memset(&smpl, 0, sizeof(kstring_t));
while (ks_getuntil(v->ks, '\n', &v->line, &dret) >= 0) {
if (v->line.l < 2) continue;
- if (v->line.s[0] != '#') return 0; // no sample line
+ if (v->line.s[0] != '#') {
+ free(meta.s);
+ free(smpl.s);
+ free(h);
+ return 0; // no sample line
+ }
if (v->line.s[0] == '#' && v->line.s[1] == '#') {
kputsn(v->line.s, v->line.l, &meta); kputc('\n', &meta);
} else if (v->line.s[0] == '#') {
return bp;
}
+int vcf_dictread(bcf_t *bp, bcf_hdr_t *h, const char *fn)
+{
+ vcf_t *v;
+ gzFile fp;
+ kstream_t *ks;
+ kstring_t s, rn;
+ int dret;
+ if (bp == 0) return -1;
+ if (!bp->is_vcf) return 0;
+ s.l = s.m = 0; s.s = 0;
+ rn.m = rn.l = h->l_nm; rn.s = h->name;
+ v = (vcf_t*)bp->v;
+ fp = gzopen(fn, "r");
+ ks = ks_init(fp);
+ while (ks_getuntil(ks, 0, &s, &dret) >= 0) {
+ bcf_str2id_add(v->refhash, strdup(s.s));
+ kputs(s.s, &rn); kputc('\0', &rn);
+ if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
+ }
+ ks_destroy(ks);
+ gzclose(fp);
+ h->l_nm = rn.l; h->name = rn.s;
+ bcf_hdr_sync(h);
+ free(s.s);
+ return 0;
+}
+
int vcf_close(bcf_t *bp)
{
vcf_t *v;
}
if (v->fpout) fclose(v->fpout);
free(v->line.s);
- bcf_str2id_destroy(v->refhash);
+ bcf_str2id_thorough_destroy(v->refhash);
free(v);
free(bp);
return 0;
int vcf_hdr_write(bcf_t *bp, const bcf_hdr_t *h)
{
vcf_t *v = (vcf_t*)bp->v;
- int i;
+ int i, has_ver = 0;
if (!bp->is_vcf) return bcf_hdr_write(bp, h);
- if (h->l_txt > 0) fwrite(h->txt, 1, h->l_txt - 1, v->fpout);
+ if (h->l_txt > 0) {
+ if (strstr(h->txt, "##fileformat=")) has_ver = 1;
+ if (has_ver == 0) fprintf(v->fpout, "##fileformat=VCFv4.1\n");
+ fwrite(h->txt, 1, h->l_txt - 1, v->fpout);
+ }
+ if (h->l_txt == 0) fprintf(v->fpout, "##fileformat=VCFv4.1\n");
fprintf(v->fpout, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT");
for (i = 0; i < h->n_smpl; ++i)
fprintf(v->fpout, "\t%s", h->sns[i]);
str.l = 0; str.m = b->m_str; str.s = b->str;
rn.l = rn.m = h->l_nm; rn.s = h->name;
if (ks_getuntil(v->ks, '\n', &v->line, &dret) < 0) return -1;
+ b->n_smpl = h->n_smpl;
for (p = kstrtok(v->line.s, "\t", &aux), k = 0; p; p = kstrtok(0, 0, &aux), ++k) {
*(char*)aux.p = 0;
if (k == 0) { // ref
int tid = bcf_str2id(v->refhash, p);
if (tid < 0) {
- tid = bcf_str2id_add(v->refhash, p);
- kputs(p, &rn);
+ tid = bcf_str2id_add(v->refhash, strdup(p));
+ kputs(p, &rn); kputc('\0', &rn);
sync = 1;
}
b->tid = tid;
} else if (k == 1) { // pos
- b->pos = atoi(p);
+ b->pos = atoi(p) - 1;
} else if (k == 5) { // qual
- b->qual = (p[0] >= '0' && p[0] <= '9')? atoi(p) : 0;
+ b->qual = (p[0] >= '0' && p[0] <= '9')? atof(p) : 0;
} else if (k <= 8) { // variable length strings
kputs(p, &str); kputc('\0', &str);
b->l_str = str.l; b->m_str = str.m; b->str = str.s;
- if (k == 8) bcf_sync(h->n_smpl, b);
- } else {
+ if (k == 8) bcf_sync(b);
+ } else { // k > 9
+ if (strncmp(p, "./.", 3) == 0) {
+ for (i = 0; i < b->n_gi; ++i) {
+ if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
+ ((uint8_t*)b->gi[i].data)[k-9] = 1<<7;
+ } else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
+ ((uint8_t*)b->gi[i].data)[k-9] = 0;
+ } else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
+ ((int32_t*)b->gi[i].data)[k-9] = 0;
+ } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("DV", 2)) {
+ ((uint16_t*)b->gi[i].data)[k-9] = 0;
+ } else if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
+ int y = b->n_alleles * (b->n_alleles + 1) / 2;
+ memset((uint8_t*)b->gi[i].data + (k - 9) * y, 0, y);
+ } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
+ int y = b->n_alleles * (b->n_alleles + 1) / 2;
+ memset((float*)b->gi[i].data + (k - 9) * y, 0, y * 4);
+ }
+ }
+ goto endblock;
+ }
for (q = kstrtok(p, ":", &a2), i = 0; q && i < b->n_gi; q = kstrtok(0, 0, &a2), ++i) {
if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
((uint8_t*)b->gi[i].data)[k-9] = (q[0] - '0')<<3 | (q[2] - '0') | (q[1] == '/'? 0 : 1) << 6;
} else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
- int x = strtol(q, &q, 10);
+ double _x = strtod(q, &q);
+ int x = (int)(_x + .499);
if (x > 255) x = 255;
((uint8_t*)b->gi[i].data)[k-9] = x;
- } else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
+ } else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
+ int x = strtol(q, &q, 10);
+ if (x > 0xffff) x = 0xffff;
+ ((uint32_t*)b->gi[i].data)[k-9] = x;
+ } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("DV", 2)) {
int x = strtol(q, &q, 10);
if (x > 0xffff) x = 0xffff;
((uint16_t*)b->gi[i].data)[k-9] = x;
+ } else if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
+ int x, y, j;
+ uint8_t *data = (uint8_t*)b->gi[i].data;
+ y = b->n_alleles * (b->n_alleles + 1) / 2;
+ for (j = 0; j < y; ++j) {
+ x = strtol(q, &q, 10);
+ if (x > 255) x = 255;
+ data[(k-9) * y + j] = x;
+ ++q;
+ }
+ } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
+ int j, y;
+ float x, *data = (float*)b->gi[i].data;
+ y = b->n_alleles * (b->n_alleles + 1) / 2;
+ for (j = 0; j < y; ++j) {
+ x = strtod(q, &q);
+ data[(k-9) * y + j] = x > 0? -x/10. : x;
+ ++q;
+ }
}
}
+ endblock: i = i;
}
}
h->l_nm = rn.l; h->name = rn.s;
projects / samtools.git / blobdiff