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[samtools.git] / bam.c
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 }