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Remove residual processing tracker arguments

This commit is contained in:
Mark DePristo 2011-10-03 09:50:01 -07:00
parent 89ac50e86e
commit 8ee0f91904
2 changed files with 0 additions and 39 deletions
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34
public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -218,26 +218,6 @@ public class GATKArgumentCollection {
// distributed GATK arguments
//
// --------------------------------------------------------------------------------------------------------------
@Element(required=false)
@Argument(fullName="processingTracker",shortName="C",doc="A lockable, shared file for coordinating distributed GATK runs",required=false)
@Hidden
public File processingTrackerFile = null;
@Element(required=false)
@Argument(fullName="restartProcessingTracker",shortName="RPT",doc="Should we delete the processing tracker file at startup?",required=false)
@Hidden
public boolean restartProcessingTracker = false;
@Element(required=false)
@Argument(fullName="processingTrackerStatusFile",shortName="CSF",doc="If provided, a detailed accounting of the state of the process tracker is written to this file. For debugging, only",required=false)
@Hidden
public File processingTrackerStatusFile = null;
@Element(required=false)
@Argument(fullName="processingTrackerID",shortName="CID",doc="If provided, an integer ID (starting at 1) indicating a unique id for this process within the distributed GATK group",required=false)
@Hidden
public int processTrackerID = -1;
@Element(required = false)
@Argument(fullName="allow_intervals_with_unindexed_bam",doc="Allow interval processing with an unsupported BAM. NO INTEGRATION TESTS are available. Use at your own risk.",required=false)
@Hidden
@ -405,20 +385,6 @@ public class GATKArgumentCollection {
(other.performanceLog != null && !other.performanceLog.equals(this.performanceLog)))
return false;
if ((other.processingTrackerFile == null && this.processingTrackerFile != null) ||
(other.processingTrackerFile != null && !other.processingTrackerFile.equals(this.processingTrackerFile)))
return false;
if ((other.processingTrackerStatusFile == null && this.processingTrackerStatusFile != null) ||
(other.processingTrackerStatusFile != null && !other.processingTrackerStatusFile.equals(this.processingTrackerStatusFile)))
return false;
if ( restartProcessingTracker != other.restartProcessingTracker )
return false;
if ( processTrackerID != other.processTrackerID )
return false;
if (allowIntervalsWithUnindexedBAM != other.allowIntervalsWithUnindexedBAM)
return false;

5
public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
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@ -84,12 +84,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
*/
protected HierarchicalMicroScheduler(GenomeAnalysisEngine engine, Walker walker, SAMDataSource reads, IndexedFastaSequenceFile reference, Collection<ReferenceOrderedDataSource> rods, int nThreadsToUse ) {
super(engine, walker, reads, reference, rods);
this.threadPool = Executors.newFixedThreadPool(nThreadsToUse);
if (engine.getArguments().processingTrackerFile != null) {
throw new UserException.BadArgumentValue("-C", "Distributed GATK calculations currently not supported in multi-threaded mode. Complain to Mark depristo@broadinstitute.org to implement and test this code path");
}
}
public Object execute( Walker walker, ShardStrategy shardStrategy ) {