forked from samtools/samtools
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathbam_tview.c
443 lines (406 loc) · 15.9 KB
/
bam_tview.c
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
/* bam_tview.c -- tview subcommand.
Copyright (C) 2008-2014 Genome Research Ltd.
Portions copyright (C) 2013 Pierre Lindenbaum, Institut du Thorax, INSERM U1087, Université de Nantes.
Author: Heng Li <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notices and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */
#include <regex.h>
#include <assert.h>
#include "bam_tview.h"
#include <htslib/faidx.h>
#include <htslib/sam.h>
#include <htslib/bgzf.h>
/*! @typedef
@abstract Type of function to be called by sam_fetch().
@param b the alignment
@param data user provided data
*/
typedef int (*sam_fetch_f)(const bam1_t *b, void *data);
int sam_fetch(samFile *fp, const hts_idx_t *idx, int tid, int beg, int end, void *data, sam_fetch_f func)
{
int ret;
hts_itr_t* iter;
bam1_t* b = bam_init1();
iter = sam_itr_queryi(idx, tid, beg, end);
while ((ret = sam_itr_next(fp, iter, b)) >= 0) func(b, data);
hts_itr_destroy(iter);
bam_destroy1(b);
return (ret == -1)? 0 : ret;
}
khash_t(kh_rg)* get_rg_sample(const char* header, const char* sample)
{
khash_t(kh_rg)* rg_hash = kh_init(kh_rg);
// given sample id return all the RD ID's
const char rg_regex[] = "^@RG.*\tID:([!-)+-<>-~][ !-~]*)(\t.*$|$)";
regex_t rg_id;
regmatch_t* matches = (regmatch_t*)calloc(2, sizeof(regmatch_t));
if (matches == NULL) { perror("out of memory"); exit(-1); }
regcomp(&rg_id, rg_regex, REG_EXTENDED|REG_NEWLINE);
char* text = strdup(header);
char* end = text + strlen(header);
char* tofree = text;
while (end > text && regexec(&rg_id, text, 2, matches, 0) == 0) { // foreach rg id in header
int ret;
text[matches[1].rm_eo] = '\0';
kh_put(kh_rg, rg_hash, strdup(text+matches[1].rm_so), &ret); // Add the RG to the list
text += matches[0].rm_eo + 1; // Move search pointer forward
}
free(tofree);
return rg_hash;
}
int base_tv_init(tview_t* tv, const char *fn, const char *fn_fa, const char *samples)
{
assert(tv!=NULL);
assert(fn!=NULL);
tv->mrow = 24; tv->mcol = 80;
tv->color_for = TV_COLOR_MAPQ;
tv->is_dot = 1;
tv->fp = sam_open(fn, "r");
if(tv->fp == NULL)
{
fprintf(stderr,"sam_open %s. %s\n", fn,fn_fa);
exit(EXIT_FAILURE);
}
// TODO bgzf_set_cache_size(tv->fp->fp.bgzf, 8 * 1024 *1024);
assert(tv->fp);
tv->header = sam_hdr_read(tv->fp);
if(tv->header == NULL)
{
fprintf(stderr,"Cannot read '%s'.\n", fn);
exit(EXIT_FAILURE);
}
tv->idx = sam_index_load(tv->fp, fn);
if (tv->idx == NULL)
{
fprintf(stderr,"Cannot read index for '%s'.\n", fn);
exit(EXIT_FAILURE);
}
tv->lplbuf = bam_lplbuf_init(tv_pl_func, tv);
if (fn_fa) tv->fai = fai_load(fn_fa);
tv->bca = bcf_call_init(0.83, 13);
tv->ins = 1;
// If the user has asked for specific samples find out create a list of readgroups make up these samples
if ( samples )
{
tv->rg_hash = get_rg_sample(tv->header->text, samples); // Init the list of rg's
}
return 0;
}
void base_tv_destroy(tview_t* tv)
{
bam_lplbuf_destroy(tv->lplbuf);
bcf_call_destroy(tv->bca);
hts_idx_destroy(tv->idx);
if (tv->fai) fai_destroy(tv->fai);
free(tv->ref);
bam_hdr_destroy(tv->header);
sam_close(tv->fp);
}
int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
{
extern const char bam_nt16_nt4_table[];
tview_t *tv = (tview_t*)data;
int i, j, c, rb, attr, max_ins = 0;
uint32_t call = 0;
if (pos < tv->left_pos || tv->ccol > tv->mcol) return 0; // out of screen
// print reference
rb = (tv->ref && pos - tv->left_pos < tv->l_ref)? tv->ref[pos - tv->left_pos] : 'N';
for (i = tv->last_pos + 1; i < pos; ++i) {
if (i%10 == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,0, tv->ccol, "%-d", i+1);
c = tv->ref? tv->ref[i - tv->left_pos] : 'N';
tv->my_mvaddch(tv,1, tv->ccol++, c);
}
if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,0, tv->ccol, "%-d", pos+1);
{ // call consensus
bcf_callret1_t bcr;
memset(&bcr, 0, sizeof bcr);
int qsum[4], a1, a2, tmp;
double p[3], prior = 30;
bcf_call_glfgen(n, pl, seq_nt16_table[rb], tv->bca, &bcr);
for (i = 0; i < 4; ++i) qsum[i] = ((int)bcr.qsum[i])<<2 | i;
for (i = 1; i < 4; ++i) // insertion sort
for (j = i; j > 0 && qsum[j] > qsum[j-1]; --j)
tmp = qsum[j], qsum[j] = qsum[j-1], qsum[j-1] = tmp;
a1 = qsum[0]&3; a2 = qsum[1]&3;
p[0] = bcr.p[a1*5+a1]; p[1] = bcr.p[a1*5+a2] + prior; p[2] = bcr.p[a2*5+a2];
if ("ACGT"[a1] != toupper(rb)) p[0] += prior + 3;
if ("ACGT"[a2] != toupper(rb)) p[2] += prior + 3;
if (p[0] < p[1] && p[0] < p[2]) call = (1<<a1)<<16 | (int)((p[1]<p[2]?p[1]:p[2]) - p[0] + .499);
else if (p[2] < p[1] && p[2] < p[0]) call = (1<<a2)<<16 | (int)((p[0]<p[1]?p[0]:p[1]) - p[2] + .499);
else call = (1<<a1|1<<a2)<<16 | (int)((p[0]<p[2]?p[0]:p[2]) - p[1] + .499);
}
attr = tv->my_underline(tv);
c = ",ACMGRSVTWYHKDBN"[call>>16&0xf];
i = (call&0xffff)/10+1;
if (i > 4) i = 4;
attr |= tv->my_colorpair(tv,i);
if (c == toupper(rb)) c = '.';
tv->my_attron(tv,attr);
tv->my_mvaddch(tv,2, tv->ccol, c);
tv->my_attroff(tv,attr);
if(tv->ins) {
// calculate maximum insert
for (i = 0; i < n; ++i) {
const bam_pileup1_t *p = pl + i;
if (p->indel > 0 && max_ins < p->indel) max_ins = p->indel;
}
}
// core loop
for (j = 0; j <= max_ins; ++j) {
for (i = 0; i < n; ++i) {
const bam_pileup1_t *p = pl + i;
int row = TV_MIN_ALNROW + p->level - tv->row_shift;
if (j == 0) {
if (!p->is_del) {
if (tv->base_for == TV_BASE_COLOR_SPACE &&
(c = bam_aux_getCSi(p->b, p->qpos))) {
// assume that if we found one color, we will be able to get the color error
if (tv->is_dot && '-' == bam_aux_getCEi(p->b, p->qpos)) c = bam_is_rev(p->b)? ',' : '.';
} else {
if (tv->show_name) {
char *name = bam_get_qname(p->b);
c = (p->qpos + 1 >= p->b->core.l_qname)? ' ' : name[p->qpos];
} else {
c = seq_nt16_str[bam_seqi(bam_get_seq(p->b), p->qpos)];
if (tv->is_dot && toupper(c) == toupper(rb)) c = bam_is_rev(p->b)? ',' : '.';
}
}
} else c = p->is_refskip? (bam_is_rev(p->b)? '<' : '>') : '*';
} else { // padding
if (j > p->indel) c = '*';
else { // insertion
if (tv->base_for == TV_BASE_NUCL) {
if (tv->show_name) {
char *name = bam_get_qname(p->b);
c = (p->qpos + j + 1 >= p->b->core.l_qname)? ' ' : name[p->qpos + j];
} else {
c = seq_nt16_str[bam_seqi(bam_get_seq(p->b), p->qpos + j)];
if (j == 0 && tv->is_dot && toupper(c) == toupper(rb)) c = bam_is_rev(p->b)? ',' : '.';
}
} else {
c = bam_aux_getCSi(p->b, p->qpos + j);
if (tv->is_dot && '-' == bam_aux_getCEi(p->b, p->qpos + j)) c = bam_is_rev(p->b)? ',' : '.';
}
}
}
if (row > TV_MIN_ALNROW && row < tv->mrow) {
int x;
attr = 0;
if (((p->b->core.flag&BAM_FPAIRED) && !(p->b->core.flag&BAM_FPROPER_PAIR))
|| (p->b->core.flag & BAM_FSECONDARY)) attr |= tv->my_underline(tv);
if (tv->color_for == TV_COLOR_BASEQ) {
x = bam_get_qual(p->b)[p->qpos]/10 + 1;
if (x > 4) x = 4;
attr |= tv->my_colorpair(tv,x);
} else if (tv->color_for == TV_COLOR_MAPQ) {
x = p->b->core.qual/10 + 1;
if (x > 4) x = 4;
attr |= tv->my_colorpair(tv,x);
} else if (tv->color_for == TV_COLOR_NUCL) {
x = bam_nt16_nt4_table[bam_seqi(bam_get_seq(p->b), p->qpos)] + 5;
attr |= tv->my_colorpair(tv,x);
} else if(tv->color_for == TV_COLOR_COL) {
x = 0;
switch(bam_aux_getCSi(p->b, p->qpos)) {
case '0': x = 0; break;
case '1': x = 1; break;
case '2': x = 2; break;
case '3': x = 3; break;
case '4': x = 4; break;
default: x = bam_nt16_nt4_table[bam_seqi(bam_get_seq(p->b), p->qpos)]; break;
}
x+=5;
attr |= tv->my_colorpair(tv,x);
} else if(tv->color_for == TV_COLOR_COLQ) {
x = bam_aux_getCQi(p->b, p->qpos);
if(0 == x) x = bam_get_qual(p->b)[p->qpos];
x = x/10 + 1;
if (x > 4) x = 4;
attr |= tv->my_colorpair(tv,x);
}
tv->my_attron(tv,attr);
tv->my_mvaddch(tv,row, tv->ccol, bam_is_rev(p->b)? tolower(c) : toupper(c));
tv->my_attroff(tv,attr);
}
}
c = j? '*' : rb;
if (c == '*') {
attr = tv->my_colorpair(tv,8);
tv->my_attron(tv,attr);
tv->my_mvaddch(tv,1, tv->ccol++, c);
tv->my_attroff(tv,attr);
} else tv->my_mvaddch(tv,1, tv->ccol++, c);
}
tv->last_pos = pos;
return 0;
}
int tv_fetch_func(const bam1_t *b, void *data)
{
tview_t *tv = (tview_t*)data;
/* If we are restricted to specific readgroups check RG is in the list */
if ( tv->rg_hash )
{
const uint8_t *rg = bam_aux_get(b, "RG");
if ( !rg ) return 0; // If we don't have an RG tag exclude read
khiter_t k = kh_get(kh_rg, tv->rg_hash, (const char*)(rg + 1));
if ( k == kh_end(tv->rg_hash) ) return 0; // if RG tag is not in list of allowed tags exclude read
}
if (tv->no_skip) {
uint32_t *cigar = bam_get_cigar(b); // this is cheating...
int i;
for (i = 0; i <b->core.n_cigar; ++i) {
if ((cigar[i]&0xf) == BAM_CREF_SKIP)
cigar[i] = cigar[i]>>4<<4 | BAM_CDEL;
}
}
bam_lplbuf_push(b, tv->lplbuf);
return 0;
}
int base_draw_aln(tview_t *tv, int tid, int pos)
{
assert(tv!=NULL);
// reset
tv->my_clear(tv);
tv->curr_tid = tid; tv->left_pos = pos;
tv->last_pos = tv->left_pos - 1;
tv->ccol = 0;
// print ref and consensus
if (tv->fai) {
char *str;
if (tv->ref) free(tv->ref);
assert(tv->curr_tid>=0);
str = (char*)calloc(strlen(tv->header->target_name[tv->curr_tid]) + 30, 1);
assert(str!=NULL);
sprintf(str, "%s:%d-%d", tv->header->target_name[tv->curr_tid], tv->left_pos + 1, tv->left_pos + tv->mcol);
tv->ref = fai_fetch(tv->fai, str, &tv->l_ref);
free(str);
if ( !tv->ref )
{
fprintf(stderr,"Could not read the reference sequence. Is it seekable (plain text or compressed + .gzi indexed with bgzip)?\n");
exit(1);
}
}
// draw aln
bam_lplbuf_reset(tv->lplbuf);
sam_fetch(tv->fp, tv->idx, tv->curr_tid, tv->left_pos, tv->left_pos + tv->mcol, tv, tv_fetch_func);
bam_lplbuf_push(0, tv->lplbuf);
while (tv->ccol < tv->mcol) {
int pos = tv->last_pos + 1;
if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,0, tv->ccol, "%-d", pos+1);
tv->my_mvaddch(tv,1, tv->ccol++, (tv->ref && pos < tv->l_ref)? tv->ref[pos - tv->left_pos] : 'N');
++tv->last_pos;
}
return 0;
}
static void error(const char *format, ...)
{
if ( !format )
{
fprintf(stderr,
"Usage: samtools tview [options] <aln.bam> [ref.fasta]\n"
"Options:\n"
" -d display output as (H)tml or (C)urses or (T)ext \n"
" -p chr:pos go directly to this position\n"
" -s STR display only reads from this sample or group\n");
}
else
{
va_list ap;
va_start(ap, format);
vfprintf(stderr, format, ap);
va_end(ap);
}
exit(-1);
}
enum dipsay_mode {display_ncurses,display_html,display_text};
extern tview_t* curses_tv_init(const char *fn, const char *fn_fa, const char *samples);
extern tview_t* html_tv_init(const char *fn, const char *fn_fa, const char *samples);
extern tview_t* text_tv_init(const char *fn, const char *fn_fa, const char *samples);
int bam_tview_main(int argc, char *argv[])
{
int view_mode=display_ncurses;
tview_t* tv=NULL;
char *samples=NULL, *position=NULL;
int c;
while ((c = getopt(argc, argv, "s:p:d:")) >= 0) {
switch (c) {
case 's': samples=optarg; break;
case 'p': position=optarg; break;
case 'd':
{
switch(optarg[0])
{
case 'H': case 'h': view_mode=display_html;break;
case 'T': case 't': view_mode=display_text;break;
case 'C': case 'c': view_mode=display_ncurses;break;
default: view_mode=display_ncurses;break;
}
break;
}
default: error(NULL);
}
}
if (argc==optind) error(NULL);
switch(view_mode)
{
case display_ncurses:
{
tv = curses_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples);
break;
}
case display_text:
{
tv = text_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples);
break;
}
case display_html:
{
tv = html_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples);
break;
}
}
if (tv==NULL)
{
error("cannot create view");
return EXIT_FAILURE;
}
if ( position )
{
int tid, beg, end;
*(char *)hts_parse_reg(position, &beg, &end) = '\0';
tid = bam_name2id(tv->header, position);
if (tid >= 0) { tv->curr_tid = tid; tv->left_pos = beg; }
}
else if ( tv->fai )
{
// find the first sequence present in both BAM and the reference file
int i;
for (i=0; i<tv->header->n_targets; i++)
{
if ( faidx_has_seq(tv->fai, tv->header->target_name[i]) ) break;
}
if ( i==tv->header->n_targets )
{
fprintf(stderr,"None of the BAM sequence names present in the fasta file\n");
exit(EXIT_FAILURE);
}
tv->curr_tid = i;
}
tv->my_drawaln(tv, tv->curr_tid, tv->left_pos);
tv->my_loop(tv);
tv->my_destroy(tv);
return EXIT_SUCCESS;
}