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Slightly better error message for the common error of only providing a dbsnp track but giving it zero clustering weight. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4114 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-08-25 18:41:21 +00:00
parent 5623e01602
commit ac58eb3cbb
2 changed files with 3 additions and 3 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
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@ -230,7 +230,7 @@ public class GenerateVariantClustersWalker extends RodWalker<ExpandingArrayList<
final VariantDataManager dataManager = new VariantDataManager( reduceSum, annotationKeys ); final VariantDataManager dataManager = new VariantDataManager( reduceSum, annotationKeys );
reduceSum.clear(); // Don't need this ever again, clean up some memory reduceSum.clear(); // Don't need this ever again, clean up some memory
logger.info( "There are " + dataManager.numVariants + " variants with >0 clustering weight and " + dataManager.numAnnotations + " annotations." ); logger.info( "There are " + dataManager.numVariants + " variants with > 0 clustering weight and " + dataManager.numAnnotations + " annotations." );
logger.info( "The annotations are: " + annotationKeys ); logger.info( "The annotations are: " + annotationKeys );
dataManager.normalizeData(); // Each data point is now [ (x - mean) / standard deviation ] dataManager.normalizeData(); // Each data point is now [ (x - mean) / standard deviation ]

4
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
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@ -53,7 +53,7 @@ public class VariantDataManager {
numVariants = dataList.size(); numVariants = dataList.size();
data = dataList.toArray( new VariantDatum[numVariants] ); data = dataList.toArray( new VariantDatum[numVariants] );
if( numVariants <= 0 ) { if( numVariants <= 0 ) {
throw new StingException( "There are zero variants! (or possibly a problem with integer overflow)" ); throw new StingException( "There are zero variants with > 0 clustering weight!" );
} }
if( _annotationKeys == null ) { if( _annotationKeys == null ) {
numAnnotations = 0; numAnnotations = 0;
@ -62,7 +62,7 @@ public class VariantDataManager {
} else { } else {
numAnnotations = _annotationKeys.size(); numAnnotations = _annotationKeys.size();
if( numAnnotations <= 0 ) { if( numAnnotations <= 0 ) {
throw new StingException( "There are zero annotations! (or possibly a problem with integer overflow)" ); throw new StingException( "There are zero annotations!" );
} }
meanVector = new double[numAnnotations]; meanVector = new double[numAnnotations];
varianceVector = new double[numAnnotations]; varianceVector = new double[numAnnotations];