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root/gclib/gclib/GBam.h
Revision: 144
Committed: Thu Dec 22 19:15:46 2011 UTC (7 years, 9 months ago) by gpertea
File size: 11467 byte(s)
Log Message:
added GBitVec.h; removed operator> requirement for sorted vectors; swap() is now template Gswap()

Line File contents
1 #ifndef _G_BAM_H
2 #define _G_BAM_H
3 #include "GBase.h"
4 #include "GList.hh"
5 #include "bam.h"
6 #include "sam.h"
7
8
9 class GBamReader;
10 class GBamWriter;
11
12 class GBamRecord: public GSeg {
13 friend class GBamReader;
14 friend class GBamWriter;
15 bam1_t* b;
16 // b->data has the following strings concatenated:
17 // qname (including the terminal \0)
18 // +cigar (each event encoded on 32 bits)
19 // +seq (4bit-encoded)
20 // +qual
21 // +aux
22 //bool novel; //created from scratch, not from a given bam1_t* record
23 bam_header_t* bam_header;
24
25 public:
26 GVec<GSeg> exons;
27 //created from a reader:
28 GBamRecord(bam1_t* from_b=NULL, bam_header_t* b_header=NULL):exons(1) {
29 bam_header=NULL;
30 if (from_b==NULL) {
31 b=bam_init1();
32 //novel=true;
33 }
34 else {
35 b=from_b; //it'll take over from_b and FREE it when destroyed
36 //novel=false;
37 }
38 bam_header=b_header;
39 setupCoordinates();//sets start, end coordinate and populates exons array
40 }
41
42 const GBamRecord& operator=(GBamRecord& r) {
43 //make a new copy of the bam1_t record etc.
44 clear();
45 b=bam_dup1(r.b);
46 //novel=true; //will also free b when destroyed
47 start=r.start;
48 end=r.end;
49 exons = r.exons;
50 return *this;
51 }
52
53 void setupCoordinates();
54 void clear() {
55 //if (novel) {
56 bam_destroy1(b);
57 // novel=false;
58 // }
59 b=NULL;
60 exons.Clear();
61 bam_header=NULL;
62 }
63
64 ~GBamRecord() {
65 clear();
66 }
67
68 void parse_error(const char* s) {
69 GError("BAM parsing error: %s\n", s);
70 }
71
72 bam1_t* get_b() { return b; }
73
74 void set_mdata(int32_t mtid, int32_t m0pos, //0-based coordinate, -1 if not available
75 int32_t isize=0) { //mate info for current record
76 b->core.mtid=mtid;
77 b->core.mpos=m0pos; // should be -1 if '*'
78 b->core.isize=isize; //should be 0 if not available
79 }
80
81 void set_flags(uint16_t flags) {
82 b->core.flag=flags;
83 }
84
85 //creates a new record from 1-based alignment coordinate
86 //quals should be given as Phred33
87 //Warning: pos and mate_pos must be given 1-based!
88 GBamRecord(const char* qname, int32_t gseq_tid,
89 int pos, bool reverse, const char* qseq, const char* cigar=NULL, const char* quals=NULL);
90 GBamRecord(const char* qname, int32_t flags, int32_t g_tid,
91 int pos, int map_qual, const char* cigar, int32_t mg_tid, int mate_pos,
92 int insert_size, const char* qseq, const char* quals=NULL,
93 GVec<char*>* aux_strings=NULL);
94 //const std::vector<std::string>* aux_strings=NULL);
95 void set_cigar(const char* cigar); //converts and adds CIGAR string given in plain SAM text format
96 void add_sequence(const char* qseq, int slen=-1); //adds the DNA sequence given in plain text format
97 void add_quals(const char* quals); //quality values string in Phred33 format
98 void add_aux(const char* str); //adds one aux field in plain SAM text format (e.g. "NM:i:1")
99 void add_aux(const char tag[2], char atype, int len, uint8_t *data) {
100 int ori_len = b->data_len;
101 b->data_len += 3 + len;
102 b->l_aux += 3 + len;
103 if (b->m_data < b->data_len) {
104 b->m_data = b->data_len;
105 kroundup32(b->m_data);
106 b->data = (uint8_t*)realloc(b->data, b->m_data);
107 }
108 b->data[ori_len] = tag[0]; b->data[ori_len + 1] = tag[1];
109 b->data[ori_len + 2] = atype;
110 memcpy(b->data + ori_len + 3, data, len);
111 }
112 void add_tag(const char tag[2], char atype, int len, uint8_t *data) {
113 //same with add_aux()
114 add_aux(tag,atype,len,data);
115 }
116 //--query methods:
117 uint32_t flags() { return b->core.flag; }
118 bool isUnmapped() { return ((b->core.flag & BAM_FUNMAP) != 0); }
119 bool isMapped() { return ((b->core.flag & BAM_FUNMAP) == 0); }
120 bool isPaired() { return ((b->core.flag & BAM_FPAIRED) != 0); }
121 const char* name() { return bam1_qname(b); }
122 int pairOrder() {
123 //which read in the pair: 0 = unpaired, 1=first read, 2=second read
124 int r=0;
125 if ((b->core.flag & BAM_FREAD1) != 0) r=1;
126 else if ((b->core.flag & BAM_FREAD2) != 0) r=2;
127 return r;
128 }
129 bool revStrand() {
130 //this is the raw alignment strand, NOT the transcription (XS) strand
131 return ((b->core.flag & BAM_FREVERSE) != 0);
132 }
133 const char* refName() {
134 return (bam_header!=NULL) ?
135 ((b->core.tid<0) ? "*" : bam_header->target_name[b->core.tid]) : NULL;
136 }
137 int32_t refId() { return b->core.tid; }
138 int32_t mate_refId() { return b->core.mtid; }
139 const char* mate_refName() {
140 return (bam_header!=NULL) ?
141 ((b->core.mtid<0) ? "*" : bam_header->target_name[b->core.mtid]) : NULL;
142 }
143 int32_t insertSize() { return b->core.isize; }
144 int32_t mate_start() { return b->core.mpos<0? 0 : b->core.mpos+1; }
145
146 int find_tag(const char tag[2], uint8_t* & s, char& tag_type);
147 //position s at the beginning of tag data, tag_type is set to the found tag type
148 //returns length of tag data, or 0 if tag not found
149
150 char* tag_str(const char tag[2]); //return tag value for tag type 'Z'
151 int tag_int(const char tag[2]); //return numeric value of tag (for numeric types)
152 char tag_char(const char tag[2]); //return char value of tag (for type 'A')
153 char spliceStrand(); // '+', '-' from the XS tag, or '.' if no XS tag
154
155 char* sequence(); //user should free after use
156 char* qualities();//user should free after use
157 char* cigar(); //returns text version of the CIGAR string; user must free
158 };
159
160
161 class GBamReader {
162 samfile_t* bam_file;
163 char* fname;
164 public:
165 void bopen(const char* filename) {
166 if (strcmp(filename, "-")==0) {
167 //if stdin was given, we HAVE to assume it's text SAM format, sorry
168 bam_file=samopen(filename, "r", 0);
169 }
170 else {
171 //BAM files have the zlib signature bytes at the beginning: 1F 8B 08
172 //if that's not present, we assume sam file
173 FILE* f=fopen(filename, "rb");
174 if (f==NULL) GError("Error opening file %s!\n", filename);
175 byte fsig[3];
176 size_t rd=fread(fsig, 1, 3, f);
177 if (rd<3) GError("Error reading from file %s!\n",filename);
178 if ((fsig[0]==0x1F && fsig[1]==0x8B && fsig[2]==0x08) ||
179 (fsig[0]=='B' && fsig[1]=='A' && fsig[2]=='M')) {
180 bam_file=samopen(filename, "rb", 0); //BAM or uncompressed BAM
181 }
182 else { //assume text SAM file
183 bam_file=samopen(filename, "r", 0);
184 }
185 }
186 if (bam_file==NULL)
187 GError("Error: could not open SAM file %s!\n",filename);
188 fname=Gstrdup(filename);
189 }
190 GBamReader(const char* fn) {
191 bam_file=NULL;
192 fname=NULL;
193 bopen(fn);
194 }
195
196 bam_header_t* header() {
197 return bam_file? bam_file->header : NULL;
198 }
199 void bclose() {
200 if (bam_file) {
201 samclose(bam_file);
202 bam_file=NULL;
203 }
204 }
205 ~GBamReader() {
206 bclose();
207 GFREE(fname);
208 }
209 void rewind() {
210 if (fname==NULL) {
211 GMessage("Warning: GBamReader::rewind() called without a file name.\n");
212 return;
213 }
214 bclose();
215 char* ifname=fname;
216 bopen(ifname);
217 GFREE(ifname);
218 }
219
220 GBamRecord* next() {
221 if (bam_file==NULL)
222 GError("Warning: GBamReader::next() called with no open file.\n");
223 bam1_t* b = bam_init1();
224 if (samread(bam_file, b) >= 0) {
225 GBamRecord* bamrec=new GBamRecord(b, bam_file->header);
226 return bamrec;
227 }
228 else {
229 bam_destroy1(b);
230 return NULL;
231 }
232 }
233 };
234
235
236 class GBamWriter {
237 samfile_t* bam_file;
238 bam_header_t* bam_header;
239 public:
240 void create(const char* fname, bool uncompressed=false) {
241 if (bam_header==NULL)
242 GError("Error: no bam_header for GBamWriter::create()!\n");
243 if (uncompressed) {
244 bam_file=samopen(fname, "wbu", bam_header);
245 }
246 else {
247 bam_file=samopen(fname, "wb", bam_header);
248 }
249 if (bam_file==NULL)
250 GError("Error: could not create BAM file %s!\n",fname);
251 }
252 void create(const char* fname, bam_header_t* bh, bool uncompressed=false) {
253 bam_header=bh;
254 create(fname,uncompressed);
255 }
256
257 GBamWriter(const char* fname, bam_header_t* bh, bool uncompressed=false) {
258 create(fname, bh, uncompressed);
259 }
260
261 GBamWriter(const char* fname, const char* samfname, bool uncompressed=false) {
262 tamFile samf_in=sam_open(samfname);
263 if (samf_in==NULL)
264 GError("Error: could not open SAM file %s\n", samfname);
265 bam_header=sam_header_read(samf_in);
266 if (bam_header==NULL)
267 GError("Error: could not read SAM header from %s!\n",samfname);
268 sam_close(samf_in);
269 create(fname, uncompressed);
270 }
271
272 ~GBamWriter() {
273 samclose(bam_file);
274 bam_header_destroy(bam_header);
275 }
276 bam_header_t* get_header() { return bam_header; }
277 int32_t get_tid(const char *seq_name) {
278 if (bam_header==NULL)
279 GError("Error: missing SAM header (get_tid())\n");
280 return bam_get_tid(bam_header, seq_name);
281 }
282
283 //just a convenience function for creating a new record, but it's NOT written
284 //given pos must be 1-based (so it'll be stored as pos-1 because BAM is 0-based)
285 GBamRecord* new_record(const char* qname, const char* gseqname,
286 int pos, bool reverse, const char* qseq, const char* cigar=NULL, const char* qual=NULL) {
287 int32_t gseq_tid=get_tid(gseqname);
288 if (gseq_tid < 0 && strcmp(gseqname, "*")) {
289 if (bam_header->n_targets == 0) {
290 GError("Error: missing/invalid SAM header\n");
291 } else
292 GMessage("Warning: reference '%s' not found in header, will consider it '*'.\n",
293 gseqname);
294 }
295
296 return (new GBamRecord(qname, gseq_tid, pos, reverse, qseq, cigar, qual));
297 }
298
299 GBamRecord* new_record(const char* qname, int32_t flags, const char* gseqname,
300 int pos, int map_qual, const char* cigar, const char* mgseqname, int mate_pos,
301 int insert_size, const char* qseq, const char* quals=NULL,
302 GVec<char*>* aux_strings=NULL) {
303 int32_t gseq_tid=get_tid(gseqname);
304 if (gseq_tid < 0 && strcmp(gseqname, "*")) {
305 if (bam_header->n_targets == 0) {
306 GError("Error: missing/invalid SAM header\n");
307 } else
308 GMessage("Warning: reference '%s' not found in header, will consider it '*'.\n",
309 gseqname);
310 }
311 int32_t mgseq_tid=-1;
312 if (mgseqname!=NULL) {
313 if (strcmp(mgseqname, "=")==0) {
314 mgseq_tid=gseq_tid;
315 }
316 else {
317 mgseq_tid=get_tid(mgseqname);
318 if (mgseq_tid < 0 && strcmp(mgseqname, "*")) {
319 GMessage("Warning: reference '%s' not found in header, will consider it '*'.\n",
320 mgseqname);
321 }
322 }
323 }
324 return (new GBamRecord(qname, flags, gseq_tid, pos, map_qual, cigar,
325 mgseq_tid, mate_pos, insert_size, qseq, quals, aux_strings));
326 }
327
328 void write(GBamRecord* brec) {
329 if (brec!=NULL)
330 samwrite(this->bam_file,brec->get_b());
331 }
332 void write(bam1_t* b) {
333 samwrite(this->bam_file, b);
334 }
335 };
336
337 #endif