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comparison PsiCLASS-1.0.2/samtools-0.1.19/bam.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 #include <stdio.h>
2 #include <ctype.h>
3 #include <errno.h>
4 #include <assert.h>
5 #include "bam.h"
6 #include "bam_endian.h"
7 #include "kstring.h"
8 #include "sam_header.h"
9
10 int bam_is_be = 0, bam_verbose = 2, bam_no_B = 0;
11 char *bam_flag2char_table = "pPuUrR12sfd\0\0\0\0\0";
12
13 /**************************
14 * CIGAR related routines *
15 **************************/
16
17 uint32_t bam_calend(const bam1_core_t *c, const uint32_t *cigar)
18 {
19 int k, end = c->pos;
20 for (k = 0; k < c->n_cigar; ++k) {
21 int op = bam_cigar_op(cigar[k]);
22 int len = bam_cigar_oplen(cigar[k]);
23 if (op == BAM_CBACK) { // move backward
24 int l, u, v;
25 if (k == c->n_cigar - 1) break; // skip trailing 'B'
26 for (l = k - 1, u = v = 0; l >= 0; --l) {
27 int op1 = bam_cigar_op(cigar[l]);
28 int len1 = bam_cigar_oplen(cigar[l]);
29 if (bam_cigar_type(op1)&1) { // consume query
30 if (u + len1 >= len) { // stop
31 if (bam_cigar_type(op1)&2) v += len - u;
32 break;
33 } else u += len1;
34 }
35 if (bam_cigar_type(op1)&2) v += len1;
36 }
37 end = l < 0? c->pos : end - v;
38 } else if (bam_cigar_type(op)&2) end += bam_cigar_oplen(cigar[k]);
39 }
40 return end;
41 }
42
43 int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar)
44 {
45 uint32_t k;
46 int32_t l = 0;
47 for (k = 0; k < c->n_cigar; ++k)
48 if (bam_cigar_type(bam_cigar_op(cigar[k]))&1)
49 l += bam_cigar_oplen(cigar[k]);
50 return l;
51 }
52
53 /********************
54 * BAM I/O routines *
55 ********************/
56
57 bam_header_t *bam_header_init()
58 {
59 bam_is_be = bam_is_big_endian();
60 return (bam_header_t*)calloc(1, sizeof(bam_header_t));
61 }
62
63 void bam_header_destroy(bam_header_t *header)
64 {
65 int32_t i;
66 extern void bam_destroy_header_hash(bam_header_t *header);
67 if (header == 0) return;
68 if (header->target_name) {
69 for (i = 0; i < header->n_targets; ++i)
70 free(header->target_name[i]);
71 free(header->target_name);
72 free(header->target_len);
73 }
74 free(header->text);
75 if (header->dict) sam_header_free(header->dict);
76 if (header->rg2lib) sam_tbl_destroy(header->rg2lib);
77 bam_destroy_header_hash(header);
78 free(header);
79 }
80
81 bam_header_t *bam_header_read(bamFile fp)
82 {
83 bam_header_t *header;
84 char buf[4];
85 int magic_len;
86 int32_t i = 1, name_len;
87 // check EOF
88 i = bgzf_check_EOF(fp);
89 if (i < 0) {
90 // If the file is a pipe, checking the EOF marker will *always* fail
91 // with ESPIPE. Suppress the error message in this case.
92 if (errno != ESPIPE) perror("[bam_header_read] bgzf_check_EOF");
93 }
94 else if (i == 0) fprintf(stderr, "[bam_header_read] EOF marker is absent. The input is probably truncated.\n");
95 // read "BAM1"
96 magic_len = bam_read(fp, buf, 4);
97 if (magic_len != 4 || strncmp(buf, "BAM\001", 4) != 0) {
98 fprintf(stderr, "[bam_header_read] invalid BAM binary header (this is not a BAM file).\n");
99 return 0;
100 }
101 header = bam_header_init();
102 // read plain text and the number of reference sequences
103 bam_read(fp, &header->l_text, 4);
104 if (bam_is_be) bam_swap_endian_4p(&header->l_text);
105 header->text = (char*)calloc(header->l_text + 1, 1);
106 bam_read(fp, header->text, header->l_text);
107 bam_read(fp, &header->n_targets, 4);
108 if (bam_is_be) bam_swap_endian_4p(&header->n_targets);
109 // read reference sequence names and lengths
110 header->target_name = (char**)calloc(header->n_targets, sizeof(char*));
111 header->target_len = (uint32_t*)calloc(header->n_targets, 4);
112 for (i = 0; i != header->n_targets; ++i) {
113 bam_read(fp, &name_len, 4);
114 if (bam_is_be) bam_swap_endian_4p(&name_len);
115 header->target_name[i] = (char*)calloc(name_len, 1);
116 bam_read(fp, header->target_name[i], name_len);
117 bam_read(fp, &header->target_len[i], 4);
118 if (bam_is_be) bam_swap_endian_4p(&header->target_len[i]);
119 }
120 return header;
121 }
122
123 int bam_header_write(bamFile fp, const bam_header_t *header)
124 {
125 char buf[4];
126 int32_t i, name_len, x;
127 // write "BAM1"
128 strncpy(buf, "BAM\001", 4);
129 bam_write(fp, buf, 4);
130 // write plain text and the number of reference sequences
131 if (bam_is_be) {
132 x = bam_swap_endian_4(header->l_text);
133 bam_write(fp, &x, 4);
134 if (header->l_text) bam_write(fp, header->text, header->l_text);
135 x = bam_swap_endian_4(header->n_targets);
136 bam_write(fp, &x, 4);
137 } else {
138 bam_write(fp, &header->l_text, 4);
139 if (header->l_text) bam_write(fp, header->text, header->l_text);
140 bam_write(fp, &header->n_targets, 4);
141 }
142 // write sequence names and lengths
143 for (i = 0; i != header->n_targets; ++i) {
144 char *p = header->target_name[i];
145 name_len = strlen(p) + 1;
146 if (bam_is_be) {
147 x = bam_swap_endian_4(name_len);
148 bam_write(fp, &x, 4);
149 } else bam_write(fp, &name_len, 4);
150 bam_write(fp, p, name_len);
151 if (bam_is_be) {
152 x = bam_swap_endian_4(header->target_len[i]);
153 bam_write(fp, &x, 4);
154 } else bam_write(fp, &header->target_len[i], 4);
155 }
156 bgzf_flush(fp);
157 return 0;
158 }
159
160 static void swap_endian_data(const bam1_core_t *c, int data_len, uint8_t *data)
161 {
162 uint8_t *s;
163 uint32_t i, *cigar = (uint32_t*)(data + c->l_qname);
164 s = data + c->n_cigar*4 + c->l_qname + c->l_qseq + (c->l_qseq + 1)/2;
165 for (i = 0; i < c->n_cigar; ++i) bam_swap_endian_4p(&cigar[i]);
166 while (s < data + data_len) {
167 uint8_t type;
168 s += 2; // skip key
169 type = toupper(*s); ++s; // skip type
170 if (type == 'C' || type == 'A') ++s;
171 else if (type == 'S') { bam_swap_endian_2p(s); s += 2; }
172 else if (type == 'I' || type == 'F') { bam_swap_endian_4p(s); s += 4; }
173 else if (type == 'D') { bam_swap_endian_8p(s); s += 8; }
174 else if (type == 'Z' || type == 'H') { while (*s) ++s; ++s; }
175 else if (type == 'B') {
176 int32_t n, Bsize = bam_aux_type2size(*s);
177 memcpy(&n, s + 1, 4);
178 if (1 == Bsize) {
179 } else if (2 == Bsize) {
180 for (i = 0; i < n; i += 2)
181 bam_swap_endian_2p(s + 5 + i);
182 } else if (4 == Bsize) {
183 for (i = 0; i < n; i += 4)
184 bam_swap_endian_4p(s + 5 + i);
185 }
186 bam_swap_endian_4p(s+1);
187 }
188 }
189 }
190
191 int bam_read1(bamFile fp, bam1_t *b)
192 {
193 bam1_core_t *c = &b->core;
194 int32_t block_len, ret, i;
195 uint32_t x[8];
196
197 assert(BAM_CORE_SIZE == 32);
198 if ((ret = bam_read(fp, &block_len, 4)) != 4) {
199 if (ret == 0) return -1; // normal end-of-file
200 else return -2; // truncated
201 }
202 if (bam_read(fp, x, BAM_CORE_SIZE) != BAM_CORE_SIZE) return -3;
203 if (bam_is_be) {
204 bam_swap_endian_4p(&block_len);
205 for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i);
206 }
207 c->tid = x[0]; c->pos = x[1];
208 c->bin = x[2]>>16; c->qual = x[2]>>8&0xff; c->l_qname = x[2]&0xff;
209 c->flag = x[3]>>16; c->n_cigar = x[3]&0xffff;
210 c->l_qseq = x[4];
211 c->mtid = x[5]; c->mpos = x[6]; c->isize = x[7];
212 b->data_len = block_len - BAM_CORE_SIZE;
213 if (b->m_data < b->data_len) {
214 b->m_data = b->data_len;
215 kroundup32(b->m_data);
216 b->data = (uint8_t*)realloc(b->data, b->m_data);
217 }
218 if (bam_read(fp, b->data, b->data_len) != b->data_len) return -4;
219 b->l_aux = b->data_len - c->n_cigar * 4 - c->l_qname - c->l_qseq - (c->l_qseq+1)/2;
220 if (bam_is_be) swap_endian_data(c, b->data_len, b->data);
221 if (bam_no_B) bam_remove_B(b);
222 return 4 + block_len;
223 }
224
225 inline int bam_write1_core(bamFile fp, const bam1_core_t *c, int data_len, uint8_t *data)
226 {
227 uint32_t x[8], block_len = data_len + BAM_CORE_SIZE, y;
228 int i;
229 assert(BAM_CORE_SIZE == 32);
230 x[0] = c->tid;
231 x[1] = c->pos;
232 x[2] = (uint32_t)c->bin<<16 | c->qual<<8 | c->l_qname;
233 x[3] = (uint32_t)c->flag<<16 | c->n_cigar;
234 x[4] = c->l_qseq;
235 x[5] = c->mtid;
236 x[6] = c->mpos;
237 x[7] = c->isize;
238 bgzf_flush_try(fp, 4 + block_len);
239 if (bam_is_be) {
240 for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i);
241 y = block_len;
242 bam_write(fp, bam_swap_endian_4p(&y), 4);
243 swap_endian_data(c, data_len, data);
244 } else bam_write(fp, &block_len, 4);
245 bam_write(fp, x, BAM_CORE_SIZE);
246 bam_write(fp, data, data_len);
247 if (bam_is_be) swap_endian_data(c, data_len, data);
248 return 4 + block_len;
249 }
250
251 int bam_write1(bamFile fp, const bam1_t *b)
252 {
253 return bam_write1_core(fp, &b->core, b->data_len, b->data);
254 }
255
256 char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of)
257 {
258 uint8_t *s = bam1_seq(b), *t = bam1_qual(b);
259 int i;
260 const bam1_core_t *c = &b->core;
261 kstring_t str;
262 str.l = str.m = 0; str.s = 0;
263
264 kputsn(bam1_qname(b), c->l_qname-1, &str); kputc('\t', &str);
265 if (of == BAM_OFDEC) { kputw(c->flag, &str); kputc('\t', &str); }
266 else if (of == BAM_OFHEX) ksprintf(&str, "0x%x\t", c->flag);
267 else { // BAM_OFSTR
268 for (i = 0; i < 16; ++i)
269 if ((c->flag & 1<<i) && bam_flag2char_table[i])
270 kputc(bam_flag2char_table[i], &str);
271 kputc('\t', &str);
272 }
273 if (c->tid < 0) kputsn("*\t", 2, &str);
274 else {
275 if (header) kputs(header->target_name[c->tid] , &str);
276 else kputw(c->tid, &str);
277 kputc('\t', &str);
278 }
279 kputw(c->pos + 1, &str); kputc('\t', &str); kputw(c->qual, &str); kputc('\t', &str);
280 if (c->n_cigar == 0) kputc('*', &str);
281 else {
282 uint32_t *cigar = bam1_cigar(b);
283 for (i = 0; i < c->n_cigar; ++i) {
284 kputw(bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, &str);
285 kputc(bam_cigar_opchr(cigar[i]), &str);
286 }
287 }
288 kputc('\t', &str);
289 if (c->mtid < 0) kputsn("*\t", 2, &str);
290 else if (c->mtid == c->tid) kputsn("=\t", 2, &str);
291 else {
292 if (header) kputs(header->target_name[c->mtid], &str);
293 else kputw(c->mtid, &str);
294 kputc('\t', &str);
295 }
296 kputw(c->mpos + 1, &str); kputc('\t', &str); kputw(c->isize, &str); kputc('\t', &str);
297 if (c->l_qseq) {
298 for (i = 0; i < c->l_qseq; ++i) kputc(bam_nt16_rev_table[bam1_seqi(s, i)], &str);
299 kputc('\t', &str);
300 if (t[0] == 0xff) kputc('*', &str);
301 else for (i = 0; i < c->l_qseq; ++i) kputc(t[i] + 33, &str);
302 } else kputsn("*\t*", 3, &str);
303 s = bam1_aux(b);
304 while (s < b->data + b->data_len) {
305 uint8_t type, key[2];
306 key[0] = s[0]; key[1] = s[1];
307 s += 2; type = *s; ++s;
308 kputc('\t', &str); kputsn((char*)key, 2, &str); kputc(':', &str);
309 if (type == 'A') { kputsn("A:", 2, &str); kputc(*s, &str); ++s; }
310 else if (type == 'C') { kputsn("i:", 2, &str); kputw(*s, &str); ++s; }
311 else if (type == 'c') { kputsn("i:", 2, &str); kputw(*(int8_t*)s, &str); ++s; }
312 else if (type == 'S') { kputsn("i:", 2, &str); kputw(*(uint16_t*)s, &str); s += 2; }
313 else if (type == 's') { kputsn("i:", 2, &str); kputw(*(int16_t*)s, &str); s += 2; }
314 else if (type == 'I') { kputsn("i:", 2, &str); kputuw(*(uint32_t*)s, &str); s += 4; }
315 else if (type == 'i') { kputsn("i:", 2, &str); kputw(*(int32_t*)s, &str); s += 4; }
316 else if (type == 'f') { ksprintf(&str, "f:%g", *(float*)s); s += 4; }
317 else if (type == 'd') { ksprintf(&str, "d:%lg", *(double*)s); s += 8; }
318 else if (type == 'Z' || type == 'H') { kputc(type, &str); kputc(':', &str); while (*s) kputc(*s++, &str); ++s; }
319 else if (type == 'B') {
320 uint8_t sub_type = *(s++);
321 int32_t n;
322 memcpy(&n, s, 4);
323 s += 4; // no point to the start of the array
324 kputc(type, &str); kputc(':', &str); kputc(sub_type, &str); // write the typing
325 for (i = 0; i < n; ++i) {
326 kputc(',', &str);
327 if ('c' == sub_type || 'c' == sub_type) { kputw(*(int8_t*)s, &str); ++s; }
328 else if ('C' == sub_type) { kputw(*(uint8_t*)s, &str); ++s; }
329 else if ('s' == sub_type) { kputw(*(int16_t*)s, &str); s += 2; }
330 else if ('S' == sub_type) { kputw(*(uint16_t*)s, &str); s += 2; }
331 else if ('i' == sub_type) { kputw(*(int32_t*)s, &str); s += 4; }
332 else if ('I' == sub_type) { kputuw(*(uint32_t*)s, &str); s += 4; }
333 else if ('f' == sub_type) { ksprintf(&str, "%g", *(float*)s); s += 4; }
334 }
335 }
336 }
337 return str.s;
338 }
339
340 char *bam_format1(const bam_header_t *header, const bam1_t *b)
341 {
342 return bam_format1_core(header, b, BAM_OFDEC);
343 }
344
345 void bam_view1(const bam_header_t *header, const bam1_t *b)
346 {
347 char *s = bam_format1(header, b);
348 puts(s);
349 free(s);
350 }
351
352 int bam_validate1(const bam_header_t *header, const bam1_t *b)
353 {
354 char *s;
355
356 if (b->core.tid < -1 || b->core.mtid < -1) return 0;
357 if (header && (b->core.tid >= header->n_targets || b->core.mtid >= header->n_targets)) return 0;
358
359 if (b->data_len < b->core.l_qname) return 0;
360 s = memchr(bam1_qname(b), '\0', b->core.l_qname);
361 if (s != &bam1_qname(b)[b->core.l_qname-1]) return 0;
362
363 // FIXME: Other fields could also be checked, especially the auxiliary data
364
365 return 1;
366 }
367
368 // FIXME: we should also check the LB tag associated with each alignment
369 const char *bam_get_library(bam_header_t *h, const bam1_t *b)
370 {
371 const uint8_t *rg;
372 if (h->dict == 0) h->dict = sam_header_parse2(h->text);
373 if (h->rg2lib == 0) h->rg2lib = sam_header2tbl(h->dict, "RG", "ID", "LB");
374 rg = bam_aux_get(b, "RG");
375 return (rg == 0)? 0 : sam_tbl_get(h->rg2lib, (const char*)(rg + 1));
376 }
377
378 /************
379 * Remove B *
380 ************/
381
382 int bam_remove_B(bam1_t *b)
383 {
384 int i, j, end_j, k, l, no_qual;
385 uint32_t *cigar, *new_cigar;
386 uint8_t *seq, *qual, *p;
387 // test if removal is necessary
388 if (b->core.flag & BAM_FUNMAP) return 0; // unmapped; do nothing
389 cigar = bam1_cigar(b);
390 for (k = 0; k < b->core.n_cigar; ++k)
391 if (bam_cigar_op(cigar[k]) == BAM_CBACK) break;
392 if (k == b->core.n_cigar) return 0; // no 'B'
393 if (bam_cigar_op(cigar[0]) == BAM_CBACK) goto rmB_err; // cannot be removed
394 // allocate memory for the new CIGAR
395 if (b->data_len + (b->core.n_cigar + 1) * 4 > b->m_data) { // not enough memory
396 b->m_data = b->data_len + b->core.n_cigar * 4;
397 kroundup32(b->m_data);
398 b->data = (uint8_t*)realloc(b->data, b->m_data);
399 cigar = bam1_cigar(b); // after realloc, cigar may be changed
400 }
401 new_cigar = (uint32_t*)(b->data + (b->m_data - b->core.n_cigar * 4)); // from the end of b->data
402 // the core loop
403 seq = bam1_seq(b); qual = bam1_qual(b);
404 no_qual = (qual[0] == 0xff); // test whether base quality is available
405 i = j = 0; end_j = -1;
406 for (k = l = 0; k < b->core.n_cigar; ++k) {
407 int op = bam_cigar_op(cigar[k]);
408 int len = bam_cigar_oplen(cigar[k]);
409 if (op == BAM_CBACK) { // the backward operation
410 int t, u;
411 if (k == b->core.n_cigar - 1) break; // ignore 'B' at the end of CIGAR
412 if (len > j) goto rmB_err; // an excessively long backward
413 for (t = l - 1, u = 0; t >= 0; --t) { // look back
414 int op1 = bam_cigar_op(new_cigar[t]);
415 int len1 = bam_cigar_oplen(new_cigar[t]);
416 if (bam_cigar_type(op1)&1) { // consume the query
417 if (u + len1 >= len) { // stop
418 new_cigar[t] -= (len - u) << BAM_CIGAR_SHIFT;
419 break;
420 } else u += len1;
421 }
422 }
423 if (bam_cigar_oplen(new_cigar[t]) == 0) --t; // squeeze out the zero-length operation
424 l = t + 1;
425 end_j = j; j -= len;
426 } else { // other CIGAR operations
427 new_cigar[l++] = cigar[k];
428 if (bam_cigar_type(op)&1) { // consume the query
429 if (i != j) { // no need to copy if i == j
430 int u, c, c0;
431 for (u = 0; u < len; ++u) { // construct the consensus
432 c = bam1_seqi(seq, i+u);
433 if (j + u < end_j) { // in an overlap
434 c0 = bam1_seqi(seq, j+u);
435 if (c != c0) { // a mismatch; choose the better base
436 if (qual[j+u] < qual[i+u]) { // the base in the 2nd segment is better
437 bam1_seq_seti(seq, j+u, c);
438 qual[j+u] = qual[i+u] - qual[j+u];
439 } else qual[j+u] -= qual[i+u]; // the 1st is better; reduce base quality
440 } else qual[j+u] = qual[j+u] > qual[i+u]? qual[j+u] : qual[i+u];
441 } else { // not in an overlap; copy over
442 bam1_seq_seti(seq, j+u, c);
443 qual[j+u] = qual[i+u];
444 }
445 }
446 }
447 i += len, j += len;
448 }
449 }
450 }
451 if (no_qual) qual[0] = 0xff; // in very rare cases, this may be modified
452 // merge adjacent operations if possible
453 for (k = 1; k < l; ++k)
454 if (bam_cigar_op(new_cigar[k]) == bam_cigar_op(new_cigar[k-1]))
455 new_cigar[k] += new_cigar[k-1] >> BAM_CIGAR_SHIFT << BAM_CIGAR_SHIFT, new_cigar[k-1] &= 0xf;
456 // kill zero length operations
457 for (k = i = 0; k < l; ++k)
458 if (new_cigar[k] >> BAM_CIGAR_SHIFT)
459 new_cigar[i++] = new_cigar[k];
460 l = i;
461 // update b
462 memcpy(cigar, new_cigar, l * 4); // set CIGAR
463 p = b->data + b->core.l_qname + l * 4;
464 memmove(p, seq, (j+1)>>1); p += (j+1)>>1; // set SEQ
465 memmove(p, qual, j); p += j; // set QUAL
466 memmove(p, bam1_aux(b), b->l_aux); p += b->l_aux; // set optional fields
467 b->core.n_cigar = l, b->core.l_qseq = j; // update CIGAR length and query length
468 b->data_len = p - b->data; // update record length
469 return 0;
470
471 rmB_err:
472 b->core.flag |= BAM_FUNMAP;
473 return -1;
474 }