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Fixing NPE in VQSR for the case of very small callsets.

This commit is contained in:
Ryan Poplin 2012-04-17 10:20:43 -04:00
parent 27e7e17dc7
commit adad76b36f
1 changed files with 2 additions and 2 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
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@ -165,9 +165,9 @@ public class VariantDataManager {
bottomPercentage = ((float) numToAdd) / ((float) data.size()); bottomPercentage = ((float) numToAdd) / ((float) data.size());
} }
int index = 0, numAdded = 0; int index = 0, numAdded = 0;
while( numAdded < numToAdd ) { while( numAdded < numToAdd && index < data.size() ) {
final VariantDatum datum = data.get(index++); final VariantDatum datum = data.get(index++);
if( !datum.atAntiTrainingSite && !datum.failingSTDThreshold && !Double.isInfinite(datum.lod) ) { if( datum != null && !datum.atAntiTrainingSite && !datum.failingSTDThreshold && !Double.isInfinite(datum.lod) ) {
datum.atAntiTrainingSite = true; datum.atAntiTrainingSite = true;
trainingData.add( datum ); trainingData.add( datum );
numAdded++; numAdded++;