From 052819bed5cac74417894f397239a49ed1a1af40 Mon Sep 17 00:00:00 2001 From: hanna Date: Mon, 11 May 2009 22:33:00 +0000 Subject: [PATCH] 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 --- .../gatk/executive/HierarchicalMicroScheduler.java | 6 +++--- .../sting/gatk/executive/ShardTraverser.java | 4 ++-- .../org/broadinstitute/sting/gatk/walkers/Walker.java | 10 +++++----- .../playground/gatk/walkers/CoverageBySample.java | 2 +- .../sting/playground/gatk/walkers/ListSampleIds.java | 4 ++-- .../sting/playground/gatk/walkers/PoolCaller.java | 6 +++--- .../playground/gatk/walkers/PoolCallingExperiment.java | 2 +- .../sting/playground/gatk/walkers/PopPriorWalker.java | 3 +-- 8 files changed, 18 insertions(+), 19 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java b/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java index c98ad4f18..b98b30928 100755 --- a/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java +++ b/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java @@ -5,7 +5,7 @@ import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategy; 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.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData; @@ -176,7 +176,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Reduce * the final data streams. */ protected void mergeExistingOutput() { - OutputTracker outputTracker = GenomeAnalysisTK.Instance.getOutputTracker(); + OutputTracker outputTracker = GenomeAnalysisEngine.instance.getOutputTracker(); while( isOutputMergeReady() ) 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. */ protected void mergeRemainingOutput() { - OutputTracker outputTracker = GenomeAnalysisTK.Instance.getOutputTracker(); + OutputTracker outputTracker = GenomeAnalysisEngine.instance.getOutputTracker(); while( outputMergeTasks.size() > 0 ) { OutputMerger outputMerger = outputMergeTasks.remove(); synchronized(outputMerger) { diff --git a/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java b/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java index 2d828f6ac..93d8f3236 100755 --- a/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java +++ b/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.executive; import org.broadinstitute.sting.gatk.dataSources.providers.ShardDataProvider; import org.broadinstitute.sting.gatk.dataSources.shards.Shard; 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.walkers.Walker; @@ -44,7 +44,7 @@ public class ShardTraverser implements Callable { public Object call() { Object accumulator = walker.reduceInit(); - OutputTracker outputTracker = GenomeAnalysisTK.Instance.getOutputTracker(); + OutputTracker outputTracker = GenomeAnalysisEngine.instance.getOutputTracker(); outputTracker.setLocalStreams( output.getOutStream(), output.getErrStream() ); try { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java b/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java index aceb10672..999b35764 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java @@ -5,7 +5,7 @@ import java.util.HashMap; import java.util.Map; 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.Pair; import org.apache.log4j.Logger; @@ -33,8 +33,8 @@ public abstract class Walker { protected PrintStream err = null; protected Walker() { - if( GenomeAnalysisTK.Instance != null ) { - GenomeAnalysisTK gatk = GenomeAnalysisTK.Instance; + if( GenomeAnalysisEngine.instance != null ) { + GenomeAnalysisEngine gatk = GenomeAnalysisEngine.instance; out = new PrintStream( gatk.getOutputTracker().getOutStream() ); err = new PrintStream( gatk.getOutputTracker().getErrStream() ); } @@ -50,8 +50,8 @@ public abstract class Walker { * team. * @return The genome analysis toolkit. */ - protected GenomeAnalysisTK getToolkit() { - return GenomeAnalysisTK.Instance; + protected GenomeAnalysisEngine getToolkit() { + return GenomeAnalysisEngine.instance; } public void initialize() { } diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageBySample.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageBySample.java index 5063c394f..c51c31eb2 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageBySample.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageBySample.java @@ -20,7 +20,7 @@ public class CoverageBySample extends LocusWalker public void initialize() { - GenomeAnalysisTK toolkit = this.getToolkit(); + GenomeAnalysisEngine toolkit = this.getToolkit(); SAMFileHeader header = toolkit.getSamReader().getFileHeader(); List read_groups = header.getReadGroups(); diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ListSampleIds.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ListSampleIds.java index 710402b09..b0c7b0dce 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ListSampleIds.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ListSampleIds.java @@ -4,7 +4,7 @@ package org.broadinstitute.sting.playground.gatk.walkers; import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMFileHeader; 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.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.LocusWalker; @@ -15,7 +15,7 @@ public class ListSampleIds extends LocusWalker { public void initialize() { - GenomeAnalysisTK toolkit = this.getToolkit(); + GenomeAnalysisEngine toolkit = this.getToolkit(); SAMFileHeader header = toolkit.getEngine().getSAMHeader(); List read_groups = header.getReadGroups(); diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java index 67845a8bb..b57c287f8 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java @@ -4,7 +4,7 @@ package org.broadinstitute.sting.playground.gatk.walkers; import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMReadGroupRecord; 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.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.LocusWalker; @@ -32,12 +32,12 @@ public class PoolCaller extends LocusWalker public void initialize() { - GenomeAnalysisTK toolkit = this.getToolkit(); + GenomeAnalysisEngine toolkit = this.getToolkit(); this.header = toolkit.getEngine().getSAMHeader(); List read_groups = header.getReadGroups(); /* - GenomeAnalysisTK toolkit = this.getToolkit(); + GenomeAnalysisEngine toolkit = this.getToolkit(); SAMFileHeader header = toolkit.getSamReader().getFileHeader(); List read_groups = header.getReadGroups(); */ diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCallingExperiment.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCallingExperiment.java index 94786e5f1..27d7590f6 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCallingExperiment.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCallingExperiment.java @@ -33,7 +33,7 @@ public class PoolCallingExperiment extends LocusWalker read_groups = header.getReadGroups(); diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PopPriorWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PopPriorWalker.java index 7a2f6f3a5..ec631066b 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PopPriorWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PopPriorWalker.java @@ -1,7 +1,6 @@ package org.broadinstitute.sting.playground.gatk.walkers; import org.broadinstitute.sting.gatk.LocusContext; -import org.broadinstitute.sting.gatk.GenomeAnalysisTK; import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.refdata.rodDbSNP; @@ -420,4 +419,4 @@ public class PopPriorWalker extends LocusWalker { } -} \ No newline at end of file +}