From cba88a8861f9e55a8a92f39cfa7acd4c56f47def Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 24 Feb 2011 21:32:35 +0000
Subject: [PATCH] Elegant solution to the determinism problem: force testNG to
 run tests in the order that I want it to.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5312 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../indels/IndelRealignerIntegrationTest.java | 29 +++++++++++--------
 1 file changed, 17 insertions(+), 12 deletions(-)

diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
index fff021803..e70ca9d14 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
@@ -14,45 +14,50 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
     private static final String knownIndels = validationDataLocation + "indelRealignerTest.pilot1.ceu.vcf";
     private static final String baseCommandPrefix = "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + mainTestBam + " -targetIntervals " + mainTestIntervals + " -compress 0 -L 20:49,500-55,500 ";
     private static final String baseCommand = baseCommandPrefix + "-o %s ";
+    private static final String base_md5 = "282070822dc5495eb20dad157d827133";
 
     @Test
     public void testDefaults() {
-        String md5 = "282070822dc5495eb20dad157d827133";
 
         WalkerTestSpec spec1 = new WalkerTestSpec(
                 baseCommand,
                 1,
-                Arrays.asList(md5));
+                Arrays.asList(base_md5));
         executeTest("test realigner defaults", spec1);
 
         WalkerTestSpec spec2 = new WalkerTestSpec(
                 baseCommand + "-B:indels,vcf " + knownIndels,
                 1,
-                Arrays.asList(md5));
+                Arrays.asList(base_md5));
         executeTest("test realigner defaults with VCF", spec2);
 
         WalkerTestSpec spec3 = new WalkerTestSpec(
                 baseCommand + "-D " + GATKDataLocation + "dbsnp_129_b36.rod",
                 1,
-                Arrays.asList(md5));
+                Arrays.asList(base_md5));
         executeTest("realigner defaults with dbsnp", spec3);
 
     }
 
-    @Test
+    @Test(dependsOnMethods = { "testNoTags" })
     public void testStats() {
-        WalkerTestSpec spec = new WalkerTestSpec(
+        WalkerTestSpec spec1 = new WalkerTestSpec(
                 baseCommandPrefix + "-stats %s -o /dev/null",
                 1,
                 Arrays.asList("ed5a207ddf5bdda4bb76899fb3eae35c"));
-        executeTest("realigner stats", spec);
+        executeTest("realigner stats", spec1);
 
+        WalkerTestSpec spec2 = new WalkerTestSpec(
+                baseCommandPrefix + "-LOD 60 -stats %s -o /dev/null",
+                1,
+                Arrays.asList("ffab7d9ca19daa8a21e0b8f0072d39e9"));
+        executeTest("realigner stats", spec2);        
     }
 
-    @Test
+    @Test(dependsOnMethods = { "testKnownsOnly" })
     public void testLods() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( "-LOD 60", "282070822dc5495eb20dad157d827133" );
+        e.put( "-LOD 60", base_md5 );
         e.put( "-LOD 1",  "c98d699d94f01bd0089f12646c764dfc" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
@@ -64,7 +69,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
         }
     }
 
-    @Test
+    @Test(dependsOnMethods = { "testDefaults" })
     public void testKnownsOnly() {
         WalkerTestSpec spec1 = new WalkerTestSpec(
                 baseCommand + "-knownsOnly -B:indels,vcf " + knownIndels,
@@ -79,7 +84,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
         executeTest("realigner known indels only from dbsnp", spec2);
     }
 
-    @Test
+    @Test(dependsOnMethods = { "testLongRun" })
     public void testNoTags() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseCommand + "--noOriginalAlignmentTags",
@@ -88,7 +93,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
         executeTest("realigner no output tags", spec);
     }
 
-    @Test
+    @Test(dependsOnMethods = { "testLods" })
     public void testLongRun() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10,000,000-11,000,000 -targetIntervals " + validationDataLocation + "indelRealignerTest.NA12878.chrom1.intervals -compress 0 -o %s",