Mercurial > repos > ashvark > qiime_1_8_0
diff bwa-0.6.2/bwtgap.h @ 2:a294fbfcb1db draft default tip
Uploaded BWA
author | ashvark |
---|---|
date | Fri, 18 Jul 2014 07:55:59 -0400 |
parents | dd1186b11b3b |
children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bwa-0.6.2/bwtgap.h Fri Jul 18 07:55:59 2014 -0400 @@ -0,0 +1,39 @@ +#ifndef BWTGAP_H_ +#define BWTGAP_H_ + +#include "bwt.h" +#include "bwtaln.h" + +typedef struct { // recursion stack + u_int32_t info; // score<<21 | i + u_int32_t n_mm:8, n_gapo:8, n_gape:8, state:2, n_seed_mm:6; + bwtint_t k, l; // (k,l) is the SA region of [i,n-1] + int last_diff_pos; +} gap_entry_t; + +typedef struct { + int n_entries, m_entries; + gap_entry_t *stack; +} gap_stack1_t; + +typedef struct { + int n_stacks, best, n_entries; + gap_stack1_t *stacks; +} gap_stack_t; + +#ifdef __cplusplus +extern "C" { +#endif + + gap_stack_t *gap_init_stack2(int max_score); + gap_stack_t *gap_init_stack(int max_mm, int max_gapo, int max_gape, const gap_opt_t *opt); + void gap_destroy_stack(gap_stack_t *stack); + bwt_aln1_t *bwt_match_gap(bwt_t *const bwt, int len, const ubyte_t *seq, bwt_width_t *w, + bwt_width_t *seed_w, const gap_opt_t *opt, int *_n_aln, gap_stack_t *stack); + void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s); + +#ifdef __cplusplus +} +#endif + +#endif