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

This commit is contained in:
Mark DePristo 2012-09-05 17:37:56 -04:00
parent c5f1ceaa95
commit e11915aa0a
11 changed files with 14 additions and 12 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
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@ -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);
}

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

2
public/java/src/org/broadinstitute/sting/gatk/walkers/ThreadSafeMapReduce.java → public/java/src/org/broadinstitute/sting/gatk/walkers/NanoSchedulable.java
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@ -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 {
}

2
public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java
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@ -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

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

2
public/java/src/org/broadinstitute/sting/gatk/walkers/TreeReducible.java
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@ -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.

2
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
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@ -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

2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -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();

3
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java
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@ -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;

3
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java
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@ -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;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java
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@ -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;
}