1 #ifndef MMPRIV2_H
2 #define MMPRIV2_H
3
4 #include <assert.h>
5 #include "minimap.h"
6 #include "bseq.h"
7 #include "kseq.h"
8
9 #define MM_PARENT_UNSET (-1)
10 #define MM_PARENT_TMP_PRI (-2)
11
12 #define MM_DBG_NO_KALLOC 0x1
13 #define MM_DBG_PRINT_QNAME 0x2
14 #define MM_DBG_PRINT_SEED 0x4
15 #define MM_DBG_PRINT_ALN_SEQ 0x8
16 #define MM_DBG_PRINT_CHAIN 0x10
17
18 #define MM_SEED_LONG_JOIN (1ULL<<40)
19 #define MM_SEED_IGNORE (1ULL<<41)
20 #define MM_SEED_TANDEM (1ULL<<42)
21 #define MM_SEED_SELF (1ULL<<43)
22
23 #define MM_SEED_SEG_SHIFT 48
24 #define MM_SEED_SEG_MASK (0xffULL<<(MM_SEED_SEG_SHIFT))
25
26 #ifndef kroundup32
27 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
28 #endif
29
30 #define mm_seq4_set(s, i, c) ((s)[(i)>>3] |= (uint32_t)(c) << (((i)&7)<<2))
31 #define mm_seq4_get(s, i) ((s)[(i)>>3] >> (((i)&7)<<2) & 0xf)
32
33 #define MALLOC(type, len) ((type*)malloc((len) * sizeof(type)))
34 #define CALLOC(type, len) ((type*)calloc((len), sizeof(type)))
35
36 #ifdef __cplusplus
37 extern "C" {
38 #endif
39
40 typedef struct {
41 uint32_t n;
42 uint32_t q_pos;
43 uint32_t q_span:31, flt:1;
44 uint32_t seg_id:31, is_tandem:1;
45 const uint64_t *cr;
46 } mm_seed_t;
47
48 typedef struct {
49 int n_u, n_a;
50 uint64_t *u;
51 mm128_t *a;
52 } mm_seg_t;
53
54 double cputime(void);
55 double realtime(void);
56 long peakrss(void);
57
58 void radix_sort_128x(mm128_t *beg, mm128_t *end);
59 void radix_sort_64(uint64_t *beg, uint64_t *end);
60 uint32_t ks_ksmall_uint32_t(size_t n, uint32_t arr[], size_t kk);
61
62 void mm_sketch(void *km, const char *str, int len, int w, int k, uint32_t rid, int is_hpc, mm128_v *p);
63
64 mm_seed_t *mm_collect_matches(void *km, int *_n_m, int qlen, int max_occ, int max_max_occ, int dist, const mm_idx_t *mi, const mm128_v *mv, int64_t *n_a, int *rep_len, int *n_mini_pos, uint64_t **mini_pos);
65 void mm_seed_mz_flt(void *km, mm128_v *mv, int32_t q_occ_max, float q_occ_frac);
66
67 double mm_event_identity(const mm_reg1_t *r);
68 int mm_write_sam_hdr(const mm_idx_t *mi, const char *rg, const char *ver, int argc, char *argv[]);
69 void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int64_t opt_flag);
70 void mm_write_paf3(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int64_t opt_flag, int rep_len);
71 void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, int n_regs, const mm_reg1_t *regs);
72 void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int seg_idx, int reg_idx, int n_seg, const int *n_regs, const mm_reg1_t *const* regs, void *km, int64_t opt_flag);
73 void mm_write_sam3(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int seg_idx, int reg_idx, int n_seg, const int *n_regss, const mm_reg1_t *const* regss, void *km, int64_t opt_flag, int rep_len);
74
75 void mm_idxopt_init(mm_idxopt_t *opt);
76 const uint64_t *mm_idx_get(const mm_idx_t *mi, uint64_t minier, int *n);
77 int32_t mm_idx_cal_max_occ(const mm_idx_t *mi, float f);
78 int mm_idx_getseq2(const mm_idx_t *mi, int is_rev, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq);
79 mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, const char *qstr, int *n_regs_, mm_reg1_t *regs, mm128_t *a);
80 mm_reg1_t *mm_gen_regs(void *km, uint32_t hash, int qlen, int n_u, uint64_t *u, mm128_t *a, int is_qstrand);
81
82 mm128_t *mm_chain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int max_iter, int min_cnt, int min_sc, float gap_scale,
83 int is_cdna, int n_segs, int64_t n, mm128_t *a, int *n_u_, uint64_t **_u, void *km);
84 mm128_t *mg_lchain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int max_iter, int min_cnt, int min_sc, float chn_pen_gap, float chn_pen_skip,
85 int is_cdna, int n_segs, int64_t n, mm128_t *a, int *n_u_, uint64_t **_u, void *km);
86 mm128_t *mg_lchain_rmq(int max_dist, int max_dist_inner, int bw, int max_chn_skip, int cap_rmq_size, int min_cnt, int min_sc, float chn_pen_gap, float chn_pen_skip,
87 int64_t n, mm128_t *a, int *n_u_, uint64_t **_u, void *km);
88
89 void mm_mark_alt(const mm_idx_t *mi, int n, mm_reg1_t *r);
90 void mm_split_reg(mm_reg1_t *r, mm_reg1_t *r2, int n, int qlen, mm128_t *a, int is_qstrand);
91 void mm_sync_regs(void *km, int n_regs, mm_reg1_t *regs);
92 int mm_squeeze_a(void *km, int n_regs, mm_reg1_t *regs, mm128_t *a);
93 int mm_set_sam_pri(int n, mm_reg1_t *r);
94 void mm_set_parent(void *km, float mask_level, int mask_len, int n, mm_reg1_t *r, int sub_diff, int hard_mask_level, float alt_diff_frac);
95 void mm_select_sub(void *km, float pri_ratio, int min_diff, int best_n, int check_strand, int min_strand_sc, int *n_, mm_reg1_t *r);
96 void mm_select_sub_multi(void *km, float pri_ratio, float pri1, float pri2, int max_gap_ref, int min_diff, int best_n, int n_segs, const int *qlens, int *n_, mm_reg1_t *r);
97 int mm_filter_strand_retained(int n_regs, mm_reg1_t *r);
98 void mm_filter_regs(const mm_mapopt_t *opt, int qlen, int *n_regs, mm_reg1_t *regs);
99 void mm_hit_sort(void *km, int *n_regs, mm_reg1_t *r, float alt_diff_frac);
100 void mm_set_mapq(void *km, int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, int rep_len, int is_sr);
101 void mm_update_dp_max(int qlen, int n_regs, mm_reg1_t *regs, float frac, int a, int b);
102
103 void mm_est_err(const mm_idx_t *mi, int qlen, int n_regs, mm_reg1_t *regs, const mm128_t *a, int32_t n, const uint64_t *mini_pos);
104
105 mm_seg_t *mm_seg_gen(void *km, uint32_t hash, int n_segs, const int *qlens, int n_regs0, const mm_reg1_t *regs0, int *n_regs, mm_reg1_t **regs, const mm128_t *a);
106 void mm_seg_free(void *km, int n_segs, mm_seg_t *segs);
107 void mm_pair(void *km, int max_gap_ref, int dp_bonus, int sub_diff, int match_sc, const int *qlens, int *n_regs, mm_reg1_t **regs);
108
109 FILE *mm_split_init(const char *prefix, const mm_idx_t *mi);
110 mm_idx_t *mm_split_merge_prep(const char *prefix, int n_splits, FILE **fp, uint32_t *n_seq_part);
111 int mm_split_merge(int n_segs, const char **fn, const mm_mapopt_t *opt, int n_split_idx);
112 void mm_split_rm_tmp(const char *prefix, int n_splits);
113
114 void mm_err_puts(const char *str);
115 void mm_err_fwrite(const void *p, size_t size, size_t nitems, FILE *fp);
116 void mm_err_fread(void *p, size_t size, size_t nitems, FILE *fp);
117
mg_log2(float x)118 static inline float mg_log2(float x) // NB: this doesn't work when x<2
119 {
120 union { float f; uint32_t i; } z = { x };
121 float log_2 = ((z.i >> 23) & 255) - 128;
122 z.i &= ~(255 << 23);
123 z.i += 127 << 23;
124 log_2 += (-0.34484843f * z.f + 2.02466578f) * z.f - 0.67487759f;
125 return log_2;
126 }
127
128 #ifdef __cplusplus
129 }
130 #endif
131
132 #endif
133