* samtools-0.1.8-18 (r763)

[samtools.git] / bcftools / vcf.c

diff --git a/bcftools/vcf.c b/bcftools/vcf.c
index d441d7f0b278bf0d6d72eb05d0e641a0926b04ef..ebca869ed999faaed7e782f3a3c410badc062c1b 100644 (file)
--- a/bcftools/vcf.c
+++ b/bcftools/vcf.c
@@ -102,13 +102,6 @@ int vcf_hdr_write(bcf_t *bp, const bcf_hdr_t *h)
                if (strstr(h->txt, "##SQ=")) has_ref = 1;
        }
        if (has_ver == 0) fprintf(v->fpout, "##fileformat=VCFv4.0\n");
-       if (!has_ref) {
-               fprintf(v->fpout, "##SQ=");
-               for (i = 0; i < h->n_ref; ++i) {
-                       fprintf(v->fpout, "%s", h->ns[i]);
-                       fputc(i == h->n_ref - 1? '\n' : ',', v->fpout);
-               }
-       }
        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]);
@@ -139,6 +132,7 @@ int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
        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
@@ -156,7 +150,7 @@ int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
                } 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);
+                       if (k == 8) bcf_sync(b);
                } else { // k > 9
                        if (strncmp(p, "./.", 3) == 0) {
                                for (i = 0; i < b->n_gi; ++i) {