4 #include "bam_endian.h"
8 /**************************
9 * CIGAR related routines *
10 **************************/
12 int bam_segreg(int32_t pos, const bam1_core_t *c, const uint32_t *cigar, bam_segreg_t *reg)
15 int32_t x = c->pos, y = 0;
17 for (k = 0; k < c->n_cigar; ++k) {
18 int op = cigar[k] & BAM_CIGAR_MASK; // operation
19 int l = cigar[k] >> BAM_CIGAR_SHIFT; // length
20 if (state == 0 && (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CINS) && x + l > pos) {
21 reg->tbeg = x; reg->qbeg = y; reg->cbeg = k;
24 if (op == BAM_CMATCH) { x += l; y += l; }
25 else if (op == BAM_CDEL || op == BAM_CREF_SKIP) x += l;
26 else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
27 if (state == 1 && (op == BAM_CSOFT_CLIP || op == BAM_CHARD_CLIP || op == BAM_CREF_SKIP || k == c->n_cigar - 1)) {
28 reg->tend = x; reg->qend = y; reg->cend = k;
34 uint32_t bam_calend(const bam1_core_t *c, const uint32_t *cigar)
38 for (k = 0; k < c->n_cigar; ++k) {
39 int op = cigar[k] & BAM_CIGAR_MASK;
40 if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP)
41 end += cigar[k] >> BAM_CIGAR_SHIFT;
46 int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar)
50 for (k = 0; k < c->n_cigar; ++k) {
51 int op = cigar[k] & BAM_CIGAR_MASK;
52 if (op == BAM_CMATCH || op == BAM_CINS || op == BAM_CSOFT_CLIP)
53 l += cigar[k] >> BAM_CIGAR_SHIFT;
62 bam_header_t *bam_header_init()
64 bam_is_be = bam_is_big_endian();
65 return (bam_header_t*)calloc(1, sizeof(bam_header_t));
68 void bam_header_destroy(bam_header_t *header)
71 extern void bam_destroy_header_hash(bam_header_t *header);
72 if (header == 0) return;
73 if (header->target_name) {
74 for (i = 0; i < header->n_targets; ++i)
75 free(header->target_name[i]);
76 free(header->target_name);
77 free(header->target_len);
81 bam_destroy_header_hash(header);
86 bam_header_t *bam_header_read(bamFile fp)
92 if (bam_read(fp, buf, 4) != 4) return 0;
93 if (strncmp(buf, "BAM\001", 4)) {
94 fprintf(stderr, "[bam_header_read] wrong header\n");
97 header = bam_header_init();
98 // read plain text and the number of reference sequences
99 bam_read(fp, &header->l_text, 4);
100 if (bam_is_be) bam_swap_endian_4p(&header->l_text);
101 header->text = (char*)calloc(header->l_text + 1, 1);
102 bam_read(fp, header->text, header->l_text);
103 bam_read(fp, &header->n_targets, 4);
104 if (bam_is_be) bam_swap_endian_4p(&header->n_targets);
105 assert(header->n_targets > 0);
106 // read reference sequence names and lengths
107 header->target_name = (char**)calloc(header->n_targets, sizeof(char*));
108 header->target_len = (uint32_t*)calloc(header->n_targets, 4);
109 for (i = 0; i != header->n_targets; ++i) {
110 bam_read(fp, &name_len, 4);
111 if (bam_is_be) bam_swap_endian_4p(&name_len);
112 header->target_name[i] = (char*)calloc(name_len, 1);
113 bam_read(fp, header->target_name[i], name_len);
114 bam_read(fp, &header->target_len[i], 4);
115 if (bam_is_be) bam_swap_endian_4p(&header->target_len[i]);
120 int bam_header_write(bamFile fp, const bam_header_t *header)
123 int32_t i, name_len, x;
125 strncpy(buf, "BAM\001", 4);
126 bam_write(fp, buf, 4);
127 // write plain text and the number of reference sequences
129 x = bam_swap_endian_4(header->l_text);
130 bam_write(fp, &x, 4);
131 if (header->l_text) bam_write(fp, header->text, header->l_text);
132 x = bam_swap_endian_4(header->n_targets);
133 bam_write(fp, &x, 4);
135 bam_write(fp, &header->l_text, 4);
136 if (header->l_text) bam_write(fp, header->text, header->l_text);
137 bam_write(fp, &header->n_targets, 4);
139 // write sequence names and lengths
140 for (i = 0; i != header->n_targets; ++i) {
141 char *p = header->target_name[i];
142 name_len = strlen(p) + 1;
144 x = bam_swap_endian_4(name_len);
145 bam_write(fp, &x, 4);
146 } else bam_write(fp, &name_len, 4);
147 bam_write(fp, p, name_len);
149 x = bam_swap_endian_4(header->target_len[i]);
150 bam_write(fp, &x, 4);
151 } else bam_write(fp, &header->target_len[i], 4);
156 static void swap_endian_data(const bam1_core_t *c, int data_len, uint8_t *data)
159 uint32_t i, *cigar = (uint32_t*)(data + c->l_qname);
160 s = data + c->n_cigar*4 + c->l_qname + c->l_qseq + (c->l_qseq + 1)/2;
161 for (i = 0; i < c->n_cigar; ++i) bam_swap_endian_4p(&cigar[i]);
162 while (s < data + data_len) {
165 type = toupper(*s); ++s; // skip type
166 if (type == 'C' || type == 'A') ++s;
167 else if (type == 'S') { bam_swap_endian_2p(s); s += 2; }
168 else if (type == 'I' || type == 'F') { bam_swap_endian_4p(s); s += 4; }
169 else if (type == 'Z' || type == 'H') { while (*s) ++s; ++s; }
173 int bam_read1(bamFile fp, bam1_t *b)
175 bam1_core_t *c = &b->core;
176 int32_t block_len, ret, i;
179 assert(BAM_CORE_SIZE == 32);
180 if ((ret = bam_read(fp, &block_len, 4)) != 4) {
181 if (ret == 0) return -1; // normal end-of-file
182 else return -2; // truncated
184 if (bam_read(fp, x, BAM_CORE_SIZE) != BAM_CORE_SIZE) return -3;
186 bam_swap_endian_4p(&block_len);
187 for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i);
189 c->tid = x[0]; c->pos = x[1];
190 c->bin = x[2]>>16; c->qual = x[2]>>8&0xff; c->l_qname = x[2]&0xff;
191 c->flag = x[3]>>16; c->n_cigar = x[3]&0xffff;
193 c->mtid = x[5]; c->mpos = x[6]; c->isize = x[7];
194 b->data_len = block_len - BAM_CORE_SIZE;
195 if (b->m_data < b->data_len) {
196 b->m_data = b->data_len;
197 kroundup32(b->m_data);
198 b->data = (uint8_t*)realloc(b->data, b->m_data);
200 if (bam_read(fp, b->data, b->data_len) != b->data_len) return -4;
201 b->l_aux = b->data_len - c->n_cigar * 4 - c->l_qname - c->l_qseq - (c->l_qseq+1)/2;
202 if (bam_is_be) swap_endian_data(c, b->data_len, b->data);
203 return 4 + block_len;
206 inline int bam_write1_core(bamFile fp, const bam1_core_t *c, int data_len, uint8_t *data)
208 uint32_t x[8], block_len = data_len + BAM_CORE_SIZE, y;
210 assert(BAM_CORE_SIZE == 32);
213 x[2] = (uint32_t)c->bin<<16 | c->qual<<8 | c->l_qname;
214 x[3] = (uint32_t)c->flag<<16 | c->n_cigar;
220 for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i);
222 bam_write(fp, bam_swap_endian_4p(&y), 4);
223 swap_endian_data(c, data_len, data);
224 } else bam_write(fp, &block_len, 4);
225 bam_write(fp, x, BAM_CORE_SIZE);
226 bam_write(fp, data, data_len);
227 if (bam_is_be) swap_endian_data(c, data_len, data);
228 return 4 + block_len;
231 int bam_write1(bamFile fp, const bam1_t *b)
233 return bam_write1_core(fp, &b->core, b->data_len, b->data);
236 void bam_view1(const bam_header_t *header, const bam1_t *b)
238 uint8_t *s = bam1_seq(b), *t = bam1_qual(b);
240 const bam1_core_t *c = &b->core;
241 printf("%s\t%d\t", bam1_qname(b), c->flag);
242 if (c->tid < 0) printf("*\t");
243 else printf("%s\t", header->target_name[c->tid]);
244 printf("%d\t%d\t", c->pos + 1, c->qual);
245 if (c->n_cigar == 0) putchar('*');
247 for (i = 0; i < c->n_cigar; ++i)
248 printf("%d%c", bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, "MIDNSHP"[bam1_cigar(b)[i]&BAM_CIGAR_MASK]);
251 if (c->mtid < 0) printf("*\t");
252 else if (c->mtid == c->tid) printf("=\t");
253 else printf("%s\t", header->target_name[c->mtid]);
254 printf("%d\t%d\t", c->mpos + 1, c->isize);
255 for (i = 0; i < c->l_qseq; ++i) putchar(bam_nt16_rev_table[bam1_seqi(s, i)]);
257 for (i = 0; i < c->l_qseq; ++i) putchar(t[i] + 33);
259 while (s < b->data + b->data_len) {
260 uint8_t type, key[2];
261 key[0] = s[0]; key[1] = s[1];
262 s += 2; type = *s; ++s;
263 printf("\t%c%c:", key[0], key[1]);
264 if (type == 'A') { printf("A:%c", *s); ++s; }
265 else if (type == 'C') { printf("i:%u", *s); ++s; }
266 else if (type == 'c') { printf("i:%d", *s); ++s; }
267 else if (type == 'S') { printf("i:%u", *(uint16_t*)s); s += 2; }
268 else if (type == 's') { printf("i:%d", *(int16_t*)s); s += 2; }
269 else if (type == 'I') { printf("i:%u", *(uint32_t*)s); s += 4; }
270 else if (type == 'i') { printf("i:%d", *(int32_t*)s); s += 4; }
271 else if (type == 'f') { printf("f:%g", *(float*)s); s += 4; }
272 else if (type == 'Z' || type == 'H') { printf("%c:", type); while (*s) putchar(*s++); ++s; }