From 8ee0f91904433e89cef8a3a3599504e5a71390da Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Mon, 3 Oct 2011 09:50:01 -0700
Subject: [PATCH] Remove residual processing tracker arguments

---
 .../arguments/GATKArgumentCollection.java     | 34 -------------------
 .../executive/HierarchicalMicroScheduler.java |  5 ---
 2 files changed, 39 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
index fd39d46b0..9ce402cf3 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
@@ -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;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
index 3b9e35311..a07f735fa 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
@@ -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 ) {