Mercurial > repos > siyuan > prada
diff pyPRADA_1.2/tools/bwa-0.5.7-mh/bwtsw2.h @ 0:acc2ca1a3ba4
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author | siyuan |
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date | Thu, 20 Feb 2014 00:44:58 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pyPRADA_1.2/tools/bwa-0.5.7-mh/bwtsw2.h Thu Feb 20 00:44:58 2014 -0500 @@ -0,0 +1,51 @@ +#ifndef LH3_BWTSW2_H +#define LH3_BWTSW2_H + +#include <stdint.h> +#include "bntseq.h" +#include "bwt_lite.h" +#include "bwt.h" + +typedef struct { + int a, b, q, r, t, qr, bw; + int z, is, t_seeds, hard_clip; + float yita, mask_level, coef; + int n_threads, chunk_size; +} bsw2opt_t; + +typedef struct { + uint32_t k, l, flag:18, n_seeds:14; + int len, G, G2; + int beg, end; +} bsw2hit_t; + +typedef struct { + int n, max; + bsw2hit_t *hits; + int *n_cigar; + uint32_t **cigar; +} bwtsw2_t; + +typedef struct { + void *stack; + int max_l; + uint8_t *aln_mem; +} bsw2global_t; + +#ifdef __cplusplus +extern "C" { +#endif + + bsw2opt_t *bsw2_init_opt(); + bwtsw2_t **bsw2_core(const bsw2opt_t *opt, const bwtl_t *target, const bwt_t *query, bsw2global_t *pool); + void bsw2_aln(const bsw2opt_t *opt, const bntseq_t *bns, bwt_t * const target[2], const char *fn); + void bsw2_destroy(bwtsw2_t *b); + + bsw2global_t *bsw2_global_init(); + void bsw2_global_destroy(bsw2global_t *_pool); + +#ifdef __cplusplus +} +#endif + +#endif