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Multi-allelic indels were not being printed out correctly in VariantsToTable; fixed.

This commit is contained in:
Eric Banks 2012-02-06 22:49:29 -05:00
parent 5961868a7f
commit 9d1a19bbaa
1 changed files with 7 additions and 10 deletions
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17
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
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@ -272,12 +272,11 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
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<Integer, Integer> {
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();