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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 BWT_BNTSEQ_H
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29 #define BWT_BNTSEQ_H
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30
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31 #include <stdint.h>
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32 #include <zlib.h>
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33
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34 #ifndef BWA_UBYTE
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35 #define BWA_UBYTE
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36 typedef uint8_t ubyte_t;
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37 #endif
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38
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39 typedef struct {
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40 int64_t offset;
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41 int32_t len;
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42 int32_t n_ambs;
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43 uint32_t gi;
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44 char *name, *anno;
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45 } bntann1_t;
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46
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47 typedef struct {
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48 int64_t offset;
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49 int32_t len;
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50 char amb;
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51 } bntamb1_t;
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52
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53 typedef struct {
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54 int64_t l_pac;
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55 int32_t n_seqs;
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56 uint32_t seed;
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57 bntann1_t *anns; // n_seqs elements
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58 int32_t n_holes;
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59 bntamb1_t *ambs; // n_holes elements
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60 FILE *fp_pac;
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61 } bntseq_t;
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62
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63 extern unsigned char nst_nt4_table[256];
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64
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65 #ifdef __cplusplus
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66 extern "C" {
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67 #endif
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68
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69 void bns_dump(const bntseq_t *bns, const char *prefix);
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70 bntseq_t *bns_restore(const char *prefix);
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71 bntseq_t *bns_restore_core(const char *ann_filename, const char* amb_filename, const char* pac_filename);
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72 void bns_destroy(bntseq_t *bns);
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73 int64_t bns_fasta2bntseq(gzFile fp_fa, const char *prefix, int for_only);
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74 int bns_cnt_ambi(const bntseq_t *bns, int64_t pos_f, int len, int *ref_id);
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75
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76 #ifdef __cplusplus
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77 }
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78 #endif
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79
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80 static inline int64_t bns_depos(const bntseq_t *bns, int64_t pos, int *is_rev)
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81 {
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82 return (*is_rev = (pos >= bns->l_pac))? (bns->l_pac<<1) - 1 - pos : pos;
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83 }
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84
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85 #endif
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