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

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author siyuan
date Thu, 20 Feb 2014 00:44:58 -0500
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1 #include <zlib.h>
2 #include <stdio.h>
3 #include <ctype.h>
4 #include <string.h>
5 #include <stdlib.h>
6 #include <unistd.h>
7 #include <assert.h>
8 #ifdef _WIN32
9 #include <fcntl.h>
10 #endif
11 #include "kstring.h"
12 #include "bam.h"
13 #include "sam_header.h"
14 #include "kseq.h"
15 #include "khash.h"
16
17 KSTREAM_INIT(gzFile, gzread, 8192)
18 KHASH_MAP_INIT_STR(ref, uint64_t)
19
20 void bam_init_header_hash(bam_header_t *header);
21 void bam_destroy_header_hash(bam_header_t *header);
22 int32_t bam_get_tid(const bam_header_t *header, const char *seq_name);
23
24 unsigned char bam_nt16_table[256] = {
25 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
26 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
27 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
28 1, 2, 4, 8, 15,15,15,15, 15,15,15,15, 15, 0 /*=*/,15,15,
29 15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
30 15,15, 5, 6, 8,15, 7, 9, 15,10,15,15, 15,15,15,15,
31 15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
32 15,15, 5, 6, 8,15, 7, 9, 15,10,15,15, 15,15,15,15,
33 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
34 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
35 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
36 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
37 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
38 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
39 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
40 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
41 };
42
43 unsigned short bam_char2flag_table[256] = {
44 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
45 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
46 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
47 0,BAM_FREAD1,BAM_FREAD2,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
48 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
49 BAM_FPROPER_PAIR,0,BAM_FMREVERSE,0, 0,BAM_FMUNMAP,0,0, 0,0,0,0, 0,0,0,0,
50 0,0,0,0, BAM_FDUP,0,BAM_FQCFAIL,0, 0,0,0,0, 0,0,0,0,
51 BAM_FPAIRED,0,BAM_FREVERSE,BAM_FSECONDARY, 0,BAM_FUNMAP,0,0, 0,0,0,0, 0,0,0,0,
52 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
53 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
54 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
55 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
56 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
57 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
58 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
59 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0
60 };
61
62 char *bam_nt16_rev_table = "=ACMGRSVTWYHKDBN";
63
64 struct __tamFile_t {
65 gzFile fp;
66 kstream_t *ks;
67 kstring_t *str;
68 uint64_t n_lines;
69 int is_first;
70 };
71
72 char **__bam_get_lines(const char *fn, int *_n) // for bam_plcmd.c only
73 {
74 char **list = 0, *s;
75 int n = 0, dret, m = 0;
76 gzFile fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
77 kstream_t *ks;
78 kstring_t *str;
79 str = (kstring_t*)calloc(1, sizeof(kstring_t));
80 ks = ks_init(fp);
81 while (ks_getuntil(ks, '\n', str, &dret) > 0) {
82 if (n == m) {
83 m = m? m << 1 : 16;
84 list = (char**)realloc(list, m * sizeof(char*));
85 }
86 if (str->s[str->l-1] == '\r')
87 str->s[--str->l] = '\0';
88 s = list[n++] = (char*)calloc(str->l + 1, 1);
89 strcpy(s, str->s);
90 }
91 ks_destroy(ks);
92 gzclose(fp);
93 free(str->s); free(str);
94 *_n = n;
95 return list;
96 }
97
98 static bam_header_t *hash2header(const kh_ref_t *hash)
99 {
100 bam_header_t *header;
101 khiter_t k;
102 header = bam_header_init();
103 header->n_targets = kh_size(hash);
104 header->target_name = (char**)calloc(kh_size(hash), sizeof(char*));
105 header->target_len = (uint32_t*)calloc(kh_size(hash), 4);
106 for (k = kh_begin(hash); k != kh_end(hash); ++k) {
107 if (kh_exist(hash, k)) {
108 int i = (int)kh_value(hash, k);
109 header->target_name[i] = (char*)kh_key(hash, k);
110 header->target_len[i] = kh_value(hash, k)>>32;
111 }
112 }
113 bam_init_header_hash(header);
114 return header;
115 }
116 bam_header_t *sam_header_read2(const char *fn)
117 {
118 bam_header_t *header;
119 int c, dret, ret, error = 0;
120 gzFile fp;
121 kstream_t *ks;
122 kstring_t *str;
123 kh_ref_t *hash;
124 khiter_t k;
125 if (fn == 0) return 0;
126 fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
127 if (fp == 0) return 0;
128 hash = kh_init(ref);
129 ks = ks_init(fp);
130 str = (kstring_t*)calloc(1, sizeof(kstring_t));
131 while (ks_getuntil(ks, 0, str, &dret) > 0) {
132 char *s = strdup(str->s);
133 int len, i;
134 i = kh_size(hash);
135 ks_getuntil(ks, 0, str, &dret);
136 len = atoi(str->s);
137 k = kh_put(ref, hash, s, &ret);
138 if (ret == 0) {
139 fprintf(stderr, "[sam_header_read2] duplicated sequence name: %s\n", s);
140 error = 1;
141 }
142 kh_value(hash, k) = (uint64_t)len<<32 | i;
143 if (dret != '\n')
144 while ((c = ks_getc(ks)) != '\n' && c != -1);
145 }
146 ks_destroy(ks);
147 gzclose(fp);
148 free(str->s); free(str);
149 fprintf(stderr, "[sam_header_read2] %d sequences loaded.\n", kh_size(hash));
150 if (error) return 0;
151 header = hash2header(hash);
152 kh_destroy(ref, hash);
153 return header;
154 }
155 static inline uint8_t *alloc_data(bam1_t *b, int size)
156 {
157 if (b->m_data < size) {
158 b->m_data = size;
159 kroundup32(b->m_data);
160 b->data = (uint8_t*)realloc(b->data, b->m_data);
161 }
162 return b->data;
163 }
164 static inline void parse_error(int64_t n_lines, const char * __restrict msg)
165 {
166 fprintf(stderr, "Parse error at line %lld: %s\n", (long long)n_lines, msg);
167 abort();
168 }
169 static inline void append_text(bam_header_t *header, kstring_t *str)
170 {
171 size_t x = header->l_text, y = header->l_text + str->l + 2; // 2 = 1 byte dret + 1 byte null
172 kroundup32(x); kroundup32(y);
173 if (x < y)
174 {
175 header->n_text = y;
176 header->text = (char*)realloc(header->text, y);
177 if ( !header->text )
178 {
179 fprintf(stderr,"realloc failed to alloc %ld bytes\n", y);
180 abort();
181 }
182 }
183 // Sanity check
184 if ( header->l_text+str->l+1 >= header->n_text )
185 {
186 fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n", header->l_text+str->l+1,header->n_text,x,y);
187 abort();
188 }
189 strncpy(header->text + header->l_text, str->s, str->l+1); // we cannot use strcpy() here.
190 header->l_text += str->l + 1;
191 header->text[header->l_text] = 0;
192 }
193
194 int sam_header_parse(bam_header_t *h)
195 {
196 char **tmp;
197 int i;
198 free(h->target_len); free(h->target_name);
199 h->n_targets = 0; h->target_len = 0; h->target_name = 0;
200 if (h->l_text < 3) return 0;
201 if (h->dict == 0) h->dict = sam_header_parse2(h->text);
202 tmp = sam_header2list(h->dict, "SQ", "SN", &h->n_targets);
203 if (h->n_targets == 0) return 0;
204 h->target_name = calloc(h->n_targets, sizeof(void*));
205 for (i = 0; i < h->n_targets; ++i)
206 h->target_name[i] = strdup(tmp[i]);
207 free(tmp);
208 tmp = sam_header2list(h->dict, "SQ", "LN", &h->n_targets);
209 h->target_len = calloc(h->n_targets, 4);
210 for (i = 0; i < h->n_targets; ++i)
211 h->target_len[i] = atoi(tmp[i]);
212 free(tmp);
213 return h->n_targets;
214 }
215
216 bam_header_t *sam_header_read(tamFile fp)
217 {
218 int ret, dret;
219 bam_header_t *header = bam_header_init();
220 kstring_t *str = fp->str;
221 while ((ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret)) >= 0 && str->s[0] == '@') { // skip header
222 str->s[str->l] = dret; // note that str->s is NOT null terminated!!
223 append_text(header, str);
224 if (dret != '\n') {
225 ret = ks_getuntil(fp->ks, '\n', str, &dret);
226 str->s[str->l] = '\n'; // NOT null terminated!!
227 append_text(header, str);
228 }
229 ++fp->n_lines;
230 }
231 sam_header_parse(header);
232 bam_init_header_hash(header);
233 fp->is_first = 1;
234 return header;
235 }
236
237 int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
238 {
239 int ret, doff, doff0, dret, z = 0;
240 bam1_core_t *c = &b->core;
241 kstring_t *str = fp->str;
242 kstream_t *ks = fp->ks;
243
244 if (fp->is_first) {
245 fp->is_first = 0;
246 ret = str->l;
247 } else {
248 do { // special consideration for empty lines
249 ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret);
250 if (ret >= 0) z += str->l + 1;
251 } while (ret == 0);
252 }
253 if (ret < 0) return -1;
254 ++fp->n_lines;
255 doff = 0;
256
257 { // name
258 c->l_qname = strlen(str->s) + 1;
259 memcpy(alloc_data(b, doff + c->l_qname) + doff, str->s, c->l_qname);
260 doff += c->l_qname;
261 }
262 { // flag
263 long flag;
264 char *s;
265 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
266 flag = strtol((char*)str->s, &s, 0);
267 if (*s) { // not the end of the string
268 flag = 0;
269 for (s = str->s; *s; ++s)
270 flag |= bam_char2flag_table[(int)*s];
271 }
272 c->flag = flag;
273 }
274 { // tid, pos, qual
275 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->tid = bam_get_tid(header, str->s);
276 if (c->tid < 0 && strcmp(str->s, "*")) {
277 if (header->n_targets == 0) {
278 fprintf(stderr, "[sam_read1] missing header? Abort!\n");
279 exit(1);
280 } else fprintf(stderr, "[sam_read1] reference '%s' is recognized as '*'.\n", str->s);
281 }
282 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->pos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
283 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->qual = isdigit(str->s[0])? atoi(str->s) : 0;
284 if (ret < 0) return -2;
285 }
286 { // cigar
287 char *s, *t;
288 int i, op;
289 long x;
290 c->n_cigar = 0;
291 if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -3;
292 z += str->l + 1;
293 if (str->s[0] != '*') {
294 for (s = str->s; *s; ++s) {
295 if (isalpha(*s)) ++c->n_cigar;
296 else if (!isdigit(*s)) parse_error(fp->n_lines, "invalid CIGAR character");
297 }
298 b->data = alloc_data(b, doff + c->n_cigar * 4);
299 for (i = 0, s = str->s; i != c->n_cigar; ++i) {
300 x = strtol(s, &t, 10);
301 op = toupper(*t);
302 if (op == 'M' || op == '=' || op == 'X') op = BAM_CMATCH;
303 else if (op == 'I') op = BAM_CINS;
304 else if (op == 'D') op = BAM_CDEL;
305 else if (op == 'N') op = BAM_CREF_SKIP;
306 else if (op == 'S') op = BAM_CSOFT_CLIP;
307 else if (op == 'H') op = BAM_CHARD_CLIP;
308 else if (op == 'P') op = BAM_CPAD;
309 else parse_error(fp->n_lines, "invalid CIGAR operation");
310 s = t + 1;
311 bam1_cigar(b)[i] = x << BAM_CIGAR_SHIFT | op;
312 }
313 if (*s) parse_error(fp->n_lines, "unmatched CIGAR operation");
314 c->bin = bam_reg2bin(c->pos, bam_calend(c, bam1_cigar(b)));
315 doff += c->n_cigar * 4;
316 } else {
317 if (!(c->flag&BAM_FUNMAP)) {
318 fprintf(stderr, "Parse warning at line %lld: mapped sequence without CIGAR\n", (long long)fp->n_lines);
319 c->flag |= BAM_FUNMAP;
320 }
321 c->bin = bam_reg2bin(c->pos, c->pos + 1);
322 }
323 }
324 { // mtid, mpos, isize
325 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
326 c->mtid = strcmp(str->s, "=")? bam_get_tid(header, str->s) : c->tid;
327 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
328 c->mpos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
329 ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
330 c->isize = (str->s[0] == '-' || isdigit(str->s[0]))? atoi(str->s) : 0;
331 if (ret < 0) return -4;
332 }
333 { // seq and qual
334 int i;
335 uint8_t *p = 0;
336 if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -5; // seq
337 z += str->l + 1;
338 if (strcmp(str->s, "*")) {
339 c->l_qseq = strlen(str->s);
340 if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b)))
341 parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
342 p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;
343 memset(p, 0, (c->l_qseq+1)/2);
344 for (i = 0; i < c->l_qseq; ++i)
345 p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2);
346 } else c->l_qseq = 0;
347 if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -6; // qual
348 z += str->l + 1;
349 if (strcmp(str->s, "*") && c->l_qseq != strlen(str->s))
350 parse_error(fp->n_lines, "sequence and quality are inconsistent");
351 p += (c->l_qseq+1)/2;
352 if (strcmp(str->s, "*") == 0) for (i = 0; i < c->l_qseq; ++i) p[i] = 0xff;
353 else for (i = 0; i < c->l_qseq; ++i) p[i] = str->s[i] - 33;
354 doff += c->l_qseq + (c->l_qseq+1)/2;
355 }
356 doff0 = doff;
357 if (dret != '\n' && dret != '\r') { // aux
358 while (ks_getuntil(ks, KS_SEP_TAB, str, &dret) >= 0) {
359 uint8_t *s, type, key[2];
360 z += str->l + 1;
361 if (str->l < 6 || str->s[2] != ':' || str->s[4] != ':')
362 parse_error(fp->n_lines, "missing colon in auxiliary data");
363 key[0] = str->s[0]; key[1] = str->s[1];
364 type = str->s[3];
365 s = alloc_data(b, doff + 3) + doff;
366 s[0] = key[0]; s[1] = key[1]; s += 2; doff += 2;
367 if (type == 'A' || type == 'a' || type == 'c' || type == 'C') { // c and C for backward compatibility
368 s = alloc_data(b, doff + 2) + doff;
369 *s++ = 'A'; *s = str->s[5];
370 doff += 2;
371 } else if (type == 'I' || type == 'i') {
372 long long x;
373 s = alloc_data(b, doff + 5) + doff;
374 x = (long long)atoll(str->s + 5);
375 if (x < 0) {
376 if (x >= -127) {
377 *s++ = 'c'; *(int8_t*)s = (int8_t)x;
378 s += 1; doff += 2;
379 } else if (x >= -32767) {
380 *s++ = 's'; *(int16_t*)s = (int16_t)x;
381 s += 2; doff += 3;
382 } else {
383 *s++ = 'i'; *(int32_t*)s = (int32_t)x;
384 s += 4; doff += 5;
385 if (x < -2147483648ll)
386 fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",
387 (long long)fp->n_lines, x);
388 }
389 } else {
390 if (x <= 255) {
391 *s++ = 'C'; *s++ = (uint8_t)x;
392 doff += 2;
393 } else if (x <= 65535) {
394 *s++ = 'S'; *(uint16_t*)s = (uint16_t)x;
395 s += 2; doff += 3;
396 } else {
397 *s++ = 'I'; *(uint32_t*)s = (uint32_t)x;
398 s += 4; doff += 5;
399 if (x > 4294967295ll)
400 fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",
401 (long long)fp->n_lines, x);
402 }
403 }
404 } else if (type == 'f') {
405 s = alloc_data(b, doff + 5) + doff;
406 *s++ = 'f';
407 *(float*)s = (float)atof(str->s + 5);
408 s += 4; doff += 5;
409 } else if (type == 'd') {
410 s = alloc_data(b, doff + 9) + doff;
411 *s++ = 'd';
412 *(float*)s = (float)atof(str->s + 9);
413 s += 8; doff += 9;
414 } else if (type == 'Z' || type == 'H') {
415 int size = 1 + (str->l - 5) + 1;
416 if (type == 'H') { // check whether the hex string is valid
417 int i;
418 if ((str->l - 5) % 2 == 1) parse_error(fp->n_lines, "length of the hex string not even");
419 for (i = 0; i < str->l - 5; ++i) {
420 int c = toupper(str->s[5 + i]);
421 if (!((c >= '0' && c <= '9') || (c >= 'A' && c <= 'F')))
422 parse_error(fp->n_lines, "invalid hex character");
423 }
424 }
425 s = alloc_data(b, doff + size) + doff;
426 *s++ = type;
427 memcpy(s, str->s + 5, str->l - 5);
428 s[str->l - 5] = 0;
429 doff += size;
430 } else if (type == 'B') {
431 int32_t n = 0, Bsize, k = 0, size;
432 char *p;
433 if (str->l < 8) parse_error(fp->n_lines, "too few values in aux type B");
434 Bsize = bam_aux_type2size(str->s[5]); // the size of each element
435 for (p = (char*)str->s + 6; *p; ++p) // count the number of elements in the array
436 if (*p == ',') ++n;
437 p = str->s + 7; // now p points to the first number in the array
438 size = 6 + Bsize * n; // total number of bytes allocated to this tag
439 s = alloc_data(b, doff + 6 * Bsize * n) + doff; // allocate memory
440 *s++ = 'B'; *s++ = str->s[5];
441 memcpy(s, &n, 4); s += 4; // write the number of elements
442 if (str->s[5] == 'c') while (p < str->s + str->l) ((int8_t*)s)[k++] = (int8_t)strtol(p, &p, 0), ++p;
443 else if (str->s[5] == 'C') while (p < str->s + str->l) ((uint8_t*)s)[k++] = (uint8_t)strtol(p, &p, 0), ++p;
444 else if (str->s[5] == 's') while (p < str->s + str->l) ((int16_t*)s)[k++] = (int16_t)strtol(p, &p, 0), ++p; // FIXME: avoid unaligned memory
445 else if (str->s[5] == 'S') while (p < str->s + str->l) ((uint16_t*)s)[k++] = (uint16_t)strtol(p, &p, 0), ++p;
446 else if (str->s[5] == 'i') while (p < str->s + str->l) ((int32_t*)s)[k++] = (int32_t)strtol(p, &p, 0), ++p;
447 else if (str->s[5] == 'I') while (p < str->s + str->l) ((uint32_t*)s)[k++] = (uint32_t)strtol(p, &p, 0), ++p;
448 else if (str->s[5] == 'f') while (p < str->s + str->l) ((float*)s)[k++] = (float)strtof(p, &p), ++p;
449 else parse_error(fp->n_lines, "unrecognized array type");
450 s += Bsize * n; doff += size;
451 } else parse_error(fp->n_lines, "unrecognized type");
452 if (dret == '\n' || dret == '\r') break;
453 }
454 }
455 b->l_aux = doff - doff0;
456 b->data_len = doff;
457 return z;
458 }
459
460 tamFile sam_open(const char *fn)
461 {
462 tamFile fp;
463 gzFile gzfp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "rb") : gzopen(fn, "rb");
464 if (gzfp == 0) return 0;
465 fp = (tamFile)calloc(1, sizeof(struct __tamFile_t));
466 fp->str = (kstring_t*)calloc(1, sizeof(kstring_t));
467 fp->fp = gzfp;
468 fp->ks = ks_init(fp->fp);
469 return fp;
470 }
471
472 void sam_close(tamFile fp)
473 {
474 if (fp) {
475 ks_destroy(fp->ks);
476 gzclose(fp->fp);
477 free(fp->str->s); free(fp->str);
478 free(fp);
479 }
480 }