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root/gclib/gclib/GBam.h
Revision: 225
Committed: Mon Mar 26 12:07:13 2012 UTC (7 years, 7 months ago) by gpertea
File size: 11742 byte(s)
Log Message:
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1 gpertea 121 #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 gpertea 225 bool novel; //created from scratch, not from a given bam1_t* record
23 gpertea 121 bam_header_t* bam_header;
24 gpertea 225 char tag[2];
25     uint8_t abuf[512];
26 gpertea 121 public:
27 gpertea 126 GVec<GSeg> exons;
28     //created from a reader:
29 gpertea 124 GBamRecord(bam1_t* from_b=NULL, bam_header_t* b_header=NULL):exons(1) {
30 gpertea 121 bam_header=NULL;
31     if (from_b==NULL) {
32     b=bam_init1();
33 gpertea 225 novel=true;
34 gpertea 121 }
35     else {
36 gpertea 225 b=from_b; //it'll take over from_b but not free it when destroyed
37     novel=false;
38 gpertea 121 }
39     bam_header=b_header;
40     setupCoordinates();//sets start, end coordinate and populates exons array
41     }
42 gpertea 126
43     const GBamRecord& operator=(GBamRecord& r) {
44     //make a new copy of the bam1_t record etc.
45     clear();
46     b=bam_dup1(r.b);
47 gpertea 225 novel=true; //will also free b when destroyed
48 gpertea 126 start=r.start;
49     end=r.end;
50     exons = r.exons;
51     return *this;
52     }
53    
54 gpertea 121 void setupCoordinates();
55     void clear() {
56 gpertea 225 if (novel) {
57     bam_destroy1(b);
58     novel=false;
59     }
60 gpertea 126 b=NULL;
61     exons.Clear();
62     bam_header=NULL;
63 gpertea 121 }
64    
65     ~GBamRecord() {
66 gpertea 126 clear();
67 gpertea 121 }
68    
69     void parse_error(const char* s) {
70     GError("BAM parsing error: %s\n", s);
71     }
72    
73     bam1_t* get_b() { return b; }
74    
75     void set_mdata(int32_t mtid, int32_t m0pos, //0-based coordinate, -1 if not available
76     int32_t isize=0) { //mate info for current record
77     b->core.mtid=mtid;
78     b->core.mpos=m0pos; // should be -1 if '*'
79     b->core.isize=isize; //should be 0 if not available
80     }
81    
82     void set_flags(uint16_t flags) {
83     b->core.flag=flags;
84     }
85    
86     //creates a new record from 1-based alignment coordinate
87     //quals should be given as Phred33
88     //Warning: pos and mate_pos must be given 1-based!
89     GBamRecord(const char* qname, int32_t gseq_tid,
90     int pos, bool reverse, const char* qseq, const char* cigar=NULL, const char* quals=NULL);
91     GBamRecord(const char* qname, int32_t flags, int32_t g_tid,
92     int pos, int map_qual, const char* cigar, int32_t mg_tid, int mate_pos,
93     int insert_size, const char* qseq, const char* quals=NULL,
94     GVec<char*>* aux_strings=NULL);
95     //const std::vector<std::string>* aux_strings=NULL);
96     void set_cigar(const char* cigar); //converts and adds CIGAR string given in plain SAM text format
97     void add_sequence(const char* qseq, int slen=-1); //adds the DNA sequence given in plain text format
98     void add_quals(const char* quals); //quality values string in Phred33 format
99     void add_aux(const char* str); //adds one aux field in plain SAM text format (e.g. "NM:i:1")
100     void add_aux(const char tag[2], char atype, int len, uint8_t *data) {
101 gpertea 225 //IMPORTANT: strings (Z,H) should include the terminal \0
102     int addz=0;
103     if ((atype=='Z' || atype=='H') && data[len-1]!=0) {
104     addz=1;
105     }
106 gpertea 121 int ori_len = b->data_len;
107 gpertea 225 b->data_len += 3 + len + addz;
108     b->l_aux += 3 + len + addz;
109 gpertea 121 if (b->m_data < b->data_len) {
110     b->m_data = b->data_len;
111     kroundup32(b->m_data);
112     b->data = (uint8_t*)realloc(b->data, b->m_data);
113     }
114     b->data[ori_len] = tag[0]; b->data[ori_len + 1] = tag[1];
115     b->data[ori_len + 2] = atype;
116 gpertea 225 if (addz) {
117     b->data[ori_len+len+4]=0;
118     }
119 gpertea 121 memcpy(b->data + ori_len + 3, data, len);
120     }
121 gpertea 225
122 gpertea 121 void add_tag(const char tag[2], char atype, int len, uint8_t *data) {
123     //same with add_aux()
124     add_aux(tag,atype,len,data);
125     }
126     //--query methods:
127     uint32_t flags() { return b->core.flag; }
128     bool isUnmapped() { return ((b->core.flag & BAM_FUNMAP) != 0); }
129     bool isMapped() { return ((b->core.flag & BAM_FUNMAP) == 0); }
130     bool isPaired() { return ((b->core.flag & BAM_FPAIRED) != 0); }
131 gpertea 124 const char* name() { return bam1_qname(b); }
132 gpertea 132 int pairOrder() {
133     //which read in the pair: 0 = unpaired, 1=first read, 2=second read
134 gpertea 121 int r=0;
135     if ((b->core.flag & BAM_FREAD1) != 0) r=1;
136     else if ((b->core.flag & BAM_FREAD2) != 0) r=2;
137     return r;
138     }
139 gpertea 132 bool revStrand() {
140     //this is the raw alignment strand, NOT the transcription (XS) strand
141     return ((b->core.flag & BAM_FREVERSE) != 0);
142     }
143     const char* refName() {
144     return (bam_header!=NULL) ?
145     ((b->core.tid<0) ? "*" : bam_header->target_name[b->core.tid]) : NULL;
146     }
147 gpertea 121 int32_t refId() { return b->core.tid; }
148 gpertea 132 int32_t mate_refId() { return b->core.mtid; }
149     const char* mate_refName() {
150     return (bam_header!=NULL) ?
151     ((b->core.mtid<0) ? "*" : bam_header->target_name[b->core.mtid]) : NULL;
152     }
153     int32_t insertSize() { return b->core.isize; }
154     int32_t mate_start() { return b->core.mpos<0? 0 : b->core.mpos+1; }
155 gpertea 121
156 gpertea 124 int find_tag(const char tag[2], uint8_t* & s, char& tag_type);
157 gpertea 132 //position s at the beginning of tag data, tag_type is set to the found tag type
158     //returns length of tag data, or 0 if tag not found
159    
160 gpertea 124 char* tag_str(const char tag[2]); //return tag value for tag type 'Z'
161     int tag_int(const char tag[2]); //return numeric value of tag (for numeric types)
162     char tag_char(const char tag[2]); //return char value of tag (for type 'A')
163     char spliceStrand(); // '+', '-' from the XS tag, or '.' if no XS tag
164 gpertea 132
165     char* sequence(); //user should free after use
166     char* qualities();//user should free after use
167     char* cigar(); //returns text version of the CIGAR string; user must free
168 gpertea 121 };
169    
170    
171     class GBamReader {
172     samfile_t* bam_file;
173     char* fname;
174     public:
175 gpertea 126 void bopen(const char* filename) {
176 gpertea 144 if (strcmp(filename, "-")==0) {
177     //if stdin was given, we HAVE to assume it's text SAM format, sorry
178     bam_file=samopen(filename, "r", 0);
179     }
180     else {
181     //BAM files have the zlib signature bytes at the beginning: 1F 8B 08
182     //if that's not present, we assume sam file
183     FILE* f=fopen(filename, "rb");
184     if (f==NULL) GError("Error opening file %s!\n", filename);
185     byte fsig[3];
186     size_t rd=fread(fsig, 1, 3, f);
187     if (rd<3) GError("Error reading from file %s!\n",filename);
188     if ((fsig[0]==0x1F && fsig[1]==0x8B && fsig[2]==0x08) ||
189     (fsig[0]=='B' && fsig[1]=='A' && fsig[2]=='M')) {
190     bam_file=samopen(filename, "rb", 0); //BAM or uncompressed BAM
191     }
192     else { //assume text SAM file
193     bam_file=samopen(filename, "r", 0);
194     }
195     }
196 gpertea 121 if (bam_file==NULL)
197     GError("Error: could not open SAM file %s!\n",filename);
198     fname=Gstrdup(filename);
199     }
200 gpertea 129 GBamReader(const char* fn) {
201 gpertea 126 bam_file=NULL;
202 gpertea 121 fname=NULL;
203 gpertea 129 bopen(fn);
204 gpertea 121 }
205    
206 gpertea 126 bam_header_t* header() {
207     return bam_file? bam_file->header : NULL;
208     }
209     void bclose() {
210     if (bam_file) {
211     samclose(bam_file);
212     bam_file=NULL;
213     }
214     }
215 gpertea 121 ~GBamReader() {
216 gpertea 126 bclose();
217 gpertea 121 GFREE(fname);
218     }
219 gpertea 126 void rewind() {
220     if (fname==NULL) {
221     GMessage("Warning: GBamReader::rewind() called without a file name.\n");
222     return;
223     }
224     bclose();
225     char* ifname=fname;
226     bopen(ifname);
227     GFREE(ifname);
228     }
229 gpertea 121
230 gpertea 126 GBamRecord* next() {
231     if (bam_file==NULL)
232     GError("Warning: GBamReader::next() called with no open file.\n");
233     bam1_t* b = bam_init1();
234     if (samread(bam_file, b) >= 0) {
235     GBamRecord* bamrec=new GBamRecord(b, bam_file->header);
236     return bamrec;
237     }
238     else {
239     bam_destroy1(b);
240     return NULL;
241     }
242     }
243 gpertea 121 };
244    
245    
246     class GBamWriter {
247     samfile_t* bam_file;
248     bam_header_t* bam_header;
249     public:
250     void create(const char* fname, bool uncompressed=false) {
251     if (bam_header==NULL)
252     GError("Error: no bam_header for GBamWriter::create()!\n");
253     if (uncompressed) {
254     bam_file=samopen(fname, "wbu", bam_header);
255     }
256     else {
257     bam_file=samopen(fname, "wb", bam_header);
258     }
259     if (bam_file==NULL)
260     GError("Error: could not create BAM file %s!\n",fname);
261     }
262     void create(const char* fname, bam_header_t* bh, bool uncompressed=false) {
263     bam_header=bh;
264     create(fname,uncompressed);
265     }
266    
267     GBamWriter(const char* fname, bam_header_t* bh, bool uncompressed=false) {
268     create(fname, bh, uncompressed);
269     }
270    
271     GBamWriter(const char* fname, const char* samfname, bool uncompressed=false) {
272     tamFile samf_in=sam_open(samfname);
273     if (samf_in==NULL)
274     GError("Error: could not open SAM file %s\n", samfname);
275     bam_header=sam_header_read(samf_in);
276     if (bam_header==NULL)
277     GError("Error: could not read SAM header from %s!\n",samfname);
278     sam_close(samf_in);
279     create(fname, uncompressed);
280     }
281    
282     ~GBamWriter() {
283     samclose(bam_file);
284     bam_header_destroy(bam_header);
285     }
286     bam_header_t* get_header() { return bam_header; }
287     int32_t get_tid(const char *seq_name) {
288     if (bam_header==NULL)
289     GError("Error: missing SAM header (get_tid())\n");
290     return bam_get_tid(bam_header, seq_name);
291     }
292    
293     //just a convenience function for creating a new record, but it's NOT written
294     //given pos must be 1-based (so it'll be stored as pos-1 because BAM is 0-based)
295     GBamRecord* new_record(const char* qname, const char* gseqname,
296     int pos, bool reverse, const char* qseq, const char* cigar=NULL, const char* qual=NULL) {
297     int32_t gseq_tid=get_tid(gseqname);
298     if (gseq_tid < 0 && strcmp(gseqname, "*")) {
299     if (bam_header->n_targets == 0) {
300     GError("Error: missing/invalid SAM header\n");
301     } else
302     GMessage("Warning: reference '%s' not found in header, will consider it '*'.\n",
303     gseqname);
304     }
305    
306     return (new GBamRecord(qname, gseq_tid, pos, reverse, qseq, cigar, qual));
307     }
308    
309     GBamRecord* new_record(const char* qname, int32_t flags, const char* gseqname,
310     int pos, int map_qual, const char* cigar, const char* mgseqname, int mate_pos,
311     int insert_size, const char* qseq, const char* quals=NULL,
312     GVec<char*>* aux_strings=NULL) {
313     int32_t gseq_tid=get_tid(gseqname);
314     if (gseq_tid < 0 && strcmp(gseqname, "*")) {
315     if (bam_header->n_targets == 0) {
316     GError("Error: missing/invalid SAM header\n");
317     } else
318     GMessage("Warning: reference '%s' not found in header, will consider it '*'.\n",
319     gseqname);
320     }
321     int32_t mgseq_tid=-1;
322     if (mgseqname!=NULL) {
323     if (strcmp(mgseqname, "=")==0) {
324     mgseq_tid=gseq_tid;
325     }
326     else {
327     mgseq_tid=get_tid(mgseqname);
328     if (mgseq_tid < 0 && strcmp(mgseqname, "*")) {
329     GMessage("Warning: reference '%s' not found in header, will consider it '*'.\n",
330     mgseqname);
331     }
332     }
333     }
334     return (new GBamRecord(qname, flags, gseq_tid, pos, map_qual, cigar,
335     mgseq_tid, mate_pos, insert_size, qseq, quals, aux_strings));
336     }
337    
338     void write(GBamRecord* brec) {
339     if (brec!=NULL)
340     samwrite(this->bam_file,brec->get_b());
341     }
342     void write(bam1_t* b) {
343     samwrite(this->bam_file, b);
344     }
345     };
346    
347     #endif