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comparison pyPRADA_1.2/tools/bwa-0.5.7-mh/bwase.c~ @ 0:acc2ca1a3ba4

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author siyuan
date Thu, 20 Feb 2014 00:44:58 -0500
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1 #include <unistd.h>
2 #include <string.h>
3 #include <stdio.h>
4 #include <stdlib.h>
5 #include <math.h>
6 #include <time.h>
7 #include "stdaln.h"
8 #include "bwase.h"
9 #include "bwtaln.h"
10 #include "bntseq.h"
11 #include "utils.h"
12 #include "kstring.h"
13
14 static int g_log_n[256];
15
16 void bwa_aln2seq_core(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s, int set_main, int n_multi)
17 {
18 int i, cnt, best;
19 if (n_aln == 0) {
20 s->type = BWA_TYPE_NO_MATCH;
21 s->c1 = s->c2 = 0;
22 return;
23 }
24
25 if (set_main) {
26 best = aln[0].score;
27 for (i = cnt = 0; i < n_aln; ++i) {
28 const bwt_aln1_t *p = aln + i;
29 if (p->score > best) break;
30 if (drand48() * (p->l - p->k + 1) > (double)cnt) {
31 s->n_mm = p->n_mm; s->n_gapo = p->n_gapo; s->n_gape = p->n_gape; s->strand = p->a;
32 s->score = p->score;
33 s->sa = p->k + (bwtint_t)((p->l - p->k + 1) * drand48());
34 }
35 cnt += p->l - p->k + 1;
36 }
37 s->c1 = cnt;
38 for (; i < n_aln; ++i) cnt += aln[i].l - aln[i].k + 1;
39 s->c2 = cnt - s->c1;
40 s->type = s->c1 > 1? BWA_TYPE_REPEAT : BWA_TYPE_UNIQUE;
41 }
42
43 if (n_multi) {
44 int k, rest, n_occ, z = 0;
45 for (k = n_occ = 0; k < n_aln; ++k) {
46 const bwt_aln1_t *q = aln + k;
47 n_occ += q->l - q->k + 1;
48 }
49 if (s->multi) free(s->multi);
50 if (n_occ > n_multi + 1) { // if there are too many hits, generate none of them
51 s->multi = 0; s->n_multi = 0;
52 return;
53 }
54 /* The following code is more flexible than what is required
55 * here. In principle, due to the requirement above, we can
56 * simply output all hits, but the following samples "rest"
57 * number of random hits. */
58 rest = n_occ > n_multi + 1? n_multi + 1 : n_occ; // find one additional for ->sa
59 s->multi = calloc(rest, rest * sizeof(bwt_multi1_t));
60 for (k = 0; k < n_aln; ++k) {
61 const bwt_aln1_t *q = aln + k;
62 if (q->l - q->k + 1 <= rest) {
63 bwtint_t l;
64 for (l = q->k; l <= q->l; ++l) {
65 s->multi[z].pos = l;
66 s->multi[z].gap = q->n_gapo + q->n_gape;
67 s->multi[z].mm = q->n_mm;
68 s->multi[z++].strand = q->a;
69 }
70 rest -= q->l - q->k + 1;
71 } else { // Random sampling (http://code.activestate.com/recipes/272884/). In fact, we never come here.
72 int j, i, k;
73 for (j = rest, i = q->l - q->k + 1, k = 0; j > 0; --j) {
74 double p = 1.0, x = drand48();
75 while (x < p) p -= p * j / (i--);
76 s->multi[z].pos = q->l - i;
77 s->multi[z].gap = q->n_gapo + q->n_gape;
78 s->multi[z].mm = q->n_mm;
79 s->multi[z++].strand = q->a;
80 }
81 rest = 0;
82 break;
83 }
84 }
85 s->n_multi = z;
86 for (k = z = 0; k < s->n_multi; ++k)
87 if (s->multi[k].pos != s->sa)
88 s->multi[z++] = s->multi[k];
89 s->n_multi = z < n_multi? z : n_multi;
90 }
91 }
92
93 void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s)
94 {
95 bwa_aln2seq_core(n_aln, aln, s, 1, 0);
96 }
97
98 /* *aln points to alignments found for the current sequence, n_aln is the
99 size of the array pointed to by *aln. Array *s of size n_seq is a collection
100 of SAM records that must be replicas, i.e. initialized with the same current sequence.
101 This method updates sequence records in *s with placements recorded in *aln,
102 until all n_seq replicas are updated. For each separate alignment record in array *aln,
103 each placement corresponding to this record will be assigned to a separate record in *s
104 if there are enough elements remaining in *s, otherwise a random subset of the placements will
105 be assigned to the remaining elements in *s. The total number of best placements and total
106 number of non-best placements will be computed from the whole array *aln (regardless of whether it
107 fits completely into *s or not) and assigned to each updated record in *s.
108 */
109 void bwa_aln2seq_all(int n_aln, const bwt_aln1_t *aln, int n_seq, bwa_seq_t *s)
110 {
111 int i, cnt1, cnt2, j, best, N;
112 if (n_aln == 0) {
113 /* there is no match found for *s */
114 s->type = BWA_TYPE_NO_MATCH;
115 s->c1 = s->c2 = 0;
116 return;
117 }
118
119 N = n_seq; // remember the size of the array
120 best = aln[0].score;
121
122 cnt1 = 0; // total number of already processed alignments (i.e. distinct placements, NOT alignment records) with best score
123 cnt2 = 0; // total number of already processed alignments with inferior score(s)
124 for (i = 0; i < n_aln && n_seq > 0 ; ++i) {
125 const bwt_aln1_t *p_aln = aln + i;
126
127 int N_aligns = p_aln->l-p_aln->k +1 ; // number of placements (alignments) in the current alignment record p_aln
128
129 if (N_aligns <= n_seq) { /* we have space to save all the alignments stored in 'p_aln' */
130
131 for ( j = 0 ; j < N_aligns ; j++ ) {
132
133 bwa_seq_t * seq = s + cnt1+ cnt2+j ;
134 seq->n_mm = p_aln->n_mm; seq->n_gapo = p_aln->n_gapo; seq->n_gape = p_aln->n_gape; seq->strand = p_aln->a;
135 seq->score = p_aln->score;
136 seq->sa = p_aln->k + j;
137 }
138 n_seq -= N_aligns; // we have n_seq slots remaining to store more alignments
139 } else { // See also: http://code.activestate.com/recipes/272884/
140 // we have to truncate, so let's select few remaining alignments randomly:
141 int xj, xi, xk;
142 for (xj = n_seq, xi = N_aligns, xk = 0; xj > 0; --xj, ++xk) {
143 double p = 1.0, x = drand48();
144 while (x < p) p -= p * xj / (xi--);
145
146 bwa_seq_t * seq = s+cnt1+cnt2+xk ;
147 seq->n_mm = p_aln->n_mm; seq->n_gapo = p_aln->n_gapo; seq->n_gape = p_aln->n_gape; seq->strand = p_aln->a;
148 seq->score = p_aln->score;
149 seq->sa = p_aln->l - xi;
150
151 }
152 n_seq = 0;
153 }
154 // cnt1 + cnt2 is the total count of hits processed so far:
155 if ( p_aln->score == best ) cnt1 += N_aligns; // we found N_aligns more placements with best score
156 else cnt2 += N_aligns; // N_aligns more placements with inferior score
157 }
158
159 // we filled all available slots in the array *s, but there can be more alignments
160 // left; we need to count them:
161 for (; i < n_aln; ++i) {
162 if ( aln[i].score == best ) cnt1 += aln[i].l-aln[i].k+1;
163 else cnt2 += aln[i].l-aln[i].k+1;
164 }
165
166 // now cnt1 is the total number of found alignments (placements) with best score
167 // and cnt2 is the total number of found placements with worse score
168
169 /* set counts and flags for all hits: */
170 for (i = 0; i < N ; ++i) {
171 bwa_seq_t * seq = s+i ;
172
173 seq->c1 = cnt1;
174 seq->c2 = cnt2;
175 seq->type = seq->c1 > 1? BWA_TYPE_REPEAT : BWA_TYPE_UNIQUE;
176 }
177 }
178
179
180
181 int bwa_approx_mapQ(const bwa_seq_t *p, int mm)
182 {
183 int n;
184 if (p->c1 == 0) return 23;
185 if (p->c1 > 1) return 0;
186 if (p->n_mm == mm) return 25;
187 if (p->c2 == 0) return 37;
188 n = (p->c2 >= 255)? 255 : p->c2;
189 return (23 < g_log_n[n])? 0 : 23 - g_log_n[n];
190 }
191
192 /**
193 * Derive the actual position in the read from the given suffix array
194 * coordinates. Note that the position will be approximate based on
195 * whether indels appear in the read and whether calculations are
196 * performed from the start or end of the read.
197 */
198 void bwa_cal_pac_pos_core(const bwt_t *forward_bwt, const bwt_t *reverse_bwt, int n_seqs, bwa_seq_t *s, const int max_mm, const float fnr)
199 {
200 int max_diff;
201 bwa_seq_t *seq;
202 int i;
203
204 for ( i = 0 ; i < n_seqs ; i++ ) {
205 seq = s + i;
206 if (seq->type != BWA_TYPE_UNIQUE && seq->type != BWA_TYPE_REPEAT) continue;
207
208 max_diff = fnr > 0.0? bwa_cal_maxdiff(seq->len, BWA_AVG_ERR, fnr) : max_mm;
209 if (seq->strand) { // reverse strand only
210 seq->pos = bwt_sa(forward_bwt, seq->sa);
211 seq->seQ = seq->mapQ = bwa_approx_mapQ(seq, max_diff);
212 } else { // forward strand only
213 /* NB: For gapped alignment, p->pos may not be correct, which
214 * will be fixed in refine_gapped_core(). This line also
215 * determines the way "x" is calculated in
216 * refine_gapped_core() when (ext < 0 && is_end == 0). */
217 seq->pos = reverse_bwt->seq_len - (bwt_sa(reverse_bwt, seq->sa) + seq->len);
218 seq->seQ = seq->mapQ = bwa_approx_mapQ(seq, max_diff);
219 }
220 }
221 }
222
223 void bwa_cal_pac_pos(const char *prefix, int n_seqs, bwa_seq_t *seqs, int max_mm, float fnr)
224 {
225 int i, j;
226 char str[1024];
227 bwt_t *bwt;
228 // load forward SA
229 strcpy(str, prefix); strcat(str, ".bwt"); bwt = bwt_restore_bwt(str);
230 strcpy(str, prefix); strcat(str, ".sa"); bwt_restore_sa(str, bwt);
231 for (i = 0; i != n_seqs; ++i) {
232 if (seqs[i].strand) bwa_cal_pac_pos_core(bwt, 0, 1, &seqs[i], max_mm, fnr);
233 for (j = 0; j < seqs[i].n_multi; ++j) {
234 bwt_multi1_t *p = seqs[i].multi + j;
235 if (p->strand) p->pos = bwt_sa(bwt, p->pos);
236 }
237 }
238 bwt_destroy(bwt);
239 // load reverse BWT and SA
240 strcpy(str, prefix); strcat(str, ".rbwt"); bwt = bwt_restore_bwt(str);
241 strcpy(str, prefix); strcat(str, ".rsa"); bwt_restore_sa(str, bwt);
242 for (i = 0; i != n_seqs; ++i) {
243 if (!seqs[i].strand) bwa_cal_pac_pos_core(0, bwt, 1, &seqs[i], max_mm, fnr);
244 for (j = 0; j < seqs[i].n_multi; ++j) {
245 bwt_multi1_t *p = seqs[i].multi + j;
246 if (!p->strand) p->pos = bwt->seq_len - (bwt_sa(bwt, p->pos) + seqs[i].len);
247 }
248 }
249 bwt_destroy(bwt);
250 }
251
252 /* is_end_correct == 1 if (*pos+len) gives the correct coordinate on
253 * forward strand. This happens when p->pos is calculated by
254 * bwa_cal_pac_pos(). is_end_correct==0 if (*pos) gives the correct
255 * coordinate. This happens only for color-converted alignment. */
256 static bwa_cigar_t *refine_gapped_core(bwtint_t l_pac, const ubyte_t *pacseq, int len, const ubyte_t *seq, bwtint_t *_pos,
257 int ext, int *n_cigar, int is_end_correct)
258 {
259 bwa_cigar_t *cigar = 0;
260 ubyte_t *ref_seq;
261 int l = 0, path_len, ref_len;
262 AlnParam ap = aln_param_bwa;
263 path_t *path;
264 int64_t k, __pos = *_pos > l_pac? (int64_t)((int32_t)*_pos) : *_pos;
265
266 ref_len = len + abs(ext);
267 if (ext > 0) {
268 ref_seq = (ubyte_t*)calloc(ref_len, 1);
269 for (k = __pos; k < __pos + ref_len && k < l_pac; ++k)
270 ref_seq[l++] = pacseq[k>>2] >> ((~k&3)<<1) & 3;
271 } else {
272 int64_t x = __pos + (is_end_correct? len : ref_len);
273 ref_seq = (ubyte_t*)calloc(ref_len, 1);
274 for (l = 0, k = x - ref_len > 0? x - ref_len : 0; k < x && k < l_pac; ++k)
275 ref_seq[l++] = pacseq[k>>2] >> ((~k&3)<<1) & 3;
276 }
277 path = (path_t*)calloc(l+len, sizeof(path_t));
278
279 aln_global_core(ref_seq, l, (ubyte_t*)seq, len, &ap, path, &path_len);
280 cigar = bwa_aln_path2cigar(path, path_len, n_cigar);
281
282 if (ext < 0 && is_end_correct) { // fix coordinate for reads mapped on the forward strand
283 for (l = k = 0; k < *n_cigar; ++k) {
284 if (__cigar_op(cigar[k]) == FROM_D) l -= __cigar_len(cigar[k]);
285 else if (__cigar_op(cigar[k]) == FROM_I) l += __cigar_len(cigar[k]);
286 }
287 __pos += l;
288 }
289
290 if (__cigar_op(cigar[0]) == FROM_D) { // deletion at the 5'-end
291 __pos += __cigar_len(cigar[0]);
292 for (k = 0; k < *n_cigar - 1; ++k) cigar[k] = cigar[k+1];
293 --(*n_cigar);
294 }
295 if (__cigar_op(cigar[*n_cigar-1]) == FROM_D) --(*n_cigar); // deletion at the 3'-end
296
297 // change "I" at either end of the read to S. just in case. This should rarely happen...
298 if (__cigar_op(cigar[*n_cigar-1]) == FROM_I) cigar[*n_cigar-1] = __cigar_create(3, (__cigar_len(cigar[*n_cigar-1])));
299 if (__cigar_op(cigar[0]) == FROM_I) cigar[0] = __cigar_create(3, (__cigar_len(cigar[0])));
300
301 *_pos = (bwtint_t)__pos;
302 free(ref_seq); free(path);
303 return cigar;
304 }
305
306 char *bwa_cal_md1(int n_cigar, bwa_cigar_t *cigar, int len, bwtint_t pos, ubyte_t *seq,
307 bwtint_t l_pac, ubyte_t *pacseq, kstring_t *str, int *_nm)
308 {
309 bwtint_t x, y;
310 int z, u, c, nm = 0;
311 str->l = 0; // reset
312 x = pos; y = 0;
313 if (cigar) {
314 int k, l;
315 for (k = u = 0; k < n_cigar; ++k) {
316 l = __cigar_len(cigar[k]);
317 if (__cigar_op(cigar[k]) == FROM_M) {
318 for (z = 0; z < l && x+z < l_pac; ++z) {
319 c = pacseq[(x+z)>>2] >> ((~(x+z)&3)<<1) & 3;
320 if (c > 3 || seq[y+z] > 3 || c != seq[y+z]) {
321 ksprintf(str, "%d", u);
322 kputc("ACGTN"[c], str);
323 ++nm;
324 u = 0;
325 } else ++u;
326 }
327 x += l; y += l;
328 /* } else if (cigar[k]>>14 == FROM_I || cigar[k]>>14 == 3) { */
329 } else if (__cigar_op(cigar[k]) == FROM_I || __cigar_op(cigar[k]) == FROM_S) {
330 y += l;
331 if (__cigar_op(cigar[k]) == FROM_I) nm += l;
332 } else if (__cigar_op(cigar[k]) == FROM_D) {
333 ksprintf(str, "%d", u);
334 kputc('^', str);
335 for (z = 0; z < l && x+z < l_pac; ++z)
336 kputc("ACGT"[pacseq[(x+z)>>2] >> ((~(x+z)&3)<<1) & 3], str);
337 u = 0;
338 x += l; nm += l;
339 }
340 }
341 } else { // no gaps
342 for (z = u = 0; z < (bwtint_t)len; ++z) {
343 c = pacseq[(x+z)>>2] >> ((~(x+z)&3)<<1) & 3;
344 if (c > 3 || seq[y+z] > 3 || c != seq[y+z]) {
345 ksprintf(str, "%d", u);
346 kputc("ACGTN"[c], str);
347 ++nm;
348 u = 0;
349 } else ++u;
350 }
351 }
352 ksprintf(str, "%d", u);
353 *_nm = nm;
354 return strdup(str->s);
355 }
356
357 void bwa_correct_trimmed(bwa_seq_t *s)
358 {
359 if (s->len == s->full_len) return;
360 if (s->strand == 0) { // forward
361 if (s->cigar && __cigar_op(s->cigar[s->n_cigar-1]) == FROM_S) { // the last is S
362 s->cigar[s->n_cigar-1] += s->full_len - s->len;
363 } else {
364 if (s->cigar == 0) {
365 s->n_cigar = 2;
366 s->cigar = calloc(s->n_cigar, sizeof(bwa_cigar_t));
367 s->cigar[0] = __cigar_create(0, s->len);
368 } else {
369 ++s->n_cigar;
370 s->cigar = realloc(s->cigar, s->n_cigar * sizeof(bwa_cigar_t));
371 }
372 s->cigar[s->n_cigar-1] = __cigar_create(3, (s->full_len - s->len));
373 }
374 } else { // reverse
375 if (s->cigar && __cigar_op(s->cigar[0]) == FROM_S) { // the first is S
376 s->cigar[0] += s->full_len - s->len;
377 } else {
378 if (s->cigar == 0) {
379 s->n_cigar = 2;
380 s->cigar = calloc(s->n_cigar, sizeof(bwa_cigar_t));
381 s->cigar[1] = __cigar_create(0, s->len);
382 } else {
383 ++s->n_cigar;
384 s->cigar = realloc(s->cigar, s->n_cigar * sizeof(bwa_cigar_t));
385 memmove(s->cigar + 1, s->cigar, (s->n_cigar-1) * sizeof(bwa_cigar_t));
386 }
387 s->cigar[0] = __cigar_create(3, (s->full_len - s->len));
388 }
389 }
390 s->len = s->full_len;
391 }
392
393 void bwa_refine_gapped(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t *_pacseq, bntseq_t *ntbns)
394 {
395 ubyte_t *pacseq, *ntpac = 0;
396 int i, j;
397 kstring_t *str;
398
399 if (ntbns) { // in color space
400 ntpac = (ubyte_t*)calloc(ntbns->l_pac/4+1, 1);
401 rewind(ntbns->fp_pac);
402 fread(ntpac, 1, ntbns->l_pac/4 + 1, ntbns->fp_pac);
403 }
404
405 if (!_pacseq) {
406 pacseq = (ubyte_t*)calloc(bns->l_pac/4+1, 1);
407 rewind(bns->fp_pac);
408 fread(pacseq, 1, bns->l_pac/4+1, bns->fp_pac);
409 } else pacseq = _pacseq;
410 for (i = 0; i != n_seqs; ++i) {
411 bwa_seq_t *s = seqs + i;
412 seq_reverse(s->len, s->seq, 0); // IMPORTANT: s->seq is reversed here!!!
413 for (j = 0; j < s->n_multi; ++j) {
414 bwt_multi1_t *q = s->multi + j;
415 int n_cigar;
416 if (q->gap == 0) continue;
417 q->cigar = refine_gapped_core(bns->l_pac, pacseq, s->len, q->strand? s->rseq : s->seq, &q->pos,
418 (q->strand? 1 : -1) * q->gap, &n_cigar, 1);
419 q->n_cigar = n_cigar;
420 }
421 if (s->type == BWA_TYPE_NO_MATCH || s->type == BWA_TYPE_MATESW || s->n_gapo == 0) continue;
422 s->cigar = refine_gapped_core(bns->l_pac, pacseq, s->len, s->strand? s->rseq : s->seq, &s->pos,
423 (s->strand? 1 : -1) * (s->n_gapo + s->n_gape), &s->n_cigar, 1);
424 }
425
426 if (ntbns) { // in color space
427 for (i = 0; i < n_seqs; ++i) {
428 bwa_seq_t *s = seqs + i;
429 bwa_cs2nt_core(s, bns->l_pac, ntpac);
430 for (j = 0; j < s->n_multi; ++j) {
431 bwt_multi1_t *q = s->multi + j;
432 int n_cigar;
433 if (q->gap == 0) continue;
434 free(q->cigar);
435 q->cigar = refine_gapped_core(bns->l_pac, ntpac, s->len, q->strand? s->rseq : s->seq, &q->pos,
436 (q->strand? 1 : -1) * q->gap, &n_cigar, 0);
437 q->n_cigar = n_cigar;
438 }
439 if (s->type != BWA_TYPE_NO_MATCH && s->cigar) { // update cigar again
440 free(s->cigar);
441 s->cigar = refine_gapped_core(bns->l_pac, ntpac, s->len, s->strand? s->rseq : s->seq, &s->pos,
442 (s->strand? 1 : -1) * (s->n_gapo + s->n_gape), &s->n_cigar, 0);
443 }
444 }
445 }
446
447 // generate MD tag
448 str = (kstring_t*)calloc(1, sizeof(kstring_t));
449 for (i = 0; i != n_seqs; ++i) {
450 bwa_seq_t *s = seqs + i;
451 if (s->type != BWA_TYPE_NO_MATCH) {
452 int nm;
453 s->md = bwa_cal_md1(s->n_cigar, s->cigar, s->len, s->pos, s->strand? s->rseq : s->seq,
454 bns->l_pac, ntbns? ntpac : pacseq, str, &nm);
455 s->nm = nm;
456 }
457 }
458 free(str->s); free(str);
459
460 // correct for trimmed reads
461 if (!ntbns) // trimming is only enabled for Illumina reads
462 for (i = 0; i < n_seqs; ++i) bwa_correct_trimmed(seqs + i);
463
464 if (!_pacseq) free(pacseq);
465 free(ntpac);
466 }
467
468 int64_t pos_end(const bwa_seq_t *p)
469 {
470 if (p->cigar) {
471 int j;
472 int64_t x = p->pos;
473 for (j = 0; j != p->n_cigar; ++j) {
474 int op = __cigar_op(p->cigar[j]);
475 if (op == 0 || op == 2) x += __cigar_len(p->cigar[j]);
476 }
477 return x;
478 } else return p->pos + p->len;
479 }
480
481 int64_t pos_end_multi(const bwt_multi1_t *p, int len) // analogy to pos_end()
482 {
483 if (p->cigar) {
484 int j;
485 int64_t x = p->pos;
486 for (j = 0; j != p->n_cigar; ++j) {
487 int op = __cigar_op(p->cigar[j]);
488 if (op == 0 || op == 2) x += __cigar_len(p->cigar[j]);
489 }
490 return x;
491 } else return p->pos + len;
492 }
493
494 static int64_t pos_5(const bwa_seq_t *p)
495 {
496 if (p->type != BWA_TYPE_NO_MATCH)
497 return p->strand? pos_end(p) : p->pos;
498 return -1;
499 }
500
501 /* Prints <bases>\t<quals> of the sequence *p into STDOUT;
502 */
503 void bwa_print_seq_and_qual(bwa_seq_t *p) {
504 int j;
505
506 if (p->strand == 0)
507 for (j = 0; j != p->full_len; ++j) putchar("ACGTN"[(int)p->seq[j]]);
508 else for (j = 0; j != p->full_len; ++j) putchar("TGCAN"[p->seq[p->full_len - 1 - j]]);
509 putchar('\t');
510 if (p->qual) {
511 if (p->strand) seq_reverse(p->len, p->qual, 0); // reverse quality
512 printf("%s", p->qual);
513 } else printf("*");
514
515 }
516
517
518
519 void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, int mode, int max_top2)
520 {
521 int j;
522 if (p->type != BWA_TYPE_NO_MATCH || (mate && mate->type != BWA_TYPE_NO_MATCH)) {
523 int seqid, nn, am = 0, flag = p->extra_flag;
524 char XT;
525
526 if (p->type == BWA_TYPE_NO_MATCH) {
527 p->pos = mate->pos;
528 p->strand = mate->strand;
529 flag |= SAM_FSU;
530 j = 1;
531 } else j = pos_end(p) - p->pos; // j is the length of the reference in the alignment
532
533 // get seqid
534 nn = bns_coor_pac2real(bns, p->pos, j, &seqid);
535 if (p->type != BWA_TYPE_NO_MATCH && p->pos + j - bns->anns[seqid].offset > bns->anns[seqid].len)
536 flag |= SAM_FSU; // flag UNMAP as this alignment bridges two adjacent reference sequences
537
538 // update flag and print it
539 if (p->strand) flag |= SAM_FSR;
540 if (mate) {
541 if (mate->type != BWA_TYPE_NO_MATCH) {
542 if (mate->strand) flag |= SAM_FMR;
543 } else flag |= SAM_FMU;
544 }
545 printf("%s\t%d\t%s\t", p->name, flag, bns->anns[seqid].name);
546 printf("%d\t%d\t", (int)(p->pos - bns->anns[seqid].offset + 1), p->mapQ);
547
548 // print CIGAR
549 if (p->cigar) {
550 for (j = 0; j != p->n_cigar; ++j)
551 printf("%d%c", __cigar_len(p->cigar[j]), "MIDS"[__cigar_op(p->cigar[j])]);
552 } else if (p->type == BWA_TYPE_NO_MATCH) printf("*");
553 else printf("%dM", p->len);
554
555 // print mate coordinate
556 if (mate && mate->type != BWA_TYPE_NO_MATCH) {
557 int m_seqid, m_is_N;
558 long long isize;
559 am = mate->seQ < p->seQ? mate->seQ : p->seQ; // smaller single-end mapping quality
560 // redundant calculation here, but should not matter too much
561 m_is_N = bns_coor_pac2real(bns, mate->pos, mate->len, &m_seqid);
562 printf("\t%s\t", (seqid == m_seqid)? "=" : bns->anns[m_seqid].name);
563 isize = (seqid == m_seqid)? pos_5(mate) - pos_5(p) : 0;
564 if (p->type == BWA_TYPE_NO_MATCH) isize = 0;
565 printf("%d\t%lld\t", (int)(mate->pos - bns->anns[m_seqid].offset + 1), isize);
566 } else if (mate) printf("\t=\t%d\t0\t", (int)(p->pos - bns->anns[seqid].offset + 1));
567 else printf("\t*\t0\t0\t");
568
569 // print sequence and quality
570 bwa_print_seq_and_qual(p);
571
572 if (p->clip_len < p->full_len) printf("\tXC:i:%d", p->clip_len);
573 if (p->type != BWA_TYPE_NO_MATCH) {
574 int i;
575 // calculate XT tag
576 XT = "NURM"[p->type];
577 if (nn > 10) XT = 'N';
578 // print tags
579 printf("\tXT:A:%c\t%s:i:%d", XT, (mode & BWA_MODE_COMPREAD)? "NM" : "CM", p->nm);
580 if (nn) printf("\tXN:i:%d", nn);
581 if (mate) printf("\tSM:i:%d\tAM:i:%d", p->seQ, am);
582 if (p->type != BWA_TYPE_MATESW) { // X0 and X1 are not available for this type of alignment
583 printf("\tX0:i:%d", p->c1);
584 if (p->c1 <= max_top2) printf("\tX1:i:%d", p->c2);
585 }
586 printf("\tXM:i:%d\tXO:i:%d\tXG:i:%d", p->n_mm, p->n_gapo, p->n_gapo+p->n_gape);
587 if (p->md) printf("\tMD:Z:%s", p->md);
588 // print multiple hits
589 if (p->n_multi) {
590 printf("\tXA:Z:");
591 for (i = 0; i < p->n_multi; ++i) {
592 bwt_multi1_t *q = p->multi + i;
593 int k;
594 j = pos_end_multi(q, p->len) - q->pos;
595 nn = bns_coor_pac2real(bns, q->pos, j, &seqid);
596 printf("%s,%c%d,", bns->anns[seqid].name, q->strand? '-' : '+',
597 (int)(q->pos - bns->anns[seqid].offset + 1));
598 if (q->cigar) {
599 for (k = 0; k < q->n_cigar; ++k)
600 printf("%d%c", __cigar_len(q->cigar[k]), "MIDS"[__cigar_op(q->cigar[k])]);
601 } else printf("%dM", p->len);
602 printf(",%d;", q->gap + q->mm);
603 }
604 }
605 }
606 putchar('\n');
607 } else { // this read has no match
608 ubyte_t *s = p->strand? p->rseq : p->seq;
609 int flag = p->extra_flag | SAM_FSU;
610 if (mate && mate->type == BWA_TYPE_NO_MATCH) flag |= SAM_FMU;
611 printf("%s\t%d\t*\t0\t0\t*\t*\t0\t0\t", p->name, flag);
612 for (j = 0; j != p->len; ++j) putchar("ACGTN"[(int)s[j]]);
613 putchar('\t');
614 if (p->qual) {
615 if (p->strand) seq_reverse(p->len, p->qual, 0); // reverse quality
616 printf("%s", p->qual);
617 } else printf("*");
618 if (p->clip_len < p->full_len) printf("\tXC:i:%d", p->clip_len);
619 putchar('\n');
620 }
621 }
622
623 /* UNUSED
624 void bwa_print_partial_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, int mode, int max_top2)
625 {
626 int j;
627 if (p->type != BWA_TYPE_NO_MATCH || (mate && mate->type != BWA_TYPE_NO_MATCH)) {
628 int seqid, nn, am = 0, flag = p->extra_flag;
629 char XT;
630
631 if (p->type == BWA_TYPE_NO_MATCH) {
632 p->pos = mate->pos;
633 p->strand = mate->strand;
634 flag |= SAM_FSU;
635 j = 1;
636 } else j = pos_end(p) - p->pos; // j is the length of the reference in the alignment
637
638 // get seqid
639 nn = bns_coor_pac2real(bns, p->pos, j, &seqid);
640 if (p->type != BWA_TYPE_NO_MATCH && p->pos + j - bns->anns[seqid].offset > bns->anns[seqid].len)
641 flag |= SAM_FSU; // flag UNMAP as this alignment bridges two adjacent reference sequences
642
643 // update flag and print it
644 if (p->strand) flag |= SAM_FSR;
645 if (mate) {
646 if (mate->type != BWA_TYPE_NO_MATCH) {
647 if (mate->strand) flag |= SAM_FMR;
648 } else flag |= SAM_FMU;
649 }
650 printf("%s\t%d\t%s\t", p->name, flag, bns->anns[seqid].name);
651 printf("%d\t%d\t", (int)(p->pos - bns->anns[seqid].offset + 1), p->mapQ);
652
653 // print CIGAR
654 if (p->cigar) {
655 for (j = 0; j != p->n_cigar; ++j)
656 printf("%d%c", __cigar_len(p->cigar[j]), "MIDS"[__cigar_op(p->cigar[j])]);
657 } else if (p->type == BWA_TYPE_NO_MATCH) printf("*");
658 else printf("%dM", p->len);
659
660 // print mate coordinate
661 if (mate && mate->type != BWA_TYPE_NO_MATCH) {
662 int m_seqid, m_is_N;
663 long long isize;
664 am = mate->seQ < p->seQ? mate->seQ : p->seQ; // smaller single-end mapping quality
665 // redundant calculation here, but should not matter too much
666 m_is_N = bns_coor_pac2real(bns, mate->pos, mate->len, &m_seqid);
667 printf("\t%s\t", (seqid == m_seqid)? "=" : bns->anns[m_seqid].name);
668 isize = (seqid == m_seqid)? pos_5(mate) - pos_5(p) : 0;
669 if (p->type == BWA_TYPE_NO_MATCH) isize = 0;
670 printf("%d\t%lld\t", (int)(mate->pos - bns->anns[m_seqid].offset + 1), isize);
671 } else if (mate) printf("\t=\t%d\t0\t", (int)(p->pos - bns->anns[seqid].offset + 1));
672 else printf("\t*\t0\t0\t");
673
674
675 if (p->clip_len < p->full_len) printf("\tXC:i:%d", p->clip_len);
676 if (p->type != BWA_TYPE_NO_MATCH) {
677 int i;
678 // calculate XT tag
679 XT = "NURM"[p->type];
680 if (nn > 10) XT = 'N';
681 // print tags
682 printf("\tXT:A:%c\t%s:i:%d", XT, (mode & BWA_MODE_COMPREAD)? "NM" : "CM", p->nm);
683 if (nn) printf("\tXN:i:%d", nn);
684 if (mate) printf("\tSM:i:%d\tAM:i:%d", p->seQ, am);
685 printf("\tXM:i:%d\tXO:i:%d\tXG:i:%d", p->n_mm, p->n_gapo, p->n_gapo+p->n_gape);
686 if (p->md) printf("\tMD:Z:%s", p->md);
687 }
688 putchar('\n');
689 } else { // this read has no match
690 ubyte_t *s = p->strand? p->rseq : p->seq;
691 int flag = p->extra_flag | SAM_FSU;
692 if (mate && mate->type == BWA_TYPE_NO_MATCH) flag |= SAM_FMU;
693 printf("%d\t*\t0\t0\t*\t*\t0\t0\t", flag);
694 if (p->clip_len < p->full_len) printf("\tXC:i:%d", p->clip_len);
695 putchar('\n');
696 }
697 }
698
699 */
700
701 bntseq_t *bwa_open_nt(const char *prefix)
702 {
703 bntseq_t *ntbns;
704 char *str;
705 str = (char*)calloc(strlen(prefix) + 10, 1);
706 strcat(strcpy(str, prefix), ".nt");
707 ntbns = bns_restore(str);
708 free(str);
709 return ntbns;
710 }
711
712 void bwa_print_sam_SQ(const bntseq_t *bns)
713 {
714 int i;
715 for (i = 0; i < bns->n_seqs; ++i)
716 printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[i].name, bns->anns[i].len);
717 }
718
719 void bwase_initialize()
720 {
721 int i;
722 for (i = 1; i != 256; ++i) g_log_n[i] = (int)(4.343 * log(i) + 0.5);
723 }
724
725 void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_fa, int n_occ)
726 {
727 int i, n_seqs, tot_seqs = 0, m_aln;
728 bwt_aln1_t *aln = 0;
729 bwa_seq_t *seqs;
730 bwa_seqio_t *ks;
731 clock_t t;
732 bntseq_t *bns, *ntbns = 0;
733 FILE *fp_sa;
734 gap_opt_t opt;
735
736 // initialization
737 bwase_initialize();
738 bns = bns_restore(prefix);
739 srand48(bns->seed);
740 ks = bwa_seq_open(fn_fa);
741 fp_sa = xopen(fn_sa, "r");
742
743 // core loop
744 m_aln = 0;
745 fread(&opt, sizeof(gap_opt_t), 1, fp_sa);
746 if (!(opt.mode & BWA_MODE_COMPREAD)) // in color space; initialize ntpac
747 ntbns = bwa_open_nt(prefix);
748 bwa_print_sam_SQ(bns);
749 while ((seqs = bwa_read_seq(ks, 0x40000, &n_seqs, opt.mode & BWA_MODE_COMPREAD, opt.trim_qual)) != 0) {
750 tot_seqs += n_seqs;
751 t = clock();
752
753 // read alignment
754 for (i = 0; i < n_seqs; ++i) {
755 bwa_seq_t *p = seqs + i;
756 int n_aln;
757 fread(&n_aln, 4, 1, fp_sa);
758 if (n_aln > m_aln) {
759 m_aln = n_aln;
760 aln = (bwt_aln1_t*)realloc(aln, sizeof(bwt_aln1_t) * m_aln);
761 }
762 fread(aln, sizeof(bwt_aln1_t), n_aln, fp_sa);
763 bwa_aln2seq_core(n_aln, aln, p, 1, n_occ);
764 }
765
766 fprintf(stderr, "[bwa_aln_core] convert to sequence coordinate... ");
767 bwa_cal_pac_pos(prefix, n_seqs, seqs, opt.max_diff, opt.fnr); // forward bwt will be destroyed here
768 fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
769
770 fprintf(stderr, "[bwa_aln_core] refine gapped alignments... ");
771 bwa_refine_gapped(bns, n_seqs, seqs, 0, ntbns);
772 fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
773
774 fprintf(stderr, "[bwa_aln_core] print alignments... ");
775 for (i = 0; i < n_seqs; ++i)
776 bwa_print_sam1(bns, seqs + i, 0, opt.mode, opt.max_top2);
777 fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
778
779 bwa_free_read_seq(n_seqs, seqs);
780 fprintf(stderr, "[bwa_aln_core] %d sequences have been processed.\n", tot_seqs);
781 }
782
783 // destroy
784 bwa_seq_close(ks);
785 if (ntbns) bns_destroy(ntbns);
786 bns_destroy(bns);
787 fclose(fp_sa);
788 free(aln);
789 }
790
791 void bwa_print_all_hits(const char *prefix, const char *fn_sa, const char *fn_fa, int max_extra_occ)
792 {
793 int i, n_seqs, tot_seqs = 0, m_aln, m_rest;
794 bwt_aln1_t *aln = 0;
795 bwa_seq_t *seqs;
796 bwa_seqio_t *ks;
797 clock_t t,t_convert, t_refine, t_write;;
798 bntseq_t *bns, *ntbns = 0;
799 FILE *fp_sa;
800 gap_opt_t opt;
801
802 //****** below modified (added) for multiple hit printout:
803
804 bwa_seq_t * rest_seqs = 0; // this array will keep (shallow) replicas of the current sequence;
805 // each of the replicas will be updated with its own alignment
806 // selected from all the (multiple) alignmens available for the current seq.
807
808 bwt_t *bwt[2];
809 char str[1024];
810 ubyte_t *pacseq;
811
812 t = clock();
813 fprintf(stderr, "[bwa_aln_core] Data structures initialized: ");
814
815
816 strcpy(str, prefix); strcat(str, ".bwt"); bwt[0] = bwt_restore_bwt(str);
817 strcpy(str, prefix); strcat(str, ".sa"); bwt_restore_sa(str, bwt[0]);
818
819 // load reverse BWT and SA
820 strcpy(str, prefix); strcat(str, ".rbwt"); bwt[1] = bwt_restore_bwt(str);
821 strcpy(str, prefix); strcat(str, ".rsa"); bwt_restore_sa(str, bwt[1]);
822 //***************
823
824 // initialization
825 bwase_initialize();
826 bns = bns_restore(prefix);
827 srand48(bns->seed);
828 ks = bwa_seq_open(fn_fa);
829 fp_sa = xopen(fn_sa, "r");
830
831 pacseq = (ubyte_t*)calloc(bns->l_pac/4+1, 1);
832 rewind(bns->fp_pac);
833 fread(pacseq, 1, bns->l_pac/4+1, bns->fp_pac);
834
835
836 // core loop
837 m_aln = 0;
838 m_rest = 0;
839
840 fread(&opt, sizeof(gap_opt_t), 1, fp_sa);
841 if (!(opt.mode & BWA_MODE_COMPREAD)) // in color space; initialize ntpac
842 ntbns = bwa_open_nt(prefix);
843 bwa_print_sam_SQ(bns);
844
845 fprintf(stderr, "%.2f sec\n", (float)(clock()-t) / CLOCKS_PER_SEC);
846
847 t = clock();
848
849 max_extra_occ++; // now this variable holds TOTAL number of alignments we want to print (1+requested extra).
850
851 while ((seqs = bwa_read_seq(ks, 0x40000, &n_seqs, opt.mode & BWA_MODE_COMPREAD, opt.trim_qual)) != 0) {
852 tot_seqs += n_seqs;
853 t_convert = 0;
854 t_refine = 0;
855 t_write = 0;
856
857 fprintf(stderr, "[bwa_aln_core] %d sequences loaded: ",n_seqs);
858 fprintf(stderr, "%.2f sec\n", (float)(clock()-t) / CLOCKS_PER_SEC);
859
860
861 // read alignment
862 for (i = 0; i < n_seqs; ++i) {
863
864 bwa_seq_t *p = seqs + i;
865 int n_aln, n_occ, k, rest;
866 fread(&n_aln, 4, 1, fp_sa);
867 if (n_aln > m_aln) {
868 m_aln = n_aln;
869 aln = (bwt_aln1_t*)realloc(aln, sizeof(bwt_aln1_t) * m_aln);
870 }
871
872 fread(aln, sizeof(bwt_aln1_t), n_aln, fp_sa);
873 for ( k = n_occ = 0 ; k < n_aln; ++k ) {
874 const bwt_aln1_t *q = aln + k;
875 n_occ += q->l - q->k + 1;
876 } /* n_occ is now keeping total number of available alignments to the reference
877 (i.e. placements, NOT bwa records, each of which can describe few placements)
878 */
879
880 // we are going to keep and print 'rest' alignments:
881 rest = ((n_occ > max_extra_occ)? max_extra_occ : n_occ);
882
883 if ( rest == 0 ) rest++; /* we need at least one record, even if it is going to say "UNMAPPED" */
884
885 if ( rest > m_rest ) {
886 // reallocate rest_seqs array (only if needed) to ensure it can keep 'rest' records
887 m_rest = rest;
888 rest_seqs = (bwa_seq_t*)realloc(rest_seqs,sizeof(bwa_seq_t)*m_rest);
889 }
890 // initialize 'rest' replicas of the current sequence record
891 for ( k = 0 ; k < rest ; k++ ) {
892 rest_seqs[k] = *p; /* clone current sequence p; IMPORTANT: it's a shallow copy */
893 }
894
895 bwa_aln2seq_all(n_aln, aln, rest,rest_seqs);
896 // now each of the replicas carries its own bwa alignment selected from all alignments
897 // available for the current sequence *p.
898
899 /* compute positions of the alignments on the ref: */
900 t = clock();
901
902 bwa_cal_pac_pos_core(bwt[0],bwt[1], rest, rest_seqs, opt.max_diff, opt.fnr );
903 t_convert += ( clock() - t );
904
905 /* compute positions of the alignments on the ref: */
906 t = clock();
907
908 bwa_cal_pac_pos_core(bwt[0],bwt[1], rest, rest_seqs, opt.max_diff, opt.fnr );
909 t_convert += ( clock() - t );
910
911 t = clock();
912
913 bwa_refine_gapped(bns,rest,rest_seqs,pacseq,ntbns); // refine all gapped aligns in our replicas;
914 // side effect: cigars will be allocated for each replica
915 t_refine += ( clock() - t );
916
917 t = clock();
918 // for ( k = 0 ; k < n_seqs ; k++ ) {
919 for ( k = 0 ; k < rest ; k++ ) {
920
921 bwa_print_sam1(bns, rest_seqs + k, 0, opt.mode, opt.max_top2);
922 // cigar was allocated for us in every replica as a side effect, free it now:
923 free ( (rest_seqs+k)->cigar );
924 }
925 t_write+= ( clock()-t);
926
927 }
928
929 bwa_free_read_seq(n_seqs, seqs);
930
931 fprintf(stderr, "[bwa_aln_core] convert %d sequences to sequence coordinate: ",n_seqs);
932 fprintf(stderr, "%.2f sec\n", (float)t_convert / CLOCKS_PER_SEC);
933 fprintf(stderr, "[bwa_aln_core] refine gapped alignments for %d sequences: ", n_seqs);
934 fprintf(stderr, "%.2f sec\n", (float)t_refine / CLOCKS_PER_SEC);
935 fprintf(stderr, "[bwa_aln_core] print alignments for %d sequences: ", n_seqs);
936 fprintf(stderr, "%.2f sec\n", (float)t_write/ CLOCKS_PER_SEC);
937 fprintf(stderr, "[bwa_aln_core] %d sequences have been processed.\n", tot_seqs);
938
939 t = clock();
940 }
941
942 // destroy
943 bwt_destroy(bwt[0]);
944 bwt_destroy(bwt[1]);
945
946 free(rest_seqs);
947 free(pacseq);
948
949 bwa_seq_close(ks);
950 if (ntbns) bns_destroy(ntbns);
951 bns_destroy(bns);
952 fclose(fp_sa);
953 free(aln);
954 }
955
956 int bwa_sai2sam_se(int argc, char *argv[])
957 {
958 int c, n_occ = 3;
959 int do_full_sam = 0;
960 while ((c = getopt(argc, argv, "hsn:f:")) >= 0) {
961 switch (c) {
962 case 'h': break;
963 case 's': do_full_sam = 1; break;
964 case 'n': n_occ = atoi(optarg); break;
965 case 'f': freopen(optarg, "w", stdout); break;
966 default: return 1;
967 }
968 }
969
970 if (optind + 3 > argc) {
971 fprintf(stderr, "Usage: bwa samse [-n max_occ [-s] ] [-f out.sam] <prefix> <in.sai> <in.fq>\n");
972 return 1;
973 }
974 if ( do_full_sam ) bwa_print_all_hits(argv[optind], argv[optind+1], argv[optind+2], n_occ);
975 else bwa_sai2sam_se_core(argv[optind], argv[optind+1], argv[optind+2], n_occ);
976 return 0;
977 }