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root/gclib/gclib/GBam.cpp
Revision: 232
Committed: Wed Apr 4 18:36:58 2012 UTC (7 years, 6 months ago) by gpertea
File size: 14390 byte(s)
Log Message:
Daehwan fixed an egregious bug in find_tag()

Line User Rev File contents
1 gpertea 121 #include "GBam.h"
2     #include <ctype.h>
3 gpertea 124 #include "kstring.h"
4 gpertea 121
5 gpertea 133 //auxiliary functions for low level BAM record creation
6 gpertea 121 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 gpertea 124 int pos, bool reverse, const char* qseq,
34     const char* cigar, const char* quals):exons(1) {
35 gpertea 225 novel=true;
36 gpertea 121 bam_header=NULL;
37     b=bam_init1();
38 gpertea 225 if (pos<=0 || gseq_tid<0) {
39 gpertea 121 b->core.pos=-1; //unmapped
40     b->core.flag |= BAM_FUNMAP;
41 gpertea 225 gseq_tid=-1;
42 gpertea 121 }
43     else b->core.pos=pos-1; //BAM is 0-based
44 gpertea 225 b->core.tid=gseq_tid;
45 gpertea 121 b->core.qual=255;
46 gpertea 225 b->core.mtid=-1;
47     b->core.mpos=-1;
48 gpertea 121 int l_qseq=strlen(qseq);
49     //this may not be accurate, setting CIGAR is the correct way
50     //b->core.bin = bam_reg2bin(b->core.pos, b->core.pos+l_qseq-1);
51     b->core.l_qname=strlen(qname)+1; //includes the \0 at the end
52     memcpy(realloc_bdata(b, b->core.l_qname), qname, b->core.l_qname);
53     set_cigar(cigar); //this will also set core.bin
54     add_sequence(qseq, l_qseq);
55     add_quals(quals); //quals must be given as Phred33
56     if (reverse) { b->core.flag |= BAM_FREVERSE ; }
57     }
58    
59     GBamRecord::GBamRecord(const char* qname, int32_t flags, int32_t g_tid,
60     int pos, int map_qual, const char* cigar, int32_t mg_tid, int mate_pos,
61     int insert_size, const char* qseq, const char* quals,
62 gpertea 124 GVec<char*>* aux_strings):exons(1) {
63 gpertea 225 novel=true;
64 gpertea 121 bam_header=NULL;
65     b=bam_init1();
66     b->core.tid=g_tid;
67     b->core.pos = (pos<=0) ? -1 : pos-1; //BAM is 0-based
68     b->core.qual=map_qual;
69     int l_qseq=strlen(qseq);
70     b->core.l_qname=strlen(qname)+1; //includes the \0 at the end
71     memcpy(realloc_bdata(b, b->core.l_qname), qname, b->core.l_qname);
72     set_cigar(cigar); //this will also set core.bin
73     add_sequence(qseq, l_qseq);
74     add_quals(quals); //quals must be given as Phred33
75     set_flags(flags);
76     set_mdata(mg_tid, (int32_t)(mate_pos-1), (int32_t)insert_size);
77     if (aux_strings!=NULL) {
78     for (int i=0;i<aux_strings->Count();i++) {
79     add_aux(aux_strings->Get(i));
80     }
81     }
82     }
83 gpertea 124
84 gpertea 121 void GBamRecord::set_cigar(const char* cigar) {
85     //requires b->core.pos and b->core.flag to have been set properly PRIOR to this call
86     int doff=b->core.l_qname;
87     uint8_t* after_cigar=NULL;
88     int after_cigar_len=0;
89     uint8_t* prev_bdata=NULL;
90     if (b->data_len>doff) {
91     //cigar string already allocated, replace it
92     int d=b->core.l_qname + b->core.n_cigar * 4;//offset of after-cigar data
93     after_cigar=b->data+d;
94     after_cigar_len=b->data_len-d;
95     }
96     const char *s;
97     char *t;
98     int i, op;
99     long x;
100     b->core.n_cigar = 0;
101     if (cigar != NULL && strcmp(cigar, "*") != 0) {
102     for (s = cigar; *s; ++s) {
103     if (isalpha(*s)) b->core.n_cigar++;
104     else if (!isdigit(*s)) {
105     GError("Error: invalid CIGAR character (%s)\n",cigar);
106     }
107     }
108     if (after_cigar_len>0) { //replace/insert into existing full data
109     prev_bdata=dupalloc_bdata(b, doff + b->core.n_cigar * 4 + after_cigar_len);
110     memcpy((void*)(b->data+doff+b->core.n_cigar*4),(void*)after_cigar, after_cigar_len);
111     free(prev_bdata);
112     }
113     else {
114     realloc_bdata(b, doff + b->core.n_cigar * 4);
115     }
116     for (i = 0, s = cigar; i != b->core.n_cigar; ++i) {
117     x = strtol(s, &t, 10);
118     op = toupper(*t);
119     if (op == 'M' || op == '=' || op == 'X') op = BAM_CMATCH;
120     else if (op == 'I') op = BAM_CINS;
121     else if (op == 'D') op = BAM_CDEL;
122     else if (op == 'N') op = BAM_CREF_SKIP;
123     else if (op == 'S') op = BAM_CSOFT_CLIP;
124     else if (op == 'H') op = BAM_CHARD_CLIP;
125     else if (op == 'P') op = BAM_CPAD;
126     else GError("Error: invalid CIGAR operation (%s)\n",cigar);
127     s = t + 1;
128     bam1_cigar(b)[i] = x << BAM_CIGAR_SHIFT | op;
129     }
130     if (*s) GError("Error: unmatched CIGAR operation (%s)\n",cigar);
131     b->core.bin = bam_reg2bin(b->core.pos, bam_calend(&b->core, bam1_cigar(b)));
132     } else {//no CIGAR string given
133     if (!(b->core.flag&BAM_FUNMAP)) {
134     GMessage("Warning: mapped sequence without CIGAR (%s)\n", (char*)b->data);
135     b->core.flag |= BAM_FUNMAP;
136     }
137     b->core.bin = bam_reg2bin(b->core.pos, b->core.pos + 1);
138     }
139 gpertea 124 setupCoordinates();
140 gpertea 121 } //set_cigar()
141    
142     void GBamRecord::add_sequence(const char* qseq, int slen) {
143     //must be called AFTER set_cigar (cannot replace existing sequence for now)
144     if (qseq==NULL) return; //should we ever care about this?
145     if (slen<0) slen=strlen(qseq);
146     int doff = b->core.l_qname + b->core.n_cigar * 4;
147     if (strcmp(qseq, "*")!=0) {
148     b->core.l_qseq=slen;
149     if (b->core.n_cigar && b->core.l_qseq != (int32_t)bam_cigar2qlen(&b->core, bam1_cigar(b)))
150     GError("Error: CIGAR and sequence length are inconsistent!(%s)\n",
151     qseq);
152     uint8_t* p = (uint8_t*)realloc_bdata(b, doff + (b->core.l_qseq+1)/2 + b->core.l_qseq) + doff;
153     //also allocated quals memory
154     memset(p, 0, (b->core.l_qseq+1)/2);
155     for (int i = 0; i < b->core.l_qseq; ++i)
156     p[i/2] |= bam_nt16_table[(int)qseq[i]] << 4*(1-i%2);
157     } else b->core.l_qseq = 0;
158     }
159    
160     void GBamRecord::add_quals(const char* quals) {
161     //requires core.l_qseq already set
162     //and must be called AFTER add_sequence(), which also allocates the memory for quals
163     uint8_t* p = b->data+(b->core.l_qname + b->core.n_cigar * 4 + (b->core.l_qseq+1)/2);
164     if (quals==NULL || strcmp(quals, "*") == 0) {
165     for (int i=0;i < b->core.l_qseq; i++) p[i] = 0xff;
166     return;
167     }
168     for (int i=0;i < b->core.l_qseq; i++) p[i] = quals[i]-33;
169     }
170    
171     void GBamRecord::add_aux(const char* str) {
172     //requires: being called AFTER add_quals()
173     int strl=strlen(str);
174     //int doff = b->core.l_qname + b->core.n_cigar*4 + (b->core.l_qseq+1)/2 + b->core.l_qseq + b->l_aux;
175     //int doff0=doff;
176     if (strl < 6 || str[2] != ':' || str[4] != ':')
177     parse_error("missing colon in auxiliary data");
178     tag[0] = str[0]; tag[1] = str[1];
179     uint8_t atype = str[3];
180     uint8_t* adata=abuf;
181     int alen=0;
182     if (atype == 'A' || atype == 'a' || atype == 'c' || atype == 'C') { // c and C for backward compatibility
183     atype='A';
184     alen=1;
185     adata=(uint8_t*)&str[5];
186     }
187     else if (atype == 'I' || atype == 'i') {
188     long long x=(long long)atoll(str + 5);
189     if (x < 0) {
190     if (x >= -127) {
191     atype='c';
192     abuf[0] = (int8_t)x;
193     alen=1;
194     }
195     else if (x >= -32767) {
196     atype = 's';
197     *(int16_t*)abuf = (int16_t)x;
198     alen=2;
199     }
200     else {
201     atype='i';
202     *(int32_t*)abuf = (int32_t)x;
203     alen=4;
204     if (x < -2147483648ll)
205     GMessage("Parse warning: integer %lld is out of range.", x);
206     }
207     } else { //x >=0
208     if (x <= 255) {
209     atype = 'C';
210     abuf[0] = (uint8_t)x;
211     alen=1;
212     }
213     else if (x <= 65535) {
214     atype='S';
215     *(uint16_t*)abuf = (uint16_t)x;
216     alen=2;
217     }
218     else {
219     atype='I';
220     *(uint32_t*)abuf = (uint32_t)x;
221     alen=4;
222     if (x > 4294967295ll)
223     GMessage("Parse warning: integer %lld is out of range.", x);
224     }
225     }
226     } //integer type
227     else if (atype == 'f') {
228     *(float*)abuf = (float)atof(str + 5);
229     alen = sizeof(float);
230     }
231     else if (atype == 'd') { //?
232     *(float*)abuf = (float)atof(str + 9);
233     alen=8;
234     }
235     else if (atype == 'Z' || atype == 'H') {
236     if (atype == 'H') { // check whether the hex string is valid
237     if ((strl - 5) % 2 == 1) parse_error("length of the hex string not even");
238     for (int i = 0; i < strl - 5; ++i) {
239     int c = toupper(str[5 + i]);
240     if (!((c >= '0' && c <= '9') || (c >= 'A' && c <= 'F')))
241     parse_error("invalid hex character");
242     }
243     }
244     memcpy(abuf, str + 5, strl - 5);
245     abuf[strl-5] = 0;
246     alen=strl-4;
247     } else parse_error("unrecognized aux type");
248     this->add_aux(tag, atype, alen, adata);
249     }//add_aux()
250    
251    
252     void GBamRecord::setupCoordinates() {
253     uint32_t *cigar = bam1_cigar(b);
254     const bam1_core_t *c = &b->core;
255 gpertea 124 if (c->flag & BAM_FUNMAP) return; /* skip unmapped reads */
256 gpertea 121 int l=0;
257 gpertea 124 start=c->pos+1;
258     int exstart=c->pos;
259     for (int i = 0; i < c->n_cigar; ++i) {
260     int op = cigar[i]&0xf;
261     if (op == BAM_CMATCH || op==BAM_CEQUAL ||
262     op == BAM_CDIFF || op == BAM_CDEL) {
263 gpertea 121 l += cigar[i]>>4;
264 gpertea 124 }
265     else if (op == BAM_CREF_SKIP) { //N
266     //intron starts
267     //exon ends here
268 gpertea 130 GSeg exon(exstart+1,c->pos+l);
269 gpertea 126 exons.Add(exon);
270 gpertea 124 l += cigar[i]>>4;
271     exstart=c->pos+l;
272     }
273     }
274 gpertea 130 GSeg exon(exstart+1,c->pos+l);
275 gpertea 126 exons.Add(exon);
276 gpertea 124 end=c->pos+l;
277 gpertea 121 }
278 gpertea 124
279     int GBamRecord::find_tag(const char tag[2], uint8_t* & s, char& tag_type) {
280     //position s at the beginning of tag "data" (after the type char)
281     //returns the length of tag data, and tag type in tag_type
282 gpertea 214 uint8_t* aux_start=bam1_aux(b);
283     s=aux_start;
284     while (s < aux_start + b->l_aux - 1) {
285 gpertea 124 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 gpertea 214 if (m_inc==0)
323 gpertea 232 GError("Error: invalid 'B' array subtype (%c)!\n",sub_type);
324 gpertea 124 inc += m_inc*n;
325     break;
326     case 'H':
327     case 'Z':
328     while (*(s+inc)) ++inc;
329 gpertea 232 ++inc; // to skip the terminating \0
330 gpertea 124 break;
331     } //switch (tag_type)
332 gpertea 232 if (tag[0]==key[0] && tag[1]==key[1]) {
333 gpertea 124 return inc;
334 gpertea 232 }
335 gpertea 127 s+=inc;
336 gpertea 124 }//while aux data
337     return 0;
338     }
339    
340     char GBamRecord::tag_char(const char tag[2]) { //retrieve tag data as single char
341     uint8_t *s;
342     char tag_type=0;
343     int vlen=find_tag(tag, s, tag_type);
344     if (vlen==0) return 0;
345     //if (vlen>1) GWarning("Warning: tag %c%c value has length %d, but char was expected.\n",
346     // tag[0],tag[1],vlen);
347     return (char)s[0];
348     }
349    
350     int GBamRecord::tag_int(const char tag[2]) { //get the numeric value of tag
351     uint8_t *s;
352     char tag_type=0;
353     int vlen=find_tag(tag, s, tag_type);
354     if (vlen==0) return 0;
355     if (vlen==1) return (int)(*(int8_t*)s);
356     else if (vlen==2) return (int)(*(int16_t*)s);
357     else if (vlen==4) return (int)(*(int32_t*)s);
358     else GMessage("Warning: tag %c%c value has length %d, but int type was expected.\n",
359     tag[0],tag[1], vlen);
360     return 0;
361     }
362    
363     char* GBamRecord::tag_str(const char tag[2]) { //return string value for a tag
364     uint8_t *s;
365     char tag_type=0;
366     int vlen=find_tag(tag, s, tag_type);
367     if (vlen==0) return NULL; //not found
368     //if (vlen>1) GWarning("Warning: tag %c%c value has length %d, but char was expected.\n",
369     // tag[0],tag[1],vlen);
370     return (char *)s;
371     }
372    
373     char GBamRecord::spliceStrand() { // '+', '-' from the XS tag, or 0 if no XS tag
374     uint8_t *s;
375     char tag_type=0;
376     int vlen=find_tag("XS", s, tag_type);
377     if (vlen==0) return '.';
378     return (char)s[0];
379     }
380    
381     char* GBamRecord::sequence() { //user must free this after use
382     char *s = (char*)bam1_seq(b);
383     char* qseq=NULL;
384     GMALLOC(qseq, (b->core.l_qseq+1));
385     int i;
386     for (i=0;i<(b->core.l_qseq);i++) {
387     int8_t v = bam1_seqi(s,i);
388     qseq[i] = bam_nt16_rev_table[v];
389     }
390     qseq[i] = 0;
391     return qseq;
392     }
393    
394     char* GBamRecord::qualities() {//user must free this after use
395     char *qual = (char*)bam1_qual(b);
396     char* qv=NULL;
397     GMALLOC(qv, (b->core.l_qseq+1) );
398     int i;
399     for(i=0;i<(b->core.l_qseq);i++) {
400     qv[i]=qual[i]+33;
401     }
402     qv[i]=0;
403     return qv;
404     }
405    
406     char* GBamRecord::cigar() { //returns text version of the CIGAR string; must be freed by user
407     kstring_t str;
408     str.l = str.m = 0; str.s = 0;
409     if (b->core.n_cigar == 0) kputc('*', &str);
410     else {
411     for (int i = 0; i < b->core.n_cigar; ++i) {
412     kputw(bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, &str);
413     kputc("MIDNSHP=X"[bam1_cigar(b)[i]&BAM_CIGAR_MASK], &str);
414     }
415     }
416     return str.s;
417     }