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Just because there's a ref base doesn't mean the VC needs to be padded

This commit is contained in:
Eric Banks 2011-08-25 22:42:14 -04:00
parent 09a729da3a
commit 9b7512fd94
1 changed files with 2 additions and 2 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
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@ -271,7 +271,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
getters.put("REF", new Getter() { getters.put("REF", new Getter() {
public String get(VariantContext vc) { public String get(VariantContext vc) {
String x = ""; String x = "";
if ( vc.hasReferenceBaseForIndel() ) { if ( vc.hasReferenceBaseForIndel() && !vc.isSNP() ) {
Byte refByte = vc.getReferenceBaseForIndel(); Byte refByte = vc.getReferenceBaseForIndel();
x=x+new String(new byte[]{refByte}); x=x+new String(new byte[]{refByte});
} }
@ -283,7 +283,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
StringBuilder x = new StringBuilder(); StringBuilder x = new StringBuilder();
int n = vc.getAlternateAlleles().size(); int n = vc.getAlternateAlleles().size();
if ( n == 0 ) return "."; if ( n == 0 ) return ".";
if ( vc.hasReferenceBaseForIndel() ) { if ( vc.hasReferenceBaseForIndel() && !vc.isSNP() ) {
Byte refByte = vc.getReferenceBaseForIndel(); Byte refByte = vc.getReferenceBaseForIndel();
x.append(new String(new byte[]{refByte})); x.append(new String(new byte[]{refByte}));
} }