X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fvcf.c;h=81a38eaa7f2d853908ce3df575416c9092735d76;hb=27eec65490fb3461f0af054868d9a0949e1843ed;hp=d8cb1e6d3efc56b8c119f677b25d292f696e3428;hpb=29e08d7455e9b283ef4650af7fde6fe0310d8158;p=samtools.git

diff --git a/bcftools/vcf.c b/bcftools/vcf.c
index d8cb1e6..81a38ea 100644
--- a/bcftools/vcf.c
+++ b/bcftools/vcf.c
@@ -182,8 +182,10 @@ 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("SP", 2)) {
+						((int32_t*)b->gi[i].data)[k-9] = 0;
 					} else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
 						((uint16_t*)b->gi[i].data)[k-9] = 0;
 					} else if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
@@ -199,11 +201,15 @@ 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("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)) {
 					int x = strtol(q, &q, 10);
 					if (x > 0xffff) x = 0xffff;