45 lines
879 B
C
45 lines
879 B
C
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#ifndef BWA_H_
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#define BWA_H_
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#include <stdint.h>
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#define BWA_DEF_MAX_SCORE 2048
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#define BWA_MAX_QUERY_LEN 1024
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struct bwa_idx_t;
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typedef struct bwa_idx_t bwa_idx_t;
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struct bwa_aux_t;
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typedef struct bwa_aux_t bwa_aux_t;
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typedef struct {
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int s_gapo, s_gape; // the mismatch penalty is fixed at 3
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int max_diff, max_gapo, max_gape;
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int seed_len, max_seed_diff;
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float fnr;
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} bwa_opt_t;
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typedef struct {
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uint32_t n_mm:16, n_gapo:8, n_gape:8;
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int score;
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uint64_t k, l;
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} bwa_alnpre_t;
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extern bwa_opt_t bwa_def_opt;
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#ifdef __cplusplus
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extern "C" {
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#endif
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bwa_idx_t *bwa_idx_load(const char *prefix);
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void bwa_idx_destroy(bwa_idx_t *p);
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bwa_aux_t *bwa_aux_init(const bwa_opt_t *opt, int max_score);
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void bwa_aux_destroy(bwa_aux_t *p);
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bwa_alnpre_t *bwa_aln_pre(const bwa_idx_t *idx, bwa_aux_t *aux, const char *seq, int *n_aln);
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#ifdef __cplusplus
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}
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#endif
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#endif
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