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);
17 b->fp->owned_file = 1;
22 int bcf_close(bcf_t *b)
26 ret = bgzf_close(b->fp);
31 int bcf_hdr_write(bcf_t *b, const bcf_hdr_t *h)
33 if (b == 0 || h == 0) return -1;
34 bgzf_write(b->fp, "BCF\4", 4);
35 bgzf_write(b->fp, &h->l_nm, 4);
36 bgzf_write(b->fp, h->name, h->l_nm);
37 bgzf_write(b->fp, &h->l_smpl, 4);
38 bgzf_write(b->fp, h->sname, h->l_smpl);
39 bgzf_write(b->fp, &h->l_txt, 4);
40 bgzf_write(b->fp, h->txt, h->l_txt);
42 return 16 + h->l_nm + h->l_smpl + h->l_txt;
45 bcf_hdr_t *bcf_hdr_read(bcf_t *b)
50 h = calloc(1, sizeof(bcf_hdr_t));
51 bgzf_read(b->fp, magic, 4);
52 bgzf_read(b->fp, &h->l_nm, 4);
53 h->name = malloc(h->l_nm);
54 bgzf_read(b->fp, h->name, h->l_nm);
55 bgzf_read(b->fp, &h->l_smpl, 4);
56 h->sname = malloc(h->l_smpl);
57 bgzf_read(b->fp, h->sname, h->l_smpl);
58 bgzf_read(b->fp, &h->l_txt, 4);
59 h->txt = malloc(h->l_txt);
60 bgzf_read(b->fp, h->txt, h->l_txt);
65 void bcf_hdr_destroy(bcf_hdr_t *h)
68 free(h->name); free(h->sname); free(h->txt); free(h->ns); free(h->sns);
72 static inline char **cnt_null(int l, char *str, int *_n)
77 if (l == 0 || str == 0) return 0;
78 for (p = str; p != str + l; ++p)
81 list = calloc(n, sizeof(void*));
83 for (p = str, n = 1; p < str + l - 1; ++p)
84 if (*p == 0) list[n++] = p + 1;
88 int bcf_hdr_sync(bcf_hdr_t *b)
90 if (b == 0) return -1;
91 if (b->ns) free(b->ns);
92 if (b->sns) free(b->sns);
93 if (b->l_nm) b->ns = cnt_null(b->l_nm, b->name, &b->n_ref);
94 else b->ns = 0, b->n_ref = 0;
95 b->sns = cnt_null(b->l_smpl, b->sname, &b->n_smpl);
99 int bcf_sync(bcf1_t *b)
102 int i, n, n_smpl = b->n_smpl;
104 // set ref, alt, flt, info, fmt
105 b->ref = b->alt = b->flt = b->info = b->fmt = 0;
106 for (p = b->str, n = 0; p < b->str + b->l_str; ++p)
107 if (*p == 0 && p+1 != b->str + b->l_str) tmp[n++] = p + 1;
109 fprintf(stderr, "[%s] incorrect number of fields (%d != 5) at %d:%d\n", __func__, n, b->tid, b->pos);
112 b->ref = tmp[0]; b->alt = tmp[1]; b->flt = tmp[2]; b->info = tmp[3]; b->fmt = tmp[4];
114 if (*b->alt == 0) b->n_alleles = 1;
116 for (p = b->alt, n = 1; *p; ++p)
118 b->n_alleles = n + 1;
120 // set n_gi and gi[i].fmt
121 for (p = b->fmt, n = 1; *p; ++p)
127 b->gi = realloc(b->gi, b->m_gi * sizeof(bcf_ginfo_t));
128 memset(b->gi + old_m, 0, (b->m_gi - old_m) * sizeof(bcf_ginfo_t));
131 for (p = kstrtok(b->fmt, ":", &aux), n = 0; p; p = kstrtok(0, 0, &aux))
132 b->gi[n++].fmt = bcf_str2int(p, aux.p - p);
134 for (i = 0; i < b->n_gi; ++i) {
135 if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
136 b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2;
137 } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("HQ", 2)) {
139 } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("GT", 2)
140 || b->gi[i].fmt == bcf_str2int("SP", 2))
143 } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
144 b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2 * 4;
146 b->gi[i].data = realloc(b->gi[i].data, n_smpl * b->gi[i].len);
151 int bcf_write(bcf_t *bp, const bcf_hdr_t *h, const bcf1_t *b)
154 if (b == 0) return -1;
155 bgzf_write(bp->fp, &b->tid, 4);
156 bgzf_write(bp->fp, &b->pos, 4);
157 bgzf_write(bp->fp, &b->qual, 4);
158 bgzf_write(bp->fp, &b->l_str, 4);
159 bgzf_write(bp->fp, b->str, b->l_str);
161 for (i = 0; i < b->n_gi; ++i) {
162 bgzf_write(bp->fp, b->gi[i].data, b->gi[i].len * h->n_smpl);
163 l += b->gi[i].len * h->n_smpl;
168 int bcf_read(bcf_t *bp, const bcf_hdr_t *h, bcf1_t *b)
171 if (b == 0) return -1;
172 if (bgzf_read(bp->fp, &b->tid, 4) == 0) return -1;
173 b->n_smpl = h->n_smpl;
174 bgzf_read(bp->fp, &b->pos, 4);
175 bgzf_read(bp->fp, &b->qual, 4);
176 bgzf_read(bp->fp, &b->l_str, 4);
177 if (b->l_str > b->m_str) {
179 kroundup32(b->m_str);
180 b->str = realloc(b->str, b->m_str);
182 bgzf_read(bp->fp, b->str, b->l_str);
184 if (bcf_sync(b) < 0) return -2;
185 for (i = 0; i < b->n_gi; ++i) {
186 bgzf_read(bp->fp, b->gi[i].data, b->gi[i].len * h->n_smpl);
187 l += b->gi[i].len * h->n_smpl;
192 int bcf_destroy(bcf1_t *b)
195 if (b == 0) return -1;
197 for (i = 0; i < b->m_gi; ++i)
204 static inline void fmt_str(const char *p, kstring_t *s)
206 if (*p == 0) kputc('.', s);
210 void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s)
214 if (h->n_ref) kputs(h->ns[b->tid], s);
215 else kputw(b->tid, s);
217 kputw(b->pos + 1, s); kputc('\t', s);
218 fmt_str(b->str, s); kputc('\t', s);
219 fmt_str(b->ref, s); kputc('\t', s);
220 fmt_str(b->alt, s); kputc('\t', s);
221 ksprintf(s, "%.3g", b->qual); kputc('\t', s);
222 fmt_str(b->flt, s); kputc('\t', s);
228 x = b->n_alleles * (b->n_alleles + 1) / 2;
229 if (b->n_gi == 0) return;
230 for (j = 0; j < h->n_smpl; ++j) {
232 for (i = 0; i < b->n_gi; ++i) {
233 if (i) kputc(':', s);
234 if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
235 uint8_t *d = (uint8_t*)b->gi[i].data + j * x;
237 for (k = 0; k < x; ++k) {
238 if (k > 0) kputc(',', s);
241 } else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
242 kputw(((uint16_t*)b->gi[i].data)[j], s);
243 } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("SP", 2)) {
244 kputw(((uint8_t*)b->gi[i].data)[j], s);
245 } else if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
246 int y = ((uint8_t*)b->gi[i].data)[j];
250 kputc('0' + (y>>3&7), s);
251 kputc("/|"[y>>6&1], s);
252 kputc('0' + (y&7), s);
254 } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
255 float *d = (float*)b->gi[i].data + j * x;
257 //printf("- %lx\n", d);
258 for (k = 0; k < x; ++k) {
259 if (k > 0) kputc(',', s);
260 ksprintf(s, "%.2f", d[k]);
267 char *bcf_fmt(const bcf_hdr_t *h, bcf1_t *b)
270 s.l = s.m = 0; s.s = 0;
271 bcf_fmt_core(h, b, &s);
275 int bcf_append_info(bcf1_t *b, const char *info, int l)
277 int shift = b->fmt - b->str;
278 int l_fmt = b->l_str - shift;
280 if (b->l_str + l > b->m_str) { // enlarge if necessary
281 b->m_str = b->l_str + l;
282 kroundup32(b->m_str);
283 b->str = realloc(b->str, b->m_str);
285 memmove(b->str + shift + l, b->str + shift, l_fmt); // move the FORMAT field
286 memcpy(b->str + shift - 1, info, l); // append to the INFO field
287 b->str[shift + l - 1] = '\0';
288 b->fmt = b->str + shift + l;
290 if (ori != b->str) bcf_sync(b); // synchronize when realloc changes the pointer
294 int bcf_cpy(bcf1_t *r, const bcf1_t *b)
297 bcf_ginfo_t *t2 = r->gi;
298 int i, t3 = r->m_str, t4 = r->m_gi;
300 r->str = t1; r->gi = t2; r->m_str = t3; r->m_gi = t4;
301 if (r->m_str < b->m_str) {
303 r->str = realloc(r->str, r->m_str);
305 memcpy(r->str, b->str, r->m_str);
306 bcf_sync(r); // calling bcf_sync() is simple but inefficient
307 for (i = 0; i < r->n_gi; ++i)
308 memcpy(r->gi[i].data, b->gi[i].data, r->n_smpl * r->gi[i].len);
312 int bcf_is_indel(const bcf1_t *b)
315 if (strlen(b->ref) > 1) return 1;
316 for (p = b->alt; *p; ++p)
317 if (*p != ',' && p[1] != ',' && p[1] != '\0')