GSA-515 Nanoscheduler GSA-550 ThreadSafeMapReduce shouldn't be super interface of TreeReducible

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

@@ -116,7 +116,7 @@ public abstract class MicroScheduler implements MicroSchedulerMBean {
                 return new HierarchicalMicroScheduler(engine, walker, reads, reference, rods, threadAllocation);
             }
         } else {
-            if ( threadAllocation.getNumCPUThreadsPerDataThread() > 1 && ! (walker instanceof ThreadSafeMapReduce) )
+            if ( threadAllocation.getNumCPUThreadsPerDataThread() > 1 && ! (walker instanceof NanoSchedulable) )
                 throw badNT("cnt", engine, walker);
             return new LinearMicroScheduler(engine, walker, reads, reference, rods, threadAllocation);
         }

public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStat.java

@@ -45,7 +45,7 @@ import java.text.NumberFormat;
  */
 @DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
 @Requires({DataSource.READS})
-public class FlagStat extends ReadWalker<FlagStat.FlagStatus, FlagStat.FlagStatus> implements ThreadSafeMapReduce {
+public class FlagStat extends ReadWalker<FlagStat.FlagStatus, FlagStat.FlagStatus> implements NanoSchedulable {
     @Output
     PrintStream out;
 

public/java/src/org/broadinstitute/sting/gatk/walkers/NanoSchedulable.java

@@ -27,5 +27,5 @@ package org.broadinstitute.sting.gatk.walkers;
  * declare that their map function is thread-safe and so multiple
  * map calls can be run in parallel in the same JVM instance.
  */
-public interface ThreadSafeMapReduce {
+public interface NanoSchedulable {
 }

public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java

@@ -52,7 +52,7 @@ import java.util.List;
  * samtools pileup [-f in.ref.fasta] [-t in.ref_list] [-l in.site_list] [-iscg] [-T theta] [-N nHap] [-r pairDiffRate] <in.alignment>
  */
 @DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
-public class Pileup extends LocusWalker<String, Integer> implements TreeReducible<Integer> {
+public class Pileup extends LocusWalker<String, Integer> implements TreeReducible<Integer>, NanoSchedulable {
 
     private static final String verboseDelimiter = "@"; // it's ugly to use "@" but it's literally the only usable character not allowed in read names
 

public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java

@@ -93,7 +93,7 @@ import java.util.*;
 @ReadTransformersMode(ApplicationTime = ReadTransformer.ApplicationTime.HANDLED_IN_WALKER)
 @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = ReadTransformer.ApplicationTime.HANDLED_IN_WALKER)
 @Requires({DataSource.READS, DataSource.REFERENCE})
-public class PrintReads extends ReadWalker<GATKSAMRecord, SAMFileWriter> implements ThreadSafeMapReduce {
+public class PrintReads extends ReadWalker<GATKSAMRecord, SAMFileWriter> implements NanoSchedulable {
 
     @Output(doc="Write output to this BAM filename instead of STDOUT", required = true)
     SAMFileWriter out;

public/java/src/org/broadinstitute/sting/gatk/walkers/TreeReducible.java

@@ -13,7 +13,7 @@ package org.broadinstitute.sting.gatk.walkers;
  * shards of the data can reduce with each other, and the composite result
  * can be reduced with other composite results.
  */
-public interface TreeReducible<ReduceType> extends ThreadSafeMapReduce {
+public interface TreeReducible<ReduceType> {
     /**
      * A composite, 'reduce of reduces' function.
      * @param lhs 'left-most' portion of data in the composite reduce.

public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java

@@ -109,7 +109,7 @@ import java.util.ArrayList;
 @ReadFilters({MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class}) // only look at covered loci, not every loci of the reference file
 @Requires({DataSource.READS, DataSource.REFERENCE}) // filter out all reads with zero or unavailable mapping quality
 @PartitionBy(PartitionType.LOCUS) // this walker requires both -I input.bam and -R reference.fasta
-public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeReducible<Long> {
+public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeReducible<Long>, NanoSchedulable {
     @ArgumentCollection
     private final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection(); // all the command line arguments for BQSR and it's covariates
 

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java

@@ -125,7 +125,7 @@ import java.util.*;
 // TODO -- When LocusIteratorByState gets cleaned up, we should enable multiple @By sources:
 // TODO -- @By( {DataSource.READS, DataSource.REFERENCE_ORDERED_DATA} )
 @Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=250)
-public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, UnifiedGenotyper.UGStatistics> implements TreeReducible<UnifiedGenotyper.UGStatistics>, AnnotatorCompatible {
+public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, UnifiedGenotyper.UGStatistics> implements TreeReducible<UnifiedGenotyper.UGStatistics>, AnnotatorCompatible, NanoSchedulable {
 
     @ArgumentCollection
     private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java

@@ -6,6 +6,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.gatk.walkers.NanoSchedulable;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 
@@ -40,7 +41,7 @@ import java.io.PrintStream;
  *
  */
 @DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
-public class CountLoci extends LocusWalker<Integer, Long> implements TreeReducible<Long> {
+public class CountLoci extends LocusWalker<Integer, Long> implements TreeReducible<Long>, NanoSchedulable {
     @Output(doc="Write count to this file instead of STDOUT")
     PrintStream out;
 

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java

@@ -37,6 +37,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
+import org.broadinstitute.sting.gatk.walkers.NanoSchedulable;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.utils.GenomeLoc;
@@ -73,7 +74,7 @@ import java.util.*;
  *
  */
 @DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
-public class CountRODs extends RodWalker<CountRODs.Datum, Pair<ExpandingArrayList<Long>, Long>> implements TreeReducible<Pair<ExpandingArrayList<Long>, Long>> {
+public class CountRODs extends RodWalker<CountRODs.Datum, Pair<ExpandingArrayList<Long>, Long>> implements TreeReducible<Pair<ExpandingArrayList<Long>, Long>>, NanoSchedulable {
     @Output
     public PrintStream out;
 

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java

@@ -4,9 +4,9 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.DataSource;
+import org.broadinstitute.sting.gatk.walkers.NanoSchedulable;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.Requires;
-import org.broadinstitute.sting.gatk.walkers.ThreadSafeMapReduce;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
@@ -41,7 +41,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
  */
 @DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
 @Requires({DataSource.READS, DataSource.REFERENCE})
-public class CountReads extends ReadWalker<Integer, Integer> implements ThreadSafeMapReduce {
+public class CountReads extends ReadWalker<Integer, Integer> implements NanoSchedulable {
     public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) {
         return 1;
     }