Clean up the code a bit following the introduction of reduceByInterval.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2887 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java

@@ -47,7 +47,7 @@ public class AllLocusView extends LocusView {
     public AllLocusView(ShardDataProvider provider) {                
         super( provider );
         // Seed the state tracking members with the first possible seek position and the first possible locus context.
-        locusIterator = new GenomeLocusIterator( Collections.singletonList(provider.getLocus()) );
+        locusIterator = new GenomeLocusIterator(provider.getLocus());
         if( locusIterator.hasNext() ) {
             nextPosition = locusIterator.next();
             nextLocus = hasNextLocus() ? nextLocus() : createEmptyLocus(nextPosition);

java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShardStrategy.java

@@ -66,20 +66,7 @@ public class IndexDelimitedLocusShardStrategy implements ShardStrategy {
             throw new StingException("Cannot power an IndexDelimitedLocusShardStrategy with this data source.");
 
         blockDrivenDataSource = (BlockDrivenSAMDataSource)dataSource;
-
+        filePointers.addAll(batchLociIntoBins(locations.toList(),blockDrivenDataSource.getNumIndexLevels()-1));
-        // Create a list of contig name -> genome loc, sorted in INSERTION ORDER.
-        LinkedHashMap<String,List<GenomeLoc>> locationToReference = new LinkedHashMap<String,List<GenomeLoc>>();
-        for(GenomeLoc location: locations) {
-            if(!locationToReference.containsKey(location.getContig()))
-                locationToReference.put(location.getContig(),new ArrayList<GenomeLoc>());
-            locationToReference.get(location.getContig()).add(location);
-        }
-
-        // TODO: Not sure there's any reason to pre-separate the contigs now that we're using a streaming approach to file pointer allocation.
-        for(String contig: locationToReference.keySet()) {
-            filePointers.addAll(batchLociIntoBins(locationToReference.get(contig),blockDrivenDataSource.getNumIndexLevels()-1));
-        }
-
         filePointerIterator = filePointers.iterator();
     }
 

java/src/org/broadinstitute/sting/gatk/iterators/GenomeLocusIterator.java

@@ -5,7 +5,6 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
 
 import java.util.NoSuchElementException;
 import java.util.Iterator;
-import java.util.List;
 /**
  * User: hanna
  * Date: May 12, 2009
@@ -24,28 +23,24 @@ import java.util.List;
  */
 public class GenomeLocusIterator implements Iterator<GenomeLoc> {
     /**
-     * An iterator to the entire data structure over which we're iterating.
+     * The entire region over which we're iterating.
      */
-    private final Iterator<GenomeLoc> locusIterator;
+    private GenomeLoc completeLocus;
 
     /**
-     * The multi-base pair long locus referring to the current locus.
+     * The current position in the traversal.
      */
-    private GenomeLoc currentLocus = null;
+    private GenomeLoc currentLocus;
-
-    /**
-     * The 1 base pair long location.
-     */
-    private GenomeLoc currentLocation = null;
 
     /**
      * Creates an iterator that can traverse over the entire
      * reference specified in the given ShardDataProvider.
-     * @param loci the list of loci over which to iterate.
+     * @param completeLocus Data provider to use as a backing source.
+     *                 Provider must have a reference (hasReference() == true).
      */
-    public GenomeLocusIterator( List<GenomeLoc> loci ) {
+    public GenomeLocusIterator( GenomeLoc completeLocus ) {
-        this.locusIterator = loci.iterator();
+        this.completeLocus = completeLocus;
-        seedNextLocus();
+        this.currentLocus = GenomeLocParser.createGenomeLoc(completeLocus.getContig(),completeLocus.getStart());
     }
 
     /**
@@ -53,7 +48,7 @@ public class GenomeLocusIterator implements Iterator<GenomeLoc> {
      * @return True if the iterator has more elements.  False otherwise. 
      */
     public boolean hasNext() {
-        return currentLocation != null;
+        return !currentLocus.isPast(completeLocus);    
     }
 
     /**
@@ -63,29 +58,12 @@ public class GenomeLocusIterator implements Iterator<GenomeLoc> {
     public GenomeLoc next() {
         if( !hasNext() )
             throw new NoSuchElementException("No elements remaining in bounded reference region.");
-        GenomeLoc toReturn = currentLocation.clone();
+        GenomeLoc toReturn = (GenomeLoc)currentLocus.clone();
-        seedNextLocus();
+        currentLocus = GenomeLocParser.incPos(currentLocus);
         return toReturn;
     }
 
     public void remove() {
         throw new UnsupportedOperationException( "ReferenceLocusIterator is read-only" );
     }
-
-    /**
-     * Position currentLocation at the next locus, if possible.
-     */
-    private void seedNextLocus() {
-        if(currentLocus != null && currentLocation != null)
-            currentLocation = GenomeLocParser.incPos(currentLocation);
-
-        // If initializing or the location was pushed off the current locus, reinitialize using the next locus.
-        if(currentLocus == null || currentLocation == null || currentLocation.isPast(currentLocus)) {
-            currentLocus = currentLocation = null;
-            if(locusIterator.hasNext()){
-                currentLocus = locusIterator.next();
-                currentLocation = GenomeLocParser.createGenomeLoc(currentLocus.getContig(),currentLocus.getStart());
-            }
-        }
-    }
 }

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

@@ -89,9 +89,9 @@ public class LocusReferenceViewTest extends ReferenceViewTemplate {
      */
     protected void validateLocation( GenomeLoc loc ) {
         Shard shard = new LocusShard(Collections.singletonList(loc));
-        GenomeLocusIterator shardIterator = new GenomeLocusIterator(shard.getGenomeLocs());
+        GenomeLocusIterator shardIterator = new GenomeLocusIterator(loc);
 
-        ShardDataProvider dataProvider = new ShardDataProvider(shard, shard.getGenomeLocs().get(0), null, sequenceFile, null);
+        ShardDataProvider dataProvider = new ShardDataProvider(shard, loc, null, sequenceFile, null);
         LocusReferenceView view = new LocusReferenceView(dataProvider);
 
         while (shardIterator.hasNext()) {