From 3163970ad5516b95dc37f0726237ea77b4463145 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 6 Jan 2011 15:34:40 +0000
Subject: [PATCH] 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
---
 .../walkers/varianteval/FunctionalClassBySample.java       | 4 ++--
 .../walkers/varianteval/SimpleMetricsBySample.java         | 2 +-
 .../walkers/varianteval/VariantEvaluatorBySample.java      | 7 ++++---
 3 files changed, 7 insertions(+), 6 deletions(-)

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();
     }