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Switched dependencies of GenomeAnalysisTK to depend on GenomeAnalysisEngine. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@656 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-05-11 22:33:00 +00:00
parent ff1b92acc4
commit 052819bed5
8 changed files with 18 additions and 19 deletions
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6
java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
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@ -5,7 +5,7 @@ import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategy; import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategy;
import org.broadinstitute.sting.gatk.dataSources.shards.Shard; import org.broadinstitute.sting.gatk.dataSources.shards.Shard;
import org.broadinstitute.sting.gatk.GenomeAnalysisTK; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.OutputTracker; import org.broadinstitute.sting.gatk.OutputTracker;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
@ -176,7 +176,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Reduce
* the final data streams. * the final data streams.
*/ */
protected void mergeExistingOutput() { protected void mergeExistingOutput() {
OutputTracker outputTracker = GenomeAnalysisTK.Instance.getOutputTracker(); OutputTracker outputTracker = GenomeAnalysisEngine.instance.getOutputTracker();
while( isOutputMergeReady() ) while( isOutputMergeReady() )
outputMergeTasks.remove().mergeInto( outputTracker.getGlobalOutStream(), outputTracker.getGlobalErrStream() ); outputMergeTasks.remove().mergeInto( outputTracker.getGlobalOutStream(), outputTracker.getGlobalErrStream() );
} }
@ -185,7 +185,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Reduce
* Merge any output that hasn't yet been taken care of by the blocking thread. * Merge any output that hasn't yet been taken care of by the blocking thread.
*/ */
protected void mergeRemainingOutput() { protected void mergeRemainingOutput() {
OutputTracker outputTracker = GenomeAnalysisTK.Instance.getOutputTracker(); OutputTracker outputTracker = GenomeAnalysisEngine.instance.getOutputTracker();
while( outputMergeTasks.size() > 0 ) { while( outputMergeTasks.size() > 0 ) {
OutputMerger outputMerger = outputMergeTasks.remove(); OutputMerger outputMerger = outputMergeTasks.remove();
synchronized(outputMerger) { synchronized(outputMerger) {

4
java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
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@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.executive;
import org.broadinstitute.sting.gatk.dataSources.providers.ShardDataProvider; import org.broadinstitute.sting.gatk.dataSources.providers.ShardDataProvider;
import org.broadinstitute.sting.gatk.dataSources.shards.Shard; import org.broadinstitute.sting.gatk.dataSources.shards.Shard;
import org.broadinstitute.sting.gatk.traversals.TraverseLociByReference; import org.broadinstitute.sting.gatk.traversals.TraverseLociByReference;
import org.broadinstitute.sting.gatk.GenomeAnalysisTK; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.OutputTracker; import org.broadinstitute.sting.gatk.OutputTracker;
import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.walkers.Walker;
@ -44,7 +44,7 @@ public class ShardTraverser implements Callable {
public Object call() { public Object call() {
Object accumulator = walker.reduceInit(); Object accumulator = walker.reduceInit();
OutputTracker outputTracker = GenomeAnalysisTK.Instance.getOutputTracker(); OutputTracker outputTracker = GenomeAnalysisEngine.instance.getOutputTracker();
outputTracker.setLocalStreams( output.getOutStream(), output.getErrStream() ); outputTracker.setLocalStreams( output.getOutStream(), output.getErrStream() );
try { try {

10
java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
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@ -5,7 +5,7 @@ import java.util.HashMap;
import java.util.Map; import java.util.Map;
import java.util.List; import java.util.List;
import org.broadinstitute.sting.gatk.GenomeAnalysisTK; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Pair; import org.broadinstitute.sting.utils.Pair;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
@ -33,8 +33,8 @@ public abstract class Walker<MapType, ReduceType> {
protected PrintStream err = null; protected PrintStream err = null;
protected Walker() { protected Walker() {
if( GenomeAnalysisTK.Instance != null ) { if( GenomeAnalysisEngine.instance != null ) {
GenomeAnalysisTK gatk = GenomeAnalysisTK.Instance; GenomeAnalysisEngine gatk = GenomeAnalysisEngine.instance;
out = new PrintStream( gatk.getOutputTracker().getOutStream() ); out = new PrintStream( gatk.getOutputTracker().getOutStream() );
err = new PrintStream( gatk.getOutputTracker().getErrStream() ); err = new PrintStream( gatk.getOutputTracker().getErrStream() );
} }
@ -50,8 +50,8 @@ public abstract class Walker<MapType, ReduceType> {
* team. * team.
* @return The genome analysis toolkit. * @return The genome analysis toolkit.
*/ */
protected GenomeAnalysisTK getToolkit() { protected GenomeAnalysisEngine getToolkit() {
return GenomeAnalysisTK.Instance; return GenomeAnalysisEngine.instance;
} }
public void initialize() { } public void initialize() { }

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageBySample.java
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@ -20,7 +20,7 @@ public class CoverageBySample extends LocusWalker<String, String>
public void initialize() public void initialize()
{ {
GenomeAnalysisTK toolkit = this.getToolkit(); GenomeAnalysisEngine toolkit = this.getToolkit();
SAMFileHeader header = toolkit.getSamReader().getFileHeader(); SAMFileHeader header = toolkit.getSamReader().getFileHeader();
List<SAMReadGroupRecord> read_groups = header.getReadGroups(); List<SAMReadGroupRecord> read_groups = header.getReadGroups();

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/ListSampleIds.java
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@ -4,7 +4,7 @@ package org.broadinstitute.sting.playground.gatk.walkers;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMReadGroupRecord;
import org.broadinstitute.sting.gatk.GenomeAnalysisTK; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.LocusContext; import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.LocusWalker;
@ -15,7 +15,7 @@ public class ListSampleIds extends LocusWalker<Boolean, Boolean>
{ {
public void initialize() public void initialize()
{ {
GenomeAnalysisTK toolkit = this.getToolkit(); GenomeAnalysisEngine toolkit = this.getToolkit();
SAMFileHeader header = toolkit.getEngine().getSAMHeader(); SAMFileHeader header = toolkit.getEngine().getSAMHeader();
List<SAMReadGroupRecord> read_groups = header.getReadGroups(); List<SAMReadGroupRecord> read_groups = header.getReadGroups();

6
java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java
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@ -4,7 +4,7 @@ package org.broadinstitute.sting.playground.gatk.walkers;
import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.GenomeAnalysisTK; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.LocusContext; import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.LocusWalker;
@ -32,12 +32,12 @@ public class PoolCaller extends LocusWalker<AlleleFrequencyEstimate, String>
public void initialize() public void initialize()
{ {
GenomeAnalysisTK toolkit = this.getToolkit(); GenomeAnalysisEngine toolkit = this.getToolkit();
this.header = toolkit.getEngine().getSAMHeader(); this.header = toolkit.getEngine().getSAMHeader();
List<SAMReadGroupRecord> read_groups = header.getReadGroups(); List<SAMReadGroupRecord> read_groups = header.getReadGroups();
/* /*
GenomeAnalysisTK toolkit = this.getToolkit(); GenomeAnalysisEngine toolkit = this.getToolkit();
SAMFileHeader header = toolkit.getSamReader().getFileHeader(); SAMFileHeader header = toolkit.getSamReader().getFileHeader();
List<SAMReadGroupRecord> read_groups = header.getReadGroups(); List<SAMReadGroupRecord> read_groups = header.getReadGroups();
*/ */

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCallingExperiment.java
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@ -33,7 +33,7 @@ public class PoolCallingExperiment extends LocusWalker<AlleleFrequencyEstimate,
public void initialize() public void initialize()
{ {
GenomeAnalysisTK toolkit = this.getToolkit(); GenomeAnalysisEngine toolkit = this.getToolkit();
SAMFileHeader header = toolkit.getEngine().getSAMHeader(); SAMFileHeader header = toolkit.getEngine().getSAMHeader();
List<SAMReadGroupRecord> read_groups = header.getReadGroups(); List<SAMReadGroupRecord> read_groups = header.getReadGroups();

3
java/src/org/broadinstitute/sting/playground/gatk/walkers/PopPriorWalker.java
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@ -1,7 +1,6 @@
package org.broadinstitute.sting.playground.gatk.walkers; package org.broadinstitute.sting.playground.gatk.walkers;
import org.broadinstitute.sting.gatk.LocusContext; import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.GenomeAnalysisTK;
import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.rodDbSNP; import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
@ -420,4 +419,4 @@ public class PopPriorWalker extends LocusWalker<Integer, Integer> {
} }
} }