annotate pyPRADA_1.2/tools/bwa-0.5.7-mh/bwtsw2.h @ 0:acc2ca1a3ba4

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author siyuan
date Thu, 20 Feb 2014 00:44:58 -0500
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1 #ifndef LH3_BWTSW2_H
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2 #define LH3_BWTSW2_H
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3
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4 #include <stdint.h>
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5 #include "bntseq.h"
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6 #include "bwt_lite.h"
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7 #include "bwt.h"
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8
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9 typedef struct {
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10 int a, b, q, r, t, qr, bw;
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11 int z, is, t_seeds, hard_clip;
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12 float yita, mask_level, coef;
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13 int n_threads, chunk_size;
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14 } bsw2opt_t;
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16 typedef struct {
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17 uint32_t k, l, flag:18, n_seeds:14;
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18 int len, G, G2;
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19 int beg, end;
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20 } bsw2hit_t;
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22 typedef struct {
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23 int n, max;
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24 bsw2hit_t *hits;
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25 int *n_cigar;
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26 uint32_t **cigar;
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27 } bwtsw2_t;
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28
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29 typedef struct {
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30 void *stack;
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31 int max_l;
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32 uint8_t *aln_mem;
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33 } bsw2global_t;
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34
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35 #ifdef __cplusplus
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36 extern "C" {
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37 #endif
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38
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39 bsw2opt_t *bsw2_init_opt();
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40 bwtsw2_t **bsw2_core(const bsw2opt_t *opt, const bwtl_t *target, const bwt_t *query, bsw2global_t *pool);
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41 void bsw2_aln(const bsw2opt_t *opt, const bntseq_t *bns, bwt_t * const target[2], const char *fn);
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42 void bsw2_destroy(bwtsw2_t *b);
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44 bsw2global_t *bsw2_global_init();
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45 void bsw2_global_destroy(bsw2global_t *_pool);
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46
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47 #ifdef __cplusplus
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48 }
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49 #endif
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51 #endif