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view bwa-0.7.9a/bwa.h @ 0:ce5a8082bbb8 draft
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author | xilinxu |
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date | Thu, 14 Aug 2014 02:16:48 -0400 |
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#ifndef BWA_H_ #define BWA_H_ #include <stdint.h> #include "bntseq.h" #include "bwt.h" #define BWA_IDX_BWT 0x1 #define BWA_IDX_BNS 0x2 #define BWA_IDX_PAC 0x4 #define BWA_IDX_ALL 0x7 typedef struct { bwt_t *bwt; // FM-index bntseq_t *bns; // information on the reference sequences uint8_t *pac; // the actual 2-bit encoded reference sequences with 'N' converted to a random base } bwaidx_t; typedef struct { int l_seq; char *name, *comment, *seq, *qual, *sam; } bseq1_t; extern int bwa_verbose; extern char bwa_rg_id[256]; #ifdef __cplusplus extern "C" { #endif bseq1_t *bseq_read(int chunk_size, int *n_, void *ks1_, void *ks2_); void bwa_fill_scmat(int a, int b, int8_t mat[25]); uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar, int *NM); uint32_t *bwa_gen_cigar2(const int8_t mat[25], int o_del, int e_del, int o_ins, int e_ins, int w_, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar, int *NM); char *bwa_idx_infer_prefix(const char *hint); bwt_t *bwa_idx_load_bwt(const char *hint); bwaidx_t *bwa_idx_load(const char *hint, int which); void bwa_idx_destroy(bwaidx_t *idx); void bwa_print_sam_hdr(const bntseq_t *bns, const char *rg_line); char *bwa_set_rg(const char *s); #ifdef __cplusplus } #endif #endif