First stage of ROD plumbing for MicroScheduler.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@614 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -105,6 +105,9 @@ public class GenomeAnalysisTK extends CommandLineProgram {
     @Argument(fullName="numthreads",shortName="nt",doc="How many threads should be allocated to running this analysis.",required=false)    
     protected int numThreads = 1;
 
+    @Argument(fullName="rodBind",shortName="B",doc="",required=false)
+    protected ArrayList<String> ROD_BINDINGS = new ArrayList<String>();    
+
     /**
      * Collection of output streams used by the walker.
      */
@@ -115,8 +118,6 @@ public class GenomeAnalysisTK extends CommandLineProgram {
      */
     private static Logger logger = Logger.getLogger(GenomeAnalysisTK.class);
 
-    @Argument(fullName="rodBind",shortName="B",doc="",required=false)    
-    protected static ArrayList<String> ROD_BINDINGS = new ArrayList<String>();
 
 
     /**
@@ -168,7 +169,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
      * @param type
      * @param file
      */
-    private static void bindConvenienceRods(final String name, final String type, final String file )
+    private void bindConvenienceRods(final String name, final String type, final String file )
     {
         ROD_BINDINGS.add(name);
         ROD_BINDINGS.add(type);
@@ -247,7 +248,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
                     //                                  is not filtered.
                     if( !DISABLE_THREADING ) {
                         logger.warn("Preliminary threading support ENABLED");
-                        microScheduler = MicroScheduler.create( walker, INPUT_FILES, REF_FILE_ARG, numThreads );
+                        microScheduler = MicroScheduler.create( walker, INPUT_FILES, REF_FILE_ARG, rods, numThreads );
                         this.engine = microScheduler.getTraversalEngine();
                     }
                     else {

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

@@ -9,6 +9,8 @@ import org.broadinstitute.sting.gatk.dataSources.shards.Shard;
 import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.SAMDataSource;
 import org.broadinstitute.sting.gatk.GenomeAnalysisTK;
 import org.broadinstitute.sting.gatk.OutputTracker;
+import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.threading.ThreadPoolMonitor;
@@ -58,12 +60,12 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Reduce
      * @param refFile Reference for driving the traversal.
      * @param nThreadsToUse maximum number of threads to use to do the work
      */
-    protected HierarchicalMicroScheduler( List<File> reads, File refFile, int nThreadsToUse ) {
+    protected HierarchicalMicroScheduler( List<File> reads, File refFile, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods, int nThreadsToUse ) {
         super( reads, refFile );
 
 
         this.threadPool = Executors.newFixedThreadPool(nThreadsToUse);        
-        traversalEngine = new TraverseLociByReference( reads, refFile, new java.util.ArrayList() );
+        traversalEngine = new TraverseLociByReference( reads, refFile, rods );
     }
 
     public TraversalEngine getTraversalEngine() {

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

@@ -14,6 +14,8 @@ import org.broadinstitute.sting.gatk.traversals.TraverseReads;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
+import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
 import java.io.File;
@@ -37,16 +39,16 @@ public class LinearMicroScheduler extends MicroScheduler {
      * @param reads   Reads file(s) to process.
      * @param refFile Reference for driving the traversal.
      */
-    protected LinearMicroScheduler(List<File> reads, File refFile, Walker walker) {
+    protected LinearMicroScheduler(List<File> reads, File refFile, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods, Walker walker) {
         super(reads, refFile);
 
         // determine if we're a read walker: they get a slightly different, but not in any way worse execute methodology. I pinky swear...
         isAReadWalker = (walker instanceof ReadWalker) ? true : false;
 
         if (isAReadWalker) {
-            traversalEngine = new TraverseByReads(reads, refFile, new java.util.ArrayList());
+            traversalEngine = new TraverseByReads(reads, refFile, rods);
         } else {
-            traversalEngine = new TraverseLociByReference(reads, refFile, new java.util.ArrayList());
+            traversalEngine = new TraverseLociByReference(reads, refFile, rods);
         }
     }
 

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

@@ -9,6 +9,8 @@ import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.SimpleDataSou
 import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.gatk.walkers.Walker;
+import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 
@@ -42,14 +44,14 @@ public abstract class MicroScheduler {
      * @param nThreadsToUse Number of threads to utilize.
      * @return The best-fit microscheduler.
      */
-    public static MicroScheduler create( Walker walker, List<File> reads, File ref, int nThreadsToUse ) {
+    public static MicroScheduler create( Walker walker, List<File> reads, File ref, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods, int nThreadsToUse ) {
         if( walker instanceof TreeReducible && nThreadsToUse > 1 ) {
             logger.info("Creating hierarchical microscheduler");
-            return new HierarchicalMicroScheduler( reads, ref, nThreadsToUse );
+            return new HierarchicalMicroScheduler( reads, ref, rods, nThreadsToUse );
         }
         else {
             logger.info("Creating linear microscheduler");
-            return new LinearMicroScheduler( reads, ref, walker );
+            return new LinearMicroScheduler( reads, ref, rods, walker );
         }
     }
 

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

@@ -76,7 +76,7 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
     // Given result of map function
     public Integer reduceInit() { return 0; }
     public Integer reduce(Integer value, Integer sum) {
-        return reduce(sum,value);
+        return treeReduce(sum,value);
     }
     public Integer treeReduce(Integer lhs, Integer rhs) {
         return lhs + rhs;