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comparison pyPRADA_1.2/tools/samtools-0.1.16/bam.c @ 0:acc2ca1a3ba4

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author siyuan
date Thu, 20 Feb 2014 00:44:58 -0500
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-1:000000000000 0:acc2ca1a3ba4
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;
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 uint32_t k, end;
20 end = c->pos;
21 for (k = 0; k < c->n_cigar; ++k) {
22 int op = cigar[k] & BAM_CIGAR_MASK;
23 if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP)
24 end += cigar[k] >> BAM_CIGAR_SHIFT;
25 }
26 return end;
27 }
28
29 int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar)
30 {
31 uint32_t k;
32 int32_t l = 0;
33 for (k = 0; k < c->n_cigar; ++k) {
34 int op = cigar[k] & BAM_CIGAR_MASK;
35 if (op == BAM_CMATCH || op == BAM_CINS || op == BAM_CSOFT_CLIP)
36 l += cigar[k] >> BAM_CIGAR_SHIFT;
37 }
38 return l;
39 }
40
41 /********************
42 * BAM I/O routines *
43 ********************/
44
45 bam_header_t *bam_header_init()
46 {
47 bam_is_be = bam_is_big_endian();
48 return (bam_header_t*)calloc(1, sizeof(bam_header_t));
49 }
50
51 void bam_header_destroy(bam_header_t *header)
52 {
53 int32_t i;
54 extern void bam_destroy_header_hash(bam_header_t *header);
55 if (header == 0) return;
56 if (header->target_name) {
57 for (i = 0; i < header->n_targets; ++i)
58 free(header->target_name[i]);
59 free(header->target_name);
60 free(header->target_len);
61 }
62 free(header->text);
63 if (header->dict) sam_header_free(header->dict);
64 if (header->rg2lib) sam_tbl_destroy(header->rg2lib);
65 bam_destroy_header_hash(header);
66 free(header);
67 }
68
69 bam_header_t *bam_header_read(bamFile fp)
70 {
71 bam_header_t *header;
72 char buf[4];
73 int magic_len;
74 int32_t i = 1, name_len;
75 // check EOF
76 i = bgzf_check_EOF(fp);
77 if (i < 0) {
78 // If the file is a pipe, checking the EOF marker will *always* fail
79 // with ESPIPE. Suppress the error message in this case.
80 if (errno != ESPIPE) perror("[bam_header_read] bgzf_check_EOF");
81 }
82 else if (i == 0) fprintf(stderr, "[bam_header_read] EOF marker is absent. The input is probably truncated.\n");
83 // read "BAM1"
84 magic_len = bam_read(fp, buf, 4);
85 if (magic_len != 4 || strncmp(buf, "BAM\001", 4) != 0) {
86 fprintf(stderr, "[bam_header_read] invalid BAM binary header (this is not a BAM file).\n");
87 return 0;
88 }
89 header = bam_header_init();
90 // read plain text and the number of reference sequences
91 bam_read(fp, &header->l_text, 4);
92 if (bam_is_be) bam_swap_endian_4p(&header->l_text);
93 header->text = (char*)calloc(header->l_text + 1, 1);
94 bam_read(fp, header->text, header->l_text);
95 bam_read(fp, &header->n_targets, 4);
96 if (bam_is_be) bam_swap_endian_4p(&header->n_targets);
97 // read reference sequence names and lengths
98 header->target_name = (char**)calloc(header->n_targets, sizeof(char*));
99 header->target_len = (uint32_t*)calloc(header->n_targets, 4);
100 for (i = 0; i != header->n_targets; ++i) {
101 bam_read(fp, &name_len, 4);
102 if (bam_is_be) bam_swap_endian_4p(&name_len);
103 header->target_name[i] = (char*)calloc(name_len, 1);
104 bam_read(fp, header->target_name[i], name_len);
105 bam_read(fp, &header->target_len[i], 4);
106 if (bam_is_be) bam_swap_endian_4p(&header->target_len[i]);
107 }
108 return header;
109 }
110
111 int bam_header_write(bamFile fp, const bam_header_t *header)
112 {
113 char buf[4];
114 int32_t i, name_len, x;
115 // write "BAM1"
116 strncpy(buf, "BAM\001", 4);
117 bam_write(fp, buf, 4);
118 // write plain text and the number of reference sequences
119 if (bam_is_be) {
120 x = bam_swap_endian_4(header->l_text);
121 bam_write(fp, &x, 4);
122 if (header->l_text) bam_write(fp, header->text, header->l_text);
123 x = bam_swap_endian_4(header->n_targets);
124 bam_write(fp, &x, 4);
125 } else {
126 bam_write(fp, &header->l_text, 4);
127 if (header->l_text) bam_write(fp, header->text, header->l_text);
128 bam_write(fp, &header->n_targets, 4);
129 }
130 // write sequence names and lengths
131 for (i = 0; i != header->n_targets; ++i) {
132 char *p = header->target_name[i];
133 name_len = strlen(p) + 1;
134 if (bam_is_be) {
135 x = bam_swap_endian_4(name_len);
136 bam_write(fp, &x, 4);
137 } else bam_write(fp, &name_len, 4);
138 bam_write(fp, p, name_len);
139 if (bam_is_be) {
140 x = bam_swap_endian_4(header->target_len[i]);
141 bam_write(fp, &x, 4);
142 } else bam_write(fp, &header->target_len[i], 4);
143 }
144 bgzf_flush(fp);
145 return 0;
146 }
147
148 static void swap_endian_data(const bam1_core_t *c, int data_len, uint8_t *data)
149 {
150 uint8_t *s;
151 uint32_t i, *cigar = (uint32_t*)(data + c->l_qname);
152 s = data + c->n_cigar*4 + c->l_qname + c->l_qseq + (c->l_qseq + 1)/2;
153 for (i = 0; i < c->n_cigar; ++i) bam_swap_endian_4p(&cigar[i]);
154 while (s < data + data_len) {
155 uint8_t type;
156 s += 2; // skip key
157 type = toupper(*s); ++s; // skip type
158 if (type == 'C' || type == 'A') ++s;
159 else if (type == 'S') { bam_swap_endian_2p(s); s += 2; }
160 else if (type == 'I' || type == 'F') { bam_swap_endian_4p(s); s += 4; }
161 else if (type == 'D') { bam_swap_endian_8p(s); s += 8; }
162 else if (type == 'Z' || type == 'H') { while (*s) ++s; ++s; }
163 else if (type == 'B') {
164 int32_t n, Bsize = bam_aux_type2size(*s);
165 memcpy(&n, s + 1, 4);
166 if (1 == Bsize) {
167 } else if (2 == Bsize) {
168 for (i = 0; i < n; i += 2)
169 bam_swap_endian_2p(s + 5 + i);
170 } else if (4 == Bsize) {
171 for (i = 0; i < n; i += 4)
172 bam_swap_endian_4p(s + 5 + i);
173 }
174 bam_swap_endian_4p(s+1);
175 }
176 }
177 }
178
179 int bam_read1(bamFile fp, bam1_t *b)
180 {
181 bam1_core_t *c = &b->core;
182 int32_t block_len, ret, i;
183 uint32_t x[8];
184
185 assert(BAM_CORE_SIZE == 32);
186 if ((ret = bam_read(fp, &block_len, 4)) != 4) {
187 if (ret == 0) return -1; // normal end-of-file
188 else return -2; // truncated
189 }
190 if (bam_read(fp, x, BAM_CORE_SIZE) != BAM_CORE_SIZE) return -3;
191 if (bam_is_be) {
192 bam_swap_endian_4p(&block_len);
193 for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i);
194 }
195 c->tid = x[0]; c->pos = x[1];
196 c->bin = x[2]>>16; c->qual = x[2]>>8&0xff; c->l_qname = x[2]&0xff;
197 c->flag = x[3]>>16; c->n_cigar = x[3]&0xffff;
198 c->l_qseq = x[4];
199 c->mtid = x[5]; c->mpos = x[6]; c->isize = x[7];
200 b->data_len = block_len - BAM_CORE_SIZE;
201 if (b->m_data < b->data_len) {
202 b->m_data = b->data_len;
203 kroundup32(b->m_data);
204 b->data = (uint8_t*)realloc(b->data, b->m_data);
205 }
206 if (bam_read(fp, b->data, b->data_len) != b->data_len) return -4;
207 b->l_aux = b->data_len - c->n_cigar * 4 - c->l_qname - c->l_qseq - (c->l_qseq+1)/2;
208 if (bam_is_be) swap_endian_data(c, b->data_len, b->data);
209 return 4 + block_len;
210 }
211
212 inline int bam_write1_core(bamFile fp, const bam1_core_t *c, int data_len, uint8_t *data)
213 {
214 uint32_t x[8], block_len = data_len + BAM_CORE_SIZE, y;
215 int i;
216 assert(BAM_CORE_SIZE == 32);
217 x[0] = c->tid;
218 x[1] = c->pos;
219 x[2] = (uint32_t)c->bin<<16 | c->qual<<8 | c->l_qname;
220 x[3] = (uint32_t)c->flag<<16 | c->n_cigar;
221 x[4] = c->l_qseq;
222 x[5] = c->mtid;
223 x[6] = c->mpos;
224 x[7] = c->isize;
225 bgzf_flush_try(fp, 4 + block_len);
226 if (bam_is_be) {
227 for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i);
228 y = block_len;
229 bam_write(fp, bam_swap_endian_4p(&y), 4);
230 swap_endian_data(c, data_len, data);
231 } else bam_write(fp, &block_len, 4);
232 bam_write(fp, x, BAM_CORE_SIZE);
233 bam_write(fp, data, data_len);
234 if (bam_is_be) swap_endian_data(c, data_len, data);
235 return 4 + block_len;
236 }
237
238 int bam_write1(bamFile fp, const bam1_t *b)
239 {
240 return bam_write1_core(fp, &b->core, b->data_len, b->data);
241 }
242
243 char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of)
244 {
245 uint8_t *s = bam1_seq(b), *t = bam1_qual(b);
246 int i;
247 const bam1_core_t *c = &b->core;
248 kstring_t str;
249 str.l = str.m = 0; str.s = 0;
250
251 kputsn(bam1_qname(b), c->l_qname-1, &str); kputc('\t', &str);
252 if (of == BAM_OFDEC) { kputw(c->flag, &str); kputc('\t', &str); }
253 else if (of == BAM_OFHEX) ksprintf(&str, "0x%x\t", c->flag);
254 else { // BAM_OFSTR
255 for (i = 0; i < 16; ++i)
256 if ((c->flag & 1<<i) && bam_flag2char_table[i])
257 kputc(bam_flag2char_table[i], &str);
258 kputc('\t', &str);
259 }
260 if (c->tid < 0) kputsn("*\t", 2, &str);
261 else {
262 if (header) kputs(header->target_name[c->tid] , &str);
263 else kputw(c->tid, &str);
264 kputc('\t', &str);
265 }
266 kputw(c->pos + 1, &str); kputc('\t', &str); kputw(c->qual, &str); kputc('\t', &str);
267 if (c->n_cigar == 0) kputc('*', &str);
268 else {
269 for (i = 0; i < c->n_cigar; ++i) {
270 kputw(bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, &str);
271 kputc("MIDNSHP"[bam1_cigar(b)[i]&BAM_CIGAR_MASK], &str);
272 }
273 }
274 kputc('\t', &str);
275 if (c->mtid < 0) kputsn("*\t", 2, &str);
276 else if (c->mtid == c->tid) kputsn("=\t", 2, &str);
277 else {
278 if (header) kputs(header->target_name[c->mtid], &str);
279 else kputw(c->mtid, &str);
280 kputc('\t', &str);
281 }
282 kputw(c->mpos + 1, &str); kputc('\t', &str); kputw(c->isize, &str); kputc('\t', &str);
283 if (c->l_qseq) {
284 for (i = 0; i < c->l_qseq; ++i) kputc(bam_nt16_rev_table[bam1_seqi(s, i)], &str);
285 kputc('\t', &str);
286 if (t[0] == 0xff) kputc('*', &str);
287 else for (i = 0; i < c->l_qseq; ++i) kputc(t[i] + 33, &str);
288 } else kputsn("*\t*", 3, &str);
289 s = bam1_aux(b);
290 while (s < b->data + b->data_len) {
291 uint8_t type, key[2];
292 key[0] = s[0]; key[1] = s[1];
293 s += 2; type = *s; ++s;
294 kputc('\t', &str); kputsn((char*)key, 2, &str); kputc(':', &str);
295 if (type == 'A') { kputsn("A:", 2, &str); kputc(*s, &str); ++s; }
296 else if (type == 'C') { kputsn("i:", 2, &str); kputw(*s, &str); ++s; }
297 else if (type == 'c') { kputsn("i:", 2, &str); kputw(*(int8_t*)s, &str); ++s; }
298 else if (type == 'S') { kputsn("i:", 2, &str); kputw(*(uint16_t*)s, &str); s += 2; }
299 else if (type == 's') { kputsn("i:", 2, &str); kputw(*(int16_t*)s, &str); s += 2; }
300 else if (type == 'I') { kputsn("i:", 2, &str); kputuw(*(uint32_t*)s, &str); s += 4; }
301 else if (type == 'i') { kputsn("i:", 2, &str); kputw(*(int32_t*)s, &str); s += 4; }
302 else if (type == 'f') { ksprintf(&str, "f:%g", *(float*)s); s += 4; }
303 else if (type == 'd') { ksprintf(&str, "d:%lg", *(double*)s); s += 8; }
304 else if (type == 'Z' || type == 'H') { kputc(type, &str); kputc(':', &str); while (*s) kputc(*s++, &str); ++s; }
305 else if (type == 'B') {
306 uint8_t sub_type = *(s++);
307 int32_t n;
308 memcpy(&n, s, 4);
309 s += 4; // no point to the start of the array
310 kputc(type, &str); kputc(':', &str); kputc(sub_type, &str); // write the typing
311 for (i = 0; i < n; ++i) {
312 kputc(',', &str);
313 if ('c' == sub_type || 'c' == sub_type) { kputw(*(int8_t*)s, &str); ++s; }
314 else if ('C' == sub_type) { kputw(*(uint8_t*)s, &str); ++s; }
315 else if ('s' == sub_type) { kputw(*(int16_t*)s, &str); s += 2; }
316 else if ('S' == sub_type) { kputw(*(uint16_t*)s, &str); s += 2; }
317 else if ('i' == sub_type) { kputw(*(int32_t*)s, &str); s += 4; }
318 else if ('I' == sub_type) { kputuw(*(uint32_t*)s, &str); s += 4; }
319 else if ('f' == sub_type) { ksprintf(&str, "%g", *(float*)s); s += 4; }
320 }
321 }
322 }
323 return str.s;
324 }
325
326 char *bam_format1(const bam_header_t *header, const bam1_t *b)
327 {
328 return bam_format1_core(header, b, BAM_OFDEC);
329 }
330
331 void bam_view1(const bam_header_t *header, const bam1_t *b)
332 {
333 char *s = bam_format1(header, b);
334 puts(s);
335 free(s);
336 }
337
338 int bam_validate1(const bam_header_t *header, const bam1_t *b)
339 {
340 char *s;
341
342 if (b->core.tid < -1 || b->core.mtid < -1) return 0;
343 if (header && (b->core.tid >= header->n_targets || b->core.mtid >= header->n_targets)) return 0;
344
345 if (b->data_len < b->core.l_qname) return 0;
346 s = memchr(bam1_qname(b), '\0', b->core.l_qname);
347 if (s != &bam1_qname(b)[b->core.l_qname-1]) return 0;
348
349 // FIXME: Other fields could also be checked, especially the auxiliary data
350
351 return 1;
352 }
353
354 // FIXME: we should also check the LB tag associated with each alignment
355 const char *bam_get_library(bam_header_t *h, const bam1_t *b)
356 {
357 const uint8_t *rg;
358 if (h->dict == 0) h->dict = sam_header_parse2(h->text);
359 if (h->rg2lib == 0) h->rg2lib = sam_header2tbl(h->dict, "RG", "ID", "LB");
360 rg = bam_aux_get(b, "RG");
361 return (rg == 0)? 0 : sam_tbl_get(h->rg2lib, (const char*)(rg + 1));
362 }