diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java old mode 100644 new mode 100755 diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java old mode 100644 new mode 100755 index 6ff0384a0..4b4ebe450 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java @@ -55,10 +55,14 @@ public class TableFeature implements Feature { } public List getAllValues() { - return getValuesTo(values.size()-1); + return getValuesTo(values.size()); } public List getValuesTo(int columnPosition) { return values.subList(0,columnPosition); } + + public List getHeader() { + return keys; + } } diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java index a9ba46159..901de6fae 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java @@ -108,7 +108,7 @@ public class Allele implements Comparable { this.bases = bases; if ( ! acceptableAlleleBases(bases) ) - throw new IllegalArgumentException("Unexpected base in allele bases " + new String(bases)); + throw new IllegalArgumentException("Unexpected base in allele bases \'" + new String(bases)+"\'"); } private Allele(String bases, boolean isRef) {