From 60003aeacacc6b78c2f01a3bb89fc0ca90384aa0 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 3 Sep 2010 13:31:49 +0000
Subject: [PATCH] Bug fix in VariantRecalibrator. Only add sample names from
 the input rod bindings, not from all rod bindings.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4206 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/variantrecalibration/ApplyVariantCuts.java     | 2 +-
 .../variantrecalibration/VariantGaussianMixtureModel.java  | 7 +------
 .../walkers/variantrecalibration/VariantRecalibrator.java  | 2 +-
 3 files changed, 3 insertions(+), 8 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java
index 9dcd6d9ba..c4ebbacef 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java
@@ -165,7 +165,7 @@ public class ApplyVariantCuts extends RodWalker<Integer, Integer> {
         hInfo.add(new VCFInfoHeaderLine("OQ", 1, VCFHeaderLineType.Float, "The original variant quality score"));
         hInfo.add(new VCFHeaderLine("source", "ApplyVariantCuts"));
         final TreeSet<String> samples = new TreeSet<String>();
-        samples.addAll(SampleUtils.getSampleListWithVCFHeader(getToolkit(), null));
+        samples.addAll(SampleUtils.getUniqueSamplesFromRods(getToolkit()));
         
         for( int iii = 1; iii < filterName.size(); iii++ ) {
             hInfo.add(new VCFFilterHeaderLine(filterName.get(iii), String.format("FDR tranche level at qual " + qCuts.get(iii))));
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java
index b451e4edc..b35784865 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java
@@ -51,11 +51,6 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel
 
     protected final static Logger logger = Logger.getLogger(VariantGaussianMixtureModel.class);
 
-    /**
-     * Est. FP rate for singleton calls.  Used to estimate FP rate as a function of AC
-     */
-    private double singletonFPRate = -1;
-
     public final VariantDataManager dataManager;
     private final int maxGaussians;
     private final int maxIterations;
@@ -65,7 +60,6 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel
 
     private final double SHRINKAGE;
     private final double DIRICHLET_PARAMETER;
-
     private final boolean FORCE_INDEPENDENT_ANNOTATIONS;
 
     private final double[][] mu; // The means for each cluster
@@ -74,6 +68,7 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel
     private double[] pClusterLog10;
     private final double[] determinant;
     private final double stdThreshold;
+    private double singletonFPRate = -1; // Est. FP rate for singleton calls.  Used to estimate FP rate as a function of AC
 
     private double[] empiricalMu;
     private Matrix empiricalSigma;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index 559431c8c..e75b6bff7 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -175,7 +175,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames));
         hInfo.add(new VCFInfoHeaderLine("OQ", 1, VCFHeaderLineType.Float, "The original variant quality score"));
         hInfo.add(new VCFHeaderLine("source", "VariantRecalibrator"));
-        samples.addAll(SampleUtils.getUniqueSamplesFromRods(getToolkit()));
+        samples.addAll(SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames));
 
         final VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
         vcfWriter.writeHeader(vcfHeader);