Mercurial > repos > siyuan > prada
comparison pyPRADA_1.2/tools/samtools-0.1.16/bam_md.c @ 0:acc2ca1a3ba4
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author | siyuan |
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date | Thu, 20 Feb 2014 00:44:58 -0500 |
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-1:000000000000 | 0:acc2ca1a3ba4 |
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1 #include <unistd.h> | |
2 #include <assert.h> | |
3 #include <string.h> | |
4 #include <ctype.h> | |
5 #include <math.h> | |
6 #include "faidx.h" | |
7 #include "sam.h" | |
8 #include "kstring.h" | |
9 #include "kaln.h" | |
10 #include "kprobaln.h" | |
11 | |
12 char bam_nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 }; | |
13 | |
14 void bam_fillmd1_core(bam1_t *b, char *ref, int is_equal, int max_nm) | |
15 { | |
16 uint8_t *seq = bam1_seq(b); | |
17 uint32_t *cigar = bam1_cigar(b); | |
18 bam1_core_t *c = &b->core; | |
19 int i, x, y, u = 0; | |
20 kstring_t *str; | |
21 uint8_t *old_md, *old_nm; | |
22 int32_t old_nm_i = -1, nm = 0; | |
23 | |
24 str = (kstring_t*)calloc(1, sizeof(kstring_t)); | |
25 for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) { | |
26 int j, l = cigar[i]>>4, op = cigar[i]&0xf; | |
27 if (op == BAM_CMATCH) { | |
28 for (j = 0; j < l; ++j) { | |
29 int z = y + j; | |
30 int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]]; | |
31 if (ref[x+j] == 0) break; // out of boundary | |
32 if ((c1 == c2 && c1 != 15 && c2 != 15) || c1 == 0) { // a match | |
33 if (is_equal) seq[z/2] &= (z&1)? 0xf0 : 0x0f; | |
34 ++u; | |
35 } else { | |
36 ksprintf(str, "%d", u); | |
37 kputc(ref[x+j], str); | |
38 u = 0; ++nm; | |
39 } | |
40 } | |
41 if (j < l) break; | |
42 x += l; y += l; | |
43 } else if (op == BAM_CDEL) { | |
44 ksprintf(str, "%d", u); | |
45 kputc('^', str); | |
46 for (j = 0; j < l; ++j) { | |
47 if (ref[x+j] == 0) break; | |
48 kputc(ref[x+j], str); | |
49 } | |
50 u = 0; | |
51 if (j < l) break; | |
52 x += l; nm += l; | |
53 } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) { | |
54 y += l; | |
55 if (op == BAM_CINS) nm += l; | |
56 } else if (op == BAM_CREF_SKIP) { | |
57 x += l; | |
58 } | |
59 } | |
60 ksprintf(str, "%d", u); | |
61 // apply max_nm | |
62 if (max_nm > 0 && nm >= max_nm) { | |
63 for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) { | |
64 int j, l = cigar[i]>>4, op = cigar[i]&0xf; | |
65 if (op == BAM_CMATCH) { | |
66 for (j = 0; j < l; ++j) { | |
67 int z = y + j; | |
68 int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]]; | |
69 if (ref[x+j] == 0) break; // out of boundary | |
70 if ((c1 == c2 && c1 != 15 && c2 != 15) || c1 == 0) { // a match | |
71 seq[z/2] |= (z&1)? 0x0f : 0xf0; | |
72 bam1_qual(b)[z] = 0; | |
73 } | |
74 } | |
75 if (j < l) break; | |
76 x += l; y += l; | |
77 } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) x += l; | |
78 else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l; | |
79 } | |
80 } | |
81 // update NM | |
82 old_nm = bam_aux_get(b, "NM"); | |
83 if (c->flag & BAM_FUNMAP) return; | |
84 if (old_nm) old_nm_i = bam_aux2i(old_nm); | |
85 if (!old_nm) bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm); | |
86 else if (nm != old_nm_i) { | |
87 fprintf(stderr, "[bam_fillmd1] different NM for read '%s': %d -> %d\n", bam1_qname(b), old_nm_i, nm); | |
88 bam_aux_del(b, old_nm); | |
89 bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm); | |
90 } | |
91 // update MD | |
92 old_md = bam_aux_get(b, "MD"); | |
93 if (!old_md) bam_aux_append(b, "MD", 'Z', str->l + 1, (uint8_t*)str->s); | |
94 else { | |
95 int is_diff = 0; | |
96 if (strlen((char*)old_md+1) == str->l) { | |
97 for (i = 0; i < str->l; ++i) | |
98 if (toupper(old_md[i+1]) != toupper(str->s[i])) | |
99 break; | |
100 if (i < str->l) is_diff = 1; | |
101 } else is_diff = 1; | |
102 if (is_diff) { | |
103 fprintf(stderr, "[bam_fillmd1] different MD for read '%s': '%s' -> '%s'\n", bam1_qname(b), old_md+1, str->s); | |
104 bam_aux_del(b, old_md); | |
105 bam_aux_append(b, "MD", 'Z', str->l + 1, (uint8_t*)str->s); | |
106 } | |
107 } | |
108 free(str->s); free(str); | |
109 } | |
110 | |
111 void bam_fillmd1(bam1_t *b, char *ref, int is_equal) | |
112 { | |
113 bam_fillmd1_core(b, ref, is_equal, 0); | |
114 } | |
115 | |
116 int bam_cap_mapQ(bam1_t *b, char *ref, int thres) | |
117 { | |
118 uint8_t *seq = bam1_seq(b), *qual = bam1_qual(b); | |
119 uint32_t *cigar = bam1_cigar(b); | |
120 bam1_core_t *c = &b->core; | |
121 int i, x, y, mm, q, len, clip_l, clip_q; | |
122 double t; | |
123 if (thres < 0) thres = 40; // set the default | |
124 mm = q = len = clip_l = clip_q = 0; | |
125 for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) { | |
126 int j, l = cigar[i]>>4, op = cigar[i]&0xf; | |
127 if (op == BAM_CMATCH) { | |
128 for (j = 0; j < l; ++j) { | |
129 int z = y + j; | |
130 int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]]; | |
131 if (ref[x+j] == 0) break; // out of boundary | |
132 if (c2 != 15 && c1 != 15 && qual[z] >= 13) { // not ambiguous | |
133 ++len; | |
134 if (c1 && c1 != c2 && qual[z] >= 13) { // mismatch | |
135 ++mm; | |
136 q += qual[z] > 33? 33 : qual[z]; | |
137 } | |
138 } | |
139 } | |
140 if (j < l) break; | |
141 x += l; y += l; len += l; | |
142 } else if (op == BAM_CDEL) { | |
143 for (j = 0; j < l; ++j) | |
144 if (ref[x+j] == 0) break; | |
145 if (j < l) break; | |
146 x += l; | |
147 } else if (op == BAM_CSOFT_CLIP) { | |
148 for (j = 0; j < l; ++j) clip_q += qual[y+j]; | |
149 clip_l += l; | |
150 y += l; | |
151 } else if (op == BAM_CHARD_CLIP) { | |
152 clip_q += 13 * l; | |
153 clip_l += l; | |
154 } else if (op == BAM_CINS) y += l; | |
155 else if (op == BAM_CREF_SKIP) x += l; | |
156 } | |
157 for (i = 0, t = 1; i < mm; ++i) | |
158 t *= (double)len / (i+1); | |
159 t = q - 4.343 * log(t) + clip_q / 5.; | |
160 if (t > thres) return -1; | |
161 if (t < 0) t = 0; | |
162 t = sqrt((thres - t) / thres) * thres; | |
163 // fprintf(stderr, "%s %lf %d\n", bam1_qname(b), t, q); | |
164 return (int)(t + .499); | |
165 } | |
166 | |
167 int bam_prob_realn_core(bam1_t *b, const char *ref, int flag) | |
168 { | |
169 int k, i, bw, x, y, yb, ye, xb, xe, apply_baq = flag&1, extend_baq = flag>>1&1; | |
170 uint32_t *cigar = bam1_cigar(b); | |
171 bam1_core_t *c = &b->core; | |
172 kpa_par_t conf = kpa_par_def; | |
173 uint8_t *bq = 0, *zq = 0, *qual = bam1_qual(b); | |
174 if ((c->flag & BAM_FUNMAP) || b->core.l_qseq == 0) return -1; // do nothing | |
175 // test if BQ or ZQ is present | |
176 if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq; | |
177 if ((zq = bam_aux_get(b, "ZQ")) != 0 && *zq == 'Z') ++zq; | |
178 if (bq && zq) { // remove the ZQ tag | |
179 bam_aux_del(b, zq-1); | |
180 zq = 0; | |
181 } | |
182 if (bq || zq) { | |
183 if ((apply_baq && zq) || (!apply_baq && bq)) return -3; // in both cases, do nothing | |
184 if (bq && apply_baq) { // then convert BQ to ZQ | |
185 for (i = 0; i < c->l_qseq; ++i) | |
186 qual[i] = qual[i] + 64 < bq[i]? 0 : qual[i] - ((int)bq[i] - 64); | |
187 *(bq - 3) = 'Z'; | |
188 } else if (zq && !apply_baq) { // then convert ZQ to BQ | |
189 for (i = 0; i < c->l_qseq; ++i) | |
190 qual[i] += (int)zq[i] - 64; | |
191 *(zq - 3) = 'B'; | |
192 } | |
193 return 0; | |
194 } | |
195 // find the start and end of the alignment | |
196 x = c->pos, y = 0, yb = ye = xb = xe = -1; | |
197 for (k = 0; k < c->n_cigar; ++k) { | |
198 int op, l; | |
199 op = cigar[k]&0xf; l = cigar[k]>>4; | |
200 if (op == BAM_CMATCH) { | |
201 if (yb < 0) yb = y; | |
202 if (xb < 0) xb = x; | |
203 ye = y + l; xe = x + l; | |
204 x += l; y += l; | |
205 } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l; | |
206 else if (op == BAM_CDEL) x += l; | |
207 else if (op == BAM_CREF_SKIP) return -1; // do nothing if there is a reference skip | |
208 } | |
209 // set bandwidth and the start and the end | |
210 bw = 7; | |
211 if (abs((xe - xb) - (ye - yb)) > bw) | |
212 bw = abs((xe - xb) - (ye - yb)) + 3; | |
213 conf.bw = bw; | |
214 xb -= yb + bw/2; if (xb < 0) xb = 0; | |
215 xe += c->l_qseq - ye + bw/2; | |
216 if (xe - xb - c->l_qseq > bw) | |
217 xb += (xe - xb - c->l_qseq - bw) / 2, xe -= (xe - xb - c->l_qseq - bw) / 2; | |
218 { // glocal | |
219 uint8_t *s, *r, *q, *seq = bam1_seq(b), *bq; | |
220 int *state; | |
221 bq = calloc(c->l_qseq + 1, 1); | |
222 memcpy(bq, qual, c->l_qseq); | |
223 s = calloc(c->l_qseq, 1); | |
224 for (i = 0; i < c->l_qseq; ++i) s[i] = bam_nt16_nt4_table[bam1_seqi(seq, i)]; | |
225 r = calloc(xe - xb, 1); | |
226 for (i = xb; i < xe; ++i) { | |
227 if (ref[i] == 0) { xe = i; break; } | |
228 r[i-xb] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[i]]]; | |
229 } | |
230 state = calloc(c->l_qseq, sizeof(int)); | |
231 q = calloc(c->l_qseq, 1); | |
232 kpa_glocal(r, xe-xb, s, c->l_qseq, qual, &conf, state, q); | |
233 if (!extend_baq) { // in this block, bq[] is capped by base quality qual[] | |
234 for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) { | |
235 int op = cigar[k]&0xf, l = cigar[k]>>4; | |
236 if (op == BAM_CMATCH) { | |
237 for (i = y; i < y + l; ++i) { | |
238 if ((state[i]&3) != 0 || state[i]>>2 != x - xb + (i - y)) bq[i] = 0; | |
239 else bq[i] = bq[i] < q[i]? bq[i] : q[i]; | |
240 } | |
241 x += l; y += l; | |
242 } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l; | |
243 else if (op == BAM_CDEL) x += l; | |
244 } | |
245 for (i = 0; i < c->l_qseq; ++i) bq[i] = qual[i] - bq[i] + 64; // finalize BQ | |
246 } else { // in this block, bq[] is BAQ that can be larger than qual[] (different from the above!) | |
247 uint8_t *left, *rght; | |
248 left = calloc(c->l_qseq, 1); rght = calloc(c->l_qseq, 1); | |
249 for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) { | |
250 int op = cigar[k]&0xf, l = cigar[k]>>4; | |
251 if (op == BAM_CMATCH) { | |
252 for (i = y; i < y + l; ++i) | |
253 bq[i] = ((state[i]&3) != 0 || state[i]>>2 != x - xb + (i - y))? 0 : q[i]; | |
254 for (left[y] = bq[y], i = y + 1; i < y + l; ++i) | |
255 left[i] = bq[i] > left[i-1]? bq[i] : left[i-1]; | |
256 for (rght[y+l-1] = bq[y+l-1], i = y + l - 2; i >= y; --i) | |
257 rght[i] = bq[i] > rght[i+1]? bq[i] : rght[i+1]; | |
258 for (i = y; i < y + l; ++i) | |
259 bq[i] = left[i] < rght[i]? left[i] : rght[i]; | |
260 x += l; y += l; | |
261 } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l; | |
262 else if (op == BAM_CDEL) x += l; | |
263 } | |
264 for (i = 0; i < c->l_qseq; ++i) bq[i] = 64 + (qual[i] <= bq[i]? 0 : qual[i] - bq[i]); // finalize BQ | |
265 free(left); free(rght); | |
266 } | |
267 if (apply_baq) { | |
268 for (i = 0; i < c->l_qseq; ++i) qual[i] -= bq[i] - 64; // modify qual | |
269 bam_aux_append(b, "ZQ", 'Z', c->l_qseq + 1, bq); | |
270 } else bam_aux_append(b, "BQ", 'Z', c->l_qseq + 1, bq); | |
271 free(bq); free(s); free(r); free(q); free(state); | |
272 } | |
273 return 0; | |
274 } | |
275 | |
276 int bam_prob_realn(bam1_t *b, const char *ref) | |
277 { | |
278 return bam_prob_realn_core(b, ref, 1); | |
279 } | |
280 | |
281 int bam_fillmd(int argc, char *argv[]) | |
282 { | |
283 int c, is_equal, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed, max_nm, is_realn, capQ, baq_flag; | |
284 samfile_t *fp, *fpout = 0; | |
285 faidx_t *fai; | |
286 char *ref = 0, mode_w[8], mode_r[8]; | |
287 bam1_t *b; | |
288 | |
289 is_equal = is_bam_out = is_sam_in = is_uncompressed = is_realn = max_nm = capQ = baq_flag = 0; | |
290 mode_w[0] = mode_r[0] = 0; | |
291 strcpy(mode_r, "r"); strcpy(mode_w, "w"); | |
292 while ((c = getopt(argc, argv, "EreubSC:n:A")) >= 0) { | |
293 switch (c) { | |
294 case 'r': is_realn = 1; break; | |
295 case 'e': is_equal = 1; break; | |
296 case 'b': is_bam_out = 1; break; | |
297 case 'u': is_uncompressed = is_bam_out = 1; break; | |
298 case 'S': is_sam_in = 1; break; | |
299 case 'n': max_nm = atoi(optarg); break; | |
300 case 'C': capQ = atoi(optarg); break; | |
301 case 'A': baq_flag |= 1; break; | |
302 case 'E': baq_flag |= 2; break; | |
303 default: fprintf(stderr, "[bam_fillmd] unrecognized option '-%c'\n", c); return 1; | |
304 } | |
305 } | |
306 if (!is_sam_in) strcat(mode_r, "b"); | |
307 if (is_bam_out) strcat(mode_w, "b"); | |
308 else strcat(mode_w, "h"); | |
309 if (is_uncompressed) strcat(mode_w, "u"); | |
310 if (optind + 1 >= argc) { | |
311 fprintf(stderr, "\n"); | |
312 fprintf(stderr, "Usage: samtools fillmd [-eubrS] <aln.bam> <ref.fasta>\n\n"); | |
313 fprintf(stderr, "Options: -e change identical bases to '='\n"); | |
314 fprintf(stderr, " -u uncompressed BAM output (for piping)\n"); | |
315 fprintf(stderr, " -b compressed BAM output\n"); | |
316 fprintf(stderr, " -S the input is SAM with header\n"); | |
317 fprintf(stderr, " -A modify the quality string\n"); | |
318 fprintf(stderr, " -r compute the BQ tag (without -A) or cap baseQ by BAQ (with -A)\n"); | |
319 fprintf(stderr, " -E extended BAQ for better sensitivity but lower specificity\n\n"); | |
320 return 1; | |
321 } | |
322 fp = samopen(argv[optind], mode_r, 0); | |
323 if (fp == 0) return 1; | |
324 if (is_sam_in && (fp->header == 0 || fp->header->n_targets == 0)) { | |
325 fprintf(stderr, "[bam_fillmd] input SAM does not have header. Abort!\n"); | |
326 return 1; | |
327 } | |
328 fpout = samopen("-", mode_w, fp->header); | |
329 fai = fai_load(argv[optind+1]); | |
330 | |
331 b = bam_init1(); | |
332 while ((ret = samread(fp, b)) >= 0) { | |
333 if (b->core.tid >= 0) { | |
334 if (tid != b->core.tid) { | |
335 free(ref); | |
336 ref = fai_fetch(fai, fp->header->target_name[b->core.tid], &len); | |
337 tid = b->core.tid; | |
338 if (ref == 0) | |
339 fprintf(stderr, "[bam_fillmd] fail to find sequence '%s' in the reference.\n", | |
340 fp->header->target_name[tid]); | |
341 } | |
342 if (is_realn) bam_prob_realn_core(b, ref, baq_flag); | |
343 if (capQ > 10) { | |
344 int q = bam_cap_mapQ(b, ref, capQ); | |
345 if (b->core.qual > q) b->core.qual = q; | |
346 } | |
347 if (ref) bam_fillmd1_core(b, ref, is_equal, max_nm); | |
348 } | |
349 samwrite(fpout, b); | |
350 } | |
351 bam_destroy1(b); | |
352 | |
353 free(ref); | |
354 fai_destroy(fai); | |
355 samclose(fp); samclose(fpout); | |
356 return 0; | |
357 } |