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