From 11052918d99ebf328390f39988a8d50d67173c8d Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 3 May 2011 18:37:25 +0000
Subject: [PATCH] Better exception text for common error in VQSR.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5734 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/variantrecalibration/TrancheManager.java  | 2 +-
 .../walkers/variantrecalibration/VariantRecalibrator.java  | 7 +++++--
 .../VariantRecalibratorArgumentCollection.java             | 2 +-
 3 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/TrancheManager.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/TrancheManager.java
index 559cc5618..3bae46247 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/TrancheManager.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/TrancheManager.java
@@ -132,7 +132,7 @@ public class TrancheManager {
 
             if ( t == null ) {
                 if ( tranches.size() == 0 )
-                    throw new UserException(String.format("Couldn't find any tranche containing variants with a %s > %.2f", metric.getName(), metric.getThreshold(trancheThreshold)));
+                    throw new UserException(String.format("Couldn't find any tranche containing variants with a %s > %.2f. Are you sure the truth files contain unfiltered variants which overlap the input data?", metric.getName(), metric.getThreshold(trancheThreshold)));
                 break;
             }
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index e8b9705d7..4250866f1 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -161,6 +161,8 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
                     datum.isSNP = vc.isSNP() && vc.isBiallelic();
                     datum.isTransition = datum.isSNP && VariantContextUtils.isTransition(vc);
                     datum.usedForTraining = 0;
+
+                    // Loop through the training data sets and if they overlap this loci then update the prior and training status appropriately
                     dataManager.parseTrainingSets( tracker, ref, context, vc, datum, TRUST_ALL_POLYMORPHIC );
                     double priorFactor = QualityUtils.qualToProb( datum.prior );
                     if( datum.consensusCount != 0 ) {
@@ -168,6 +170,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
                         priorFactor = 1.0 - ((1.0 - priorFactor) * (1.0 - consensusPrior));
                     }
                     datum.prior = Math.log10( priorFactor ) - Math.log10( 1.0 - priorFactor );
+
                     mapList.add( datum );
                 }
             }
@@ -224,8 +227,8 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         TRANCHES_FILE.print(Tranche.tranchesString( tranches ));
 
         double lodCutoff = 0.0;
-        for(final Tranche tranche : tranches) {
-            if(MathUtils.compareDoubles(tranche.ts, TS_FILTER_LEVEL, 0.0001)==0) {
+        for( final Tranche tranche : tranches ) {
+            if( MathUtils.compareDoubles(tranche.ts, TS_FILTER_LEVEL, 0.0001)==0 ) {
                 lodCutoff = tranche.minVQSLod;
             }
         }
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
index e12fc20b5..bd1d030bb 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
@@ -16,7 +16,7 @@ public class VariantRecalibratorArgumentCollection {
         BOTH
     }
 
-    @Argument(fullName = "mode", shortName = "mode", doc = "Recalibration mode to employ: 1.) SNP for recalibrating only SNPs (emitting indels untouched in the output VCF); 2.) INDEL for indels; and 3.) BOTH for recalibrating both SNPs and indels simultaneously.", required = false)
+    @Argument(fullName = "mode", shortName = "mode", doc = "Recalibration mode to employ: 1.) SNP for recalibrating only snps (emitting indels untouched in the output VCF); 2.) INDEL for indels; and 3.) BOTH for recalibrating both snps and indels simultaneously.", required = false)
     public VariantRecalibratorArgumentCollection.Mode MODE = VariantRecalibratorArgumentCollection.Mode.SNP;
     @Argument(fullName="maxGaussians", shortName="mG", doc="The maximum number of Gaussians to try during variational Bayes algorithm", required=false)
     public int MAX_GAUSSIANS = 10;