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Updates that slipped from my last commit: fixed some imports and calls to super(). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4951 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2011-01-06 15:34:40 +00:00
parent 3b76034d50
commit 3163970ad5
3 changed files with 7 additions and 6 deletions
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4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/FunctionalClassBySample.java
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@ -5,7 +5,7 @@ import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; 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 org.broadinstitute.sting.utils.report.tags.Analysis;
import java.util.ArrayList; 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 * 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. * 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 class FunctionalClassBySample extends VariantEvaluatorBySample {
public FunctionalClassBySample(VariantEvalWalker parent) { super(parent); } public FunctionalClassBySample(VariantEvalWalker parent) { super(parent); }

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/SimpleMetricsBySample.java
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@ -6,7 +6,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; 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 org.broadinstitute.sting.utils.report.tags.Analysis;
import java.util.ArrayList; import java.util.ArrayList;

7
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/VariantEvaluatorBySample.java
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@ -5,7 +5,8 @@ import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; 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.tags.DataPoint;
import org.broadinstitute.sting.utils.report.utils.TableType; import org.broadinstitute.sting.utils.report.utils.TableType;
@ -18,11 +19,11 @@ import java.util.*;
* @Author chartl * @Author chartl
*/ */
public abstract class VariantEvaluatorBySample extends VariantEvaluator { 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; EvalBySample evalBySample;
public VariantEvaluatorBySample(VariantEvalWalker parent) { public VariantEvaluatorBySample(VariantEvalWalker parent) {
super(parent); //super(parent);
evalBySample = initializeTable(); evalBySample = initializeTable();
} }