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);
19 int bcf_close(bcf_t *b)
23 ret = bgzf_close(b->fp);
28 int bcf_hdr_write(bcf_t *b, const bcf_hdr_t *h)
30 if (b == 0 || h == 0) return -1;
31 bgzf_write(b->fp, "BCF\4", 4);
32 bgzf_write(b->fp, &h->l_nm, 4);
33 bgzf_write(b->fp, h->name, h->l_nm);
34 bgzf_write(b->fp, &h->l_smpl, 4);
35 bgzf_write(b->fp, h->sname, h->l_smpl);
36 bgzf_write(b->fp, &h->l_txt, 4);
37 bgzf_write(b->fp, h->txt, h->l_txt);
39 return 16 + h->l_nm + h->l_smpl + h->l_txt;
42 bcf_hdr_t *bcf_hdr_read(bcf_t *b)
47 h = calloc(1, sizeof(bcf_hdr_t));
48 bgzf_read(b->fp, magic, 4);
49 bgzf_read(b->fp, &h->l_nm, 4);
50 h->name = malloc(h->l_nm);
51 bgzf_read(b->fp, h->name, h->l_nm);
52 bgzf_read(b->fp, &h->l_smpl, 4);
53 h->sname = malloc(h->l_smpl);
54 bgzf_read(b->fp, h->sname, h->l_smpl);
55 bgzf_read(b->fp, &h->l_txt, 4);
56 h->txt = malloc(h->l_txt);
57 bgzf_read(b->fp, h->txt, h->l_txt);
62 void bcf_hdr_destroy(bcf_hdr_t *h)
65 free(h->name); free(h->sname); free(h->txt); free(h->ns); free(h->sns);
69 static inline char **cnt_null(int l, char *str, int *_n)
74 if (l == 0 || str == 0) return 0;
75 for (p = str; p != str + l; ++p)
78 list = calloc(n, sizeof(void*));
80 for (p = str, n = 1; p < str + l - 1; ++p)
81 if (*p == 0) list[n++] = p + 1;
85 int bcf_hdr_sync(bcf_hdr_t *b)
87 if (b == 0) return -1;
88 if (b->ns) free(b->ns);
89 if (b->sns) free(b->sns);
90 if (b->l_nm) b->ns = cnt_null(b->l_nm, b->name, &b->n_ref);
91 else b->ns = 0, b->n_ref = 0;
92 b->sns = cnt_null(b->l_smpl, b->sname, &b->n_smpl);
96 int bcf_sync(bcf1_t *b)
99 int i, n, n_smpl = b->n_smpl;
101 // set ref, alt, flt, info, fmt
102 b->ref = b->alt = b->flt = b->info = b->fmt = 0;
103 for (p = b->str, n = 0; p < b->str + b->l_str; ++p) {
104 if (*p == 0 && p+1 != b->str + b->l_str) {
108 } else tmp[n++] = p + 1;
112 fprintf(stderr, "[%s] incorrect number of fields (%d != 5) at %d:%d\n", __func__, n, b->tid, b->pos);
115 b->ref = tmp[0]; b->alt = tmp[1]; b->flt = tmp[2]; b->info = tmp[3]; b->fmt = tmp[4];
117 if (*b->alt == 0) b->n_alleles = 1;
119 for (p = b->alt, n = 1; *p; ++p)
121 b->n_alleles = n + 1;
123 // set n_gi and gi[i].fmt
124 for (p = b->fmt, n = 1; *p; ++p)
130 b->gi = realloc(b->gi, b->m_gi * sizeof(bcf_ginfo_t));
131 memset(b->gi + old_m, 0, (b->m_gi - old_m) * sizeof(bcf_ginfo_t));
134 for (p = kstrtok(b->fmt, ":", &aux), n = 0; p; p = kstrtok(0, 0, &aux))
135 b->gi[n++].fmt = bcf_str2int(p, aux.p - p);
137 for (i = 0; i < b->n_gi; ++i) {
138 if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
139 b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2;
140 } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("HQ", 2) || b->gi[i].fmt == bcf_str2int("DV", 2)) {
142 } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("GT", 2)) {
144 } else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
146 } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
147 b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2 * 4;
149 b->gi[i].data = realloc(b->gi[i].data, n_smpl * b->gi[i].len);
154 int bcf_write(bcf_t *bp, const bcf_hdr_t *h, const bcf1_t *b)
157 if (b == 0) return -1;
158 bgzf_write(bp->fp, &b->tid, 4);
159 bgzf_write(bp->fp, &b->pos, 4);
160 bgzf_write(bp->fp, &b->qual, 4);
161 bgzf_write(bp->fp, &b->l_str, 4);
162 bgzf_write(bp->fp, b->str, b->l_str);
164 for (i = 0; i < b->n_gi; ++i) {
165 bgzf_write(bp->fp, b->gi[i].data, b->gi[i].len * h->n_smpl);
166 l += b->gi[i].len * h->n_smpl;
171 int bcf_read(bcf_t *bp, const bcf_hdr_t *h, bcf1_t *b)
174 if (b == 0) return -1;
175 if (bgzf_read(bp->fp, &b->tid, 4) == 0) return -1;
176 b->n_smpl = h->n_smpl;
177 bgzf_read(bp->fp, &b->pos, 4);
178 bgzf_read(bp->fp, &b->qual, 4);
179 bgzf_read(bp->fp, &b->l_str, 4);
180 if (b->l_str > b->m_str) {
182 kroundup32(b->m_str);
183 b->str = realloc(b->str, b->m_str);
185 bgzf_read(bp->fp, b->str, b->l_str);
187 if (bcf_sync(b) < 0) return -2;
188 for (i = 0; i < b->n_gi; ++i) {
189 bgzf_read(bp->fp, b->gi[i].data, b->gi[i].len * h->n_smpl);
190 l += b->gi[i].len * h->n_smpl;
195 int bcf_destroy(bcf1_t *b)
198 if (b == 0) return -1;
200 for (i = 0; i < b->m_gi; ++i)
207 static inline void fmt_str(const char *p, kstring_t *s)
209 if (*p == 0) kputc('.', s);
213 void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s)
217 if (h->n_ref) kputs(h->ns[b->tid], s);
218 else kputw(b->tid, s);
220 kputw(b->pos + 1, s); kputc('\t', s);
221 fmt_str(b->str, s); kputc('\t', s);
222 fmt_str(b->ref, s); kputc('\t', s);
223 fmt_str(b->alt, s); kputc('\t', s);
224 ksprintf(s, "%.3g", b->qual); kputc('\t', s);
225 fmt_str(b->flt, s); kputc('\t', s);
231 x = b->n_alleles * (b->n_alleles + 1) / 2;
232 if (b->n_gi == 0) return;
234 if ( b->n_alleles > 2 ) {
235 for (i=0; i<b->n_gi; i++) {
236 if ( b->gi[i].fmt == bcf_str2int("PL", 2) ) {
242 for (j = 0; j < h->n_smpl; ++j) {
244 // Determine GT with maximum PL (multiple ALT sites only)
247 uint8_t *d = (uint8_t*)b->gi[iPL].data + j * x;
252 if ( identical && d[k]!=d[k-1] ) identical = 0;
253 if ( d[k]<d[imax] ) imax = k;
255 // If all lks are identical, leave GT untouched
256 if ( identical ) imax = -1;
259 for (i = 0; i < b->n_gi; ++i) {
260 if (i) kputc(':', s);
261 if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
262 uint8_t *d = (uint8_t*)b->gi[i].data + j * x;
264 for (k = 0; k < x; ++k) {
265 if (k > 0) kputc(',', s);
268 } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("DV", 2)) {
269 kputw(((uint16_t*)b->gi[i].data)[j], s);
270 } else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
271 kputw(((uint8_t*)b->gi[i].data)[j], s);
272 } else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
273 kputw(((int32_t*)b->gi[i].data)[j], s);
274 } else if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
275 int y = ((uint8_t*)b->gi[i].data)[j];
280 kputc('0' + (y>>3&7), s);
281 kputc("/|"[y>>6&1], s);
282 kputc('0' + (y&7), s);
286 // Arguably, the while loop will be faster than two sqrts
295 kputw(imax-n+row, s);
296 kputc("/|"[y>>6&1], s);
299 } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
300 float *d = (float*)b->gi[i].data + j * x;
302 //printf("- %lx\n", d);
303 for (k = 0; k < x; ++k) {
304 if (k > 0) kputc(',', s);
305 ksprintf(s, "%.2f", d[k]);
307 } else kputc('.', s); // custom fields
312 char *bcf_fmt(const bcf_hdr_t *h, bcf1_t *b)
315 s.l = s.m = 0; s.s = 0;
316 bcf_fmt_core(h, b, &s);
320 int bcf_append_info(bcf1_t *b, const char *info, int l)
322 int shift = b->fmt - b->str;
323 int l_fmt = b->l_str - shift;
325 if (b->l_str + l > b->m_str) { // enlarge if necessary
326 b->m_str = b->l_str + l;
327 kroundup32(b->m_str);
328 b->str = realloc(b->str, b->m_str);
330 memmove(b->str + shift + l, b->str + shift, l_fmt); // move the FORMAT field
331 memcpy(b->str + shift - 1, info, l); // append to the INFO field
332 b->str[shift + l - 1] = '\0';
333 b->fmt = b->str + shift + l;
335 if (ori != b->str) bcf_sync(b); // synchronize when realloc changes the pointer
339 int bcf_cpy(bcf1_t *r, const bcf1_t *b)
342 bcf_ginfo_t *t2 = r->gi;
343 int i, t3 = r->m_str, t4 = r->m_gi;
345 r->str = t1; r->gi = t2; r->m_str = t3; r->m_gi = t4;
346 if (r->m_str < b->m_str) {
348 r->str = realloc(r->str, r->m_str);
350 memcpy(r->str, b->str, r->m_str);
351 bcf_sync(r); // calling bcf_sync() is simple but inefficient
352 for (i = 0; i < r->n_gi; ++i)
353 memcpy(r->gi[i].data, b->gi[i].data, r->n_smpl * r->gi[i].len);
357 int bcf_is_indel(const bcf1_t *b)
360 if (strlen(b->ref) > 1) return 1;
361 for (p = b->alt; *p; ++p)
362 if (*p != ',' && p[1] != ',' && p[1] != '\0')