X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fbcf.c;h=6e45695cfb8c35a22dc4699728e445129293a699;hb=82797ab5f5ba03634967e19822e11a491c8e6198;hp=035eddc70386bd011f710970026e50358a502be4;hpb=f221655a2515b417a545caece40b6985e927fb83;p=samtools.git

diff --git a/bcftools/bcf.c b/bcftools/bcf.c
index 035eddc..6e45695 100644
--- a/bcftools/bcf.c
+++ b/bcftools/bcf.c
@@ -13,7 +13,9 @@ bcf_t *bcf_open(const char *fn, const char *mode)
 	} else {
 		b->fp = strcmp(fn, "-")? bgzf_open(fn, mode) : bgzf_fdopen(fileno(stdin), mode);
 	}
+#ifndef BCF_LITE
 	b->fp->owned_file = 1;
+#endif
 	return b;
 }
 
@@ -135,7 +137,7 @@ int bcf_sync(bcf1_t *b)
 		} 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)
-				   || b->gi[i].fmt == bcf_str2int("ST", 2))
+				   || b->gi[i].fmt == bcf_str2int("SP", 2))
 		{
 			b->gi[i].len = 1;
 		} else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
@@ -179,7 +181,7 @@ int bcf_read(bcf_t *bp, const bcf_hdr_t *h, bcf1_t *b)
 	}
 	bgzf_read(bp->fp, b->str, b->l_str);
 	l = 12 + b->l_str;
-	bcf_sync(b);
+	if (bcf_sync(b) < 0) return -2;
 	for (i = 0; i < b->n_gi; ++i) {
 		bgzf_read(bp->fp, b->gi[i].data, b->gi[i].len * h->n_smpl);
 		l += b->gi[i].len * h->n_smpl;
@@ -238,7 +240,7 @@ 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) || b->gi[i].fmt == bcf_str2int("ST", 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];
@@ -306,3 +308,13 @@ int bcf_cpy(bcf1_t *r, const bcf1_t *b)
 		memcpy(r->gi[i].data, b->gi[i].data, r->n_smpl * r->gi[i].len);
 	return 0;
 }
+
+int bcf_is_indel(const bcf1_t *b)
+{
+	char *p;
+	if (strlen(b->ref) > 1) return 1;
+	for (p = b->alt; *p; ++p)
+		if (*p != ',' && p[1] != ',' && p[1] != '\0')
+			return 1;
+	return 0;
+}