X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fvcf.c;h=bc110847dab9e2b97d0248ddfef92312de561ce1;hb=da45f88bac09817fcd87916d3e104f0e4bc53874;hp=81a38eaa7f2d853908ce3df575416c9092735d76;hpb=27eec65490fb3461f0af054868d9a0949e1843ed;p=samtools.git

diff --git a/bcftools/vcf.c b/bcftools/vcf.c
index 81a38ea..bc11084 100644
--- a/bcftools/vcf.c
+++ b/bcftools/vcf.c
@@ -124,10 +124,10 @@ int vcf_hdr_write(bcf_t *bp, const bcf_hdr_t *h)
 	if (!bp->is_vcf) return bcf_hdr_write(bp, h);
 	if (h->l_txt > 0) {
 		if (strstr(h->txt, "##fileformat=")) has_ver = 1;
-		if (has_ver == 0) fprintf(v->fpout, "##fileformat=VCFv4.0\n");
+		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=VCFv4.0\n");
+	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]);
@@ -186,7 +186,7 @@ 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 +210,7 @@ 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;