Mercurial > repos > ashvark > qiime_1_8_0
diff bwa-0.6.2/bwtsw2.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/bwtsw2.h Fri Jul 18 07:55:59 2014 -0400 @@ -0,0 +1,69 @@ +#ifndef LH3_BWTSW2_H +#define LH3_BWTSW2_H + +#include <stdint.h> +#include "bntseq.h" +#include "bwt_lite.h" +#include "bwt.h" + +#define BSW2_FLAG_MATESW 0x100 +#define BSW2_FLAG_TANDEM 0x200 +#define BSW2_FLAG_MOVED 0x400 +#define BSW2_FLAG_RESCUED 0x800 + +typedef struct { + int skip_sw:16, hard_clip:16; + int a, b, q, r, t, qr, bw, max_ins; + int z, is, t_seeds, multi_2nd; + float mask_level, coef; + int n_threads, chunk_size; +} bsw2opt_t; + +typedef struct { + bwtint_t k, l; + uint32_t flag:18, n_seeds:13, is_rev:1; + int len, G, G2; + int beg, end; +} bsw2hit_t; + +typedef struct { + int flag, nn, n_cigar, chr, pos, qual, mchr, mpos, pqual, isize, nm; + uint32_t *cigar; +} bsw2aux_t; + +typedef struct { + int n, max; + bsw2hit_t *hits; + bsw2aux_t *aux; +} bwtsw2_t; + +typedef struct { + void *stack; + int max_l; + uint8_t *aln_mem; +} bsw2global_t; + +typedef struct { + int l, tid; + char *name, *seq, *qual, *sam; +} bsw2seq1_t; + +#ifdef __cplusplus +extern "C" { +#endif + + bsw2opt_t *bsw2_init_opt(); + bwtsw2_t **bsw2_core(const bntseq_t *bns, 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, const char *fn, const char *fn2); + void bsw2_destroy(bwtsw2_t *b); + + bsw2global_t *bsw2_global_init(); + void bsw2_global_destroy(bsw2global_t *_pool); + + void bsw2_pair(const bsw2opt_t *opt, int64_t l_pac, const uint8_t *pac, int n, bsw2seq1_t *seq, bwtsw2_t **hit); + +#ifdef __cplusplus +} +#endif + +#endif