Removed annoying FastaSequenceIndexBuilderProgressListener infrastructure that was just a boolean switch on whether to print progress or not.

public/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java

@@ -25,7 +25,6 @@
 
 package net.sf.picard.reference;
 
-import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSourceProgressListener;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import static net.sf.picard.reference.FastaSequenceIndexBuilder.Status.*;
@@ -39,8 +38,8 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
  * Produces fai file with same output as samtools faidx
  */
 public class FastaSequenceIndexBuilder {
-    public File fastaFile;
+    final public File fastaFile;
-    ReferenceDataSourceProgressListener progress;  // interface that provides a method for updating user on progress of reading file
+    final boolean printProgress;
 
     // keep track of location in file
     long bytesRead, endOfLastLine, lastTimestamp, fileLength;  // initialized to -1 to keep 0-indexed position in file;
@@ -55,10 +54,10 @@ public class FastaSequenceIndexBuilder {
     public enum Status { NONE, CONTIG, FIRST_SEQ_LINE, SEQ_LINE, COMMENT }
     Status status = Status.NONE; // keeps state of what is currently being read. better to use int instead of enum?
 
-    public FastaSequenceIndexBuilder(File fastaFile, ReferenceDataSourceProgressListener progress) {
+    public FastaSequenceIndexBuilder(File fastaFile, boolean printProgress) {
-        this.progress = progress;
         this.fastaFile = fastaFile;
         fileLength = fastaFile.length();
+        this.printProgress = printProgress;
     }
 
     /**
@@ -252,8 +251,8 @@ public class FastaSequenceIndexBuilder {
 
         if (System.currentTimeMillis() - lastTimestamp > 10000) {
             int percentProgress = (int) (100*bytesRead/fileLength);
-            if (progress != null)
+            if (printProgress)
-                progress.percentProgress(percentProgress);
+                System.out.println(String.format("PROGRESS UPDATE: file is %d percent complete", percentProgress));
             lastTimestamp = System.currentTimeMillis();
         }
     }

public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

@@ -926,9 +926,6 @@ public class GenomeAnalysisEngine {
                                                                             GenomeLocParser genomeLocParser,
                                                                             ValidationExclusion.TYPE validationExclusionType) {
         RMDTrackBuilder builder = new RMDTrackBuilder(sequenceDictionary,genomeLocParser,validationExclusionType);
-        // try and make the tracks given their requests
-        // create of live instances of the tracks
-        List<RMDTrack> tracks = new ArrayList<RMDTrack>();
 
         List<ReferenceOrderedDataSource> dataSources = new ArrayList<ReferenceOrderedDataSource>();
         for (RMDTriplet fileDescriptor : referenceMetaDataFiles)

public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java

@@ -41,7 +41,7 @@ import java.io.File;
  * Loads reference data from fasta file
  * Looks for fai and dict files, and tries to create them if they don't exist
  */
-public class ReferenceDataSource implements ReferenceDataSourceProgressListener {
+public class ReferenceDataSource {
     private IndexedFastaSequenceFile index;
 
     /** our log, which we want to capture anything from this class */
@@ -75,7 +75,7 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener
                 // get exclusive lock
                 if (!indexLock.exclusiveLock())
                     throw new UserException.CouldNotCreateReferenceIndexFileBecauseOfLock(dictFile);
-                FastaSequenceIndexBuilder faiBuilder = new FastaSequenceIndexBuilder(fastaFile, this);
+                FastaSequenceIndexBuilder faiBuilder = new FastaSequenceIndexBuilder(fastaFile, true);
                 FastaSequenceIndex sequenceIndex = faiBuilder.createIndex();
                 FastaSequenceIndexBuilder.saveAsFaiFile(sequenceIndex, indexFile);
             }
@@ -194,13 +194,4 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener
     public IndexedFastaSequenceFile getReference() {
         return this.index;
     }
-
-    /**
-     * Notify user of progress in creating fai file
-     * @param percent Percent of fasta file read as a percent
-     */
-    public void percentProgress(int percent) {
-        System.out.println(String.format("PROGRESS UPDATE: file is %d percent complete", percent));
-    }
-
 }

public/java/test/net/sf/picard/reference/FastaSequenceIndexBuilderUnitTest.java

@@ -27,7 +27,6 @@ package net.sf.picard.reference;
 
 import org.testng.Assert;
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSourceProgressListener;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
@@ -40,7 +39,6 @@ import java.io.FileNotFoundException;
 public class FastaSequenceIndexBuilderUnitTest extends BaseTest {
 
     private FastaSequenceIndexBuilder builder;
-    private ReferenceDataSourceProgressListener progress;
     private File fastaFile;
     private FastaSequenceIndex controlIndex;
 
@@ -58,7 +56,7 @@ public class FastaSequenceIndexBuilderUnitTest extends BaseTest {
         logger.warn("Executing unixFileTest");
 
         fastaFile = new File(validationDataLocation + "exampleFASTA.fasta");
-        builder = new FastaSequenceIndexBuilder(fastaFile, progress);
+        builder = new FastaSequenceIndexBuilder(fastaFile, false);
         FastaSequenceIndex index = builder.createIndex();
         controlIndex.add(new FastaSequenceIndexEntry("chr1", 6, 100000, 60, 61,0));
 
@@ -75,7 +73,7 @@ public class FastaSequenceIndexBuilderUnitTest extends BaseTest {
         logger.warn("Executing windowsFileTest");
 
         fastaFile = new File(validationDataLocation + "exampleFASTA-windows.fasta");
-        builder = new FastaSequenceIndexBuilder(fastaFile, progress);
+        builder = new FastaSequenceIndexBuilder(fastaFile, false);
         FastaSequenceIndex index = builder.createIndex();
         controlIndex.add(new FastaSequenceIndexEntry("chr2", 7, 29, 7, 9,0));
 
@@ -91,7 +89,7 @@ public class FastaSequenceIndexBuilderUnitTest extends BaseTest {
         logger.warn("Executing combinedWindowsUnix");
 
         fastaFile = new File(validationDataLocation + "exampleFASTA-combined.fasta");
-        builder = new FastaSequenceIndexBuilder(fastaFile, progress);
+        builder = new FastaSequenceIndexBuilder(fastaFile, false);
         FastaSequenceIndex index = builder.createIndex();
         controlIndex.add(new FastaSequenceIndexEntry("chr1", 6, 100000, 60, 61,0));
         controlIndex.add(new FastaSequenceIndexEntry("chr2", 101680, 29, 7, 9,1));
@@ -108,7 +106,7 @@ public class FastaSequenceIndexBuilderUnitTest extends BaseTest {
         logger.warn("Executing threeVariableLengthContigs");
 
         fastaFile = new File(validationDataLocation + "exampleFASTA-3contigs.fasta");
-        builder = new FastaSequenceIndexBuilder(fastaFile, progress);
+        builder = new FastaSequenceIndexBuilder(fastaFile, false);
         FastaSequenceIndex index = builder.createIndex();
         controlIndex.add(new FastaSequenceIndexEntry("chr1", 6, 17, 5, 6,0));
         controlIndex.add(new FastaSequenceIndexEntry("chr2", 35, 21, 7, 8,1));