39 lines
942 B
C
39 lines
942 B
C
#ifndef BWTGAP_H_
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#define BWTGAP_H_
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#include "bwt.h"
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#include "bwtaln.h"
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typedef struct { // recursion stack
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u_int32_t info; // score<<21 | a<<20 | i
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u_int32_t n_mm:8, n_gapo:8, n_gape:8, state:2, n_seed_mm:6;
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bwtint_t k, l; // (k,l) is the SA region of [i,n-1]
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int last_diff_pos;
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} gap_entry_t;
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typedef struct {
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int n_entries, m_entries;
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gap_entry_t *stack;
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} gap_stack1_t;
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typedef struct {
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int n_stacks, best, n_entries;
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gap_stack1_t *stacks;
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} gap_stack_t;
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#ifdef __cplusplus
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extern "C" {
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#endif
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gap_stack_t *gap_init_stack(int max_mm, int max_gapo, int max_gape, const gap_opt_t *opt);
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void gap_destroy_stack(gap_stack_t *stack);
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bwt_aln1_t *bwt_match_gap(bwt_t *const bwt[2], int len, const ubyte_t *seq[2], bwt_width_t *w[2],
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bwt_width_t *seed_w[2], const gap_opt_t *opt, int *_n_aln, gap_stack_t *stack);
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void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s);
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#ifdef __cplusplus
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}
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#endif
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#endif
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