X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fbcf.c;h=035eddc70386bd011f710970026e50358a502be4;hb=f221655a2515b417a545caece40b6985e927fb83;hp=3531647e18775cd5049954385a1022d39a17ec6f;hpb=032937695157a15fb0ce042deda22afc30be1616;p=samtools.git

diff --git a/bcftools/bcf.c b/bcftools/bcf.c
index 3531647..035eddc 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("ST", 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("ST", 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];
@@ -283,8 +285,7 @@ int bcf_append_info(bcf1_t *b, const char *info, int l)
 	b->str[shift + l - 1] = '\0';
 	b->fmt = b->str + shift + l;
 	b->l_str += l;
-	bcf_sync(b);
-//	if (ori != b->str) bcf_sync(b); // synchronize when realloc changes the pointer
+	if (ori != b->str) bcf_sync(b); // synchronize when realloc changes the pointer
 	return 0;
 }