bcf_callret1_t *bcr = 0;
bcf_call_t bc;
bcf_t *bp = 0;
+ bcf_hdr_t *bh = 0;
memset(&bc, 0, sizeof(bcf_call_t));
data = calloc(n, sizeof(void*));
// write the VCF header
if (conf->flag & MPLP_GLF) {
kstring_t s;
+ bh = calloc(1, sizeof(bcf_hdr_t));
s.l = s.m = 0; s.s = 0;
bp = bcf_open("-", (conf->flag&MPLP_NO_COMP)? "wu" : "w");
for (i = 0; i < h->n_targets; ++i) {
kputs(h->target_name[i], &s);
kputc('\0', &s);
}
- bp->h.l_nm = s.l;
- bp->h.name = malloc(s.l);
- memcpy(bp->h.name, s.s, s.l);
+ bh->l_nm = s.l;
+ bh->name = malloc(s.l);
+ memcpy(bh->name, s.s, s.l);
s.l = 0;
for (i = 0; i < n; ++i) {
const char *p;
else kputs(fn[i], &s);
kputc('\0', &s);
}
- bp->h.l_smpl = s.l;
- bp->h.sname = malloc(s.l);
- memcpy(bp->h.sname, s.s, s.l);
- bp->h.l_txt = 0;
+ bh->l_smpl = s.l;
+ bh->sname = malloc(s.l);
+ memcpy(bh->sname, s.s, s.l);
+ bh->l_txt = 0;
free(s.s);
- bcf_hdr_sync(&bp->h);
- bcf_hdr_write(bp);
+ bcf_hdr_sync(bh);
+ bcf_hdr_write(bp, bh);
} else if (conf->flag & MPLP_VCF) {
kstring_t s;
s.l = s.m = 0; s.s = 0;
bcf_call_glfgen(n_plp[i], plp[i], ref16, bca, bcr + i);
bcf_call_combine(n, bcr, ref16, &bc);
bcf_call2bcf(tid, pos, &bc, b);
- bcf_write(bp, b);
+ bcf_write(bp, bh, b);
//fprintf(stderr, "%d,%d,%d\n", b->tid, b->pos, b->l_str);
bcf_destroy(b);
} else if (conf->flag & MPLP_VCF) {
if (kh_exist(hash, k)) free(kh_val(hash, k));
kh_destroy(64, hash);
}
- bcf_call_destroy(bca); free(bc.PL); free(bcr);
+ bcf_hdr_destroy(bh); bcf_call_destroy(bca); free(bc.PL); free(bcr);
mc_destroy(ma);
bam_mplp_destroy(iter);
bam_header_destroy(h);