59 lines
1.2 KiB
C
59 lines
1.2 KiB
C
#ifndef BWAMEM_H_
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#define BWAMEM_H_
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#include "bwt.h"
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struct __smem_i;
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typedef struct __smem_i smem_i;
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typedef struct {
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int64_t rbeg;
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int32_t qbeg, len;
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} mem_seed_t;
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typedef struct {
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int a, b, q, r, w;
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int min_seed_len, max_occ, max_chain_gap;
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int8_t mat[25]; // scoring matrix; mat[0] == 0 if unset
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float mask_level, chain_drop_ratio;
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} mem_opt_t;
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typedef struct {
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int n, m;
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int64_t pos;
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mem_seed_t *seeds;
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} mem_chain1_t;
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typedef struct {
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int n, m;
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mem_chain1_t *chains;
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} mem_chain_t;
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typedef struct {
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int64_t pos, rb, re;
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int n_cigar, len, score, qb, qe, is_all;
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uint32_t *cigar;
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} mem_aln_t;
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#ifdef __cplusplus
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extern "C" {
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#endif
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smem_i *smem_itr_init(const bwt_t *bwt);
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void smem_itr_destroy(smem_i *itr);
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void smem_set_query(smem_i *itr, int len, const uint8_t *query);
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const bwtintv_v *smem_next(smem_i *itr, int split_len);
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mem_opt_t *mem_opt_init(void);
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void mem_fill_scmat(int a, int b, int8_t mat[25]);
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mem_chain_t mem_chain(const mem_opt_t *opt, const bwt_t *bwt, int len, const uint8_t *seq);
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void mem_chain_flt(const mem_opt_t *opt, mem_chain_t *chn);
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void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain1_t *c, mem_aln_t *a);
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#ifdef __cplusplus
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}
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#endif
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#endif
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