144 lines
3.8 KiB
C
144 lines
3.8 KiB
C
#ifndef MINIMAP2_H
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#define MINIMAP2_H
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#include <stdint.h>
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#include <stdio.h>
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#include <sys/types.h>
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#define MM_IDX_DEF_B 14
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#define MM_F_NO_SELF 0x01
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#define MM_F_AVA 0x02
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#define MM_F_CIGAR 0x04
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#define MM_F_OUT_SAM 0x08
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#define MM_F_NO_QUAL 0x10
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#define MM_IDX_MAGIC "MMI\2"
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typedef struct {
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uint64_t x, y;
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} mm128_t;
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typedef struct { size_t n, m; mm128_t *a; } mm128_v;
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typedef struct { size_t n, m; uint64_t *a; } uint64_v;
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typedef struct { size_t n, m; uint32_t *a; } uint32_v;
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typedef struct {
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mm128_v a; // (minimizer, position) array
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int32_t n; // size of the _p_ array
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uint64_t *p; // position array for minimizers appearing >1 times
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void *h; // hash table indexing _p_ and minimizers appearing once
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} mm_idx_bucket_t;
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typedef struct {
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char *name; // name of the db sequence
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uint64_t offset; // offset in mm_idx_t::S
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uint32_t len; // length
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} mm_idx_seq_t;
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typedef struct {
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int32_t b, w, k, is_hpc;
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uint32_t n_seq; // number of reference sequences
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mm_idx_seq_t *seq; // sequence name, length and offset
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uint32_t *S; // 4-bit packed sequence
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mm_idx_bucket_t *B; // index
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} mm_idx_t;
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typedef struct {
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uint32_t capacity;
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int32_t dp_score, dp_max, dp_max2;
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uint32_t blen;
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uint32_t n_diff, n_ambi;
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uint32_t n_cigar;
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uint32_t cigar[];
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} mm_extra_t;
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typedef struct {
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int32_t id;
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uint32_t cnt:31, rev:1;
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uint32_t rid:31, rep:1;
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int32_t score;
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int32_t qs, qe, rs, re;
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int32_t parent, subsc;
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int32_t as;
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int32_t fuzzy_mlen, fuzzy_blen;
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uint32_t mapq:8, split:2, sam_pri:1, n_sub:21; // TODO: n_sub is not used for now
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mm_extra_t *p;
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} mm_reg1_t;
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typedef struct {
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float max_occ_frac;
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float mid_occ_frac;
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int sdust_thres; // score threshold for SDUST; 0 to disable
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int flag; // see MM_F_* macros
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int bw; // bandwidth
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int max_gap; // break a chain if there are no minimizers in a max_gap window
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int max_chain_skip;
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int min_cnt;
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int min_chain_score;
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float mask_level;
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float pri_ratio;
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int best_n;
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int max_join_long, max_join_short;
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int min_join_flank_sc;
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int a, b, q, e, q2, e2; // matching score, mismatch, gap-open and gap-ext penalties
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int zdrop;
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int min_dp_max;
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int min_ksw_len;
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int max_occ;
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int mid_occ;
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} mm_mapopt_t;
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extern int mm_verbose, mm_dbg_flag;
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extern double mm_realtime0;
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struct mm_tbuf_s;
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typedef struct mm_tbuf_s mm_tbuf_t;
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struct bseq_file_s;
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#define mm_seq4_set(s, i, c) ((s)[(i)>>3] |= (uint32_t)(c) << (((i)&7)<<2))
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#define mm_seq4_get(s, i) ((s)[(i)>>3] >> (((i)&7)<<2) & 0xf)
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#ifdef __cplusplus
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extern "C" {
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#endif
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// compute minimizers
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void mm_sketch(void *km, const char *str, int len, int w, int k, uint32_t rid, int is_hpc, mm128_v *p);
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// minimizer indexing
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mm_idx_t *mm_idx_init(int w, int k, int b, int is_hpc);
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void mm_idx_destroy(mm_idx_t *mi);
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mm_idx_t *mm_idx_gen(struct bseq_file_s *fp, int w, int k, int b, int is_hpc, int mini_batch_size, int n_threads, uint64_t batch_size, int keep_name);
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uint32_t mm_idx_cal_max_occ(const mm_idx_t *mi, float f);
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void mm_idx_stat(const mm_idx_t *idx);
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const uint64_t *mm_idx_get(const mm_idx_t *mi, uint64_t minier, int *n);
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int mm_idx_getseq(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq);
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mm_idx_t *mm_idx_build(const char *fn, int w, int k, int is_hpc, int n_threads);
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// minimizer index I/O
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void mm_idx_dump(FILE *fp, const mm_idx_t *mi);
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mm_idx_t *mm_idx_load(FILE *fp);
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// mapping
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void mm_mapopt_init(mm_mapopt_t *opt);
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void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi);
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mm_tbuf_t *mm_tbuf_init(void);
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void mm_tbuf_destroy(mm_tbuf_t *b);
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mm_reg1_t *mm_map(const mm_idx_t *mi, int l_seq, const char *seq, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *name);
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int mm_map_file(const mm_idx_t *idx, const char *fn, const mm_mapopt_t *opt, int n_threads, int tbatch_size);
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#ifdef __cplusplus
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}
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#endif
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#endif // MINIMAP2_H
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