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Fix: GSA-531 ApplyRecalibration writing to BCF: java.lang.String cannot be cast to java.lang.Double 

-- LOD must be added a double to attributes, not as string, so that it can be written out as BCF
This commit is contained in:
Mark DePristo 2012-08-30 16:56:36 -04:00
parent 76853806b0
commit 82b2845b9f
1 changed files with 3 additions and 3 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
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@ -39,11 +39,11 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import java.io.File;
import java.util.*;
@ -218,7 +218,7 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> implements T
String filterString = null;
// Annotate the new record with its VQSLOD and the worst performing annotation
builder.attribute(VariantRecalibrator.VQS_LOD_KEY, lodString); // use the String representation so that we don't lose precision on output
builder.attribute(VariantRecalibrator.VQS_LOD_KEY, lod);
builder.attribute(VariantRecalibrator.CULPRIT_KEY, recalDatum.getAttribute(VariantRecalibrator.CULPRIT_KEY));
for( int i = tranches.size() - 1; i >= 0; i-- ) {