Unit test fixed - Tribble codecs aren't designed to be stateless, but I was

using one as though it was.  Fixed, and debug code reverted.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4917 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java

@@ -60,13 +60,10 @@ public class TableCodec implements ReferenceDependentFeatureCodec {
 
     @Override
     public Object readHeader(LineReader reader) {
-        System.out.printf("  TableCodec.readHeader:%n  ");
-        new Exception().printStackTrace(System.out);
         String line = "";
         try {
             while ((line = reader.readLine()) != null) {
                 if (line.startsWith(headerDelimiter)) {
-                    System.out.printf("  Line w/ header delimiter: %s%n",line);
                     if (header.size() > 0) throw new IllegalStateException("Input table file seems to have two header lines.  The second is = " + line);
                     String spl[] = line.split(delimiterRegex);
                     for (String s : spl) header.add(s);

java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java

@@ -237,14 +237,12 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
         FeatureSource featureSource = null;
         SAMSequenceDictionary sequenceDictionary = null;
 
-        FeatureCodec codec = createCodec(targetClass, name);
-
         // Detect whether or not this source should be indexed.
         boolean canBeIndexed = (storageType == RMDStorageType.FILE);
 
         if(canBeIndexed) {
             try {
-                Index index = loadIndex(inputFile, codec);
+                Index index = loadIndex(inputFile, createCodec(targetClass, name));
                 try { logger.info(String.format("  Index for %s has size in bytes %d", inputFile, Sizeof.getObjectGraphSize(index))); }
                 catch (ReviewedStingException e) { }
 
@@ -257,7 +255,7 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
                     sequenceDictionary = getSequenceDictionaryFromProperties(index);
                 }
 
-                featureSource = new BasicFeatureSource(inputFile.getAbsolutePath(), index, codec);
+                featureSource = new BasicFeatureSource(inputFile.getAbsolutePath(), index, createCodec(targetClass, name));
             }
             catch (TribbleException e) {
                 throw new UserException(e.getMessage());
@@ -267,7 +265,7 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
             }
         }
         else {
-            featureSource = BasicFeatureSource.getFeatureSource(inputFile.getAbsolutePath(),codec,false);
+            featureSource = BasicFeatureSource.getFeatureSource(inputFile.getAbsolutePath(),createCodec(targetClass, name),false);
         }
 
         return new Pair<FeatureSource,SAMSequenceDictionary>(featureSource,sequenceDictionary);

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

@@ -64,14 +64,12 @@ public class ReferenceOrderedViewUnitTest extends BaseTest {
      */
     @Test
     public void testNoBindings() {
-        System.out.printf("Starting testNoBindings%n");
         Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chrM",1,30)));
         LocusShardDataProvider provider = new LocusShardDataProvider(shard, null, genomeLocParser, shard.getGenomeLocs().get(0), null, seq, Collections.<ReferenceOrderedDataSource>emptyList());
         ReferenceOrderedView view = new ManagingReferenceOrderedView( provider );
 
         RefMetaDataTracker tracker = view.getReferenceOrderedDataAtLocus(genomeLocParser.createGenomeLoc("chrM",10));
         Assert.assertEquals(tracker.getAllRods().size(), 0, "The tracker should not have produced any data");
-        System.out.printf("Ending testNoBindings%n");
     }
 
     /**
@@ -79,7 +77,6 @@ public class ReferenceOrderedViewUnitTest extends BaseTest {
      */
     @Test
     public void testSingleBinding() {
-        System.out.printf("Starting testSingleBinding%n");
         String fileName = testDir + "TabularDataTest.dat";
         RMDTriplet triplet = new RMDTriplet("tableTest","Table",fileName,RMDStorageType.FILE);
         ReferenceOrderedDataSource dataSource = new ReferenceOrderedDataSource(triplet,builder,seq.getSequenceDictionary(),genomeLocParser,false);
@@ -95,7 +92,6 @@ public class ReferenceOrderedViewUnitTest extends BaseTest {
         Assert.assertEquals(datum.get("COL1"),"C","datum parameter for COL1 is incorrect");
         Assert.assertEquals(datum.get("COL2"),"D","datum parameter for COL2 is incorrect");
         Assert.assertEquals(datum.get("COL3"),"E","datum parameter for COL3 is incorrect");
-        System.out.printf("Ending testSingleBinding%n");
     }
 
     /**
@@ -103,7 +99,6 @@ public class ReferenceOrderedViewUnitTest extends BaseTest {
      */
     @Test
     public void testMultipleBinding() {
-        System.out.printf("Starting testMultipleBinding%n");
         File file = new File(testDir + "TabularDataTest.dat");
 
         RMDTriplet testTriplet1 = new RMDTriplet("tableTest1","Table",file.getAbsolutePath(),RMDStorageType.FILE);
@@ -129,6 +124,5 @@ public class ReferenceOrderedViewUnitTest extends BaseTest {
         Assert.assertEquals(datum2.get("COL1"),"C","datum2 parameter for COL1 is incorrect");
         Assert.assertEquals(datum2.get("COL2"),"D","datum2 parameter for COL2 is incorrect");
         Assert.assertEquals(datum2.get("COL3"),"E","datum2 parameter for COL3 is incorrect");
-        System.out.printf("Ending testMultipleBinding%n");
     }
 }