Clear the ReadCovariates keysCache before runs of individual Unit Tests

- normal runs have a constant covariate count, so this is not necessary

protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java

@@ -78,6 +78,14 @@ public class ReadCovariates {
         }
     };
 
+    /**
+     * The keys cache is only valid for a single covariate count.  Normally this will remain constant for the analysis.
+     * If running multiple analyses (or the unit test suite), it's necessary to clear the cache.
+     */
+    public static void clearKeysCache() {
+        keysCache.remove();
+    }
+
     /**
      * Our keys, indexed by event type x read length x covariate
      */

protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfoUnitTest.java

@@ -53,6 +53,7 @@ import org.broadinstitute.sting.utils.recalibration.ReadCovariates;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
+import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
@@ -62,6 +63,11 @@ import java.util.EnumMap;
 import java.util.List;
 
 public final class ReadRecalibrationInfoUnitTest extends BaseTest {
+    @BeforeMethod
+    public void init() {
+        ReadCovariates.clearKeysCache();
+    }
+
     @DataProvider(name = "InfoProvider")
     public Object[][] createCombineTablesProvider() {
         List<Object[]> tests = new ArrayList<Object[]>();
@@ -74,7 +80,6 @@ public final class ReadRecalibrationInfoUnitTest extends BaseTest {
 
         return tests.toArray(new Object[][]{});
     }
-
     @Test(dataProvider = "InfoProvider")
     public void testReadInfo(final int readLength, final boolean includeIndelErrors) {
         final ReadCovariates covariates = new ReadCovariates(readLength, 2);

protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/ContextCovariateUnitTest.java

@@ -55,6 +55,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
 /**
@@ -70,7 +71,11 @@ public class ContextCovariateUnitTest {
         RAC = new RecalibrationArgumentCollection();
         covariate = new ContextCovariate();
         covariate.initialize(RAC);
+    }
 
+    @BeforeMethod
+    public void initCache() {
+        ReadCovariates.clearKeysCache();
     }
 
     @Test(enabled = true)

protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/CycleCovariateUnitTest.java

@@ -54,6 +54,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
 /**
@@ -71,6 +72,11 @@ public class CycleCovariateUnitTest {
         covariate.initialize(RAC);
     }
 
+    @BeforeMethod
+    public void initCache() {
+        ReadCovariates.clearKeysCache();
+    }
+
     @Test(enabled = true)
     public void testSimpleCycles() {
         short readLength = 10;

protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/ReadCovariatesUnitTest.java

@@ -53,6 +53,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.testng.Assert;
+import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
 import java.util.Random;
@@ -63,9 +64,14 @@ import java.util.Random;
  */
 public class ReadCovariatesUnitTest {
 
+    @BeforeMethod
+    public void init() {
+        ReadCovariates.clearKeysCache();
+    }
+
     @Test(enabled = false)
     public void testCovariateGeneration() {
-         final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();
+        final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();
         final String RGID = "id";
 
         ReadGroupCovariate rgCov = new ReadGroupCovariate();

protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/ReadGroupCovariateUnitTest.java

@@ -53,6 +53,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
 /**
@@ -70,6 +71,11 @@ public class ReadGroupCovariateUnitTest {
         covariate.initialize(RAC);
     }
 
+    @BeforeMethod
+    public void initCache() {
+        ReadCovariates.clearKeysCache();
+    }
+
     @Test(enabled = true)
     public void testSingleRecord() {
         final String expected = "SAMPLE.1";

protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java

@@ -54,6 +54,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.testng.Assert;
+import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
 import java.util.*;
@@ -63,6 +64,11 @@ import java.util.*;
  * @since 4/21/12
  */
 public class RecalibrationReportUnitTest {
+    @BeforeMethod
+    public void init() {
+        ReadCovariates.clearKeysCache();
+    }
+
     private static RecalDatum createRandomRecalDatum(int maxObservations, int maxErrors) {
         final Random random = new Random();
         final int nObservations = random.nextInt(maxObservations);

protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/recalibration/RepeatCovariatesUnitTest.java

@@ -56,6 +56,7 @@ import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
 import java.util.ArrayList;
@@ -82,6 +83,11 @@ public class RepeatCovariatesUnitTest {
         rurlCovariate.initialize(RAC);
     }
 
+    @BeforeMethod
+    public void initCache() {
+        ReadCovariates.clearKeysCache();
+    }
+
 
     @Test(enabled = true)
     public void testFindNumberOfRepetitions() {