X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fvcf.c;h=bc110847dab9e2b97d0248ddfef92312de561ce1;hb=543a9fc2055575dcc17a7bb9c83ecca17a32cec6;hp=d8cb1e6d3efc56b8c119f677b25d292f696e3428;hpb=c8e59c53055a63e697e98a5942a2d811eb4db5b9;p=samtools.git

diff --git a/bcftools/vcf.c b/bcftools/vcf.c
index d8cb1e6..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]);
@@ -182,9 +182,11 @@ int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
 				for (i = 0; i < b->n_gi; ++i) {
 					if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
 						((uint8_t*)b->gi[i].data)[k-9] = 1<<7;
-					} else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("SP", 2)) {
+					} else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
 						((uint8_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("SP", 2)) {
+						((int32_t*)b->gi[i].data)[k-9] = 0;
+					} 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;
@@ -199,12 +201,16 @@ int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
 			for (q = kstrtok(p, ":", &a2), i = 0; q && i < b->n_gi; q = kstrtok(0, 0, &a2), ++i) {
 				if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
 					((uint8_t*)b->gi[i].data)[k-9] = (q[0] - '0')<<3 | (q[2] - '0') | (q[1] == '/'? 0 : 1) << 6;
-				} else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("SP", 2)) {
+				} else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
 					double _x = strtod(q, &q);
 					int x = (int)(_x + .499);
 					if (x > 255) x = 255;
 					((uint8_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("SP", 2)) {
+					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) || 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;