diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java index 043e5e185..652f7f96f 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java @@ -587,7 +587,7 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec int nParts = ParsingUtils.split(str, genotypeParts, VCFConstants.FIELD_SEPARATOR_CHAR); if ( nParts != genotypeParts.length ) - generateException("there are " + (nParts-1) + " genotypes while the header requires that " + (genotypeParts.length-1) + " genotypes be present for all records", lineNo); + generateException("there are " + (nParts-1) + " genotypes while the header requires that " + (genotypeParts.length-1) + " genotypes be present for all records at " + chr + ":" + pos, lineNo); ArrayList genotypes = new ArrayList(nParts); diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriterManager.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriterManager.java index 7b8224568..9c63a69e7 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriterManager.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriterManager.java @@ -76,7 +76,6 @@ public class BCF2FieldWriterManager { if ( map.containsKey(field) ) throw new ReviewedStingException("BUG: field " + field + " already seen in VCFHeader while building BCF2 field encoders"); map.put(field, writer); - if ( logger.isDebugEnabled() ) logger.debug(writer); } // ----------------------------------------------------------------- diff --git a/settings/repository/org.broad/tribble-110.jar b/settings/repository/org.broad/tribble-119.jar similarity index 78% rename from settings/repository/org.broad/tribble-110.jar rename to settings/repository/org.broad/tribble-119.jar index f8e312ad9..ab456938a 100644 Binary files a/settings/repository/org.broad/tribble-110.jar and b/settings/repository/org.broad/tribble-119.jar differ diff --git a/settings/repository/org.broad/tribble-110.xml b/settings/repository/org.broad/tribble-119.xml similarity index 79% rename from settings/repository/org.broad/tribble-110.xml rename to settings/repository/org.broad/tribble-119.xml index 84a550b27..08037b20e 100644 --- a/settings/repository/org.broad/tribble-110.xml +++ b/settings/repository/org.broad/tribble-119.xml @@ -1,3 +1,3 @@ - +