A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests.

Thanks!



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3135 348d0f76-0448-11de-a6fe-93d51630548a

java/test/org/broadinstitute/sting/WalkerTest.java

@@ -6,10 +6,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.utils.Pair;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
-import org.junit.Before;
 import org.junit.Test;
-import org.apache.log4j.Appender;
-import org.apache.log4j.WriterAppender;
 
 import java.io.File;
 import java.io.FileInputStream;
@@ -202,7 +199,7 @@ public class WalkerTest extends BaseTest {
     }
 
     @Test
-    public void testWalkerTest() {
+    public void testWalkerUnitTest() {
         //System.out.println("WalkerTest is just a framework");
     }
 }

java/test/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollectionUnitTest.java

@@ -46,7 +46,7 @@ import net.sf.samtools.SAMFileReader;
  * <p/>
  * Test out the argument collection class
  */
-public class GATKArgumentCollectionTest extends BaseTest {
+public class GATKArgumentCollectionUnitTest extends BaseTest {
 
     // our collection of arguments
     private GATKArgumentCollection collect;

java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/AlleleUnitTest.java

@@ -26,7 +26,7 @@ import org.junit.Test;
 /**
  * Basic unit test for RecalData
  */
-public class AlleleTest extends BaseTest {
+public class AlleleUnitTest extends BaseTest {
     Allele ARef, del, delRef, A, T, ATIns, ATCIns, NoCall;
     
     @Before

java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUnitTest.java

@@ -23,7 +23,7 @@ import net.sf.picard.reference.ReferenceSequenceFile;
 /**
  * Basic unit test for RecalData
  */
-public class VariantContextTest extends BaseTest {
+public class VariantContextUnitTest extends BaseTest {
     private static ReferenceSequenceFile seq;
 
     @BeforeClass

java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantJEXLContextUnitTest.java

@@ -43,11 +43,11 @@ import java.util.Map;
  * 
  * @author aaron 
  * 
- * Class VariantJEXLContextTest
+ * Class VariantJEXLContextUnitTest
  *
  * Test out parts of the VariantJEXLContext
  */
-public class VariantJEXLContextTest extends BaseTest {
+public class VariantJEXLContextUnitTest extends BaseTest {
 
 
     private static String expression = "QUAL > 500.0";

java/test/org/broadinstitute/sting/gatk/datasources/providers/AllLocusViewUnitTest.java

@@ -23,7 +23,7 @@ import java.util.List;
 /**
  * Test the view of all loci.
  */
-public class AllLocusViewTest extends LocusViewTemplate {
+public class AllLocusViewUnitTest extends LocusViewTemplate {
 
     @Override
     protected LocusView createView(LocusShardDataProvider provider) {

java/test/org/broadinstitute/sting/gatk/datasources/providers/CoveredLocusViewUnitTest.java

@@ -23,7 +23,7 @@ import java.util.List;
 /**
  * Test the CoveredLocusView.
  */
-public class CoveredLocusViewTest extends LocusViewTemplate {
+public class CoveredLocusViewUnitTest extends LocusViewTemplate {
 
     /**
      * Retrieve a covered locus view.

java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewUnitTest.java

@@ -41,7 +41,7 @@ import java.util.Collections;
 
 /** Tests for viewing the reference from the perspective of a locus. */
 
-public class LocusReferenceViewTest extends ReferenceViewTemplate {
+public class LocusReferenceViewUnitTest extends ReferenceViewTemplate {
 
 //
 //    /** Multiple-base pair queries should generate exceptions. */

java/test/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedViewUnitTest.java

@@ -27,7 +27,7 @@ import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTrackerTest;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTrackerUnitTest;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
@@ -45,11 +45,11 @@ import java.util.*;
 /**
  * @author aaron
  *         <p/>
- *         Class ReadBasedReferenceOrderedViewTest
+ *         Class ReadBasedReferenceOrderedViewUnitTest
  *         <p/>
  *         test out the ReadBasedReferenceOrderedView class
  */
-public class ReadBasedReferenceOrderedViewTest extends BaseTest {
+public class ReadBasedReferenceOrderedViewUnitTest extends BaseTest {
 
     private static int startingChr = 1;
     private static int endingChr = 2;
@@ -131,7 +131,7 @@ class FakePeekingRODIterator implements LocationAwareSeekableRODIterator {
     @Override
     public RODRecordList next() {
         System.err.println("Next -> " + location);
-        curROD = new ReadMetaDataTrackerTest.FakeRODatum(location, name);
+        curROD = new ReadMetaDataTrackerUnitTest.FakeRODatum(location, name);
         location = GenomeLocParser.createGenomeLoc(location.getContigIndex(), location.getStart() + 1, location.getStop() + 1);
         FakeRODRecordList list = new FakeRODRecordList();
         list.add(curROD);

java/test/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceViewUnitTest.java

@@ -44,7 +44,7 @@ import net.sf.picard.reference.ReferenceSequence;
  * Test reading the reference for a given read.
  */
 
-public class ReadReferenceViewTest extends ReferenceViewTemplate {
+public class ReadReferenceViewUnitTest extends ReferenceViewTemplate {
 
 
     /**

java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java

@@ -35,7 +35,7 @@ import java.util.Collections;
  * Test the transparent view into the reference-ordered data.  At the moment, just do some basic bindings and make
  * sure the data comes through correctly.
  */
-public class ReferenceOrderedViewTest extends BaseTest {
+public class ReferenceOrderedViewUnitTest extends BaseTest {
     /**
      * Sequence file.
      */

java/test/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProviderUnitTest.java

@@ -26,7 +26,7 @@ import java.util.Arrays;
  * Test basic functionality of the shard data provider.
  */
 
-public class ShardDataProviderTest extends BaseTest {
+public class ShardDataProviderUnitTest extends BaseTest {
     /**
      * Provider to test.  Should be recreated for every test.
      */

java/test/org/broadinstitute/sting/gatk/datasources/shards/IntervalShardStrategyUnitTest.java

@@ -41,7 +41,7 @@ import net.sf.samtools.SAMFileHeader;
 /**
  * @author aaron
  *         <p/>
- *         Class ReadIntervalShardStrategyTest
+ *         Class ReadIntervalShardStrategyUnitTest
  *         <p/>
  *         Tests the ReadIntervalShardStrategy class
  *
@@ -51,7 +51,7 @@ import net.sf.samtools.SAMFileHeader;
  * back in the future, the expected number of shards should change from 1 to > 1.
  *
  */
-public class IntervalShardStrategyTest extends BaseTest {
+public class IntervalShardStrategyUnitTest extends BaseTest {
 
     private GenomeLocSortedSet mSortedSet = null;
     private SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(NUMBER_OF_CHROMOSOMES, STARTING_CHROMOSOME, CHROMOSOME_SIZE);

java/test/org/broadinstitute/sting/gatk/datasources/shards/IntervalShardUnitTest.java

@@ -43,7 +43,7 @@ import net.sf.samtools.SAMFileHeader;
  *         <p/>
  *         Tests for the IntervalReadShard class.
  */
-public class IntervalShardTest extends BaseTest {
+public class IntervalShardUnitTest extends BaseTest {
 
     private IntervalShard intervalShard = null;
     private SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(NUMBER_OF_CHROMOSOMES, STARTING_CHROMOSOME, CHROMOSOME_SIZE);

java/test/org/broadinstitute/sting/gatk/datasources/shards/LinearLocusShardStrategyUnitTest.java

@@ -43,7 +43,7 @@ import net.sf.samtools.SAMFileHeader;
  *         <p/>
  *         Test for the Locus Shard Strategy
  */
-public class LinearLocusShardStrategyTest extends BaseTest {
+public class LinearLocusShardStrategyUnitTest extends BaseTest {
 
     private GenomeLocSortedSet mSortedSet = null;
     private SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(NUMBER_OF_CHROMOSOMES, STARTING_CHROMOSOME, CHROMOSOME_SIZE);

java/test/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactoryUnitTest.java

@@ -32,7 +32,7 @@ import static org.junit.Assert.assertTrue;
  * @author aaron
  * @version 1.0
  */
-public class ShardStrategyFactoryTest extends BaseTest {
+public class ShardStrategyFactoryUnitTest extends BaseTest {
 
     private SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(NUMBER_OF_CHROMOSOMES, STARTING_CHROMOSOME, CHROMOSOME_SIZE);
     private static final int NUMBER_OF_CHROMOSOMES = 5;

java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataPoolUnitTest.java

@@ -35,7 +35,7 @@ import static org.junit.Assert.assertTrue;
  * Test the contents and number of iterators in the pool.
  */
 
-public class ReferenceOrderedDataPoolTest extends BaseTest {
+public class ReferenceOrderedDataPoolUnitTest extends BaseTest {
 
     private RMDTrack rod = null;
 

java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMBAMDataSourceUnitTest.java

@@ -43,11 +43,11 @@ import java.util.List;
  * @version 1.0
  * @date Apr 8, 2009
  * <p/>
- * Class SAMBAMDataSourceTest
+ * Class SAMBAMDataSourceUnitTest
  * <p/>
  * The test of the SAMBAM simple data source.
  */
-public class SAMBAMDataSourceTest extends BaseTest {
+public class SAMBAMDataSourceUnitTest extends BaseTest {
 
     private List<File> fl;
     private ReferenceSequenceFile seq;

java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMByIntervalUnitTest.java

@@ -48,11 +48,11 @@ import net.sf.samtools.SAMRecord;
 /**
  * @author aaron
  *         <p/>
- *         Class SAMByIntervalTest
+ *         Class SAMByIntervalUnitTest
  *         <p/>
  *         Test that the SAM data source behaves well given intervals
  */
-public class SAMByIntervalTest extends BaseTest {
+public class SAMByIntervalUnitTest extends BaseTest {
     private List<File> fl;
     ShardStrategy shardStrategy;
     Reads reads;
@@ -65,7 +65,7 @@ public class SAMByIntervalTest extends BaseTest {
     protected final int STARTING_CHROMO;
     protected final int UNMAPPED_READ_COUNT;
 
-    public SAMByIntervalTest() {
+    public SAMByIntervalUnitTest() {
         READ_COUNT = 100;
         ENDING_CHROMO = 10;
         STARTING_CHROMO = 1;

java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMByReadsUnitTest.java

@@ -39,7 +39,7 @@ import java.util.List;
  * @author aaron
  * @version 1.0
  */
-public class SAMByReadsTest extends BaseTest {
+public class SAMByReadsUnitTest extends BaseTest {
 
 
     private List<File> fl;

java/test/org/broadinstitute/sting/gatk/executive/ReduceTreeUnitTest.java

@@ -30,7 +30,7 @@ import java.util.ArrayList;
  * Make sure the reduce tree organizes reduces in the correct way.
  */
 
-public class ReduceTreeTest extends BaseTest implements ReduceTree.TreeReduceNotifier {
+public class ReduceTreeUnitTest extends BaseTest implements ReduceTree.TreeReduceNotifier {
 
     /**
      * The tree indicating reduce order.

java/test/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java

@@ -15,7 +15,7 @@ import java.util.List;
 import java.util.ArrayList;
 import java.util.Collections;
 
-public class ReadGroupBlackListFilterTest extends BaseTest {
+public class ReadGroupBlackListFilterUnitTest extends BaseTest {
     private static final int READ_GROUP_COUNT = 5;
     private static final String READ_GROUP_PREFIX = "ReadGroup";
     private static final String SAMPLE_NAME_PREFIX = "Sample";

java/test/org/broadinstitute/sting/gatk/io/OutputTrackerUnitTest.java

@@ -27,9 +27,9 @@ import java.util.Scanner;
  * For the file opening and closing mechanisms.
  */
 
-public class OutputTrackerTest extends BaseTest {
-    public static final String OUTPUT_FILENAME = "OutputTrackerTest.out";
-    public static final String ERROR_FILENAME = "OutputTrackerTest.err";
+public class OutputTrackerUnitTest extends BaseTest {
+    public static final String OUTPUT_FILENAME = "OutputTrackerUnitTest.out";
+    public static final String ERROR_FILENAME = "OutputTrackerUnitTest.err";
 
     @After
     public void cleanupTestFiles() {

java/test/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorUnitTest.java

@@ -61,11 +61,11 @@ import java.util.List;
  * @version 1.0
  * @date Apr 14, 2009
  * <p/>
- * Class BoundedReadIteratorTest
+ * Class BoundedReadIteratorUnitTest
  * <p/>
  * tests for the bounded read iterator.
  */
-public class BoundedReadIteratorTest extends BaseTest {
+public class BoundedReadIteratorUnitTest extends BaseTest {
 
     /** the file list and the fasta sequence */
     private List<File> fl;

java/test/org/broadinstitute/sting/gatk/iterators/IntervalOverlapIteratorUnitTest.java

@@ -23,7 +23,7 @@ import java.util.Iterator;
  *         <p/>
  *         test the DuplicateDetectorIterator class.
  */
-public class IntervalOverlapIteratorTest extends BaseTest {
+public class IntervalOverlapIteratorUnitTest extends BaseTest {
     private final File bam = new File(validationDataLocation + "index_test.bam");
     private static IndexedFastaSequenceFile seq;
     private int chromosomeOneReadCount = 885;

java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java

@@ -22,7 +22,7 @@ import java.util.List;
 /**
  * testing of the LocusIteratorByState
  */
-public class LocusIteratorByStateTest extends BaseTest {
+public class LocusIteratorByStateUnitTest extends BaseTest {
 
     private final int MAX_READS = 10;
     private static SAMFileHeader header;

java/test/org/broadinstitute/sting/gatk/iterators/LocusOverflowTrackerUnitTest.java

@@ -16,11 +16,11 @@ import org.junit.Test;
 /**
  * @author aaron
  *         <p/>
- *         Class LocusOverflowTrackerTest
+ *         Class LocusOverflowTrackerUnitTest
  *         <p/>
  *         test out the locus overflow tracker
  */
-public class LocusOverflowTrackerTest extends BaseTest {
+public class LocusOverflowTrackerUnitTest extends BaseTest {
 
     private LocusOverflowTracker tracker;
     private final int MAX_READS = 10;

java/test/org/broadinstitute/sting/gatk/iterators/PlusOneFixIteratorUnitTest.java

@@ -22,7 +22,7 @@ import net.sf.samtools.SAMRecord;
  * Date: Nov 4, 2009
  * Time: 11:02:24 PM
  */
-public class PlusOneFixIteratorTest extends BaseTest {
+public class PlusOneFixIteratorUnitTest extends BaseTest {
     private final File bam = new File(validationDataLocation + "index_test.bam");
     private static IndexedFastaSequenceFile seq;
     private int chromosomeOneReadCount = 885;

java/test/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapterUnitTest.java

@@ -34,7 +34,7 @@ import java.util.Iterator;
  * <p/>
  * Tests the StingSAMIteratorAdapter class.
  */
-public class StingSAMIteratorAdapterTest extends BaseTest {
+public class StingSAMIteratorAdapterUnitTest extends BaseTest {
 
     class MyTestIterator implements Iterator<SAMRecord> {
 

java/test/org/broadinstitute/sting/gatk/refdata/PlinkRodUnitTest.java

@@ -24,7 +24,7 @@ import java.util.*;
  * Time: 11:27:33 PM
  * To change this template use File | Settings | File Templates.
  *
-public class PlinkRodTest extends BaseTest {
+public class PlinkRodUnitTest extends BaseTest {
     // todo :: get the isIndel() isInsertion() and isDeletion() tests working again -- this may require new
     // todo :: methods in the objects themselves
     private static IndexedFastaSequenceFile seq;

java/test/org/broadinstitute/sting/gatk/refdata/ReadMetaDataTrackerUnitTest.java

@@ -42,11 +42,11 @@ import java.util.*;
 /**
  * @author aaron
  *         <p/>
- *         Class ReadMetaDataTrackerTest
+ *         Class ReadMetaDataTrackerUnitTest
  *         <p/>
  *         test out the ReadMetaDataTracker
  */
-public class ReadMetaDataTrackerTest extends BaseTest {
+public class ReadMetaDataTrackerUnitTest extends BaseTest {
     private static int startingChr = 1;
     private static int endingChr = 2;
     private static int readCount = 100;

java/test/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedDataUnitTest.java

@@ -12,12 +12,12 @@ import java.util.List;
  * 
  * @author aaron 
  * 
- * Class ReferenceOrderedDataTest
+ * Class ReferenceOrderedDataUnitTest
  *
  * some functionality to test parts of the reference ordered data system that I've added.  This is by NO MEANS
  * a complete test suite, but additions would be extremely welcome
  */
-public class ReferenceOrderedDataTest extends BaseTest {
+public class ReferenceOrderedDataUnitTest extends BaseTest {
     @Test
     public void extractRodsFromFileTest() {
         String file = validationDataLocation + "testRODFileImpl.csv";

java/test/org/broadinstitute/sting/gatk/refdata/RodGLFUnitTest.java

@@ -26,7 +26,7 @@ import java.io.File;
  * <p/>
  * You'll notice that the first is a hom ref, and the other two are hom alt SNP's
  */
-public class RodGLFTest extends BaseTest {
+public class RodGLFUnitTest extends BaseTest {
     static final File glfFile = new File(validationDataLocation + "glfTestFile.glf");
     static final int finalRecordCount = 100; // the number of records in the above file
     static final int contigCount = 1;

java/test/org/broadinstitute/sting/gatk/refdata/RodVCFUnitTest.java

@@ -24,11 +24,11 @@ import java.util.List;
 /**
  * @author aaron
  *         <p/>
- *         Class RodVCFTest
+ *         Class RodVCFUnitTest
  *         <p/>
  *         test out the rod VCF
  */
-public class RodVCFTest extends BaseTest {
+public class RodVCFUnitTest extends BaseTest {
 
     private static File vcfFile = new File(validationDataLocation + "vcfexample.vcf");
     private VCFHeader mHeader;

java/test/org/broadinstitute/sting/gatk/refdata/TabularRODUnitTest.java

@@ -28,7 +28,7 @@ import static org.junit.Assert.assertTrue;
  * Basic unit test for TabularROD
  *
  */
-public class TabularRODTest extends BaseTest {
+public class TabularRODUnitTest extends BaseTest {
     private static ReferenceSequenceFile seq;
     private ReferenceOrderedData ROD;
     private LocationAwareSeekableRODIterator iter;

java/test/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptorsUnitTest.java

@@ -26,12 +26,12 @@ import java.util.List;
  * 
  * @author aaron 
  * 
- * Class VariantContextAdaptorsTest
+ * Class VariantContextAdaptorsUnitTest
  *
  * This test class exists to test input -> output of variant formats
  * run through the VariantContext class.  
  */
-public class VariantContextAdaptorsTest extends BaseTest {
+public class VariantContextAdaptorsUnitTest extends BaseTest {
     public static IndexedFastaSequenceFile seq = null;
 
     @BeforeClass

java/test/org/broadinstitute/sting/gatk/refdata/rodDbSNPUnitTest.java

@@ -14,11 +14,11 @@ import java.io.*;
 /**
  * @author aaron
  *         <p/>
- *         Class rodDbSNPTest
+ *         Class rodDbSNPUnitTest
  *         <p/>
  *         A descriptions should go here. Blame aaron if it's missing.
  */
-public class rodDbSNPTest extends BaseTest {
+public class rodDbSNPUnitTest extends BaseTest {
     private static IndexedFastaSequenceFile seq;
 
     @BeforeClass

java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManagerUnitTest.java

@@ -41,10 +41,10 @@ import java.util.Iterator;
 import java.util.List;
 
 /**
- * class RMDTrackManagerTest
+ * class RMDTrackManagerUnitTest
  * tests out the ability of the RMDTrackManager to correctly create RMDtracks based on the requested types.
  */
-public class RMDTrackManagerTest extends BaseTest {
+public class RMDTrackManagerUnitTest extends BaseTest {
     List<String> triplets;
     List<RMDTrack> tracks;
 

java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java

@@ -34,11 +34,11 @@ import java.util.Map;
  * 
  * @author aaron 
  * 
- * Class TribbleRMDTrackBuilderTest
+ * Class TribbleRMDTrackBuilderUnitTest
  *
  * Testing out the builder for tribble Tracks (not really a functional test right now)
  */
-public class TribbleRMDTrackBuilderTest extends BaseTest {
+public class TribbleRMDTrackBuilderUnitTest extends BaseTest {
     private TribbleRMDTrackBuilder builder;
 
     @Before

java/test/org/broadinstitute/sting/gatk/refdata/utils/FlashBackIteratorUnitTest.java

@@ -21,11 +21,11 @@ import java.util.List;
 /**
  * @author aaron
  *         <p/>
- *         Class FlashBackIteratorTest
+ *         Class FlashBackIteratorUnitTest
  *         <p/>
  *         just like a greatful dead show...this will be prone to flashbacks
  */
-public class FlashBackIteratorTest extends BaseTest {
+public class FlashBackIteratorUnitTest extends BaseTest {
     private SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(NUMBER_OF_CHROMOSOMES, STARTING_CHROMOSOME, CHROMOSOME_SIZE);
     private static final int NUMBER_OF_CHROMOSOMES = 5;
     private static final int STARTING_CHROMOSOME = 1;

java/test/org/broadinstitute/sting/gatk/traversals/TraverseDuplicatesUnitTest.java

@@ -18,11 +18,11 @@ import java.util.Set;
 /**
  * @author aaron
  *         <p/>
- *         Class TraverseDuplicatesTest
+ *         Class TraverseDuplicatesUnitTest
  *         <p/>
  *         test the meat of the traverse dupplicates.
  */
-public class TraverseDuplicatesTest extends BaseTest {
+public class TraverseDuplicatesUnitTest extends BaseTest {
 
     private TraverseDuplicates obj = new TraverseDuplicates();
     private SAMFileHeader header;

java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java

@@ -48,11 +48,11 @@ import java.util.List;
  * @version 1.0
  * @date Apr 24, 2009
  * <p/>
- * Class TraverseReadsTest
+ * Class TraverseReadsUnitTest
  * <p/>
  * test traversing reads
  */
-public class TraverseReadsTest extends BaseTest {
+public class TraverseReadsUnitTest extends BaseTest {
 
     private ReferenceSequenceFile seq;
     private File bam = new File(validationDataLocation + "index_test.bam"); // TCGA-06-0188.aligned.duplicates_marked.bam");

java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsWalkerUnitTest.java

@@ -42,11 +42,11 @@ import net.sf.samtools.SAMFileHeader;
 /**
  * @author aaron
  *         <p/>
- *         Class PrintReadsWalkerTest
+ *         Class PrintReadsWalkerUnitTest
  *         <p/>
  *         This tests the print reads walker, using the artificial reads traversal
  */
-public class PrintReadsWalkerTest extends BaseTest {
+public class PrintReadsWalkerUnitTest extends BaseTest {
 
     /**
      * our private fake reads traversal.  This traversal seeds the

java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsUnitTest.java

@@ -7,7 +7,7 @@ import org.junit.Assert;
 
 import static java.lang.Math.log10;
 
-public class GenotypeLikelihoodsTest extends BaseTest {
+public class GenotypeLikelihoodsUnitTest extends BaseTest {
     private final static double DELTA = 1e-8;
 
     @Test

java/test/org/broadinstitute/sting/playground/gatk/walkers/ConcordanceTruthTableUnitTest.java

@@ -19,7 +19,7 @@ import java.util.ArrayList;
  * Time: 9:40:51 AM
  * To change this template use File | Settings | File Templates.
  */
-public class ConcordanceTruthTableTest extends BaseTest {
+public class ConcordanceTruthTableUnitTest extends BaseTest {
 
     @Test
     public void testAlleleFrequencyCalculation() {

java/test/org/broadinstitute/sting/playground/gatk/walkers/poolseq/PowerUnitTest.java

@@ -16,7 +16,7 @@ import java.math.BigDecimal;
  * Time: 10:19:53 AM
  * To change this template use File | Settings | File Templates.
  */
-public class PowerTest extends BaseTest {
+public class PowerUnitTest extends BaseTest {
     // test for various items involved in PowerBelowFrequency
     @Test
     public void testBinomialProbabilityLog() {

java/test/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScannerUnitTest.java

@@ -11,11 +11,11 @@ import org.junit.Test;
 /**
  * @author aaron
  *         <p/>
- *         Class AnalysisModuleScannerTest
+ *         Class AnalysisModuleScannerUnitTest
  *         <p/>
  *         Test out the analysis scanner, which takes an analysis module and extracts out basic data
  */
-public class AnalysisModuleScannerTest extends BaseTest {
+public class AnalysisModuleScannerUnitTest extends BaseTest {
 
     @Test
     public void testBasicScan() {

java/test/org/broadinstitute/sting/playground/utils/report/ReportMarshallerUnitTest.java

@@ -30,11 +30,11 @@ import org.junit.Test;
 /**
  * @author aaron
  *         <p/>
- *         Class ReportMarshallerTest
+ *         Class ReportMarshallerUnitTest
  *         <p/>
  *         test out the marshaller
  */
-public class ReportMarshallerTest extends BaseTest {
+public class ReportMarshallerUnitTest extends BaseTest {
     @Test
     public void testMarshalling() {
         /*Configuration cfg = new Configuration();

java/test/org/broadinstitute/sting/utils/BaseUtilsUnitTest.java

@@ -5,7 +5,7 @@ import org.junit.Test;
 import org.junit.BeforeClass;
 import org.junit.Assert;
 
-public class BaseUtilsTest extends BaseTest {
+public class BaseUtilsUnitTest extends BaseTest {
     @BeforeClass
     public static void init() { }
 

java/test/org/broadinstitute/sting/utils/ExpandingArrayListUnitTest.java

@@ -13,7 +13,7 @@ import java.util.Arrays;
 /**
  * Basic unit test for RecalData
  */
-public class ExpandingArrayListTest extends BaseTest {
+public class ExpandingArrayListUnitTest extends BaseTest {
     ExpandingArrayList<Integer> empty, initCap10, hasOne, hasTen;
 
     @Before

java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java

@@ -17,11 +17,11 @@ import java.util.List;
 /**
  * @author aaron
  *         <p/>
- *         Class GenomeLocParserTest
+ *         Class GenomeLocParserUnitTest
  *         <p/>
  *         Test out the functionality of the new genome loc parser
  */
-public class GenomeLocParserTest extends BaseTest {
+public class GenomeLocParserUnitTest extends BaseTest {
     @Test(expected = StingException.class)
     public void testUnsetupException() {
         GenomeLocParser.contigInfo = null;

java/test/org/broadinstitute/sting/utils/GenomeLocSortedSetUnitTest.java

@@ -36,7 +36,7 @@ import java.util.Arrays;
  * <p/>
  * This tests the functions of the GenomeLocSet
  */
-public class GenomeLocSortedSetTest extends BaseTest {
+public class GenomeLocSortedSetUnitTest extends BaseTest {
 
     private GenomeLocSortedSet mSortedSet = null;
     private SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(NUMBER_OF_CHROMOSOMES, STARTING_CHROMOSOME, CHROMOSOME_SIZE);
@@ -207,15 +207,15 @@ public class GenomeLocSortedSetTest extends BaseTest {
     public void fromSequenceDictionary() {
         mSortedSet = GenomeLocSortedSet.createSetFromSequenceDictionary(this.header.getSequenceDictionary());
         // we should have sequence
-        assertTrue(mSortedSet.size() == GenomeLocSortedSetTest.NUMBER_OF_CHROMOSOMES);
+        assertTrue(mSortedSet.size() == GenomeLocSortedSetUnitTest.NUMBER_OF_CHROMOSOMES);
         int seqNumber = 0;
         for (GenomeLoc loc : mSortedSet) {
             assertTrue(loc.getStart() == 1);
-            assertTrue(loc.getStop() == GenomeLocSortedSetTest.CHROMOSOME_SIZE);
+            assertTrue(loc.getStop() == GenomeLocSortedSetUnitTest.CHROMOSOME_SIZE);
             assertTrue(loc.getContigIndex() == seqNumber);
             ++seqNumber;
         }
-        assertTrue(seqNumber == GenomeLocSortedSetTest.NUMBER_OF_CHROMOSOMES);
+        assertTrue(seqNumber == GenomeLocSortedSetUnitTest.NUMBER_OF_CHROMOSOMES);
     }
 
     @Test
@@ -223,9 +223,9 @@ public class GenomeLocSortedSetTest extends BaseTest {
         mSortedSet = GenomeLocSortedSet.createSetFromSequenceDictionary(this.header.getSequenceDictionary());
         GenomeLocSortedSet set = GenomeLocSortedSet.createSetFromSequenceDictionary(this.header.getSequenceDictionary());
         // we should have sequence
-        assertTrue(mSortedSet.size() == GenomeLocSortedSetTest.NUMBER_OF_CHROMOSOMES);
+        assertTrue(mSortedSet.size() == GenomeLocSortedSetUnitTest.NUMBER_OF_CHROMOSOMES);
         mSortedSet.addAllRegions(set.toList());
-        assertTrue(mSortedSet.size() == GenomeLocSortedSetTest.NUMBER_OF_CHROMOSOMES);                        
+        assertTrue(mSortedSet.size() == GenomeLocSortedSetUnitTest.NUMBER_OF_CHROMOSOMES);                        
     }
 
     @Test

java/test/org/broadinstitute/sting/utils/GenomeLocUnitTest.java

@@ -18,7 +18,7 @@ import net.sf.picard.reference.ReferenceSequenceFile;
 /**
  * Basic unit test for GenomeLoc
  */
-public class GenomeLocTest extends BaseTest {
+public class GenomeLocUnitTest extends BaseTest {
     private static ReferenceSequenceFile seq;
 
     @BeforeClass

java/test/org/broadinstitute/sting/utils/ListUtilsUnitTest.java

@@ -13,7 +13,7 @@ import java.util.Collections;
 /**
  * Basic unit test for MathUtils
  */
-public class ListUtilsTest extends BaseTest {
+public class ListUtilsUnitTest extends BaseTest {
     @BeforeClass
     public static void init() { }
 

java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java

@@ -12,7 +12,7 @@ import java.io.File;
 /**
  * Basic unit test for MathUtils
  */
-public class MathUtilsTest extends BaseTest {
+public class MathUtilsUnitTest extends BaseTest {
     @BeforeClass
     public static void init() { }
 

java/test/org/broadinstitute/sting/utils/PathUtilsUnitTest.java

@@ -7,7 +7,7 @@ import org.junit.Assert;
 
 import java.io.File;
 
-public class PathUtilsTest extends BaseTest {
+public class PathUtilsUnitTest extends BaseTest {
     @BeforeClass
     public static void init() { }
 

java/test/org/broadinstitute/sting/utils/UtilsUnitTest.java

@@ -38,7 +38,7 @@ import java.util.Map;
  * @version 0.1
  */
 
-public class UtilsTest extends BaseTest {
+public class UtilsUnitTest extends BaseTest {
 
     @Test
     public void testDupStringNoChars() {

java/test/org/broadinstitute/sting/utils/bed/BedParserUnitTest.java

@@ -15,7 +15,7 @@ import java.io.FileNotFoundException;
 import java.util.List;
 
 
-public class BedParserTest extends BaseTest {
+public class BedParserUnitTest extends BaseTest {
 
     private static IndexedFastaSequenceFile seq;
     private File bedFile = new File("testdata/sampleBedFile.bed");

java/test/org/broadinstitute/sting/utils/cmdLine/ParsingEngineUnitTest.java

@@ -25,7 +25,7 @@ import java.util.EnumSet;
 /**
  * Test suite for the parsing engine.
  */
-public class ParsingEngineTest extends BaseTest {
+public class ParsingEngineUnitTest extends BaseTest {
     private ParsingEngine parsingEngine;
 
     @Before

java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceIndexUnitTest.java

@@ -14,7 +14,7 @@ import java.util.Iterator;
 /**
  * Test the fasta sequence index reader.
  */
-public class FastaSequenceIndexTest extends BaseTest {
+public class FastaSequenceIndexUnitTest extends BaseTest {
     // our basic human 18 fai
     private static String sequenceIndexName = null;
     private FastaSequenceIndex sequenceIndex = null;

java/test/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFileUnitTest.java

@@ -18,7 +18,7 @@ import net.sf.samtools.util.StringUtil;
 /**
  * Test the indexed fasta sequence file reader.
  */
-public class IndexedFastaSequenceFileTest extends BaseTest {
+public class IndexedFastaSequenceFileUnitTest extends BaseTest {
     private static String sequenceFileName;
     private IndexedFastaSequenceFile sequenceFile = null;
 

java/test/org/broadinstitute/sting/utils/genotype/BasicGenotypeUnitTest.java

@@ -16,11 +16,11 @@ import java.io.FileNotFoundException;
  * 
  * @author aaron 
  * 
- * Class BasicGenotypeTest
+ * Class BasicGenotypeUnitTest
  *
  * tests the basic genotype class
  */
-public class BasicGenotypeTest extends BaseTest {
+public class BasicGenotypeUnitTest extends BaseTest {
     private static IndexedFastaSequenceFile seq;
 
        @BeforeClass

java/test/org/broadinstitute/sting/utils/genotype/BasicVariationUnitTest.java

@@ -19,7 +19,7 @@ import java.io.FileNotFoundException;
  * <p/>
  * some quick tests for the BasicVariation class
  */
-public class BasicVariationTest extends BaseTest {
+public class BasicVariationUnitTest extends BaseTest {
     private static IndexedFastaSequenceFile seq;
 
     @BeforeClass

java/test/org/broadinstitute/sting/utils/genotype/DiploidGenotypeUnitTest.java

@@ -9,11 +9,11 @@ import org.junit.Test;
  * 
  * @author aaron 
  * 
- * Class DiploidGenotypeTest
+ * Class DiploidGenotypeUnitTest
  *
  * Testing the basic functionality of the diploid genotype class
  */
-public class DiploidGenotypeTest extends BaseTest {
+public class DiploidGenotypeUnitTest extends BaseTest {
 
     @Test
     public void testCreateDiploidFromString() {

java/test/org/broadinstitute/sting/utils/genotype/LikelihoodObjectUnitTest.java

@@ -36,11 +36,11 @@ import static junit.framework.Assert.assertTrue;
 /**
  * @author aaron
  *         <p/>
- *         Class LikelihoodObjectTest
+ *         Class LikelihoodObjectUnitTest
  *         <p/>
  *         Tests the Likelihood object.
  */
-public class LikelihoodObjectTest extends BaseTest {
+public class LikelihoodObjectUnitTest extends BaseTest {
 
     private LikelihoodObject mLO = null;
 

java/test/org/broadinstitute/sting/utils/genotype/glf/GLFReaderUnitTest.java

@@ -12,11 +12,11 @@ import java.util.List;
 /**
  * @author aaron
  *         <p/>
- *         Class GLFReaderTest
+ *         Class GLFReaderUnitTest
  *         <p/>
  *         A descriptions should go here. Blame aaron if it's missing.
  */
-public class GLFReaderTest extends BaseTest {
+public class GLFReaderUnitTest extends BaseTest {
 
 
     // our test file

java/test/org/broadinstitute/sting/utils/genotype/glf/GLFRecordUnitTest.java

@@ -9,11 +9,11 @@ import org.junit.Test;
  * 
  * @author aaron 
  * 
- * Class GLFRecordTest
+ * Class GLFRecordUnitTest
  *
  * Test out the basics of a GLFRecord
  */
-public class GLFRecordTest extends BaseTest {
+public class GLFRecordUnitTest extends BaseTest {
 
     @Test
     public void testConstructingGLFRecord() {

java/test/org/broadinstitute/sting/utils/genotype/glf/GLFWriterUnitTest.java

@@ -49,7 +49,7 @@ import net.sf.samtools.SAMSequenceRecord;
  *         <p/>
  *         Tests for the GLFRecord class
  */
-public class GLFWriterTest extends BaseTest {
+public class GLFWriterUnitTest extends BaseTest {
 
     /** some made up values that we use to generate the GLF */
     private final String header = "";

java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeEncodingUnitTest.java

@@ -8,11 +8,11 @@ import org.junit.Test;
 /**
  * @author aaron
  *         <p/>
- *         Class VCFGenotypeEncodingTest
+ *         Class VCFGenotypeEncodingUnitTest
  *         <p/>
  *         test the VCFGenotypeEncoding class
  */
-public class VCFGenotypeEncodingTest extends BaseTest {
+public class VCFGenotypeEncodingUnitTest extends BaseTest {
     @Test
     public void testDecodingSingle() {
         VCFGenotypeEncoding enc = new VCFGenotypeEncoding("A");

java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderUnitTest.java

@@ -11,11 +11,11 @@ import java.util.*;
  * 
  * @author aaron 
  * 
- * Class VCFHeaderTest
+ * Class VCFHeaderUnitTest
  *
  * Test the VCF Header class
  */
-public class VCFHeaderTest extends BaseTest {
+public class VCFHeaderUnitTest extends BaseTest {
 
     private Set<VCFHeaderLine> metaData = new HashSet<VCFHeaderLine>();
     private Set<String> additionalColumns = new HashSet<String>();

java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFReaderUnitTest.java

@@ -22,7 +22,7 @@ import org.junit.BeforeClass;
 import org.junit.Test;
 
 /** test the VCFReader class test */
-public class VCFReaderTest extends BaseTest {
+public class VCFReaderUnitTest extends BaseTest {
 
     private static final File vcfFile = new File(validationDataLocation + "vcfexample.vcf");
     private static final File multiSampleVCF = new File(validationDataLocation + "MultiSample.vcf");

java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFRecordUnitTest.java

@@ -16,11 +16,11 @@ import java.io.FileNotFoundException;
 /**
  * @author aaron
  *         <p/>
- *         Class VCFRecordTest
+ *         Class VCFRecordUnitTest
  *         <p/>
  *         test the basic functionality of the vcf record
  */
-public class VCFRecordTest extends BaseTest {
+public class VCFRecordUnitTest extends BaseTest {
 
     @BeforeClass
     public static void beforeTests() {

java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java

@@ -16,11 +16,11 @@ import java.util.*;
 /**
  * @author aaron
  *         <p/>
- *         Class VCFWriterTest
+ *         Class VCFWriterUnitTest
  *         <p/>
  *         This class tests out the ability of the VCF writer to correctly write VCF files
  */
-public class VCFWriterTest extends BaseTest {
+public class VCFWriterUnitTest extends BaseTest {
     private Set<VCFHeaderLine> metaData = new HashSet<VCFHeaderLine>();
     private Set<String> additionalColumns = new HashSet<String>();
     private File fakeVCFFile = new File("FAKEVCFFILEFORTESTING.vcf");

java/test/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java

@@ -38,12 +38,12 @@ import net.sf.samtools.SAMRecord;
  * 
  * @author aaron 
  * 
- * Class ArtificialPatternedSAMIteratorTest
+ * Class ArtificialPatternedSAMIteratorUnitTest
  *
  * tests ArtificialPatternedSAMIterator, making sure that if you specify in order
  * you get reads in order, and if you specify out of order you get them out of order.  
  */
-public class ArtificialPatternedSAMIteratorTest extends BaseTest {
+public class ArtificialPatternedSAMIteratorUnitTest extends BaseTest {
 
     // our artifical patterned iterator
     ArtificialPatternedSAMIterator iter;

java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriterUnitTest.java

@@ -44,7 +44,7 @@ import java.util.List;
  *         <p/>
  *         Test out the ArtificialSAMFileWriter class
  */
-public class ArtificialSAMFileWriterTest extends BaseTest {
+public class ArtificialSAMFileWriterUnitTest extends BaseTest {
 
     /** the artificial sam writer */
     private ArtificialSAMFileWriter writer;

java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIteratorUnitTest.java

@@ -35,11 +35,11 @@ import static junit.framework.Assert.assertTrue;
 /**
  * @author aaron
  *         <p/>
- *         Class ArtificialSAMQueryIteratorTest
+ *         Class ArtificialSAMQueryIteratorUnitTest
  *         <p/>
  *         a test for the ArtificialSAMQueryIterator class.
  */
-public class ArtificialSAMQueryIteratorTest extends BaseTest {
+public class ArtificialSAMQueryIteratorUnitTest extends BaseTest {
 
     @Test
     public void testWholeChromosomeQuery() {

java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMUtilsUnitTest.java

@@ -15,7 +15,7 @@ import net.sf.samtools.SAMRecord;
  * Time: 3:09:34 AM
  * To change this template use File | Settings | File Templates.
  */
-public class ArtificialSAMUtilsTest extends BaseTest {
+public class ArtificialSAMUtilsUnitTest extends BaseTest {
 
 
     @Test

java/test/org/broadinstitute/sting/utils/threading/ThreadPoolMonitorUnitTest.java

@@ -22,7 +22,7 @@ import java.util.concurrent.Executors;
  * Tests for the thread pool monitor class.
  */
 
-public class ThreadPoolMonitorTest extends BaseTest {
+public class ThreadPoolMonitorUnitTest extends BaseTest {
     private ExecutorService threadPool = Executors.newFixedThreadPool(1);
 
     /**