X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fbcf.c;h=494dcccd3641b3c1b0856a8e88c0d065399ca8a7;hb=896d270d34b71e0422ddca4a0d62136cb2e537be;hp=9044b93b0b514fd9566f037a705f8769f60ecc54;hpb=b28a2f58cecab24d2872964dabe53e3b3caaf476;p=samtools.git

diff --git a/bcftools/bcf.c b/bcftools/bcf.c
index 9044b93..494dccc 100644
--- a/bcftools/bcf.c
+++ b/bcftools/bcf.c
@@ -134,7 +134,9 @@ int bcf_sync(bcf1_t *b)
 			b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2;
 		} else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("HQ", 2)) {
 			b->gi[i].len = 2;
-		} else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("GT", 2)) {
+		} else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("GT", 2)
+				   || b->gi[i].fmt == bcf_str2int("SP", 2))
+		{
 			b->gi[i].len = 1;
 		} else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
 			b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2 * 4;
@@ -236,7 +238,7 @@ void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s)
 				}
 			} else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
 				kputw(((uint16_t*)b->gi[i].data)[j], s);
-			} else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
+			} else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("SP", 2)) {
 				kputw(((uint8_t*)b->gi[i].data)[j], s);
 			} else if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
 				int y = ((uint8_t*)b->gi[i].data)[j];