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Cleaning up help text for the -numBad argument.

This commit is contained in:
Ryan Poplin 2013-08-12 09:45:41 -04:00
parent 163d796ae7
commit 59f56bef30
3 changed files with 4 additions and 4 deletions
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4
protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
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@ -264,7 +264,7 @@ public class VariantDataManager {
Collections.sort( data, new VariantDatum.VariantDatumLODComparator() ); Collections.sort( data, new VariantDatum.VariantDatumLODComparator() );
final int numToAdd = minimumNumber - trainingData.size(); final int numToAdd = minimumNumber - trainingData.size();
if( numToAdd > data.size() ) { if( numToAdd > data.size() ) {
throw new UserException.BadInput( "Error during negative model training. Minimum number of variants to use in training is larger than the whole call set. One can attempt to lower the --minNumBadVariants arugment but this is unsafe." ); throw new UserException.BadInput( "Error during negative model training. Minimum number of variants to use in training is larger than the whole call set. One can attempt to lower the --numBadVariants arugment but this is unsafe." );
} }
int index = 0, numAdded = 0; int index = 0, numAdded = 0;
while( numAdded < numToAdd && index < data.size() ) { while( numAdded < numToAdd && index < data.size() ) {
@ -275,7 +275,7 @@ public class VariantDataManager {
numAdded++; numAdded++;
} }
} }
logger.info( "Additionally training with worst " + numToAdd + "% of passing data --> " + (trainingData.size() - numBadSitesAdded) + " variants with LOD <= " + String.format("%.4f", data.get(index).lod) + "." ); logger.info( "Additionally training with worst " + numToAdd + " scoring variants --> " + (trainingData.size() - numBadSitesAdded) + " variants with LOD <= " + String.format("%.4f", data.get(index).lod) + "." );
return trainingData; return trainingData;
} }

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
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@ -335,7 +335,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
engine.evaluateData( dataManager.getData(), badModel, true ); engine.evaluateData( dataManager.getData(), badModel, true );
if( badModel.failedToConverge || goodModel.failedToConverge ) { if( badModel.failedToConverge || goodModel.failedToConverge ) {
throw new UserException("NaN LOD value assigned. Clustering with this few variants and these annotations is unsafe. Please consider raising the number of variants used to train the negative model (via --minNumBad, for example) or lowering the maximum number of Gaussians to use in the model (via --maxGaussians 4, for example)"); throw new UserException("NaN LOD value assigned. Clustering with this few variants and these annotations is unsafe. Please consider " + (badModel.failedToConverge ? "raising the number of variants used to train the negative model (via --numBad 3000, for example)." : "lowering the maximum number of Gaussians allowed for use in the model (via --maxGaussians 4, for example).") );
} }
engine.calculateWorstPerformingAnnotation( dataManager.getData(), goodModel, badModel ); engine.calculateWorstPerformingAnnotation( dataManager.getData(), goodModel, badModel );

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
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@ -94,6 +94,6 @@ public class VariantRecalibratorArgumentCollection {
public double DIRICHLET_PARAMETER = 0.001; public double DIRICHLET_PARAMETER = 0.001;
@Argument(fullName="priorCounts", shortName="priorCounts", doc="The number of prior counts to use in the variational Bayes algorithm.", required=false) @Argument(fullName="priorCounts", shortName="priorCounts", doc="The number of prior counts to use in the variational Bayes algorithm.", required=false)
public double PRIOR_COUNTS = 20.0; public double PRIOR_COUNTS = 20.0;
@Argument(fullName="numBadVariants", shortName="numBad", doc="The number of worst scoring variants to use when building the Gaussian mixture model of bad variants. Will override -percentBad argument if necessary.", required=false) @Argument(fullName="numBadVariants", shortName="numBad", doc="The number of worst scoring variants to use when building the Gaussian mixture model of bad variants.", required=false)
public int NUM_BAD_VARIANTS = 1000; public int NUM_BAD_VARIANTS = 1000;
} }