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comparison PsiCLASS-1.0.2/samtools-0.1.19/bam_plcmd.c @ 0:903fc43d6227 draft default tip

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author lsong10
date Fri, 26 Mar 2021 16:52:45 +0000
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-1:000000000000 0:903fc43d6227
1 #include <math.h>
2 #include <stdio.h>
3 #include <unistd.h>
4 #include <ctype.h>
5 #include <string.h>
6 #include <errno.h>
7 #include <sys/stat.h>
8 #include <getopt.h>
9 #include "sam.h"
10 #include "faidx.h"
11 #include "kstring.h"
12 #include "sam_header.h"
13
14 static inline int printw(int c, FILE *fp)
15 {
16 char buf[16];
17 int l, x;
18 if (c == 0) return fputc('0', fp);
19 for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
20 if (c < 0) buf[l++] = '-';
21 buf[l] = 0;
22 for (x = 0; x < l/2; ++x) {
23 int y = buf[x]; buf[x] = buf[l-1-x]; buf[l-1-x] = y;
24 }
25 fputs(buf, fp);
26 return 0;
27 }
28
29 static inline void pileup_seq(const bam_pileup1_t *p, int pos, int ref_len, const char *ref)
30 {
31 int j;
32 if (p->is_head) {
33 putchar('^');
34 putchar(p->b->core.qual > 93? 126 : p->b->core.qual + 33);
35 }
36 if (!p->is_del) {
37 int c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
38 if (ref) {
39 int rb = pos < ref_len? ref[pos] : 'N';
40 if (c == '=' || bam_nt16_table[c] == bam_nt16_table[rb]) c = bam1_strand(p->b)? ',' : '.';
41 else c = bam1_strand(p->b)? tolower(c) : toupper(c);
42 } else {
43 if (c == '=') c = bam1_strand(p->b)? ',' : '.';
44 else c = bam1_strand(p->b)? tolower(c) : toupper(c);
45 }
46 putchar(c);
47 } else putchar(p->is_refskip? (bam1_strand(p->b)? '<' : '>') : '*');
48 if (p->indel > 0) {
49 putchar('+'); printw(p->indel, stdout);
50 for (j = 1; j <= p->indel; ++j) {
51 int c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + j)];
52 putchar(bam1_strand(p->b)? tolower(c) : toupper(c));
53 }
54 } else if (p->indel < 0) {
55 printw(p->indel, stdout);
56 for (j = 1; j <= -p->indel; ++j) {
57 int c = (ref && (int)pos+j < ref_len)? ref[pos+j] : 'N';
58 putchar(bam1_strand(p->b)? tolower(c) : toupper(c));
59 }
60 }
61 if (p->is_tail) putchar('$');
62 }
63
64 #include <assert.h>
65 #include "bam2bcf.h"
66 #include "sample.h"
67
68 #define MPLP_GLF 0x10
69 #define MPLP_NO_COMP 0x20
70 #define MPLP_NO_ORPHAN 0x40
71 #define MPLP_REALN 0x80
72 #define MPLP_NO_INDEL 0x400
73 #define MPLP_REDO_BAQ 0x800
74 #define MPLP_ILLUMINA13 0x1000
75 #define MPLP_IGNORE_RG 0x2000
76 #define MPLP_PRINT_POS 0x4000
77 #define MPLP_PRINT_MAPQ 0x8000
78 #define MPLP_PER_SAMPLE 0x10000
79
80 void *bed_read(const char *fn);
81 void bed_destroy(void *_h);
82 int bed_overlap(const void *_h, const char *chr, int beg, int end);
83
84 typedef struct {
85 int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth, fmt_flag;
86 int rflag_require, rflag_filter;
87 int openQ, extQ, tandemQ, min_support; // for indels
88 double min_frac; // for indels
89 char *reg, *pl_list, *fai_fname;
90 faidx_t *fai;
91 void *bed, *rghash;
92 } mplp_conf_t;
93
94 typedef struct {
95 bamFile fp;
96 bam_iter_t iter;
97 bam_header_t *h;
98 int ref_id;
99 char *ref;
100 const mplp_conf_t *conf;
101 } mplp_aux_t;
102
103 typedef struct {
104 int n;
105 int *n_plp, *m_plp;
106 bam_pileup1_t **plp;
107 } mplp_pileup_t;
108
109 static int mplp_func(void *data, bam1_t *b)
110 {
111 extern int bam_realn(bam1_t *b, const char *ref);
112 extern int bam_prob_realn_core(bam1_t *b, const char *ref, int);
113 extern int bam_cap_mapQ(bam1_t *b, char *ref, int thres);
114 mplp_aux_t *ma = (mplp_aux_t*)data;
115 int ret, skip = 0;
116 do {
117 int has_ref;
118 ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b);
119 if (ret < 0) break;
120 if (b->core.tid < 0 || (b->core.flag&BAM_FUNMAP)) { // exclude unmapped reads
121 skip = 1;
122 continue;
123 }
124 if (ma->conf->rflag_require && !(ma->conf->rflag_require&b->core.flag)) { skip = 1; continue; }
125 if (ma->conf->rflag_filter && ma->conf->rflag_filter&b->core.flag) { skip = 1; continue; }
126 if (ma->conf->bed) { // test overlap
127 skip = !bed_overlap(ma->conf->bed, ma->h->target_name[b->core.tid], b->core.pos, bam_calend(&b->core, bam1_cigar(b)));
128 if (skip) continue;
129 }
130 if (ma->conf->rghash) { // exclude read groups
131 uint8_t *rg = bam_aux_get(b, "RG");
132 skip = (rg && bcf_str2id(ma->conf->rghash, (const char*)(rg+1)) >= 0);
133 if (skip) continue;
134 }
135 if (ma->conf->flag & MPLP_ILLUMINA13) {
136 int i;
137 uint8_t *qual = bam1_qual(b);
138 for (i = 0; i < b->core.l_qseq; ++i)
139 qual[i] = qual[i] > 31? qual[i] - 31 : 0;
140 }
141 has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0;
142 skip = 0;
143 if (has_ref && (ma->conf->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, (ma->conf->flag & MPLP_REDO_BAQ)? 7 : 3);
144 if (has_ref && ma->conf->capQ_thres > 10) {
145 int q = bam_cap_mapQ(b, ma->ref, ma->conf->capQ_thres);
146 if (q < 0) skip = 1;
147 else if (b->core.qual > q) b->core.qual = q;
148 }
149 else if (b->core.qual < ma->conf->min_mq) skip = 1;
150 else if ((ma->conf->flag&MPLP_NO_ORPHAN) && (b->core.flag&1) && !(b->core.flag&2)) skip = 1;
151 } while (skip);
152 return ret;
153 }
154
155 static void group_smpl(mplp_pileup_t *m, bam_sample_t *sm, kstring_t *buf,
156 int n, char *const*fn, int *n_plp, const bam_pileup1_t **plp, int ignore_rg)
157 {
158 int i, j;
159 memset(m->n_plp, 0, m->n * sizeof(int));
160 for (i = 0; i < n; ++i) {
161 for (j = 0; j < n_plp[i]; ++j) {
162 const bam_pileup1_t *p = plp[i] + j;
163 uint8_t *q;
164 int id = -1;
165 q = ignore_rg? 0 : bam_aux_get(p->b, "RG");
166 if (q) id = bam_smpl_rg2smid(sm, fn[i], (char*)q+1, buf);
167 if (id < 0) id = bam_smpl_rg2smid(sm, fn[i], 0, buf);
168 if (id < 0 || id >= m->n) {
169 assert(q); // otherwise a bug
170 fprintf(stderr, "[%s] Read group %s used in file %s but absent from the header or an alignment missing read group.\n", __func__, (char*)q+1, fn[i]);
171 exit(1);
172 }
173 if (m->n_plp[id] == m->m_plp[id]) {
174 m->m_plp[id] = m->m_plp[id]? m->m_plp[id]<<1 : 8;
175 m->plp[id] = realloc(m->plp[id], sizeof(bam_pileup1_t) * m->m_plp[id]);
176 }
177 m->plp[id][m->n_plp[id]++] = *p;
178 }
179 }
180 }
181
182 static int mpileup(mplp_conf_t *conf, int n, char **fn)
183 {
184 extern void *bcf_call_add_rg(void *rghash, const char *hdtext, const char *list);
185 extern void bcf_call_del_rghash(void *rghash);
186 mplp_aux_t **data;
187 int i, tid, pos, *n_plp, tid0 = -1, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid = -1, max_depth, max_indel_depth;
188 const bam_pileup1_t **plp;
189 bam_mplp_t iter;
190 bam_header_t *h = 0;
191 char *ref;
192 void *rghash = 0;
193
194 bcf_callaux_t *bca = 0;
195 bcf_callret1_t *bcr = 0;
196 bcf_call_t bc;
197 bcf_t *bp = 0;
198 bcf_hdr_t *bh = 0;
199
200 bam_sample_t *sm = 0;
201 kstring_t buf;
202 mplp_pileup_t gplp;
203
204 memset(&gplp, 0, sizeof(mplp_pileup_t));
205 memset(&buf, 0, sizeof(kstring_t));
206 memset(&bc, 0, sizeof(bcf_call_t));
207 data = calloc(n, sizeof(void*));
208 plp = calloc(n, sizeof(void*));
209 n_plp = calloc(n, sizeof(int*));
210 sm = bam_smpl_init();
211
212 // read the header and initialize data
213 for (i = 0; i < n; ++i) {
214 bam_header_t *h_tmp;
215 data[i] = calloc(1, sizeof(mplp_aux_t));
216 data[i]->fp = strcmp(fn[i], "-") == 0? bam_dopen(fileno(stdin), "r") : bam_open(fn[i], "r");
217 if ( !data[i]->fp )
218 {
219 fprintf(stderr, "[%s] failed to open %s: %s\n", __func__, fn[i], strerror(errno));
220 exit(1);
221 }
222 data[i]->conf = conf;
223 h_tmp = bam_header_read(data[i]->fp);
224 if ( !h_tmp ) {
225 fprintf(stderr,"[%s] fail to read the header of %s\n", __func__, fn[i]);
226 exit(1);
227 }
228 data[i]->h = i? h : h_tmp; // for i==0, "h" has not been set yet
229 bam_smpl_add(sm, fn[i], (conf->flag&MPLP_IGNORE_RG)? 0 : h_tmp->text);
230 rghash = bcf_call_add_rg(rghash, h_tmp->text, conf->pl_list);
231 if (conf->reg) {
232 int beg, end;
233 bam_index_t *idx;
234 idx = bam_index_load(fn[i]);
235 if (idx == 0) {
236 fprintf(stderr, "[%s] fail to load index for %s\n", __func__, fn[i]);
237 exit(1);
238 }
239 if (bam_parse_region(h_tmp, conf->reg, &tid, &beg, &end) < 0) {
240 fprintf(stderr, "[%s] malformatted region or wrong seqname for %s\n", __func__, fn[i]);
241 exit(1);
242 }
243 if (i == 0) tid0 = tid, beg0 = beg, end0 = end;
244 data[i]->iter = bam_iter_query(idx, tid, beg, end);
245 bam_index_destroy(idx);
246 }
247 if (i == 0) h = h_tmp;
248 else {
249 // FIXME: to check consistency
250 bam_header_destroy(h_tmp);
251 }
252 }
253 gplp.n = sm->n;
254 gplp.n_plp = calloc(sm->n, sizeof(int));
255 gplp.m_plp = calloc(sm->n, sizeof(int));
256 gplp.plp = calloc(sm->n, sizeof(void*));
257
258 fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, sm->n, n);
259 // write the VCF header
260 if (conf->flag & MPLP_GLF) {
261 kstring_t s;
262 bh = calloc(1, sizeof(bcf_hdr_t));
263 s.l = s.m = 0; s.s = 0;
264 bp = bcf_open("-", (conf->flag&MPLP_NO_COMP)? "wu" : "w");
265 for (i = 0; i < h->n_targets; ++i) {
266 kputs(h->target_name[i], &s);
267 kputc('\0', &s);
268 }
269 bh->l_nm = s.l;
270 bh->name = malloc(s.l);
271 memcpy(bh->name, s.s, s.l);
272 s.l = 0;
273 for (i = 0; i < sm->n; ++i) {
274 kputs(sm->smpl[i], &s); kputc('\0', &s);
275 }
276 bh->l_smpl = s.l;
277 bh->sname = malloc(s.l);
278 memcpy(bh->sname, s.s, s.l);
279 s.l = 0;
280 ksprintf(&s, "##samtoolsVersion=%s\n", BAM_VERSION);
281 if (conf->fai_fname) ksprintf(&s, "##reference=file://%s\n", conf->fai_fname);
282 h->dict = sam_header_parse2(h->text);
283 int nseq;
284 const char *tags[] = {"SN","LN","UR","M5",NULL};
285 char **tbl = sam_header2tbl_n(h->dict, "SQ", tags, &nseq);
286 for (i=0; i<nseq; i++)
287 {
288 ksprintf(&s, "##contig=<ID=%s", tbl[4*i]);
289 if ( tbl[4*i+1] ) ksprintf(&s, ",length=%s", tbl[4*i+1]);
290 if ( tbl[4*i+2] ) ksprintf(&s, ",URL=%s", tbl[4*i+2]);
291 if ( tbl[4*i+3] ) ksprintf(&s, ",md5=%s", tbl[4*i+3]);
292 kputs(">\n", &s);
293 }
294 if (tbl) free(tbl);
295 bh->txt = s.s;
296 bh->l_txt = 1 + s.l;
297 bcf_hdr_sync(bh);
298 bcf_hdr_write(bp, bh);
299 bca = bcf_call_init(-1., conf->min_baseQ);
300 bcr = calloc(sm->n, sizeof(bcf_callret1_t));
301 bca->rghash = rghash;
302 bca->openQ = conf->openQ, bca->extQ = conf->extQ, bca->tandemQ = conf->tandemQ;
303 bca->min_frac = conf->min_frac;
304 bca->min_support = conf->min_support;
305 bca->per_sample_flt = conf->flag & MPLP_PER_SAMPLE;
306 }
307 if (tid0 >= 0 && conf->fai) { // region is set
308 ref = faidx_fetch_seq(conf->fai, h->target_name[tid0], 0, 0x7fffffff, &ref_len);
309 ref_tid = tid0;
310 for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid0;
311 } else ref_tid = -1, ref = 0;
312 iter = bam_mplp_init(n, mplp_func, (void**)data);
313 max_depth = conf->max_depth;
314 if (max_depth * sm->n > 1<<20)
315 fprintf(stderr, "(%s) Max depth is above 1M. Potential memory hog!\n", __func__);
316 if (max_depth * sm->n < 8000) {
317 max_depth = 8000 / sm->n;
318 fprintf(stderr, "<%s> Set max per-file depth to %d\n", __func__, max_depth);
319 }
320 max_indel_depth = conf->max_indel_depth * sm->n;
321 bam_mplp_set_maxcnt(iter, max_depth);
322 while (bam_mplp_auto(iter, &tid, &pos, n_plp, plp) > 0) {
323 if (conf->reg && (pos < beg0 || pos >= end0)) continue; // out of the region requested
324 if (conf->bed && tid >= 0 && !bed_overlap(conf->bed, h->target_name[tid], pos, pos+1)) continue;
325 if (tid != ref_tid) {
326 free(ref); ref = 0;
327 if (conf->fai) ref = faidx_fetch_seq(conf->fai, h->target_name[tid], 0, 0x7fffffff, &ref_len);
328 for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid;
329 ref_tid = tid;
330 }
331 if (conf->flag & MPLP_GLF) {
332 int total_depth, _ref0, ref16;
333 bcf1_t *b = calloc(1, sizeof(bcf1_t));
334 for (i = total_depth = 0; i < n; ++i) total_depth += n_plp[i];
335 group_smpl(&gplp, sm, &buf, n, fn, n_plp, plp, conf->flag & MPLP_IGNORE_RG);
336 _ref0 = (ref && pos < ref_len)? ref[pos] : 'N';
337 ref16 = bam_nt16_table[_ref0];
338 for (i = 0; i < gplp.n; ++i)
339 bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i);
340 bcf_call_combine(gplp.n, bcr, bca, ref16, &bc);
341 bcf_call2bcf(tid, pos, &bc, b, bcr, conf->fmt_flag, 0, 0);
342 bcf_write(bp, bh, b);
343 bcf_destroy(b);
344 // call indels
345 if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, rghash) >= 0) {
346 for (i = 0; i < gplp.n; ++i)
347 bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i);
348 if (bcf_call_combine(gplp.n, bcr, bca, -1, &bc) >= 0) {
349 b = calloc(1, sizeof(bcf1_t));
350 bcf_call2bcf(tid, pos, &bc, b, bcr, conf->fmt_flag, bca, ref);
351 bcf_write(bp, bh, b);
352 bcf_destroy(b);
353 }
354 }
355 } else {
356 printf("%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');
357 for (i = 0; i < n; ++i) {
358 int j, cnt;
359 for (j = cnt = 0; j < n_plp[i]; ++j) {
360 const bam_pileup1_t *p = plp[i] + j;
361 if (bam1_qual(p->b)[p->qpos] >= conf->min_baseQ) ++cnt;
362 }
363 printf("\t%d\t", cnt);
364 if (n_plp[i] == 0) {
365 printf("*\t*"); // FIXME: printf() is very slow...
366 if (conf->flag & MPLP_PRINT_POS) printf("\t*");
367 } else {
368 for (j = 0; j < n_plp[i]; ++j) {
369 const bam_pileup1_t *p = plp[i] + j;
370 if (bam1_qual(p->b)[p->qpos] >= conf->min_baseQ)
371 pileup_seq(plp[i] + j, pos, ref_len, ref);
372 }
373 putchar('\t');
374 for (j = 0; j < n_plp[i]; ++j) {
375 const bam_pileup1_t *p = plp[i] + j;
376 int c = bam1_qual(p->b)[p->qpos];
377 if (c >= conf->min_baseQ) {
378 c = c + 33 < 126? c + 33 : 126;
379 putchar(c);
380 }
381 }
382 if (conf->flag & MPLP_PRINT_MAPQ) {
383 putchar('\t');
384 for (j = 0; j < n_plp[i]; ++j) {
385 int c = plp[i][j].b->core.qual + 33;
386 if (c > 126) c = 126;
387 putchar(c);
388 }
389 }
390 if (conf->flag & MPLP_PRINT_POS) {
391 putchar('\t');
392 for (j = 0; j < n_plp[i]; ++j) {
393 if (j > 0) putchar(',');
394 printf("%d", plp[i][j].qpos + 1); // FIXME: printf() is very slow...
395 }
396 }
397 }
398 }
399 putchar('\n');
400 }
401 }
402
403 bcf_close(bp);
404 bam_smpl_destroy(sm); free(buf.s);
405 for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]);
406 free(gplp.plp); free(gplp.n_plp); free(gplp.m_plp);
407 bcf_call_del_rghash(rghash);
408 bcf_hdr_destroy(bh); bcf_call_destroy(bca); free(bc.PL); free(bcr);
409 bam_mplp_destroy(iter);
410 bam_header_destroy(h);
411 for (i = 0; i < n; ++i) {
412 bam_close(data[i]->fp);
413 if (data[i]->iter) bam_iter_destroy(data[i]->iter);
414 free(data[i]);
415 }
416 free(data); free(plp); free(ref); free(n_plp);
417 return 0;
418 }
419
420 #define MAX_PATH_LEN 1024
421 int read_file_list(const char *file_list,int *n,char **argv[])
422 {
423 char buf[MAX_PATH_LEN];
424 int len, nfiles = 0;
425 char **files = NULL;
426 struct stat sb;
427
428 *n = 0;
429 *argv = NULL;
430
431 FILE *fh = fopen(file_list,"r");
432 if ( !fh )
433 {
434 fprintf(stderr,"%s: %s\n", file_list,strerror(errno));
435 return 1;
436 }
437
438 files = calloc(nfiles,sizeof(char*));
439 nfiles = 0;
440 while ( fgets(buf,MAX_PATH_LEN,fh) )
441 {
442 // allow empty lines and trailing spaces
443 len = strlen(buf);
444 while ( len>0 && isspace(buf[len-1]) ) len--;
445 if ( !len ) continue;
446
447 // check sanity of the file list
448 buf[len] = 0;
449 if (stat(buf, &sb) != 0)
450 {
451 // no such file, check if it is safe to print its name
452 int i, safe_to_print = 1;
453 for (i=0; i<len; i++)
454 if (!isprint(buf[i])) { safe_to_print = 0; break; }
455 if ( safe_to_print )
456 fprintf(stderr,"The file list \"%s\" appears broken, could not locate: %s\n", file_list,buf);
457 else
458 fprintf(stderr,"Does the file \"%s\" really contain a list of files and do all exist?\n", file_list);
459 return 1;
460 }
461
462 nfiles++;
463 files = realloc(files,nfiles*sizeof(char*));
464 files[nfiles-1] = strdup(buf);
465 }
466 fclose(fh);
467 if ( !nfiles )
468 {
469 fprintf(stderr,"No files read from %s\n", file_list);
470 return 1;
471 }
472 *argv = files;
473 *n = nfiles;
474 return 0;
475 }
476 #undef MAX_PATH_LEN
477
478 int bam_mpileup(int argc, char *argv[])
479 {
480 int c;
481 const char *file_list = NULL;
482 char **fn = NULL;
483 int nfiles = 0, use_orphan = 0;
484 mplp_conf_t mplp;
485 memset(&mplp, 0, sizeof(mplp_conf_t));
486 mplp.max_mq = 60;
487 mplp.min_baseQ = 13;
488 mplp.capQ_thres = 0;
489 mplp.max_depth = 250; mplp.max_indel_depth = 250;
490 mplp.openQ = 40; mplp.extQ = 20; mplp.tandemQ = 100;
491 mplp.min_frac = 0.002; mplp.min_support = 1;
492 mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN;
493 static struct option lopts[] =
494 {
495 {"rf",1,0,1}, // require flag
496 {"ff",1,0,2}, // filter flag
497 {0,0,0,0}
498 };
499 while ((c = getopt_long(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:L:b:P:po:e:h:Im:F:EG:6OsV1:2:",lopts,NULL)) >= 0) {
500 switch (c) {
501 case 1 : mplp.rflag_require = strtol(optarg,0,0); break;
502 case 2 : mplp.rflag_filter = strtol(optarg,0,0); break;
503 case 'f':
504 mplp.fai = fai_load(optarg);
505 if (mplp.fai == 0) return 1;
506 mplp.fai_fname = optarg;
507 break;
508 case 'd': mplp.max_depth = atoi(optarg); break;
509 case 'r': mplp.reg = strdup(optarg); break;
510 case 'l': mplp.bed = bed_read(optarg); break;
511 case 'P': mplp.pl_list = strdup(optarg); break;
512 case 'p': mplp.flag |= MPLP_PER_SAMPLE; break;
513 case 'g': mplp.flag |= MPLP_GLF; break;
514 case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_GLF; break;
515 case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN; break;
516 case 'B': mplp.flag &= ~MPLP_REALN; break;
517 case 'D': mplp.fmt_flag |= B2B_FMT_DP; break;
518 case 'S': mplp.fmt_flag |= B2B_FMT_SP; break;
519 case 'V': mplp.fmt_flag |= B2B_FMT_DV; break;
520 case 'I': mplp.flag |= MPLP_NO_INDEL; break;
521 case 'E': mplp.flag |= MPLP_REDO_BAQ; break;
522 case '6': mplp.flag |= MPLP_ILLUMINA13; break;
523 case 'R': mplp.flag |= MPLP_IGNORE_RG; break;
524 case 's': mplp.flag |= MPLP_PRINT_MAPQ; break;
525 case 'O': mplp.flag |= MPLP_PRINT_POS; break;
526 case 'C': mplp.capQ_thres = atoi(optarg); break;
527 case 'M': mplp.max_mq = atoi(optarg); break;
528 case 'q': mplp.min_mq = atoi(optarg); break;
529 case 'Q': mplp.min_baseQ = atoi(optarg); break;
530 case 'b': file_list = optarg; break;
531 case 'o': mplp.openQ = atoi(optarg); break;
532 case 'e': mplp.extQ = atoi(optarg); break;
533 case 'h': mplp.tandemQ = atoi(optarg); break;
534 case 'A': use_orphan = 1; break;
535 case 'F': mplp.min_frac = atof(optarg); break;
536 case 'm': mplp.min_support = atoi(optarg); break;
537 case 'L': mplp.max_indel_depth = atoi(optarg); break;
538 case 'G': {
539 FILE *fp_rg;
540 char buf[1024];
541 mplp.rghash = bcf_str2id_init();
542 if ((fp_rg = fopen(optarg, "r")) == 0)
543 fprintf(stderr, "(%s) Fail to open file %s. Continue anyway.\n", __func__, optarg);
544 while (!feof(fp_rg) && fscanf(fp_rg, "%s", buf) > 0) // this is not a good style, but forgive me...
545 bcf_str2id_add(mplp.rghash, strdup(buf));
546 fclose(fp_rg);
547 }
548 break;
549 }
550 }
551 if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN;
552 if (argc == 1) {
553 fprintf(stderr, "\n");
554 fprintf(stderr, "Usage: samtools mpileup [options] in1.bam [in2.bam [...]]\n\n");
555 fprintf(stderr, "Input options:\n\n");
556 fprintf(stderr, " -6 assume the quality is in the Illumina-1.3+ encoding\n");
557 fprintf(stderr, " -A count anomalous read pairs\n");
558 fprintf(stderr, " -B disable BAQ computation\n");
559 fprintf(stderr, " -b FILE list of input BAM filenames, one per line [null]\n");
560 fprintf(stderr, " -C INT parameter for adjusting mapQ; 0 to disable [0]\n");
561 fprintf(stderr, " -d INT max per-BAM depth to avoid excessive memory usage [%d]\n", mplp.max_depth);
562 fprintf(stderr, " -E recalculate extended BAQ on the fly thus ignoring existing BQs\n");
563 fprintf(stderr, " -f FILE faidx indexed reference sequence file [null]\n");
564 fprintf(stderr, " -G FILE exclude read groups listed in FILE [null]\n");
565 fprintf(stderr, " -l FILE list of positions (chr pos) or regions (BED) [null]\n");
566 fprintf(stderr, " -M INT cap mapping quality at INT [%d]\n", mplp.max_mq);
567 fprintf(stderr, " -r STR region in which pileup is generated [null]\n");
568 fprintf(stderr, " -R ignore RG tags\n");
569 fprintf(stderr, " -q INT skip alignments with mapQ smaller than INT [%d]\n", mplp.min_mq);
570 fprintf(stderr, " -Q INT skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp.min_baseQ);
571 fprintf(stderr, " --rf INT required flags: skip reads with mask bits unset []\n");
572 fprintf(stderr, " --ff INT filter flags: skip reads with mask bits set []\n");
573 fprintf(stderr, "\nOutput options:\n\n");
574 fprintf(stderr, " -D output per-sample DP in BCF (require -g/-u)\n");
575 fprintf(stderr, " -g generate BCF output (genotype likelihoods)\n");
576 fprintf(stderr, " -O output base positions on reads (disabled by -g/-u)\n");
577 fprintf(stderr, " -s output mapping quality (disabled by -g/-u)\n");
578 fprintf(stderr, " -S output per-sample strand bias P-value in BCF (require -g/-u)\n");
579 fprintf(stderr, " -u generate uncompress BCF output\n");
580 fprintf(stderr, "\nSNP/INDEL genotype likelihoods options (effective with `-g' or `-u'):\n\n");
581 fprintf(stderr, " -e INT Phred-scaled gap extension seq error probability [%d]\n", mplp.extQ);
582 fprintf(stderr, " -F FLOAT minimum fraction of gapped reads for candidates [%g]\n", mplp.min_frac);
583 fprintf(stderr, " -h INT coefficient for homopolymer errors [%d]\n", mplp.tandemQ);
584 fprintf(stderr, " -I do not perform indel calling\n");
585 fprintf(stderr, " -L INT max per-sample depth for INDEL calling [%d]\n", mplp.max_indel_depth);
586 fprintf(stderr, " -m INT minimum gapped reads for indel candidates [%d]\n", mplp.min_support);
587 fprintf(stderr, " -o INT Phred-scaled gap open sequencing error probability [%d]\n", mplp.openQ);
588 fprintf(stderr, " -p apply -m and -F per-sample to increase sensitivity\n");
589 fprintf(stderr, " -P STR comma separated list of platforms for indels [all]\n");
590 fprintf(stderr, "\n");
591 fprintf(stderr, "Notes: Assuming diploid individuals.\n\n");
592 return 1;
593 }
594 bam_no_B = 1;
595 if (file_list) {
596 if ( read_file_list(file_list,&nfiles,&fn) ) return 1;
597 mpileup(&mplp,nfiles,fn);
598 for (c=0; c<nfiles; c++) free(fn[c]);
599 free(fn);
600 } else mpileup(&mplp, argc - optind, argv + optind);
601 if (mplp.rghash) bcf_str2id_thorough_destroy(mplp.rghash);
602 free(mplp.reg); free(mplp.pl_list);
603 if (mplp.fai) fai_destroy(mplp.fai);
604 if (mplp.bed) bed_destroy(mplp.bed);
605 return 0;
606 }