Moving StingException

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4262 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/alignment/Alignment.java

@@ -2,7 +2,6 @@ package org.broadinstitute.sting.alignment;
 
 import net.sf.samtools.*;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.Utils;
 

java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java

@@ -30,7 +30,6 @@ import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
 import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;

java/src/org/broadinstitute/sting/alignment/bwa/BWAConfiguration.java

@@ -1,7 +1,5 @@
 package org.broadinstitute.sting.alignment.bwa;
 
-import org.broadinstitute.sting.utils.StingException;
-
 /**
  * Configuration for the BWA/C aligner.
  *

java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java

@@ -1,8 +1,6 @@
 package org.broadinstitute.sting.alignment.bwa;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
 import org.broadinstitute.sting.alignment.reference.bwt.BWT;

java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java

@@ -3,7 +3,6 @@ package org.broadinstitute.sting.alignment.bwa.c;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMFileHeader;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.alignment.Alignment;
 import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
 import org.broadinstitute.sting.alignment.bwa.BWTFiles;

java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java

@@ -3,7 +3,6 @@ package org.broadinstitute.sting.alignment.bwa.java;
 import org.broadinstitute.sting.alignment.Aligner;
 import org.broadinstitute.sting.alignment.Alignment;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.BaseUtils;
 
 import java.io.File;

java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java

@@ -1,8 +1,6 @@
 package org.broadinstitute.sting.alignment.bwa.java;
 
-import org.broadinstitute.sting.alignment.bwa.java.AlignmentState;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.Deque;
 import java.util.ArrayDeque;

java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java

@@ -1,11 +1,7 @@
 package org.broadinstitute.sting.alignment.bwa.java;
 
 import org.broadinstitute.sting.alignment.Alignment;
-import org.broadinstitute.sting.alignment.bwa.java.BWAJavaAligner;
-import org.broadinstitute.sting.alignment.bwa.java.AlignmentMatchSequence;
-import org.broadinstitute.sting.alignment.bwa.java.AlignmentState;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import net.sf.samtools.Cigar;
 
 /**

java/src/org/broadinstitute/sting/alignment/reference/bwt/BWT.java

@@ -2,7 +2,6 @@ package org.broadinstitute.sting.alignment.reference.bwt;
 
 import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 /**
  * Represents the Burrows-Wheeler Transform of a reference sequence.

java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java

@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream;
 import org.broadinstitute.sting.alignment.reference.packing.BasePackedInputStream;
 import org.broadinstitute.sting.alignment.reference.packing.PackUtils;

java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java

@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream;
 import org.broadinstitute.sting.alignment.reference.packing.BasePackedOutputStream;
 

java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java

@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.*;
 

java/src/org/broadinstitute/sting/alignment/reference/bwt/Counts.java

@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.HashMap;
 import java.util.Map;

java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java

@@ -32,7 +32,6 @@ import net.sf.picard.reference.ReferenceSequence;
 import java.io.*;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
 
 /**

java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java

@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.Comparator;
 import java.util.TreeSet;

java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java

@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream;
 import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
 

java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java

@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream;
 
 import java.io.*;

java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java

@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.packing;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.io.*;
 import java.nio.ByteOrder;

java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java

@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.packing;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.io.*;
 import java.nio.ByteBuffer;

java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java

@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.packing;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.io.File;
 import java.io.IOException;

java/src/org/broadinstitute/sting/commandline/ArgumentDefinition.java

@@ -25,7 +25,6 @@
 
 package org.broadinstitute.sting.commandline;
 
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
 
 import java.lang.annotation.Annotation;

java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java

@@ -26,7 +26,6 @@
 package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.List;
 import java.util.Collections;

java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java

@@ -26,7 +26,6 @@
 package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.Set;
 import java.util.HashSet;

java/src/org/broadinstitute/sting/commandline/ArgumentIOType.java

@@ -25,7 +25,6 @@
 package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.lang.annotation.Annotation;
 

java/src/org/broadinstitute/sting/commandline/ArgumentSource.java

@@ -26,10 +26,8 @@
 package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.lang.reflect.Field;
-import java.lang.annotation.Annotation;
 import java.util.Arrays;
 import java.util.List;
 

java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java

@@ -26,8 +26,6 @@
 package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.classloader.JVMUtils;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 

java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java

@@ -29,14 +29,8 @@ import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.commandline.CommandLineProgram;
 import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
 import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
-import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.text.XReadLines;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.PrintStream;
 import java.util.*;
 
 import net.sf.picard.filter.SamRecordFilter;

java/src/org/broadinstitute/sting/gatk/ReadMetrics.java

@@ -31,7 +31,6 @@ import java.util.HashMap;
 import java.util.Collections;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 /**
  * Holds a bunch of basic information about the traversal.

java/src/org/broadinstitute/sting/gatk/WalkerManager.java

@@ -32,7 +32,6 @@ import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 import org.broadinstitute.sting.utils.help.DescriptionTaglet;
 import org.broadinstitute.sting.utils.help.DisplayNameTaglet;

java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java

@@ -28,7 +28,6 @@ package org.broadinstitute.sting.gatk.arguments;
 import net.sf.samtools.SAMFileReader;
 import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Input;
@@ -77,7 +76,7 @@ public class GATKArgumentCollection {
 
     @Element(required = false)
     @Argument(fullName = "phone_home", shortName = "et", doc="What kind of GATK run report should we generate?  Standard is the default, can be verbose or NO_ET so nothing is posted to the run repository", required = false)
-    public GATKRunReport.PhoneHomeOption phoneHomeType = GATKRunReport.PhoneHomeOption.NO_ET;
+    public GATKRunReport.PhoneHomeOption phoneHomeType = GATKRunReport.PhoneHomeOption.STANDARD;
 
     @ElementList(required = false)
     @Argument(fullName = "read_filter", shortName = "rf", doc = "Specify filtration criteria to apply to each read individually.", required = false)

java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java

@@ -28,10 +28,8 @@ package org.broadinstitute.sting.gatk.contexts;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
 
 import java.util.*;
 

java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java

@@ -27,7 +27,6 @@ package org.broadinstitute.sting.gatk.contexts;
 
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.BaseUtils;
 import net.sf.samtools.util.StringUtil;
 

java/src/org/broadinstitute/sting/gatk/datasources/DataSourceGenerationException.java

@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 /**
  * User: aaron

java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java

@@ -3,15 +3,11 @@ package org.broadinstitute.sting.gatk.datasources.providers;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.walkers.Window;
 import org.broadinstitute.sting.gatk.walkers.Reference;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import net.sf.picard.reference.ReferenceSequence;
-import net.sf.samtools.util.StringUtil;
-
-import java.util.List;
 /*
  * Copyright (c) 2009 The Broad Institute
  *

java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java

@@ -1,11 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
 import net.sf.samtools.SAMRecord;
-import net.sf.samtools.SAMSequenceRecord;
-import net.sf.samtools.util.StringUtil;
-import net.sf.picard.reference.ReferenceSequence;
-import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;

java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java

@@ -3,7 +3,6 @@ package org.broadinstitute.sting.gatk.datasources.providers;
 import org.broadinstitute.sting.gatk.datasources.shards.Shard;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.ArrayList;
 import java.util.List;

java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java

@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources.shards;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.gatk.ReadMetrics;
 import org.broadinstitute.sting.gatk.ReadProperties;

java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShardStrategy.java

@@ -1,16 +1,12 @@
 package org.broadinstitute.sting.gatk.datasources.shards;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
 
 import java.util.Iterator;
 import java.util.NoSuchElementException;
 import java.util.List;
 
-import net.sf.samtools.SAMSequenceDictionary;
-
 /**
  * Create a giant shard representing all the data in the input BAM(s).
  *

java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactory.java

@@ -3,7 +3,6 @@ package org.broadinstitute.sting.gatk.datasources.shards;
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
 

java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ResourcePool.java

@@ -2,7 +2,6 @@ package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
 
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 
 import java.util.List;

java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceLoadException.java

@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 /**
  *

java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceSplitException.java

@@ -3,7 +3,6 @@ package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
 
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 
 /*

java/src/org/broadinstitute/sting/gatk/datasources/utilities/BAMFileStat.java

@@ -28,7 +28,6 @@ package org.broadinstitute.sting.gatk.datasources.utilities;
 import org.broadinstitute.sting.commandline.CommandLineProgram;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.instrumentation.Sizeof;
 
 import java.io.File;

java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java

@@ -33,7 +33,6 @@ import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.ArrayList;
 import java.util.List;

java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java

@@ -8,9 +8,7 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.io.*;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.ReadMetrics;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.threading.ThreadPoolMonitor;
 
 import javax.management.MBeanServer;

java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java

@@ -9,7 +9,6 @@ import org.broadinstitute.sting.gatk.io.ThreadLocalOutputTracker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.concurrent.Callable;
 /**

java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java

@@ -2,7 +2,6 @@ package org.broadinstitute.sting.gatk.executive;
 
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.concurrent.Callable;
 import java.util.concurrent.Future;

java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java

@@ -27,7 +27,6 @@ package org.broadinstitute.sting.gatk.io;
 
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.commandline.ArgumentSource;
 import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder;
 import org.broadinstitute.sting.gatk.walkers.Walker;
@@ -36,7 +35,6 @@ import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub;
 import org.broadinstitute.sting.gatk.io.stubs.Stub;
 import org.broadinstitute.sting.gatk.io.storage.StorageFactory;
 import org.broadinstitute.sting.gatk.io.storage.Storage;
-import org.broadinstitute.sting.gatk.io.storage.OutputStreamStorage;
 
 import java.io.*;
 import java.lang.reflect.Field;

java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java

@@ -30,7 +30,6 @@ import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub;
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub;
 import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.io.File;
 

java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java

@@ -26,16 +26,12 @@
 package org.broadinstitute.sting.gatk.io.stubs;
 
 import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 
 import java.io.OutputStream;
 import java.io.File;
 import java.lang.reflect.Constructor;
-import java.lang.reflect.InvocationTargetException;
-import java.lang.reflect.Field;
 
 /**
  * Insert an OutputStreamStub instead of a full-fledged concrete OutputStream implementations.

java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java

@@ -29,11 +29,9 @@ import net.sf.samtools.util.CloseableIterator;
 
 import java.util.Queue;
 import java.util.LinkedList;
-import java.util.Iterator;
 import java.util.NoSuchElementException;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 /**
  * Buffers access to a large stream of reads, replenishing the buffer only when the reads  

java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapter.java

@@ -5,9 +5,6 @@ import net.sf.samtools.util.CloseableIterator;
 
 import java.util.Iterator;
 
-import org.broadinstitute.sting.gatk.ReadProperties;
-import org.broadinstitute.sting.utils.StingException;
-
 /**
  *
  * User: aaron

java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java

@@ -31,7 +31,6 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
 import org.simpleframework.xml.Element;
 import org.simpleframework.xml.ElementList;

java/src/org/broadinstitute/sting/gatk/refdata/IntervalRod.java

@@ -2,9 +2,7 @@ package org.broadinstitute.sting.gatk.refdata;
 
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.StingException;
 
-import java.util.Iterator;
 import java.io.File;
 import java.io.IOException;
 

java/src/org/broadinstitute/sting/gatk/refdata/PlinkRod.java

@@ -4,7 +4,6 @@ import org.broad.tribble.util.variantcontext.Allele;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.io.*;
 import java.util.*;

java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java

@@ -4,7 +4,6 @@ import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.*;
 

java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java

@@ -7,7 +7,6 @@ import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.ArrayList;
 import java.util.List;

java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackCreationException.java

@@ -24,7 +24,6 @@
 package org.broadinstitute.sting.gatk.refdata.tracks;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 
 /**

java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java

@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.analyzeannotations;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.Comparator;
 

java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java

@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.fasta;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.io.PrintStream;
 

java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java

@@ -26,7 +26,6 @@
 package org.broadinstitute.sting.gatk.walkers.filters;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.*;
 

java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java

@@ -4,7 +4,6 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMFileWriter;
 

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java

@@ -8,7 +8,6 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
 import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 
 @Analysis(name = "Count Variants", description = "Counts different classes of variants in the sample")

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelLengthHistogram.java

@@ -8,7 +8,6 @@ import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
 import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
 import org.broadinstitute.sting.playground.utils.report.utils.TableType;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 /**
  * IF THERE IS NO JAVADOC RIGHT HERE, YELL AT chartl

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java

@@ -9,7 +9,6 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
 import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.List;
 import java.util.Arrays;

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/SimpleMetricsByAC.java

@@ -9,7 +9,6 @@ import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
 import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
 import org.broadinstitute.sting.playground.utils.report.utils.TableType;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.ArrayList;
 

java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java

@@ -25,22 +25,14 @@
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.*;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.Reference;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.gatk.walkers.Window;
-import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
 
 import java.io.PrintStream;
 import java.util.*;

java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java

@@ -37,7 +37,6 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.io.PrintStream;
 import java.util.*;

java/src/org/broadinstitute/sting/oneoffprojects/walkers/DesignFileGeneratorWalker.java

@@ -10,7 +10,6 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.commandline.Output;
 
 import java.util.*;

java/src/org/broadinstitute/sting/oneoffprojects/walkers/DownsamplingValidationWalker.java

@@ -31,7 +31,6 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.commandline.Argument;
 
 import java.util.ArrayList;

java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java

@@ -13,7 +13,6 @@ import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 
 import java.io.File;

java/src/org/broadinstitute/sting/playground/analyzeconcordance/AnalyzeConcordance.java

@@ -29,7 +29,6 @@ import org.broadinstitute.sting.commandline.CommandLineProgram;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.PathUtils;
 import org.broadinstitute.sting.playground.utils.ProcessUtils;

java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java

@@ -40,7 +40,6 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
 import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.pileup.PileupElement;

java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/CoverageAcrossBaitsWalker.java

@@ -36,7 +36,6 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/Biallele.java

@@ -26,7 +26,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.phasing;
 import org.broad.tribble.util.variantcontext.Allele;
 import org.broad.tribble.util.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
+
 import java.util.ArrayList;
 import java.util.List;
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/BialleleSNP.java

@@ -27,7 +27,6 @@ import org.broad.tribble.util.variantcontext.Allele;
 import org.broad.tribble.util.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 public class BialleleSNP extends Biallele {
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java

@@ -11,7 +11,6 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.io.*;
 import java.math.BigInteger;

java/src/org/broadinstitute/sting/playground/utils/ProcessUtils.java

@@ -27,7 +27,6 @@ package org.broadinstitute.sting.playground.utils;
 
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.utils.StingException;
 import org.apache.log4j.Logger;
 
 /**

java/src/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScanner.java

@@ -27,11 +27,9 @@ import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
 import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
 import org.broadinstitute.sting.playground.utils.report.tags.Param;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.lang.annotation.Annotation;
 import java.lang.reflect.Field;
-import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.Map;
 

java/src/org/broadinstitute/sting/playground/utils/report/ReportMarshaller.java

@@ -28,7 +28,6 @@ import org.broadinstitute.sting.playground.utils.report.templates.ReportFormat;
 import org.broadinstitute.sting.playground.utils.report.utils.ComplexDataUtils;
 import org.broadinstitute.sting.playground.utils.report.utils.Node;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.io.*;
 import java.lang.reflect.Field;

java/src/org/broadinstitute/sting/playground/utils/report/VE2ReportFactory.java

@@ -2,7 +2,6 @@ package org.broadinstitute.sting.playground.utils.report;
 
 import org.broadinstitute.sting.playground.utils.report.templates.*;
 import org.broadinstitute.sting.playground.utils.report.utils.Node;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 
 import java.io.*;

java/src/org/broadinstitute/sting/playground/utils/report/utils/Node.java

@@ -1,7 +1,5 @@
 package org.broadinstitute.sting.playground.utils.report.utils;
 
-import org.broadinstitute.sting.utils.StingException;
-
 import java.util.*;
 
 /**

java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java

@@ -40,7 +40,6 @@ import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescripto
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackManager;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.io.File;
 import java.io.IOException;

java/src/org/broadinstitute/sting/utils/GATKException.java

@@ -24,6 +24,8 @@
 
 package org.broadinstitute.sting.utils;
 
+import org.broadinstitute.sting.utils.exceptions.StingException;
+
 /**
  * Temp class to track split from Sting exception to UserException
  */

java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java

@@ -26,7 +26,6 @@
 package org.broadinstitute.sting.utils.classloader;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.lang.reflect.Modifier;
 import java.lang.reflect.Field;
@@ -34,7 +33,6 @@ import java.io.File;
 import java.io.IOException;
 import java.util.List;
 import java.util.ArrayList;
-import java.util.Collections;
 import java.util.Arrays;
 
 /**

java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java

@@ -27,9 +27,7 @@ package org.broadinstitute.sting.utils.classloader;
 
 import ch.qos.logback.classic.Level;
 import ch.qos.logback.classic.Logger;
-import ch.qos.logback.classic.LoggerContext;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 import org.reflections.Reflections;
 import org.reflections.scanners.SubTypesScanner;

java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java

@@ -26,8 +26,6 @@
 package org.broadinstitute.sting.utils.classloader;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.classloader.PackageUtils;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 
 import java.util.HashMap;

java/src/org/broadinstitute/sting/utils/collections/CircularArray.java

@@ -26,7 +26,6 @@
 package org.broadinstitute.sting.utils.collections;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 
 /** This class, closely resembling a deque (except that it is not dynamically grown), 

java/src/org/broadinstitute/sting/utils/collections/MergingIterator.java

@@ -29,7 +29,6 @@ import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODItera
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.*;
 

java/src/org/broadinstitute/sting/utils/fasta/ArtificialFastaUtils.java

@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.utils.fasta;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;

java/src/org/broadinstitute/sting/utils/fastq/FastqRecord.java

@@ -1,10 +1,5 @@
 package org.broadinstitute.sting.utils.fastq;
 
-import org.broadinstitute.sting.utils.StingException;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-
 public class FastqRecord {
     private String seqHeader;
     private String seqLine;

java/src/org/broadinstitute/sting/utils/file/FSLockWithShared.java

@@ -2,7 +2,6 @@ package org.broadinstitute.sting.utils.file;
 
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.io.File;
 import java.io.IOException;

java/src/org/broadinstitute/sting/utils/genotype/LikelihoodObject.java

@@ -4,7 +4,6 @@ import edu.mit.broad.picard.genotype.DiploidGenotype;
 import edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods;
 import net.sf.samtools.SAMFileHeader;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.HashMap;
 

java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java

@@ -2,7 +2,6 @@ package org.broadinstitute.sting.utils.genotype.glf;
 
 import net.sf.samtools.util.BinaryCodec;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 
 /*

java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java

@@ -27,7 +27,6 @@ package org.broadinstitute.sting.utils.help;
 
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.commandline.CommandLineProgram;
 
 import java.util.List;

java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java

@@ -32,7 +32,6 @@ import java.io.PrintStream;
 import java.io.IOException;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.gatk.walkers.Walker;

java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java

@@ -25,7 +25,6 @@
 package org.broadinstitute.sting.utils.instrumentation;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.lang.instrument.Instrumentation;
 import java.lang.reflect.Field;

java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java

@@ -24,10 +24,8 @@
 
 package org.broadinstitute.sting.utils.pileup;
 
-import net.sf.samtools.SAMReadGroupRecord;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.gatk.iterators.IterableIterator;
 

java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java

@@ -25,7 +25,6 @@ package org.broadinstitute.sting.utils.pileup;
 
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.collections.Pair;
 
 import java.util.*;

java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java

@@ -33,7 +33,6 @@ import net.sf.samtools.util.StringUtil;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.pileup.*;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
 
 import java.util.ArrayList;