// Find/add and then update a header record
void vcf_misc_add_update_hrec(bcf_hrec_t *hrec, char *key, char *val)
{
int keyidx = bcf_hrec_find_key(hrec, key);
if(keyidx < 0) {
status("Adding sample key [%s] => [%s]", key, val);
bcf_hrec_add_key(hrec, key, strlen(key));
keyidx = hrec->nkeys-1;
}
bcf_hrec_set_val(hrec, keyidx, val, strlen(val), 0); // 0 => not quoted
}
bcf_hrec_t *bcf_hdr_parse_line(const bcf_hdr_t *h, char *line, int *len)
{
char *p = line;
if (p[0] != '#' || p[1] != '#') { *len = 0; return NULL; }
p += 2;
char *q = p;
while ( *q && *q!='=' ) q++;
int n = q-p;
if ( *q!='=' || !n ) { *len = q-line+1; return NULL; } // wrong format
bcf_hrec_t *hrec = (bcf_hrec_t*) calloc(1,sizeof(bcf_hrec_t));
hrec->key = (char*) malloc(sizeof(char)*(n+1));
memcpy(hrec->key,p,n);
hrec->key[n] = 0;
p = ++q;
if ( *p!='<' ) // generic field, e.g. ##samtoolsVersion=0.1.18-r579
{
while ( *q && *q!='\n' ) q++;
hrec->value = (char*) malloc((q-p+1)*sizeof(char));
memcpy(hrec->value, p, q-p);
hrec->value[q-p] = 0;
*len = q-line+1;
return hrec;
}
// structured line, e.g. ##INFO=<ID=PV1,Number=1,Type=Float,Description="P-value for baseQ bias">
while ( *q && *q!='\n' )
{
p = ++q;
while ( *q && *q!='=' ) q++;
n = q-p;
if ( *q!='=' || !n ) { *len = q-line+1; return NULL; } // wrong format
bcf_hrec_add_key(hrec, p, q-p);
p = ++q;
int quoted = *p=='"' ? 1 : 0;
if ( quoted ) p++, q++;
while (1)
{
if ( !*q ) break;
if ( quoted ) { if ( *q=='"' && !is_escaped(p,q) ) break; }
else { if ( *q==',' || *q=='>' ) break; }
q++;
}
bcf_hrec_set_val(hrec, hrec->nkeys-1, p, q-p, quoted);
if ( quoted ) q++;
if ( *q=='>' ) { q++; break; }
}
*len = q-line+1;
return hrec;
}
bcf_hdr_t *vcf_hdr_read(htsFile *fp)
{
if (!fp->is_bin) {
kstring_t txt, *s = &fp->line;
bcf_hdr_t *h;
h = bcf_hdr_init();
txt.l = txt.m = 0; txt.s = 0;
while (hts_getline(fp, KS_SEP_LINE, s) >= 0) {
if (s->l == 0) continue;
if (s->s[0] != '#') {
if (hts_verbose >= 2)
fprintf(stderr, "[E::%s] no sample line\n", __func__);
free(txt.s);
bcf_hdr_destroy(h);
return 0;
}
if (s->s[1] != '#' && fp->fn_aux) { // insert contigs here
int dret;
gzFile f;
kstream_t *ks;
kstring_t tmp;
tmp.l = tmp.m = 0; tmp.s = 0;
f = gzopen(fp->fn_aux, "r");
ks = ks_init(f);
while (ks_getuntil(ks, 0, &tmp, &dret) >= 0) {
int c;
kputs("##contig=<ID=", &txt); kputs(tmp.s, &txt);
ks_getuntil(ks, 0, &tmp, &dret);
kputs(",length=", &txt); kputw(atol(tmp.s), &txt);
kputsn(">\n", 2, &txt);
if (dret != '\n')
while ((c = ks_getc(ks)) != '\n' && c != -1); // skip the rest of the line
}
free(tmp.s);
ks_destroy(ks);
gzclose(f);
}
kputsn(s->s, s->l, &txt);
if (s->s[1] != '#') break;
kputc('\n', &txt);
}
h->l_text = txt.l + 1; // including NULL
h->text = txt.s;
bcf_hdr_parse(h);
// check tabix index, are all contigs listed in the header? add the missing ones
tbx_t *idx = tbx_index_load(fp->fn);
if ( idx )
{
int i, n, need_sync = 0;
const char **names = tbx_seqnames(idx, &n);
for (i=0; i<n; i++)
{
bcf_hrec_t *hrec = bcf_hdr_get_hrec(h, BCF_DT_CTG, (char*) names[i]);
if ( hrec ) continue;
hrec = (bcf_hrec_t*) calloc(1,sizeof(bcf_hrec_t));
hrec->key = strdup("contig");
bcf_hrec_add_key(hrec, "ID", strlen("ID"));
bcf_hrec_set_val(hrec, hrec->nkeys-1, (char*) names[i], strlen(names[i]), 0);
bcf_hrec_add_key(hrec, "length", strlen("length"));
bcf_hrec_set_val(hrec, hrec->nkeys-1, "-1", strlen("-1"), 0); // what is a good default value?
bcf_hdr_add_hrec(h, hrec);
need_sync = 1;
}
free(names);
tbx_destroy(idx);
if ( need_sync )
{
bcf_hdr_sync(h);
bcf_hdr_fmt_text(h);
}
}
return h;
} else return bcf_hdr_read((BGZF*)fp->fp);
}
