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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
This commit is contained in:
hanna 2009-05-06 23:26:21 +00:00
parent 5136724884
commit dc944ec69b
5 changed files with 20 additions and 13 deletions
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9
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
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@ -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 {

6
java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
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@ -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() {

8
java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
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@ -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);
}
}

8
java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
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@ -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 );
}
}

2
java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
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@ -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;