diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java index 4b3aa4864..e43d54e14 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java @@ -272,12 +272,11 @@ public class VariantsToTable extends RodWalker { getters.put("POS", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getStart()); } }); getters.put("REF", new Getter() { public String get(VariantContext vc) { - String x = ""; - if ( vc.hasReferenceBaseForIndel() && !vc.isSNP() ) { - Byte refByte = vc.getReferenceBaseForIndel(); - x=x+new String(new byte[]{refByte}); - } - return x+vc.getReference().getDisplayString(); + StringBuilder x = new StringBuilder(); + if ( vc.hasReferenceBaseForIndel() && !vc.isSNP() ) + x.append((char)vc.getReferenceBaseForIndel().byteValue()); + x.append(vc.getReference().getDisplayString()); + return x.toString(); } }); getters.put("ALT", new Getter() { @@ -285,13 +284,11 @@ public class VariantsToTable extends RodWalker { StringBuilder x = new StringBuilder(); int n = vc.getAlternateAlleles().size(); if ( n == 0 ) return "."; - if ( vc.hasReferenceBaseForIndel() && !vc.isSNP() ) { - Byte refByte = vc.getReferenceBaseForIndel(); - x.append(new String(new byte[]{refByte})); - } for ( int i = 0; i < n; i++ ) { if ( i != 0 ) x.append(","); + if ( vc.hasReferenceBaseForIndel() && !vc.isSNP() ) + x.append((char)vc.getReferenceBaseForIndel().byteValue()); x.append(vc.getAlternateAllele(i).getDisplayString()); } return x.toString();