Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

Removing PSP and CSM

Conflicts:

	public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java
	public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java

build.xml

@@ -780,6 +780,50 @@
         </sequential>
     </macrodef>
 
+    <!-- FAILED-TEST -->
+    <macrodef name="run-failed-test">
+        <attribute name="xmlfailedtestfile" />
+        <sequential>
+            <!-- Get the pipeline run type.  Default to dry.  -->
+            <condition property="pipeline.run" value="dry" else="${pipeline.run}">
+                <equals arg1="${pipeline.run}" arg2="$${pipeline.run}" />
+            </condition>
+
+            <condition property="cofoja.jvm.args" value="-javaagent:${cofoja.jar} -Dcom.google.java.contract.log.contract=false" else="">
+                <isset property="include.contracts" />
+            </condition>
+
+            <mkdir dir="${report}/failed_rerun" />
+            <echo message="Sting: Running @{xmlfailedtestfile} test cases!"/>
+            <taskdef resource="testngtasks" classpath="${lib.dir}/testng-5.14.1.jar"/>
+            <testng outputDir="${report}/failed_rerun"
+                    haltOnFailure="false" failureProperty="test.failure"
+                    verbose="2"
+                    workingDir="${basedir}"
+                    useDefaultListeners="false"
+                    listeners="org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.sting.StingTextReporter">
+                <jvmarg value="-Xmx${test.maxmemory}" />
+                <jvmarg value="-Djava.awt.headless=true" />
+                <jvmarg value="-Dpipeline.run=${pipeline.run}" />
+                <jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
+                <jvmarg line="${cofoja.jvm.args}"/>
+<!--                 <jvmarg value="-Xdebug"/> -->
+<!--                 <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> -->
+                <classpath>
+                    <path refid="external.dependencies" />
+                    <pathelement location="${java.classes}" />
+                    <pathelement location="${scala.classes}" />
+                    <pathelement location="${java.contracts}" />
+                    <pathelement location="${java.test.classes}" />
+                    <pathelement location="${scala.test.classes}" />
+                </classpath>
+
+                <xmlfileset dir="${basedir}" includes="@{xmlfailedtestfile}" />
+            </testng>
+
+            <fail message="test failed" if="test.failure" />
+        </sequential>
+    </macrodef>
 
     <!-- our three different test conditions: Test, IntegrationTest, PerformanceTest -->
     <target name="test" depends="test.compile,tribble.test" description="Run unit tests">
@@ -814,6 +858,22 @@
         <run-test testtype="${pipetype}"/>
     </target>
 
+    <target name="failed-test" depends="test.compile">
+        <run-failed-test xmlfailedtestfile="${report}/*UnitTest/testng-failed.xml" />
+    </target>
+
+    <target name="failed-integration" depends="test.compile">
+        <run-failed-test xmlfailedtestfile="${report}/*IntegrationTest/testng-failed.xml" />
+    </target>
+
+    <target name="failed-performance" depends="test.compile">
+        <run-failed-test xmlfailedtestfile="${report}/*PerformanceTest/testng-failed.xml" />
+    </target>
+
+    <target name="failed-pipeline" depends="test.compile">
+        <run-failed-test xmlfailedtestfile="${report}/*PipelineTest/testng-failed.xml" />
+    </target>
+
     <!-- ***************************************************************************** -->
     <!-- ***********                     Tribble                             ********* -->
     <!-- ***************************************************************************** -->

public/java/src/org/broadinstitute/sting/alignment/Aligner.java

@@ -1,10 +1,7 @@
 package org.broadinstitute.sting.alignment;
 
-import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMFileHeader;
-
-import java.util.List;
-import java.util.Iterator;
+import net.sf.samtools.SAMRecord;
 
 /**
  * Create perfect alignments from the read to the genome represented by the given BWT / suffix array. 

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

@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.alignment;
 
 import net.sf.samtools.*;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 /**
  * Represents an alignment of a read to a site in the reference genome.

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

@@ -25,16 +25,16 @@
 
 package org.broadinstitute.sting.alignment;
 
-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.BaseUtils;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
 import org.broadinstitute.sting.alignment.bwa.BWTFiles;
-import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.Iterator;
 

public/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java

@@ -25,21 +25,22 @@
 
 package org.broadinstitute.sting.alignment;
 
-import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
-import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.walkers.WalkerName;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
+import net.sf.picard.reference.ReferenceSequenceFileFactory;
+import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMSequenceDictionary;
 import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
 import org.broadinstitute.sting.alignment.bwa.BWTFiles;
-import net.sf.samtools.*;
-import net.sf.picard.reference.ReferenceSequenceFileFactory;
+import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.walkers.WalkerName;
 
 import java.io.File;
-import java.io.PrintStream;
 
 /**
  * Aligns reads to a given reference using Heng Li's BWA aligner, presenting the resulting alignments in SAM or BAM format.

public/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java

@@ -25,18 +25,21 @@
 
 package org.broadinstitute.sting.alignment;
 
-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.alignment.bwa.BWTFiles;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
+import org.broadinstitute.sting.alignment.bwa.BWTFiles;
 import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
-import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 
-import java.util.*;
 import java.io.PrintStream;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.SortedMap;
+import java.util.TreeMap;
 
 /**
  * Counts the number of best alignments as presented by BWA and outputs a histogram of number of placements vs. the

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

@@ -1,21 +1,15 @@
 package org.broadinstitute.sting.alignment.bwa;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
-import org.broadinstitute.sting.alignment.reference.bwt.BWT;
-import org.broadinstitute.sting.alignment.reference.bwt.BWTWriter;
-import org.broadinstitute.sting.alignment.reference.bwt.SuffixArray;
-import org.broadinstitute.sting.alignment.reference.bwt.SuffixArrayWriter;
-import org.broadinstitute.sting.alignment.reference.bwt.ANNWriter;
-import org.broadinstitute.sting.alignment.reference.bwt.AMBWriter;
-
-import java.io.File;
-import java.io.IOException;
-
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.SAMSequenceRecord;
 import net.sf.samtools.util.StringUtil;
+import org.broadinstitute.sting.alignment.reference.bwt.*;
+import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+
+import java.io.File;
+import java.io.IOException;
 
 /**
  * Support files for BWT.

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

@@ -1,14 +1,15 @@
 package org.broadinstitute.sting.alignment.bwa.c;
 
-import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMFileHeader;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.alignment.Alignment;
+import org.broadinstitute.sting.alignment.bwa.BWAAligner;
 import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
 import org.broadinstitute.sting.alignment.bwa.BWTFiles;
-import org.broadinstitute.sting.alignment.bwa.BWAAligner;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.*;
+import java.util.Arrays;
+import java.util.Iterator;
 
 /**
  * An aligner using the BWA/C implementation.

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

@@ -1,16 +1,15 @@
 package org.broadinstitute.sting.alignment.bwa.java;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import net.sf.samtools.*;
 import org.broadinstitute.sting.alignment.Aligner;
 import org.broadinstitute.sting.alignment.Alignment;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.File;
 import java.io.FileNotFoundException;
 
-import net.sf.samtools.*;
-import net.sf.picard.reference.IndexedFastaSequenceFile;
-
 /**
  * A test harness to ensure that the perfect aligner works.
  *

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

@@ -1,14 +1,13 @@
 package org.broadinstitute.sting.alignment.bwa.java;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-
-import java.util.Deque;
-import java.util.ArrayDeque;
-import java.util.Iterator;
-
 import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
 import net.sf.samtools.CigarOperator;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+
+import java.util.ArrayDeque;
+import java.util.Deque;
+import java.util.Iterator;
 
 /**
  * Represents a sequence of matches.

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

@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.alignment.bwa.java;
 
+import net.sf.samtools.Cigar;
 import org.broadinstitute.sting.alignment.Alignment;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import net.sf.samtools.Cigar;
 
 /**
  * An alignment object to be used incrementally as the BWA aligner

public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java

@@ -1,17 +1,18 @@
 package org.broadinstitute.sting.alignment.bwa.java;
 
-import org.broadinstitute.sting.alignment.reference.bwt.*;
+import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.alignment.Alignment;
 import org.broadinstitute.sting.alignment.bwa.BWAAligner;
 import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
-import org.broadinstitute.sting.alignment.Alignment;
+import org.broadinstitute.sting.alignment.reference.bwt.*;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.Utils;
 
 import java.io.File;
-import java.util.*;
-
-import net.sf.samtools.SAMRecord;
-import net.sf.samtools.SAMFileHeader;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.PriorityQueue;
 
 /**
  * Create imperfect alignments from the read to the genome represented by the given BWT / suffix array. 

public/java/src/org/broadinstitute/sting/alignment/bwa/java/LowerBound.java

@@ -1,10 +1,10 @@
 package org.broadinstitute.sting.alignment.bwa.java;
 
-import java.util.List;
-import java.util.ArrayList;
-
 import org.broadinstitute.sting.alignment.reference.bwt.BWT;
 
+import java.util.ArrayList;
+import java.util.List;
+
 /**
  * At any point along the given read, what is a good lower bound for the
  * total number of differences?

public/java/src/org/broadinstitute/sting/alignment/reference/bwt/AMBWriter.java

@@ -3,10 +3,10 @@ package org.broadinstitute.sting.alignment.reference.bwt;
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.SAMSequenceRecord;
 
-import java.io.PrintStream;
 import java.io.File;
 import java.io.IOException;
 import java.io.OutputStream;
+import java.io.PrintStream;
 
 /**
  * Writes .amb files - a file indicating where 'holes' (indeterminant bases)

public/java/src/org/broadinstitute/sting/alignment/reference/bwt/ANNWriter.java

@@ -3,10 +3,10 @@ package org.broadinstitute.sting.alignment.reference.bwt;
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.SAMSequenceRecord;
 
-import java.io.PrintStream;
 import java.io.File;
 import java.io.IOException;
 import java.io.OutputStream;
+import java.io.PrintStream;
 
 /**
  * Writes .ann files - an alternate sequence dictionary format

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

@@ -1,11 +1,14 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream;
 import org.broadinstitute.sting.alignment.reference.packing.BasePackedInputStream;
 import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
+import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.io.*;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
 import java.nio.ByteOrder;
 /**
  * Reads a BWT from a given file.

public/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTSupplementaryFileGenerator.java

@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
-import net.sf.picard.reference.ReferenceSequenceFileFactory;
 import net.sf.picard.reference.ReferenceSequenceFile;
+import net.sf.picard.reference.ReferenceSequenceFileFactory;
 import net.sf.samtools.SAMSequenceDictionary;
 
 import java.io.File;

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

@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream;
 import org.broadinstitute.sting.alignment.reference.packing.BasePackedOutputStream;
+import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.*;
 import java.nio.ByteOrder;

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

@@ -25,14 +25,14 @@
 
 package org.broadinstitute.sting.alignment.reference.bwt;
 
+import net.sf.picard.reference.ReferenceSequence;
 import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.picard.reference.ReferenceSequenceFileFactory;
-import net.sf.picard.reference.ReferenceSequence;
-
-import java.io.*;
-
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+
+import java.io.File;
+import java.io.IOException;
 
 /**
  * Create a suffix array data structure.

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

@@ -1,12 +1,11 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
+import net.sf.samtools.util.StringUtil;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.Comparator;
 import java.util.TreeSet;
 
-import net.sf.samtools.util.StringUtil;
-
 /**
  * An in-memory representation of a suffix array.
  *

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

@@ -1,10 +1,13 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream;
 import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
+import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.io.*;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
 import java.nio.ByteOrder;
 
 /**

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

@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.*;
 import java.nio.ByteOrder;

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

@@ -2,9 +2,12 @@ package org.broadinstitute.sting.alignment.reference.packing;
 
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.io.*;
-import java.nio.ByteOrder;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
 import java.nio.ByteBuffer;
+import java.nio.ByteOrder;
 import java.nio.channels.FileChannel;
 
 /**

public/java/src/org/broadinstitute/sting/alignment/reference/packing/CreatePACFromReference.java

@@ -25,12 +25,12 @@
 
 package org.broadinstitute.sting.alignment.reference.packing;
 
+import net.sf.picard.reference.ReferenceSequence;
 import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.picard.reference.ReferenceSequenceFileFactory;
-import net.sf.picard.reference.ReferenceSequence;
 
-import java.io.*;
-import java.nio.ByteOrder;
+import java.io.File;
+import java.io.IOException;
 
 /**
  * Generate a .PAC file from a given reference.

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

@@ -3,9 +3,9 @@ package org.broadinstitute.sting.alignment.reference.packing;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.File;
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.OutputStream;
-import java.io.FileOutputStream;
 import java.nio.ByteOrder;
 
 /**

public/java/src/org/broadinstitute/sting/alignment/reference/packing/UnsignedIntPackedInputStream.java

@@ -1,6 +1,8 @@
 package org.broadinstitute.sting.alignment.reference.packing;
 
-import java.io.*;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
 import java.nio.channels.FileChannel;

public/java/src/org/broadinstitute/sting/alignment/reference/packing/UnsignedIntPackedOutputStream.java

@@ -25,7 +25,10 @@
 
 package org.broadinstitute.sting.alignment.reference.packing;
 
-import java.io.*;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
 

public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java

@@ -25,20 +25,21 @@
 
 package org.broadinstitute.sting.analyzecovariates;
 
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.CommandLineProgram;
 import org.broadinstitute.sting.commandline.Input;
-import org.broadinstitute.sting.gatk.walkers.recalibration.*;
+import org.broadinstitute.sting.gatk.walkers.recalibration.Covariate;
+import org.broadinstitute.sting.gatk.walkers.recalibration.RecalDatum;
+import org.broadinstitute.sting.gatk.walkers.recalibration.RecalibrationArgumentCollection;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.commandline.CommandLineProgram;
-import org.broadinstitute.sting.commandline.Argument;
 
+import java.io.*;
 import java.util.ArrayList;
 import java.util.Collection;
-import java.util.List;
 import java.util.Map;
 import java.util.regex.Pattern;
-import java.io.*;
 
 /**
  * Created by IntelliJ IDEA.

public/java/src/org/broadinstitute/sting/commandline/Argument.java

@@ -25,12 +25,7 @@
 
 package org.broadinstitute.sting.commandline;
 
-import java.lang.annotation.Documented;
-import java.lang.annotation.ElementType;
-import java.lang.annotation.Inherited;
-import java.lang.annotation.Retention;
-import java.lang.annotation.RetentionPolicy;
-import java.lang.annotation.Target;
+import java.lang.annotation.*;
 
 /**
  * Created by IntelliJ IDEA.

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

@@ -27,10 +27,10 @@ package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.List;
-import java.util.Collections;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.Iterator;
+import java.util.List;
 
 /**
  * A group of argument definitions.

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

@@ -27,10 +27,10 @@ package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.Set;
-import java.util.HashSet;
 import java.util.Collection;
+import java.util.HashSet;
 import java.util.Iterator;
+import java.util.Set;
 
 /**
  * A collection of argument definitions.

public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java

@@ -25,12 +25,12 @@
 
 package org.broadinstitute.sting.commandline;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.classloader.JVMUtils;
+import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.walkers.Multiplex;
 import org.broadinstitute.sting.gatk.walkers.Multiplexer;
-import org.apache.log4j.Logger;
+import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.lang.annotation.Annotation;

public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java

@@ -25,14 +25,20 @@
 
 package org.broadinstitute.sting.commandline;
 
-import org.apache.log4j.*;
+import org.apache.log4j.FileAppender;
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import org.apache.log4j.PatternLayout;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.help.ApplicationDetails;
 import org.broadinstitute.sting.utils.help.HelpFormatter;
 
 import java.io.IOException;
-import java.util.*;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.EnumSet;
+import java.util.Locale;
 
 public abstract class CommandLineProgram {
 

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

@@ -25,11 +25,17 @@
 
 package org.broadinstitute.sting.commandline;
 
-import org.apache.log4j.*;
+import org.apache.log4j.Appender;
+import org.apache.log4j.ConsoleAppender;
+import org.apache.log4j.Logger;
+import org.apache.log4j.PatternLayout;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.*;
 import java.lang.annotation.Annotation;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.LinkedHashMap;
+import java.util.Map;
 
 /**
  * Static utility methods for working with command-line arguments.

public/java/src/org/broadinstitute/sting/commandline/MissingArgumentValueException.java

@@ -26,8 +26,6 @@ package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.utils.Utils;
 
-import java.util.Collection;
-
 /**
  * Specifies that a value was missing when attempting to populate an argument.
  */

public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java

@@ -25,16 +25,16 @@
 
 package org.broadinstitute.sting.commandline;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.classloader.JVMUtils;
+import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.classloader.JVMUtils;
+import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.ApplicationDetails;
 import org.broadinstitute.sting.utils.help.HelpFormatter;
-import org.apache.log4j.Logger;
 
-import java.lang.reflect.*;
+import java.lang.reflect.Field;
 import java.util.*;
 
 /**

public/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java

@@ -27,10 +27,8 @@ package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.utils.Utils;
 
-import java.util.regex.Pattern;
 import java.util.regex.Matcher;
-import java.util.List;
-import java.util.ArrayList;
+import java.util.regex.Pattern;
 
 /**
  * Holds a pattern, along with how to get to the argument definitions that could match that pattern.

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

@@ -25,30 +25,21 @@
 
 package org.broadinstitute.sting.gatk;
 
-import org.broadinstitute.sting.commandline.Tags;
-import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
-import org.broadinstitute.sting.commandline.CommandLineProgram;
 import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
-import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
+import org.broadinstitute.sting.commandline.CommandLineProgram;
+import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.filters.ReadFilter;
 import org.broadinstitute.sting.gatk.io.stubs.OutputStreamArgumentTypeDescriptor;
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileReaderArgumentTypeDescriptor;
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor;
 import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor;
 import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
-import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
-import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;
-import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
 import org.broadinstitute.sting.gatk.walkers.Walker;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.util.*;
-
-import net.sf.picard.filter.SamRecordFilter;
-import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.ListFileUtils;
-import org.broadinstitute.sting.utils.text.XReadLines;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
 
 /**
  * @author aaron

public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java

@@ -26,13 +26,15 @@
 package org.broadinstitute.sting.gatk;
 
 import org.broad.tribble.TribbleException;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.ArgumentCollection;
+import org.broadinstitute.sting.commandline.CommandLineProgram;
 import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.walkers.Attribution;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.text.TextFormattingUtils;
-import org.broadinstitute.sting.utils.help.ApplicationDetails;
-import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.walkers.Walker;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.help.ApplicationDetails;
+import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 
 import java.util.*;
 

public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

@@ -28,24 +28,14 @@ import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.samtools.*;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.commandline.ArgumentException;
-import org.broadinstitute.sting.commandline.ArgumentSource;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.commandline.CommandLineUtils;
-import org.broadinstitute.sting.commandline.ParsingEngine;
-import org.broadinstitute.sting.commandline.Tags;
+import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
-import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
-import org.broadinstitute.sting.gatk.datasources.reads.Shard;
+import org.broadinstitute.sting.gatk.datasources.reads.*;
 import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
 import org.broadinstitute.sting.gatk.datasources.sample.SampleDataSource;
-import org.broadinstitute.sting.gatk.datasources.reads.MonolithicShardStrategy;
-import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategy;
-import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategyFactory;
-import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
 import org.broadinstitute.sting.gatk.executive.MicroScheduler;
 import org.broadinstitute.sting.gatk.filters.FilterManager;
 import org.broadinstitute.sting.gatk.filters.ReadFilter;
@@ -65,6 +55,7 @@ import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.interval.IntervalUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
 import java.util.*;

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

@@ -25,13 +25,12 @@
 package org.broadinstitute.sting.gatk;
 
 import net.sf.picard.filter.SamRecordFilter;
-
-import java.util.Map;
-import java.util.HashMap;
-import java.util.Collections;
-
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+
 /**
  * Holds a bunch of basic information about the traversal.
  */

public/java/src/org/broadinstitute/sting/gatk/ReadProperties.java

@@ -1,6 +1,5 @@
 package org.broadinstitute.sting.gatk;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMFileReader;

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

@@ -25,19 +25,18 @@
 
 package org.broadinstitute.sting.gatk;
 
-import net.sf.picard.filter.SamRecordFilter;
 import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.filters.FilterManager;
 import org.broadinstitute.sting.gatk.filters.ReadFilter;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
-import org.broadinstitute.sting.utils.text.TextFormattingUtils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.help.DescriptionTaglet;
 import org.broadinstitute.sting.utils.help.DisplayNameTaglet;
 import org.broadinstitute.sting.utils.help.SummaryTaglet;
-import org.broadinstitute.sting.utils.baq.BAQ;
+import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 
 import java.util.*;
 

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

@@ -26,17 +26,16 @@
 package org.broadinstitute.sting.gatk.arguments;
 
 import net.sf.samtools.SAMFileReader;
-import org.broadinstitute.sting.commandline.Hidden;
-import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
-import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.gatk.DownsampleType;
 import org.broadinstitute.sting.gatk.DownsamplingMethod;
-import org.broadinstitute.sting.utils.interval.IntervalSetRule;
+import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
 import org.broadinstitute.sting.utils.baq.BAQ;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
+import org.broadinstitute.sting.utils.interval.IntervalSetRule;
 import org.simpleframework.xml.*;
 import org.simpleframework.xml.core.Persister;
 import org.simpleframework.xml.stream.Format;

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

@@ -26,13 +26,13 @@
 package org.broadinstitute.sting.gatk.contexts;
 
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.HasGenomeLocation;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
-import java.util.*;
+import java.util.List;
 
 /**
  * Useful class for forwarding on locusContext data from this iterator

public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java

@@ -27,8 +27,8 @@ package org.broadinstitute.sting.gatk.contexts;
 
 import net.sf.samtools.SAMReadGroupRecord;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pileup.*;
 

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

@@ -25,11 +25,12 @@
 
 package org.broadinstitute.sting.gatk.contexts;
 
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.BaseUtils;
+import com.google.java.contract.Ensures;
+import com.google.java.contract.Requires;
 import net.sf.samtools.util.StringUtil;
-import com.google.java.contract.*;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 
 /**
  * The section of the reference that overlaps with the given

public/java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java

@@ -1,16 +1,14 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.iterators.GenomeLocusIterator;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
+
+import java.util.Collections;
 import java.util.List;
 import java.util.NoSuchElementException;
-import java.util.ArrayList;
-import java.util.Collections;
-
-import org.broadinstitute.sting.gatk.iterators.GenomeLocusIterator;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
 /**
  * User: hanna
  * Date: May 13, 2009

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

@@ -1,13 +1,12 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
+import net.sf.picard.reference.ReferenceSequence;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.walkers.Reference;
 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 org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 /*
  * Copyright (c) 2009 The Broad Institute
  *

public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java

@@ -1,16 +1,15 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.datasources.reads.Shard;
-import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.iterators.LocusIterator;
-import org.broadinstitute.sting.gatk.ReadProperties;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 
 import java.util.Collection;
 
-import net.sf.picard.reference.IndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-
 /**
  * Presents data sharded by locus to the traversal engine.
  *

public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java

@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
-import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.DownsampleType;
+import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.iterators.LocusIterator;
 import org.broadinstitute.sting.utils.GenomeLoc;

public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java

@@ -5,10 +5,10 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
-import java.util.List;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
+import java.util.List;
 /**
  * User: hanna
  * Date: May 21, 2009

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

@@ -1,9 +1,8 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.utils.GenomeLoc;
 /*
  * Copyright (c) 2009 The Broad Institute
  *

public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java

@@ -1,14 +1,13 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.gatk.datasources.reads.Shard;
-import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
+import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 
 import java.util.Collection;
 
-import net.sf.picard.reference.IndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-
 /**
  * Present data sharded by read to a traversal engine.
  *

public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java

@@ -1,11 +1,10 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
 
-import java.util.Collection;
 import java.util.Arrays;
-
-import net.sf.samtools.SAMRecord;
+import java.util.Collection;
 /**
  * User: hanna
  * Date: May 22, 2009

public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java

@@ -1,16 +1,16 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
-import org.broadinstitute.sting.utils.*;
-
-import java.util.Collections;
-import java.util.Collection;
-import java.util.Arrays;
-
-import net.sf.samtools.SAMSequenceRecord;
-import net.sf.samtools.SAMRecord;
-import net.sf.picard.reference.ReferenceSequence;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
+import net.sf.picard.reference.ReferenceSequence;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMSequenceRecord;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
 /**
  * User: hanna
  * Date: May 22, 2009

public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java

@@ -25,9 +25,9 @@
 
 package org.broadinstitute.sting.gatk.datasources.providers;
 
-import org.broadinstitute.sting.gatk.refdata.*;
-import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.utils.GenomeLoc;

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

@@ -1,15 +1,14 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.gatk.datasources.reads.Shard;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.ArrayList;
-import java.util.List;
 import java.util.Collection;
-
-import net.sf.picard.reference.IndexedFastaSequenceFile;
+import java.util.List;
 /**
  * User: hanna
  * Date: May 8, 2009

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMBlockStartIterator.java

@@ -24,9 +24,6 @@
 
 package org.broadinstitute.sting.gatk.datasources.reads;
 
-import net.sf.samtools.SAMFileReader;
-import net.sf.samtools.SAMRecord;
-import org.apache.commons.lang.ArrayUtils;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 
 import java.io.File;
@@ -35,9 +32,7 @@ import java.io.IOException;
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
 import java.nio.channels.FileChannel;
-import java.util.ArrayList;
 import java.util.Iterator;
-import java.util.List;
 
 /**
  * Created by IntelliJ IDEA.

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java

@@ -39,12 +39,7 @@ import java.io.RandomAccessFile;
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
 import java.nio.channels.FileChannel;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 
 /**
  * Writes schedules for a single BAM file to a target output file.

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java

@@ -26,20 +26,10 @@ package org.broadinstitute.sting.gatk.datasources.reads;
 
 import net.sf.picard.util.PeekableIterator;
 import net.sf.samtools.GATKBAMFileSpan;
-import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-import java.util.NoSuchElementException;
+import java.util.*;
 
 /**
  * Assign intervals to the most appropriate blocks, keeping as little as possible in memory at once.

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java

@@ -29,19 +29,11 @@ import net.sf.samtools.GATKBAMFileSpan;
 import net.sf.samtools.SAMFileSpan;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.utils.interval.IntervalUtils;
 
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.SortedMap;
-import java.util.TreeMap;
+import java.util.*;
 
 /**
  * Represents a small section of a BAM file, and every associated interval.

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java

@@ -23,24 +23,18 @@
  */
 package org.broadinstitute.sting.gatk.datasources.reads;
 
-import net.sf.samtools.Bin;
-
-import net.sf.samtools.GATKBAMFileSpan;
-import net.sf.samtools.GATKBin;
-import net.sf.samtools.GATKChunk;
-import net.sf.samtools.LinearIndex;
-import net.sf.samtools.SAMException;
-import net.sf.samtools.util.RuntimeIOException;
+import net.sf.samtools.*;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
-import java.lang.ref.SoftReference;
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
 import java.nio.channels.FileChannel;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
 
 /**
  * A basic interface for querying BAM indices.

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java

@@ -24,11 +24,7 @@
 
 package org.broadinstitute.sting.gatk.datasources.reads;
 
-import net.sf.samtools.Bin;
-import net.sf.samtools.GATKBAMFileSpan;
-import net.sf.samtools.GATKBin;
-import net.sf.samtools.GATKChunk;
-import net.sf.samtools.LinearIndex;
+import net.sf.samtools.*;
 
 import java.util.ArrayList;
 import java.util.Collections;

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java

@@ -35,16 +35,7 @@ import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-import java.util.NoSuchElementException;
-import java.util.PriorityQueue;
-import java.util.Queue;
+import java.util.*;
 
 /**
  * Shard intervals based on position within the BAM file.

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources.reads;
 
+import net.sf.samtools.SAMFileSpan;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.Utils;
@@ -7,8 +8,6 @@ import org.broadinstitute.sting.utils.Utils;
 import java.util.List;
 import java.util.Map;
 
-import net.sf.samtools.SAMFileSpan;
-
 /**
  * Handles locus shards of BAM information.
  * @author aaron

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShardStrategy.java

@@ -24,17 +24,18 @@
 
 package org.broadinstitute.sting.gatk.datasources.reads;
 
-import net.sf.samtools.GATKBAMFileSpan;
-import org.broadinstitute.sting.utils.GenomeLocSortedSet;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMFileSpan;
+import net.sf.samtools.SAMSequenceRecord;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 
-import java.util.*;
-
-import net.sf.samtools.SAMFileHeader;
-import net.sf.samtools.SAMSequenceRecord;
-import net.sf.samtools.SAMFileSpan;
-import net.sf.picard.reference.IndexedFastaSequenceFile;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
 
 /**
  * A sharding strategy for loci based on reading of the index.

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShard.java

@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.gatk.datasources.reads;
 
+import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.GenomeLoc;
 
 import java.util.List;
 

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShardStrategy.java

@@ -4,8 +4,8 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 
 import java.util.Iterator;
-import java.util.NoSuchElementException;
 import java.util.List;
+import java.util.NoSuchElementException;
 
 /**
  * Create a giant shard representing all the data in the input BAM(s).

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java

@@ -1,15 +1,17 @@
 package org.broadinstitute.sting.gatk.datasources.reads;
 
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
-import org.broadinstitute.sting.gatk.iterators.StingSAMIteratorAdapter;
-
-import java.util.*;
-
 import net.sf.samtools.SAMFileSpan;
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
+import org.broadinstitute.sting.gatk.iterators.StingSAMIteratorAdapter;
+import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+
 /**
  *
  * User: aaron

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShardStrategy.java

@@ -25,12 +25,11 @@
 package org.broadinstitute.sting.gatk.datasources.reads;
 
 import net.sf.samtools.SAMFileSpan;
-
-import java.util.*;
-
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 
+import java.util.*;
+
 /**
  * The sharding strategy for reads using a simple counting mechanism.  Each read shard
  * has a specific number of reads (default to 10K) which is configured in the constructor.

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java

@@ -24,21 +24,19 @@
 
 package org.broadinstitute.sting.gatk.datasources.reads;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import net.sf.picard.sam.MergingSamRecordIterator;
+import net.sf.picard.sam.SamFileHeaderMerger;
 import net.sf.samtools.*;
 import net.sf.samtools.util.CloseableIterator;
-import net.sf.picard.filter.SamRecordFilter;
-import net.sf.picard.sam.SamFileHeaderMerger;
-import net.sf.picard.sam.MergingSamRecordIterator;
-import net.sf.picard.reference.IndexedFastaSequenceFile;
-
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.DownsamplingMethod;
-import org.broadinstitute.sting.gatk.filters.ReadFilter;
-import org.broadinstitute.sting.gatk.iterators.*;
-import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.ReadMetrics;
+import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.filters.CountingFilteringIterator;
+import org.broadinstitute.sting.gatk.filters.ReadFilter;
+import org.broadinstitute.sting.gatk.iterators.*;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.baq.BAQ;

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/Shard.java

@@ -2,17 +2,13 @@ package org.broadinstitute.sting.gatk.datasources.reads;
 
 import net.sf.samtools.SAMFileSpan;
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
-import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
-import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
-import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.gatk.ReadMetrics;
 import org.broadinstitute.sting.gatk.ReadProperties;
+import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
+import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.HasGenomeLocation;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.io.Serializable;
 import java.util.Collections;
 import java.util.List;
 import java.util.Map;

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardStrategyFactory.java

@@ -1,10 +1,10 @@
 package org.broadinstitute.sting.gatk.datasources.reads;
 
-import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
+import net.sf.samtools.SAMSequenceDictionary;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 /**
  *

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

@@ -25,17 +25,17 @@
 
 package org.broadinstitute.sting.gatk.datasources.reads.utilities;
 
-import org.broadinstitute.sting.commandline.CommandLineProgram;
+import net.sf.samtools.BAMIndex;
+import net.sf.samtools.SAMFileReader;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.CommandLineProgram;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.instrumentation.Sizeof;
 
 import java.io.File;
 import java.lang.reflect.Field;
-import java.util.Map;
 import java.util.List;
-
-import net.sf.samtools.*;
+import java.util.Map;
 
 /**
  *

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java

@@ -24,12 +24,12 @@
 
 package org.broadinstitute.sting.gatk.datasources.reads.utilities;
 
-import org.broadinstitute.sting.commandline.CommandLineProgram;
-import org.broadinstitute.sting.commandline.Argument;
-import net.sf.samtools.SAMFileWriter;
 import net.sf.samtools.SAMFileReader;
-import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMFileWriter;
 import net.sf.samtools.SAMFileWriterFactory;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.CommandLineProgram;
 
 import java.io.File;
 

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBGZFBounds.java

@@ -24,7 +24,6 @@
 
 package org.broadinstitute.sting.gatk.datasources.reads.utilities;
 
-import net.sf.samtools.SAMFileReader;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.CommandLineProgram;
 

public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java

@@ -25,16 +25,15 @@
 
 package org.broadinstitute.sting.gatk.datasources.reference;
 
-import net.sf.picard.reference.ReferenceSequenceFileFactory;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import net.sf.picard.reference.FastaSequenceIndexBuilder;
-import net.sf.picard.sam.CreateSequenceDictionary;
-import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.picard.reference.FastaSequenceIndex;
+import net.sf.picard.reference.FastaSequenceIndexBuilder;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import net.sf.picard.sam.CreateSequenceDictionary;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.file.FSLockWithShared;
 import org.broadinstitute.sting.utils.file.FileSystemInabilityToLockException;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
 
 import java.io.File;
 

public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ResourcePool.java

@@ -28,11 +28,7 @@ import net.sf.samtools.SAMSequenceDictionary;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 
 /**
  * A pool of open resources, all of which can create a closeable iterator.

public/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java

@@ -3,11 +3,10 @@ package org.broadinstitute.sting.gatk.datasources.sample;
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMReadGroupRecord;
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.exceptions.StingException;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.yaml.snakeyaml.TypeDescription;
 import org.yaml.snakeyaml.Yaml;
 import org.yaml.snakeyaml.constructor.Constructor;

public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java

@@ -1,15 +1,20 @@
 
 package org.broadinstitute.sting.gatk.examples;
 
-import net.sf.samtools.*;
-import org.broadinstitute.sting.gatk.refdata.*;
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.gatk.contexts.*;
-import org.broadinstitute.sting.utils.pileup.*;
+import net.sf.samtools.SAMReadGroupRecord;
 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.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
-import java.util.*;
 import java.io.PrintStream;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
 
 /**
  * Computes the coverage per sample.

public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java

@@ -25,6 +25,8 @@
 
 package org.broadinstitute.sting.gatk.examples;
 
+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.refdata.RefMetaDataTracker;
@@ -32,8 +34,6 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidSNPGenotypePriors;
 import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
 import java.io.PrintStream;

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

@@ -25,18 +25,18 @@
 
 package org.broadinstitute.sting.gatk.executive;
 
-import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
-import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider;
+import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
+import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
+import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.ArrayList;
-import java.util.List;
 import java.util.Iterator;
+import java.util.List;
 /**
  * Manages the
  */

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

@@ -1,27 +1,27 @@
 package org.broadinstitute.sting.gatk.executive;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
 import org.broadinstitute.sting.gatk.datasources.reads.Shard;
-import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategy;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.gatk.io.*;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.gatk.io.OutputTracker;
+import org.broadinstitute.sting.gatk.io.ThreadLocalOutputTracker;
+import org.broadinstitute.sting.gatk.walkers.TreeReducible;
+import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.threading.ThreadPoolMonitor;
 
-import java.util.Queue;
-import java.util.LinkedList;
 import java.util.Collection;
-import java.util.concurrent.Executors;
+import java.util.LinkedList;
+import java.util.Queue;
 import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
 import java.util.concurrent.Future;
 import java.util.concurrent.FutureTask;
 
-import net.sf.picard.reference.IndexedFastaSequenceFile;
-
 /**
  * A microscheduler that schedules shards according to a tree-like structure.
  * Requires a special walker tagged with a 'TreeReducible' interface.

public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java

@@ -1,22 +1,21 @@
 package org.broadinstitute.sting.gatk.executive;
 
-import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider;
 import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider;
+import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
 import org.broadinstitute.sting.gatk.datasources.reads.Shard;
 import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategy;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.io.DirectOutputTracker;
 import org.broadinstitute.sting.gatk.io.OutputTracker;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.gatk.walkers.Walker;
 
 import java.util.Collection;
 
-import net.sf.picard.reference.IndexedFastaSequenceFile;
-
 
 /** A micro-scheduling manager for single-threaded execution of a traversal. */
 public class LinearMicroScheduler extends MicroScheduler {

public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java

@@ -25,26 +25,18 @@
 
 package org.broadinstitute.sting.gatk.executive;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.apache.log4j.Logger;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
-import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.datasources.reads.Shard;
 import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategy;
+import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
+import org.broadinstitute.sting.gatk.io.OutputTracker;
+import org.broadinstitute.sting.gatk.iterators.NullSAMIterator;
+import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
 import org.broadinstitute.sting.gatk.traversals.*;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.gatk.io.OutputTracker;
-import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
-import org.broadinstitute.sting.gatk.iterators.NullSAMIterator;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.ReadMetrics;
-
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.PrintStream;
-import java.lang.management.ManagementFactory;
-import java.util.*;
-
-import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.threading.*;
@@ -52,6 +44,11 @@ import org.broadinstitute.sting.utils.threading.*;
 import javax.management.JMException;
 import javax.management.MBeanServer;
 import javax.management.ObjectName;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.PrintStream;
+import java.lang.management.ManagementFactory;
+import java.util.Collection;
 
 
 /**

public/java/src/org/broadinstitute/sting/gatk/executive/OutputMergeTask.java

@@ -1,10 +1,9 @@
 package org.broadinstitute.sting.gatk.executive;
 
 import org.broadinstitute.sting.gatk.io.storage.Storage;
-import org.broadinstitute.sting.gatk.io.OutputTracker;
 
-import java.util.Collection;
 import java.util.ArrayList;
+import java.util.Collection;
 
 /**
  * User: hanna

public/java/src/org/broadinstitute/sting/gatk/executive/ReduceTree.java

@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.executive;
 
-import java.util.Queue;
-import java.util.List;
 import java.util.ArrayList;
 import java.util.LinkedList;
+import java.util.List;
+import java.util.Queue;
 import java.util.concurrent.Future;
 /**
  * User: hanna

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

@@ -1,13 +1,13 @@
 package org.broadinstitute.sting.gatk.executive;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
 import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider;
+import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
 import org.broadinstitute.sting.gatk.datasources.reads.Shard;
-import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
 import org.broadinstitute.sting.gatk.io.ThreadLocalOutputTracker;
-import org.broadinstitute.sting.gatk.walkers.Walker;
+import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.concurrent.Callable;

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

@@ -4,8 +4,8 @@ import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.concurrent.Callable;
-import java.util.concurrent.Future;
 import java.util.concurrent.ExecutionException;
+import java.util.concurrent.Future;
 /**
  * User: hanna
  * Date: Apr 29, 2009

public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java

@@ -1,17 +1,20 @@
 package org.broadinstitute.sting.gatk.executive;
 
-import org.broadinstitute.sting.gatk.datasources.reads.Shard;
-import org.broadinstitute.sting.gatk.datasources.sample.SampleDataSource;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.gatk.iterators.*;
+import net.sf.picard.util.PeekableIterator;
 import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-
-import java.util.*;
-
-import net.sf.picard.util.PeekableIterator;
+import org.broadinstitute.sting.gatk.datasources.reads.Shard;
+import org.broadinstitute.sting.gatk.datasources.sample.SampleDataSource;
+import org.broadinstitute.sting.gatk.iterators.LocusIterator;
+import org.broadinstitute.sting.gatk.iterators.LocusIteratorByState;
+import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
+import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 
+import java.util.Iterator;
+import java.util.List;
+import java.util.NoSuchElementException;
+
 /**
  * Buffer shards of data which may or may not contain multiple loci into
  * iterators of all data which cover an interval.  Its existence is an homage

public/java/src/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java

@@ -24,8 +24,10 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
-import net.sf.samtools.*;
+import net.sf.samtools.Cigar;
+import net.sf.samtools.CigarElement;
+import net.sf.samtools.CigarOperator;
+import net.sf.samtools.SAMRecord;
 
 /**
  * Filter out reads with wonky cigar strings.

public/java/src/org/broadinstitute/sting/gatk/filters/BadMateFilter.java

@@ -24,7 +24,6 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 
 /**

public/java/src/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java

@@ -23,17 +23,16 @@
  */
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.samtools.util.CloserUtil;
-
-import java.util.Iterator;
-import java.util.NoSuchElementException;
-import java.util.Collection;
-
+import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.util.CloseableIterator;
-import net.sf.picard.filter.SamRecordFilter;
+import net.sf.samtools.util.CloserUtil;
 import org.broadinstitute.sting.gatk.ReadMetrics;
 
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.NoSuchElementException;
+
 /**
  * Filtering Iterator which takes a filter and an iterator and iterates
  * through only those records which are not rejected by the filter.

public/java/src/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java

@@ -1,6 +1,5 @@
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 
 /*

public/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckReadFilter.java

@@ -24,7 +24,6 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 
 /**

public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java

@@ -25,11 +25,8 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 
-import net.sf.picard.filter.SamRecordFilter;
-
 import java.util.Collection;
 
 /**

public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java

@@ -24,8 +24,8 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMSequenceRecord;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 

public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java

@@ -25,7 +25,6 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.commandline.Argument;
 

public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableReadFilter.java

@@ -24,7 +24,6 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.util.QualityUtil;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.QualityUtils;