From: Heng Li <lh3@live.co.uk>
Date: Thu, 24 Feb 2011 14:35:06 +0000 (+0000)
Subject:  * automatically fix errors in GL
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=c8e59c53055a63e697e98a5942a2d811eb4db5b9;p=samtools.git

 * automatically fix errors in GL
 * output unrecognized FORMAT as "."
---

diff --git a/bcftools/bcf.c b/bcftools/bcf.c
index b749847..88ba1ba 100644
--- a/bcftools/bcf.c
+++ b/bcftools/bcf.c
@@ -259,7 +259,7 @@ 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
 		}
 	}
 }
diff --git a/bcftools/vcf.c b/bcftools/vcf.c
index 6d3abaa..d8cb1e6 100644
--- a/bcftools/vcf.c
+++ b/bcftools/vcf.c
@@ -224,7 +224,7 @@ int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
 					y = b->n_alleles * (b->n_alleles + 1) / 2;
 					for (j = 0; j < y; ++j) {
 						x = strtod(q, &q);
-						data[(k-9) * y + j] = x;
+						data[(k-9) * y + j] = x > 0? -x/10. : x;
 						++q;
 					}
 				}