Rev tribble.

Just added more documentation for diffEngine and pointer to new wiki:

http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine

public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java

@@ -209,7 +209,7 @@ public class DiffEngine {
     protected void printSummaryReport(List<Difference> sortedSummaries, SummaryReportParams params ) {
         GATKReport report = new GATKReport();
         final String tableName = "diffences";
-        report.addTable(tableName, "Summarized differences between the master and test files.\nSee http://www.broadinstitute.org/gsa/wiki/index.php/DiffObjectsWalker_and_SummarizedDifferences for more information");
+        report.addTable(tableName, "Summarized differences between the master and test files.\nSee http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine for more information");
         GATKReportTable table = report.getTable(tableName);
         table.addPrimaryKey("Difference", true);
         table.addColumn("NumberOfOccurrences", 0);

public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java

@@ -39,12 +39,27 @@ import java.io.File;
  */
 public interface DiffableReader {
     @Ensures("result != null")
+    /**
+     * Return the name of this DiffableReader type.  For example, the VCF reader returns 'VCF' and the
+     * bam reader 'BAM'
+     */
     public String getName();
 
     @Ensures("result != null")
     @Requires("file != null")
+    /**
+     * Read up to maxElementsToRead DiffElements from file, and return them.
+     */
     public DiffElement readFromFile(File file, int maxElementsToRead);
 
+    /**
+     * Return true if the file can be read into DiffElement objects with this reader. This should
+     * be uniquely true/false for all readers, as the system will use the first reader that can read the
+     * file.  This routine should never throw an exception.  The VCF reader, for example, looks at the
+     * first line of the file for the ##format=VCF4.1 header, and the BAM reader for the BAM_MAGIC value
+     * @param file
+     * @return
+     */
     @Requires("file != null")
     public boolean canRead(File file);
 }

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

@@ -75,7 +75,7 @@ public class WalkerTest extends BaseTest {
         Index indexFromOutputFile = IndexFactory.createIndex(resultFile, new VCFCodec());
         Index dynamicIndex = IndexFactory.loadIndex(indexFile.getAbsolutePath());
 
-        if ( ! indexFromOutputFile.equals(dynamicIndex) ) {
+        if ( ! indexFromOutputFile.equalsIgnoreTimestamp(dynamicIndex) ) {
             Assert.fail(String.format("Index on disk from indexing on the fly not equal to the index created after the run completed.  FileIndex %s vs. on-the-fly %s%n",
                     indexFromOutputFile.getProperties(),
                     dynamicIndex.getProperties()));