From 59f56bef30fec9e0ee3fe256748e0df77046e9e7 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Mon, 12 Aug 2013 09:45:41 -0400
Subject: [PATCH] Cleaning up help text for the -numBad argument.

---
 .../gatk/walkers/variantrecalibration/VariantDataManager.java | 4 ++--
 .../walkers/variantrecalibration/VariantRecalibrator.java     | 2 +-
 .../VariantRecalibratorArgumentCollection.java                | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
index 358787e51..9752ab5f5 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -264,7 +264,7 @@ public class VariantDataManager {
         Collections.sort( data, new VariantDatum.VariantDatumLODComparator() );
         final int numToAdd = minimumNumber - trainingData.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;
         while( numAdded < numToAdd && index < data.size() ) {
@@ -275,7 +275,7 @@ public class VariantDataManager {
                 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;
     }
 
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index 496d4fd2b..1c56f7fff 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -335,7 +335,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         engine.evaluateData( dataManager.getData(), badModel, true );
 
         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 );
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
index b376874fc..5a319d8f5 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
@@ -94,6 +94,6 @@ public class VariantRecalibratorArgumentCollection {
     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)
     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;
 }