diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/FunctionalClassBySample.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/FunctionalClassBySample.java index b8e6b1f77..dd0f1cefa 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/FunctionalClassBySample.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/FunctionalClassBySample.java @@ -5,7 +5,7 @@ import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.*; +import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; import org.broadinstitute.sting.utils.report.tags.Analysis; import java.util.ArrayList; @@ -15,7 +15,7 @@ import java.util.List; * Extends the Per-sample variant evaluator class and returns, for each sample, the number of variants, the Ti/Tv, and * the comp overlap. It does this only on sites where the sample is identified as hom var, or het. */ -@Analysis(name="FunctionalClassBySample",description="Count of SNPs by functional class by sample") +@org.broadinstitute.sting.utils.report.tags.Analysis(name="FunctionalClassBySample",description="Count of SNPs by functional class by sample") public class FunctionalClassBySample extends VariantEvaluatorBySample { public FunctionalClassBySample(VariantEvalWalker parent) { super(parent); } diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/SimpleMetricsBySample.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/SimpleMetricsBySample.java index ea57ee539..33edd32ec 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/SimpleMetricsBySample.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/SimpleMetricsBySample.java @@ -6,7 +6,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.*; +import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; import org.broadinstitute.sting.utils.report.tags.Analysis; import java.util.ArrayList; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/VariantEvaluatorBySample.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/VariantEvaluatorBySample.java index c5f065f03..3e3268bc1 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/VariantEvaluatorBySample.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/VariantEvaluatorBySample.java @@ -5,7 +5,8 @@ import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.*; +import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; +import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.evaluators.VariantEvaluator; import org.broadinstitute.sting.utils.report.tags.DataPoint; import org.broadinstitute.sting.utils.report.utils.TableType; @@ -18,11 +19,11 @@ import java.util.*; * @Author chartl */ public abstract class VariantEvaluatorBySample extends VariantEvaluator { - @DataPoint(name="VariantEvaluatorBySample",description="Evaluation broken down by sample") + @org.broadinstitute.sting.utils.report.tags.DataPoint(name="VariantEvaluatorBySample",description="Evaluation broken down by sample") EvalBySample evalBySample; public VariantEvaluatorBySample(VariantEvalWalker parent) { - super(parent); + //super(parent); evalBySample = initializeTable(); }