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OK, this time REALLY fix cut and paste error 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5880 348d0f76-0448-11de-a6fe-93d51630548a
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delangel 2011-05-26 19:47:12 +00:00
parent dab269160b
commit 6ecbfa9013
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
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@ -10,7 +10,6 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.collections.ExpandingArrayList; import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import sun.awt.SunHints;
import java.io.PrintStream; import java.io.PrintStream;
import java.util.*; import java.util.*;
@ -220,6 +219,7 @@ public class VariantDataManager {
if( jitter && ( annotationKey.equalsIgnoreCase("HRUN") || annotationKey.equalsIgnoreCase("FS") ) ) { // Integer valued annotations must be jittered a bit to work in this GMM if( jitter && ( annotationKey.equalsIgnoreCase("HRUN") || annotationKey.equalsIgnoreCase("FS") ) ) { // Integer valued annotations must be jittered a bit to work in this GMM
value += -0.25 + 0.5 * GenomeAnalysisEngine.getRandomGenerator().nextDouble(); value += -0.25 + 0.5 * GenomeAnalysisEngine.getRandomGenerator().nextDouble();
} }
if(annotationKey.equals("HaplotypeScore") && MathUtils.compareDoubles(value, 0.0, 0.0001) == 0 ) { value = -0.2 + 0.4*GenomeAnalysisEngine.getRandomGenerator().nextDouble(); }
} catch( final Exception e ) { } catch( final Exception e ) {
value = Double.NaN; // The VQSR works with missing data now by marginalizing over the missing dimension when evaluating clusters. value = Double.NaN; // The VQSR works with missing data now by marginalizing over the missing dimension when evaluating clusters.