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root/gclib/gclib/GBam.cpp
Revision: 133
Committed: Fri Dec 9 15:59:14 2011 UTC (7 years, 10 months ago) by gpertea
File size: 14340 byte(s)
Log Message:
TODO: detect sam/bam input for samopen

Line File contents
1 #include "GBam.h"
2 #include <ctype.h>
3 #include "kstring.h"
4
5 //auxiliary functions for low level BAM record creation
6 uint8_t* realloc_bdata(bam1_t *b, int size) {
7 if (b->m_data < size) {
8 b->m_data = size;
9 kroundup32(b->m_data);
10 b->data = (uint8_t*)realloc(b->data, b->m_data);
11 }
12 if (b->data_len<size) b->data_len=size;
13 return b->data;
14 }
15
16 uint8_t* dupalloc_bdata(bam1_t *b, int size) {
17 //same as realloc_bdata, but does not free previous data
18 //but returns it instead
19 //it ALWAYS duplicates data
20 b->m_data = size;
21 kroundup32(b->m_data);
22 uint8_t* odata=b->data;
23 b->data = (uint8_t*)malloc(b->m_data);
24 memcpy((void*)b->data, (void*)odata, b->data_len);
25 b->data_len=size;
26 return odata; //user must FREE this after
27 }
28
29 //from bam_import.c
30 extern unsigned short bam_char2flag_table[];
31
32 GBamRecord::GBamRecord(const char* qname, int32_t gseq_tid,
33 int pos, bool reverse, const char* qseq,
34 const char* cigar, const char* quals):exons(1) {
35 //novel=true;
36 bam_header=NULL;
37 b=bam_init1();
38 b->core.tid=gseq_tid;
39 if (pos<=0) {
40 b->core.pos=-1; //unmapped
41 //if (gseq_tid<0)
42 b->core.flag |= BAM_FUNMAP;
43 }
44 else b->core.pos=pos-1; //BAM is 0-based
45 b->core.qual=255;
46 int l_qseq=strlen(qseq);
47 //this may not be accurate, setting CIGAR is the correct way
48 //b->core.bin = bam_reg2bin(b->core.pos, b->core.pos+l_qseq-1);
49 b->core.l_qname=strlen(qname)+1; //includes the \0 at the end
50 memcpy(realloc_bdata(b, b->core.l_qname), qname, b->core.l_qname);
51 set_cigar(cigar); //this will also set core.bin
52 add_sequence(qseq, l_qseq);
53 add_quals(quals); //quals must be given as Phred33
54 if (reverse) { b->core.flag |= BAM_FREVERSE ; }
55 }
56
57 GBamRecord::GBamRecord(const char* qname, int32_t flags, int32_t g_tid,
58 int pos, int map_qual, const char* cigar, int32_t mg_tid, int mate_pos,
59 int insert_size, const char* qseq, const char* quals,
60 GVec<char*>* aux_strings):exons(1) {
61 //novel=true;
62 bam_header=NULL;
63 b=bam_init1();
64 b->core.tid=g_tid;
65 b->core.pos = (pos<=0) ? -1 : pos-1; //BAM is 0-based
66 b->core.qual=map_qual;
67 int l_qseq=strlen(qseq);
68 b->core.l_qname=strlen(qname)+1; //includes the \0 at the end
69 memcpy(realloc_bdata(b, b->core.l_qname), qname, b->core.l_qname);
70 set_cigar(cigar); //this will also set core.bin
71 add_sequence(qseq, l_qseq);
72 add_quals(quals); //quals must be given as Phred33
73 set_flags(flags);
74 set_mdata(mg_tid, (int32_t)(mate_pos-1), (int32_t)insert_size);
75 if (aux_strings!=NULL) {
76 for (int i=0;i<aux_strings->Count();i++) {
77 add_aux(aux_strings->Get(i));
78 }
79 }
80 }
81
82 void GBamRecord::set_cigar(const char* cigar) {
83 //requires b->core.pos and b->core.flag to have been set properly PRIOR to this call
84 int doff=b->core.l_qname;
85 uint8_t* after_cigar=NULL;
86 int after_cigar_len=0;
87 uint8_t* prev_bdata=NULL;
88 if (b->data_len>doff) {
89 //cigar string already allocated, replace it
90 int d=b->core.l_qname + b->core.n_cigar * 4;//offset of after-cigar data
91 after_cigar=b->data+d;
92 after_cigar_len=b->data_len-d;
93 }
94 const char *s;
95 char *t;
96 int i, op;
97 long x;
98 b->core.n_cigar = 0;
99 if (cigar != NULL && strcmp(cigar, "*") != 0) {
100 for (s = cigar; *s; ++s) {
101 if (isalpha(*s)) b->core.n_cigar++;
102 else if (!isdigit(*s)) {
103 GError("Error: invalid CIGAR character (%s)\n",cigar);
104 }
105 }
106 if (after_cigar_len>0) { //replace/insert into existing full data
107 prev_bdata=dupalloc_bdata(b, doff + b->core.n_cigar * 4 + after_cigar_len);
108 memcpy((void*)(b->data+doff+b->core.n_cigar*4),(void*)after_cigar, after_cigar_len);
109 free(prev_bdata);
110 }
111 else {
112 realloc_bdata(b, doff + b->core.n_cigar * 4);
113 }
114 for (i = 0, s = cigar; i != b->core.n_cigar; ++i) {
115 x = strtol(s, &t, 10);
116 op = toupper(*t);
117 if (op == 'M' || op == '=' || op == 'X') op = BAM_CMATCH;
118 else if (op == 'I') op = BAM_CINS;
119 else if (op == 'D') op = BAM_CDEL;
120 else if (op == 'N') op = BAM_CREF_SKIP;
121 else if (op == 'S') op = BAM_CSOFT_CLIP;
122 else if (op == 'H') op = BAM_CHARD_CLIP;
123 else if (op == 'P') op = BAM_CPAD;
124 else GError("Error: invalid CIGAR operation (%s)\n",cigar);
125 s = t + 1;
126 bam1_cigar(b)[i] = x << BAM_CIGAR_SHIFT | op;
127 }
128 if (*s) GError("Error: unmatched CIGAR operation (%s)\n",cigar);
129 b->core.bin = bam_reg2bin(b->core.pos, bam_calend(&b->core, bam1_cigar(b)));
130 } else {//no CIGAR string given
131 if (!(b->core.flag&BAM_FUNMAP)) {
132 GMessage("Warning: mapped sequence without CIGAR (%s)\n", (char*)b->data);
133 b->core.flag |= BAM_FUNMAP;
134 }
135 b->core.bin = bam_reg2bin(b->core.pos, b->core.pos + 1);
136 }
137 setupCoordinates();
138 } //set_cigar()
139
140 void GBamRecord::add_sequence(const char* qseq, int slen) {
141 //must be called AFTER set_cigar (cannot replace existing sequence for now)
142 if (qseq==NULL) return; //should we ever care about this?
143 if (slen<0) slen=strlen(qseq);
144 int doff = b->core.l_qname + b->core.n_cigar * 4;
145 if (strcmp(qseq, "*")!=0) {
146 b->core.l_qseq=slen;
147 if (b->core.n_cigar && b->core.l_qseq != (int32_t)bam_cigar2qlen(&b->core, bam1_cigar(b)))
148 GError("Error: CIGAR and sequence length are inconsistent!(%s)\n",
149 qseq);
150 uint8_t* p = (uint8_t*)realloc_bdata(b, doff + (b->core.l_qseq+1)/2 + b->core.l_qseq) + doff;
151 //also allocated quals memory
152 memset(p, 0, (b->core.l_qseq+1)/2);
153 for (int i = 0; i < b->core.l_qseq; ++i)
154 p[i/2] |= bam_nt16_table[(int)qseq[i]] << 4*(1-i%2);
155 } else b->core.l_qseq = 0;
156 }
157
158 void GBamRecord::add_quals(const char* quals) {
159 //requires core.l_qseq already set
160 //and must be called AFTER add_sequence(), which also allocates the memory for quals
161 uint8_t* p = b->data+(b->core.l_qname + b->core.n_cigar * 4 + (b->core.l_qseq+1)/2);
162 if (quals==NULL || strcmp(quals, "*") == 0) {
163 for (int i=0;i < b->core.l_qseq; i++) p[i] = 0xff;
164 return;
165 }
166 for (int i=0;i < b->core.l_qseq; i++) p[i] = quals[i]-33;
167 }
168
169 void GBamRecord::add_aux(const char* str) {
170 //requires: being called AFTER add_quals()
171 static char tag[2];
172 static uint8_t abuf[512];
173 //requires: being called AFTER add_quals()
174 int strl=strlen(str);
175 //int doff = b->core.l_qname + b->core.n_cigar*4 + (b->core.l_qseq+1)/2 + b->core.l_qseq + b->l_aux;
176 //int doff0=doff;
177 if (strl < 6 || str[2] != ':' || str[4] != ':')
178 parse_error("missing colon in auxiliary data");
179 tag[0] = str[0]; tag[1] = str[1];
180 uint8_t atype = str[3];
181 uint8_t* adata=abuf;
182 int alen=0;
183 if (atype == 'A' || atype == 'a' || atype == 'c' || atype == 'C') { // c and C for backward compatibility
184 atype='A';
185 alen=1;
186 adata=(uint8_t*)&str[5];
187 }
188 else if (atype == 'I' || atype == 'i') {
189 long long x=(long long)atoll(str + 5);
190 if (x < 0) {
191 if (x >= -127) {
192 atype='c';
193 abuf[0] = (int8_t)x;
194 alen=1;
195 }
196 else if (x >= -32767) {
197 atype = 's';
198 *(int16_t*)abuf = (int16_t)x;
199 alen=2;
200 }
201 else {
202 atype='i';
203 *(int32_t*)abuf = (int32_t)x;
204 alen=4;
205 if (x < -2147483648ll)
206 GMessage("Parse warning: integer %lld is out of range.", x);
207 }
208 } else { //x >=0
209 if (x <= 255) {
210 atype = 'C';
211 abuf[0] = (uint8_t)x;
212 alen=1;
213 }
214 else if (x <= 65535) {
215 atype='S';
216 *(uint16_t*)abuf = (uint16_t)x;
217 alen=2;
218 }
219 else {
220 atype='I';
221 *(uint32_t*)abuf = (uint32_t)x;
222 alen=4;
223 if (x > 4294967295ll)
224 GMessage("Parse warning: integer %lld is out of range.", x);
225 }
226 }
227 } //integer type
228 else if (atype == 'f') {
229 *(float*)abuf = (float)atof(str + 5);
230 alen = sizeof(float);
231 }
232 else if (atype == 'd') { //?
233 *(float*)abuf = (float)atof(str + 9);
234 alen=8;
235 }
236 else if (atype == 'Z' || atype == 'H') {
237 if (atype == 'H') { // check whether the hex string is valid
238 if ((strl - 5) % 2 == 1) parse_error("length of the hex string not even");
239 for (int i = 0; i < strl - 5; ++i) {
240 int c = toupper(str[5 + i]);
241 if (!((c >= '0' && c <= '9') || (c >= 'A' && c <= 'F')))
242 parse_error("invalid hex character");
243 }
244 }
245 memcpy(abuf, str + 5, strl - 5);
246 abuf[strl-5] = 0;
247 alen=strl-4;
248 } else parse_error("unrecognized aux type");
249 this->add_aux(tag, atype, alen, adata);
250 }//add_aux()
251
252
253 void GBamRecord::setupCoordinates() {
254 uint32_t *cigar = bam1_cigar(b);
255 const bam1_core_t *c = &b->core;
256 if (c->flag & BAM_FUNMAP) return; /* skip unmapped reads */
257 int l=0;
258 start=c->pos+1;
259 int exstart=c->pos;
260 for (int i = 0; i < c->n_cigar; ++i) {
261 int op = cigar[i]&0xf;
262 if (op == BAM_CMATCH || op==BAM_CEQUAL ||
263 op == BAM_CDIFF || op == BAM_CDEL) {
264 l += cigar[i]>>4;
265 }
266 else if (op == BAM_CREF_SKIP) { //N
267 //intron starts
268 //exon ends here
269 GSeg exon(exstart+1,c->pos+l);
270 exons.Add(exon);
271 l += cigar[i]>>4;
272 exstart=c->pos+l;
273 }
274 }
275 GSeg exon(exstart+1,c->pos+l);
276 exons.Add(exon);
277 end=c->pos+l;
278 }
279
280 int GBamRecord::find_tag(const char tag[2], uint8_t* & s, char& tag_type) {
281 //position s at the beginning of tag "data" (after the type char)
282 //returns the length of tag data, and tag type in tag_type
283 s=bam1_aux(b);
284 while (s < b->data + b->data_len) {
285 char key[2];
286 key[0] = (char)s[0]; key[1] = (char)s[1];
287 s += 2; tag_type = (char)*s; ++s;
288 int inc=0;
289 int m_inc=0; //for 'B' case
290 uint8_t sub_type=0; // --,,--
291 switch (tag_type) {
292 case 'A':
293 case 'C':
294 case 'c':
295 inc=1;
296 break;
297 case 'S':
298 case 's':
299 inc=2;
300 break;
301 case 'I':
302 case 'i':
303 case 'f':
304 inc=4;
305 break;
306 case 'd':
307 inc=8;
308 break;
309 case 'B':
310 sub_type = *(s+1);
311 int32_t n;
312 memcpy(&n, s+1, 4);
313 inc += 5;
314 //kputc(type, &str); kputc(':', &str); kputc(sub_type, &str);
315 m_inc=0;
316 if (sub_type == 'c' || sub_type == 'C')
317 { m_inc=1; }
318 else if (sub_type == 's' || sub_type == 'S')
319 { m_inc = 2; }
320 else if ('i' == sub_type || 'I' == sub_type || 'f' == sub_type)
321 { m_inc = 4; }
322 if (m_inc==0) GError("Error: invalid 'B' array subtype (%c)!\n",sub_type);
323 inc += m_inc*n;
324 break;
325 case 'H':
326 case 'Z':
327 while (*(s+inc)) ++inc;
328 break;
329 } //switch (tag_type)
330 if (tag[0]==key[0] && tag[1]==key[1])
331 return inc;
332 s+=inc;
333 }//while aux data
334 return 0;
335 }
336
337 char GBamRecord::tag_char(const char tag[2]) { //retrieve tag data as single char
338 uint8_t *s;
339 char tag_type=0;
340 int vlen=find_tag(tag, s, tag_type);
341 if (vlen==0) return 0;
342 //if (vlen>1) GWarning("Warning: tag %c%c value has length %d, but char was expected.\n",
343 // tag[0],tag[1],vlen);
344 return (char)s[0];
345 }
346
347 int GBamRecord::tag_int(const char tag[2]) { //get the numeric value of tag
348 uint8_t *s;
349 char tag_type=0;
350 int vlen=find_tag(tag, s, tag_type);
351 if (vlen==0) return 0;
352 if (vlen==1) return (int)(*(int8_t*)s);
353 else if (vlen==2) return (int)(*(int16_t*)s);
354 else if (vlen==4) return (int)(*(int32_t*)s);
355 else GMessage("Warning: tag %c%c value has length %d, but int type was expected.\n",
356 tag[0],tag[1], vlen);
357 return 0;
358 }
359
360 char* GBamRecord::tag_str(const char tag[2]) { //return string value for a tag
361 uint8_t *s;
362 char tag_type=0;
363 int vlen=find_tag(tag, s, tag_type);
364 if (vlen==0) return NULL; //not found
365 //if (vlen>1) GWarning("Warning: tag %c%c value has length %d, but char was expected.\n",
366 // tag[0],tag[1],vlen);
367 return (char *)s;
368 }
369
370 char GBamRecord::spliceStrand() { // '+', '-' from the XS tag, or 0 if no XS tag
371 uint8_t *s;
372 char tag_type=0;
373 int vlen=find_tag("XS", s, tag_type);
374 if (vlen==0) return '.';
375 return (char)s[0];
376 }
377
378 char* GBamRecord::sequence() { //user must free this after use
379 char *s = (char*)bam1_seq(b);
380 char* qseq=NULL;
381 GMALLOC(qseq, (b->core.l_qseq+1));
382 int i;
383 for (i=0;i<(b->core.l_qseq);i++) {
384 int8_t v = bam1_seqi(s,i);
385 qseq[i] = bam_nt16_rev_table[v];
386 }
387 qseq[i] = 0;
388 return qseq;
389 }
390
391 char* GBamRecord::qualities() {//user must free this after use
392 char *qual = (char*)bam1_qual(b);
393 char* qv=NULL;
394 GMALLOC(qv, (b->core.l_qseq+1) );
395 int i;
396 for(i=0;i<(b->core.l_qseq);i++) {
397 qv[i]=qual[i]+33;
398 }
399 qv[i]=0;
400 return qv;
401 }
402
403 char* GBamRecord::cigar() { //returns text version of the CIGAR string; must be freed by user
404 kstring_t str;
405 str.l = str.m = 0; str.s = 0;
406 if (b->core.n_cigar == 0) kputc('*', &str);
407 else {
408 for (int i = 0; i < b->core.n_cigar; ++i) {
409 kputw(bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, &str);
410 kputc("MIDNSHP=X"[bam1_cigar(b)[i]&BAM_CIGAR_MASK], &str);
411 }
412 }
413 return str.s;
414 }