X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bcftools%2Fbcf.c;h=84a8e767ec58adb397630f609a52670779f99c89;hp=fd5c0c9ae24971f15168f488452afe2077258dd0;hb=2347ad62090e036841008e054c234868e21f7a80;hpb=e3b3a0177339fb8c099346986e965e3bd5b85999

diff --git a/bcftools/bcf.c b/bcftools/bcf.c
index fd5c0c9..84a8e76 100644
--- a/bcftools/bcf.c
+++ b/bcftools/bcf.c
@@ -103,10 +103,16 @@ int bcf_sync(bcf1_t *b)
 	ks_tokaux_t aux;
 	// set ref, alt, flt, info, fmt
 	b->ref = b->alt = b->flt = b->info = b->fmt = 0;
-	for (p = b->str, n = 0; p < b->str + b->l_str; ++p)
-		if (*p == 0 && p+1 != b->str + b->l_str) tmp[n++] = p + 1;
+	for (p = b->str, n = 0; p < b->str + b->l_str; ++p) {
+		if (*p == 0 && p+1 != b->str + b->l_str) {
+			if (n == 5) {
+				++n;
+				break;
+			} else tmp[n++] = p + 1;
+		}
+	}
 	if (n != 5) {
-		fprintf(stderr, "[%s] incorrect number of fields (%d != 5). Corrupted file?\n", __func__, n);
+		fprintf(stderr, "[%s] incorrect number of fields (%d != 5) at %d:%d\n", __func__, n, b->tid, b->pos);
 		return -1;
 	}
 	b->ref = tmp[0]; b->alt = tmp[1]; b->flt = tmp[2]; b->info = tmp[3]; b->fmt = tmp[4];
@@ -136,10 +142,10 @@ 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)
-				   || b->gi[i].fmt == bcf_str2int("SP", 2))
-		{
+		} else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("GT", 2)) {
 			b->gi[i].len = 1;
+		} else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
+			b->gi[i].len = 4;
 		} else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
 			b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2 * 4;
 		}
@@ -181,7 +187,7 @@ 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;
@@ -240,8 +246,10 @@ 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("SP", 2)) {
+			} else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
 				kputw(((uint8_t*)b->gi[i].data)[j], s);
+			} else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
+				kputw(((int32_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];
 				if (y>>7&1) {
@@ -259,7 +267,7 @@ void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s)
 					if (k > 0) kputc(',', s);
 					ksprintf(s, "%.2f", d[k]);
 				}
-			}
+			} else kputc('.', s); // custom fields
 		}
 	}
 }