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comparison rDiff/src/tools/read_utils/get_reads_direct.cpp @ 0:0f80a5141704

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version 0.3 uploaded
author vipints
date Thu, 14 Feb 2013 23:38:36 -0500
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-1:000000000000 0:0f80a5141704
1 /* written by Jonas Behr, Regina Bohnert and Gunnar Raetsch, FML Tuebingen, Germany, 2010 */
2
3 #include <stdio.h>
4 #include <assert.h>
5 #include "sam.h"
6 #include "get_reads_direct.h"
7
8 #include <vector>
9 using std::vector;
10 #include <string>
11 using std::string;
12
13 #ifdef __cplusplus
14 extern "C" {
15 #endif
16
17 typedef struct {
18 int beg, end;
19 samfile_t *in;
20 } tmpstruct_t;
21
22 typedef struct {
23 uint64_t u, v;
24 } pair64_t;
25
26 static inline int is_overlap(uint32_t beg, uint32_t end, const bam1_t *b)
27 {
28 uint32_t rbeg = b->core.pos;
29 uint32_t rend = b->core.n_cigar? bam_calend(&b->core, bam1_cigar(b)) : b->core.pos + 1;
30 return (rend > beg && rbeg < end);
31 }
32
33 pair64_t * get_chunk_coordinates(const bam_index_t *idx, int tid, int beg, int end, int* cnt_off);
34
35 int bam_fetch_reads(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_header_t* header, vector<CRead*>* reads, char strand);
36
37 // callback for bam_plbuf_init()
38 static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
39 {
40 //tmpstruct_t *tmp = (tmpstruct_t*)data;
41 //if ((int)pos >= tmp->beg && (int)pos < tmp->end)
42 // printf("%s\t%d\t%d\n", tmp->in->header->target_name[tid], pos + 1, n);
43 return 0;
44 }
45 #ifdef __cplusplus
46 }
47 #endif
48 int parse_sam_line(char* line, CRead* read);
49 //int set_strand(char c);
50 //void parse_cigar(bam1_t* b, CRead* read);
51
52
53 int get_reads_from_bam(char* filename, char* region, vector<CRead*>* reads, char strand, int lsubsample)
54 {
55 subsample = lsubsample;
56 //set_strand(strand);
57
58 srand (time(NULL));
59 //srand (1234);
60 tmpstruct_t tmp;
61 tmp.in = samopen(filename, "rb", 0);
62 if (tmp.in == 0) {
63 fprintf(stderr, "Fail to open BAM file %s\n", filename);
64 return 1;
65 }
66 int ref;
67 bam_index_t *idx;
68 bam_plbuf_t *buf;
69 idx = bam_index_load(filename); // load BAM index
70 if (idx == 0) {
71 fprintf(stderr, "BAM indexing file is not available.\n");
72 samclose(tmp.in);
73 return 1;
74 }
75 bam_parse_region(tmp.in->header, region, &ref,
76 &tmp.beg, &tmp.end); // parse the region
77 if (ref < 0) {
78 fprintf(stderr, "Invalid region %s\n", region);
79 bam_index_destroy(idx);
80 samclose(tmp.in);
81 return 1;
82 }
83
84 buf = bam_plbuf_init(pileup_func, &tmp); // initialize pileup
85
86 bam_fetch_reads(tmp.in->x.bam, idx, ref, tmp.beg, tmp.end, buf, tmp.in->header, reads, strand);
87 //fprintf(stdout, "intron_list: %d \n", intron_list->size());
88
89 bam_plbuf_push(0, buf); // finalize pileup
90 bam_index_destroy(idx);
91 bam_plbuf_destroy(buf);
92 samclose(tmp.in);
93 return 0;
94 }
95
96
97 int bam_fetch_reads(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_header_t* header, vector<CRead*>* reads, char strand)
98 {
99 int n_off;
100 pair64_t *off = get_chunk_coordinates(idx, tid, beg, end, &n_off);
101 if (off == 0) return 0;
102 {
103 // retrive alignments
104 uint64_t curr_off;
105 int i, ret, n_seeks;
106 n_seeks = 0; i = -1; curr_off = 0;
107 bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t));
108 for (;;) {
109 if (curr_off == 0 || curr_off >= off[i].v) { // then jump to the next chunk
110 if (i == n_off - 1) break; // no more chunks
111 if (i >= 0) assert(curr_off == off[i].v); // otherwise bug
112 if (i < 0 || off[i].v != off[i+1].u) { // not adjacent chunks; then seek
113 bam_seek(fp, off[i+1].u, SEEK_SET);
114 curr_off = bam_tell(fp);
115 ++n_seeks;
116 }
117 ++i;
118 }
119 if ((ret = bam_read1(fp, b)) > 0) {
120 curr_off = bam_tell(fp);
121 if (b->core.tid != tid || b->core.pos >= end) break; // no need to proceed
122 else if (is_overlap(beg, end, b))
123 {
124 int rr = rand();
125 if ((rr%1000 < subsample))
126 {
127 CRead* read = new CRead();
128 parse_cigar(b, read, header);
129
130 if (strand == '0' || strand==read->strand[0] || read->strand[0]=='0')
131 {
132 reads->push_back(read);
133 }
134 else
135 {
136 delete read;
137 }
138 //else if (read->strand[0]=='0'&&((b->core.flag & g_flag_off) >0))
139 //{
140 // //fprintf(stdout, "(-)-strand; read->strand[0]==0, num_exons: %i \n", read->block_starts.size());
141 // // this flag means that the read has been reversed for alignment
142 // // flag bit set and (-)-strand requested
143 // reads->push_back(read);
144 //}
145 //else if (read->strand[0]=='0'&&(g_flag_on>0&&(b->core.flag & g_flag_on)==0))
146 //{
147 // //fprintf(stdout, "(+)-strand; read->strand[0]==0, num_exons: %i \n", read->block_starts.size());
148 // // (+)-strand requested and flag bit not set
149 // reads->push_back(read);
150 //}
151 }
152 }
153 } else break; // end of file
154 }
155 // fprintf(stderr, "[bam_fetch] # seek calls: %d\n", n_seeks);
156 bam_destroy1(b);
157 }
158 free(off);
159 return 0;
160 }
161
162 void parse_cigar(bam1_t* b, CRead* read, bam_header_t* header)
163 {
164 read->left = (b->core.flag & left_flag_mask) >0;
165 read->right = (b->core.flag & right_flag_mask) >0;
166 read->reverse = (b->core.flag & reverse_flag_mask) >0;
167
168 read->start_pos = b->core.pos+1;
169 read->set_strand('0');
170 read->read_id = new char[1000];
171 //sprintf(read->read_id, "%s\0", bam1_qname(b));
172 sprintf(read->read_id, "%s", bam1_qname(b));
173
174 for (int k = 0; k < b->core.n_cigar; ++k)
175 {
176 int op = bam1_cigar(b)[k] & BAM_CIGAR_MASK; // operation
177 int l = bam1_cigar(b)[k] >> BAM_CIGAR_SHIFT; // length
178 //int op = bam_cigar_op(bam1_cigar(b)[k]); // operation
179 //int l = bam_cigar_oplen(bam1_cigar(b)[k]); // length
180 //fprintf(stdout, "op:%d l:%d\n", op, l);
181 if (op == BAM_CMATCH)
182 {
183 if (k==0)
184 {
185 read->block_lengths.push_back(l);
186 read->block_starts.push_back(0);
187 }
188 else
189 {
190 int op_prev = bam1_cigar(b)[k-1] & BAM_CIGAR_MASK;
191 int l_prev = bam1_cigar(b)[k-1] >> BAM_CIGAR_SHIFT;
192 if (op_prev==BAM_CREF_SKIP)// intron before
193 {
194 if (read->block_lengths.size()>=1)
195 {
196 int last_block_start = (*(read->block_starts.end()-1));
197 int intron_start = last_block_start+(*(read->block_lengths.end()-1));
198 read->block_lengths.push_back(l);
199 read->block_starts.push_back(intron_start+l_prev);
200 }
201 else
202 {
203 // start of first block was not a match
204 read->block_lengths.push_back(l);
205 read->block_starts.push_back(0);
206 }
207 }
208 else
209 {
210 if (read->block_lengths.size()>=1)
211 (*(read->block_lengths.end()-1))+=l;
212 else
213 {
214 read->block_lengths.push_back(l);
215 read->block_starts.push_back(0);
216 }
217 }
218 }
219 }
220 else if (op == BAM_CDEL)
221 {
222 if (k>0 && read->block_lengths.size()>=1)
223 (*(read->block_lengths.end()-1))+=l;
224 }
225 else if (op == BAM_CREF_SKIP)//intron
226 {}
227 else if (op == BAM_CINS)
228 {}
229 else if (op == BAM_CSOFT_CLIP || op == BAM_CHARD_CLIP)
230 {
231 read->is_clipped = true;
232 }
233 }
234 // parse auxiliary data
235 uint8_t* s = bam1_aux(b);
236 uint8_t* end = b->data + b->data_len;
237 while (s < end)
238 {
239 uint8_t type, key[2];
240 key[0] = s[0]; key[1] = s[1];
241 s += 2; type = *s; ++s;
242 //fprintf(stdout, "\n%c%c:%c\n", key[0], key[1], type);
243 if (type == 'A')
244 {
245 if ( key[0] =='X' && key[1] == 'S')
246 {
247 read->set_strand((char) *s);
248 }
249 ++s;
250 }
251 else if (type == 'C')
252 {
253 if ( key[0] =='H' && key[1] == '0')
254 {
255 uint8_t matches = *s;
256 read->matches = (int) matches;
257 }
258 if ( key[0] =='N' && key[1] == 'M')
259 {
260 uint8_t mismatches = *s;
261 read->mismatches = (int) mismatches;
262 }
263 if ( key[0] =='H' && key[1] == 'I')
264 {
265 uint8_t mai = *s;
266 read->multiple_alignment_index = (int) mai;
267 }
268
269 ++s;
270 }
271 else if (type == 'c') { ++s; }
272 else if (type == 'S') { s += 2; }
273 else if (type == 's') { s += 2; }
274 else if (type == 'I') { s += 4; }
275 else if (type == 'i') { s += 4; }
276 else if (type == 'f') { s += 4; }
277 else if (type == 'd') { s += 8; }
278 else if (type == 'Z') { ++s; }
279 else if (type == 'H') { ++s; }
280 }
281 }
282
283 //int set_strand(char c)
284 //{
285 // if (c=='+')
286 // {
287 // char* fl = (char*) "0x0010";
288 // g_flag_on = strtol(fl, 0, 0);
289 // g_flag_off = 0;
290 // }
291 // else if (c=='-')
292 // {
293 // char* fl = (char*) "0x0010";
294 // g_flag_off = strtol(fl, 0, 0);
295 // g_flag_on = 0;
296 // }
297 // return 0;
298 //}
299