103 lines
2.8 KiB
C
103 lines
2.8 KiB
C
#ifndef BWAMEM_H_
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#define BWAMEM_H_
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#include "bwt.h"
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#include "bntseq.h"
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#include "utils.h"
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#define MEM_MAPQ_COEF 40.0
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#define MEM_MAPQ_MAX 60
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struct __smem_i;
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typedef struct __smem_i smem_i;
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typedef struct {
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int64_t rbeg;
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int32_t qbeg, len;
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} mem_seed_t;
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#define MEM_F_HARDCLIP 0x1
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#define MEM_F_PE 0x2
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#define MEM_F_NOPAIRING 0x4
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typedef struct {
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int a, b, q, r, w;
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int flag;
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int split_width;
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int min_seed_len, max_occ, max_chain_gap;
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int n_threads, chunk_size;
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int pe_dir;
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float mask_level;
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float chain_drop_ratio;
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float split_factor; // split into a seed if MEM is longer than min_seed_len*split_factor
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int pen_unpaired; // phred-scaled penalty for unpaired reads
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int max_ins; // maximum insert size
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int8_t mat[25]; // scoring matrix; mat[0] == 0 if unset
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} mem_opt_t;
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typedef struct {
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int n, m;
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int64_t pos;
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mem_seed_t *seeds;
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} mem_chain_t;
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typedef struct {
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int64_t rb, re;
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int score, qb, qe, seedcov, sub, csub; // sub: suboptimal score; csub: suboptimal inside the chain
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int sub_n; // approximate number of suboptimal hits
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int secondary; // non-negative if the hit is secondary
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} mem_alnreg_t;
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typedef struct {
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int low, high, failed;
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double avg, std;
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} mem_pestat_t;
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typedef struct {
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int64_t rb, re;
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int qb, qe, flag, qual;
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// optional info
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int score, sub;
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} bwahit_t;
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typedef struct { size_t n, m; mem_chain_t *a; } mem_chain_v;
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typedef struct { size_t n, m; mem_alnreg_t *a; } mem_alnreg_v;
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extern int mem_verbose;
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#ifdef __cplusplus
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extern "C" {
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#endif
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smem_i *smem_itr_init(const bwt_t *bwt);
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void smem_itr_destroy(smem_i *itr);
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void smem_set_query(smem_i *itr, int len, const uint8_t *query);
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const bwtintv_v *smem_next(smem_i *itr, int split_len, int split_width);
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mem_opt_t *mem_opt_init(void);
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void mem_fill_scmat(int a, int b, int8_t mat[25]);
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mem_chain_v mem_chain(const mem_opt_t *opt, const bwt_t *bwt, int len, const uint8_t *seq);
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int mem_chain_flt(const mem_opt_t *opt, int n_chn, mem_chain_t *chains);
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void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain_t *c, mem_alnreg_v *a);
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uint32_t *mem_gen_cigar(const mem_opt_t *opt, 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);
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int mem_process_seqs(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int n, bseq1_t *seqs);
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void mem_pestat(const mem_opt_t *opt, int64_t l_pac, int n, const mem_alnreg_v *regs, mem_pestat_t pes[4]);
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#ifdef __cplusplus
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}
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#endif
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static inline int mem_infer_dir(int64_t l_pac, int64_t b1, int64_t b2, int64_t *dist)
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{
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int64_t p2;
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int r1 = (b1 >= l_pac), r2 = (b2 >= l_pac);
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p2 = r1 == r2? b2 : (l_pac<<1) - 1 - b2; // p2 is the coordinate of read 2 on the read 1 strand
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*dist = p2 > b1? p2 - b1 : b1 - p2;
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return (r1 == r2? 0 : 1) ^ (p2 > b1? 0 : 3);
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}
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#endif
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