Updated samtools to 0.1.19

[rsem.git] / sam / bcftools / vcf.c

diff --git a/sam/bcftools/vcf.c b/sam/bcftools/vcf.c
index 9daa845cba6c13b7d2190fbf77f4877b7979178c..e8526a38706357c4aa2d067fcf9c64dadd8978f6 100644 (file)
--- a/sam/bcftools/vcf.c
+++ b/sam/bcftools/vcf.c
@@ -30,7 +30,12 @@ bcf_hdr_t *vcf_hdr_read(bcf_t *bp)
        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] == '#') {
@@ -186,7 +191,7 @@ int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
                                                ((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)) {
+                                       } 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;
@@ -210,7 +215,7 @@ int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
                                        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)) {
+                               } 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;