ruby-minigraph 0.0.20.0

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Files changed (89) hide show
  1. checksums.yaml +7 -0
  2. data/LICENSE.txt +21 -0
  3. data/README.md +62 -0
  4. data/ext/Rakefile +56 -0
  5. data/ext/cmappy/cmappy.c +7 -0
  6. data/ext/cmappy/cmappy.h +8 -0
  7. data/ext/minigraph/LICENSE.txt +23 -0
  8. data/ext/minigraph/Makefile +66 -0
  9. data/ext/minigraph/NEWS.md +317 -0
  10. data/ext/minigraph/README.md +207 -0
  11. data/ext/minigraph/algo.c +194 -0
  12. data/ext/minigraph/algo.h +33 -0
  13. data/ext/minigraph/asm-call.c +147 -0
  14. data/ext/minigraph/bseq.c +133 -0
  15. data/ext/minigraph/bseq.h +76 -0
  16. data/ext/minigraph/cal_cov.c +139 -0
  17. data/ext/minigraph/doc/example1.png +0 -0
  18. data/ext/minigraph/doc/example2.png +0 -0
  19. data/ext/minigraph/doc/examples.graffle +0 -0
  20. data/ext/minigraph/format.c +241 -0
  21. data/ext/minigraph/galign.c +140 -0
  22. data/ext/minigraph/gchain1.c +532 -0
  23. data/ext/minigraph/gcmisc.c +223 -0
  24. data/ext/minigraph/gfa-aug.c +260 -0
  25. data/ext/minigraph/gfa-base.c +526 -0
  26. data/ext/minigraph/gfa-bbl.c +372 -0
  27. data/ext/minigraph/gfa-ed.c +617 -0
  28. data/ext/minigraph/gfa-io.c +395 -0
  29. data/ext/minigraph/gfa-priv.h +154 -0
  30. data/ext/minigraph/gfa.h +166 -0
  31. data/ext/minigraph/ggen.c +182 -0
  32. data/ext/minigraph/ggen.h +21 -0
  33. data/ext/minigraph/ggsimple.c +570 -0
  34. data/ext/minigraph/gmap.c +211 -0
  35. data/ext/minigraph/index.c +230 -0
  36. data/ext/minigraph/kalloc.c +224 -0
  37. data/ext/minigraph/kalloc.h +82 -0
  38. data/ext/minigraph/kavl.h +414 -0
  39. data/ext/minigraph/kdq.h +134 -0
  40. data/ext/minigraph/ketopt.h +116 -0
  41. data/ext/minigraph/khashl.h +348 -0
  42. data/ext/minigraph/krmq.h +474 -0
  43. data/ext/minigraph/kseq.h +256 -0
  44. data/ext/minigraph/ksort.h +164 -0
  45. data/ext/minigraph/kstring.h +165 -0
  46. data/ext/minigraph/kthread.c +159 -0
  47. data/ext/minigraph/kthread.h +15 -0
  48. data/ext/minigraph/kvec-km.h +105 -0
  49. data/ext/minigraph/kvec.h +110 -0
  50. data/ext/minigraph/lchain.c +441 -0
  51. data/ext/minigraph/main.c +301 -0
  52. data/ext/minigraph/map-algo.c +500 -0
  53. data/ext/minigraph/mgpriv.h +128 -0
  54. data/ext/minigraph/minigraph.1 +359 -0
  55. data/ext/minigraph/minigraph.h +176 -0
  56. data/ext/minigraph/miniwfa.c +834 -0
  57. data/ext/minigraph/miniwfa.h +95 -0
  58. data/ext/minigraph/misc/mgutils.js +1451 -0
  59. data/ext/minigraph/misc.c +12 -0
  60. data/ext/minigraph/options.c +134 -0
  61. data/ext/minigraph/shortk.c +251 -0
  62. data/ext/minigraph/sketch.c +109 -0
  63. data/ext/minigraph/sys.c +147 -0
  64. data/ext/minigraph/sys.h +20 -0
  65. data/ext/minigraph/test/MT-chimp.fa +277 -0
  66. data/ext/minigraph/test/MT-human.fa +239 -0
  67. data/ext/minigraph/test/MT-orangA.fa +276 -0
  68. data/ext/minigraph/test/MT.gfa +19 -0
  69. data/ext/minigraph/tex/Makefile +13 -0
  70. data/ext/minigraph/tex/minigraph.bib +676 -0
  71. data/ext/minigraph/tex/minigraph.tex +986 -0
  72. data/ext/minigraph/tex/plots/CHM13-f1-90.bb.anno.gp +42 -0
  73. data/ext/minigraph/tex/plots/CHM13-f1-90.bb.anno.tbl +13 -0
  74. data/ext/minigraph/tex/plots/CHM13-f1-90.bb.mini-inter-none.win.gp +269 -0
  75. data/ext/minigraph/tex/plots/CHM13-f1-90.bb.mini-inter-none.win.sh +7 -0
  76. data/ext/minigraph/tex/plots/CHM13v1.cen.bed +23 -0
  77. data/ext/minigraph/tex/plots/CHM13v1.size +23 -0
  78. data/ext/minigraph/tex/plots/anno2tbl.js +40 -0
  79. data/ext/minigraph/tex/plots/bedutils.js +367 -0
  80. data/ext/minigraph/tex/plots/chr-plot.js +130 -0
  81. data/ext/minigraph/tex/plots/gen-anno.mak +24 -0
  82. data/ext/minigraph.patch +21 -0
  83. data/lib/minigraph/ffi/constants.rb +230 -0
  84. data/lib/minigraph/ffi/functions.rb +70 -0
  85. data/lib/minigraph/ffi/mappy.rb +8 -0
  86. data/lib/minigraph/ffi.rb +27 -0
  87. data/lib/minigraph/version.rb +5 -0
  88. data/lib/minigraph.rb +72 -0
  89. metadata +159 -0
@@ -0,0 +1,834 @@
1
+ #include <string.h>
2
+ #include <assert.h>
3
+ #include <stdlib.h>
4
+ #include <stdio.h>
5
+ #include "miniwfa.h"
6
+ #include "kalloc.h"
7
+
8
+ /*
9
+ * Default setting
10
+ */
11
+ void mwf_opt_init(mwf_opt_t *opt)
12
+ {
13
+ memset(opt, 0, sizeof(*opt));
14
+ opt->x = 4; // corresponding SW score: m=1, x=3, o1=4, e1=3/2, o2=15, e2=1/2
15
+ opt->o1 = 4, opt->e1 = 2;
16
+ opt->o2 = 15, opt->e2 = 1;
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+ opt->kmer = 13, opt->max_occ = 2, opt->min_len = 30;
18
+ }
19
+
20
+ /*
21
+ * Structs and simple functions for traceback
22
+ */
23
+ typedef struct {
24
+ int32_t lo, hi;
25
+ uint8_t *x;
26
+ } wf_tb1_t;
27
+
28
+ typedef struct {
29
+ int32_t m, n;
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+ wf_tb1_t *a;
31
+ } wf_tb_t;
32
+
33
+ static wf_tb1_t *wf_tb_add(void *km, wf_tb_t *tb, int32_t lo, int32_t hi)
34
+ {
35
+ wf_tb1_t *p;
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+ if (tb->n == tb->m) {
37
+ tb->m += (tb->m>>1) + 4;
38
+ tb->a = Krealloc(km, wf_tb1_t, tb->a, tb->m);
39
+ }
40
+ p = &tb->a[tb->n++];
41
+ p->lo = lo, p->hi = hi;
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+ p->x = Kcalloc(km, uint8_t, hi - lo + 1);
43
+ return p;
44
+ }
45
+
46
+ typedef struct {
47
+ int32_t m, n;
48
+ uint32_t *cigar;
49
+ } wf_cigar_t;
50
+
51
+ static void wf_cigar_push1(void *km, wf_cigar_t *c, int32_t op, int32_t len)
52
+ {
53
+ if (c->n && op == (c->cigar[c->n-1]&0xf)) {
54
+ c->cigar[c->n-1] += len<<4;
55
+ } else {
56
+ if (c->n == c->m) {
57
+ c->m = c->m + (c->m>>1) + 4;
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+ c->cigar = Krealloc(km, uint32_t, c->cigar, c->m);
59
+ }
60
+ c->cigar[c->n++] = len<<4 | op;
61
+ }
62
+ }
63
+
64
+ /*
65
+ * The stripe data structure
66
+ */
67
+ #define WF_NEG_INF (-0x40000000)
68
+
69
+ typedef struct {
70
+ int32_t lo, hi;
71
+ int32_t *mem, *H, *E1, *E2, *F1, *F2;
72
+ } wf_slice_t;
73
+
74
+ typedef struct {
75
+ int32_t s, top, n, max_pen, lo, hi;
76
+ wf_slice_t *a;
77
+ } wf_stripe_t;
78
+
79
+ void wf_stripe_add(void *km, wf_stripe_t *wf, int32_t lo, int32_t hi)
80
+ {
81
+ int32_t i, n, m1 = wf->max_pen + 1, m2 = m1 * 2;
82
+ wf_slice_t *f;
83
+ ++wf->s;
84
+ ++wf->top;
85
+ if (wf->top == wf->n) wf->top = 0;
86
+ f = &wf->a[wf->top];
87
+ f->lo = lo, f->hi = hi;
88
+ n = hi - lo + 1;
89
+ kfree(km, f->mem);
90
+ f->mem = Kmalloc(km, int32_t, 5 * (n + m2));
91
+ f->H = f->mem + m1;
92
+ f->E1 = f->H + n + m2;
93
+ f->F1 = f->E1 + n + m2;
94
+ f->E2 = f->F1 + n + m2;
95
+ f->F2 = f->E2 + n + m2;
96
+ for (i = -m1; i < 0; ++i)
97
+ f->H[i] = f->E1[i] = f->E2[i] = f->F1[i] = f->F2[i] = WF_NEG_INF;
98
+ for (i = n; i < n + m1; ++i)
99
+ f->H[i] = f->E1[i] = f->E2[i] = f->F1[i] = f->F2[i] = WF_NEG_INF;
100
+ f->H -= lo, f->E1 -= lo, f->E2 -= lo, f->F1 -= lo, f->F2 -= lo; // such that f->H[lo] points to 0
101
+ }
102
+
103
+ static wf_stripe_t *wf_stripe_init(void *km, int32_t max_pen)
104
+ {
105
+ int32_t i;
106
+ wf_stripe_t *wf;
107
+ wf = Kcalloc(km, wf_stripe_t, 1);
108
+ wf->max_pen = max_pen;
109
+ wf->n = max_pen + 1;
110
+ wf->a = Kcalloc(km, wf_slice_t, wf->n);
111
+ wf->lo = wf->hi = 0;
112
+ for (i = 0; i < wf->n; ++i) {
113
+ wf_slice_t *f;
114
+ wf_stripe_add(km, wf, 0, 0);
115
+ f = &wf->a[wf->top];
116
+ f->H[0] = f->E1[0] = f->E2[0] = f->F1[0] = f->F2[0] = WF_NEG_INF;
117
+ }
118
+ wf->s = 0;
119
+ wf->a[wf->top].H[0] = -1;
120
+ return wf;
121
+ }
122
+
123
+ static void wf_stripe_destroy(void *km, wf_stripe_t *wf)
124
+ {
125
+ int32_t i;
126
+ for (i = 0; i < wf->n; ++i)
127
+ kfree(km, wf->a[i].mem);
128
+ kfree(km, wf->a);
129
+ kfree(km, wf);
130
+ }
131
+
132
+ static inline wf_slice_t *wf_stripe_get(const wf_stripe_t *wf, int32_t x)
133
+ {
134
+ int32_t y = wf->top - x;
135
+ if (y < 0) y += wf->n;
136
+ return &wf->a[y];
137
+ }
138
+
139
+ static inline int good_diag(int32_t d, int32_t k, int32_t tl, int32_t ql) // check if (d,k) falls within the DP matrix
140
+ {
141
+ return ((k >= -1 && k < tl) && (d + k >= -1 && d + k < ql));
142
+ }
143
+
144
+ static void wf_stripe_shrink(wf_stripe_t *wf, int32_t tl, int32_t ql)
145
+ {
146
+ int32_t j, d;
147
+ for (d = wf->lo; d <= wf->hi; ++d) {
148
+ for (j = 0; j < wf->n; ++j) {
149
+ wf_slice_t *p = &wf->a[(wf->top + 1 + j) % wf->n];
150
+ if (d < p->lo || d > p->hi) continue;
151
+ if (good_diag(d, p->H[d], tl, ql)) break;
152
+ if (good_diag(d, p->E1[d], tl, ql) || good_diag(d, p->F1[d], tl, ql)) break;
153
+ if (good_diag(d, p->E2[d], tl, ql) || good_diag(d, p->F2[d], tl, ql)) break;
154
+ }
155
+ if (j < wf->n) break; // stop when we see a "good diagonal" in the stripe
156
+ }
157
+ assert(d <= wf->hi); // should never happen
158
+ wf->lo = d;
159
+ for (d = wf->hi; d >= wf->lo; --d) {
160
+ for (j = 0; j < wf->n; ++j) {
161
+ wf_slice_t *p = &wf->a[(wf->top + 1 + j) % wf->n];
162
+ if (d < p->lo || d > p->hi) continue;
163
+ if (good_diag(d, p->H[d], tl, ql)) break;
164
+ if (good_diag(d, p->E1[d], tl, ql) || good_diag(d, p->F1[d], tl, ql)) break;
165
+ if (good_diag(d, p->E2[d], tl, ql) || good_diag(d, p->F2[d], tl, ql)) break;
166
+ }
167
+ if (j < wf->n) break;
168
+ }
169
+ assert(d >= wf->lo);
170
+ wf->hi = d;
171
+ }
172
+
173
+ typedef struct {
174
+ int32_t s, d;
175
+ } wf_chkpt_t;
176
+
177
+ /*
178
+ * Extend a diagonal along exact matches
179
+ */
180
+
181
+ // pad strings with distinct characters
182
+ static void wf_pad_str(void *km, int32_t tl, const char *ts, int32_t ql, const char *qs, char **pts, char **pqs)
183
+ {
184
+ uint8_t t[256];
185
+ int32_t i, c1 = -1, c2 = -1;
186
+ char *s1, *s2;
187
+ *pts = *pqs = 0;
188
+ // collect all used characters
189
+ memset(t, 0, 256);
190
+ for (i = 0; i < tl; ++i)
191
+ if (t[(uint8_t)ts[i]] == 0)
192
+ t[(uint8_t)ts[i]] = 1;
193
+ for (i = 0; i < ql; ++i)
194
+ if (t[(uint8_t)qs[i]] == 0)
195
+ t[(uint8_t)qs[i]] = 1;
196
+ for (i = 0; i < 256; ++i)
197
+ if (t[i] == 0) {
198
+ if (c1 < 0) c1 = i;
199
+ else if (c2 < 0) c2 = i;
200
+ }
201
+ if (c1 < 0 || c2 < 0) return; // The two strings use >=255 characters. Unlikely for bio strings.
202
+ s1 = Kmalloc(km, char, tl + ql + 16); // the two strings are allocated together
203
+ s2 = s1 + tl + 8;
204
+ memcpy(s1, ts, tl);
205
+ for (i = tl; i < tl + 8; ++i) s1[i] = c1; // pad with c1
206
+ memcpy(s2, qs, ql);
207
+ for (i = ql; i < ql + 8; ++i) s2[i] = c2; // pad with c2
208
+ *pts = s1, *pqs = s2;
209
+ }
210
+
211
+ // Extend a diagonal along exact matches.
212
+ static inline int32_t wf_extend1_padded(const char *ts, const char *qs, int32_t k, int32_t d)
213
+ {
214
+ uint64_t cmp = 0;
215
+ const char *ts_ = ts + 1;
216
+ const char *qs_ = qs + d + 1;
217
+ while (1) {
218
+ uint64_t x = *(uint64_t*)(ts_ + k); // warning: unaligned memory access
219
+ uint64_t y = *(uint64_t*)(qs_ + k);
220
+ cmp = x ^ y;
221
+ if (cmp == 0) k += 8;
222
+ else break;
223
+ }
224
+ k += __builtin_ctzl(cmp) >> 3;
225
+ return k;
226
+ }
227
+
228
+ /*
229
+ * Core wf_next() routines
230
+ */
231
+
232
+ // Force loop vectorization. Learned from WFA.
233
+ #if defined(__clang__)
234
+ #define PRAGMA_LOOP_VECTORIZE _Pragma("clang loop vectorize(enable)")
235
+ #elif defined(__GNUC__)
236
+ #define PRAGMA_LOOP_VECTORIZE _Pragma("GCC ivdep")
237
+ #else
238
+ #define PRAGMA_LOOP_VECTORIZE _Pragma("ivdep")
239
+ #endif
240
+
241
+ #define wf_max(a, b) ((a) >= (b)? (a) : (b))
242
+
243
+ static void wf_next_prep(void *km, const mwf_opt_t *opt, wf_stripe_t *wf, int32_t lo, int32_t hi,
244
+ int32_t **H, int32_t **E1, int32_t **F1, int32_t **E2, int32_t **F2,
245
+ const int32_t **pHx, const int32_t **pHo1, const int32_t **pHo2,
246
+ const int32_t **pE1, const int32_t **pF1, const int32_t **pE2, const int32_t **pF2)
247
+ {
248
+ const wf_slice_t *fx, *fo1, *fo2, *fe1, *fe2;
249
+ wf_slice_t *ft;
250
+ wf_stripe_add(km, wf, lo, hi);
251
+ ft = &wf->a[wf->top];
252
+ fx = wf_stripe_get(wf, opt->x);
253
+ fo1 = wf_stripe_get(wf, opt->o1 + opt->e1);
254
+ fo2 = wf_stripe_get(wf, opt->o2 + opt->e2);
255
+ fe1 = wf_stripe_get(wf, opt->e1);
256
+ fe2 = wf_stripe_get(wf, opt->e2);
257
+ *pHx = fx->H, *pHo1 = fo1->H, *pHo2 = fo2->H, *pE1 = fe1->E1, *pE2 = fe2->E2, *pF1 = fe1->F1, *pF2 = fe2->F2;
258
+ *H = ft->H, *E1 = ft->E1, *E2 = ft->E2, *F1 = ft->F1, *F2 = ft->F2;
259
+ }
260
+
261
+ static void wf_next_score(int32_t lo, int32_t hi, int32_t *H, int32_t *E1, int32_t *F1, int32_t *E2, int32_t *F2,
262
+ const int32_t *pHx, const int32_t *pHo1, const int32_t *pHo2,
263
+ const int32_t *pE1, const int32_t *pF1, const int32_t *pE2, const int32_t *pF2)
264
+ {
265
+ int32_t d;
266
+ PRAGMA_LOOP_VECTORIZE
267
+ for (d = lo; d <= hi; ++d) {
268
+ int32_t h, f, e;
269
+ E1[d] = wf_max(pHo1[d-1], pE1[d-1]);
270
+ E2[d] = wf_max(pHo2[d-1], pE2[d-1]);
271
+ e = wf_max(E1[d], E2[d]);
272
+ F1[d] = wf_max(pHo1[d+1], pF1[d+1]) + 1;
273
+ F2[d] = wf_max(pHo2[d+1], pF2[d+1]) + 1;
274
+ f = wf_max(F1[d], F2[d]);
275
+ h = wf_max(e, f);
276
+ H[d] = wf_max(pHx[d] + 1, h);
277
+ // if (H[d] >= -1) fprintf(stderr, "s=%d, d=%d, k=%d, (%d,%d)\n", wf->s, d, H[d], E1[d], F1[d]);
278
+ }
279
+ }
280
+
281
+ static void wf_next_tb(int32_t lo, int32_t hi, int32_t *H, int32_t *E1, int32_t *F1, int32_t *E2, int32_t *F2, uint8_t *ax,
282
+ const int32_t *pHx, const int32_t *pHo1, const int32_t *pHo2,
283
+ const int32_t *pE1, const int32_t *pF1, const int32_t *pE2, const int32_t *pF2)
284
+ {
285
+ int32_t d;
286
+ PRAGMA_LOOP_VECTORIZE
287
+ for (d = lo; d <= hi; ++d) {
288
+ int32_t h, f, e;
289
+ uint8_t x = 0, ze, zf, z;
290
+ x |= pHo1[d-1] >= pE1[d-1]? 0 : 0x08;
291
+ E1[d] = wf_max(pHo1[d-1], pE1[d-1]);
292
+ x |= pHo2[d-1] >= pE2[d-1]? 0 : 0x20;
293
+ E2[d] = wf_max(pHo2[d-1], pE2[d-1]);
294
+ ze = E1[d] >= E2[d]? 1 : 3;
295
+ e = wf_max(E1[d], E2[d]);
296
+ x |= pHo1[d+1] >= pF1[d+1]? 0 : 0x10;
297
+ F1[d] = wf_max(pHo1[d+1], pF1[d+1]) + 1;
298
+ x |= pHo2[d+1] >= pF2[d+1]? 0 : 0x40;
299
+ F2[d] = wf_max(pHo2[d+1], pF2[d+1]) + 1;
300
+ zf = F1[d] >= F2[d]? 2 : 4;
301
+ f = wf_max(F1[d], F2[d]);
302
+ z = e >= f? ze : zf;
303
+ h = wf_max(e, f);
304
+ z = pHx[d] + 1 >= h? 0 : z;
305
+ H[d] = wf_max(pHx[d] + 1, h);
306
+ ax[d] = x | z;
307
+ }
308
+ }
309
+
310
+ /*
311
+ * Core algorithm
312
+ */
313
+ static void wf_next_basic(void *km, void *km_tb, const mwf_opt_t *opt, wf_stripe_t *wf, wf_tb_t *tb, int32_t lo, int32_t hi)
314
+ {
315
+ int32_t *H, *E1, *E2, *F1, *F2;
316
+ const int32_t *pHx, *pHo1, *pHo2, *pE1, *pE2, *pF1, *pF2;
317
+ wf_next_prep(km, opt, wf, lo, hi, &H, &E1, &F1, &E2, &F2, &pHx, &pHo1, &pHo2, &pE1, &pF1, &pE2, &pF2);
318
+ if (tb) {
319
+ uint8_t *ax;
320
+ ax = wf_tb_add(km_tb, tb, lo, hi)->x - lo;
321
+ wf_next_tb(lo, hi, H, E1, F1, E2, F2, ax, pHx, pHo1, pHo2, pE1, pF1, pE2, pF2);
322
+ } else {
323
+ wf_next_score(lo, hi, H, E1, F1, E2, F2, pHx, pHo1, pHo2, pE1, pF1, pE2, pF2);
324
+ }
325
+ if (H[lo] >= -1 || E1[lo] >= -1 || F1[lo] >= -1 || E2[lo] >= -1 || F2[lo] >= -1) wf->lo = lo;
326
+ if (H[hi] >= -1 || E1[hi] >= -1 || F1[hi] >= -1 || E2[hi] >= -1 || F2[hi] >= -1) wf->hi = hi;
327
+ }
328
+
329
+ static uint32_t *wf_traceback(void *km, const mwf_opt_t *opt, wf_tb_t *tb, int32_t t_end, const char *ts, int32_t q_end, const char *qs, int32_t last, int32_t *n_cigar)
330
+ {
331
+ wf_cigar_t cigar = {0,0,0};
332
+ int32_t i = q_end, k = t_end, s = tb->n - 1;
333
+ while (i >= 0 && k >= 0) {
334
+ int32_t k0 = k, j, x, state, ext;
335
+ if (last == 0) { // if the previous state is 0, check exact matches
336
+ while (i >= 0 && k >= 0 && qs[i] == ts[k])
337
+ --i, --k;
338
+ if (k0 - k > 0)
339
+ wf_cigar_push1(km, &cigar, 7, k0 - k);
340
+ if (i < 0 || k < 0) break;
341
+ }
342
+ assert(s >= 0);
343
+ j = i - k - tb->a[s].lo;
344
+ assert(j <= tb->a[s].hi - tb->a[s].lo);
345
+ x = tb->a[s].x[j];
346
+ state = last == 0? x&7 : last;
347
+ ext = state > 0? x>>(state+2)&1 : 0; // whether an extension
348
+ //fprintf(stderr, "s=%d, %d->%d, ext=%d%d%d%d, i=%d, k=%d\n", s, last, state, x>>3&1, x>>4&1, x>>5&1, x>>6&1, i, k);
349
+ if (state == 0) {
350
+ wf_cigar_push1(km, &cigar, 8, 1);
351
+ --i, --k, s -= opt->x;
352
+ } else if (state == 1) {
353
+ wf_cigar_push1(km, &cigar, 1, 1);
354
+ --i, s -= ext? opt->e1 : opt->o1 + opt->e1;
355
+ } else if (state == 3) {
356
+ wf_cigar_push1(km, &cigar, 1, 1);
357
+ --i, s -= ext? opt->e2 : opt->o2 + opt->e2;
358
+ } else if (state == 2) {
359
+ wf_cigar_push1(km, &cigar, 2, 1);
360
+ --k, s -= ext? opt->e1 : opt->o1 + opt->e1;
361
+ } else if (state == 4) {
362
+ wf_cigar_push1(km, &cigar, 2, 1);
363
+ --k, s -= ext? opt->e2 : opt->o2 + opt->e2;
364
+ } else abort();
365
+ last = state > 0 && ext? state : 0;
366
+ }
367
+ if (opt->flag&MWF_F_DEBUG) fprintf(stderr, "s0=%d, s=%d, i=%d, k=%d\n", tb->n-1, s, i, k);
368
+ if (i >= 0) wf_cigar_push1(km, &cigar, 1, i + 1);
369
+ else if (k >= 0) wf_cigar_push1(km, &cigar, 2, k + 1);
370
+ for (i = 0; i < cigar.n>>1; ++i) { // reverse to the input order
371
+ uint32_t t = cigar.cigar[i];
372
+ cigar.cigar[i] = cigar.cigar[cigar.n - i - 1];
373
+ cigar.cigar[cigar.n - i - 1] = t;
374
+ }
375
+ *n_cigar = cigar.n;
376
+ return cigar.cigar;
377
+ }
378
+
379
+ // pts and pqs MUST BE padded with wf_pad_str()
380
+ static void mwf_wfa_core(void *km, const mwf_opt_t *opt, int32_t tl, const char *pts, int32_t ql, const char *pqs, int32_t n_seg, wf_chkpt_t *seg, mwf_rst_t *r)
381
+ {
382
+ int32_t max_pen, sid, is_tb = !!(opt->flag&MWF_F_CIGAR), last_state = 0, stopped = 0;
383
+ wf_stripe_t *wf;
384
+ wf_tb_t tb = {0,0,0};
385
+ void *km_tb, *km_st;
386
+
387
+ memset(r, 0, sizeof(*r));
388
+ km_tb = is_tb && !(opt->flag&MWF_F_NO_KALLOC)? km_init2(km, 0) : 0;
389
+ km_st = !(opt->flag&MWF_F_NO_KALLOC)? km_init2(km, 0) : 0;
390
+ max_pen = opt->x;
391
+ max_pen = max_pen > opt->o1 + opt->e1? max_pen : opt->o1 + opt->e1;
392
+ max_pen = max_pen > opt->o2 + opt->e2? max_pen : opt->o2 + opt->e2;
393
+ wf = wf_stripe_init(km_st, max_pen);
394
+ assert(pts);
395
+
396
+ sid = 0;
397
+ while (1) {
398
+ wf_slice_t *p = &wf->a[wf->top];
399
+ int32_t d, lo, hi, *H = p->H;
400
+ for (d = p->lo; d <= p->hi; ++d) {
401
+ int32_t k = 0;
402
+ if (H[d] < -1 || d + H[d] < -1 || H[d] >= tl || d + H[d] >= ql) continue;
403
+ k = wf_extend1_padded(pts, pqs, H[d], d);
404
+ //fprintf(stderr, "[s=%d] [%d,%d]:%d %d->%d,%d,%d,%d,%d\n", wf->s, p->lo, p->hi, d, H[d], k, wf->a[wf->top].E1[d], wf->a[wf->top].F1[d], wf->a[wf->top].E2[d], wf->a[wf->top].F2[d]);
405
+ if (k == tl - 1 && d + k == ql - 1) {
406
+ if (k == H[d] && is_tb)
407
+ last_state = tb.a[tb.n-1].x[d - tb.a[tb.n-1].lo] & 7;
408
+ break;
409
+ }
410
+ H[d] = k;
411
+ }
412
+ if (d <= p->hi) break;
413
+ if (is_tb && seg && sid < n_seg && seg[sid].s == wf->s) {
414
+ assert(seg[sid].d >= wf->lo && seg[sid].d <= wf->hi);
415
+ wf->lo = wf->hi = seg[sid++].d;
416
+ }
417
+ lo = wf->lo > -tl? wf->lo - 1 : -tl;
418
+ hi = wf->hi < ql? wf->hi + 1 : ql;
419
+ wf_next_basic(km_st, km_tb, opt, wf, is_tb? &tb : 0, lo, hi);
420
+ if ((wf->s&0xff) == 0) wf_stripe_shrink(wf, tl, ql);
421
+ r->n_iter += hi - lo + 1;
422
+ if ((opt->max_iter > 0 && r->n_iter > opt->max_iter) || (opt->max_s > 0 && wf->s > opt->max_s)) {
423
+ stopped = 1;
424
+ break;
425
+ }
426
+ }
427
+ r->s = stopped? -1 : wf->s;
428
+ if (is_tb && !stopped)
429
+ r->cigar = wf_traceback(km, opt, &tb, tl-1, pts, ql-1, pqs, last_state, &r->n_cigar);
430
+ if (km_st == 0) wf_stripe_destroy(km_st, wf);
431
+ else km_destroy(km_st);
432
+ km_destroy(km_tb);
433
+ if (is_tb && !stopped)
434
+ r->cigar = (uint32_t*)krelocate(km, r->cigar, r->n_cigar * sizeof(*r->cigar));
435
+ }
436
+
437
+ /*
438
+ * Low-memory mode
439
+ */
440
+ typedef struct {
441
+ int32_t n, n_intv, max_s;
442
+ int32_t *x;
443
+ uint64_t *intv;
444
+ } wf_ss_t; // snapshot
445
+
446
+ typedef struct {
447
+ int32_t n, m;
448
+ wf_ss_t *a;
449
+ } wf_sss_t;
450
+
451
+ static void wf_snapshot1(void *km, wf_stripe_t *sf, wf_ss_t *ss)
452
+ {
453
+ int32_t j, k, t;
454
+ ss->n = 0, ss->max_s = sf->s;
455
+ for (j = 0; j < sf->n; ++j)
456
+ ss->n += 5 * (sf->a[j].hi - sf->a[j].lo + 1);
457
+ ss->x = Kmalloc(km, int32_t, ss->n);
458
+ ss->n_intv = sf->n;
459
+ ss->intv = Kmalloc(km, uint64_t, ss->n_intv);
460
+ for (j = 0, t = 0; j < sf->n; ++j) {
461
+ wf_slice_t *p;
462
+ k = (sf->top + 1 + j) % sf->n;
463
+ p = &sf->a[k];
464
+ ss->intv[j] = (uint64_t)p->lo << 32 | (p->hi - p->lo + 1) * 5;
465
+ for (k = p->lo; k <= p->hi; ++k) {
466
+ ss->x[t] = p->H[k], p->H[k] = t++;
467
+ ss->x[t] = p->E1[k], p->E1[k] = t++;
468
+ ss->x[t] = p->F1[k], p->F1[k] = t++;
469
+ ss->x[t] = p->E2[k], p->E2[k] = t++;
470
+ ss->x[t] = p->F2[k], p->F2[k] = t++;
471
+ }
472
+ }
473
+ assert(t == ss->n);
474
+ }
475
+
476
+ static void wf_snapshot(void *km, wf_sss_t *sss, wf_stripe_t *sf)
477
+ {
478
+ if (sss->n == sss->m) {
479
+ sss->m += (sss->m>>1) + 8;
480
+ sss->a = Krealloc(km, wf_ss_t, sss->a, sss->m);
481
+ }
482
+ wf_snapshot1(km, sf, &sss->a[sss->n++]);
483
+ }
484
+
485
+ static void wf_snapshot_free(void *km, wf_sss_t *sss)
486
+ {
487
+ int32_t j;
488
+ for (j = 0; j < sss->n; ++j) {
489
+ kfree(km, sss->a[j].x);
490
+ kfree(km, sss->a[j].intv);
491
+ }
492
+ kfree(km, sss->a);
493
+ }
494
+
495
+ static void wf_next_seg(void *km, const mwf_opt_t *opt, uint8_t *xbuf, wf_stripe_t *wf, wf_stripe_t *sf, int32_t lo, int32_t hi)
496
+ {
497
+ int32_t d, *H, *E1, *E2, *F1, *F2;
498
+ const int32_t *pHx, *pHo1, *pHo2, *pE1, *pE2, *pF1, *pF2;
499
+ uint8_t *ax = xbuf - lo;
500
+
501
+ wf_next_prep(km, opt, wf, lo, hi, &H, &E1, &F1, &E2, &F2, &pHx, &pHo1, &pHo2, &pE1, &pF1, &pE2, &pF2);
502
+ wf_next_tb(lo, hi, H, E1, F1, E2, F2, ax, pHx, pHo1, pHo2, pE1, pF1, pE2, pF2);
503
+ wf_next_prep(km, opt, sf, lo, hi, &H, &E1, &F1, &E2, &F2, &pHx, &pHo1, &pHo2, &pE1, &pF1, &pE2, &pF2);
504
+ PRAGMA_LOOP_VECTORIZE
505
+ for (d = lo; d <= hi; ++d) { // FIXME: merge this loop into the loop in wf_next_tb(). I tried but couldn't make clang vectorize.
506
+ uint8_t x = ax[d];
507
+ int32_t a, b, e1, f1, e2, f2, h;
508
+ a = pHo1[d-1], b = pE1[d-1];
509
+ e1 = E1[d] = (x&0x08) == 0? a : b;
510
+ a = pHo1[d+1], b = pF1[d+1];
511
+ f1 = F1[d] = (x&0x10) == 0? a : b;
512
+ a = pHo2[d-1], b = pE2[d-1];
513
+ e2 = E2[d] = (x&0x20) == 0? a : b;
514
+ a = pHo2[d+1], b = pF2[d+1];
515
+ f2 = F2[d] = (x&0x40) == 0? a : b;
516
+ x &= 7;
517
+ h = pHx[d];
518
+ h = x == 1? e1 : h;
519
+ h = x == 2? f1 : h;
520
+ h = x == 3? e2 : h;
521
+ h = x == 4? f2 : h;
522
+ H[d] = h;
523
+ }
524
+ if (H[lo] >= -1 || E1[lo] >= -1 || F1[lo] >= -1 || E2[lo] >= -1 || F2[lo] >= -1) wf->lo = lo;
525
+ if (H[hi] >= -1 || E1[hi] >= -1 || F1[hi] >= -1 || E2[hi] >= -1 || F2[hi] >= -1) wf->hi = hi;
526
+ }
527
+
528
+ static wf_chkpt_t *wf_traceback_seg(void *km, wf_sss_t *sss, int32_t last, int32_t *n_seg)
529
+ {
530
+ int32_t j;
531
+ wf_chkpt_t *seg;
532
+ *n_seg = sss->n;
533
+ seg = Kmalloc(km, wf_chkpt_t, sss->n);
534
+ for (j = sss->n - 1; j >= 0; --j) {
535
+ int32_t k, m;
536
+ wf_ss_t *p = &sss->a[j];
537
+ for (k = 0, m = 0; k < p->n_intv; ++k) {
538
+ if (last >= m && last < m + (int32_t)p->intv[k])
539
+ break;
540
+ m += (int32_t)p->intv[k];
541
+ }
542
+ assert(k < p->n_intv);
543
+ seg[j].s = p->max_s - (p->n_intv - k - 1);
544
+ seg[j].d = (int32_t)(p->intv[k]>>32) + (last - m) / 5;
545
+ last = p->x[last];
546
+ }
547
+ assert(last == -1);
548
+ return seg;
549
+ }
550
+
551
+ wf_chkpt_t *mwf_wfa_seg(void *km, const mwf_opt_t *opt, int32_t tl, const char *pts, int32_t ql, const char *pqs, int32_t *n_seg_)
552
+ {
553
+ int32_t max_pen, last, n_seg;
554
+ wf_stripe_t *wf, *sf;
555
+ wf_sss_t sss = {0,0,0};
556
+ uint8_t *xbuf;
557
+ wf_chkpt_t *seg;
558
+ void *km_st;
559
+
560
+ km_st = !(opt->flag&MWF_F_NO_KALLOC)? km_init2(km, 0) : 0;
561
+ max_pen = opt->x;
562
+ max_pen = max_pen > opt->o1 + opt->e1? max_pen : opt->o1 + opt->e1;
563
+ max_pen = max_pen > opt->o2 + opt->e2? max_pen : opt->o2 + opt->e2;
564
+ xbuf = Kcalloc(km_st, uint8_t, tl + ql + 1);
565
+ wf = wf_stripe_init(km_st, max_pen);
566
+ sf = wf_stripe_init(km_st, max_pen);
567
+ assert(pts);
568
+
569
+ while (1) {
570
+ wf_slice_t *p = &wf->a[wf->top];
571
+ int32_t d, lo, hi, *H = p->H;
572
+ for (d = p->lo; d <= p->hi; ++d) {
573
+ int32_t k;
574
+ if (H[d] < -1 || d + H[d] < -1 || H[d] >= tl || d + H[d] >= ql) continue;
575
+ k = wf_extend1_padded(pts, pqs, H[d], d);
576
+ if (k == tl - 1 && d + k == ql - 1) {
577
+ last = sf->a[sf->top].H[d];
578
+ break;
579
+ }
580
+ H[d] = k;
581
+ }
582
+ if (d <= p->hi) break;
583
+ lo = wf->lo > -tl? wf->lo - 1 : -tl;
584
+ hi = wf->hi < ql? wf->hi + 1 : ql;
585
+ if ((wf->s + 1) % opt->step == 0)
586
+ wf_snapshot(km_st, &sss, sf);
587
+ wf_next_seg(km_st, opt, xbuf, wf, sf, lo, hi);
588
+ if ((wf->s&0xff) == 0) wf_stripe_shrink(wf, tl, ql);
589
+ }
590
+ seg = wf_traceback_seg(km, &sss, last, &n_seg);
591
+ if (km_st == 0) {
592
+ wf_snapshot_free(km_st, &sss);
593
+ wf_stripe_destroy(km_st, wf);
594
+ wf_stripe_destroy(km_st, sf);
595
+ kfree(km_st, xbuf);
596
+ } else km_destroy(km_st);
597
+
598
+ seg = (wf_chkpt_t*)krelocate(km, seg, n_seg * sizeof(*seg));
599
+ *n_seg_ = n_seg;
600
+ return seg;
601
+ }
602
+
603
+ void mwf_wfa_exact(void *km, const mwf_opt_t *opt, int32_t tl, const char *ts, int32_t ql, const char *qs, mwf_rst_t *r)
604
+ {
605
+ int32_t n_seg = 0;
606
+ wf_chkpt_t *seg = 0;
607
+ char *pts, *pqs;
608
+
609
+ wf_pad_str(km, tl, ts, ql, qs, &pts, &pqs);
610
+ if (opt->step > 0)
611
+ seg = mwf_wfa_seg(km, opt, tl, pts, ql, pqs, &n_seg);
612
+ mwf_wfa_core(km, opt, tl, pts, ql, pqs, n_seg, seg, r);
613
+ kfree(km, seg);
614
+ kfree(km, pts);
615
+ }
616
+
617
+ /*
618
+ * Heuristics
619
+ */
620
+ static int32_t mg_lis_64(void *km, int32_t n, const uint64_t *a, int32_t *b)
621
+ {
622
+ int32_t i, k, L = 0, *M, *P = b;
623
+ KMALLOC(km, M, n+1);
624
+ for (i = 0; i < n; ++i) {
625
+ int32_t lo = 1, hi = L, newL;
626
+ while (lo <= hi) {
627
+ int32_t mid = (lo + hi + 1) >> 1;
628
+ if (a[M[mid]] < a[i]) lo = mid + 1;
629
+ else hi = mid - 1;
630
+ }
631
+ newL = lo, P[i] = M[newL - 1], M[newL] = i;
632
+ if (newL > L) L = newL;
633
+ }
634
+ k = M[L];
635
+ memcpy(M, P, n * sizeof(int32_t));
636
+ for (i = L - 1; i >= 0; --i) b[i] = k, k = M[k];
637
+ kfree(km, M);
638
+ return L;
639
+ }
640
+
641
+ extern void radix_sort_gfa64(uint64_t*, uint64_t*);
642
+ extern unsigned char seq_nt4_table[256];
643
+
644
+ static int32_t mg_fc_kmer(int32_t len, const char *seq, int32_t rid, int32_t k, uint64_t *a)
645
+ {
646
+ int32_t i, l, n;
647
+ uint64_t x, mask = (1ULL<<k*2) - 1;
648
+ for (i = l = 0, x = 0, n = 0; i < len; ++i) {
649
+ int32_t c = seq_nt4_table[(uint8_t)seq[i]];
650
+ if (c < 4) {
651
+ x = (x << 2 | c) & mask;
652
+ if (++l >= k) a[n++] = (x<<1|rid) << 32 | i;
653
+ } else l = 0, x = 0;
654
+ }
655
+ return n;
656
+ }
657
+
658
+ static uint64_t *mg_chain(void *km, int32_t l1, const char *s1, int32_t l2, const char *s2, int32_t k, int32_t max_occ, int32_t *n_lis_)
659
+ {
660
+ int32_t i, n_a, n_b, m_b, i0, n_lis, *lis;
661
+ uint64_t *a, *b;
662
+
663
+ *n_lis_ = 0;
664
+ if (l1 < k || l2 < k) return 0;
665
+ assert(k >= 2 && k <= 15);
666
+
667
+ // collect k-mers
668
+ KMALLOC(km, a, l1 + l2);
669
+ n_a = mg_fc_kmer(l1, s1, 0, k, a);
670
+ n_a += mg_fc_kmer(l2, s2, 1, k, &a[n_a]);
671
+ radix_sort_gfa64(a, a + n_a);
672
+
673
+ // collect k-mer matches
674
+ n_b = m_b = 0, b = 0;
675
+ for (i0 = 0, i = 1; i <= n_a; ++i) {
676
+ if (i == n_a || a[i0]>>33 != a[i]>>33) {
677
+ if (i - i0 >= 2) {
678
+ int32_t j, s, t;
679
+ for (j = i0; j < i && (a[j]>>32&1) == 0; ++j) {}
680
+ if (j > i0 && j < i && j - i0 <= max_occ && i - j <= max_occ) {
681
+ for (s = i0; s < j; ++s)
682
+ for (t = j; t < i; ++t) {
683
+ if (n_b == m_b) KEXPAND(km, b, m_b);
684
+ b[n_b++] = a[s]<<32 | (uint32_t)a[t];
685
+ }
686
+ }
687
+ }
688
+ i0 = i;
689
+ }
690
+ }
691
+ kfree(km, a);
692
+
693
+ // find co-linear chain with LIS
694
+ radix_sort_gfa64(b, b + n_b);
695
+ for (i = 0; i < n_b; ++i)
696
+ b[i] = b[i]>>32 | b[i]<<32;
697
+ KMALLOC(km, lis, n_b);
698
+ n_lis = mg_lis_64(km, n_b, b, lis);
699
+ a = Kmalloc(km, uint64_t, n_lis);
700
+ for (i = 0; i < n_lis; ++i) a[i] = b[lis[i]];
701
+ kfree(km, lis);
702
+ kfree(km, b);
703
+ b = Kmalloc(km, uint64_t, n_lis);
704
+ memcpy(b, a, sizeof(uint64_t) * n_lis);
705
+ kfree(km, a);
706
+ *n_lis_ = n_lis;
707
+ for (i = 0; i < n_lis; ++i) // switch back, such that seq1 on the high bits
708
+ b[i] = b[i]>>32 | b[i]<<32;
709
+ return b;
710
+ }
711
+
712
+ static double mwf_ksim(void *km, int32_t l1, const char *s1, int32_t l2, const char *s2, int32_t k)
713
+ {
714
+ int32_t i, i0, j, n_a, n1 = 0, n2 = 0, t1 = 0, t2 = 0;
715
+ double p1, p2;
716
+ uint64_t *a;
717
+ if (l1 < k || l2 < k) return 0;
718
+ assert(k >= 2 && k <= 15);
719
+ KMALLOC(km, a, l1 + l2);
720
+ n_a = mg_fc_kmer(l1, s1, 0, k, a);
721
+ n_a += mg_fc_kmer(l2, s2, 1, k, &a[n_a]);
722
+ radix_sort_gfa64(a, a + n_a);
723
+ for (i0 = 0, i = 1; i <= n_a; ++i) {
724
+ if (i == n_a || a[i0]>>33 != a[i]>>33) {
725
+ int32_t m1, m2, min;
726
+ for (j = i0; j < i && (a[j]>>32&1) == 0; ++j) {}
727
+ m1 = j - i0, m2 = i - j;
728
+ min = m1 < m2? m1 : m2;
729
+ n1 += m1, n2 += m2;
730
+ if (m1 > 0 && m2 > 0)
731
+ t1 += min, t2 += min;
732
+ i0 = i;
733
+ }
734
+ }
735
+ kfree(km, a);
736
+ p1 = (double)t1 / n1, p2 = (double)t2 / n2;
737
+ return p1 > p2? p1 : p2;
738
+ }
739
+
740
+ #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
741
+
742
+ static void wf_cigar_push(void *km, wf_cigar_t *c, int32_t n_cigar, const uint32_t *cigar)
743
+ {
744
+ if (n_cigar == 0) return;
745
+ wf_cigar_push1(km, c, cigar[0]&0xf, cigar[0]>>4);
746
+ if (c->n + n_cigar - 1 > c->m) {
747
+ c->m = c->n + n_cigar - 1;
748
+ kroundup32(c->m);
749
+ c->cigar = Krealloc(km, uint32_t, c->cigar, c->m);
750
+ }
751
+ memcpy(&c->cigar[c->n], &cigar[1], sizeof(*cigar) * (n_cigar - 1));
752
+ c->n += n_cigar - 1;
753
+ }
754
+
755
+ static int32_t wf_anchor_filter(int32_t n, uint64_t *a, int32_t tl, int32_t ql, int32_t k, int32_t min_l)
756
+ {
757
+ int32_t i, st, x0, y0, x1, y1, j, l, m;
758
+ for (i = 0, x0 = y0 = x1 = y1 = 0, st = -1, l = 0; i <= n; ++i) {
759
+ int32_t x, y;
760
+ if (i == n) x = tl, y = ql;
761
+ else x = (int32_t)(a[i]>>32) + 1, y = (int32_t)a[i] + 1;
762
+ if (x - x0 != y - y0) {
763
+ //fprintf(stderr, "X\t%d\t(%d,%d) -> (%d,%d)\n", l, x0, y0, x, y);
764
+ if (l < min_l)
765
+ for (j = st > 0? st : 0; j < i; ++j)
766
+ a[j] = 0;
767
+ x0 = x, y0 = y, st = i, l = k;
768
+ } else l += x - x1;
769
+ x1 = x, y1 = y;
770
+ }
771
+ for (i = 0, m = 0; i < n; ++i)
772
+ if (a[i] != 0) a[m++] = a[i];
773
+ return m;
774
+ }
775
+
776
+ void mwf_wfa_chain(void *km, const mwf_opt_t *opt, int32_t tl, const char *ts, int32_t ql, const char *qs, mwf_rst_t *r)
777
+ {
778
+ int32_t n_a, i, x0, y0;
779
+ uint64_t *a;
780
+ void *km_wfa;
781
+ wf_cigar_t c = {0,0,0};
782
+
783
+ km_wfa = !(opt->flag&MWF_F_NO_KALLOC)? km_init2(km, 0) : 0;
784
+ a = mg_chain(km_wfa, tl, ts, ql, qs, opt->kmer, opt->max_occ, &n_a);
785
+ n_a = wf_anchor_filter(n_a, a, tl, ql, opt->kmer, opt->min_len);
786
+ r->s = 0;
787
+ for (i = 0, x0 = y0 = 0; i <= n_a; ++i) {
788
+ int32_t x1, y1;
789
+ if (i == n_a) x1 = tl, y1 = ql;
790
+ else x1 = (int32_t)(a[i]>>32) + 1, y1 = (int32_t)a[i] + 1;
791
+ if (i < n_a && x1 - x0 == y1 - y0 && x1 - x0 <= opt->kmer) {
792
+ if (opt->flag&MWF_F_CIGAR)
793
+ wf_cigar_push1(km, &c, 7, x1 - x0);
794
+ } else if (x0 < x1 && y0 < y1) {
795
+ if (x1 - x0 >= 10000 && y1 - y0 >= 10000 && mwf_ksim(km, x1 - x0, &ts[x0], y1 - y0, &qs[y0], opt->kmer) < 0.02) {
796
+ if (opt->flag&MWF_F_CIGAR) {
797
+ wf_cigar_push1(km, &c, 2, x1 - x0);
798
+ wf_cigar_push1(km, &c, 1, y1 - y0);
799
+ }
800
+ r->s += opt->o2 * 2 + opt->e2 * ((x1 - x0) + (y1 - y0));
801
+ } else {
802
+ mwf_rst_t q;
803
+ mwf_wfa_exact(km_wfa, opt, x1 - x0, &ts[x0], y1 - y0, &qs[y0], &q);
804
+ if (opt->flag&MWF_F_CIGAR)
805
+ wf_cigar_push(km, &c, q.n_cigar, q.cigar);
806
+ r->s += q.s;
807
+ kfree(km_wfa, q.cigar);
808
+ }
809
+ } else if (x0 < x1) {
810
+ wf_cigar_push1(km, &c, 2, x1 - x0);
811
+ r->s += opt->o2 + (x1 - x0) * opt->e2 < opt->o1 + (x1 - x0) * opt->e1? opt->o2 + (x1 - x0) * opt->e2 : opt->o1 + (x1 - x0) * opt->e1;
812
+ } else if (y0 < y1) {
813
+ wf_cigar_push1(km, &c, 1, y1 - y0);
814
+ r->s += opt->o2 + (y1 - y0) * opt->e2 < opt->o1 + (y1 - y0) * opt->e1? opt->o2 + (y1 - y0) * opt->e2 : opt->o1 + (y1 - y0) * opt->e1;
815
+ }
816
+ x0 = x1, y0 = y1;
817
+ }
818
+ if (km_wfa == 0) kfree(km_wfa, a);
819
+ km_destroy(km_wfa);
820
+ r->n_cigar = c.n, r->cigar = c.cigar;
821
+ r->cigar = (uint32_t*)krelocate(km, r->cigar, r->n_cigar * sizeof(*r->cigar));
822
+ }
823
+
824
+ void mwf_wfa_auto(void *km, const mwf_opt_t *opt0, int32_t tl, const char *ts, int32_t ql, const char *qs, mwf_rst_t *r)
825
+ {
826
+ mwf_opt_t opt = *opt0;
827
+ opt.step = 0, opt.max_iter = 100000000;
828
+ mwf_wfa_exact(km, &opt, tl, ts, ql, qs, r);
829
+ if (r->s < 0) {
830
+ if (opt.flag & MWF_F_CIGAR) opt.step = 5000;
831
+ opt.max_iter = -1;
832
+ mwf_wfa_chain(km, &opt, tl, ts, ql, qs, r);
833
+ }
834
+ }