7 bcf_t *bcf_open(const char *fn, const char *mode)
10 b = calloc(1, sizeof(bcf_t));
11 if (strchr(mode, 'w')) {
12 b->fp = strcmp(fn, "-")? bgzf_open(fn, mode) : bgzf_fdopen(fileno(stdout), mode);
14 b->fp = strcmp(fn, "-")? bgzf_open(fn, mode) : bgzf_fdopen(fileno(stdin), mode);
16 b->fp->owned_file = 1;
20 int bcf_close(bcf_t *b)
24 ret = bgzf_close(b->fp);
29 int bcf_hdr_write(bcf_t *b, const bcf_hdr_t *h)
31 if (b == 0 || h == 0) return -1;
32 bgzf_write(b->fp, "BCF\4", 4);
33 bgzf_write(b->fp, &h->l_nm, 4);
34 bgzf_write(b->fp, h->name, h->l_nm);
35 bgzf_write(b->fp, &h->l_smpl, 4);
36 bgzf_write(b->fp, h->sname, h->l_smpl);
37 bgzf_write(b->fp, &h->l_txt, 4);
38 bgzf_write(b->fp, h->txt, h->l_txt);
40 return 16 + h->l_nm + h->l_smpl + h->l_txt;
43 bcf_hdr_t *bcf_hdr_read(bcf_t *b)
48 h = calloc(1, sizeof(bcf_hdr_t));
49 bgzf_read(b->fp, magic, 4);
50 bgzf_read(b->fp, &h->l_nm, 4);
51 h->name = malloc(h->l_nm);
52 bgzf_read(b->fp, h->name, h->l_nm);
53 bgzf_read(b->fp, &h->l_smpl, 4);
54 h->sname = malloc(h->l_smpl);
55 bgzf_read(b->fp, h->sname, h->l_smpl);
56 bgzf_read(b->fp, &h->l_txt, 4);
57 h->txt = malloc(h->l_txt);
58 bgzf_read(b->fp, h->txt, h->l_txt);
63 void bcf_hdr_destroy(bcf_hdr_t *h)
66 free(h->name); free(h->sname); free(h->txt); free(h->ns); free(h->sns);
70 static inline char **cnt_null(int l, char *str, int *_n)
75 if (l == 0 || str == 0) return 0;
76 for (p = str; p != str + l; ++p)
79 list = calloc(n, sizeof(void*));
81 for (p = str, n = 1; p < str + l - 1; ++p)
82 if (*p == 0) list[n++] = p + 1;
86 int bcf_hdr_sync(bcf_hdr_t *b)
88 if (b == 0) return -1;
89 if (b->ns) free(b->ns);
90 if (b->sns) free(b->sns);
91 if (b->l_nm) b->ns = cnt_null(b->l_nm, b->name, &b->n_ref);
92 else b->ns = 0, b->n_ref = 0;
93 b->sns = cnt_null(b->l_smpl, b->sname, &b->n_smpl);
97 int bcf_sync(bcf1_t *b)
100 int i, n, n_smpl = b->n_smpl;
102 // set ref, alt, flt, info, fmt
103 b->ref = b->alt = b->flt = b->info = b->fmt = 0;
104 for (p = b->str, n = 0; p < b->str + b->l_str; ++p)
105 if (*p == 0 && p+1 != b->str + b->l_str) tmp[n++] = p + 1;
107 fprintf(stderr, "[%s] incorrect number of fields (%d != 5). Corrupted file?\n", __func__, n);
110 b->ref = tmp[0]; b->alt = tmp[1]; b->flt = tmp[2]; b->info = tmp[3]; b->fmt = tmp[4];
112 if (*b->alt == 0) b->n_alleles = 1;
114 for (p = b->alt, n = 1; *p; ++p)
116 b->n_alleles = n + 1;
118 // set n_gi and gi[i].fmt
119 for (p = b->fmt, n = 1; *p; ++p)
125 b->gi = realloc(b->gi, b->m_gi * sizeof(bcf_ginfo_t));
126 memset(b->gi + old_m, 0, (b->m_gi - old_m) * sizeof(bcf_ginfo_t));
129 for (p = kstrtok(b->fmt, ":", &aux), n = 0; p; p = kstrtok(0, 0, &aux))
130 b->gi[n++].fmt = bcf_str2int(p, aux.p - p);
132 for (i = 0; i < b->n_gi; ++i) {
133 if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
134 b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2;
135 } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("HQ", 2)) {
137 } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("GT", 2)
138 || b->gi[i].fmt == bcf_str2int("SP", 2))
141 } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
142 b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2 * 4;
144 b->gi[i].data = realloc(b->gi[i].data, n_smpl * b->gi[i].len);
149 int bcf_write(bcf_t *bp, const bcf_hdr_t *h, const bcf1_t *b)
152 if (b == 0) return -1;
153 bgzf_write(bp->fp, &b->tid, 4);
154 bgzf_write(bp->fp, &b->pos, 4);
155 bgzf_write(bp->fp, &b->qual, 4);
156 bgzf_write(bp->fp, &b->l_str, 4);
157 bgzf_write(bp->fp, b->str, b->l_str);
159 for (i = 0; i < b->n_gi; ++i) {
160 bgzf_write(bp->fp, b->gi[i].data, b->gi[i].len * h->n_smpl);
161 l += b->gi[i].len * h->n_smpl;
166 int bcf_read(bcf_t *bp, const bcf_hdr_t *h, bcf1_t *b)
169 if (b == 0) return -1;
170 if (bgzf_read(bp->fp, &b->tid, 4) == 0) return -1;
171 b->n_smpl = h->n_smpl;
172 bgzf_read(bp->fp, &b->pos, 4);
173 bgzf_read(bp->fp, &b->qual, 4);
174 bgzf_read(bp->fp, &b->l_str, 4);
175 if (b->l_str > b->m_str) {
177 kroundup32(b->m_str);
178 b->str = realloc(b->str, b->m_str);
180 bgzf_read(bp->fp, b->str, b->l_str);
183 for (i = 0; i < b->n_gi; ++i) {
184 bgzf_read(bp->fp, b->gi[i].data, b->gi[i].len * h->n_smpl);
185 l += b->gi[i].len * h->n_smpl;
190 int bcf_destroy(bcf1_t *b)
193 if (b == 0) return -1;
195 for (i = 0; i < b->m_gi; ++i)
202 static inline void fmt_str(const char *p, kstring_t *s)
204 if (*p == 0) kputc('.', s);
208 void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s)
212 if (h->n_ref) kputs(h->ns[b->tid], s);
213 else kputw(b->tid, s);
215 kputw(b->pos + 1, s); kputc('\t', s);
216 fmt_str(b->str, s); kputc('\t', s);
217 fmt_str(b->ref, s); kputc('\t', s);
218 fmt_str(b->alt, s); kputc('\t', s);
219 ksprintf(s, "%.3g", b->qual); kputc('\t', s);
220 fmt_str(b->flt, s); kputc('\t', s);
226 x = b->n_alleles * (b->n_alleles + 1) / 2;
227 if (b->n_gi == 0) return;
228 for (j = 0; j < h->n_smpl; ++j) {
230 for (i = 0; i < b->n_gi; ++i) {
231 if (i) kputc(':', s);
232 if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
233 uint8_t *d = (uint8_t*)b->gi[i].data + j * x;
235 for (k = 0; k < x; ++k) {
236 if (k > 0) kputc(',', s);
239 } else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
240 kputw(((uint16_t*)b->gi[i].data)[j], s);
241 } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("SP", 2)) {
242 kputw(((uint8_t*)b->gi[i].data)[j], s);
243 } else if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
244 int y = ((uint8_t*)b->gi[i].data)[j];
248 kputc('0' + (y>>3&7), s);
249 kputc("/|"[y>>6&1], s);
250 kputc('0' + (y&7), s);
252 } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
253 float *d = (float*)b->gi[i].data + j * x;
255 //printf("- %lx\n", d);
256 for (k = 0; k < x; ++k) {
257 if (k > 0) kputc(',', s);
258 ksprintf(s, "%.2f", d[k]);
265 char *bcf_fmt(const bcf_hdr_t *h, bcf1_t *b)
268 s.l = s.m = 0; s.s = 0;
269 bcf_fmt_core(h, b, &s);
273 int bcf_append_info(bcf1_t *b, const char *info, int l)
275 int shift = b->fmt - b->str;
276 int l_fmt = b->l_str - shift;
278 if (b->l_str + l > b->m_str) { // enlarge if necessary
279 b->m_str = b->l_str + l;
280 kroundup32(b->m_str);
281 b->str = realloc(b->str, b->m_str);
283 memmove(b->str + shift + l, b->str + shift, l_fmt); // move the FORMAT field
284 memcpy(b->str + shift - 1, info, l); // append to the INFO field
285 b->str[shift + l - 1] = '\0';
286 b->fmt = b->str + shift + l;
288 if (ori != b->str) bcf_sync(b); // synchronize when realloc changes the pointer
292 int bcf_cpy(bcf1_t *r, const bcf1_t *b)
295 bcf_ginfo_t *t2 = r->gi;
296 int i, t3 = r->m_str, t4 = r->m_gi;
298 r->str = t1; r->gi = t2; r->m_str = t3; r->m_gi = t4;
299 if (r->m_str < b->m_str) {
301 r->str = realloc(r->str, r->m_str);
303 memcpy(r->str, b->str, r->m_str);
304 bcf_sync(r); // calling bcf_sync() is simple but inefficient
305 for (i = 0; i < r->n_gi; ++i)
306 memcpy(r->gi[i].data, b->gi[i].data, r->n_smpl * r->gi[i].len);
310 int bcf_is_indel(const bcf1_t *b)
313 if (strlen(b->ref) > 1) return 1;
314 for (p = b->alt; *p; ++p)
315 if (*p != ',' && p[1] != ',' && p[1] != '\0')