5  *
   6  */
   7
   8 /* The MIT License
   9
  10    Copyright (c) 2008 Genome Research Ltd (GRL).
  11
  12    Permission is hereby granted, free of charge, to any person obtaining
  13    a copy of this software and associated documentation files (the
  14    "Software"), to deal in the Software without restriction, including
  15    without limitation the rights to use, copy, modify, merge, publish,
  16    distribute, sublicense, and/or sell copies of the Software, and to
  17    permit persons to whom the Software is furnished to do so, subject to
  18    the following conditions:
  19
  20    The above copyright notice and this permission notice shall be
  21    included in all copies or substantial portions of the Software.
  22
  23    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
  24    EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
  25    MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
  26    NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
  27    BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
  28    ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
  29    CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  30    SOFTWARE.
  31 */
  32
  33 /* Contact: Heng Li <lh3@sanger.ac.uk> */
  34
  35 #ifndef FAIDX_H
  36 #define FAIDX_H
  37
  38 /*!
  39   @header
  40
  41   Index FASTA files and extract subsequence.
  42
  43   @copyright The Wellcome Trust Sanger Institute.
  44  */
  45
  46 struct __faidx_t;
  47 typedef struct __faidx_t faidx_t;
  48
  49 #ifdef __cplusplus
  50 extern "C" {
  51 #endif
  52
  53         /*!
  54           @abstract   Build index for a FASTA or razip compressed FASTA file.
  55           @param  fn  FASTA file name
  56           @return     0 on success; or -1 on failure
  57           @discussion File "fn.fai" will be generated.
  58          */
  59         int fai_build ( const char * fn );
  60
  61         /*!
  62           @abstract    Distroy a faidx_t struct.
  63           @param  fai  Pointer to the struct to be destroyed
  64          */
  65         void fai_destroy ( faidx_t * fai );
  66
  67         /*!
  68           @abstract   Load index from "fn.fai".
  69           @param  fn  File name of the FASTA file
  70          */
  71         faidx_t * fai_load ( const char * fn );
  72
  73         /*!
  74           @abstract    Fetch the sequence in a region.
  75           @param  fai  Pointer to the faidx_t struct
  76           @param  reg  Region in the format "chr2:20,000-30,000"
  77           @param  len  Length of the region
  78           @return      Pointer to the sequence; null on failure
  79
  80           @discussion The returned sequence is allocated by malloc family
  81           and should be destroyed by end users by calling free() on it.
  82          */
  83         char * fai_fetch ( const faidx_t * fai, const char * reg, int * len );
  84
  85         /*!
  86           @abstract    Fetch the number of sequences.
  87           @param  fai  Pointer to the faidx_t struct
  88           @return      The number of sequences
  89          */
  90         int faidx_fetch_nseq ( const faidx_t * fai );
  91
  92         /*!
  93           @abstract    Fetch the sequence in a region.
  94           @param  fai  Pointer to the faidx_t struct
  95           @param  c_name Region name
  96           @param  p_beg_i  Beginning position number (zero-based)
  97           @param  p_end_i  End position number (zero-based)
  98           @param  len  Length of the region
  99           @return      Pointer to the sequence; null on failure
 100
 101           @discussion The returned sequence is allocated by malloc family
 102           and should be destroyed by end users by calling free() on it.
 103          */
 104         char * faidx_fetch_seq ( const faidx_t * fai, char * c_name, int p_beg_i, int p_end_i, int * len );
 105
 106 #ifdef __cplusplus
 107 }
 108 #endif
 109
 110 #endif