From 7d0ac7c6f21f0406298fe806012f7dd2876ab453 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sat, 31 Oct 2009 00:00:33 +0000
Subject: [PATCH] Fix for long-term VariantEval bug plus new intergration test
 to catch it

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1951 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../varianteval/VariantEvalWalker.java        |  4 +--
 .../VariantEvalWalkerIntegrationTest.java     | 32 ++++++++++---------
 2 files changed, 19 insertions(+), 17 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java
index b01fa1a5c..663670410 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java
@@ -72,7 +72,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
 
     // the types of analysis we support, and the string tags we associate with the enumerated value
     enum ANALYSIS_TYPE {
-        ALL_SNPS("all"), SINGLETON_SNPS("singletons"), TWOHIT_SNPS("2plus_hit"), KNOWN_SNPS("2plus_hit"), NOVEL_SNPS("2plus_hit");
+        ALL_SNPS("all"), SINGLETON_SNPS("singletons"), TWOHIT_SNPS("2plus_hit"), KNOWN_SNPS("known"), NOVEL_SNPS("novel");
 
         private final String value;
         ANALYSIS_TYPE(String value) { this.value = value;}
@@ -226,7 +226,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
             Variation eval = (Variation) tracker.lookup("eval", null);
 
             // ensure that the variation we're looking at is bi-allelic
-            if (eval != null && !eval.isBiallelic())
+            if ( eval != null && ! eval.isBiallelic() )
                 eval = null;  
 
             if (eval != null)
diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java
index 8f072c837..fe742ec84 100644
--- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java
@@ -4,8 +4,7 @@ import org.broadinstitute.sting.WalkerTest;
 import org.junit.Test;
 
 import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
+import java.util.*;
 
 /**
  * @author aaron
@@ -18,8 +17,9 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
 
     @Test
     public void testEvalVariantROD() {
-        List<String> md5 = new ArrayList<String>();
-        md5.add("86582b57ec27dd9c4a6e0252eb010376");
+        HashMap<String, String> md5 = new HashMap<String, String>();
+        md5.put("", "86582b57ec27dd9c4a6e0252eb010376");
+        md5.put("-A", "ead904e334956435e6b586b697cd1905");
 
         /**
          * the above MD5 was calculated from running the following command:
@@ -34,17 +34,19 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
          * --rodBind eval,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls
          *
          */
-        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-R /broad/1KG/reference/human_b36_both.fasta" +
-                        " --rodBind eval,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" +
-                        " -T VariantEval" +
-                        " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +
-                        " -L 1:10,000,000-11,000,000" +
-                        " --outerr %s" +
-                        " --supressDateInformation",
-                1, // just one output file
-                md5);
-        List<File> result = executeTest("testEvalVariantROD", spec).getFirst();
+        for ( Map.Entry<String, String> e : md5.entrySet() ) {
+            WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                    "-R /broad/1KG/reference/human_b36_both.fasta" +
+                            " --rodBind eval,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" +
+                            " -T VariantEval" +
+                            " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +
+                            " -L 1:10,000,000-11,000,000" +
+                            " --outerr %s" +
+                            " --supressDateInformation " + e.getKey(),
+                    1, // just one output file
+                    Arrays.asList(e.getValue()));
+            List<File> result = executeTest("testEvalVariantROD", spec).getFirst();
+        }
     }
 
     @Test