Renaming for consistency

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3180 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java

@@ -64,7 +64,7 @@ public class CountVariants extends VariantEvaluator {
     @DataPoint(description = "deletion to insertion ratio")
     double deletionInsertionRatio = 0;
     
-    public CountVariants(VariantEval2Walker parent) {
+    public CountVariants(VariantEvalWalker parent) {
         // don't do anything
     }
 

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/DbSNPPercentage.java

@@ -41,7 +41,7 @@ public class DbSNPPercentage extends VariantEvaluator {
     @DataPoint(name = "% concordant", description = "the concordance rate")
     double concordantRate = 0.0;
 
-    public DbSNPPercentage(VariantEval2Walker parent) {
+    public DbSNPPercentage(VariantEvalWalker parent) {
         // don't do anything
     }
 

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java

@@ -187,7 +187,7 @@ public class GenotypeConcordance extends VariantEvaluator {
     private HashSet<VariantContext> missedValidationData = new HashSet<VariantContext>();
 
 
-    public GenotypeConcordance(VariantEval2Walker parent) {
+    public GenotypeConcordance(VariantEvalWalker parent) {
         // don't do anything
     }
 

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java

@@ -59,7 +59,7 @@ public class MendelianViolationEvaluator extends VariantEvaluator {
     @DataPoint(name="KHV->PHR",description = "number of child hom variant calls where the parent was hom ref")
     long KidHomVar_ParentHomRef;
 
-    VariantEval2Walker parent;
+    VariantEvalWalker parent;
 
     TrioStructure trio;
 
@@ -83,7 +83,7 @@ public class MendelianViolationEvaluator extends VariantEvaluator {
         }
     }
 
-    public MendelianViolationEvaluator(VariantEval2Walker parent) {
+    public MendelianViolationEvaluator(VariantEvalWalker parent) {
         this.parent = parent;
 
         if (enabled()) {

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/TiTvVariantEvaluator.java

@@ -23,7 +23,7 @@ public class TiTvVariantEvaluator extends VariantEvaluator {
     @DataPoint(name = "ti/tv ratio standard", description = "the transition to transversion ratio")
     double TiTvRatioStandard = 0.0;
 
-    public TiTvVariantEvaluator(VariantEval2Walker parent) {
+    public TiTvVariantEvaluator(VariantEvalWalker parent) {
         // don't do anything
     }
 

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ValidationRate.java

@@ -62,7 +62,7 @@ public class ValidationRate extends VariantEvaluator {
     private SiteStats evalOverlapAtMono = new SiteStats();
     private SiteStats evalOverlapAtPoly = new SiteStats();
 
-    public ValidationRate(VariantEval2Walker parent) {
+    public ValidationRate(VariantEvalWalker parent) {
         // don't do anything
     }
 
@@ -108,8 +108,6 @@ public class ValidationRate extends VariantEvaluator {
 
         if (rawValidationData!= null && rawValidationData.hasGenotypes() && rawValidationData.isNotFiltered()) {
             VariantContext validation = rawValidationData;
-            //if ( eval != null )  // todo -- remove me when I can get the header from the VariantEval engine
-            //    validation = rawValidationData.subContextFromGenotypes(eval.getGenotypes().values());
 
             SiteStats overlap;
 

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java

@@ -82,7 +82,7 @@ import java.util.*;
 /**
  * Test routine for new VariantContext object
  */
-public class VariantEval2Walker extends RodWalker<Integer, Integer> {
+public class VariantEvalWalker extends RodWalker<Integer, Integer> {
     // --------------------------------------------------------------------------------------------------------------
     //
     // walker arguments

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantQualityScore.java

@@ -207,7 +207,7 @@ public class VariantQualityScore extends VariantEvaluator {
         }
     }
 
-    public VariantQualityScore(VariantEval2Walker parent) {
+    public VariantQualityScore(VariantEvalWalker parent) {
         // don't do anything
     }
 

java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java

@@ -7,8 +7,8 @@ import java.util.Arrays;
 import java.util.HashMap;
 import java.util.Map;
 
-public class VariantEval2IntegrationTest extends WalkerTest {
-    private static String cmdRoot = "-T VariantEval2" +
+public class VariantEvalIntegrationTest extends WalkerTest {
+    private static String cmdRoot = "-T VariantEval" +
             " -R " + oneKGLocation + "reference/human_b36_both.fasta -reportType Grep -all";
 
     private static String root = cmdRoot +
@@ -16,7 +16,7 @@ public class VariantEval2IntegrationTest extends WalkerTest {
             " -B eval,VCF," + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf";
 
     @Test
-    public void testVE2Simple() {
+    public void testVESimple() {
         HashMap<String, String> expectations = new HashMap<String, String>();
         expectations.put("-L 1:1-10,000,000", "278c9c2798fed510a0cc3e65f3749b26");
         expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0", "98ceb8dab20af47e724a0b47f82ba698");
@@ -28,12 +28,12 @@ public class VariantEval2IntegrationTest extends WalkerTest {
             WalkerTestSpec spec = new WalkerTestSpec( root + " " + extraArgs + " -o %s",
                     1, // just one output file
                     Arrays.asList(md5));
-            executeTest("testVE2Simple", spec);
+            executeTest("testVESimple", spec);
         }
     }
 
     @Test
-    public void testVE2Complex() {
+    public void testVEComplex() {
         HashMap<String, String> expectations = new HashMap<String, String>();
         String extraArgs1 = "-L " + validationDataLocation + "chr1_b36_pilot3.interval_list -family NA19238+NA19239=NA19240 -MVQ 30" +
                 " -B dbsnp_130,dbSNP," + GATKDataLocation + "dbsnp_130_b36.rod" +
@@ -51,16 +51,16 @@ public class VariantEval2IntegrationTest extends WalkerTest {
             WalkerTestSpec spec = new WalkerTestSpec( root + " " + extraArgs1 + extraArgs2 + " -o %s",
                     1, // just one output file
                     Arrays.asList(md5));
-            executeTest("testVE2Complex", spec);
+            executeTest("testVEComplex", spec);
         }
     }
 
     @Test
-    public void testVE2WriteVCF() {
+    public void testVEWriteVCF() {
         String extraArgs = "-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 30";
         WalkerTestSpec spec = new WalkerTestSpec( root + " " + extraArgs + " -o %s -outputVCF %s",
                 2,
                 Arrays.asList("782b569e213b494c19598d3f4dacba49", "a3ce1d70d8ae3874807e9d61994d42af"));
-        executeTest("testVE2WriteVCF", spec);
+        executeTest("testVEWriteVCF", spec);
     }
 }