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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
This commit is contained in:
rpoplin 2010-09-03 13:31:49 +00:00
parent c119f64514
commit 60003aeaca
3 changed files with 3 additions and 8 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java
View File

@ -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))));

7
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java
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@ -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;

2
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
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@ -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);