TraverseByLocusWindow -- asstd bug fixes.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1109 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -118,11 +118,11 @@ public class GenomeAnalysisEngine {
 
         // if we're a read or a locus walker, we use the new system.  Right now we have complicated
         // branching based on the input data, but this should disapear when all the traversals are switched over
-        if (!(my_walker instanceof LocusWindowWalker) && !args.useNewTraverseByLocusWindow) {
+        if (my_walker instanceof LocusWindowWalker && !args.useNewTraverseByLocusWindow) {
-            microScheduler = createMicroscheduler(my_walker, rods);
-        } else { // we have an old style traversal, once we're done return
             legacyTraversal(my_walker, rods);
             return;
+        } else { // we have an old style traversal, once we're done return
+            microScheduler = createMicroscheduler(my_walker, rods);
         }
 
         // Prepare the sort ordering w.r.t. the sequence dictionary
@@ -194,7 +194,7 @@ public class GenomeAnalysisEngine {
         MicroScheduler microScheduler = null;
 
         // we need to verify different parameter based on the walker type
-        if (my_walker instanceof LocusWalker) {
+        if (my_walker instanceof LocusWalker || my_walker instanceof LocusWindowWalker) {
             // create the MicroScheduler
             if( argCollection.walkAllLoci )
                 Utils.scareUser("Argument --all_loci is deprecated.  Please annotate your walker with @By(DataSource.REFERENCE) to perform a by-reference traversal.");

java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java

@@ -36,10 +36,7 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrde
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
-import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
+import org.broadinstitute.sting.gatk.traversals.*;
-import org.broadinstitute.sting.gatk.traversals.TraverseDuplicates;
-import org.broadinstitute.sting.gatk.traversals.TraverseLoci;
-import org.broadinstitute.sting.gatk.traversals.TraverseReads;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
@@ -107,6 +104,8 @@ public abstract class MicroScheduler {
             traversalEngine = new TraverseReads(reads.getReadsFiles(), refFile, rods);            
         } else if (walker instanceof LocusWalker) {
             traversalEngine = new TraverseLoci(reads.getReadsFiles(), refFile, rods);
+        } else if (walker instanceof LocusWindowWalker) {
+            traversalEngine = new TraverseLocusWindows(reads.getReadsFiles(), refFile, rods);  
         } else if (walker instanceof DuplicateWalker) {
             traversalEngine = new TraverseDuplicates(reads.getReadsFiles(), refFile, rods);
         } else {
@@ -184,6 +183,13 @@ public abstract class MicroScheduler {
                         drivingDataSource.getSequenceDictionary(),
                         SHARD_SIZE, maxIterations);
             }
+        } else if (walker instanceof LocusWindowWalker) {
+            if( intervals == null )
+                throw new StingException("Unable to shard: walker is of type LocusWindow, but no intervals were provided");
+            shardStrategy = ShardStrategyFactory.shatter(ShardStrategyFactory.SHATTER_STRATEGY.INTERVAL,
+                    drivingDataSource.getSequenceDictionary(),
+                    SHARD_SIZE,
+                    intervals, maxIterations);
         } else
             throw new StingException("Unable to support walker of type" + walker.getClass().getName());
 

java/src/org/broadinstitute/sting/gatk/traversals/TraverseLocusWindows.java

@@ -47,7 +47,11 @@ public class TraverseLocusWindows extends TraversalEngine {
 
         LocusContext locus = getLocusContext(readView.iterator(), interval);
 
-        String referenceSubsequence = new String(referenceView.getReferenceBases(interval));
+        // The TraverseByLocusWindow expands intervals to cover all reads in a non-standard way.
+        // TODO: Convert this approach to the standard.
+        GenomeLoc expandedInterval = locus.getLocation();
+
+        String referenceSubsequence = new String(referenceView.getReferenceBases(expandedInterval));
 
         // Iterate forward to get all reference ordered data covering this interval
         final RefMetaDataTracker tracker = referenceOrderedDataView.getReferenceOrderedDataAtLocus(locus.getLocation());
@@ -94,4 +98,14 @@ public class TraverseLocusWindows extends TraversalEngine {
         return locus;
     }
 
+    /**
+     * Temporary override of printOnTraversalDone.
+     * TODO: Add some sort of TE.getName() function once all TraversalEngines are ported.
+     * @param sum Result of the computation.
+     * @param <T> Type of the result.
+     */
+    public <T> void printOnTraversalDone( T sum ) {
+        printOnTraversalDone( "intervals", sum );
+    }
+
 }

java/src/org/broadinstitute/sting/gatk/walkers/PrintLocusContextWalker.java

@@ -17,9 +17,9 @@ import net.sf.samtools.SAMRecord;
  * Time: 11:23:14 AM
  * To change this template use File | Settings | File Templates.
  */
-public class PrintLocusContextWalker extends LocusWalker<LocusContext, Integer> implements TreeReducible<Integer> {
+public class PrintLocusContextWalker extends LocusWindowWalker<LocusContext, Integer> implements TreeReducible<Integer> {
-    public LocusContext map(RefMetaDataTracker tracker, char ref, LocusContext context) {
+    public LocusContext map(RefMetaDataTracker tracker, String ref, LocusContext context) {
-        out.printf( "In map: ref = %c, loc = %s, reads = %s%n", ref,
+        out.printf( "In map: ref = %s, loc = %s, reads = %s%n", ref,
                                                                 context.getLocation(),
                                                                 Arrays.deepToString( getReadNames(context.getReads()) ) );
         return context;