Mercurial > repos > ryanmorin > nextgen_variant_identification
comparison SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/bam_pileup.c @ 0:74f5ea818cea
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author | ryanmorin |
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date | Wed, 12 Oct 2011 19:50:38 -0400 |
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-1:000000000000 | 0:74f5ea818cea |
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1 #include <stdio.h> | |
2 #include <stdlib.h> | |
3 #include <ctype.h> | |
4 #include <assert.h> | |
5 #include "sam.h" | |
6 | |
7 typedef struct __linkbuf_t { | |
8 bam1_t b; | |
9 uint32_t beg, end; | |
10 struct __linkbuf_t *next; | |
11 } lbnode_t; | |
12 | |
13 /* --- BEGIN: Memory pool */ | |
14 | |
15 typedef struct { | |
16 int cnt, n, max; | |
17 lbnode_t **buf; | |
18 } mempool_t; | |
19 | |
20 static mempool_t *mp_init() | |
21 { | |
22 mempool_t *mp; | |
23 mp = (mempool_t*)calloc(1, sizeof(mempool_t)); | |
24 return mp; | |
25 } | |
26 static void mp_destroy(mempool_t *mp) | |
27 { | |
28 int k; | |
29 for (k = 0; k < mp->n; ++k) { | |
30 free(mp->buf[k]->b.data); | |
31 free(mp->buf[k]); | |
32 } | |
33 free(mp->buf); | |
34 free(mp); | |
35 } | |
36 static inline lbnode_t *mp_alloc(mempool_t *mp) | |
37 { | |
38 ++mp->cnt; | |
39 if (mp->n == 0) return (lbnode_t*)calloc(1, sizeof(lbnode_t)); | |
40 else return mp->buf[--mp->n]; | |
41 } | |
42 static inline void mp_free(mempool_t *mp, lbnode_t *p) | |
43 { | |
44 --mp->cnt; p->next = 0; // clear lbnode_t::next here | |
45 if (mp->n == mp->max) { | |
46 mp->max = mp->max? mp->max<<1 : 256; | |
47 mp->buf = (lbnode_t**)realloc(mp->buf, sizeof(lbnode_t*) * mp->max); | |
48 } | |
49 mp->buf[mp->n++] = p; | |
50 } | |
51 | |
52 /* --- END: Memory pool */ | |
53 | |
54 /* --- BEGIN: Auxiliary functions */ | |
55 | |
56 static inline int resolve_cigar(bam_pileup1_t *p, uint32_t pos) | |
57 { | |
58 unsigned k; | |
59 bam1_t *b = p->b; | |
60 bam1_core_t *c = &b->core; | |
61 uint32_t x = c->pos, y = 0; | |
62 int ret = 1, is_restart = 1; | |
63 | |
64 if (c->flag&BAM_FUNMAP) return 0; // unmapped read | |
65 assert(x <= pos); // otherwise a bug | |
66 p->qpos = -1; p->indel = 0; p->is_del = p->is_head = p->is_tail = 0; | |
67 for (k = 0; k < c->n_cigar; ++k) { | |
68 int op = bam1_cigar(b)[k] & BAM_CIGAR_MASK; // operation | |
69 int l = bam1_cigar(b)[k] >> BAM_CIGAR_SHIFT; // length | |
70 if (op == BAM_CMATCH) { // NOTE: this assumes the first and the last operation MUST BE a match or a clip | |
71 if (x + l > pos) { // overlap with pos | |
72 p->indel = p->is_del = 0; | |
73 p->qpos = y + (pos - x); | |
74 if (x == pos && is_restart) p->is_head = 1; | |
75 if (x + l - 1 == pos) { // come to the end of a match | |
76 if (k < c->n_cigar - 1) { // there are additional operation(s) | |
77 uint32_t cigar = bam1_cigar(b)[k+1]; // next CIGAR | |
78 int op_next = cigar&BAM_CIGAR_MASK; // next CIGAR operation | |
79 if (op_next == BAM_CDEL) p->indel = -(int32_t)(cigar>>BAM_CIGAR_SHIFT); // del | |
80 else if (op_next == BAM_CINS) p->indel = cigar>>BAM_CIGAR_SHIFT; // ins | |
81 if (op_next == BAM_CDEL || op_next == BAM_CINS) { | |
82 if (k + 2 < c->n_cigar) op_next = bam1_cigar(b)[k+2]&BAM_CIGAR_MASK; | |
83 else p->is_tail = 1; | |
84 } | |
85 if (op_next == BAM_CSOFT_CLIP || op_next == BAM_CREF_SKIP || op_next == BAM_CHARD_CLIP) | |
86 p->is_tail = 1; // tail | |
87 } else p->is_tail = 1; // this is the last operation; set tail | |
88 } | |
89 } | |
90 x += l; y += l; | |
91 } else if (op == BAM_CDEL) { // then set ->is_del | |
92 if (x + l > pos) { | |
93 p->indel = 0; p->is_del = 1; | |
94 p->qpos = y + (pos - x); | |
95 } | |
96 x += l; | |
97 } else if (op == BAM_CREF_SKIP) x += l; | |
98 else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l; | |
99 is_restart = (op == BAM_CREF_SKIP || op == BAM_CSOFT_CLIP || op == BAM_CHARD_CLIP); | |
100 if (x > pos) { | |
101 if (op == BAM_CREF_SKIP) ret = 0; // then do not put it into pileup at all | |
102 break; | |
103 } | |
104 } | |
105 assert(x > pos); // otherwise a bug | |
106 return ret; | |
107 } | |
108 | |
109 /* --- END: Auxiliary functions */ | |
110 | |
111 struct __bam_plbuf_t { | |
112 mempool_t *mp; | |
113 lbnode_t *head, *tail, *dummy; | |
114 bam_pileup_f func; | |
115 void *func_data; | |
116 int32_t tid, pos, max_tid, max_pos; | |
117 int max_pu, is_eof; | |
118 bam_pileup1_t *pu; | |
119 int flag_mask; | |
120 }; | |
121 | |
122 void bam_plbuf_reset(bam_plbuf_t *buf) | |
123 { | |
124 lbnode_t *p, *q; | |
125 buf->max_tid = buf->max_pos = -1; | |
126 buf->tid = buf->pos = 0; | |
127 buf->is_eof = 0; | |
128 for (p = buf->head; p->next;) { | |
129 q = p->next; | |
130 mp_free(buf->mp, p); | |
131 p = q; | |
132 } | |
133 buf->head = buf->tail; | |
134 } | |
135 | |
136 void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask) | |
137 { | |
138 if (mask < 0) buf->flag_mask = BAM_DEF_MASK; | |
139 else buf->flag_mask = BAM_FUNMAP | mask; | |
140 } | |
141 | |
142 bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data) | |
143 { | |
144 bam_plbuf_t *buf; | |
145 buf = (bam_plbuf_t*)calloc(1, sizeof(bam_plbuf_t)); | |
146 buf->func = func; buf->func_data = data; | |
147 buf->mp = mp_init(); | |
148 buf->head = buf->tail = mp_alloc(buf->mp); | |
149 buf->dummy = mp_alloc(buf->mp); | |
150 buf->max_tid = buf->max_pos = -1; | |
151 buf->flag_mask = BAM_DEF_MASK; | |
152 return buf; | |
153 } | |
154 | |
155 void bam_plbuf_destroy(bam_plbuf_t *buf) | |
156 { | |
157 mp_free(buf->mp, buf->dummy); | |
158 mp_free(buf->mp, buf->head); | |
159 if (buf->mp->cnt != 0) | |
160 fprintf(stderr, "[bam_plbuf_destroy] memory leak: %d. Continue anyway.\n", buf->mp->cnt); | |
161 mp_destroy(buf->mp); | |
162 free(buf->pu); | |
163 free(buf); | |
164 } | |
165 | |
166 int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf) | |
167 { | |
168 if (b) { // fill buffer | |
169 if (b->core.tid < 0) return 0; | |
170 if (b->core.flag & buf->flag_mask) return 0; | |
171 bam_copy1(&buf->tail->b, b); | |
172 buf->tail->beg = b->core.pos; buf->tail->end = bam_calend(&b->core, bam1_cigar(b)); | |
173 if (b->core.tid < buf->max_tid) { | |
174 fprintf(stderr, "[bam_pileup_core] the input is not sorted (chromosomes out of order)\n"); | |
175 return -1; | |
176 } | |
177 if ((b->core.tid == buf->max_tid) && (buf->tail->beg < buf->max_pos)) { | |
178 fprintf(stderr, "[bam_pileup_core] the input is not sorted (reads out of order)\n"); | |
179 return -1; | |
180 } | |
181 buf->max_tid = b->core.tid; buf->max_pos = buf->tail->beg; | |
182 if (buf->tail->end > buf->pos || buf->tail->b.core.tid > buf->tid) { | |
183 buf->tail->next = mp_alloc(buf->mp); | |
184 buf->tail = buf->tail->next; | |
185 } | |
186 } else buf->is_eof = 1; | |
187 while (buf->is_eof || buf->max_tid > buf->tid || (buf->max_tid == buf->tid && buf->max_pos > buf->pos)) { | |
188 int n_pu = 0; | |
189 lbnode_t *p, *q; | |
190 buf->dummy->next = buf->head; | |
191 for (p = buf->head, q = buf->dummy; p->next; q = p, p = p->next) { | |
192 if (p->b.core.tid < buf->tid || (p->b.core.tid == buf->tid && p->end <= buf->pos)) { // then remove from the list | |
193 q->next = p->next; mp_free(buf->mp, p); p = q; | |
194 } else if (p->b.core.tid == buf->tid && p->beg <= buf->pos) { // here: p->end > pos; then add to pileup | |
195 if (n_pu == buf->max_pu) { // then double the capacity | |
196 buf->max_pu = buf->max_pu? buf->max_pu<<1 : 256; | |
197 buf->pu = (bam_pileup1_t*)realloc(buf->pu, sizeof(bam_pileup1_t) * buf->max_pu); | |
198 } | |
199 buf->pu[n_pu].b = &p->b; | |
200 if (resolve_cigar(buf->pu + n_pu, buf->pos)) ++n_pu; // skip the read if we are looking at BAM_CREF_SKIP | |
201 } | |
202 } | |
203 buf->head = buf->dummy->next; // dummy->next may be changed | |
204 if (n_pu) { // then call user defined function | |
205 buf->func(buf->tid, buf->pos, n_pu, buf->pu, buf->func_data); | |
206 } | |
207 // update tid and pos | |
208 if (buf->head->next) { | |
209 if (buf->tid > buf->head->b.core.tid) { | |
210 fprintf(stderr, "[bam_plbuf_push] unsorted input. Pileup aborts.\n"); | |
211 return 1; | |
212 } | |
213 } | |
214 if (buf->tid < buf->head->b.core.tid) { // come to a new reference sequence | |
215 buf->tid = buf->head->b.core.tid; buf->pos = buf->head->beg; // jump to the next reference | |
216 } else if (buf->pos < buf->head->beg) { // here: tid == head->b.core.tid | |
217 buf->pos = buf->head->beg; // jump to the next position | |
218 } else ++buf->pos; // scan contiguously | |
219 if (buf->is_eof && buf->head->next == 0) break; | |
220 } | |
221 return 0; | |
222 } | |
223 | |
224 int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data) | |
225 { | |
226 bam_plbuf_t *buf; | |
227 int ret; | |
228 bam1_t *b; | |
229 b = bam_init1(); | |
230 buf = bam_plbuf_init(func, func_data); | |
231 bam_plbuf_set_mask(buf, mask); | |
232 while ((ret = bam_read1(fp, b)) >= 0) | |
233 bam_plbuf_push(b, buf); | |
234 bam_plbuf_push(0, buf); | |
235 bam_plbuf_destroy(buf); | |
236 bam_destroy1(b); | |
237 return 0; | |
238 } |