From e91ae6b2659e13442627e85038991b40ffe4d16b Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Wed, 29 Jun 2011 15:00:26 -0400
Subject: [PATCH 001/161] AF matching when selecting random variants

---
 .../walkers/variantutils/SelectVariants.java  | 69 +++++++++++++++++--
 1 file changed, 64 insertions(+), 5 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index 963aa0ce5..4916c4ac4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -24,14 +24,12 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
+import org.broadinstitute.sting.commandline.Hidden;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.variantcontext.*;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.MendelianViolation;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -42,9 +40,10 @@ import org.broadinstitute.sting.gatk.walkers.RMD;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.apache.log4j.Logger;
 
 import java.io.File;
+import java.lang.annotation.AnnotationFormatError;
 import java.util.*;
 
 /**
@@ -75,12 +74,24 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
     @Argument(fullName="excludeFiltered", shortName="ef", doc="Don't include filtered loci in the analysis.", required=false)
     private boolean EXCLUDE_FILTERED = false;
 
+    @Argument(fullName="keepOriginalAC", shortName="keepOriginalAC", doc="Don't include filtered loci.", required=false)
+    private boolean KEEP_ORIGINAL_CHR_COUNTS = false;
+
     @Argument(fullName="discordance", shortName =  "disc", doc="Output variants that were not called on a ROD comparison track. Use -disc ROD_NAME", required=false)
     private String discordanceRodName = "";
 
     @Argument(fullName="concordance", shortName =  "conc", doc="Output variants that were also called on a ROD comparison track. Use -conc ROD_NAME", required=false)
     private String concordanceRodName = "";
 
+    @Hidden
+    @Argument(fullName="inputAF", shortName =  "inputAF", doc="", required=false)
+    private String inputAFRodName = "";
+
+    @Hidden
+    @Argument(fullName="keepAFSpectrum", shortName="keepAF", doc="Don't include loci found to be non-variant after the subsetting procedure.", required=false)
+    private boolean KEEP_AF_SPECTRUM = false;
+
+
     @Argument(fullName="family_structure", shortName="family", doc="USE YAML FILE INSTEAD (-SM) !!! string formatted as dad+mom=child where these parameters determine which sample names are examined", required=false)
     private String FAMILY_STRUCTURE = "";
 
@@ -178,6 +189,12 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
         // Initialize VCF header
         Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), logger);
         headerLines.add(new VCFHeaderLine("source", "SelectVariants"));
+
+        if (KEEP_ORIGINAL_CHR_COUNTS) {
+            headerLines.add(new VCFFormatHeaderLine("AC_Orig", 1, VCFHeaderLineType.Integer, "Original AC"));
+            headerLines.add(new VCFFormatHeaderLine("AF_Orig", 1, VCFHeaderLineType.Float, "Original AF"));
+            headerLines.add(new VCFFormatHeaderLine("AN_Orig", 1, VCFHeaderLineType.Integer, "Original AN"));
+        }
         vcfWriter.writeHeader(new VCFHeader(headerLines, samples));
 
         for (int i = 0; i < SELECT_EXPRESSIONS.size(); i++) {
@@ -269,6 +286,38 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
                 else if (!SELECT_RANDOM_FRACTION || GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom) {
                     vcfWriter.add(sub, ref.getBase());
                 }
+                else {
+                    if (SELECT_RANDOM_FRACTION && KEEP_AF_SPECTRUM ) {
+                        Collection<VariantContext> compVCs = tracker.getVariantContexts(ref, inputAFRodName, null, context.getLocation(), true, false);
+                        if (compVCs.isEmpty())
+                            return 0;
+
+                        // ok we have a comp VC and we need to match the AF spectrum of inputAFRodName.
+                        // We then pick a variant with probablity AF*desiredFraction
+                        for (VariantContext compVC : compVCs) {
+                            if ( compVC.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY) )  {
+                                String afo = compVC.getAttributeAsString(VCFConstants.ALLELE_FREQUENCY_KEY);
+
+                                double af;
+                                if (afo.contains(",")) {
+                                    String[] afs = afo.split(",");
+                                    afs[0] = afs[0].substring(1,afs[0].length());
+                                    afs[afs.length-1] = afs[afs.length-1].substring(0,afs[afs.length-1].length()-1);
+                                    af = Double.valueOf(afs[0]);
+
+                                }
+                                else
+                                    af = Double.valueOf(afo);
+
+                                System.out.format("%s .. %4.1f\n",afo.toString(), af);
+                                if (GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom * af)
+                                    vcfWriter.add(sub, ref.getBase());
+                            }
+                            break; // do only one vc
+                        }
+
+                    }
+                }
             }
 
         }
@@ -413,6 +462,16 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
         }
 
 
+        if (KEEP_ORIGINAL_CHR_COUNTS) {
+            if ( attributes.containsKey(VCFConstants.ALLELE_COUNT_KEY) )
+                attributes.put("AC_Orig",attributes.get(VCFConstants.ALLELE_COUNT_KEY));
+            if ( attributes.containsKey(VCFConstants.ALLELE_FREQUENCY_KEY) )
+                attributes.put("AF_Orig",attributes.get(VCFConstants.ALLELE_FREQUENCY_KEY));
+            if ( attributes.containsKey(VCFConstants.ALLELE_NUMBER_KEY) )
+                attributes.put("AN_Orig",attributes.get(VCFConstants.ALLELE_NUMBER_KEY));
+
+        }
+
         VariantContextUtils.calculateChromosomeCounts(sub,attributes,false);
         attributes.put("DP", depth);
 

From dc4f63a1a819a71815df2748a27528516176bd4f Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Wed, 29 Jun 2011 16:00:23 -0400
Subject: [PATCH 002/161] a) consensus goes to week queue b) New experimental
 TechnologyComposition annotation c) SelectVariants fixes

---
 .../annotator/TechnologyComposition.java      | 77 +++++++++++++++++++
 .../walkers/variantutils/SelectVariants.java  | 12 ++-
 2 files changed, 87 insertions(+), 2 deletions(-)
 create mode 100755 public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java
new file mode 100755
index 000000000..351117809
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java
@@ -0,0 +1,77 @@
+package org.broadinstitute.sting.gatk.walkers.annotator;
+
+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.annotator.interfaces.ExperimentalAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.utils.IndelUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.sam.ReadUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+import java.util.*;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: delangel
+ * Date: 6/29/11
+ * Time: 3:14 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class TechnologyComposition implements ExperimentalAnnotation,InfoFieldAnnotation {
+    private String nSLX = "NumSLX";
+    private String n454 ="Num454";
+    private String nSolid = "NumSOLiD";
+    private String nOther = "NumOther";
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+        if ( stratifiedContexts.size() == 0 )
+            return null;
+
+        int readsIllumina = 0;
+        int readsSolid = 0;
+        int reads454 = 0;
+        int readsOther = 0;
+
+        for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
+            AlignmentContext context = sample.getValue();
+
+            ReadBackedPileup pileup = null;
+            if (context.hasExtendedEventPileup())
+                pileup = context.getExtendedEventPileup();
+            else if (context.hasBasePileup())
+                pileup = context.getBasePileup();
+
+            if (pileup != null) {
+                for (PileupElement p : pileup ) {
+                    if(ReadUtils.is454Read(p.getRead()))
+                        reads454++;
+                    else if (ReadUtils.isSOLiDRead(p.getRead()))
+                        readsSolid++;
+                    else if (ReadUtils.isSLXRead(p.getRead()))
+                        readsIllumina++;
+                    else
+                        readsOther++;
+                }
+            }
+        }
+
+        Map<String, Object> map = new HashMap<String, Object>();
+        map.put(nSLX, String.format("%d", readsIllumina));
+        map.put(n454, String.format("%d", reads454));
+        map.put(nSolid, String.format("%d", readsSolid));
+        map.put(nOther, String.format("%d", readsOther));
+            return map;
+    }
+
+     public List<String> getKeyNames() { return Arrays.asList(nSLX,n454,nSolid,nOther); }
+
+     public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(nSLX, 1, VCFHeaderLineType.Integer, "Number of SLX reads"),
+             new VCFInfoHeaderLine(n454, 1, VCFHeaderLineType.Integer, "Number of 454 reads"),
+             new VCFInfoHeaderLine(nSolid, 1, VCFHeaderLineType.Integer, "Number of SOLiD reads"),
+             new VCFInfoHeaderLine(nOther, 1, VCFHeaderLineType.Integer, "Number of Other technology reads")); }
+
+}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index 4916c4ac4..cbac54326 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -25,6 +25,7 @@
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import org.broadinstitute.sting.commandline.Hidden;
+import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.variantcontext.*;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
@@ -303,13 +304,20 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
                                     String[] afs = afo.split(",");
                                     afs[0] = afs[0].substring(1,afs[0].length());
                                     afs[afs.length-1] = afs[afs.length-1].substring(0,afs[afs.length-1].length()-1);
-                                    af = Double.valueOf(afs[0]);
+
+                                    double[] afd = new double[afs.length];
+
+                                    for (int k=0; k < afd.length; k++)
+                                        afd[k] = Double.valueOf(afs[k]);
+
+                                    af = MathUtils.arrayMax(afd);
+                                    //af = Double.valueOf(afs[0]);
 
                                 }
                                 else
                                     af = Double.valueOf(afo);
 
-                                System.out.format("%s .. %4.1f\n",afo.toString(), af);
+                                //System.out.format("%s .. %4.4f\n",afo.toString(), af);
                                 if (GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom * af)
                                     vcfWriter.add(sub, ref.getBase());
                             }

From 2b88033ef4ab4501b5b78ae2d13b78d46c082a62 Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Wed, 29 Jun 2011 16:12:55 -0400
Subject: [PATCH 003/161] Enable considering 454 reads, just lower GOP by 15

---
 .../IndelGenotypeLikelihoodsCalculationModel.java        | 4 ++--
 .../gatk/walkers/indels/PairHMMIndelErrorModel.java      | 9 +++++++--
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
index 1f430548b..62f6ff5a6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
@@ -157,10 +157,10 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
                  GATKSAMRecord read = ReadUtils.hardClipAdaptorSequence(p.getRead());
                 if (read == null)
                     continue;     
-                if(ReadUtils.is454Read(read)) {
+         /*       if(ReadUtils.is454Read(read)) {
                     continue;
                 }
-
+            */
                 if (DEBUG && p.isIndel()) {
                     System.out.format("Read: %s, cigar: %s, aln start: %d, aln end: %d, p.len:%d, Type:%s, EventBases:%s\n",
                             read.getReadName(),read.getCigar().toString(),read.getAlignmentStart(),read.getAlignmentEnd(),
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
index e7b9cfa68..419ae694f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
@@ -105,6 +105,7 @@ public class PairHMMIndelErrorModel {
     private static final double MIN_GAP_CONT_PENALTY = 10.0;
     private static final double GAP_PENALTY_HRUN_STEP = 1.0; // each increase in hrun decreases gap penalty by this.
 
+    private static final double GOP_454_DELTA = 15.0; // lower gap penalty for 454 reads
 
     private boolean doViterbi = false;
 
@@ -771,10 +772,10 @@ public class PairHMMIndelErrorModel {
                 if (read == null)
                     continue;
 
-                if(ReadUtils.is454Read(read) && !getGapPenaltiesFromFile) {
+         /*       if(ReadUtils.is454Read(read) && !getGapPenaltiesFromFile) {
                     continue;
                 }
-
+            */
                 double[] recalQuals = null;
 
  /*
@@ -990,6 +991,10 @@ public class PairHMMIndelErrorModel {
                                }  else {
                                    currentContextGOP = Arrays.copyOfRange(gapOpenProbabilityMap.get(a), (int)indStart, (int)indStop);
                                    currentContextGCP = Arrays.copyOfRange(gapContProbabilityMap.get(a), (int)indStart, (int)indStop);
+                                   if(ReadUtils.is454Read(read)) {
+                                       for (int k=0; k <currentContextGOP.length; k++ )
+                                           currentContextGOP[k] += GOP_454_DELTA/10;
+                                   }
                                    readLikelihood = computeReadLikelihoodGivenHaplotypeAffineGaps(haplotypeBases, readBases, readQuals, currentContextGOP, currentContextGCP);
                                }
                             }

From 9644f104c49ed50c8894722ea971d68e274b74ca Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Fri, 1 Jul 2011 13:13:24 -0400
Subject: [PATCH 006/161] Fixes to the queue pipeline tests to account for the
 new directory structure.

---
 .../pipeline/examples/ExampleCountLociPipelineTest.scala    | 2 +-
 .../queue/pipeline/examples/HelloWorldPipelineTest.scala    | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala
index 2b3b51783..09f80f2c3 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala
@@ -35,7 +35,7 @@ class ExampleCountLociPipelineTest {
     val spec = new PipelineTestSpec
     spec.name = "countloci"
     spec.args = Array(
-      " -S scala/qscript/examples/ExampleCountLoci.scala",
+      " -S public/scala/qscript/examples/ExampleCountLoci.scala",
       " -R " + BaseTest.hg18Reference,
       " -I " + BaseTest.validationDataLocation + "small_bam_for_countloci.bam",
       " -o " + testOut).mkString
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala
index 8b8fa86a4..37531e791 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala
@@ -32,7 +32,7 @@ class HelloWorldPipelineTest {
   def testHelloWorld {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorld"
-    spec.args = "-S scala/qscript/examples/HelloWorld.scala"
+    spec.args = "-S public/scala/qscript/examples/HelloWorld.scala"
     PipelineTest.executeTest(spec)
   }
 
@@ -40,7 +40,7 @@ class HelloWorldPipelineTest {
   def testHelloWorldWithPrefix {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorldWithPrefix"
-    spec.args = "-S scala/qscript/examples/HelloWorld.scala -jobPrefix HelloWorld"
+    spec.args = "-S public/scala/qscript/examples/HelloWorld.scala -jobPrefix HelloWorld"
     PipelineTest.executeTest(spec)
   }
 
@@ -48,7 +48,7 @@ class HelloWorldPipelineTest {
   def testHelloWorldWithPriority {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorldWithPriority"
-    spec.args = "-S scala/qscript/examples/HelloWorld.scala -jobPriority 100"
+    spec.args = "-S public/scala/qscript/examples/HelloWorld.scala -jobPriority 100"
     PipelineTest.executeTest(spec)
   }
 }

From 11d4af0e7528d0d3dd8b5da3745ad7d7bced7280 Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Fri, 1 Jul 2011 13:41:34 -0400
Subject: [PATCH 007/161] Path-related fixes to the private queue pipeline
 tests.

---
 .../pipeline/IPFLibraryPipelineTest.scala     | 71 -------------------
 1 file changed, 71 deletions(-)
 delete mode 100755 public/scala/test/org/broadinstitute/sting/queue/pipeline/IPFLibraryPipelineTest.scala

diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/IPFLibraryPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/IPFLibraryPipelineTest.scala
deleted file mode 100755
index 6b32e5c9d..000000000
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/IPFLibraryPipelineTest.scala
+++ /dev/null
@@ -1,71 +0,0 @@
-package org.broadinstitute.sting.queue.pipeline
-
-import org.testng.annotations.Test
-import org.broadinstitute.sting.BaseTest
-
-class IPFLibraryPipelineTest {
-
-  @Test
-  def testVCFExtractSites {
-    var testOut = "vcfes.vcf"
-    val spec = new PipelineTestSpec
-    spec.name = "vcfExtractSites"
-    spec.args = "-S scala/qscript/oneoffs/QTools.q -T VCFExtractSites -ivcf %s -out %s".format(
-      BaseTest.validationDataLocation + "omni_1212.subset.b37.vcf", testOut
-    )
-    spec.fileMD5s += testOut -> "4f496b8cf90302428a9edda486a337f4"
-    PipelineTest.executeTest(spec)
-  }
-
-  @Test
-  def testVCFExtractSamples {
-    var testOut = "vcf.extract.samples.vcf"
-    val spec = new PipelineTestSpec
-    spec.name = "vcfExtractSamples"
-    spec.args = "-S scala/qscript/oneoffs/QTools.q -T VCFExtractSamples -ivcf %s -out %s -sm HG00107,HG00500,NA18501,NA18942".format(
-      BaseTest.validationDataLocation + "omni_1212.subset.b37.vcf", testOut
-    )
-
-    spec.fileMD5s += testOut -> "180d5a2e7a1fbc5117de6705bde3a7c8"
-  }
-
-  @Test
-  def testVCFExtractIntervals {
-    var testOut = "vcf.extract.intervals.list"
-    val spec = new PipelineTestSpec
-    spec.name = "vcfExtractIntervals"
-    spec.args = "-S scala/qscript/oneoffs/QTools.q -T VCFExtractIntervals -ivcf %s -out %s".format(
-      BaseTest.validationDataLocation + "omni_1212.subset.b37.vcf", testOut
-    )
-
-    spec.fileMD5s += testOut ->"28589eeb28fac753577c027abf939345"
-
-  }
-
-  @Test
-  def testVCFSimpleMerge {
-    var testOut = "vcf.simplemerge.vcf"
-    val spec = new PipelineTestSpec
-    val int1 = BaseTest.validationDataLocation + "omni.subset.interleaved.1.vcf"
-    val int2 = BaseTest.validationDataLocation + "omni.subset.interleaved.2.vcf"
-    spec.name = "vcfSimpleMerge"
-    spec.args = "-S scala/qscript/oneoffs/QTools.q -T VCFSimpleMerge -vcfs %s,%s -out %s -ref %s".format(
-      int1,int2,testOut,BaseTest.b37KGReference
-    )
-
-    spec.fileMD5s += testOut -> "c59b8de64ba787a2ca3a1734bdebf277"
-  }
-
-  @Test
-  def testSortByRef {
-    var testOut = "vcf.refsorted.vcf"
-    val spec = new PipelineTestSpec
-    val unsorted = BaseTest.validationDataLocation + "omni.pos_sorted.vcf"
-    spec.name = "sortByRef"
-    spec.args = "-S scala/qscript/oneoffs/QTools.q -T SortByRef -ivcf %s -out %s -ref %s".format(
-      unsorted, testOut, BaseTest.b37KGReference
-    )
-
-    spec.fileMD5s += testOut -> "ee09af803bc94987d55d044c2ebbc0b8"
-  }
-}

From d19351f71acc60673286d5dc8b1e6516bcc7a4a3 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Fri, 1 Jul 2011 16:02:28 -0400
Subject: [PATCH 008/161] Added capability of running multiple bam files in the
 same directory.

---
 .../sting/queue/qscripts/RecalibrateBaseQualities.scala   | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
index 678b356ee..51de3a7ad 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
@@ -41,9 +41,9 @@ class RecalibrateBaseQualities extends QScript {
 
     nContigs = getNumberOfContigs(input)
 
-    val recalFile1: File = new File("recal1.csv")
-    val recalFile2: File = new File("recal2.csv")
-    val recalBam: File        = swapExt(input, ".bam", "recal.bam")
+    val recalFile1: File = swapExt(input, ".bam", "recal1.csv")
+    val recalFile2: File = swapExt(input, ".bam", "recal2.csv")
+    val recalBam: File   = swapExt(input, ".bam", "recal.bam")
     val path1: String    = "before"
     val path2: String    = "after"
     
@@ -88,4 +88,4 @@ class RecalibrateBaseQualities extends QScript {
     this.analysisName = queueLogDir + inRecalFile + ".analyze_covariates"
     this.jobName = queueLogDir + inRecalFile + ".analyze_covariates"
   }
-}
\ No newline at end of file
+}

From d647ea4fdc4274507d0456c955f2dfbf66ae70c1 Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Fri, 1 Jul 2011 16:04:30 -0400
Subject: [PATCH 009/161] Long-delayed change to
 CachingIndexedFastaSequenceFile. Made the cache non-static to avoid problems
 when multiple references are used within the same thread (eg., during
 integration tests). This should kill the intermittent
 IndelRealignerIntegrationTest failures.

---
 .../utils/fasta/CachingIndexedFastaSequenceFile.java      | 8 ++++----
 .../fasta/CachingIndexedFastaSequenceFileUnitTest.java    | 5 -----
 2 files changed, 4 insertions(+), 9 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java b/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java
index bda52dd4e..0c5085cc7 100644
--- a/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java
+++ b/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java
@@ -68,13 +68,13 @@ public class CachingIndexedFastaSequenceFile extends IndexedFastaSequenceFile {
         ReferenceSequence seq = null;
     }
 
-    private static ThreadLocal<Cache> cache;
+    private ThreadLocal<Cache> cache;
 
-    static {
+    {
         resetThreadLocalCache();
-    };
+    }
 
-    protected static void resetThreadLocalCache() {
+    protected void resetThreadLocalCache() {
         cache = new ThreadLocal<Cache> () {
             @Override protected Cache initialValue() {
                 return new Cache();
diff --git a/public/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java
index a60f1b0fe..74cd8d8fe 100644
--- a/public/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java
@@ -34,11 +34,6 @@ public class CachingIndexedFastaSequenceFileUnitTest extends BaseTest {
     private static final List<Integer> QUERY_SIZES = Arrays.asList(1, 10, 100, 1000);
     private static final List<Integer> CACHE_SIZES = Arrays.asList(-1, 10, 1000);
 
-    @BeforeMethod
-    public void clearCache() {
-        CachingIndexedFastaSequenceFile.resetThreadLocalCache();
-    }
-
     @DataProvider(name = "fastas")
     public Object[][] createData1() {
         List<Object[]> params = new ArrayList<Object[]>();

From b0fb63e20a86e5d3542a1c5301663eb8cc884795 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Fri, 1 Jul 2011 16:14:59 -0400
Subject: [PATCH 010/161] moving the example scala scripts to the qscripts
 package.

---
 .../sting/queue/qscripts}/examples/ExampleCountLoci.scala       | 2 ++
 .../sting/queue/qscripts}/examples/ExampleCountReads.scala      | 2 ++
 .../sting/queue/qscripts}/examples/ExampleCustomWalker.scala    | 2 ++
 .../queue/qscripts}/examples/ExampleUnifiedGenotyper.scala      | 2 ++
 .../sting/queue/qscripts}/examples/HelloWorld.scala             | 2 ++
 .../broadinstitute/sting/queue/qscripts}/lib/Vcf2Table.q        | 2 ++
 6 files changed, 12 insertions(+)
 rename public/scala/qscript/{ => org/broadinstitute/sting/queue/qscripts}/examples/ExampleCountLoci.scala (93%)
 rename public/scala/qscript/{ => org/broadinstitute/sting/queue/qscripts}/examples/ExampleCountReads.scala (97%)
 rename public/scala/qscript/{ => org/broadinstitute/sting/queue/qscripts}/examples/ExampleCustomWalker.scala (96%)
 rename public/scala/qscript/{ => org/broadinstitute/sting/queue/qscripts}/examples/ExampleUnifiedGenotyper.scala (98%)
 rename public/scala/qscript/{ => org/broadinstitute/sting/queue/qscripts}/examples/HelloWorld.scala (76%)
 rename public/scala/qscript/{ => org/broadinstitute/sting/queue/qscripts}/lib/Vcf2Table.q (95%)

diff --git a/public/scala/qscript/examples/ExampleCountLoci.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountLoci.scala
similarity index 93%
rename from public/scala/qscript/examples/ExampleCountLoci.scala
rename to public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountLoci.scala
index ba834e72f..4ca3cbb89 100644
--- a/public/scala/qscript/examples/ExampleCountLoci.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountLoci.scala
@@ -1,3 +1,5 @@
+package org.broadinstitute.sting.queue.qscripts.examples
+
 import org.broadinstitute.sting.queue.QScript
 import org.broadinstitute.sting.queue.extensions.gatk._
 
diff --git a/public/scala/qscript/examples/ExampleCountReads.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountReads.scala
similarity index 97%
rename from public/scala/qscript/examples/ExampleCountReads.scala
rename to public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountReads.scala
index 85f796a51..9fdd1ba4c 100644
--- a/public/scala/qscript/examples/ExampleCountReads.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountReads.scala
@@ -1,3 +1,5 @@
+package org.broadinstitute.sting.queue.qscripts.examples
+
 import org.broadinstitute.sting.queue.QScript
 import org.broadinstitute.sting.queue.extensions.gatk._
 
diff --git a/public/scala/qscript/examples/ExampleCustomWalker.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCustomWalker.scala
similarity index 96%
rename from public/scala/qscript/examples/ExampleCustomWalker.scala
rename to public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCustomWalker.scala
index 340934b5b..d3796d350 100644
--- a/public/scala/qscript/examples/ExampleCustomWalker.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCustomWalker.scala
@@ -1,3 +1,5 @@
+package org.broadinstitute.sting.queue.qscripts.examples
+
 import org.broadinstitute.sting.queue.QScript
 import org.broadinstitute.sting.queue.extensions.gatk._
 
diff --git a/public/scala/qscript/examples/ExampleUnifiedGenotyper.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala
similarity index 98%
rename from public/scala/qscript/examples/ExampleUnifiedGenotyper.scala
rename to public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala
index 2f6940d64..4a93233eb 100644
--- a/public/scala/qscript/examples/ExampleUnifiedGenotyper.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala
@@ -1,3 +1,5 @@
+package org.broadinstitute.sting.queue.qscripts.examples
+
 import org.broadinstitute.sting.queue.QScript
 import org.broadinstitute.sting.queue.extensions.gatk._
 
diff --git a/public/scala/qscript/examples/HelloWorld.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala
similarity index 76%
rename from public/scala/qscript/examples/HelloWorld.scala
rename to public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala
index 64e0c161c..9f2ce27fe 100644
--- a/public/scala/qscript/examples/HelloWorld.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala
@@ -1,3 +1,5 @@
+package org.broadinstitute.sting.queue.qscripts.examples
+
 import org.broadinstitute.sting.queue.QScript
 
 class HelloWorld extends QScript {
diff --git a/public/scala/qscript/lib/Vcf2Table.q b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/lib/Vcf2Table.q
similarity index 95%
rename from public/scala/qscript/lib/Vcf2Table.q
rename to public/scala/qscript/org/broadinstitute/sting/queue/qscripts/lib/Vcf2Table.q
index 1b66a648b..25ff8fddd 100755
--- a/public/scala/qscript/lib/Vcf2Table.q
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/lib/Vcf2Table.q
@@ -1,3 +1,5 @@
+package org.broadinstitute.sting.queue.qscripts.lib
+
 import org.broadinstitute.sting.commandline.Hidden
 import org.broadinstitute.sting.queue.extensions.gatk.{RodBind, VariantsToTable}
 import org.broadinstitute.sting.queue.QScript

From 546e7777fa1c8f6d091f75aa28e6ac490fbf3523 Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Fri, 1 Jul 2011 16:39:10 -0400
Subject: [PATCH 011/161] Re-fixing paths in pipeline tests after example
 qscripts got moved.

---
 .../pipeline/examples/ExampleCountLociPipelineTest.scala    | 2 +-
 .../queue/pipeline/examples/HelloWorldPipelineTest.scala    | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala
index 09f80f2c3..1e6c93cff 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala
@@ -35,7 +35,7 @@ class ExampleCountLociPipelineTest {
     val spec = new PipelineTestSpec
     spec.name = "countloci"
     spec.args = Array(
-      " -S public/scala/qscript/examples/ExampleCountLoci.scala",
+      " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountLoci.scala",
       " -R " + BaseTest.hg18Reference,
       " -I " + BaseTest.validationDataLocation + "small_bam_for_countloci.bam",
       " -o " + testOut).mkString
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala
index 37531e791..0871e769b 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala
@@ -32,7 +32,7 @@ class HelloWorldPipelineTest {
   def testHelloWorld {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorld"
-    spec.args = "-S public/scala/qscript/examples/HelloWorld.scala"
+    spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala"
     PipelineTest.executeTest(spec)
   }
 
@@ -40,7 +40,7 @@ class HelloWorldPipelineTest {
   def testHelloWorldWithPrefix {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorldWithPrefix"
-    spec.args = "-S public/scala/qscript/examples/HelloWorld.scala -jobPrefix HelloWorld"
+    spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala -jobPrefix HelloWorld"
     PipelineTest.executeTest(spec)
   }
 
@@ -48,7 +48,7 @@ class HelloWorldPipelineTest {
   def testHelloWorldWithPriority {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorldWithPriority"
-    spec.args = "-S public/scala/qscript/examples/HelloWorld.scala -jobPriority 100"
+    spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala -jobPriority 100"
     PipelineTest.executeTest(spec)
   }
 }

From 444eae316c8d33e4b3ff765aa5b7211f5bd746a9 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Fri, 1 Jul 2011 17:26:25 -0400
Subject: [PATCH 013/161] Moving these supported perl scripts to public

---
 public/perl/liftOverVCF.pl |  83 ++++++++++++++++++++++++
 public/perl/sortByRef.pl   | 127 +++++++++++++++++++++++++++++++++++++
 2 files changed, 210 insertions(+)
 create mode 100755 public/perl/liftOverVCF.pl
 create mode 100755 public/perl/sortByRef.pl

diff --git a/public/perl/liftOverVCF.pl b/public/perl/liftOverVCF.pl
new file mode 100755
index 000000000..21cb8bb6b
--- /dev/null
+++ b/public/perl/liftOverVCF.pl
@@ -0,0 +1,83 @@
+#!/usr/bin/perl -w
+
+# Runs the liftover tool on a VCF and properly handles the output
+
+use strict;
+use Getopt::Long;
+
+my $in = undef;
+my $gatk = undef;
+my $chain = undef;
+my $newRef = undef;
+my $oldRef = undef;
+my $out = undef;
+my $tmp = "/tmp";
+my $recordOriginalLocation = 0;
+GetOptions( "vcf=s" => \$in,
+	    "gatk=s" => \$gatk,
+	    "chain=s" => \$chain,
+	    "newRef=s" => \$newRef,
+	    "oldRef=s" => \$oldRef,
+            "out=s" => \$out,
+	    "tmp=s" => \$tmp,
+	    "recordOriginalLocation" => \$recordOriginalLocation);
+
+if ( !$in || !$gatk || !$chain || !$newRef || !$oldRef || !$out ) {
+    print "Usage: liftOverVCF.pl\n\t-vcf \t\t<input vcf>\n\t-gatk \t\t<path to gatk trunk>\n\t-chain \t\t<chain file>\n\t-newRef \t<path to new reference prefix; we will need newRef.dict, .fasta, and .fasta.fai>\n\t-oldRef \t<path to old reference prefix; we will need oldRef.fasta>\n\t-out \t\t<output vcf>\n\t-tmp \t\t<temp file location; defaults to /tmp>\n\t-recordOriginalLocation \t\t<Should we record what the original location was in the INFO field?; defaults to false>\n";
+    print "Example: ./liftOverVCF.pl\n\t-vcf /humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/1kg_snp_validation/all_validation_batches.b36.vcf\n\t-chain b36ToHg19.broad.over.chain\n\t-out lifted.hg19.vcf\n\t-gatk /humgen/gsa-scr1/ebanks/Sting_dev\n\t-newRef /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19\n\t-oldRef /humgen/1kg/reference/human_b36_both\n";
+    exit(1);
+}
+
+# generate a random number
+my $random_number = rand();
+my $tmp_prefix = "$tmp/$random_number";
+print "Writing temporary files to prefix: $tmp_prefix\n";
+my $unsorted_vcf = "$tmp_prefix.unsorted.vcf";
+
+# lift over the file
+print "Lifting over the vcf...";
+my $cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T LiftoverVariants -R $oldRef.fasta -B:variant,vcf $in -o $unsorted_vcf -chain $chain -dict $newRef.dict";
+if ($recordOriginalLocation) {
+  $cmd .= " -recordOriginalLocation";
+}
+system($cmd) == 0 or quit("The liftover step failed.  Please correct the necessary errors before retrying.");
+
+# we need to sort the lifted over file now
+print "\nRe-sorting the vcf...\n";
+my $sorted_vcf = "$tmp_prefix.sorted.vcf";
+open(SORTED, ">$sorted_vcf") or die "can't open $sorted_vcf: $!";
+
+# write the header
+open(UNSORTED, "< $unsorted_vcf") or die "can't open $unsorted_vcf: $!";
+my $inHeader = 1;
+while ( $inHeader == 1 ) {
+    my $line = <UNSORTED>;
+    if ( $line !~ m/^#/ ) {
+	$inHeader = 0;
+    } else {
+	print SORTED "$line";
+    }
+}
+close(UNSORTED);
+close(SORTED);
+
+$cmd = "grep \"^#\" -v $unsorted_vcf | sort -n -k2 -T $tmp | $gatk/public/perl/sortByRef.pl --tmp $tmp - $newRef.fasta.fai >> $sorted_vcf";
+system($cmd) == 0 or quit("The sorting step failed.  Please correct the necessary errors before retrying.");
+
+# Filter the VCF for bad records
+print "\nFixing/removing bad records...\n";
+$cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T FilterLiftedVariants -R $newRef.fasta -B:variant,vcf $sorted_vcf -o $out";
+system($cmd) == 0 or quit("The filtering step failed.  Please correct the necessary errors before retrying.");
+
+# clean up
+unlink $unsorted_vcf;
+unlink $sorted_vcf;
+my $sorted_index = "$sorted_vcf.idx";
+unlink $sorted_index;
+
+print "\nDone!\n";
+
+sub quit {
+    print "\n$_[0]\n";
+    exit(1);
+}
diff --git a/public/perl/sortByRef.pl b/public/perl/sortByRef.pl
new file mode 100755
index 000000000..71d3f4477
--- /dev/null
+++ b/public/perl/sortByRef.pl
@@ -0,0 +1,127 @@
+#!/usr/bin/perl -w
+
+use strict;
+use Getopt::Long;
+
+sub usage {
+
+    print "\nUsage:\n";
+    print "sortByRef.pl [--k POS] [--tmp dir] INPUT REF_DICT\n\n";
+
+    print " Sorts lines of the input file INFILE according\n";
+    print " to the reference contig order specified by the\n";
+    print " reference dictionary REF_DICT (.fai file).\n";
+    print " The sort is stable. If -k option is not specified,\n";
+    print " it is assumed that the contig name is the first\n";
+    print " field in each line.\n\n";
+    print "  INPUT       input file to sort. If '-' is specified, \n";
+    print "              then reads from STDIN.\n";
+    print "  REF_DICT    .fai file, or ANY file that has contigs, in the\n";
+    print "              desired soting order, as its first column.\n";
+    print "  --k POS :   contig name is in the field POS (1-based)\n";
+    print "              of input lines.\n\n";
+    print "  --tmp DIR : temp directory [default=/tmp]\n\n";
+
+    exit(1);
+}
+
+my $pos = 1;
+my $tmp = "/tmp";
+GetOptions( "k:i" => \$pos,
+	    "tmp=s" => \$tmp);
+
+$pos--;
+
+usage() if ( scalar(@ARGV) == 0 );
+
+if ( scalar(@ARGV) != 2 ) {
+    print "Wrong number of arguments\n";
+    usage();
+}
+
+my $input_file = $ARGV[0];
+my $dict_file = $ARGV[1];
+
+
+open(DICT, "< $dict_file") or die("Can not open $dict_file: $!");
+
+my %ref_order;
+
+my $n = 0;
+while ( <DICT> ) {
+    chomp;
+    my ($contig, $rest) = split "\t";
+    die("Dictionary file is probably corrupt: multiple instances of contig $contig") if ( defined $ref_order{$contig} );
+
+    $ref_order{$contig} = $n;
+    $n++;
+}
+
+close DICT;
+#we have loaded contig ordering now
+
+my $INPUT;
+if ($input_file eq "-" ) {
+    $INPUT = "STDIN";
+} else {
+    open($INPUT, "< $input_file") or die("Can not open $input_file: $!");
+}
+
+my %temp_outputs;
+
+while ( <$INPUT> ) {
+    
+    my @fields = split '\s';
+    die("Specified field position exceeds the number of fields:\n$_") 
+        if ( $pos >= scalar(@fields) );
+
+    my $contig = $fields[$pos];
+    if ( $contig =~ m/:/ ) {
+        my @loc = split(/:/, $contig);
+        # print $contig . " " . $loc[0] . "\n";
+        $contig = $loc[0]
+    }
+    chomp $contig if ( $pos == scalar(@fields) - 1 ); # if last field in line
+
+    my $order;
+    if ( defined $ref_order{$contig} ) { $order = $ref_order{$contig}; }
+    else {
+        $ref_order{$contig} = $n;
+        $order = $n; # input line has contig that was not in the dict; 
+        $n++; # this contig will go at the end of the output, 
+              # after all known contigs
+    }
+
+    my $fhandle;
+    if ( defined $temp_outputs{$order} ) { $fhandle = $temp_outputs{$order} }
+    else {
+        #print "opening $order $$ $_\n";
+        open( $fhandle, " > $tmp/sortByRef.$$.$order.tmp" ) or
+            die ( "Can not open temporary file $order: $!");
+        $temp_outputs{$order} = $fhandle;
+    }
+
+    # we got the handle to the temp file that keeps all 
+    # lines with contig $contig
+
+    print $fhandle $_; # send current line to its corresponding temp file
+}
+
+close $INPUT;
+
+foreach my $f ( values %temp_outputs ) { close $f; }
+
+# now collect back into single output stream:
+
+for ( my $i = 0 ; $i < $n ; $i++ ) {
+    # if we did not have any lines on contig $i, then there's 
+    # no temp file and nothing to do
+    next if ( ! defined $temp_outputs{$i} ) ; 
+
+    my $f; 
+    open ( $f, "< $tmp/sortByRef.$$.$i.tmp" );
+    while ( <$f> ) { print ; }
+    close $f;
+
+    unlink "$tmp/sortByRef.$$.$i.tmp";    
+}

From 0c9105ca221508c5205f61ee23d5fe779936c513 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Fri, 1 Jul 2011 18:07:35 -0400
Subject: [PATCH 014/161] Minor fix of description

---
 .../org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
index 33069f1f5..f23433bb5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
@@ -42,5 +42,5 @@ public class LowMQ implements InfoFieldAnnotation {
 
     public List<String> getKeyNames() { return Arrays.asList("LowMQ"); }
 
-    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 3, VCFHeaderLineType.Integer, "3-tuple: <fraction of reads with MQ=0>,<fraction of reads with MQ<=10>,<total nubmer of reads>")); }
+    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 3, VCFHeaderLineType.Float, "3-tuple: <fraction of reads with MQ=0>,<fraction of reads with MQ<=10>,<total number of reads>")); }
 }

From b6bc64a0c8e4c2dd616dd5a9aad86416857d6d09 Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Fri, 1 Jul 2011 20:47:03 -0400
Subject: [PATCH 015/161] Cleanup of the utils.broad package. Using Picard
 IoUtils on sample names.

---
 .../{datasources => }/pipeline/Pipeline.java  |   2 +-
 .../pipeline/PipelineProject.java             |   2 +-
 .../pipeline/PipelineSample.java              |   2 +-
 .../utils/broad/PicardAggregationUtils.java   | 149 ------------------
 .../utils/broad/PicardAnalysisFiles.java      | 108 -------------
 .../sting/utils/broad/PicardPipeline.java     | 123 ---------------
 .../sting/utils/broad/ReferenceData.java      | 135 ----------------
 .../pipeline/PipelineUnitTest.java            |   4 +-
 .../broad/PicardAggregationUtilsUnitTest.java |  61 -------
 .../broad/PicardAnalysisFilesUnitTest.java    |  56 -------
 .../utils/broad/PicardPipelineUnitTest.java   |  71 ---------
 .../utils/broad/ReferenceDataUnitTest.java    |  49 ------
 public/packages/Queue.xml                     |   2 +-
 .../sting/queue/pipeline/PipelineTest.scala   |  87 ----------
 14 files changed, 7 insertions(+), 844 deletions(-)
 rename public/java/src/org/broadinstitute/sting/{datasources => }/pipeline/Pipeline.java (97%)
 rename public/java/src/org/broadinstitute/sting/{datasources => }/pipeline/PipelineProject.java (98%)
 rename public/java/src/org/broadinstitute/sting/{datasources => }/pipeline/PipelineSample.java (97%)
 delete mode 100755 public/java/src/org/broadinstitute/sting/utils/broad/PicardAggregationUtils.java
 delete mode 100755 public/java/src/org/broadinstitute/sting/utils/broad/PicardAnalysisFiles.java
 delete mode 100755 public/java/src/org/broadinstitute/sting/utils/broad/PicardPipeline.java
 delete mode 100755 public/java/src/org/broadinstitute/sting/utils/broad/ReferenceData.java
 rename public/java/test/org/broadinstitute/sting/{datasources => }/pipeline/PipelineUnitTest.java (96%)
 delete mode 100755 public/java/test/org/broadinstitute/sting/utils/broad/PicardAggregationUtilsUnitTest.java
 delete mode 100755 public/java/test/org/broadinstitute/sting/utils/broad/PicardAnalysisFilesUnitTest.java
 delete mode 100755 public/java/test/org/broadinstitute/sting/utils/broad/PicardPipelineUnitTest.java
 delete mode 100755 public/java/test/org/broadinstitute/sting/utils/broad/ReferenceDataUnitTest.java

diff --git a/public/java/src/org/broadinstitute/sting/datasources/pipeline/Pipeline.java b/public/java/src/org/broadinstitute/sting/pipeline/Pipeline.java
similarity index 97%
rename from public/java/src/org/broadinstitute/sting/datasources/pipeline/Pipeline.java
rename to public/java/src/org/broadinstitute/sting/pipeline/Pipeline.java
index f8f8b2d29..e0e75c353 100644
--- a/public/java/src/org/broadinstitute/sting/datasources/pipeline/Pipeline.java
+++ b/public/java/src/org/broadinstitute/sting/pipeline/Pipeline.java
@@ -22,7 +22,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.datasources.pipeline;
+package org.broadinstitute.sting.pipeline;
 
 import java.util.ArrayList;
 import java.util.List;
diff --git a/public/java/src/org/broadinstitute/sting/datasources/pipeline/PipelineProject.java b/public/java/src/org/broadinstitute/sting/pipeline/PipelineProject.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/datasources/pipeline/PipelineProject.java
rename to public/java/src/org/broadinstitute/sting/pipeline/PipelineProject.java
index 7967ba5df..8d33047bf 100644
--- a/public/java/src/org/broadinstitute/sting/datasources/pipeline/PipelineProject.java
+++ b/public/java/src/org/broadinstitute/sting/pipeline/PipelineProject.java
@@ -22,7 +22,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.datasources.pipeline;
+package org.broadinstitute.sting.pipeline;
 
 import java.io.File;
 import java.util.Map;
diff --git a/public/java/src/org/broadinstitute/sting/datasources/pipeline/PipelineSample.java b/public/java/src/org/broadinstitute/sting/pipeline/PipelineSample.java
similarity index 97%
rename from public/java/src/org/broadinstitute/sting/datasources/pipeline/PipelineSample.java
rename to public/java/src/org/broadinstitute/sting/pipeline/PipelineSample.java
index 701841302..7cd25fed5 100644
--- a/public/java/src/org/broadinstitute/sting/datasources/pipeline/PipelineSample.java
+++ b/public/java/src/org/broadinstitute/sting/pipeline/PipelineSample.java
@@ -22,7 +22,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.datasources.pipeline;
+package org.broadinstitute.sting.pipeline;
 
 import java.io.File;
 import java.util.Map;
diff --git a/public/java/src/org/broadinstitute/sting/utils/broad/PicardAggregationUtils.java b/public/java/src/org/broadinstitute/sting/utils/broad/PicardAggregationUtils.java
deleted file mode 100755
index 8f3ffd741..000000000
--- a/public/java/src/org/broadinstitute/sting/utils/broad/PicardAggregationUtils.java
+++ /dev/null
@@ -1,149 +0,0 @@
-/*
- * Copyright (c) 2011, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.utils.broad;
-
-import org.apache.commons.io.filefilter.RegexFileFilter;
-
-import java.io.File;
-import java.io.FileFilter;
-import java.io.FileNotFoundException;
-import java.util.Arrays;
-
-public class PicardAggregationUtils {
-    public static final String PICARD_AGGREGATION_DIR = "/seq/picard_aggregation/";
-
-    /**
-     * Returns the path to the sample BAM.
-     * @param project Project
-     * @param sample Sample
-     * @param version Version
-     * @return The path to the sample BAM.
-     */
-    public static String getSampleBam(String project, String sample, int version) {
-        return getSampleDir(project, sample, version) + sample + ".bam";
-    }
-
-    /**
-     * Returns the path to the latest BAM.
-     * @param project Project
-     * @param sample Sample
-     * @return The path to the latest BAM.
-     * @throws FileNotFoundException If a finished directory cannot be found for a sample.
-     */
-    public static String getSampleBam(String project, String sample) throws FileNotFoundException {
-        return getSampleDir(project, sample) + sample + ".bam";
-    }
-
-    /**
-     * Returns the sample directory.
-     * @param project Project
-     * @param sample Sample
-     * @param version Version
-     * @return the sample directory.
-     */
-    public static String getSampleDir(String project, String sample, int version) {
-        return PICARD_AGGREGATION_DIR + String.format("%s/%s/v%d/", project, sample, version);
-    }
-
-    /**
-     * Returns the latest finished directory for this project sample.
-     * @param project Project
-     * @param sample Sample
-     * @return The path to the latest finished directory.
-     * @throws FileNotFoundException If a finished directory cannot be found for a sample.
-     */
-    public static String getSampleDir(String project, String sample) throws FileNotFoundException {
-        int latestVersion = getLatestVersion(project, sample);
-        if (latestVersion == 0)
-            throw new FileNotFoundException("Unable to find a finished directory for project sample " + project + "/" + sample);
-        return getSampleDir(project, sample, latestVersion);
-    }
-
-    /**
-     * Returns the latest finished version directory.
-     * Because isilon metadata operations are relatively slow this method
-     * tries not to look for every possible versioned directory.
-     * @param project Project
-     * @param sample Sample
-     * @return The highest finished version directory or 0 if a finished directory was not found.
-     */
-    public static int getLatestVersion(String project, String sample) {
-        return getLatestVersion(project, sample, 0);
-    }
-
-    /**
-     * Returns the latest finished version directory after startVersion.
-     * Because isilon metadata operations are relatively slow this method
-     * tries not to look for every possible versioned directory.
-     * @param project Project
-     * @param sample Sample
-     * @param startVersion minimum version to return
-     * @return The highest finished version directory after startVersion
-     */
-    public static int getLatestVersion(String project, String sample, int startVersion) {
-        int version = Math.max(0, startVersion);
-        boolean nextExists = true;
-        while (nextExists) {
-            nextExists = false;
-            for (int next = 3; next > 0; next--)
-                if (isFinished(project, sample, version + next)) {
-                    version += next;
-                    nextExists = true;
-                    break;
-                }
-        }
-        // Special case when the version is 0
-        // Because isilon storage takes a while to do meta data operations only look through every file if we have to.
-        if (version == 0) {
-            File sampleDir = new File(PICARD_AGGREGATION_DIR + project + "/" + sample);
-            if (sampleDir.exists()) {
-                FileFilter filter = new RegexFileFilter("v\\d+");
-                File[] files = sampleDir.listFiles(filter);
-                int[] versions = new int[files.length];
-                for (int i = 0; i < files.length; i++)
-                    versions[i] = Integer.parseInt(files[i].getName().substring(1));
-                Arrays.sort(versions);
-                for (int i = versions.length - 1; i >= 0; i--) {
-                    if (isFinished(project, sample, versions[i])) {
-                        version = versions[i];
-                        break;
-                    }
-                }
-            }
-        }
-        return version == 0 ? startVersion : version;
-    }
-
-    /**
-     * Returns true if the project sample directory contains a finished.txt
-     * @param project Project
-     * @param sample Sample
-     * @param version Version
-     * @return true if the project sample directory contains a finished.txt
-     */
-    public static boolean isFinished(String project, String sample, int version) {
-        return new File(getSampleDir(project, sample, version), "finished.txt").exists();
-    }
-}
diff --git a/public/java/src/org/broadinstitute/sting/utils/broad/PicardAnalysisFiles.java b/public/java/src/org/broadinstitute/sting/utils/broad/PicardAnalysisFiles.java
deleted file mode 100755
index 02381916e..000000000
--- a/public/java/src/org/broadinstitute/sting/utils/broad/PicardAnalysisFiles.java
+++ /dev/null
@@ -1,108 +0,0 @@
-/*
- * Copyright (c) 2011, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.utils.broad;
-
-import org.apache.commons.lang.ArrayUtils;
-import org.broadinstitute.sting.utils.exceptions.StingException;
-import org.broadinstitute.sting.utils.text.XReadLines;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
-
-public class PicardAnalysisFiles {
-    private static final String REFERENCE_SEQUENCE_HEADER = "REFERENCE_SEQUENCE";
-    private static final String TARGET_INTERVALS_HEADER = "TARGET_INTERVALS";
-    private static final String BAIT_INTERVALS_HEADER = "BAIT_INTERVALS";
-    private static final String[] ANALYSIS_HEADERS = {REFERENCE_SEQUENCE_HEADER, TARGET_INTERVALS_HEADER, BAIT_INTERVALS_HEADER};
-    private static final String ANALYSIS_FILES = "analysis_files.txt";
-
-    private String path;
-    private Map<String,Set<String>> headerValues = new HashMap<String,Set<String>>();
-
-    public PicardAnalysisFiles(String project, String sample) throws FileNotFoundException {
-        this(PicardAggregationUtils.getSampleDir(project, sample) + ANALYSIS_FILES);
-    }
-
-    public PicardAnalysisFiles(String project, String sample, int version) throws FileNotFoundException {
-        this(PicardAggregationUtils.getSampleDir(project, sample, version) + ANALYSIS_FILES);
-    }
-
-    public PicardAnalysisFiles(String path) throws FileNotFoundException {
-        this.path = path;
-        HashMap<String,Integer> headerIndexes = null;
-        for (String line: new XReadLines(new File(path))) {
-            if (line.startsWith("#"))
-                continue;
-            String[] values = line.split("\t");
-            if (headerIndexes == null) {
-                headerIndexes = new HashMap<String,Integer>();
-                for (String header: ANALYSIS_HEADERS) {
-                    headerIndexes.put(header, ArrayUtils.indexOf(values, header));
-                    headerValues.put(header, new HashSet<String>());
-                }
-            } else {
-                for (String header: ANALYSIS_HEADERS) {
-                    int index = headerIndexes.get(header);
-                    if (values.length <= index)
-                        throw new StingException(String.format("Unable to parse line in %s: %n%s", path, line));
-                    String value = values[index];
-                    headerValues.get(header).add(value);
-                }
-            }
-        }
-    }
-
-    public String getPath() {
-        return path;
-    }
-
-    public String getReferenceSequence() {
-        return getSingle(REFERENCE_SEQUENCE_HEADER);
-    }
-
-    public String getTargetIntervals() {
-        return getSingle(TARGET_INTERVALS_HEADER);
-    }
-
-    public String getBaitIntervals() {
-        return getSingle(BAIT_INTERVALS_HEADER);
-    }
-
-    private String getSingle(String header) {
-        Set<String> values = headerValues.get(header);
-        if (values.size() > 1) {
-            throw new UnsupportedOperationException(path + " contains more than one value for " + header + ": " + values);
-        } else if (values.size() == 0) {
-            return null;
-        } else {
-            String value = values.iterator().next();
-            return "null".equals(value) ? null : value;
-        }
-    }
-}
diff --git a/public/java/src/org/broadinstitute/sting/utils/broad/PicardPipeline.java b/public/java/src/org/broadinstitute/sting/utils/broad/PicardPipeline.java
deleted file mode 100755
index 96bbb2455..000000000
--- a/public/java/src/org/broadinstitute/sting/utils/broad/PicardPipeline.java
+++ /dev/null
@@ -1,123 +0,0 @@
-/*
- * Copyright (c) 2011, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.utils.broad;
-
-import org.apache.commons.io.FilenameUtils;
-import org.apache.commons.lang.NullArgumentException;
-import org.broadinstitute.sting.datasources.pipeline.Pipeline;
-import org.broadinstitute.sting.datasources.pipeline.PipelineProject;
-import org.broadinstitute.sting.datasources.pipeline.PipelineSample;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.utils.yaml.YamlUtils;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-
-/**
- * Automatically gets the latest version using PicardAggregationUtils.
- */
-public class PicardPipeline {
-
-    protected static final String PROJECT_TAG = "SQUIDProject";
-    protected static final String SAMPLE_TAG = "CollaboratorID";
-    protected static final String PICARD_BAM_TYPE = "cleaned";
-
-    private PicardPipeline() {}
-
-    /**
-     * Creates a new PicardPipeline
-     * @param path Path to a tsv with project [tab] sample on each line or a pipeline yaml.
-     * @return a new Picard
-     * @throws FileNotFoundException when unable to find the file or any supporting files.
-     */
-    public static Pipeline parse(File path) throws FileNotFoundException {
-        if (path == null)
-            throw new NullArgumentException("path");
-
-        Pipeline pipeline;
-        if (path.getName().endsWith(".tsv")) {
-            pipeline = new Pipeline();
-            pipeline.getProject().setName(FilenameUtils.getBaseName(path.getPath()));
-            for (String line: new XReadLines(path)) {
-                String[] projectSample = line.split("\t");
-                addSample(pipeline, projectSample[0], projectSample[1]);
-            }
-        } else if (path.getName().endsWith(".yaml")) {
-            pipeline = YamlUtils.load(Pipeline.class, path);
-        } else {
-            throw new UserException.BadInput("Path does not end with .tsv or .yaml: " + path.getPath());
-        }
-
-        update(pipeline);
-        return pipeline;
-    }
-
-    private static void update(Pipeline pipeline) throws FileNotFoundException {
-        for (PipelineSample sample: pipeline.getSamples())
-            updateSample(pipeline.getProject(), sample);
-    }
-
-    private static void addSample(Pipeline pipeline, String project, String sample) {
-        PipelineSample pipelineSample = new PipelineSample();
-        pipelineSample.getTags().put(PROJECT_TAG, project);
-        pipelineSample.getTags().put(SAMPLE_TAG, sample);
-        pipeline.getSamples().add(pipelineSample);
-    }
-
-    private static void updateSample(PipelineProject pipelineProject, PipelineSample pipelineSample) throws FileNotFoundException {
-        if (!pipelineSample.getTags().containsKey(PROJECT_TAG) && !pipelineSample.getTags().containsKey(SAMPLE_TAG))
-            return;
-        String project = pipelineSample.getTags().get(PROJECT_TAG);
-        String sample = pipelineSample.getTags().get(SAMPLE_TAG);
-        int version = PicardAggregationUtils.getLatestVersion(project, sample);
-        if (version <= 0)
-            throw new UserException.BadInput("Project sample not found: " + project + "/" + sample);
-        String bam = PicardAggregationUtils.getSampleBam(project, sample, version);
-        if (pipelineSample.getId() == null)
-            pipelineSample.setId(project + "_" + sample);
-        pipelineSample.getBamFiles().put(PICARD_BAM_TYPE, new File(bam));
-
-        PicardAnalysisFiles analysis = new PicardAnalysisFiles(project, sample, version);
-        if (pipelineProject.getReferenceFile() == null) {
-            String referenceSequence = analysis.getReferenceSequence();
-            ReferenceData referenceData = ReferenceData.getByReference(referenceSequence);
-            pipelineProject.setReferenceFile(new File(referenceData.getReference()));
-            pipelineProject.setRefseqTable(new File(referenceData.getRefseq()));
-            if (analysis.getTargetIntervals() != null)
-                pipelineProject.setIntervalList(new File(analysis.getTargetIntervals()));
-            pipelineProject.setEvalDbsnp(new File(referenceData.getDbsnp(129)));
-            if (referenceData.getDbsnpVersions().contains(132)) {
-                pipelineProject.setGenotypeDbsnp(new File(referenceData.getDbsnp(132)));
-            } else {
-                pipelineProject.setGenotypeDbsnp(new File(referenceData.getDbsnp(129)));
-            }
-        } else {
-            String referenceSequence = analysis.getReferenceSequence();
-            if (!pipelineProject.getReferenceFile().getPath().equals(referenceSequence))
-                throw new UserException.BadInput("Samples sequenced with different references");
-        }
-    }
-}
diff --git a/public/java/src/org/broadinstitute/sting/utils/broad/ReferenceData.java b/public/java/src/org/broadinstitute/sting/utils/broad/ReferenceData.java
deleted file mode 100755
index 36a59ec70..000000000
--- a/public/java/src/org/broadinstitute/sting/utils/broad/ReferenceData.java
+++ /dev/null
@@ -1,135 +0,0 @@
-/*
- * Copyright (c) 2011, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.utils.broad;
-
-import java.util.Collections;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeMap;
-
-/**
- * Tracks data related to reference files at the Broad.
- */
-public enum ReferenceData {
-    /**
-     * HG18 reference data
-     */
-    HG18("hg18"),
-
-    /**
-     * HG19 reference data
-     */
-    HG19("hg19");
-
-    private static final String REFSEQ_DIR = "/humgen/gsa-hpprojects/GATK/data/Annotations/refseq/";
-    private static final String DBSNP_DIR = "/humgen/gsa-hpprojects/GATK/data/";
-
-    private final String name;
-    private final String reference;
-    private final String refseq;
-    private final Map<Integer,String> dbsnps;
-
-    ReferenceData(String name) {
-        this.name = name;
-        Map<Integer,String> dbsnps = new TreeMap<Integer,String>();
-        if ("hg18".equals(name)) {
-            this.reference = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta";
-            this.refseq = REFSEQ_DIR + "refGene-big-table-hg18.txt";
-            dbsnps.put(129, DBSNP_DIR + "dbsnp_129_hg18.rod");
-        } else if ("hg19".equals(name)) {
-            this.reference = "/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta";
-            this.refseq = REFSEQ_DIR + "refGene-big-table-hg19.txt";
-            dbsnps.put(129, DBSNP_DIR + "dbsnp_129_b37.vcf");
-            dbsnps.put(132, DBSNP_DIR + "dbsnp_132_b37.vcf");
-        } else
-            throw new UnsupportedOperationException("Unknown reference: " + name);
-        this.dbsnps = Collections.unmodifiableMap(dbsnps);
-    }
-
-    /**
-     * Returns the name of the reference.
-     * @return the name of the reference.
-     */
-    public String getName() {
-        return name;
-    }
-
-    /**
-     * Returns the path to the fasta.
-     * @return the path to the fasta.
-     */
-    public String getReference() {
-        return reference;
-    }
-
-    /**
-     * Returns the path to the refseq table.
-     * @return the path to the refseq table.
-     */
-    public String getRefseq() {
-        return refseq;
-    }
-
-    /**
-     * Returns the dbsnp versions available.
-     * @return the dbsnp versions available.
-     */
-    public Set<Integer> getDbsnpVersions() {
-        return dbsnps.keySet();
-    }
-
-    /**
-     * Returns the dbsnp path for the version.
-     * @param version version from getDbsnpVersions()
-     * @return the dbsnp path for the version.
-     */
-    public String getDbsnp(int version) {
-        return dbsnps.get(version);
-    }
-
-    /**
-     * Returns the dbsnp type for the version, "VCF" or "DBSNP".
-     * @param version version from getDbsnpVersions()
-     * @return the dbsnp type for the version, "VCF" or "DBSNP".
-     */
-    public String getDbsnpType(int version) {
-        String dbsnp = getDbsnp(version);
-        if (dbsnp == null)
-            return null;
-        return dbsnp.toLowerCase().endsWith(".vcf") ? "VCF" : "DBSNP";
-    }
-
-    /**
-     * Returns the reference data based on the path or null.
-     * @param reference path to the reference
-     * @return the reference data based on the path or null.
-     */
-    public static ReferenceData getByReference(String reference) {
-        for (ReferenceData data: ReferenceData.values())
-            if (data.reference.equals(reference))
-                return data;
-        return null;
-    }
-}
diff --git a/public/java/test/org/broadinstitute/sting/datasources/pipeline/PipelineUnitTest.java b/public/java/test/org/broadinstitute/sting/pipeline/PipelineUnitTest.java
similarity index 96%
rename from public/java/test/org/broadinstitute/sting/datasources/pipeline/PipelineUnitTest.java
rename to public/java/test/org/broadinstitute/sting/pipeline/PipelineUnitTest.java
index 8e18fac6f..891356670 100644
--- a/public/java/test/org/broadinstitute/sting/datasources/pipeline/PipelineUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/pipeline/PipelineUnitTest.java
@@ -22,8 +22,10 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.datasources.pipeline;
+package org.broadinstitute.sting.pipeline;
 
+import org.broadinstitute.sting.pipeline.Pipeline;
+import org.broadinstitute.sting.pipeline.PipelineSample;
 import org.testng.Assert;
 import org.broadinstitute.sting.utils.yaml.YamlUtils;
 
diff --git a/public/java/test/org/broadinstitute/sting/utils/broad/PicardAggregationUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/broad/PicardAggregationUtilsUnitTest.java
deleted file mode 100755
index 77a8a1ac8..000000000
--- a/public/java/test/org/broadinstitute/sting/utils/broad/PicardAggregationUtilsUnitTest.java
+++ /dev/null
@@ -1,61 +0,0 @@
-package org.broadinstitute.sting.utils.broad;
-
-import org.testng.Assert;
-import org.testng.annotations.Test;
-
-import java.io.FileNotFoundException;
-
-public class PicardAggregationUtilsUnitTest {
-    public static final String PROJECT = "C474";
-    public static final String SAMPLE = "NA19651";
-    public static final String MISSING_PROJECT = "C0";
-    public static final String MISSING_SAMPLE = "0";
-    private int latestVersion = -1;
-
-    @Test
-    public void testGetLatestVersion() {
-        latestVersion = PicardAggregationUtils.getLatestVersion(PROJECT, SAMPLE);
-        System.out.println(String.format("Latest version for %s %s is %d", PROJECT, SAMPLE, latestVersion));
-        Assert.assertTrue(latestVersion > 0);
-        Assert.assertEquals(PicardAggregationUtils.getLatestVersion(PROJECT, SAMPLE, latestVersion), latestVersion);
-    }
-
-    @Test(dependsOnMethods = "testGetLatestVersion")
-    public void testGetSampleBam() throws Exception {
-        String test = PicardAggregationUtils.getSampleBam(PROJECT, SAMPLE);
-        String latest = PicardAggregationUtils.getSampleBam(PROJECT, SAMPLE, latestVersion);
-        Assert.assertEquals(test, latest);
-    }
-
-    @Test(dependsOnMethods = "testGetLatestVersion")
-    public void testGetSampleDir() throws Exception {
-        String test = PicardAggregationUtils.getSampleDir(PROJECT, SAMPLE);
-        String latest = PicardAggregationUtils.getSampleDir(PROJECT, SAMPLE, latestVersion);
-        Assert.assertEquals(test, latest);
-    }
-
-    @Test(dependsOnMethods = "testGetLatestVersion")
-    public void testIsFinished() {
-        Assert.assertTrue(PicardAggregationUtils.isFinished(PROJECT, SAMPLE, latestVersion));
-        Assert.assertFalse(PicardAggregationUtils.isFinished(PROJECT, SAMPLE, latestVersion + 1));
-    }
-
-    @Test(expectedExceptions = FileNotFoundException.class)
-    public void testMissingSampleBam() throws Exception {
-        PicardAggregationUtils.getSampleBam(MISSING_PROJECT, MISSING_SAMPLE);
-    }
-
-    @Test(expectedExceptions = FileNotFoundException.class)
-    public void testMissingSampleDir() throws Exception {
-        PicardAggregationUtils.getSampleDir(MISSING_PROJECT, MISSING_SAMPLE);
-    }
-
-    @Test
-    public void testLatestVersionMissing() {
-        Assert.assertEquals(PicardAggregationUtils.getLatestVersion(MISSING_PROJECT, MISSING_SAMPLE), 0);
-        Assert.assertEquals(PicardAggregationUtils.getLatestVersion(MISSING_PROJECT, MISSING_SAMPLE, -1), -1);
-        Assert.assertEquals(PicardAggregationUtils.getLatestVersion(MISSING_PROJECT, MISSING_SAMPLE, 0), 0);
-        Assert.assertEquals(PicardAggregationUtils.getLatestVersion(MISSING_PROJECT, MISSING_SAMPLE, 1), 1);
-        Assert.assertEquals(PicardAggregationUtils.getLatestVersion(MISSING_PROJECT, MISSING_SAMPLE, 2), 2);
-    }
-}
diff --git a/public/java/test/org/broadinstitute/sting/utils/broad/PicardAnalysisFilesUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/broad/PicardAnalysisFilesUnitTest.java
deleted file mode 100755
index de58bf983..000000000
--- a/public/java/test/org/broadinstitute/sting/utils/broad/PicardAnalysisFilesUnitTest.java
+++ /dev/null
@@ -1,56 +0,0 @@
-package org.broadinstitute.sting.utils.broad;
-
-import org.broadinstitute.sting.BaseTest;
-import org.testng.Assert;
-import org.testng.annotations.Test;
-
-import java.io.FileNotFoundException;
-
-import static org.broadinstitute.sting.utils.broad.PicardAggregationUtilsUnitTest.*;
-
-public class PicardAnalysisFilesUnitTest extends BaseTest {
-    @Test
-    public void testParseLatest() throws Exception {
-        PicardAnalysisFiles files = new PicardAnalysisFiles(PROJECT, SAMPLE);
-        Assert.assertNotNull(files.getPath());
-        files = new PicardAnalysisFiles(PROJECT, SAMPLE, PicardAggregationUtils.getLatestVersion(PROJECT, SAMPLE));
-        Assert.assertNotNull(files.getPath());
-    }
-
-    @Test
-    public void testParseValid() throws Exception {
-        PicardAnalysisFiles file = new PicardAnalysisFiles(BaseTest.validationDataLocation + "picard_analysis_file.txt");
-        Assert.assertEquals(file.getReferenceSequence(), "/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta");
-        Assert.assertEquals(file.getTargetIntervals(), "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list");
-        Assert.assertEquals(file.getBaitIntervals(), "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.baits.interval_list");
-    }
-
-    @Test
-    public void testParseValidWithComments() throws Exception {
-        PicardAnalysisFiles file = new PicardAnalysisFiles(BaseTest.validationDataLocation + "picard_analysis_file_with_comments.txt");
-        Assert.assertEquals(file.getReferenceSequence(), "/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta");
-        Assert.assertEquals(file.getTargetIntervals(), "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list");
-        Assert.assertEquals(file.getBaitIntervals(), "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.baits.interval_list");
-    }
-
-    @Test(expectedExceptions = FileNotFoundException.class)
-    public void testParseBadPath() throws Exception {
-        new PicardAnalysisFiles(BaseTest.validationDataLocation + "non_existent_picard_analysis_file.txt");
-    }
-
-    @Test(expectedExceptions = FileNotFoundException.class)
-    public void testParseMissingLatest() throws Exception {
-        new PicardAnalysisFiles(MISSING_PROJECT, MISSING_SAMPLE);
-    }
-
-    @Test(expectedExceptions = FileNotFoundException.class)
-    public void testParseMissingVersion() throws Exception {
-        new PicardAnalysisFiles(PROJECT, SAMPLE, PicardAggregationUtils.getLatestVersion(PROJECT, SAMPLE) + 2);
-    }
-
-    @Test(expectedExceptions = UnsupportedOperationException.class)
-    public void testParseMultipleReferences() throws Exception {
-        PicardAnalysisFiles file = new PicardAnalysisFiles(BaseTest.validationDataLocation + "picard_analysis_file_with_different_references.txt");
-        file.getReferenceSequence();
-    }
-}
diff --git a/public/java/test/org/broadinstitute/sting/utils/broad/PicardPipelineUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/broad/PicardPipelineUnitTest.java
deleted file mode 100755
index 121ca4619..000000000
--- a/public/java/test/org/broadinstitute/sting/utils/broad/PicardPipelineUnitTest.java
+++ /dev/null
@@ -1,71 +0,0 @@
-package org.broadinstitute.sting.utils.broad;
-
-import org.testng.Assert;
-import org.apache.commons.io.FileUtils;
-import org.apache.commons.io.FilenameUtils;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.datasources.pipeline.Pipeline;
-import org.broadinstitute.sting.datasources.pipeline.PipelineSample;
-import org.broadinstitute.sting.utils.yaml.YamlUtils;
-import org.testng.annotations.Test;
-import static org.broadinstitute.sting.utils.broad.PicardAggregationUtilsUnitTest.*;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.Collections;
-
-public class PicardPipelineUnitTest {
-    @Test
-    public void testParseTsv() throws IOException {
-        File tsv = writeTsv(PROJECT, SAMPLE);
-        Pipeline pipeline = PicardPipeline.parse(tsv);
-        validatePipeline(pipeline, FilenameUtils.getBaseName(tsv.getPath()));
-    }
-
-    @Test
-    public void testParseTsvWithPicardComments() throws Exception {
-        File tsv = writeTsv("C460", "HG01359");
-        PicardPipeline.parse(tsv);
-    }
-
-    @Test
-    public void testParseYaml() throws IOException {
-        File yaml = writeYaml("project_name", PROJECT, SAMPLE);
-        Pipeline pipeline = PicardPipeline.parse(yaml);
-        validatePipeline(pipeline, "project_name");
-    }
-
-    private void validatePipeline(Pipeline pipeline, String name) {
-        Assert.assertEquals(pipeline.getProject().getName(), name);
-        Assert.assertTrue(pipeline.getProject().getReferenceFile().exists(), "reference not found");
-        Assert.assertTrue(pipeline.getProject().getIntervalList().exists(), "intervals not found");
-        Assert.assertTrue(pipeline.getProject().getRefseqTable().exists(), "refseq not found");
-        Assert.assertTrue(pipeline.getProject().getGenotypeDbsnp().exists(), "genotype dbsnp not found");
-        Assert.assertTrue(pipeline.getProject().getEvalDbsnp().exists(), "eval dbsnp not found");
-        Assert.assertEquals(pipeline.getSamples().size(), 1);
-        for (PipelineSample sample: pipeline.getSamples()) {
-            Assert.assertEquals(sample.getId(), PROJECT + "_" + SAMPLE);
-            Assert.assertTrue(sample.getBamFiles().get(PicardPipeline.PICARD_BAM_TYPE).exists(), "bam not found");
-            Assert.assertEquals(sample.getTags().get(PicardPipeline.PROJECT_TAG), PROJECT);
-            Assert.assertEquals(sample.getTags().get(PicardPipeline.SAMPLE_TAG), SAMPLE);
-        }
-    }
-
-    private File writeTsv(String project, String sample) throws IOException {
-        File tsv = BaseTest.createTempFile("pipeline", ".tsv");
-        FileUtils.writeLines(tsv, Collections.singletonList(project + "\t" + sample));
-        return tsv;
-    }
-
-    private File writeYaml(String projectName, String project, String sample) throws IOException {
-        File yaml = BaseTest.createTempFile("pipeline", ".yaml");
-        PipelineSample pipelineSample = new PipelineSample();
-        pipelineSample.getTags().put(PicardPipeline.PROJECT_TAG, project);
-        pipelineSample.getTags().put(PicardPipeline.SAMPLE_TAG, sample);
-        Pipeline pipeline = new Pipeline();
-        pipeline.getProject().setName(projectName);
-        pipeline.getSamples().add(pipelineSample);
-        YamlUtils.dump(pipeline, yaml);
-        return yaml;
-    }
-}
diff --git a/public/java/test/org/broadinstitute/sting/utils/broad/ReferenceDataUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/broad/ReferenceDataUnitTest.java
deleted file mode 100755
index e58ea3858..000000000
--- a/public/java/test/org/broadinstitute/sting/utils/broad/ReferenceDataUnitTest.java
+++ /dev/null
@@ -1,49 +0,0 @@
-package org.broadinstitute.sting.utils.broad;
-
-import org.broadinstitute.sting.BaseTest;
-import org.testng.Assert;
-import org.testng.annotations.Test;
-
-import java.io.File;
-
-public class ReferenceDataUnitTest {
-    @Test
-    public void testNames() {
-        Assert.assertEquals(ReferenceData.HG18.getName(), "hg18");
-        Assert.assertEquals(ReferenceData.HG19.getName(), "hg19");
-    }
-
-    @Test
-    public void testFilesExist() {
-        for (ReferenceData data: ReferenceData.values()) {
-            Assert.assertTrue(new File(data.getReference()).exists());
-            Assert.assertTrue(new File(data.getRefseq()).exists());
-            for (int version: data.getDbsnpVersions()) {
-                Assert.assertTrue(new File(data.getDbsnp(version)).exists());
-            }
-        }
-    }
-
-    @Test
-    public void testDbsnps() {
-        Assert.assertTrue(new File(ReferenceData.HG18.getDbsnp(129)).exists());
-        Assert.assertTrue(new File(ReferenceData.HG19.getDbsnp(129)).exists());
-        Assert.assertTrue(new File(ReferenceData.HG19.getDbsnp(132)).exists());
-        Assert.assertNull(ReferenceData.HG19.getDbsnp(130));
-    }
-
-    @Test
-    public void testDbsnpTypes() {
-        Assert.assertEquals(ReferenceData.HG18.getDbsnpType(129), "DBSNP");
-        Assert.assertEquals(ReferenceData.HG19.getDbsnpType(129), "VCF");
-        Assert.assertEquals(ReferenceData.HG19.getDbsnpType(132), "VCF");
-        Assert.assertNull(ReferenceData.HG19.getDbsnpType(130));
-    }
-
-    @Test
-    public void testGetByReference() {
-        Assert.assertEquals(ReferenceData.getByReference(BaseTest.hg18Reference), ReferenceData.HG18);
-        Assert.assertEquals(ReferenceData.getByReference(BaseTest.hg19Reference), ReferenceData.HG19);
-        Assert.assertEquals(ReferenceData.getByReference("none"), null);
-    }
-}
diff --git a/public/packages/Queue.xml b/public/packages/Queue.xml
index 347b24db3..58da4398e 100644
--- a/public/packages/Queue.xml
+++ b/public/packages/Queue.xml
@@ -33,7 +33,7 @@
             <package name="org.broadinstitute.sting.queue.**" />
 
             <!-- Pipeline + Utils -->
-            <package name="org.broadinstitute.sting.datasources.pipeline.**" />
+            <package name="org.broadinstitute.sting.pipeline.**" />
             <package name="org.broadinstitute.sting.utils.**" />
 
             <!-- Scala -->
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala
index 6b87981ff..dc3cfd9d4 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala
@@ -32,8 +32,6 @@ import java.util.Date
 import java.text.SimpleDateFormat
 import org.broadinstitute.sting.BaseTest
 import org.broadinstitute.sting.queue.QCommandLine
-import org.broadinstitute.sting.datasources.pipeline.{Pipeline, PipelineProject, PipelineSample}
-import org.broadinstitute.sting.utils.broad.PicardAggregationUtils
 import org.broadinstitute.sting.queue.util.{Logging, ProcessController}
 import java.io.{FileNotFoundException, File}
 import org.broadinstitute.sting.gatk.report.GATKReportParser
@@ -42,23 +40,6 @@ import org.broadinstitute.sting.queue.engine.CommandLinePluginManager
 
 object PipelineTest extends BaseTest with Logging {
 
-  case class K1gBam(squidId: String, sampleId: String, version: Int)
-
-  /** 1000G BAMs used for validation */
-  val k1gBams = List(
-    new K1gBam("C474", "NA19651", 2),
-    new K1gBam("C474", "NA19655", 2),
-    new K1gBam("C474", "NA19669", 2),
-    new K1gBam("C454", "NA19834", 2),
-    new K1gBam("C460", "HG01440", 2),
-    new K1gBam("C456", "NA12342", 2),
-    new K1gBam("C456", "NA12748", 2),
-    new K1gBam("C474", "NA19649", 2),
-    new K1gBam("C474", "NA19652", 2),
-    new K1gBam("C474", "NA19654", 2))
-
-  validateK1gBams()
-
   private val validationReportsDataLocation = "/humgen/gsa-hpprojects/GATK/validationreports/submitted/"
 
   val run = System.getProperty("pipeline.run") == "run"
@@ -92,49 +73,6 @@ object PipelineTest extends BaseTest with Logging {
    */
   private def tempDir(testName: String, jobRunner: String) = testDir(testName, jobRunner) + "temp/"
 
-  /**
-   * Creates a new pipeline from a project.
-   * @param project Pipeline project info.
-   * @param samples List of samples.
-   * @return a new pipeline project.
-   */
-  def createPipeline(project: PipelineProject, samples: List[PipelineSample]) = {
-    val pipeline = new Pipeline
-    pipeline.setProject(project)
-    pipeline.setSamples(samples)
-    pipeline
-  }
-
-  /**
-   * Creates a new pipeline project for hg19 with b37 132 dbsnp for genotyping, and b37 129 dbsnp for eval.
-   * @param projectName Name of the project.
-   * @param intervals The intervals file to use.
-   * @return a new pipeline project.
-   */
-  def createHg19Project(projectName: String, intervals: String) = {
-    val project = new PipelineProject
-    project.setName(projectName)
-    project.setReferenceFile(new File(BaseTest.hg19Reference))
-    project.setGenotypeDbsnp(new File(BaseTest.b37dbSNP132))
-    project.setEvalDbsnp(new File(BaseTest.b37dbSNP129))
-    project.setRefseqTable(new File(BaseTest.hg19Refseq))
-    project.setIntervalList(new File(intervals))
-    project
-  }
-
-  /**
-   * Creates a 1000G pipeline sample from one of the bams.
-   * @param idPrefix Text to prepend to the sample name.
-   * @param k1gBam bam to create the sample for.
-   * @return the created pipeline sample.
-   */
-  def createK1gSample(idPrefix: String, k1gBam: K1gBam) = {
-    val sample = new PipelineSample
-    sample.setId(idPrefix + "_" + k1gBam.sampleId)
-    sample.setBamFiles(Map("cleaned" -> getPicardBam(k1gBam)))
-    sample
-  }
-
   /**
    * Runs the pipelineTest.
    * @param pipelineTest test to run.
@@ -267,31 +205,6 @@ object PipelineTest extends BaseTest with Logging {
     }
   }
 
-  /**
-   * Throws an exception if any of the 1000G bams do not exist and warns if they are out of date.
-   */
-  private def validateK1gBams() {
-    var missingBams = List.empty[File]
-    for (k1gBam <- k1gBams) {
-      val latest = getLatestVersion(k1gBam)
-      val bam = getPicardBam(k1gBam)
-      if (k1gBam.version != latest)
-        logger.warn("1000G bam is not the latest version %d: %s".format(latest, k1gBam))
-      if (!bam.exists)
-        missingBams :+= bam
-    }
-    if (missingBams.size > 0) {
-      val nl = "%n".format()
-      throw new FileNotFoundException("The following 1000G bam files are missing.%n%s".format(missingBams.mkString(nl)))
-    }
-  }
-
-  private def getPicardBam(k1gBam: K1gBam): File =
-    new File(PicardAggregationUtils.getSampleBam(k1gBam.squidId, k1gBam.sampleId, k1gBam.version))
-
-  private def getLatestVersion(k1gBam: K1gBam): Int =
-    PicardAggregationUtils.getLatestVersion(k1gBam.squidId, k1gBam.sampleId, k1gBam.version)
-
   private var runningCommandLines = Set.empty[QCommandLine]
 
   Runtime.getRuntime.addShutdownHook(new Thread {

From 17ff5bb09436b8805657859b787f4f7f8714cc08 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Sat, 2 Jul 2011 09:55:35 -0400
Subject: [PATCH 017/161] Variant records coming out of the VQSR are now
 annotated with which input annotation was most divergent from the Gaussian
 mixture model. This gives a general sense for why each variant was removed
 from the callset.

---
 .../ApplyRecalibration.java                     |  8 +++++++-
 .../GaussianMixtureModel.java                   | 13 +++++++++++++
 .../VariantDataManager.java                     |  4 +++-
 .../variantrecalibration/VariantDatum.java      |  1 +
 .../VariantRecalibrator.java                    |  2 ++
 .../VariantRecalibratorEngine.java              | 17 +++++++++++++++++
 ...iantRecalibrationWalkersIntegrationTest.java |  4 ++--
 7 files changed, 45 insertions(+), 4 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
index 9877781d1..02d850211 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
@@ -55,7 +55,6 @@ import java.util.*;
 
 public class ApplyRecalibration extends RodWalker<Integer, Integer> {
 
-
     /////////////////////////////
     // Inputs
     /////////////////////////////
@@ -86,6 +85,7 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> {
     final private List<Tranche> tranches = new ArrayList<Tranche>();
     final private Set<String> inputNames = new HashSet<String>();
     final private NestedHashMap lodMap = new NestedHashMap();
+    final private NestedHashMap annotationMap = new NestedHashMap();
     final private Set<String> ignoreInputFilterSet = new TreeSet<String>();
 
     //---------------------------------------------------------------------------------------------------------------
@@ -124,6 +124,7 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> {
         final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
         hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames));
         hInfo.add(new VCFInfoHeaderLine(VariantRecalibrator.VQS_LOD_KEY, 1, VCFHeaderLineType.Float, "Log odds ratio of being a true variant versus being false under the trained gaussian mixture model"));
+        hInfo.add(new VCFInfoHeaderLine(VariantRecalibrator.CULPRIT_KEY, 1, VCFHeaderLineType.String, "The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out"));
         final TreeSet<String> samples = new TreeSet<String>();
         samples.addAll(SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames));
 
@@ -149,6 +150,7 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> {
             for ( final String line : new XReadLines( RECAL_FILE ) ) {
                 final String[] vals = line.split(",");
                 lodMap.put( Double.parseDouble(vals[3]), vals[0], Integer.parseInt(vals[1]), Integer.parseInt(vals[2]) ); // value comes before the keys
+                annotationMap.put( vals[4], vals[0], Integer.parseInt(vals[1]), Integer.parseInt(vals[2]) ); // value comes before the keys
             }
         } catch ( FileNotFoundException e ) {
             throw new UserException.CouldNotReadInputFile(RECAL_FILE, e);
@@ -174,11 +176,15 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> {
                     String filterString = null;
                     final Map<String, Object> attrs = new HashMap<String, Object>(vc.getAttributes());
                     final Double lod = (Double) lodMap.get( vc.getChr(), vc.getStart(), vc.getEnd() );
+                    final String worstAnnotation = (String) annotationMap.get( vc.getChr(), vc.getStart(), vc.getEnd() );
                     if( lod == null ) {
                         throw new UserException("Encountered input variant which isn't found in the input recal file. Please make sure VariantRecalibrator and ApplyRecalibration were run on the same set of input variants. First seen at: " + vc );
                     }
 
+                    // Annotate the new record with its VQSLOD and the worst performing annotation
                     attrs.put(VariantRecalibrator.VQS_LOD_KEY, String.format("%.4f", lod));
+                    attrs.put(VariantRecalibrator.CULPRIT_KEY, worstAnnotation);
+
                     for( int i = tranches.size() - 1; i >= 0; i-- ) {
                         final Tranche tranche = tranches.get(i);
                         if( lod >= tranche.minVQSLod ) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
index 9ffe7be7a..a09a30145 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
@@ -190,6 +190,19 @@ public class GaussianMixtureModel {
         return MathUtils.log10sumLog10(pVarInGaussianLog10); // Sum(pi_k * p(v|n,k))
     }
 
+    public Double evaluateDatumInOneDimension( final VariantDatum datum, final int iii ) {
+        if(datum.isNull[iii]) { return null; }
+
+        final Normal normal = new Normal(0.0, 1.0, null);
+        final double[] pVarInGaussianLog10 = new double[gaussians.size()];
+        int gaussianIndex = 0;
+        for( final MultivariateGaussian gaussian : gaussians ) {
+            normal.setState( gaussian.mu[iii], gaussian.sigma.get(iii, iii) );
+            pVarInGaussianLog10[gaussianIndex++] = gaussian.pMixtureLog10 + Math.log10( normal.pdf( datum.annotations[iii] ) );
+        }
+        return MathUtils.log10sumLog10(pVarInGaussianLog10); // Sum(pi_k * p(v|n,k))
+    }
+
     public double evaluateDatumMarginalized( final VariantDatum datum ) {
         int numVals = 0;
         double sumPVarInGaussian = 0.0;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
index 2fd1326fe..efff5b780 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -254,7 +254,9 @@ public class VariantDataManager {
 
     public void writeOutRecalibrationTable( final PrintStream RECAL_FILE ) {
         for( final VariantDatum datum : data ) {
-            RECAL_FILE.println(String.format("%s,%d,%d,%.4f", datum.contig, datum.start, datum.stop, datum.lod));
+            RECAL_FILE.println(String.format("%s,%d,%d,%.4f,%s",
+                    datum.contig, datum.start, datum.stop, datum.lod,
+                    (datum.worstAnnotation != -1 ? annotationKeys.get(datum.worstAnnotation) : "NULL")));
         }
     }
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java
index ac875b645..38e2affb6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java
@@ -24,6 +24,7 @@ public class VariantDatum implements Comparable<VariantDatum> {
     public String contig;
     public int start;
     public int stop;
+    public int worstAnnotation;
     public MultivariateGaussian assignment; // used in K-means implementation 
 
     public int compareTo( final VariantDatum other ) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index e651b62e0..b5fda4443 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -60,6 +60,7 @@ import java.util.*;
 public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDatum>, ExpandingArrayList<VariantDatum>> implements TreeReducible<ExpandingArrayList<VariantDatum>> {
 
     public static final String VQS_LOD_KEY = "VQSLOD";
+    public static final String CULPRIT_KEY = "culprit";
 
     @ArgumentCollection private VariantRecalibratorArgumentCollection VRAC = new VariantRecalibratorArgumentCollection();
 
@@ -232,6 +233,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         engine.evaluateData( dataManager.getData(), goodModel, false );
         final GaussianMixtureModel badModel = engine.generateModel( dataManager.selectWorstVariants( VRAC.PERCENT_BAD_VARIANTS, VRAC.MIN_NUM_BAD_VARIANTS ) );
         engine.evaluateData( dataManager.getData(), badModel, true );
+        engine.calculateWorstPerformingAnnotation( dataManager.getData(), goodModel, badModel );
 
         final ExpandingArrayList<VariantDatum> randomData = dataManager.getRandomDataForPlotting( 6000 );
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
index a0fbc572d..81e4d190c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
@@ -57,6 +57,23 @@ public class VariantRecalibratorEngine {
         }
     }
 
+    public void calculateWorstPerformingAnnotation( final List<VariantDatum> data, final GaussianMixtureModel goodModel, final GaussianMixtureModel badModel ) {
+        for( final VariantDatum datum : data ) {
+            int worstAnnotation = -1;
+            double minProb = Double.MAX_VALUE;
+            for( int iii = 0; iii < datum.annotations.length; iii++ ) {
+                final Double goodProbLog10 = goodModel.evaluateDatumInOneDimension(datum, iii);
+                final Double badProbLog10 = badModel.evaluateDatumInOneDimension(datum, iii);
+                if( goodProbLog10 != null && badProbLog10 != null ) {
+                    final double prob = goodProbLog10 - badProbLog10;
+                    if(prob < minProb) { minProb = prob; worstAnnotation = iii; }
+                }
+            }
+            datum.worstAnnotation = worstAnnotation;
+        }
+    }
+
+
     /////////////////////////////
     // Private Methods used for generating a GaussianMixtureModel
     /////////////////////////////
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
index eb6a1a4c6..9600046da 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
@@ -26,8 +26,8 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
 
     VRTest lowPass = new VRTest("phase1.projectConsensus.chr20.raw.snps.vcf",
             "d33212a84368e821cbedecd4f59756d6",  // tranches
-            "a35cd067f378442eee8cd5edeea92be0",  // recal file
-            "126d52843f4a57199ee97750ffc16a07"); // cut VCF
+            "4652dca41222bebdf9d9fda343b2a835",  // recal file
+            "5350b1a4c1250cf3b77ca45327c04711"); // cut VCF
 
     @DataProvider(name = "VRTest")
     public Object[][] createData1() {

From 5faf40b79deea87ceb0e682bf6e27721cc51f621 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Sat, 2 Jul 2011 10:39:53 -0400
Subject: [PATCH 019/161] Moving AnalyzeAnnotations into the archive because it
 has outlived its usefulness.

---
 .../R/plot_Annotations_BinnedTruthMetrics.R   | 190 ------------------
 .../AnalyzeAnnotationsWalker.java             | 154 --------------
 .../AnnotationDataManager.java                | 169 ----------------
 .../analyzeannotations/AnnotationDatum.java   | 170 ----------------
 public/packages/GenomeAnalysisTK.xml          |   1 -
 5 files changed, 684 deletions(-)
 delete mode 100644 public/R/plot_Annotations_BinnedTruthMetrics.R
 delete mode 100755 public/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnalyzeAnnotationsWalker.java
 delete mode 100755 public/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDataManager.java
 delete mode 100755 public/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java

diff --git a/public/R/plot_Annotations_BinnedTruthMetrics.R b/public/R/plot_Annotations_BinnedTruthMetrics.R
deleted file mode 100644
index 9f9ee290c..000000000
--- a/public/R/plot_Annotations_BinnedTruthMetrics.R
+++ /dev/null
@@ -1,190 +0,0 @@
-#!/bin/env Rscript
-
-args <- commandArgs(TRUE)
-verbose = TRUE
-
-input = args[1]
-annotationName = args[2]
-minBinCutoff = as.numeric(args[3])
-medianNumVariants = args[4]
-
-c <- read.table(input, header=T)
-
-all = c[c$numVariants>minBinCutoff & c$category=="all",]
-novel = c[c$numVariants>minBinCutoff & c$category=="novel",]
-dbsnp = c[c$numVariants>minBinCutoff & c$category=="dbsnp",]
-truth = c[c$numVariants>minBinCutoff & c$category=="truth",]
-
-#
-# Calculate min, max, medians
-#
-
-d = c[c$numVariants>minBinCutoff,]
-ymin = min(d$titv)
-ymax = max(d$titv)
-xmin = min(d$value)
-xmax = max(d$value)
-m = weighted.mean(all$value,all$numVariants/sum(all$numVariants))
-ma = all[all$value > m,]
-mb = all[all$value < m,]
-m75 = weighted.mean(ma$value,ma$numVariants/sum(ma$numVariants))
-m25 = weighted.mean(mb$value,mb$numVariants/sum(mb$numVariants))
-if(medianNumVariants == "true") {
-vc = cumsum( all$numVariants/sum(all$numVariants) )
-m10 = all$value[ max(which(vc<=0.10)) ]
-m25 = all$value[ max(which(vc<=0.25)) ]
-m = all$value[ max(which(vc<=0.5)) ]
-m75 = all$value[ min(which(vc>=0.75)) ]
-m90 = all$value[ min(which(vc>=0.90)) ]
-}
-
-#
-# Plot TiTv ratio as a function of the annotation
-#
-
-outfile = paste(input, ".TiTv.pdf", sep="")
-pdf(outfile, height=7, width=7)
-par(cex=1.1)
-plot(all$value,all$titv,xlab=annotationName,ylab="Ti/Tv Ratio",pch=20,ylim=c(ymin,ymax),xaxt="n",ps=14);
-axis(1,axTicks(1), format(axTicks(1), scientific=F))
-abline(v=m,lty=2,col="red")
-abline(v=m75,lty=3)
-abline(v=m25,lty=3)
-text(m, ymin, "50", col="red", cex=0.6);
-text(m75, ymin, "75", col="black", cex=0.6);
-text(m25, ymin, "25", col="black", cex=0.6);
-if(medianNumVariants == "true") {
-abline(v=m90,lty=3)
-abline(v=m10,lty=3)
-text(m10, ymin, "10", col="black", cex=0.6);
-text(m90, ymin, "90", col="black", cex=0.6);
-}
-points(novel$value,novel$titv,col="green",pch=20)
-points(dbsnp$value,dbsnp$titv,col="blue",pch=20)
-if( sum(all$truePositive==0) != length(all$truePositive) ) {
-points(truth$value,truth$titv,col="magenta",pch=20)
-legend("topleft", c("all","novel","dbsnp","truth"),col=c("black","green","blue","magenta"),pch=c(20,20,20,20))
-} else {
-legend("topleft", c("all","novel","dbsnp"),col=c("black","green","blue"),pch=c(20,20,20))
-}
-dev.off()
-
-#
-# Plot TiTv ratio as a function of the annotation, log scale on the x-axis
-#
-
-outfile = paste(input, ".TiTv_log.pdf", sep="")
-pdf(outfile, height=7, width=7)
-par(cex=1.1)
-plot(all$value,all$titv,xlab=annotationName,log="x",ylab="Ti/Tv Ratio",pch=20,ylim=c(ymin,ymax),xaxt="n",ps=14);
-axis(1,axTicks(1), format(axTicks(1), scientific=F))
-abline(v=m,lty=2,col="red")
-abline(v=m75,lty=3)
-abline(v=m25,lty=3)
-text(m, ymin, "50", col="red", cex=0.6);
-text(m75, ymin, "75", col="black", cex=0.6);
-text(m25, ymin, "25", col="black", cex=0.6);
-if(medianNumVariants == "true") {
-abline(v=m90,lty=3)
-abline(v=m10,lty=3)
-text(m10, ymin, "10", col="black", cex=0.6);
-text(m90, ymin, "90", col="black", cex=0.6);
-}
-points(novel$value,novel$titv,col="green",pch=20)
-points(dbsnp$value,dbsnp$titv,col="blue",pch=20)
-if( sum(all$truePositive==0) != length(all$truePositive) ) {
-points(truth$value,truth$titv,col="magenta",pch=20)
-legend("topleft", c("all","novel","dbsnp","truth"),col=c("black","green","blue","magenta"),pch=c(20,20,20,20))
-} else {
-legend("topleft", c("all","novel","dbsnp"),col=c("black","green","blue"),pch=c(20,20,20))
-}
-dev.off()
-
-#
-# Plot dbsnp and true positive rate as a function of the annotation
-#
-
-ymin = min(all$dbsnp)
-ymax = max(all$dbsnp)
-outfile = paste(input, ".truthRate.pdf", sep="")
-pdf(outfile, height=7, width=7)
-par(cex=1.1)
-yLabel = "DBsnp Rate"
-if( sum(all$truePositive==0) != length(all$truePositive) ) {
-t = all[all$truePositive>0,]
-yLabel = "DBsnp/True Positive Rate"
-ymin = min(min(all$dbsnp),min(t$truePositive))
-ymax = max(max(all$dbsnp),max(t$truePositive))
-}
-plot(all$value,all$dbsnp,xlab=annotationName,ylab=yLabel,pch=20,ylim=c(ymin,ymax),xaxt="n",ps=14);
-axis(1,axTicks(1), format(axTicks(1), scientific=F))
-abline(v=m,lty=2,col="red")
-abline(v=m75,lty=3)
-abline(v=m25,lty=3)
-text(m, ymin, "50", col="red", cex=0.6);
-text(m75, ymin, "75", col="black", cex=0.6);
-text(m25, ymin, "25", col="black", cex=0.6);
-if(medianNumVariants == "true") {
-abline(v=m90,lty=3)
-abline(v=m10,lty=3)
-text(m10, ymin, "10", col="black", cex=0.6);
-text(m90, ymin, "90", col="black", cex=0.6);
-}
-if( sum(all$truePositive==0) != length(all$truePositive) ) {
-points(t$value,t$truePositive,col="magenta",pch=20);
-legend("topleft", c("dbsnp","truth"),col=c("black","magenta"),pch=c(20,20))
-}
-dev.off()
-
-#
-# Plot dbsnp and true positive rate as a function of the annotation, log scale on the x-axis
-#
-
-outfile = paste(input, ".truthRate_log.pdf", sep="")
-pdf(outfile, height=7, width=7)
-par(cex=1.1)
-yLabel = "DBsnp Rate"
-if( sum(all$truePositive==0) != length(all$truePositive) ) {
-yLabel = "DBsnp/Truth Rate"
-}
-plot(all$value,all$dbsnp,xlab=annotationName,log="x",ylab=yLabel,ylim=c(ymin,ymax),pch=20,xaxt="n",ps=14);
-axis(1,axTicks(1), format(axTicks(1), scientific=F))
-abline(v=m,lty=2,col="red")
-abline(v=m75,lty=3)
-abline(v=m25,lty=3)
-text(m, ymin, "50", col="red", cex=0.6);
-text(m75, ymin, "75", col="black", cex=0.6);
-text(m25, ymin, "25", col="black", cex=0.6);
-if(medianNumVariants == "true") {
-abline(v=m90,lty=3)
-abline(v=m10,lty=3)
-text(m10, ymin, "10", col="black", cex=0.6);
-text(m90, ymin, "90", col="black", cex=0.6);
-}
-if( sum(all$truePositive==0) != length(all$truePositive) ) {
-points(t$value,t$truePositive,col="magenta",pch=20);
-legend("topleft", c("dbsnp","truth"),col=c("black","magenta"),pch=c(20,20))
-}
-dev.off()
-
-#
-# Plot histogram of the annotation's value
-#
-
-outfile = paste(input, ".Histogram.pdf", sep="")
-pdf(outfile, height=7, width=7)
-par(cex=1.1)
-plot(all$value,all$numVariants,xlab=annotationName,ylab="Num variants in bin",type="h",xaxt="n",ps=14,lwd=4);
-axis(1,axTicks(1), format(axTicks(1), scientific=F))
-dev.off()
-
-#
-# Plot histogram of the annotation's value, log scale on x-axis
-#
-
-outfile = paste(input, ".Histogram_log.pdf", sep="")
-pdf(outfile, height=7, width=7)
-par(cex=1.1)
-plot(all$value,all$numVariants,xlab=annotationName,log="x",ylab="Num variants in bin",type="h",xaxt="n",ps=14,lwd=4);
-axis(1,axTicks(1), format(axTicks(1), scientific=F))
-dev.off()
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnalyzeAnnotationsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnalyzeAnnotationsWalker.java
deleted file mode 100755
index 54fd0a20c..000000000
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnalyzeAnnotationsWalker.java
+++ /dev/null
@@ -1,154 +0,0 @@
-/*
- * Copyright (c) 2010 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.gatk.walkers.analyzeannotations;
-
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-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.RodWalker;
-import org.broadinstitute.sting.commandline.Argument;
-
-import java.util.HashMap;
-import java.util.Collection;
-
-/**
- * Takes variant calls as .vcf files and creates plots of truth metrics as a function of the various annotations found in the INFO field.
- *
- * @author rpoplin
- * @since Jan 15, 2010
- * @help.summary Takes variant calls as .vcf files and creates plots of truth metrics as a function of the various annotations found in the INFO field. 
- */
-
-public class AnalyzeAnnotationsWalker extends RodWalker<Integer, Integer> {
-
-    /////////////////////////////
-    // Command Line Arguments
-    /////////////////////////////
-    @Argument(fullName = "output_prefix", shortName = "output", doc = "The output path and name to prepend to all plots and intermediate data files", required = false)
-    private String OUTPUT_PREFIX = "analyzeAnnotations/";
-    @Argument(fullName = "path_to_Rscript", shortName = "Rscript", doc = "The path to your implementation of Rscript. For Broad users this is maybe /broad/tools/apps/R-2.6.0/bin/Rscript", required = false)
-    private String PATH_TO_RSCRIPT = "Rscript";
-    @Argument(fullName = "path_to_resources", shortName = "resources", doc = "Path to resources folder holding the Sting R scripts.", required = false)
-    private String PATH_TO_RESOURCES = "R/";
-    @Argument(fullName = "min_variants_per_bin", shortName = "minBinSize", doc = "The minimum number of variants in a bin in order to calculate truth metrics.", required = false)
-    private int MIN_VARIANTS_PER_BIN = 1000;
-    @Argument(fullName = "max_variants_per_bin", shortName = "maxBinSize", doc = "The maximum number of variants in a bin.", required = false)
-    private int MAX_VARIANTS_PER_BIN = 20000;
-    @Argument(fullName = "sampleName", shortName = "sampleName", doc = "If supplied, only process variants found in this sample.", required = false)
-    private String SAMPLE_NAME = null;
-    @Argument(fullName = "name", shortName = "name", doc = "Labels for the annotations to make plots look nicer. Each name is a separate -name argument. For example, -name DP,Depth -name AB,AlleleBalance", required = false)
-    private String[] ANNOTATION_NAMES = null;
-    @Argument(fullName = "indicate_mean_num_vars", shortName = "meanNumVars", doc = "If supplied, plots will indicate the distribution of number of variants instead of distribution of value of annotation", required = false)
-    private boolean INDICATE_MEAN_NUM_VARS = false;
-        
-    /////////////////////////////
-    // Private Member Variables
-    /////////////////////////////
-    private AnnotationDataManager dataManager;
-    
-    //---------------------------------------------------------------------------------------------------------------
-    //
-    // initialize
-    //
-    //---------------------------------------------------------------------------------------------------------------
-
-    public void initialize() {
-
-        // Create a HashMap associating the names of the annotations to full Strings that can be used as labels on plots
-        HashMap<String,String> nameMap = null;
-        if( ANNOTATION_NAMES != null ) {
-            nameMap = new HashMap<String,String>();
-            for( String nameLine : ANNOTATION_NAMES ) {
-                String[] vals = nameLine.split(",");
-                nameMap.put(vals[0],vals[1]);
-            }
-        }
-        dataManager = new AnnotationDataManager( nameMap, INDICATE_MEAN_NUM_VARS );
-
-        if( !PATH_TO_RESOURCES.endsWith("/") ) { PATH_TO_RESOURCES = PATH_TO_RESOURCES + "/"; }
-    }
-
-    //---------------------------------------------------------------------------------------------------------------
-    //
-    // map
-    //
-    //---------------------------------------------------------------------------------------------------------------
-
-    public Integer map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
-
-        if( tracker != null ) {
-            Collection<VariantContext> VCs = tracker.getAllVariantContexts(ref);
-
-            // First find out if this variant is in the truth sets
-            boolean isInTruthSet = false;
-            boolean isTrueVariant = false;
-            for ( VariantContext vc : VCs ) {
-                if( vc != null && vc.isSNP() && !vc.isFiltered() ) {
-                    if( vc.getSource().toUpperCase().startsWith("TRUTH") ) {
-                        isInTruthSet = true;
-                        if( vc.isBiallelic() && vc.isVariant() ) {
-                            isTrueVariant = true;
-                        }
-                    }
-                }
-            }
-            
-            // Add each annotation in this VCF Record to the dataManager
-            for ( VariantContext vc : VCs ) {
-                if( vc != null && vc.isSNP() && vc.isBiallelic() && !vc.isFiltered() ) {
-                    if( !vc.getSource().toUpperCase().startsWith("TRUTH") ) {
-                        if( vc.isVariant() ) {
-                            dataManager.addAnnotations( vc, SAMPLE_NAME, isInTruthSet, isTrueVariant );
-                        }
-                    }
-                }
-            }
-        }
-
-        return 1; // This value isn't actually used for anything
-    }
-
-    //---------------------------------------------------------------------------------------------------------------
-    //
-    // reduce
-    //
-    //---------------------------------------------------------------------------------------------------------------
-
-    public Integer reduceInit() {
-        return 0; // Nothing to do here
-    }
-
-    public Integer reduce( Integer value, Integer sum ) {
-        return 0; // Nothing to do here
-    }
-
-    public void onTraversalDone( Integer sum ) {
-
-        // For each annotation, decide how to cut up the data, output intermediate cumulative p(true) tables, and call RScript to plot the tables
-        dataManager.plotCumulativeTables(PATH_TO_RSCRIPT, PATH_TO_RESOURCES, OUTPUT_PREFIX, MIN_VARIANTS_PER_BIN, MAX_VARIANTS_PER_BIN);
-    }
-}
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDataManager.java
deleted file mode 100755
index 2c06b30d6..000000000
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDataManager.java
+++ /dev/null
@@ -1,169 +0,0 @@
-package org.broadinstitute.sting.gatk.walkers.analyzeannotations;
-
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
-import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-
-import java.io.File;
-import java.util.*;
-import java.io.IOException;
-import java.io.PrintStream;
-import java.io.FileNotFoundException;
-
-/*
- * Copyright (c) 2010 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-/**
- * Created by IntelliJ IDEA.
- * User: rpoplin
- * Date: Jan 18, 2010
- */
-
-public class AnnotationDataManager {
-
-    private final HashMap<String, TreeSet<AnnotationDatum>> data;
-    private final HashMap<String,String> nameMap;
-    private final boolean INDICATE_MEAN_NUM_VARS;
-
-    public AnnotationDataManager( HashMap<String,String> _nameMap, boolean _INDICATE_MEAN_NUM_VARS ) {
-        data = new HashMap<String, TreeSet<AnnotationDatum>>();
-        nameMap = _nameMap;
-        INDICATE_MEAN_NUM_VARS = _INDICATE_MEAN_NUM_VARS;
-    }
-
-    public void addAnnotations( final VariantContext vc, final String sampleName, final boolean isInTruthSet, final boolean isTrueVariant ) {
-
-        if( sampleName != null ) { // Only process variants that are found in the sample with this sampleName
-            if( vc.getGenotype(sampleName).isNoCall() ) { // This variant isn't found in this sample so break out
-                return;
-            }
-        } // else, process all samples
-
-        // Loop over each annotation in the vcf record
-        final Map<String,Object> infoField = new HashMap<String, Object>(vc.getAttributes());
-        infoField.put("QUAL", ((Double)vc.getPhredScaledQual()).toString() ); // add QUAL field to annotations
-        for( Map.Entry<String, Object> annotation : infoField.entrySet() ) {
-
-            float value;
-            try {
-                value = Float.parseFloat( annotation.getValue().toString() );
-            } catch( NumberFormatException e ) {
-                continue; // Skip over annotations that aren't floats, like "DB"
-            }
-
-            TreeSet<AnnotationDatum> treeSet = data.get( annotation.getKey() );
-            if( treeSet == null ) { // This annotation hasn't been seen before
-                treeSet = new TreeSet<AnnotationDatum>( new AnnotationDatum() ); // AnnotationDatum is a Comparator that orders variants by the value of the Annotation
-                data.put( annotation.getKey(), treeSet );
-            }
-            AnnotationDatum datum = new AnnotationDatum( value );
-            if( treeSet.contains(datum) ) { // contains() uses AnnotationDatum's equals function, so it only checks if the value field is already present
-                datum = treeSet.tailSet(datum).first();
-            } else {
-                treeSet.add(datum);
-            }
-
-            final boolean isNovelVariant = !vc.hasID() || !vc.getID().contains("rs");
-
-            // Decide if the variant is a transition or transversion
-            if( VariantContextUtils.getSNPSubstitutionType(vc).compareTo(BaseUtils.BaseSubstitutionType.TRANSITION) == 0 ) {
-                datum.incrementTi( isNovelVariant, isInTruthSet, isTrueVariant );
-            } else {
-                datum.incrementTv( isNovelVariant, isInTruthSet, isTrueVariant );
-            }
-        }
-    }
-
-    public void plotCumulativeTables( final String PATH_TO_RSCRIPT, final String PATH_TO_RESOURCES, final String OUTPUT_PREFIX,
-                                      final int MIN_VARIANTS_PER_BIN, final int MAX_VARIANTS_PER_BIN ) {
-
-        final AnnotationDatum thisAnnotationBin = new AnnotationDatum();
-        System.out.println( "\nFinished reading variants into memory. Executing RScript commands:" );
-
-        // For each annotation we've seen
-        for( final String annotationKey : data.keySet() ) {
-
-            String filename = OUTPUT_PREFIX + annotationKey + ".dat";
-            PrintStream output;
-            try {
-                output = new PrintStream(filename); // Create the intermediate data file for this annotation
-            } catch ( FileNotFoundException e ) {
-                throw new UserException.CouldNotCreateOutputFile(new File(filename), "Can't create intermediate output annotation data file. Does the output directory exist?", e);
-            }
-
-            // Output a header line
-            output.println("value\ttitv\tdbsnp\ttruePositive\tnumVariants\tcategory");
-
-            // Bin SNPs and calculate truth metrics for each bin
-            thisAnnotationBin.clearBin();
-            for( final AnnotationDatum datum : data.get( annotationKey ) ) {
-                thisAnnotationBin.combine( datum );
-                if( thisAnnotationBin.numVariants( AnnotationDatum.FULL_SET ) >= MAX_VARIANTS_PER_BIN ) { // This annotation bin is full
-                    output.println( thisAnnotationBin.value + "\t" + thisAnnotationBin.calcTiTv( AnnotationDatum.FULL_SET ) + "\t" + thisAnnotationBin.calcDBsnpRate() + "\t" + thisAnnotationBin.calcTPrate() +
-                            "\t" + thisAnnotationBin.numVariants( AnnotationDatum.FULL_SET ) + "\tall");
-                    output.println( thisAnnotationBin.value + "\t" + thisAnnotationBin.calcTiTv( AnnotationDatum.NOVEL_SET ) + "\t-1\t-1\t" + thisAnnotationBin.numVariants( AnnotationDatum.NOVEL_SET ) + "\tnovel");
-                    output.println( thisAnnotationBin.value + "\t" + thisAnnotationBin.calcTiTv( AnnotationDatum.DBSNP_SET ) + "\t-1\t-1\t" + thisAnnotationBin.numVariants( AnnotationDatum.DBSNP_SET ) + "\tdbsnp");
-                    output.println( thisAnnotationBin.value + "\t" + thisAnnotationBin.calcTiTv( AnnotationDatum.TRUTH_SET ) + "\t-1\t-1\t" + thisAnnotationBin.numVariants( AnnotationDatum.TRUTH_SET ) + "\ttruth");
-                    thisAnnotationBin.clearBin();
-                }
-                // else, continue accumulating variants because this bin isn't full yet
-            }
-
-            // One final bin that may not have been dumped out
-            if( thisAnnotationBin.numVariants( AnnotationDatum.FULL_SET ) != 0 ) {
-                output.println( thisAnnotationBin.value + "\t" + thisAnnotationBin.calcTiTv( AnnotationDatum.FULL_SET ) + "\t" + thisAnnotationBin.calcDBsnpRate() + "\t" + thisAnnotationBin.calcTPrate() +
-                            "\t" + thisAnnotationBin.numVariants( AnnotationDatum.FULL_SET ) + "\tall");
-                output.println( thisAnnotationBin.value + "\t" + thisAnnotationBin.calcTiTv( AnnotationDatum.NOVEL_SET ) + "\t-1\t-1\t" + thisAnnotationBin.numVariants( AnnotationDatum.NOVEL_SET ) + "\tnovel");
-                output.println( thisAnnotationBin.value + "\t" + thisAnnotationBin.calcTiTv( AnnotationDatum.DBSNP_SET ) + "\t-1\t-1\t" + thisAnnotationBin.numVariants( AnnotationDatum.DBSNP_SET ) + "\tdbsnp");
-                output.println( thisAnnotationBin.value + "\t" + thisAnnotationBin.calcTiTv( AnnotationDatum.TRUTH_SET ) + "\t-1\t-1\t" + thisAnnotationBin.numVariants( AnnotationDatum.TRUTH_SET ) + "\ttruth");
-                thisAnnotationBin.clearBin();
-            }
-
-            // Close the PrintStream
-            output.close();
-
-            String annotationName = null;
-            if( nameMap != null ) {
-                annotationName = nameMap.get(annotationKey);
-            }
-            if( annotationName == null ) { // This annotation is not in the name map so use the key instead
-                annotationName = annotationKey;
-            }
-
-            // Print out the command line to make it clear to the user what is being executed and how one might modify it
-            final String rScriptCommandLine = PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_Annotations_BinnedTruthMetrics.R" + " " +
-                                   OUTPUT_PREFIX + annotationKey + ".dat" + " " + annotationName + " " + MIN_VARIANTS_PER_BIN + " " + INDICATE_MEAN_NUM_VARS;
-            System.out.println( rScriptCommandLine );
-
-            // Execute the RScript command to plot the table of truth values
-            try {
-                Runtime.getRuntime().exec( rScriptCommandLine );
-            } catch ( IOException e ) {
-                throw new UserException.CannotExecuteRScript( rScriptCommandLine, e );
-            }
-        }
-    }
-}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java
deleted file mode 100755
index 888eb7e6e..000000000
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java
+++ /dev/null
@@ -1,170 +0,0 @@
-package org.broadinstitute.sting.gatk.walkers.analyzeannotations;
-
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-
-import java.util.Comparator;
-
-/*
- * Copyright (c) 2010 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-/**
- * Created by IntelliJ IDEA.
- * User: rpoplin
- * Date: Jan 18, 2010
- */
-
-public class AnnotationDatum implements Comparator<AnnotationDatum> {
-    
-    public float value;
-    private final int[] ti;
-    private final int[] tv;
-
-    public static final int FULL_SET = 0;
-    public static final int NOVEL_SET = 1;
-    public static final int DBSNP_SET = 2;
-    public static final int TRUTH_SET = 3;
-    public static final int TRUE_POSITIVE = 4;
-    private static final int NUM_SETS = 5;
-
-    public AnnotationDatum() {
-
-        value = 0.0f;
-        ti = new int[NUM_SETS];
-        tv = new int[NUM_SETS];
-        for( int iii = 0; iii < NUM_SETS; iii++ ) {
-            ti[iii] = 0;
-            tv[iii] = 0;
-        }
-    }
-
-    public AnnotationDatum( final float _value ) {
-
-        value = _value;
-        ti = new int[NUM_SETS];
-        tv = new int[NUM_SETS];
-        for( int iii = 0; iii < NUM_SETS; iii++ ) {
-            ti[iii] = 0;
-            tv[iii] = 0;
-        }
-    }
-
-    final public void incrementTi( final boolean isNovelVariant, final boolean isInTruthSet, final boolean isTrueVariant ) {
-
-        ti[FULL_SET]++;
-        if( isNovelVariant ) {
-            ti[NOVEL_SET]++;
-        } else { // Is known, in DBsnp
-            ti[DBSNP_SET]++;
-        }
-        if( isInTruthSet ) {
-            ti[TRUTH_SET]++;
-            if( isTrueVariant ) {
-                ti[TRUE_POSITIVE]++;
-            }
-        }
-    }
-
-    final public void incrementTv( final boolean isNovelVariant, final boolean isInTruthSet, final boolean isTrueVariant ) {
-
-        tv[FULL_SET]++;
-        if( isNovelVariant ) {
-            tv[NOVEL_SET]++;
-        } else { // Is known, in DBsnp
-            tv[DBSNP_SET]++;
-        }
-        if( isInTruthSet ) {
-            tv[TRUTH_SET]++;
-            if( isTrueVariant ) {
-                tv[TRUE_POSITIVE]++;
-            }
-        }
-    }
-
-    final public void combine( final AnnotationDatum that ) {
-
-        for( int iii = 0; iii < NUM_SETS; iii++ ) {
-            this.ti[iii] += that.ti[iii];
-            this.tv[iii] += that.tv[iii];
-        }
-        this.value = that.value; // Overwrite this bin's value
-    }
-
-    final public float calcTiTv( final int INDEX ) {
-
-        if( ti[INDEX] < 0 || tv[INDEX] < 0 ) {
-            throw new ReviewedStingException( "Integer overflow detected! There are too many variants piled up in one annotation bin." );
-        }
-
-        if( tv[INDEX] == 0 ) { // Don't divide by zero
-            return 0.0f;
-        }
-
-        return ((float) ti[INDEX]) / ((float) tv[INDEX]);
-    }
-
-    final public float calcDBsnpRate() {
-
-        if( ti[FULL_SET] + tv[FULL_SET] == 0 ) { // Don't divide by zero
-            return 0.0f;
-        }
-
-        return 100.0f * ((float) ti[DBSNP_SET] + tv[DBSNP_SET]) /
-                ((float) ti[FULL_SET] + tv[FULL_SET]);
-    }
-
-    final public float calcTPrate() {
-
-        if( ti[TRUTH_SET] + tv[TRUTH_SET] == 0 ) { // Don't divide by zero
-            return 0.0f;
-        }
-
-        return 100.0f * ((float) ti[TRUE_POSITIVE] + tv[TRUE_POSITIVE]) /
-                ((float) ti[TRUTH_SET] + tv[TRUTH_SET]);
-    }
-
-    final public int numVariants( final int INDEX ) {
-        return ti[INDEX] + tv[INDEX];
-    }
-
-    final public void clearBin() {
-        value = 0.0f;
-        for( int iii = 0; iii < NUM_SETS; iii++ ) {
-            ti[iii] = 0;
-            tv[iii] = 0;
-        }
-    }
-
-    public int compare( AnnotationDatum a1, AnnotationDatum a2 ) { // Function needed for this to be a Comparator
-        if( a1.value < a2.value ) { return -1; }
-        if( a1.value > a2.value ) { return 1; }
-        return 0;
-    }
-
-    public int equals( AnnotationDatum that ) { // Function needed for this to be sorted correctly in a TreeSet
-        if( this.value < that.value ) { return -1; }
-        if( this.value > that.value ) { return 1; }
-        return 0;
-    }
-}
diff --git a/public/packages/GenomeAnalysisTK.xml b/public/packages/GenomeAnalysisTK.xml
index f923ea698..14b837211 100644
--- a/public/packages/GenomeAnalysisTK.xml
+++ b/public/packages/GenomeAnalysisTK.xml
@@ -19,7 +19,6 @@
     <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java" />
     <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java" />
     <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java" />
-    <file name="public/R/plot_Annotations_BinnedTruthMetrics.R" />
     <file name="public/R/plot_Tranches.R" />
     <file name="public/R/titvFPEst.R" />
   </resources>

From 09af6bbc6c548082edc09883980e12e5d72fbfa4 Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Sat, 2 Jul 2011 16:58:57 -0400
Subject: [PATCH 022/161] Ugh - backed out experimental code not for public
 consumption unintendedly committed

---
 .../IndelGenotypeLikelihoodsCalculationModel.java        | 4 ++--
 .../gatk/walkers/indels/PairHMMIndelErrorModel.java      | 9 ++-------
 2 files changed, 4 insertions(+), 9 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
index 62f6ff5a6..1f430548b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
@@ -157,10 +157,10 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
                  GATKSAMRecord read = ReadUtils.hardClipAdaptorSequence(p.getRead());
                 if (read == null)
                     continue;     
-         /*       if(ReadUtils.is454Read(read)) {
+                if(ReadUtils.is454Read(read)) {
                     continue;
                 }
-            */
+
                 if (DEBUG && p.isIndel()) {
                     System.out.format("Read: %s, cigar: %s, aln start: %d, aln end: %d, p.len:%d, Type:%s, EventBases:%s\n",
                             read.getReadName(),read.getCigar().toString(),read.getAlignmentStart(),read.getAlignmentEnd(),
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
index 5c1f57bc7..ab7ae4184 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
@@ -105,7 +105,6 @@ public class PairHMMIndelErrorModel {
     private static final double MIN_GAP_CONT_PENALTY = 10.0;
     private static final double GAP_PENALTY_HRUN_STEP = 1.0; // each increase in hrun decreases gap penalty by this.
 
-    private static final double GOP_454_DELTA = 15.0; // lower gap penalty for 454 reads
 
     private boolean doViterbi = false;
 
@@ -772,10 +771,10 @@ public class PairHMMIndelErrorModel {
                 if (read == null)
                     continue;
 
-         /*       if(ReadUtils.is454Read(read) && !getGapPenaltiesFromFile) {
+                if(ReadUtils.is454Read(read) && !getGapPenaltiesFromFile) {
                     continue;
                 }
-            */
+
                 double[] recalQuals = null;
 
  /*
@@ -991,10 +990,6 @@ public class PairHMMIndelErrorModel {
                                }  else {
                                    currentContextGOP = Arrays.copyOfRange(gapOpenProbabilityMap.get(a), (int)indStart, (int)indStop);
                                    currentContextGCP = Arrays.copyOfRange(gapContProbabilityMap.get(a), (int)indStart, (int)indStop);
-                                   if(ReadUtils.is454Read(read)) {
-                                       for (int k=0; k <currentContextGOP.length; k++ )
-                                           currentContextGOP[k] += GOP_454_DELTA/10;
-                                   }
                                    readLikelihood = computeReadLikelihoodGivenHaplotypeAffineGaps(haplotypeBases, readBases, readQuals, currentContextGOP, currentContextGCP);
                                }
                             }

From fdc2ebb321abe0da2ea20b13b5250d016740213e Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Sat, 2 Jul 2011 17:15:13 -0400
Subject: [PATCH 023/161] Adding ability to specify in VQSR a list of bad sites
 to use when training the negative model. Just add bad=true to the list of rod
 tags for your bad sites track.

---
 .../variantrecalibration/TrainingSet.java     | 12 ++++-
 .../VariantDataManager.java                   | 44 ++++++++++++-------
 .../variantrecalibration/VariantDatum.java    |  2 +-
 .../VariantRecalibrator.java                  |  4 +-
 4 files changed, 42 insertions(+), 20 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java
index f3677421e..9bbcf395a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java
@@ -14,6 +14,7 @@ public class TrainingSet {
     public String name;
     public boolean isKnown = false;
     public boolean isTraining = false;
+    public boolean isAntiTraining = false;
     public boolean isTruth = false;
     public boolean isConsensus = false;
     public double prior = 0.0;
@@ -22,17 +23,24 @@ public class TrainingSet {
 
     public TrainingSet( final String name, final Tags tags ) {
         this.name = name;
+
+        // Parse the tags to decide which tracks have which properties
         if( tags != null ) {
             isKnown = tags.containsKey("known") && tags.getValue("known").equals("true");
             isTraining = tags.containsKey("training") && tags.getValue("training").equals("true");
+            isAntiTraining = tags.containsKey("bad") && tags.getValue("bad").equals("true");
             isTruth = tags.containsKey("truth") && tags.getValue("truth").equals("true");
             isConsensus = tags.containsKey("consensus") && tags.getValue("consensus").equals("true");
             prior = ( tags.containsKey("prior") ? Double.parseDouble(tags.getValue("prior")) : prior );
         }
-        if( !isConsensus ) {
+
+        // Report back to the user which tracks were found and the properties that were detected
+        if( !isConsensus && !isAntiTraining ) {
             logger.info( String.format( "Found %s track: \tKnown = %s \tTraining = %s \tTruth = %s \tPrior = Q%.1f", this.name, isKnown, isTraining, isTruth, prior) );
-        } else {
+        } else if( isConsensus ) {
             logger.info( String.format( "Found consensus track: %s", this.name) );
+        } else {
+            logger.info( String.format( "Found bad sites training track: %s", this.name) );
         }
     }
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
index efff5b780..cd739f9fc 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -84,7 +84,6 @@ public class VariantDataManager {
                 remove = remove || (Math.abs(val) > VRAC.STD_THRESHOLD);
             }
             datum.failingSTDThreshold = remove;
-            datum.usedForTraining = 0;
         }
     }
 
@@ -118,38 +117,47 @@ public class VariantDataManager {
         for( final VariantDatum datum : data ) {
             if( datum.atTrainingSite && !datum.failingSTDThreshold && datum.originalQual > VRAC.QUAL_THRESHOLD ) {
                 trainingData.add( datum );
-                datum.usedForTraining = 1;
             }
         }
         logger.info( "Training with " + trainingData.size() + " variants after standard deviation thresholding." );
         if( trainingData.size() < VRAC.MIN_NUM_BAD_VARIANTS ) {
-            logger.warn("WARNING: Training with very few variant sites! Please check the model reporting PDF to ensure the quality of the model is reliable.");
+            logger.warn( "WARNING: Training with very few variant sites! Please check the model reporting PDF to ensure the quality of the model is reliable." );
         }
         return trainingData;
     }
 
     public ExpandingArrayList<VariantDatum> selectWorstVariants( double bottomPercentage, final int minimumNumber ) {
-        Collections.sort( data );
+        // The return value is the list of training variants
         final ExpandingArrayList<VariantDatum> trainingData = new ExpandingArrayList<VariantDatum>();
-        final int numToAdd = Math.max( minimumNumber, Math.round((float)bottomPercentage * data.size()) );
-        if( numToAdd > data.size() ) {
-            throw new UserException.BadInput("Error during negative model training. Minimum number of variants to use in training is larger than the whole call set. One can attempt to lower the --minNumBadVariants arugment but this is unsafe.");
+
+        // First add to the training list all sites overlapping any bad sites training tracks
+        for( final VariantDatum datum : data ) {
+            if( datum.atAntiTrainingSite && !datum.failingSTDThreshold && !Double.isInfinite(datum.lod) ) {
+                trainingData.add( datum );
+            }
         }
-        if( numToAdd == minimumNumber ) {
-            logger.warn("WARNING: Training with very few variant sites! Please check the model reporting PDF to ensure the quality of the model is reliable.");
+        final int numBadSitesAdded = trainingData.size();
+        logger.info( "Found " + numBadSitesAdded + " variants overlapping bad sites training tracks." );
+
+        // Next, sort the variants by the LOD coming from the positive model and add to the list the bottom X percent of variants
+        Collections.sort( data );
+        final int numToAdd = Math.max( minimumNumber - trainingData.size(), Math.round((float)bottomPercentage * data.size()) );
+        if( numToAdd > data.size() ) {
+            throw new UserException.BadInput( "Error during negative model training. Minimum number of variants to use in training is larger than the whole call set. One can attempt to lower the --minNumBadVariants arugment but this is unsafe." );
+        } else if( numToAdd == minimumNumber - trainingData.size() ) {
+            logger.warn( "WARNING: Training with very few variant sites! Please check the model reporting PDF to ensure the quality of the model is reliable." );
             bottomPercentage = ((float) numToAdd) / ((float) data.size());
         }
-        int index = 0;
-        int numAdded = 0;
+        int index = 0, numAdded = 0;
         while( numAdded < numToAdd ) {
             final VariantDatum datum = data.get(index++);
             if( !datum.failingSTDThreshold && !Double.isInfinite(datum.lod) ) {
+                datum.atAntiTrainingSite = true;
                 trainingData.add( datum );
-                datum.usedForTraining = -1;
                 numAdded++;
             }
         }
-        logger.info("Training with worst " + (float) bottomPercentage * 100.0f + "% of passing data --> " + trainingData.size() + " variants with LOD <= " + String.format("%.4f", data.get(index).lod) + ".");
+        logger.info( "Additionally training with worst " + (float) bottomPercentage * 100.0f + "% of passing data --> " + (trainingData.size() - numBadSitesAdded) + " variants with LOD <= " + String.format("%.4f", data.get(index).lod) + "." );
         return trainingData;
     }
 
@@ -162,10 +170,11 @@ public class VariantDataManager {
                 returnData.add(datum);
             }
         }
-        // add an extra 5% of points from bad training set, since that set is small but interesting
+
+        // Add an extra 5% of points from bad training set, since that set is small but interesting
         for( int iii = 0; iii < Math.floor(0.05*numToAdd); iii++) {
             final VariantDatum datum = data.get(GenomeAnalysisEngine.getRandomGenerator().nextInt(data.size()));
-            if( datum.usedForTraining == -1 && !datum.failingSTDThreshold ) { returnData.add(datum); }
+            if( datum.atAntiTrainingSite && !datum.failingSTDThreshold ) { returnData.add(datum); }
             else { iii--; }
         }
 
@@ -236,6 +245,7 @@ public class VariantDataManager {
         datum.atTrainingSite = false;
         datum.prior = 2.0;
         datum.consensusCount = 0;
+
         for( final TrainingSet trainingSet : trainingSets ) {
             for( final VariantContext trainVC : tracker.getVariantContexts( ref, trainingSet.name, null, context.getLocation(), false, false ) ) {
                 if( trainVC != null && trainVC.isNotFiltered() && trainVC.isVariant() &&
@@ -248,6 +258,10 @@ public class VariantDataManager {
                     datum.prior = Math.max( datum.prior, trainingSet.prior );
                     datum.consensusCount += ( trainingSet.isConsensus ? 1 : 0 );
                 }
+                if( trainVC != null ) {
+                    datum.atAntiTrainingSite = datum.atAntiTrainingSite || trainingSet.isAntiTraining;
+                }
+
             }
         }
     }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java
index 38e2affb6..04a5a9d3e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java
@@ -14,13 +14,13 @@ public class VariantDatum implements Comparable<VariantDatum> {
     public double lod;
     public boolean atTruthSite;
     public boolean atTrainingSite;
+    public boolean atAntiTrainingSite;
     public boolean isTransition;
     public boolean isSNP;
     public boolean failingSTDThreshold;
     public double originalQual;
     public double prior;
     public int consensusCount;
-    public int usedForTraining;
     public String contig;
     public int start;
     public int stop;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index b5fda4443..b903d20af 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -175,7 +175,6 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
                     datum.originalQual = vc.getPhredScaledQual();
                     datum.isSNP = vc.isSNP() && vc.isBiallelic();
                     datum.isTransition = datum.isSNP && VariantContextUtils.isTransition(vc);
-                    datum.usedForTraining = 0;
 
                     // Loop through the training data sets and if they overlap this loci then update the prior and training status appropriately
                     dataManager.parseTrainingSets( tracker, ref, context, vc, datum, TRUST_ALL_POLYMORPHIC );
@@ -328,7 +327,8 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
 
                 stream.print("data <- c(");
                 for( final VariantDatum datum : randomData ) {
-                    stream.print(String.format("%.3f, %.3f, %.3f, %d, %d,", datum.annotations[iii], datum.annotations[jjj], (datum.lod < lodCutoff ? -1.0 : 1.0), datum.usedForTraining, (datum.isKnown ? 1 : -1)));
+                    stream.print(String.format("%.3f, %.3f, %.3f, %d, %d,", datum.annotations[iii], datum.annotations[jjj], (datum.lod < lodCutoff ? -1.0 : 1.0),
+                            (datum.atAntiTrainingSite ? -1 : (datum.atTrainingSite ? 1 : 0)), (datum.isKnown ? 1 : -1)));
                 }
                 stream.println("NA,NA,NA,NA,1)");
                 stream.println("d <- matrix(data,ncol=5,byrow=T)");

From 781c0c33a42a4df39624e33da7eb300a580c61b3 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Sat, 2 Jul 2011 17:55:10 -0400
Subject: [PATCH 025/161] Use the worst X% of calls in addition to the bad
 training sites list. Don't include the already added calls in the calculation
 of X%

---
 .../walkers/variantrecalibration/VariantDataManager.java     | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
index cd739f9fc..309d1b8fa 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -151,13 +151,13 @@ public class VariantDataManager {
         int index = 0, numAdded = 0;
         while( numAdded < numToAdd ) {
             final VariantDatum datum = data.get(index++);
-            if( !datum.failingSTDThreshold && !Double.isInfinite(datum.lod) ) {
+            if( !datum.atAntiTrainingSite && !datum.failingSTDThreshold && !Double.isInfinite(datum.lod) ) {
                 datum.atAntiTrainingSite = true;
                 trainingData.add( datum );
                 numAdded++;
             }
         }
-        logger.info( "Additionally training with worst " + (float) bottomPercentage * 100.0f + "% of passing data --> " + (trainingData.size() - numBadSitesAdded) + " variants with LOD <= " + String.format("%.4f", data.get(index).lod) + "." );
+        logger.info( "Additionally training with worst " + String.format("%0.3f", (float) bottomPercentage * 100.0f) + "% of passing data --> " + (trainingData.size() - numBadSitesAdded) + " variants with LOD <= " + String.format("%.4f", data.get(index).lod) + "." );
         return trainingData;
     }
 
@@ -243,6 +243,7 @@ public class VariantDataManager {
         datum.isKnown = false;
         datum.atTruthSite = false;
         datum.atTrainingSite = false;
+        datum.atAntiTrainingSite = false;
         datum.prior = 2.0;
         datum.consensusCount = 0;
 

From 41d46059e7cace435f9f1d558435d4fde14c8531 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Sat, 2 Jul 2011 18:09:17 -0400
Subject: [PATCH 026/161] fixing bad format statement

---
 .../gatk/walkers/variantrecalibration/VariantDataManager.java   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
index 309d1b8fa..f83e9b2f0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -157,7 +157,7 @@ public class VariantDataManager {
                 numAdded++;
             }
         }
-        logger.info( "Additionally training with worst " + String.format("%0.3f", (float) bottomPercentage * 100.0f) + "% of passing data --> " + (trainingData.size() - numBadSitesAdded) + " variants with LOD <= " + String.format("%.4f", data.get(index).lod) + "." );
+        logger.info( "Additionally training with worst " + String.format("%.3f", (float) bottomPercentage * 100.0f) + "% of passing data --> " + (trainingData.size() - numBadSitesAdded) + " variants with LOD <= " + String.format("%.4f", data.get(index).lod) + "." );
         return trainingData;
     }
 

From 38740b0ff5e70df6c5d760251d129ed22d0eeccb Mon Sep 17 00:00:00 2001
From: "Mark A. DePristo" <depristo@broadinstitute.org>
Date: Mon, 4 Jul 2011 16:11:42 -0400
Subject: [PATCH 027/161] First working version of the DiffNode readers for VCF
 and BAM files.  Unit tests confirm the readers are approximately working. 
 Skeleton of a working DiffObjects walker that will be able to provide
 detailed information about how exactly two files of the same type differ, so
 long as the files are supported by the DiffNode structure.

---
 public/testdata/diffTestMaster.vcf | 11 +++++++++++
 public/testdata/diffTestTest.vcf   | 11 +++++++++++
 2 files changed, 22 insertions(+)
 create mode 100644 public/testdata/diffTestMaster.vcf
 create mode 100644 public/testdata/diffTestTest.vcf

diff --git a/public/testdata/diffTestMaster.vcf b/public/testdata/diffTestMaster.vcf
new file mode 100644
index 000000000..549f54345
--- /dev/null
+++ b/public/testdata/diffTestMaster.vcf
@@ -0,0 +1,11 @@
+##fileformat=VCFv4.0
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878	
+chr1	2646	rs62635284	G	A	0.15	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:53,75:3:-12.40,-0.90,-0.00:9.03
+chr1	2979	rs62635286	T	G	83.67	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:31,32:9:-33.61,-2.71,-0.00:27.09
+chr1	2981	rs62028691	A	G	14.69	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:31,33:9:-32.12,-2.71,-0.00:27.08
+chr1	4536	rs11582131	G	C	0.18	PASS	AC=1;AF=0.50;AN=2	GT:AD:DP:GL:GQ	0/1:42,33:16:-41.67,-4.82,-26.29:99
+chr1	4562	rs11490464	C	G	0.14	PASS	AC=1;AF=0.50;AN=2	GT:AD:DP:GL:GQ	0/1:26,30:9:-19.64,-2.72,-14.87:99
+chr1	4770	rs6682375	A	G	0.32	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:9,111:84:-306.27,-28.58,-3.46:99
+chr1	4793	rs6682385	A	G	0.15	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:4,115:109:-350.74,-32.88,-0.10:99
+chr1	5074	rs11586607	T	G	0.01	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:29,97:39:-130.41,-11.75,-3.82:79.31
+chr1	5137	rs62636497	A	T	140.49	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:0,74:39:-148.99,-11.75,-0.01:99
diff --git a/public/testdata/diffTestTest.vcf b/public/testdata/diffTestTest.vcf
new file mode 100644
index 000000000..8699ab253
--- /dev/null
+++ b/public/testdata/diffTestTest.vcf
@@ -0,0 +1,11 @@
+##fileformat=VCFv4.0
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878	
+chr1	2646	rs62635284	G	A	0.15	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:53,75:3:-12.40,-0.90,-0.00:9.03
+chr1	2979	rs62635286	T	G	83.67	CHANGED_FILTER	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:31,32:9:-33.61,-2.71,-0.00:27.09
+chr1	2981	rs62028691	A	G	14.69	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:31,33:9:-32.12,-2.71,-0.00:27.08
+chr1	4536	rs11582131	G	C	0.18	PASS	AC=2;AF=0.50;AN=2	GT:AD:DP:GL:GQ	0/1:42,33:16:-41.67,-4.82,-26.29:99
+chr1	4562	rs11490464	C	G	0.14	PASS	AC=1;AF=0.50;AN=2	GT:AD:DP:GL:GQ	1/1:26,30:9:-19.64,-2.72,-14.87:99
+chr1	4770	rs6682375	A	G	0.32	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	0/1:9,111:84:-306.27,-28.58,-3.46:99
+chr1	4793	rs6682385	A	G	0.15	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:4,114:109:-350.74,-32.88,-0.10:99
+chr1	5074	rs11586607	T	G	0.01	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:29,97:39:-130.41,-11.74,-3.82:79.31
+chr1	5137	rs62636497	A	T	140.49	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:0,74:39:-148.99,-11.75,-0.01:9

From 080875d5daf876ebd29b059c156890d7c349983f Mon Sep 17 00:00:00 2001
From: "Mark A. DePristo" <depristo@broadinstitute.org>
Date: Tue, 5 Jul 2011 16:13:39 -0400
Subject: [PATCH 039/161] Refactored DiffNode/DiffElement/DiffValue class
 structure.  DiffElement is now a pair of Name -> Value, where value is either
 a DiffValue or its subclass DiffNode.  Code cleaned up, more tests added. 
 DiffEngine is now working, with tests.  DiffObjectWalker can now take two
 VCFs and itemize the difference between the two files correctly and
 concisely.

---
 build.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/build.xml b/build.xml
index fe1723587..21066686f 100644
--- a/build.xml
+++ b/build.xml
@@ -741,8 +741,8 @@
                 <jvmarg value="-Dpipeline.run=${pipeline.run}" />
                 <jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
                 <!-- needs to be if -->
-                <!--jvmarg value="-javaagent:lib/cofoja.jar"/-->
-                <!--jvmarg value="-Dcom.google.java.contract.log.contract=false"/-->
+<!--                 <jvmarg value="-javaagent:lib/cofoja.jar"/> -->
+<!--                 <jvmarg value="-Dcom.google.java.contract.log.contract=false"/> -->
 <!--                 <jvmarg value="-Xdebug"/> -->
 <!--                 <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> -->
                 <classpath>

From 7d3dfdfdf2e92f502c4394d338ca01c5de6287e5 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Tue, 5 Jul 2011 16:30:10 -0400
Subject: [PATCH 040/161] Updating the MDCP to use the classpath for the GATK
 jar, removing -gatk parameter.

---
 .../queue/qscripts/MethodsDevelopmentCallingPipeline.scala    | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
index d71c6ae5d..f5b639185 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
@@ -19,9 +19,6 @@ import org.broadinstitute.sting.gatk.phonehome.GATKRunReport
 class MethodsDevelopmentCallingPipeline extends QScript {
   qscript =>
 
-  @Argument(shortName="gatk", doc="gatk jar file", required=true)
-  var gatkJarFile: File = _
-
   @Argument(shortName="outputDir", doc="output directory", required=true)
   var outputDir: String = "./"
 
@@ -185,7 +182,6 @@ class MethodsDevelopmentCallingPipeline extends QScript {
 
   trait UNIVERSAL_GATK_ARGS extends CommandLineGATK {
     logging_level = "INFO";
-    jarFile = gatkJarFile;
     memoryLimit = 4;
     phone_home = if ( LOCAL_ET ) GATKRunReport.PhoneHomeOption.STANDARD else GATKRunReport.PhoneHomeOption.AWS_S3
   }

From 5298e3a942be54c05a8d765c7aaca99e9c061f8a Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Tue, 5 Jul 2011 16:30:41 -0400
Subject: [PATCH 041/161] Making the outputDir optional. Default = ./

---
 .../queue/qscripts/MethodsDevelopmentCallingPipeline.scala      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
index f5b639185..a961beca1 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
@@ -19,7 +19,7 @@ import org.broadinstitute.sting.gatk.phonehome.GATKRunReport
 class MethodsDevelopmentCallingPipeline extends QScript {
   qscript =>
 
-  @Argument(shortName="outputDir", doc="output directory", required=true)
+  @Argument(shortName="outputDir", doc="output directory", required=false)
   var outputDir: String = "./"
 
   @Argument(shortName="skipCalling", doc="skip the calling part of the pipeline and only run VQSR on preset, gold standard VCF files", required=false)

From 7b699f8b175f02bbf7ba2cb1aea420361dc4af0d Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Tue, 5 Jul 2011 21:59:00 -0400
Subject: [PATCH 042/161] Switched GridEngine from looking from environment
 variable to using embedded jar.

---
 build.xml                                     |  33 ++++++++----------
 ivy.xml                                       |   3 ++
 settings/ivysettings.xml                      |   1 +
 .../drmaa-6.2u5p2-sources.jar                 | Bin 0 -> 110692 bytes
 .../net.sf.gridscheduler/drmaa-6.2u5p2.jar    | Bin 0 -> 51479 bytes
 .../net.sf.gridscheduler/drmaa-6.2u5p2.xml    |   3 ++
 6 files changed, 21 insertions(+), 19 deletions(-)
 create mode 100644 settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2-sources.jar
 create mode 100644 settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.jar
 create mode 100644 settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.xml

diff --git a/build.xml b/build.xml
index fe1723587..a78c4d738 100644
--- a/build.xml
+++ b/build.xml
@@ -69,8 +69,6 @@
 
     <property environment="env"/>
 
-    <property name="drmaa.jar" value="${env.SGE_ROOT}/lib/drmaa.jar" />
-
     <patternset id="java.source.pattern">
         <include name="${java.public.source.dir}/**/*.java" />
         <include name="${java.private.source.dir}/**/*.java" if="include.private" />
@@ -146,11 +144,7 @@
         <property name="init.resolve.done" value="true"/>
     </target>
 
-    <target name="init.gridengine" depends="init" if="include.gridengine">
-        <copy todir="lib" file="${drmaa.jar}"/>
-    </target>
-
-    <target name="resolve" depends="init.resolve,init,init.gridengine"
+    <target name="resolve" depends="init.resolve,init"
             description="locate and download library dependencies">
         <property name="ivy.conf" value="default"/>
       <ivy:retrieve file="ivy.xml" conf="${ivy.conf}" />
@@ -178,13 +172,23 @@
         <property name="build.version" value="${git.describe.output}" />
     </target>
     
-    <target name="untagged.build.version" depends="git.describe" unless="git.describe.succeeded">
-      <exec executable="git" outputproperty="build.version" failonerror="true">
+    <target name="git.rev-parse" depends="git.describe" unless="git.describe.succeeded">
+      <exec executable="git" outputproperty="git.rev-parse.output" resultproperty="git.rev-parse.exit.value" failonerror="false">
         <arg line="rev-parse HEAD" />
       </exec>
+      <condition property="git.rev-parse.succeeded">
+        <equals arg1="${git.rev-parse.exit.value}" arg2="0" />
+      </condition>
     </target>
     
-    <target name="generate.build.version" depends="tagged.build.version, untagged.build.version" />
+    <target name="untagged.build.version" depends="git.rev-parse" if="git.rev-parse.succeeded">
+        <property name="build.version" value="${git.rev-parse.output}" />
+    </target>
+    
+    <target name="generate.build.version" depends="tagged.build.version, untagged.build.version">
+        <!-- Set build.version to exported if no other value has been set -->
+        <property name="build.version" value="exported" />
+    </target>
 
     <!-- define some key locations that might change based on how the build is run -->
     <target name="init" depends="generate.build.version">
@@ -214,12 +218,6 @@
             </or>
         </condition>
 
-        <!-- Include Grid Engine in the compile if SGE_ROOT is available. -->
-        <!-- Based off of http://wikis.sun.com/display/GridEngine/Automating+Grid+Engine+Functions+Through+DRMAA -->
-        <condition property="include.gridengine">
-            <available file="${drmaa.jar}"/>
-        </condition>
-
         <echo message="GATK build      : ${gatk.target}"/>
         <echo message="Scala build     : ${scala.target}"/>
       <echo message="source revision : ${build.version}"/>
@@ -357,7 +355,6 @@
             <src path="${scala.public.source.dir}" />
             <src path="${queue-extensions.source.dir}" />
             <include name="**/*.scala"/>
-            <exclude name="**/gridengine/**" unless="include.gridengine" />
         </scalac>    
     </target>
     
@@ -374,7 +371,6 @@
         <scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.classes}" classpathref="scala.dependencies" deprecation="yes" unchecked="yes">
             <src path="${scala.private.source.dir}" />
             <include name="**/*.scala"/>
-            <exclude name="**/gridengine/**" unless="include.gridengine" />
         </scalac>       
     </target>
 
@@ -682,7 +678,6 @@
 	        <src path="${scala.public.test.sources}" />
 	        <src path="${scala.private.test.sources}" />
             <include name="**/*.scala"/>
-            <exclude name="**/gridengine/**" unless="include.gridengine" />
             <classpath>
                 <path refid="scala.dependencies"/>
                 <pathelement location="${scala.test.classes}"/>
diff --git a/ivy.xml b/ivy.xml
index c2a6c4ccd..10e4ee570 100644
--- a/ivy.xml
+++ b/ivy.xml
@@ -48,6 +48,9 @@
     <!-- Dependencies for amazon.com S3 support -->
     <dependency org="net.java.dev.jets3t" name="jets3t" rev="0.8.0"/>
 
+    <!-- Dependencies for GridEngine -->
+    <dependency org="net.sf.gridscheduler" name="drmaa" rev="latest.integration"/>
+
     <!-- Scala dependancies -->
     <dependency org="org.scala-lang" name="scala-compiler" rev="2.8.1"/>
     <dependency org="org.scala-lang" name="scala-library" rev="2.8.1"/>
diff --git a/settings/ivysettings.xml b/settings/ivysettings.xml
index 1e47fa847..2c8fc388f 100644
--- a/settings/ivysettings.xml
+++ b/settings/ivysettings.xml
@@ -25,5 +25,6 @@
     <module organisation="javax.activation" resolver="java.net" />
     <module organisation="net.java.dev.jna" resolver="maven2-repository.dev.java.net" />
     <module organisation="com.google.code.caliper" resolver="projects" />
+    <module organisation="net.sf.gridscheduler" resolver="projects" />
   </modules>
 </ivysettings>
diff --git a/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2-sources.jar b/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2-sources.jar
new file mode 100644
index 0000000000000000000000000000000000000000..dc77c7d333c61a79fa8c7be7d8ad3345678f811c
GIT binary patch
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zat~GUFulPKTm#>Sxc|pw2M<L&jOPC#V$ScMBK|M2{Xa{%SNFr<^&b+X0v<~E>umXZ
zEk6w6{Q(pj{4YR%MMnPH+4o`K><>gh$bTUITNv%nSAV}w9>#M15Wy4nA0mDq+4)ew
z!`Q(e0_Y<Cw}9Vk`JoT{54^L)f8YUr>(TzOix18GKOo5}{{i`bGx|Ri@zARMLqtN=
zLlOUC<9-PF(3txJ@~rwH<p066`!oFgvUq5^`~h!J^AP?QL*@^l-y28%1iF6=l4|(L
ycJPy_<hvaJ7VLM%k{=y${cU^DJ@Q{oCkoQgpy%fMTr5w(Fwnrjjz9=tVE+$3(c0Aj

literal 0
HcmV?d00001

diff --git a/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.xml b/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.xml
new file mode 100644
index 000000000..c6a8da052
--- /dev/null
+++ b/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf.gridscheduler" module="drmaa" revision="6.2u5p2" status="release" />
+</ivy-module>

From 81a4d18468b85b8cdc79e6f9d06c735f5ca16d9b Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Wed, 6 Jul 2011 09:56:38 -0400
Subject: [PATCH 044/161] Mark several indel-related arguments as @Hidden

---
 .../gatk/walkers/genotyper/UnifiedArgumentCollection.java | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
index 1045ca371..055eb0b97 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
@@ -92,25 +92,31 @@ public class UnifiedArgumentCollection {
     @Argument(fullName = "indel_heterozygosity", shortName = "indelHeterozygosity", doc = "Heterozygosity for indel calling", required = false)
     public double INDEL_HETEROZYGOSITY = 1.0/8000;
 
+    @Hidden
     @Argument(fullName = "indelGapContinuationPenalty", shortName = "indelGCP", doc = "Indel gap continuation penalty", required = false)
     public double INDEL_GAP_CONTINUATION_PENALTY = 10.0;
 
+    @Hidden
     @Argument(fullName = "indelGapOpenPenalty", shortName = "indelGOP", doc = "Indel gap open penalty", required = false)
     public double INDEL_GAP_OPEN_PENALTY = 45.0;
 
+    @Hidden
     @Argument(fullName = "indelHaplotypeSize", shortName = "indelHSize", doc = "Indel haplotype size", required = false)
     public int INDEL_HAPLOTYPE_SIZE = 80;
+    @Hidden
     @Argument(fullName = "doContextDependentGapPenalties", shortName = "doCDP", doc = "Vary gap penalties by context", required = false)
      public boolean DO_CONTEXT_DEPENDENT_PENALTIES = true;
     //gdebug+
-    @Hidden
     // experimental arguments, NOT TO BE USED BY ANYONE WHOSE INITIALS AREN'T GDA!!!
+    @Hidden
     @Argument(fullName = "getGapPenaltiesFromData", shortName = "dataGP", doc = "Vary gap penalties by context - EXPERIMENTAL, DO NO USE", required = false)
     public boolean GET_GAP_PENALTIES_FROM_DATA = false;
 
+    @Hidden
     @Argument(fullName="indel_recal_file", shortName="recalFile", required=false, doc="Filename for the input covariates table recalibration .csv file - EXPERIMENTAL, DO NO USE")
     public File INDEL_RECAL_FILE = new File("indel.recal_data.csv");
 
+    @Hidden
     @Argument(fullName = "indelDebug", shortName = "indelDebug", doc = "Output indel debug info", required = false)
     public boolean OUTPUT_DEBUG_INDEL_INFO = false;
     @Hidden

From e8ed6b7f0f1c3e0e4f75d77349807b36ee37a3c7 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Wed, 6 Jul 2011 10:01:14 -0400
Subject: [PATCH 045/161] Adding more comments to main VQSR walker. Fixing
 copyright lines. Bug fix for default paths to now point to public/R/ instead
 of R/  Bug fix in VQSR for the path to the R scripts not ending in a slash.

---
 .../analyzecovariates/AnalyzeCovariates.java  |  2 +-
 .../ApplyRecalibration.java                   |  2 +-
 .../GaussianMixtureModel.java                 | 25 ++++++++++++++++++
 .../MultivariateGaussian.java                 | 25 ++++++++++++++++++
 .../variantrecalibration/TrainingSet.java     | 25 ++++++++++++++++++
 .../walkers/variantrecalibration/Tranche.java |  2 +-
 .../variantrecalibration/TrancheManager.java  | 25 ++++++++++++++++++
 .../VQSRCalibrationCurve.java                 | 26 ++++++++++++++++++-
 .../VariantDataManager.java                   | 25 ++++++++++++++++++
 .../variantrecalibration/VariantDatum.java    | 25 ++++++++++++++++++
 .../VariantRecalibrator.java                  | 15 ++++++++---
 ...VariantRecalibratorArgumentCollection.java | 25 ++++++++++++++++++
 .../VariantRecalibratorEngine.java            | 25 ++++++++++++++++++
 13 files changed, 239 insertions(+), 8 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java b/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
index 3cf43c15a..f8e298d88 100755
--- a/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
+++ b/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
@@ -61,7 +61,7 @@ public class AnalyzeCovariates extends CommandLineProgram {
     @Argument(fullName = "path_to_Rscript", shortName = "Rscript", doc = "The path to your implementation of Rscript. For Broad users this is maybe /broad/tools/apps/R-2.6.0/bin/Rscript", required = false)
     private String PATH_TO_RSCRIPT = "Rscript";
     @Argument(fullName = "path_to_resources", shortName = "resources", doc = "Path to resources folder holding the Sting R scripts.", required = false)
-    private String PATH_TO_RESOURCES = "R/";
+    private String PATH_TO_RESOURCES = "public/R/";
     @Argument(fullName = "ignoreQ", shortName = "ignoreQ", doc = "Ignore bases with reported quality less than this number.", required = false)
     private int IGNORE_QSCORES_LESS_THAN = 5;
     @Argument(fullName = "numRG", shortName = "numRG", doc = "Only process N read groups. Default value: -1 (process all read groups)", required = false)            
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
index 9877781d1..7957d35cd 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2010 The Broad Institute
+ * Copyright (c) 2011 The Broad Institute
  *
  * Permission is hereby granted, free of charge, to any person
  * obtaining a copy of this software and associated documentation
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
index 9ffe7be7a..acc1f24cc 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
@@ -1,3 +1,28 @@
+/*
+ * Copyright (c) 2011 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 import Jama.Matrix;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java
index 0b2edfd10..d077af78e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java
@@ -1,3 +1,28 @@
+/*
+ * Copyright (c) 2011 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 import Jama.Matrix;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java
index f3677421e..67132b133 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java
@@ -1,3 +1,28 @@
+/*
+ * Copyright (c) 2011 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 import org.apache.log4j.Logger;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java
index fbee64fe2..64fe36637 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2010 The Broad Institute
+ * Copyright (c) 2011 The Broad Institute
  *
  * Permission is hereby granted, free of charge, to any person
  * obtaining a copy of this software and associated documentation
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java
index 08388db21..19c6d501b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java
@@ -1,3 +1,28 @@
+/*
+ * Copyright (c) 2011 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 import org.apache.log4j.Logger;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java
index 2914385a4..5deb5d8c2 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java
@@ -1,8 +1,32 @@
+/*
+ * Copyright (c) 2011 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantQualityScore;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
index 2fd1326fe..f0a78280d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -1,3 +1,28 @@
+/*
+ * Copyright (c) 2011 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 import cern.jet.random.Normal;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java
index ac875b645..8295ec205 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java
@@ -1,3 +1,28 @@
+/*
+ * Copyright (c) 2011 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index e651b62e0..a77c5962c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -87,7 +87,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     @Argument(fullName="rscript_file", shortName="rscriptFile", doc="The output rscript file generated by the VQSR to aid in visualization of the input data and learned model", required=false)
     private String RSCRIPT_FILE = null;
     @Argument(fullName = "path_to_resources", shortName = "resources", doc = "Path to resources folder holding the Sting R scripts.", required=false)
-    private String PATH_TO_RESOURCES = "R/";
+    private String PATH_TO_RESOURCES = "public/R/";
     @Argument(fullName="ts_filter_level", shortName="ts_filter_level", doc="The truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots", required=false)
     private double TS_FILTER_LEVEL = 99.0;
 
@@ -117,6 +117,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     //---------------------------------------------------------------------------------------------------------------
 
     public void initialize() {
+        if( !PATH_TO_RESOURCES.endsWith("/") ) { PATH_TO_RESOURCES = PATH_TO_RESOURCES + "/"; }
         dataManager = new VariantDataManager( new ArrayList<String>(Arrays.asList(USE_ANNOTATIONS)), VRAC );
 
         if( IGNORE_INPUT_FILTERS != null ) {
@@ -228,18 +229,22 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     public void onTraversalDone( final ExpandingArrayList<VariantDatum> reduceSum ) {
         dataManager.setData( reduceSum );
         dataManager.normalizeData(); // Each data point is now (x - mean) / standard deviation
+
+        // Generate the positive model using the training data and evaluate each variant
         final GaussianMixtureModel goodModel = engine.generateModel( dataManager.getTrainingData() );
         engine.evaluateData( dataManager.getData(), goodModel, false );
+
+        // Generate the negative model using the worst performing data and evaluate each variant contrastively
         final GaussianMixtureModel badModel = engine.generateModel( dataManager.selectWorstVariants( VRAC.PERCENT_BAD_VARIANTS, VRAC.MIN_NUM_BAD_VARIANTS ) );
         engine.evaluateData( dataManager.getData(), badModel, true );
 
-        final ExpandingArrayList<VariantDatum> randomData = dataManager.getRandomDataForPlotting( 6000 );
-
+        // Find the VQSLOD cutoff values which correspond to the various tranches of calls requested by the user
         final int nCallsAtTruth = TrancheManager.countCallsAtTruth( dataManager.getData(), Double.NEGATIVE_INFINITY );
         final TrancheManager.SelectionMetric metric = new TrancheManager.TruthSensitivityMetric( nCallsAtTruth );
         final List<Tranche> tranches = TrancheManager.findTranches( dataManager.getData(), TS_TRANCHES, metric );
         tranchesStream.print(Tranche.tranchesString( tranches ));
 
+        // Find the filtering lodCutoff for display on the model PDFs. Red variants are those which were below the cutoff and filtered out of the final callset.
         double lodCutoff = 0.0;
         for( final Tranche tranche : tranches ) {
             if( MathUtils.compareDoubles(tranche.ts, TS_FILTER_LEVEL, 0.0001)==0 ) {
@@ -251,7 +256,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         dataManager.writeOutRecalibrationTable( RECAL_FILE );
         if( RSCRIPT_FILE != null ) {
             logger.info( "Writing out visualization Rscript file...");
-            createVisualizationScript( randomData, goodModel, badModel, lodCutoff );
+            createVisualizationScript( dataManager.getRandomDataForPlotting( 6000 ), goodModel, badModel, lodCutoff );
         }
 
         // Execute Rscript command to create the tranche plot
@@ -277,6 +282,8 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         } catch( FileNotFoundException e ) {
             throw new UserException.CouldNotCreateOutputFile(RSCRIPT_FILE, "", e);
         }
+
+        // We make extensive use of the ggplot2 library: http://had.co.nz/ggplot2/
         stream.println("library(ggplot2)");
 
         createArrangeFunction( stream );
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
index e177cebab..f597fb128 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
@@ -1,3 +1,28 @@
+/*
+ * Copyright (c) 2011 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 import org.broadinstitute.sting.commandline.Argument;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
index a0fbc572d..4deb82f6b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
@@ -1,3 +1,28 @@
+/*
+ * Copyright (c) 2011 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 import org.apache.log4j.Logger;

From c93d0b37a8334ea2ec0ec0c63008940b7bcc844b Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Wed, 6 Jul 2011 11:32:46 -0400
Subject: [PATCH 046/161] Fixed namespace of the pipeline classes.

---
 build.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.xml b/build.xml
index fe1723587..2a23f74c1 100644
--- a/build.xml
+++ b/build.xml
@@ -464,7 +464,7 @@
               <exclude name="**/utils/variantcontext/**/*.class"/>
             </fileset>
             <fileset dir="${java.classes}" includes="**/commandline/**/*.class"/>
-            <fileset dir="${java.classes}" includes="**/sting/datasources/**/*.class"/>
+            <fileset dir="${java.classes}" includes="**/sting/pipeline/**/*.class"/>
             <fileset dir="${java.classes}" includes="**/sting/jna/**/*.class"/>
             <fileset dir="${java.classes}" includes="net/sf/picard/**/*.class"/>
             <fileset dir="${java.classes}" includes="net/sf/samtools/**/*.class"/>

From 14fee4ccbd990bd32956017624dfbcdddeee75ae Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 6 Jul 2011 12:51:44 -0400
Subject: [PATCH 050/161] Patch from Bob to deal with symbolic alleles: these
 weren't getting padded but they should be.

---
 .../sting/utils/variantcontext/VariantContext.java  | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
index 3d375aba2..5787b591f 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -1343,6 +1343,15 @@ public class VariantContext implements Feature { // to enable tribble intergrati
         return (int)stop;
     }
 
+    private boolean hasSymbolicAlleles() {
+        for (Allele a: getAlleles()) {
+            if (a.isSymbolic()) {
+                return true;
+            }
+        }
+        return false;
+    }
+
     public static VariantContext createVariantContextWithPaddedAlleles(VariantContext inputVC, byte inputRefBase, boolean refBaseShouldBeAppliedToEndOfAlleles) {
         Allele refAllele = inputVC.getReference();
 
@@ -1352,7 +1361,9 @@ public class VariantContext implements Feature { // to enable tribble intergrati
         // We need to pad a VC with a common base if the length of the reference allele is less than the length of the VariantContext.
         // This happens because the position of e.g. an indel is always one before the actual event (as per VCF convention).
         long locLength = (inputVC.getEnd() - inputVC.getStart()) + 1;
-        if (refAllele.length() == locLength)
+        if (inputVC.hasSymbolicAlleles())
+            padVC = true;
+        else if (refAllele.length() == locLength)
             padVC = false;
         else if (refAllele.length() == locLength-1)
             padVC = true;

From 54121eb082eb84920770d573ff143efbe32f0340 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 6 Jul 2011 16:05:08 -0400
Subject: [PATCH 053/161] Catch malformed bams that cause the writer to run in
 infinite loops

---
 .../gatk/walkers/indels/ConstrainedMateFixingManager.java | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
index aebb0e3eb..df1f4f908 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
@@ -5,6 +5,7 @@ import net.sf.samtools.*;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.util.*;
@@ -113,9 +114,10 @@ public class ConstrainedMateFixingManager {
     HashMap<String, SAMRecordHashObject> forMateMatching = new HashMap<String, SAMRecordHashObject>();
     TreeSet<SAMRecord> waitingReads = new TreeSet<SAMRecord>(comparer);
 
-    private <T> T remove(TreeSet<T> treeSet) {
-        final T first = treeSet.first();
-        treeSet.remove(first);
+    private SAMRecord remove(TreeSet<SAMRecord> treeSet) {
+        final SAMRecord first = treeSet.first();
+        if ( !treeSet.remove(first) )
+            throw new UserException("Error caching SAM record " + first.getReadName() + ", which is usually caused by malformed SAM/BAM files in which multiple identical copies of a read are present.");
         return first;
     }
 

From ccf34f7e45164cea70beccb4cf1b0791e6acde06 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Wed, 6 Jul 2011 21:57:22 -0400
Subject: [PATCH 054/161] (1) Added very useful helper class TestDataProvider
 to BaseTest that making creating data providers for TestNG far easier (2)
 DiffEngine now officially working with with summaries.  Extensive UnitTests
 all around!

---
 .../org/broadinstitute/sting/BaseTest.java    | 55 +++++++++++++++++++
 1 file changed, 55 insertions(+)

diff --git a/public/java/test/org/broadinstitute/sting/BaseTest.java b/public/java/test/org/broadinstitute/sting/BaseTest.java
index 61bb8b34b..b469c8a41 100755
--- a/public/java/test/org/broadinstitute/sting/BaseTest.java
+++ b/public/java/test/org/broadinstitute/sting/BaseTest.java
@@ -12,6 +12,10 @@ import java.io.*;
 import java.math.BigInteger;
 import java.security.MessageDigest;
 import java.security.NoSuchAlgorithmException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 /**
  *
@@ -107,6 +111,57 @@ public abstract class BaseTest {
         }
     }
 
+    /**
+     * Simple generic utility class to creating TestNG data providers:
+     *
+     * 1: inherit this class, as in
+     *
+     *      private class SummarizeDifferenceTest extends TestDataProvider {
+     *         public SummarizeDifferenceTest() {
+     *           super(SummarizeDifferenceTest.class);
+     *         }
+     *         ...
+     *      }
+     *
+     * Provide a reference to your class to the TestDataProvider constructor.
+     *
+     * 2: Create instances of your subclass.  Return from it the call to getTests, providing
+     * the class type of your test
+     *
+     * @DataProvider(name = "summaries")
+     * public Object[][] createSummaries() {
+     *   new SummarizeDifferenceTest().addDiff("A", "A").addSummary("A:2");
+     *   new SummarizeDifferenceTest().addDiff("A", "B").addSummary("A:1", "B:1");
+     *   return SummarizeDifferenceTest.getTests(SummarizeDifferenceTest.class);
+     * }
+     *
+     * This class magically tracks created objects of this
+     */
+    public static class TestDataProvider {
+        private static final Map<Class, List<Object>> tests = new HashMap<Class, List<Object>>();
+
+        /**
+         * Create a new TestDataProvider instance bound to the class variable C
+         * @param c
+         */
+        public TestDataProvider(Class c) {
+            if ( ! tests.containsKey(c) )
+                tests.put(c, new ArrayList<Object>());
+            tests.get(c).add(this);
+        }
+
+        /**
+         * Return all of the data providers in the form expected by TestNG of type class C
+         * @param c
+         * @return
+         */
+        public static Object[][] getTests(Class c) {
+            List<Object[]> params2 = new ArrayList<Object[]>();
+            for ( Object x : tests.get(c) ) params2.add(new Object[]{x});
+            return params2.toArray(new Object[][]{});
+        }
+    }
+
     /**
      * test if the file exists
      *

From 50111db2b7920ba5b3cfe659e33f7135ebd277f5 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Thu, 7 Jul 2011 15:02:48 -0400
Subject: [PATCH 057/161] Fixing non-determinism in single-threaded VQSR by
 moving references to cern.Normal over to the static random generator
 available in GenomeAnalysisEngine

---
 .../GaussianMixtureModel.java                 | 24 ++++++++++---------
 .../VariantDataManager.java                   |  3 +--
 2 files changed, 14 insertions(+), 13 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
index acc1f24cc..41fea0896 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
@@ -26,7 +26,6 @@
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 import Jama.Matrix;
-import cern.jet.random.Normal;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.MathUtils;
@@ -97,7 +96,7 @@ public class GaussianMixtureModel {
 
         int ttt = 0;
         while( ttt++ < numIterations ) {
-            // Estep: assign each variant to the nearest cluster
+            // E step: assign each variant to the nearest cluster
             for( final VariantDatum datum : data ) {
                 double minDistance = Double.MAX_VALUE;
                 MultivariateGaussian minGaussian = null;
@@ -112,7 +111,7 @@ public class GaussianMixtureModel {
                 datum.assignment = minGaussian;
             }
 
-            // Mstep: update gaussian means based on assigned variants
+            // M step: update gaussian means based on assigned variants
             for( final MultivariateGaussian gaussian : gaussians ) {
                 gaussian.zeroOutMu();
                 int numAssigned = 0;
@@ -216,26 +215,29 @@ public class GaussianMixtureModel {
     }
 
     public double evaluateDatumMarginalized( final VariantDatum datum ) {
-        int numVals = 0;
+        int numSamples = 0;
         double sumPVarInGaussian = 0.0;
-        int numIter = 10;
+        final int numIterPerMissingAnnotation = 10; // Trade off here between speed of computation and accuracy of the marginalization
         final double[] pVarInGaussianLog10 = new double[gaussians.size()];
+        // for each dimension
         for( int iii = 0; iii < datum.annotations.length; iii++ ) {
-            // marginalize over the missing dimension by drawing X random values for the missing annotation and averaging the lod
+            // if it is missing marginalize over the missing dimension by drawing X random values for the missing annotation and averaging the lod
             if( datum.isNull[iii] ) {
-                for( int ttt = 0; ttt < numIter; ttt++ ) {
-                    datum.annotations[iii] = Normal.staticNextDouble(0.0, 1.0);
+                for( int ttt = 0; ttt < numIterPerMissingAnnotation; ttt++ ) {
+                    datum.annotations[iii] = GenomeAnalysisEngine.getRandomGenerator().nextGaussian(); // draw a random sample from the standard normal distribution
 
+                    // evaluate this random data point
                     int gaussianIndex = 0;
                     for( final MultivariateGaussian gaussian : gaussians ) {
                         pVarInGaussianLog10[gaussianIndex++] = gaussian.pMixtureLog10 + gaussian.evaluateDatumLog10( datum );
                     }
 
-                    sumPVarInGaussian += Math.pow(10.0, MathUtils.log10sumLog10(pVarInGaussianLog10));
-                    numVals++;
+                    // add this sample's probability to the pile in order to take an average in the end
+                    sumPVarInGaussian += Math.pow(10.0, MathUtils.log10sumLog10(pVarInGaussianLog10)); // p = 10 ^ Sum(pi_k * p(v|n,k))
+                    numSamples++;
                 }
             }
         }
-        return Math.log10( sumPVarInGaussian / ((double) numVals) );
+        return Math.log10( sumPVarInGaussian / ((double) numSamples) );
     }
 }
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
index f0a78280d..e1a076e76 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -25,7 +25,6 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
-import cern.jet.random.Normal;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
@@ -91,7 +90,7 @@ public class VariantDataManager {
             meanVector[iii] = theMean;
             varianceVector[iii] = theSTD;
             for( final VariantDatum datum : data ) {
-                datum.annotations[iii] = ( datum.isNull[iii] ? Normal.staticNextDouble(0.0, 1.0) : ( datum.annotations[iii] - theMean ) / theSTD );
+                datum.annotations[iii] = ( datum.isNull[iii] ? GenomeAnalysisEngine.getRandomGenerator().nextGaussian() : ( datum.annotations[iii] - theMean ) / theSTD );
                 // Each data point is now [ (x - mean) / standard deviation ]
                 if( annotationKeys.get(iii).toLowerCase().contains("ranksum") && datum.isNull[iii] && datum.annotations[iii] > 0.0 ) {
                     datum.annotations[iii] /= 3.0;

From 212e9a1a0cf766f54f70d17d0786db570f8111ae Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Thu, 7 Jul 2011 15:18:57 -0400
Subject: [PATCH 058/161] Fixing unstable build after stable commit

---
 .../gatk/walkers/variantrecalibration/GaussianMixtureModel.java  | 1 +
 1 file changed, 1 insertion(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
index b4a8c4c32..17461de2f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 import Jama.Matrix;
+import cern.jet.random.Normal;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.MathUtils;

From 3d4f0e9dd76d1ab23a7e7fdecd61067b57b8e7d7 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Thu, 7 Jul 2011 17:21:15 -0400
Subject: [PATCH 063/161] Now supports the case where you have multiple AC
 values in the info field.

---
 .../gatk/walkers/varianteval/stratifications/AlleleCount.java | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
index ff59c9e29..2cbc66e31 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
@@ -43,9 +43,9 @@ public class AlleleCount extends VariantStratifier {
 
         if (eval != null) {
             int AC = -1;
-            if ( eval.hasAttribute("AC") )
+            if ( eval.hasAttribute("AC") && eval.getAttribute("AC") instanceof Integer ) {
                 AC = eval.getAttributeAsInt("AC");
-            else if ( eval.isVariant() ) {
+            } else if ( eval.isVariant() ) {
                 for (Allele allele : eval.getAlternateAlleles())
                     AC = Math.max(AC, eval.getChromosomeCount(allele));
             } else

From 4cfe0dd857891f6c70f4d0e58b60d6c4c401a0cd Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 7 Jul 2011 23:01:03 -0400
Subject: [PATCH 066/161] Test for bad alleles so that we don't generate
 IndexOutOfBoundsExceptions

---
 .../sting/utils/codecs/vcf/AbstractVCFCodec.java            | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
index cd0f52c68..01344a117 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
@@ -225,7 +225,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
             loc = pos + alleles.get(0).length() - 1;
         } else if ( !isSingleNucleotideEvent(alleles) ) {
             ArrayList<Allele> newAlleles = new ArrayList<Allele>();
-            loc = clipAlleles(pos, ref, alleles, newAlleles);
+            loc = clipAlleles(pos, ref, alleles, newAlleles, lineNo);
             alleles = newAlleles;
         }
 
@@ -504,7 +504,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
      * @param clippedAlleles output list of clipped alleles
      * @return a list of alleles, clipped to the reference
      */
-    protected static long clipAlleles(long position, String ref, List<Allele> unclippedAlleles, List<Allele> clippedAlleles) {
+    protected static long clipAlleles(long position, String ref, List<Allele> unclippedAlleles, List<Allele> clippedAlleles, int lineNo) {
 
         // Note that the computation of forward clipping here is meant only to see whether there is a common
         // base to all alleles, and to correctly compute reverse clipping,
@@ -522,6 +522,8 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
                 }
                 if (a.length() - reverseClipped <= forwardClipping || a.length() - forwardClipping == 0)
                     clipping = false;
+                else if (ref.length() == reverseClipped)
+                    generateException("bad alleles encountered", lineNo);
                 else if (a.getBases()[a.length()-reverseClipped-1] != ref.getBytes()[ref.length()-reverseClipped-1])
                     clipping = false;
             }

From 2a4b3ae4a20ea3d5bbd3047f2c2f7842cd01e2ef Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Fri, 8 Jul 2011 12:48:33 -0400
Subject: [PATCH 069/161] Cleaning up / removing most of the monkeying around
 with annotation values that happens in VariantDataManager

---
 .../VariantDataManager.java                   | 34 +++++--------------
 .../VariantRecalibrator.java                  |  6 ++--
 ...VariantRecalibratorArgumentCollection.java |  2 +-
 3 files changed, 13 insertions(+), 29 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
index 5f35c182c..ddeda1699 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -82,19 +82,11 @@ public class VariantDataManager {
             }
 
             foundZeroVarianceAnnotation = foundZeroVarianceAnnotation || (theSTD < 1E-6);
-            if( annotationKeys.get(iii).toLowerCase().contains("ranksum") ) { // BUGBUG: to clean up
-                for( final VariantDatum datum : data ) {
-                    if( datum.annotations[iii] > 0.0 ) { datum.annotations[iii] /= 3.0; }
-                }
-            }
             meanVector[iii] = theMean;
             varianceVector[iii] = theSTD;
             for( final VariantDatum datum : data ) {
+                // Transform each data point via: (x - mean) / standard deviation
                 datum.annotations[iii] = ( datum.isNull[iii] ? GenomeAnalysisEngine.getRandomGenerator().nextGaussian() : ( datum.annotations[iii] - theMean ) / theSTD );
-                // Each data point is now [ (x - mean) / standard deviation ]
-                if( annotationKeys.get(iii).toLowerCase().contains("ranksum") && datum.isNull[iii] && datum.annotations[iii] > 0.0 ) {
-                    datum.annotations[iii] /= 3.0;
-                }
             }
         }
         if( foundZeroVarianceAnnotation ) {
@@ -163,7 +155,7 @@ public class VariantDataManager {
         final int numBadSitesAdded = trainingData.size();
         logger.info( "Found " + numBadSitesAdded + " variants overlapping bad sites training tracks." );
 
-        // Next, sort the variants by the LOD coming from the positive model and add to the list the bottom X percent of variants
+        // Next sort the variants by the LOD coming from the positive model and add to the list the bottom X percent of variants
         Collections.sort( data );
         final int numToAdd = Math.max( minimumNumber - trainingData.size(), Math.round((float)bottomPercentage * data.size()) );
         if( numToAdd > data.size() ) {
@@ -241,23 +233,15 @@ public class VariantDataManager {
         double value;
 
         try {
-            if( annotationKey.equalsIgnoreCase("QUAL") ) {
-                value = vc.getPhredScaledQual();
-            } else if( annotationKey.equalsIgnoreCase("DP") ) {
-                value = Double.parseDouble( (String)vc.getAttribute( "DP" ) ) / Double.parseDouble( (String)vc.getAttribute( "AN" ) );
-            } else {
-                value = Double.parseDouble( (String)vc.getAttribute( annotationKey ) );
-                if( Double.isInfinite(value) ) { value = Double.NaN; }
-                if( annotationKey.equalsIgnoreCase("InbreedingCoeff") && value > 0.05 ) { value = Double.NaN; }
-                if( jitter && annotationKey.equalsIgnoreCase("HRUN") ) { // Integer valued annotations must be jittered a bit to work in this GMM
-                      value += -0.25 + 0.5 * GenomeAnalysisEngine.getRandomGenerator().nextDouble();
-                }
-                if( annotationKey.equalsIgnoreCase("HaplotypeScore") && MathUtils.compareDoubles(value, 0.0, 0.0001) == 0 ) { value = -0.2 + 0.4*GenomeAnalysisEngine.getRandomGenerator().nextDouble(); }
-                if( annotationKey.equalsIgnoreCase("FS") && MathUtils.compareDoubles(value, 0.0, 0.01) == 0 ) { value = -0.2 + 0.4*GenomeAnalysisEngine.getRandomGenerator().nextDouble(); }
+            value = Double.parseDouble( (String)vc.getAttribute( annotationKey ) );
+            if( Double.isInfinite(value) ) { value = Double.NaN; }
+            if( jitter && annotationKey.equalsIgnoreCase("HRUN") ) { // Integer valued annotations must be jittered a bit to work in this GMM
+                  value += -0.25 + 0.5 * GenomeAnalysisEngine.getRandomGenerator().nextDouble();
             }
-
+            if( jitter && annotationKey.equalsIgnoreCase("HaplotypeScore") && MathUtils.compareDoubles(value, 0.0, 0.0001) == 0 ) { value = -0.2 + 0.4*GenomeAnalysisEngine.getRandomGenerator().nextDouble(); }
+            if( jitter && annotationKey.equalsIgnoreCase("FS") && MathUtils.compareDoubles(value, 0.0, 0.001) == 0 ) { value = -0.2 + 0.4*GenomeAnalysisEngine.getRandomGenerator().nextDouble(); }
         } catch( Exception e ) {
-            value = Double.NaN; // The VQSR works with missing data now by marginalizing over the missing dimension when evaluating Gaussians
+            value = Double.NaN; // The VQSR works with missing data by marginalizing over the missing dimension when evaluating the Gaussian mixture model
         }
 
         return value;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index 2c51f02d6..2d0355d7d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -284,7 +284,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
             throw new UserException.CouldNotCreateOutputFile(RSCRIPT_FILE, "", e);
         }
 
-        // We make extensive use of the ggplot2 library: http://had.co.nz/ggplot2/
+        // We make extensive use of the ggplot2 R library: http://had.co.nz/ggplot2/
         stream.println("library(ggplot2)");
 
         createArrangeFunction( stream );
@@ -378,6 +378,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         }
      }
 
+    // The Arrange function is how we place the 4 model plots on one page
     // from http://gettinggeneticsdone.blogspot.com/2010/03/arrange-multiple-ggplot2-plots-in-same.html
     private void createArrangeFunction( final PrintStream stream ) {
         stream.println("vp.layout <- function(x, y) viewport(layout.pos.row=x, layout.pos.col=y)");
@@ -402,5 +403,4 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         stream.println("}");
         stream.println("}");
     }
-
- }
+}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
index f597fb128..e1a815913 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
@@ -60,7 +60,7 @@ public class VariantRecalibratorArgumentCollection {
     @Argument(fullName="priorCounts", shortName="priorCounts", doc="The number of prior counts to use in variational Bayes algorithm.", required=false)
     public double PRIOR_COUNTS = 20.0;
     @Argument(fullName="percentBadVariants", shortName="percentBad", doc="What percentage of the worst scoring variants to use when building the Gaussian mixture model of bad variants. 0.07 means bottom 7 percent.", required=false)
-    public double PERCENT_BAD_VARIANTS = 0.015;
+    public double PERCENT_BAD_VARIANTS = 0.03;
     @Argument(fullName="minNumBadVariants", shortName="minNumBad", doc="The minimum amount of worst scoring variants to use when building the Gaussian mixture model of bad variants. Will override -percentBad arugment if necessary.", required=false)
     public int MIN_NUM_BAD_VARIANTS = 2000;
 }

From 224574424e90152ffbe4536a4dd6061eb886f9ff Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Fri, 8 Jul 2011 12:48:49 -0400
Subject: [PATCH 070/161] Bug fix: if we're genotyping a very long indel (>100
 bp) fail gracefully instead of with an array out of bounds exception

---
 .../org/broadinstitute/sting/utils/genotype/Haplotype.java  | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java b/public/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java
index cb6557408..31791e805 100755
--- a/public/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java
+++ b/public/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java
@@ -133,8 +133,12 @@ public class Haplotype {
 
 
         byte[] basesBeforeVariant = Arrays.copyOfRange(refBases,startIdxInReference,startIdxInReference+numPrefBases);
+        int startAfter = startIdxInReference+numPrefBases+ refAllele.getBases().length;
+        // protect against long events that overrun available reference context
+        if (startAfter > refBases.length)
+            startAfter = refBases.length;
         byte[] basesAfterVariant = Arrays.copyOfRange(refBases,
-                startIdxInReference+numPrefBases+ refAllele.getBases().length, refBases.length);
+                startAfter, refBases.length);
 
 
         // Create location for all haplotypes

From a3c9d9c3ff561a0a910b5313e0ebb037b7883a4b Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Fri, 8 Jul 2011 15:34:39 -0400
Subject: [PATCH 075/161] Fixing Contracts for Java, and enabling contracts by
 default for unit/integration tests.

The NullPointerException we were seeing when trying to run with contracts enabled was being caused
by an outdated version of the asm library.

To run tests without contracts and disable their compilation, pass in "-Duse.contracts=false" to ant.

Also did some minor unrelated cleanup in build.xml
---
 build.xml                                     |  70 +++++++++++-------
 ivy.xml                                       |   4 +
 settings/ivysettings.xml                      |   1 +
 .../cofoja-1.0-20110609.jar                   | Bin
 .../cofoja-1.0-20110609.xml                   |   3 +
 5 files changed, 51 insertions(+), 27 deletions(-)
 rename settings/repository/{com.google => com.google.code.cofoja}/cofoja-1.0-20110609.jar (100%)
 create mode 100644 settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.xml

diff --git a/build.xml b/build.xml
index 2a23f74c1..986d89213 100644
--- a/build.xml
+++ b/build.xml
@@ -28,6 +28,7 @@
 
     <property name="build.dir" value="build" />
     <property name="dist.dir" value="dist" />
+    <property name="lib.dir" value="lib" />
     <property name="external.dir" value="external" />
     <property name="public.dir" value="public" />
     <property name="private.dir" value="private" />
@@ -44,11 +45,11 @@
     <property name="queue-extensions.source.dir" value="${build.dir}/queue-extensions/src" />
     
     <!-- Contracts for Java -->
-    <!-- uncomment out to enable building contracts -->
-    <property name="use.contracts" value="true" /> 
+    <!-- To disable, run with -Duse.contracts=false -->
+    <property name="use.contracts" value="true" />
     <property name="java.contracts" value="${build.dir}/java/contracts" />
-    <property name="cofojaDir" value="settings/repository/com.google/"/>
-    <property name="cofoja.jar" value="${cofojaDir}/cofoja-1.0-20110609.jar"/>
+    <property name="contracts.version" value="1.0-20110609" />
+    <property name="cofoja.jar" value="${lib.dir}/cofoja-${contracts.version}.jar"/>
     
     <!-- where to find the tribble distro -->
     <property name="tribble.dir" value="tribble" />
@@ -69,7 +70,7 @@
 
     <property environment="env"/>
 
-    <property name="drmaa.jar" value="${env.SGE_ROOT}/lib/drmaa.jar" />
+    <property name="drmaa.jar" value="${env.SGE_ROOT}/${lib.dir}/drmaa.jar" />
 
     <patternset id="java.source.pattern">
         <include name="${java.public.source.dir}/**/*.java" />
@@ -103,7 +104,7 @@
     </patternset>
     
     <path id="external.dependencies">
-      <fileset dir="lib">
+      <fileset dir="${lib.dir}">
         <patternset refid="dependency.mask" />
       </fileset>
     </path>
@@ -128,14 +129,14 @@
         <!-- ivy properties -->
         <property name="ivy.install.version" value="2.2.0"/>
         <property name="ivy.home" value="${user.home}/.ant"/>
-        <property name="ivy.jar.dir" value="${ivy.home}/lib"/>
+        <property name="ivy.jar.dir" value="${ivy.home}/${lib.dir}"/>
         <property name="ivy.jar.file" value="ivy-${ivy.install.version}.jar"/>
         <property name="ivy.settings.dir" value="settings"/>
         <property file="${ivy.settings.dir}/ivysettings.properties"/>
   
-      <mkdir dir="lib"/>
+      <mkdir dir="${lib.dir}"/>
       <mkdir dir="${ivy.jar.dir}"/>
-      <copy file="${cofoja.jar}" toFile="lib/cofoja.jar"/>
+
       <get src="http://repo1.maven.org/maven2/org/apache/ivy/ivy/${ivy.install.version}/${ivy.jar.file}"
            dest="${ivy.jar.dir}/${ivy.jar.file}"
            usetimestamp="true"/>
@@ -147,7 +148,7 @@
     </target>
 
     <target name="init.gridengine" depends="init" if="include.gridengine">
-        <copy todir="lib" file="${drmaa.jar}"/>
+        <copy todir="${lib.dir}" file="${drmaa.jar}"/>
     </target>
 
     <target name="resolve" depends="init.resolve,init,init.gridengine"
@@ -229,6 +230,10 @@
         <equals arg1="${gatk.target}" arg2="private" casesensitive="false" />
       </condition>
 
+      <condition property="include.contracts">
+        <equals arg1="${use.contracts}" arg2="true" />
+      </condition>
+
       <!-- Create the build directory structure used by compile -->
       <mkdir dir="${build.dir}"/>
       <mkdir dir="${java.classes}"/>
@@ -252,7 +257,7 @@
     <target name="init.scala.compile" depends="resolve"
             description="Initializes the scala ant tasks from scala-compiler.jar">
         <path id="scala.classpath">
-            <fileset dir="lib">
+            <fileset dir="${lib.dir}">
                 <include name="scala-compiler-*.jar"/>
                 <include name="scala-library-*.jar"/>
             </fileset>
@@ -287,7 +292,7 @@
             depends="gatk.compile.public.source,gatk.compile.private.source,gatk.compile.external.source" 
             description="compile the GATK source" />
 
-   <target name="gatk.contracts.public" depends="gatk.compile.source">
+   <target name="gatk.contracts.public" depends="gatk.compile.source" if="include.contracts">
         <javac fork="true" memoryMaximumSize="512m" srcdir="${java.public.source.dir}" destdir="${java.contracts}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" >
             <classpath>
                 <path refid="external.dependencies" />
@@ -299,7 +304,16 @@
         </javac>   
    </target>
 
-   <target name="gatk.contracts.private" depends="gatk.compile.source" if="include.private">
+    <target name="check.contracts.private" depends="gatk.contracts.public">
+        <condition property="include.contracts.private">
+          <and>
+            <isset property="include.contracts" />
+            <isset property="include.private" />
+          </and>
+        </condition>
+    </target>
+
+   <target name="gatk.contracts.private" depends="check.contracts.private" if="include.contracts.private">
         <javac fork="true" memoryMaximumSize="512m" srcdir="${java.private.source.dir}" destdir="${java.contracts}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" >
             <classpath>
                 <path refid="external.dependencies" />
@@ -312,7 +326,7 @@
    </target>
 
     <target name="gatk.contracts" depends="gatk.contracts.public,gatk.contracts.private" 
-            description="create GATK contracts" if="use.contracts" />
+            description="create GATK contracts" if="include.contracts" />
     
     <target name="gatk.compile" depends="tribble,init,resolve,gatk.compile.source,gatk.contracts" />
 
@@ -452,7 +466,7 @@
     <target name="init.jar" depends="sting.compile,extracthelp">
         <mkdir dir="${dist.dir}"/>
         <copy todir="${dist.dir}">
-            <fileset dir="lib" includes="*.jar"/>
+            <fileset dir="${lib.dir}" includes="*.jar"/>
         </copy>
     </target>
 
@@ -663,7 +677,7 @@
                 <path refid="external.dependencies" />
                 <pathelement location="${java.classes}"/>
                 <pathelement location="${java.contracts}"/>
-                <pathelement location="lib/testng-5.14.1.jar"/>
+                <pathelement location="${lib.dir}/testng-5.14.1.jar"/>
             </classpath>
             <compilerarg value="-proc:none"/>
 <!-- 
@@ -687,7 +701,7 @@
                 <path refid="scala.dependencies"/>
                 <pathelement location="${scala.test.classes}"/>
                 <pathelement location="${java.test.classes}"/>
-                <pathelement location="lib/testng-5.14.1.jar"/>
+                <pathelement location="${lib.dir}/testng-5.14.1.jar"/>
             </classpath>
         </scalac>
     </target>
@@ -727,9 +741,13 @@
                 <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}/@{testtype}"/>
             <echo message="Sting: Running @{testtype} test cases!"/>
-            <taskdef resource="testngtasks" classpath="lib/testng-5.14.1.jar"/>
+            <taskdef resource="testngtasks" classpath="${lib.dir}/testng-5.14.1.jar"/>
             <testng outputDir="${report}/@{testtype}"
                     haltOnFailure="false" failureProperty="test.failure"
                     verbose="2"
@@ -740,9 +758,7 @@
                 <jvmarg value="-Djava.awt.headless=true" />
                 <jvmarg value="-Dpipeline.run=${pipeline.run}" />
                 <jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
-                <!-- needs to be if -->
-                <!--jvmarg value="-javaagent:lib/cofoja.jar"/-->
-                <!--jvmarg value="-Dcom.google.java.contract.log.contract=false"/-->
+                <jvmarg line="${cofoja.jvm.args}"/>
 <!--                 <jvmarg value="-Xdebug"/> -->
 <!--                 <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> -->
                 <classpath>
@@ -820,7 +836,7 @@
 
     <!-- copy the compiled library -->
     <target name="tribble.compile.copy" description="Copies the compiled tribble library" depends="tribble.compile" if="tribble.compile.exists">
-        <copy todir="lib">
+        <copy todir="${lib.dir}">
             <fileset dir="${tribble.dir}/dist" includes="*.jar"/>
         </copy>
     </target>
@@ -828,7 +844,7 @@
     <!-- copy the precompiled library -->
     <target name="tribble.library.copy" description="Copies the precompiled tribble library" depends="tribble.init" unless="tribble.compile.exists">
         <echo message="Copying the Tribble Library..."/>
-        <copy todir="lib">
+        <copy todir="${lib.dir}">
             <fileset dir="settings/repository/org.broad" includes="tribble*.jar"/>
         </copy>
     </target>
@@ -921,8 +937,8 @@
       <pathconvert property="required.picard.jars" pathsep=":">
         <fileset dir="${basedir}">
 	     <include name="staging" />
-	     <include name="lib/picard-*.*.*.jar" />
-	     <include name="lib/sam-*.jar" />
+	     <include name="${lib.dir}/picard-*.*.*.jar" />
+	     <include name="${lib.dir}/sam-*.jar" />
 	   </fileset>
       </pathconvert>
       <echo message="required.picard.jars=${required.picard.jars}" />
@@ -944,7 +960,7 @@
     <!-- Find bug tasks                                                                   -->
     <!-- ******************************************************************************** -->
     <path id="findbugs.classpath">
-      <fileset dir="lib" erroronmissingdir="true" includes="*.jar"/>
+      <fileset dir="${lib.dir}" erroronmissingdir="true" includes="*.jar"/>
     </path>
     <target         name="findbugs" depends="dist">
         <antcall    target  ="resolve">
@@ -969,7 +985,7 @@
     <target name="clean" description="clean up" depends="tribble.clean,clean.javadoc">
         <delete dir="out"/>
         <delete dir="${build.dir}"/>
-        <delete dir="lib"/>
+        <delete dir="${lib.dir}"/>
         <delete dir="staging"/>
         <delete dir="${dist.dir}"/>
         <delete dir="pipelinetests"/>
diff --git a/ivy.xml b/ivy.xml
index c2a6c4ccd..ce724bc3c 100644
--- a/ivy.xml
+++ b/ivy.xml
@@ -60,6 +60,10 @@
     <dependency org="net.sourceforge.findbugs" name="jsr305" rev="1.3.2" conf="test"/>
     <dependency org="com.google.code.caliper" name="caliper" rev="1.0-SNAPSHOT" conf="test" />
 
+    <!-- Contracts for Java and dependencies -->
+    <dependency org="com.google.code.cofoja" name="cofoja" rev="1.0-20110609" />
+    <dependency org="asm" name="asm-all" rev="3.3.1" />
+
     <!-- POI, for reading pipeline files -->
     <dependency org="org.apache.poi" name="poi" rev="3.8-beta3" />
     <dependency org="org.apache.poi" name="poi-ooxml" rev="3.8-beta3" />
diff --git a/settings/ivysettings.xml b/settings/ivysettings.xml
index 1e47fa847..b77414df9 100644
--- a/settings/ivysettings.xml
+++ b/settings/ivysettings.xml
@@ -25,5 +25,6 @@
     <module organisation="javax.activation" resolver="java.net" />
     <module organisation="net.java.dev.jna" resolver="maven2-repository.dev.java.net" />
     <module organisation="com.google.code.caliper" resolver="projects" />
+    <module organisation="com.google.code.cofoja" resolver="projects" />
   </modules>
 </ivysettings>
diff --git a/settings/repository/com.google/cofoja-1.0-20110609.jar b/settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.jar
similarity index 100%
rename from settings/repository/com.google/cofoja-1.0-20110609.jar
rename to settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.jar
diff --git a/settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.xml b/settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.xml
new file mode 100644
index 000000000..38d4e88f1
--- /dev/null
+++ b/settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="com.google.code.cofoja" module="cofoja" revision="1.0-20110609" status="integration" publication="20110609114800" />
+</ivy-module>

From 8a78414432226daceccccb4b38463c0826fb0f19 Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Mon, 11 Jul 2011 12:10:11 -0400
Subject: [PATCH 076/161] Removed TileCovariate as a dependency for
 AnalyzeCovariates.jar

---
 public/packages/AnalyzeCovariates.xml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/public/packages/AnalyzeCovariates.xml b/public/packages/AnalyzeCovariates.xml
index 1862d6cbb..7e31934df 100644
--- a/public/packages/AnalyzeCovariates.xml
+++ b/public/packages/AnalyzeCovariates.xml
@@ -10,7 +10,6 @@
       <class name="org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate" />
       <class name="org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate" />
       <class name="org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate" />
-      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate" />
     </dependencies>
   </executable>
   <resources>

From 86890c63574eba41bbbce6c52e2614f6c81b6f27 Mon Sep 17 00:00:00 2001
From: Christopher Hartl <chartl@broadinstitute.org>
Date: Mon, 11 Jul 2011 16:16:15 -0400
Subject: [PATCH 078/161] N and K (in binomial probability) got switched in RFA
 Walker with the last commit. No longer will NaNs be produced.

Added: TableToVCF. Kind of a longer-term project, but there are lots of variant calls available in a weird tabular format. I used this to convert Ju Et Al small indels to VCF. I'll check against the 1000G ASN superpopulation calls to see if we see a good amount of recapitulation, and if so, i'll put them in unvalidated comparisons. Minor chances to the TableCodec and TableFeatures to allow for this (the codec can sometimes drop a column, and the feature now allows you to grab on to its header).
---
 .../sting/gatk/refdata/features/table/TableCodec.java       | 0
 .../sting/gatk/refdata/features/table/TableFeature.java     | 6 +++++-
 .../broadinstitute/sting/utils/variantcontext/Allele.java   | 2 +-
 3 files changed, 6 insertions(+), 2 deletions(-)
 mode change 100644 => 100755 public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java
 mode change 100644 => 100755 public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java

diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java
old mode 100644
new mode 100755
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java
old mode 100644
new mode 100755
index 6ff0384a0..4b4ebe450
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java
@@ -55,10 +55,14 @@ public class TableFeature implements Feature {
     }
 
     public List<String> getAllValues() {
-        return getValuesTo(values.size()-1);
+        return getValuesTo(values.size());
     }
 
     public List<String> getValuesTo(int columnPosition) {
         return values.subList(0,columnPosition);
     }
+
+    public List<String> getHeader() {
+        return keys;
+    }
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java
index a9ba46159..901de6fae 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java
@@ -108,7 +108,7 @@ public class Allele implements Comparable<Allele> {
         this.bases = bases;
 
         if ( ! acceptableAlleleBases(bases) )
-            throw new IllegalArgumentException("Unexpected base in allele bases " + new String(bases));
+            throw new IllegalArgumentException("Unexpected base in allele bases \'" + new String(bases)+"\'");
     }
 
     private Allele(String bases, boolean isRef) {

From e3748675dbd518042ad67cfc653c7f1a5f89b327 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 11 Jul 2011 17:40:45 -0400
Subject: [PATCH 079/161] Support for VCF 4.1 header counts

---
 .../annotator/DepthPerAlleleBySample.java     |  3 +-
 .../ReadDepthAndAllelicFractionBySample.java  |  5 +-
 .../gatk/walkers/annotator/SampleList.java    |  3 +-
 .../utils/codecs/vcf/StandardVCFWriter.java   | 11 +--
 .../codecs/vcf/VCFCompoundHeaderLine.java     | 91 +++++++++++++++----
 .../sting/utils/codecs/vcf/VCFConstants.java  |  2 +
 .../utils/codecs/vcf/VCFFormatHeaderLine.java |  4 +
 .../utils/codecs/vcf/VCFHeaderLineCount.java  |  8 ++
 .../utils/codecs/vcf/VCFInfoHeaderLine.java   |  4 +
 9 files changed, 101 insertions(+), 30 deletions(-)
 create mode 100644 public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineCount.java

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
index 754d28dfd..ee66b50ee 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@@ -142,5 +143,5 @@ public class DepthPerAlleleBySample implements GenotypeAnnotation, StandardAnnot
  //   public String getIndelBases()
     public List<String> getKeyNames() { return Arrays.asList("AD"); }
 
-    public List<VCFFormatHeaderLine> getDescriptions() { return Arrays.asList(new VCFFormatHeaderLine(getKeyNames().get(0), VCFCompoundHeaderLine.UNBOUNDED, VCFHeaderLineType.Integer, "Allelic depths for the ref and alt alleles in the order listed")); }
+    public List<VCFFormatHeaderLine> getDescriptions() { return Arrays.asList(new VCFFormatHeaderLine(getKeyNames().get(0), VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "Allelic depths for the ref and alt alleles in the order listed")); }
 }
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java
index f287549bb..a670532af 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java
@@ -29,6 +29,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
@@ -200,8 +201,8 @@ public class ReadDepthAndAllelicFractionBySample implements GenotypeAnnotation {
                             1,
                             VCFHeaderLineType.Integer,
                             "Total read depth per sample, including MQ0"),
-                    new VCFFormatHeaderLine(getKeyNames().get(1),
-                            VCFCompoundHeaderLine.UNBOUNDED,
+                            new VCFFormatHeaderLine(getKeyNames().get(1),
+                            VCFHeaderLineCount.UNBOUNDED,
                             VCFHeaderLineType.Float,
                             "Fractions of reads (excluding MQ0 from both ref and alt) supporting each reported alternative allele, per sample"));
         }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
index 82f16be42..e2fd2a3d4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
@@ -65,5 +66,5 @@ public class SampleList implements InfoFieldAnnotation {
 
     public List<String> getKeyNames() { return Arrays.asList("Samples"); }
 
-    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("Samples", VCFInfoHeaderLine.UNBOUNDED, VCFHeaderLineType.String, "List of polymorphic samples")); }
+    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("Samples", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "List of polymorphic samples")); }
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
index 31251c089..230773310 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
@@ -360,14 +360,7 @@ public class StandardVCFWriter implements VCFWriter {
             if ( !entry.getValue().equals("") ) {
                 int numVals = 1;
                 VCFInfoHeaderLine metaData = mHeader.getInfoHeaderLine(key);
-                if ( metaData != null )
-                    numVals = metaData.getCount();
-
-                // take care of unbounded encoding
-                if ( numVals == VCFInfoHeaderLine.UNBOUNDED )
-                    numVals = 1;
-
-                if ( numVals > 0 ) {
+                if ( metaData != null && (metaData.getCountType() != VCFHeaderLineCount.INTEGER || metaData.getCount() > 0) ) {
                     mWriter.write("=");
                     mWriter.write(entry.getValue());
                 }
@@ -423,7 +416,7 @@ public class StandardVCFWriter implements VCFWriter {
 
                 VCFFormatHeaderLine metaData = mHeader.getFormatHeaderLine(key);
                 if ( metaData != null ) {
-                    int numInFormatField = metaData.getCount();
+                    int numInFormatField = metaData.getCount(vc.getAlternateAlleles().size());
                     if ( numInFormatField > 1 && val.equals(VCFConstants.MISSING_VALUE_v4) ) {
                         // If we have a missing field but multiple values are expected, we need to construct a new string with all fields.
                         // For example, if Number=2, the string has to be ".,."
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java
index a799161ad..49f9ab184 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java
@@ -24,6 +24,8 @@
 
 package org.broadinstitute.sting.utils.codecs.vcf;
 
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+
 import java.util.Arrays;
 import java.util.LinkedHashMap;
 import java.util.Map;
@@ -43,26 +45,43 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
 
     // the field types
     private String name;
-    private int count;
+    private int count = -1;
+    private VCFHeaderLineCount countType;
     private String description;
     private VCFHeaderLineType type;
 
     // access methods
     public String getName() { return name; }
-    public int getCount() { return count; }
     public String getDescription() { return description; }
     public VCFHeaderLineType getType() { return type; }
+    public VCFHeaderLineCount getCountType() { return countType; }
+    public int getCount() {
+        if ( countType != VCFHeaderLineCount.INTEGER )
+            throw new ReviewedStingException("Asking for header line count when type is not an integer");
+        return count;
+    }
 
-    //
-    public void setNumberToUnbounded() { this.count = UNBOUNDED; }
+    // utility method
+    public int getCount(int numAltAlleles) {
+        int myCount;
+        switch ( countType ) {
+            case INTEGER: myCount = count; break;
+            case UNBOUNDED: myCount = -1; break;
+            case A: myCount = numAltAlleles; break;
+            case G: myCount = ((numAltAlleles + 1) * (numAltAlleles + 2) / 2); break;
+            default: throw new ReviewedStingException("Unknown count type: " + countType);
+        }
+        return myCount;
+    }
+
+    public void setNumberToUnbounded() {
+        countType = VCFHeaderLineCount.UNBOUNDED;
+        count = -1;
+    }
 
     // our type of line, i.e. format, info, etc
     private final SupportedHeaderLineType lineType;
 
-    // line numerical values are allowed to be unbounded (or unknown), which is
-    // marked with a dot (.)
-    public static final int UNBOUNDED = -1;    // the value we store internally for unbounded types
-
     /**
      * create a VCF format header line
      *
@@ -74,6 +93,7 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
     protected VCFCompoundHeaderLine(String name, int count, VCFHeaderLineType type, String description, SupportedHeaderLineType lineType) {
         super(lineType.toString(), "");
         this.name = name;
+        this.countType = VCFHeaderLineCount.INTEGER;
         this.count = count;
         this.type = type;
         this.description = description;
@@ -81,6 +101,24 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
         validate();
     }
 
+    /**
+     * create a VCF format header line
+     *
+     * @param name         the name for this header line
+     * @param count        the count type for this header line
+     * @param type         the type for this header line
+     * @param description  the description for this header line
+     */
+    protected VCFCompoundHeaderLine(String name, VCFHeaderLineCount count, VCFHeaderLineType type, String description, SupportedHeaderLineType lineType) {
+        super(lineType.toString(), "");
+        this.name = name;
+        this.countType = count;
+        this.type = type;
+        this.description = description;
+        this.lineType = lineType;
+        validate();
+    }
+
     /**
      * create a VCF format header line
      *
@@ -92,9 +130,22 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
         super(lineType.toString(), "");
         Map<String,String> mapping = VCFHeaderLineTranslator.parseLine(version,line, Arrays.asList("ID","Number","Type","Description"));
         name = mapping.get("ID");
-        count = (version == VCFHeaderVersion.VCF4_0 || version == VCFHeaderVersion.VCF4_1) ?
-                        mapping.get("Number").equals(VCFConstants.UNBOUNDED_ENCODING_v4) ? UNBOUNDED : Integer.valueOf(mapping.get("Number")) :
-                        mapping.get("Number").equals(VCFConstants.UNBOUNDED_ENCODING_v3) ? UNBOUNDED : Integer.valueOf(mapping.get("Number"));
+        count = -1;
+        final String numberStr = mapping.get("Number");
+        if ( numberStr.equals(VCFConstants.PER_ALLELE_COUNT) ) {
+            countType = VCFHeaderLineCount.A;
+        } else if ( numberStr.equals(VCFConstants.PER_GENOTYPE_COUNT) ) {
+            countType = VCFHeaderLineCount.G;
+        } else if ( ((version == VCFHeaderVersion.VCF4_0 || version == VCFHeaderVersion.VCF4_1) &&
+                     numberStr.equals(VCFConstants.UNBOUNDED_ENCODING_v4)) ||
+                    ((version == VCFHeaderVersion.VCF3_2 || version == VCFHeaderVersion.VCF3_3) &&
+                     numberStr.equals(VCFConstants.UNBOUNDED_ENCODING_v3)) ) {
+            countType = VCFHeaderLineCount.UNBOUNDED;
+        } else {
+            countType = VCFHeaderLineCount.INTEGER;
+            count = Integer.valueOf(numberStr);
+
+        }
         type = VCFHeaderLineType.valueOf(mapping.get("Type"));
         if (type == VCFHeaderLineType.Flag && !allowFlagValues())
             throw new IllegalArgumentException("Flag is an unsupported type for this kind of field");
@@ -121,7 +172,15 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
     protected String toStringEncoding() {
         Map<String,Object> map = new LinkedHashMap<String,Object>();
         map.put("ID", name);
-        map.put("Number", count == UNBOUNDED ? VCFConstants.UNBOUNDED_ENCODING_v4 : count);
+        Object number;
+        switch ( countType ) {
+            case A: number = VCFConstants.PER_ALLELE_COUNT; break;
+            case G: number = VCFConstants.PER_GENOTYPE_COUNT; break;
+            case UNBOUNDED: number = VCFConstants.UNBOUNDED_ENCODING_v4; break;
+            case INTEGER:
+            default: number = count;
+        }
+        map.put("Number", number);
         map.put("Type", type);
         map.put("Description", description);
         return lineType.toString() + "=" + VCFHeaderLine.toStringEncoding(map);
@@ -136,15 +195,13 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
         if ( !(o instanceof VCFCompoundHeaderLine) )
             return false;
         VCFCompoundHeaderLine other = (VCFCompoundHeaderLine)o;
-        return name.equals(other.name) &&
-                count == other.count &&
-                description.equals(other.description) &&
-                type == other.type &&
-                lineType == other.lineType;
+        return equalsExcludingDescription(other) &&
+                description.equals(other.description);
     }
 
     public boolean equalsExcludingDescription(VCFCompoundHeaderLine other) {
         return count == other.count &&
+                countType == other.countType &&
                 type == other.type &&
                 lineType == other.lineType &&
                 name.equals(other.name);
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java
index 695c46c27..91cf86c70 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java
@@ -99,6 +99,8 @@ public final class VCFConstants {
     public static final String MISSING_DEPTH_v3 = "-1";
     public static final String UNBOUNDED_ENCODING_v4 = ".";
     public static final String UNBOUNDED_ENCODING_v3 = "-1";
+    public static final String PER_ALLELE_COUNT = "A";
+    public static final String PER_GENOTYPE_COUNT = "G";
     public static final String EMPTY_ALLELE = ".";
     public static final String EMPTY_GENOTYPE = "./.";
     public static final double MAX_GENOTYPE_QUAL = 99.0;
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java
index 352be3e97..f68cb670b 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java
@@ -16,6 +16,10 @@ public class VCFFormatHeaderLine extends VCFCompoundHeaderLine {
             throw new IllegalArgumentException("Flag is an unsupported type for format fields");
     }
 
+    public VCFFormatHeaderLine(String name, VCFHeaderLineCount count, VCFHeaderLineType type, String description) {
+        super(name, count, type, description, SupportedHeaderLineType.INFO);
+    }
+
     protected VCFFormatHeaderLine(String line, VCFHeaderVersion version) {
         super(line, version, SupportedHeaderLineType.FORMAT);
     }
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineCount.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineCount.java
new file mode 100644
index 000000000..d615c7c78
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineCount.java
@@ -0,0 +1,8 @@
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+/**
+ * the count encodings we use for fields in VCF header lines
+ */
+public enum VCFHeaderLineCount {
+    INTEGER, A, G, UNBOUNDED;
+}
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java
index 135a5c1a1..9b20f38a1 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java
@@ -13,6 +13,10 @@ public class VCFInfoHeaderLine extends VCFCompoundHeaderLine {
         super(name, count, type, description, SupportedHeaderLineType.INFO);
     }
 
+    public VCFInfoHeaderLine(String name, VCFHeaderLineCount count, VCFHeaderLineType type, String description) {
+        super(name, count, type, description, SupportedHeaderLineType.INFO);
+    }
+
     protected VCFInfoHeaderLine(String line, VCFHeaderVersion version) {
         super(line, version, SupportedHeaderLineType.INFO);
     }

From e93052a51e88ddb77c8ce71cf6a14a449ca3b1aa Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Mon, 11 Jul 2011 19:17:58 -0400
Subject: [PATCH 080/161] When generating the QGraph, don't regenerate if there
 aren't scatter/gather jobs. Fixed a display issue with the number of
 milliseconds that Queue has tried to contact LSF.

---
 .../sting/queue/engine/QGraph.scala           | 44 ++++++++++---------
 .../queue/engine/lsf/Lsf706JobRunner.scala    |  6 +--
 2 files changed, 26 insertions(+), 24 deletions(-)

diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala b/public/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala
index bfcc4d48c..8ed3f84c1 100755
--- a/public/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala
@@ -138,30 +138,32 @@ class QGraph extends Logging {
     validate()
 
     if (running && numMissingValues == 0) {
-      logger.info("Generating scatter gather jobs.")
       val scatterGathers = jobGraph.edgeSet.filter(edge => scatterGatherable(edge))
+      if (!scatterGathers.isEmpty) {
+        logger.info("Generating scatter gather jobs.")
 
-      var addedFunctions = List.empty[QFunction]
-      for (scatterGather <- scatterGathers) {
-        val functions = scatterGather.asInstanceOf[FunctionEdge]
-                .function.asInstanceOf[ScatterGatherableFunction]
-                .generateFunctions()
-        addedFunctions ++= functions
+        var addedFunctions = List.empty[QFunction]
+        for (scatterGather <- scatterGathers) {
+          val functions = scatterGather.asInstanceOf[FunctionEdge]
+                  .function.asInstanceOf[ScatterGatherableFunction]
+                  .generateFunctions()
+          addedFunctions ++= functions
+        }
+
+        logger.info("Removing original jobs.")
+        this.jobGraph.removeAllEdges(scatterGathers)
+        prune()
+
+        logger.info("Adding scatter gather jobs.")
+        addedFunctions.foreach(function => if (running) this.add(function))
+
+        logger.info("Regenerating graph.")
+        fill
+        val scatterGatherDotFile = if (settings.expandedDotFile != null) settings.expandedDotFile else settings.dotFile
+        if (scatterGatherDotFile != null)
+          renderToDot(scatterGatherDotFile)
+        validate()
       }
-
-      logger.info("Removing original jobs.")
-      this.jobGraph.removeAllEdges(scatterGathers)
-      prune()
-
-      logger.info("Adding scatter gather jobs.")
-      addedFunctions.foreach(function => if (running) this.add(function))
-
-      logger.info("Regenerating graph.")
-      fill
-      val scatterGatherDotFile = if (settings.expandedDotFile != null) settings.expandedDotFile else settings.dotFile
-      if (scatterGatherDotFile != null)
-        renderToDot(scatterGatherDotFile)
-      validate()
     }
   }
 
diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala b/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala
index 57d133dfe..ac2f036b4 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala
@@ -286,11 +286,11 @@ object Lsf706JobRunner extends Logging {
     // LSB_SHAREDIR/cluster_name/logdir/lsb.acct (man bacct)
     // LSB_SHAREDIR/cluster_name/logdir/lsb.events (man bhist)
     logger.debug("Job Id %s status / exitStatus / exitInfo: ??? / ??? / ???".format(runner.jobId))
-    val unknownStatusSeconds = (System.currentTimeMillis - runner.lastStatusUpdate)
-    if (unknownStatusSeconds > (unknownStatusMaxSeconds * 1000L)) {
+    val unknownStatusMillis = (System.currentTimeMillis - runner.lastStatusUpdate)
+    if (unknownStatusMillis > (unknownStatusMaxSeconds * 1000L)) {
       // Unknown status has been returned for a while now.
       runner.updateStatus(RunnerStatus.FAILED)
-      logger.error("Unable to read LSF status for %d minutes: job id %d: %s".format(unknownStatusSeconds/60, runner.jobId, runner.function.description))
+      logger.error("Unable to read LSF status for %0.2f minutes: job id %d: %s".format(unknownStatusMillis/(60 * 1000D), runner.jobId, runner.function.description))
     }
   }
 

From 5e593793af43153e844f69c0f0df367b1d56a658 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Mon, 11 Jul 2011 23:10:27 -0400
Subject: [PATCH 081/161] DiffEngine utility function simpleDiffFiles
 printSummaryReport now uses GATKReport for nice formating Moved print
 formatting arguments into inner class provided to printing functions
 themselves, not the class BAMDiffableReader only reads 1000 entries to avoid
 performance issue.  Work around for BAM files with non-unique names
 Uncommented all of the incorrectly commented out CombineVariants
 integrationtests BaseTest now uses DiffEngine to provide inline differences
 to VCF and BAM files

---
 .../org/broadinstitute/sting/BaseTest.java    |  15 +-
 .../CombineVariantsIntegrationTest.java       | 142 +++++++++---------
 2 files changed, 83 insertions(+), 74 deletions(-)

diff --git a/public/java/test/org/broadinstitute/sting/BaseTest.java b/public/java/test/org/broadinstitute/sting/BaseTest.java
index b469c8a41..b3e422ba9 100755
--- a/public/java/test/org/broadinstitute/sting/BaseTest.java
+++ b/public/java/test/org/broadinstitute/sting/BaseTest.java
@@ -4,6 +4,7 @@ import org.apache.commons.io.FileUtils;
 import org.apache.log4j.*;
 import org.apache.log4j.spi.LoggingEvent;
 import org.broadinstitute.sting.commandline.CommandLineUtils;
+import org.broadinstitute.sting.gatk.walkers.diffengine.DiffEngine;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.testng.Assert;
 
@@ -334,11 +335,14 @@ public abstract class BaseTest {
         
         if (parameterize || expectedMD5.equals("")) {
             // Don't assert
-        } else {
-            Assert.assertEquals(filemd5sum, expectedMD5, name + " Mismatching MD5s");
+        } else if ( filemd5sum.equals(expectedMD5) ) {
             System.out.println(String.format("  => %s PASSED", name));
+        } else {
+            Assert.fail(String.format("%s has mismatching MD5s: expected=%s observed=%s", name, expectedMD5, filemd5sum));
         }
 
+
+
         return filemd5sum;
     }
 
@@ -381,7 +385,12 @@ public abstract class BaseTest {
                     System.out.printf("##### Path to calculated file (MD5=%s): %s%n", filemd5sum, pathToFileMD5File);
                     System.out.printf("##### Diff command: diff %s %s%n", pathToExpectedMD5File, pathToFileMD5File);
 
-                    // todo -- add support for simple inline display of the first N differences for text file
+                    // inline differences
+                    DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(System.out, 20, 10, 0);
+                    boolean success = DiffEngine.simpleDiffFiles(new File(pathToExpectedMD5File), new File(pathToFileMD5File), params);
+                    if ( success )
+                        System.out.printf("Note that the above list is not comprehensive.  At most 20 lines of output, and 10 specific differences will be listed.  Please use -T DiffObjects -R public/testdata/exampleFASTA.fasta -m %s -t %s to explore the differences more freely%n",
+                                pathToExpectedMD5File, pathToFileMD5File);
                 }
             }
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
index 33a20f7b5..600718aa0 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
@@ -34,76 +34,76 @@ import java.util.Arrays;
  * Tests CombineVariants
  */
 public class CombineVariantsIntegrationTest extends WalkerTest {
-//    public static String baseTestString(String args) {
-//        return "-T CombineVariants -NO_HEADER -L 1:1-50,000,000 -o %s -R " + b36KGReference + args;
-//    }
-//
-//    public void test1InOut(String file, String md5, boolean vcf3) {
-//        test1InOut(file, md5, "", vcf3);
-//    }
-//
-//    public void test1InOut(String file, String md5, String args, boolean vcf3) {
-//         WalkerTestSpec spec = new WalkerTestSpec(
-//                 baseTestString(" -priority v1 -B:v1,VCF" + (vcf3 ? "3 " : " ") + validationDataLocation + file + args),
-//                 1,
-//                 Arrays.asList(md5));
-//         executeTest("testInOut1--" + file, spec);
-//    }
-//
-//    public void combine2(String file1, String file2, String args, String md5, boolean vcf3) {
-//         WalkerTestSpec spec = new WalkerTestSpec(
-//                 baseTestString(" -priority v1,v2 -B:v1,VCF" + (vcf3 ? "3 " : " ") + validationDataLocation + file1 + " -B:v2,VCF" + (vcf3 ? "3 " : " ") + validationDataLocation + file2 + args),
-//                 1,
-//                 Arrays.asList(md5));
-//         executeTest("combine2 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec);
-//    }
-//
-//    public void combineSites(String args, String md5) {
-//        String file1 = "1000G_omni2.5.b37.sites.vcf";
-//        String file2 = "hapmap_3.3.b37.sites.vcf";
-//        WalkerTestSpec spec = new WalkerTestSpec(
-//                "-T CombineVariants -NO_HEADER -o %s -R " + b37KGReference
-//                        + " -L 1:1-10,000,000 -B:omni,VCF " + validationDataLocation + file1
-//                        + " -B:hm3,VCF " + validationDataLocation + file2 + args,
-//                1,
-//                Arrays.asList(md5));
-//        executeTest("combineSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec);
-//    }
-//
-//
-//    @Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "2117fff6e0d182cd20be508e9661829c", true); }
-//    @Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "2cfaf7af3dd119df08b8a9c1f72e2f93", " -setKey foo", true); }
-//    @Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "1474ac0fde2ce42a3c24f1c97eab333e", " -setKey null", true); }
-//    @Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "7fc66df048a0ab08cf507906e1d4a308", false); } // official project VCF files in tabix format
-//
-//    @Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "ec9715f53dbf4531570557c212822f12", false); }
-//    @Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "f1072be5f5c6ee810276d9ca6537224d", false); }
-//
-//    @Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "b77a1eec725201d9d8e74ee0c45638d3", false); } // official project VCF files in tabix format
-//    @Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "802977fdfd2f4905b501bb06800f60af", false); } // official project VCF files in tabix format
-//    @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "a67157287dd2b24b5cdf7ebf8fcbbe9a", false); }
-//
-//    @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "e1f4718a179f1196538a33863da04f53", false); }
-//
-//    @Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "b3783384b7c8e877b971033e90beba48", true); }
-//
-//    @Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "902e541c87caa72134db6293fc46f0ad"); }
-//    @Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "f339ad4bb5863b58b9c919ce7d040bb9"); }
-//
-//    @Test public void threeWayWithRefs() {
-//        WalkerTestSpec spec = new WalkerTestSpec(
-//                baseTestString(" -B:NA19240_BGI,VCF "+validationDataLocation+"NA19240.BGI.RG.vcf" +
-//                        " -B:NA19240_ILLUMINA,VCF "+validationDataLocation+"NA19240.ILLUMINA.RG.vcf" +
-//                        " -B:NA19240_WUGSC,VCF "+validationDataLocation+"NA19240.WUGSC.RG.vcf" +
-//                        " -B:denovoInfo,VCF "+validationDataLocation+"yri_merged_validation_data_240610.annotated.b36.vcf" +
-//                        " -setKey centerSet" +
-//                        " -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED" +
-//                        " -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" +
-//                        " -genotypeMergeOptions UNIQUIFY -L 1"),
-//                1,
-//                Arrays.asList("a07995587b855f3214fb71940bf23c0f"));
-//        executeTest("threeWayWithRefs", spec);
-//    }
+    public static String baseTestString(String args) {
+        return "-T CombineVariants -NO_HEADER -L 1:1-50,000,000 -o %s -R " + b36KGReference + args;
+    }
+
+    public void test1InOut(String file, String md5, boolean vcf3) {
+        test1InOut(file, md5, "", vcf3);
+    }
+
+    public void test1InOut(String file, String md5, String args, boolean vcf3) {
+         WalkerTestSpec spec = new WalkerTestSpec(
+                 baseTestString(" -priority v1 -B:v1,VCF" + (vcf3 ? "3 " : " ") + validationDataLocation + file + args),
+                 1,
+                 Arrays.asList(md5));
+         executeTest("testInOut1--" + file, spec);
+    }
+
+    public void combine2(String file1, String file2, String args, String md5, boolean vcf3) {
+         WalkerTestSpec spec = new WalkerTestSpec(
+                 baseTestString(" -priority v1,v2 -B:v1,VCF" + (vcf3 ? "3 " : " ") + validationDataLocation + file1 + " -B:v2,VCF" + (vcf3 ? "3 " : " ") + validationDataLocation + file2 + args),
+                 1,
+                 Arrays.asList(md5));
+         executeTest("combine2 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec);
+    }
+
+    public void combineSites(String args, String md5) {
+        String file1 = "1000G_omni2.5.b37.sites.vcf";
+        String file2 = "hapmap_3.3.b37.sites.vcf";
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T CombineVariants -NO_HEADER -o %s -R " + b37KGReference
+                        + " -L 1:1-10,000,000 -B:omni,VCF " + validationDataLocation + file1
+                        + " -B:hm3,VCF " + validationDataLocation + file2 + args,
+                1,
+                Arrays.asList(md5));
+        executeTest("combineSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec);
+    }
+
+
+    @Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "2117fff6e0d182cd20be508e9661829c", true); }
+    @Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "2cfaf7af3dd119df08b8a9c1f72e2f93", " -setKey foo", true); }
+    @Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "1474ac0fde2ce42a3c24f1c97eab333e", " -setKey null", true); }
+    @Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "7fc66df048a0ab08cf507906e1d4a308", false); } // official project VCF files in tabix format
+
+    @Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "ec9715f53dbf4531570557c212822f12", false); }
+    @Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "f1072be5f5c6ee810276d9ca6537224d", false); }
+
+    @Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "b77a1eec725201d9d8e74ee0c45638d3", false); } // official project VCF files in tabix format
+    @Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "802977fdfd2f4905b501bb06800f60af", false); } // official project VCF files in tabix format
+    @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "a67157287dd2b24b5cdf7ebf8fcbbe9a", false); }
+
+    @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "e1f4718a179f1196538a33863da04f53", false); }
+
+    @Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "b3783384b7c8e877b971033e90beba48", true); }
+
+    @Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "902e541c87caa72134db6293fc46f0ad"); }
+    @Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "f339ad4bb5863b58b9c919ce7d040bb9"); }
+
+    @Test public void threeWayWithRefs() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString(" -B:NA19240_BGI,VCF "+validationDataLocation+"NA19240.BGI.RG.vcf" +
+                        " -B:NA19240_ILLUMINA,VCF "+validationDataLocation+"NA19240.ILLUMINA.RG.vcf" +
+                        " -B:NA19240_WUGSC,VCF "+validationDataLocation+"NA19240.WUGSC.RG.vcf" +
+                        " -B:denovoInfo,VCF "+validationDataLocation+"yri_merged_validation_data_240610.annotated.b36.vcf" +
+                        " -setKey centerSet" +
+                        " -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED" +
+                        " -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" +
+                        " -genotypeMergeOptions UNIQUIFY -L 1"),
+                1,
+                Arrays.asList("a07995587b855f3214fb71940bf23c0f"));
+        executeTest("threeWayWithRefs", spec);
+    }
 
 
     // complex examples with filtering, indels, and multiple alleles
@@ -119,7 +119,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
         executeTest("combineComplexSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec);
     }
 
-    @Test public void complexTestFull() { combineComplexSites("", "64b991fd3850f83614518f7d71f0532f"); }
+//    @Test public void complexTestFull() { combineComplexSites("", "64b991fd3850f83614518f7d71f0532f"); }
     @Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "0db9ef50fe54b60426474273d7c7fa99"); }
     @Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "d20acb3d53ba0a02ce92d540ebeda2a9"); }
     @Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "8d1b3d120515f8b56b5a0d10bc5da713"); }

From 893cc2e103e25daf01018c86382869ddac0e1f4a Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Mon, 11 Jul 2011 23:15:08 -0400
Subject: [PATCH 082/161] Making the package public, so there's no dependances
 from public -> private

---
 .../walkers/diffengine/BAMDiffableReader.java | 122 +++++
 .../gatk/walkers/diffengine/DiffElement.java  | 118 +++++
 .../gatk/walkers/diffengine/DiffEngine.java   | 423 ++++++++++++++++++
 .../gatk/walkers/diffengine/DiffNode.java     | 239 ++++++++++
 .../walkers/diffengine/DiffObjectsWalker.java | 113 +++++
 .../gatk/walkers/diffengine/DiffValue.java    |  90 ++++
 .../walkers/diffengine/DiffableReader.java    |  50 +++
 .../gatk/walkers/diffengine/Difference.java   |  58 +++
 .../walkers/diffengine/VCFDiffableReader.java | 119 +++++
 9 files changed, 1332 insertions(+)
 create mode 100644 public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
 create mode 100644 public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java
 create mode 100644 public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
 create mode 100644 public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java
 create mode 100644 public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
 create mode 100644 public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java
 create mode 100644 public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java
 create mode 100644 public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java
 create mode 100644 public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
new file mode 100644
index 000000000..f7a395d9d
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
@@ -0,0 +1,122 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+import net.sf.samtools.*;
+import net.sf.samtools.util.BlockCompressedInputStream;
+import org.broad.tribble.readers.AsciiLineReader;
+import org.broad.tribble.readers.LineReader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+import java.io.DataInputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.Map;
+import java.util.zip.GZIPInputStream;
+
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: depristo
+ * Date: 7/4/11
+ * Time: 1:09 PM
+ *
+ * Class implementing diffnode reader for VCF
+ */
+public class BAMDiffableReader implements DiffableReader {
+    private final static int MAX_RECORDS_TO_READ = 1000;
+    @Override
+    public String getName() { return "BAM"; }
+
+    @Override
+    public DiffElement readFromFile(File file) {
+        final SAMFileReader reader = new SAMFileReader(file, null); // null because we don't want it to look for the index
+        reader.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
+
+        DiffNode root = DiffNode.rooted(file.getName());
+        SAMRecordIterator iterator = reader.iterator();
+
+        int count = 0;
+        while ( iterator.hasNext() ) {
+            if ( count++ > MAX_RECORDS_TO_READ )
+                break;
+            final SAMRecord record = iterator.next();
+
+            // name is the read name + first of pair
+            String name = record.getReadName().replace('.', '_');
+            if ( record.getReadPairedFlag() ) {
+                name += record.getFirstOfPairFlag() ? "_1" : "_2";
+            }
+
+            DiffNode readRoot = DiffNode.empty(name, root);
+
+            // add fields
+            readRoot.add("NAME", record.getReadName());
+            readRoot.add("FLAGS", record.getFlags());
+            readRoot.add("RNAME", record.getReferenceName());
+            readRoot.add("POS", record.getAlignmentStart());
+            readRoot.add("MAPQ", record.getMappingQuality());
+            readRoot.add("CIGAR", record.getCigarString());
+            readRoot.add("RNEXT", record.getMateReferenceName());
+            readRoot.add("PNEXT", record.getMateAlignmentStart());
+            readRoot.add("TLEN", record.getInferredInsertSize());
+            readRoot.add("SEQ", record.getReadString());
+            readRoot.add("QUAL", record.getBaseQualityString());
+
+            for ( SAMRecord.SAMTagAndValue xt : record.getAttributes() ) {
+                readRoot.add(xt.tag, xt.value);
+            }
+
+            // add record to root
+            if ( ! root.hasElement(name) )
+                // protect ourselves from malformed files
+                root.add(readRoot);
+        }
+
+        reader.close();
+
+        return root.getBinding();
+    }
+
+    @Override
+    public boolean canRead(File file) {
+        final byte[] BAM_MAGIC = "BAM\1".getBytes();
+        final byte[] buffer = new byte[BAM_MAGIC.length];
+        try {
+            FileInputStream fstream = new FileInputStream(file);
+            new BlockCompressedInputStream(fstream).read(buffer,0,BAM_MAGIC.length);
+            return Arrays.equals(buffer, BAM_MAGIC);
+        } catch ( IOException e ) {
+            return false;
+        } catch ( net.sf.samtools.FileTruncatedException e ) {
+            return false;
+        }
+    }
+}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java
new file mode 100644
index 000000000..eff24bb88
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java
@@ -0,0 +1,118 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+import com.google.java.contract.*;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: depristo
+ * Date: 7/4/11
+ * Time: 12:55 PM
+ *
+ * An interface that must be implemented to allow us to calculate differences
+ * between structured objects
+ */
+@Invariant({
+        "name != null",
+        "value != null",
+        "parent != null || name.equals(\"ROOT\")",
+        "value == null || value.getBinding() == this"})
+public class DiffElement {
+    public final static DiffElement ROOT = new DiffElement();
+
+    final private String name;
+    final private DiffElement parent;
+    final private DiffValue value;
+
+    /**
+     * For ROOT only
+     */
+    private DiffElement() {
+        this.name = "ROOT";
+        this.parent = null;
+        this.value = new DiffValue(this, "ROOT");
+    }
+
+    @Requires({"name != null", "parent != null", "value != null"})
+    public DiffElement(String name, DiffElement parent, DiffValue value) {
+        if ( name.equals("ROOT") ) throw new IllegalArgumentException("Cannot use reserved name ROOT");
+        this.name = name;
+        this.parent = parent;
+        this.value = value;
+        this.value.setBinding(this);
+    }
+
+    @Ensures({"result != null"})
+    public String getName() {
+        return name;
+    }
+
+    public DiffElement getParent() {
+        return parent;
+    }
+
+    @Ensures({"result != null"})
+    public DiffValue getValue() {
+        return value;
+    }
+
+    public boolean isRoot() { return this == ROOT; }
+
+    @Ensures({"result != null"})
+    @Override
+    public String toString() {
+        return getName() + "=" + getValue().toString();
+    }
+
+    public String toString(int offset) {
+        return (offset > 0 ? Utils.dupString(' ', offset) : 0) + getName() + "=" + getValue().toString(offset);
+    }
+
+    @Ensures({"result != null"})
+    public final String fullyQualifiedName() {
+        if ( isRoot() )
+            return "";
+        else if ( parent.isRoot() )
+            return name;
+        else
+            return parent.fullyQualifiedName() + "." + name;
+    }
+
+    @Ensures({"result != null"})
+    public String toOneLineString() {
+        return getName() + "=" + getValue().toOneLineString();
+    }
+
+    @Ensures({"result != null"})
+    public DiffNode getValueAsNode() {
+        if ( getValue().isCompound() )
+            return (DiffNode)getValue();
+        else
+            throw new ReviewedStingException("Illegal request conversion of a DiffValue into a DiffNode: " + this);
+    }
+}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
new file mode 100644
index 000000000..ba2713bff
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
@@ -0,0 +1,423 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+import com.google.java.contract.Requires;
+import org.apache.log4j.Logger;
+import org.broadinstitute.sting.gatk.report.GATKReport;
+import org.broadinstitute.sting.gatk.report.GATKReportTable;
+import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.classloader.PluginManager;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+
+import java.io.File;
+import java.io.PrintStream;
+import java.util.*;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: depristo
+ * Date: 7/4/11
+ * Time: 12:51 PM
+ * A generic engine for comparing tree-structured objects
+ */
+public class DiffEngine {
+    final protected static Logger logger = Logger.getLogger(DiffEngine.class);
+
+    private final Map<String, DiffableReader> readers = new HashMap<String, DiffableReader>();
+
+    public DiffEngine() {
+        loadDiffableReaders();
+    }
+
+    // --------------------------------------------------------------------------------
+    //
+    // difference calculation
+    //
+    // --------------------------------------------------------------------------------
+
+    public List<Difference> diff(DiffElement master, DiffElement test) {
+        DiffValue masterValue = master.getValue();
+        DiffValue testValue = test.getValue();
+
+        if ( masterValue.isCompound() && masterValue.isCompound() ) {
+            return diff(master.getValueAsNode(), test.getValueAsNode());
+        } else if ( masterValue.isAtomic() && testValue.isAtomic() ) {
+            return diff(masterValue, testValue);
+        } else {
+            // structural difference in types.  one is node, other is leaf
+            return Arrays.asList(new Difference(master, test));
+        }
+    }
+
+    public List<Difference> diff(DiffNode master, DiffNode test) {
+        Set<String> allNames = new HashSet<String>(master.getElementNames());
+        allNames.addAll(test.getElementNames());
+        List<Difference> diffs = new ArrayList<Difference>();
+
+        for ( String name : allNames ) {
+            DiffElement masterElt = master.getElement(name);
+            DiffElement testElt = test.getElement(name);
+            if ( masterElt == null && testElt == null ) {
+                throw new ReviewedStingException("BUG: unexceptedly got two null elements for field: " + name);
+            } else if ( masterElt == null || testElt == null ) { // if either is null, we are missing a value
+                // todo -- should one of these be a special MISSING item?
+                diffs.add(new Difference(masterElt, testElt));
+            } else {
+                diffs.addAll(diff(masterElt, testElt));
+            }
+        }
+
+        return diffs;
+    }
+
+    public List<Difference> diff(DiffValue master, DiffValue test) {
+        if ( master.getValue().equals(test.getValue()) ) {
+            return Collections.emptyList();
+        } else {
+            return Arrays.asList(new Difference(master.getBinding(), test.getBinding()));
+        }
+    }
+
+    // --------------------------------------------------------------------------------
+    //
+    // Summarizing differences
+    //
+    // --------------------------------------------------------------------------------
+
+    /**
+     * Emits a summary of the diffs to out.  Suppose you have the following three differences:
+     *
+     *   A.X.Z:1!=2
+     *   A.Y.Z:3!=4
+     *   B.X.Z:5!=6
+     *
+     * The above is the itemized list of the differences.  The summary looks for common differences
+     * in the name hierarchy, counts those shared elements, and emits the differences that occur
+     * in order of decreasing counts.
+     *
+     * So, in the above example, what are the shared elements?
+     *
+     * A.X.Z and B.X.Z share X.Z, so there's a *.X.Z with count 2
+     * A.X.Z, A.Y.Z, and B.X.Z all share *.*.Z, with count 3
+     * Each of A.X.Z, A.Y.Z, and B.X.Z are individually unique, with count 1
+     *
+     * So we would emit the following summary:
+     *
+     * *.*.Z: 3
+     * *.X.Z: 2
+     * A.X.Z: 1 [specific difference: 1!=2]
+     * A.Y.Z: 1 [specific difference: 3!=4]
+     * B.X.Z: 1 [specific difference: 5!=6]
+     *
+     * The algorithm to accomplish this calculation is relatively simple. Start with all of the
+     * concrete differences.  For each pair of differences A1.A2....AN and B1.B2....BN:
+     *
+     * find the longest common subsequence Si.Si+1...SN where Ai = Bi = Si
+     * If i == 0, then there's no shared substructure
+     * If i > 0, then generate the summarized value X = *.*...Si.Si+1...SN
+     * if X is a known summary, increment it's count, otherwise set its count to 1
+     *
+     * Not that only pairs of the same length are considered as potentially equivalent
+     *
+     * @param params determines how we display the items
+     * @param diffs
+     */
+    public void reportSummarizedDifferences(List<Difference> diffs, SummaryReportParams params ) {
+        printSummaryReport(summarizeDifferences(diffs), params );
+    }
+
+    public List<SummarizedDifference> summarizeDifferences(List<Difference> diffs) {
+        List<String[]> diffPaths = new ArrayList<String[]>(diffs.size());
+
+        for ( Difference diff1 : diffs ) {
+            diffPaths.add(diffNameToPath(diff1.getFullyQualifiedName()));
+        }
+
+        return summarizedDifferencesOfPaths(diffPaths);
+    }
+
+    final protected static String[] diffNameToPath(String diffName) {
+        return diffName.split("\\.");
+    }
+
+    protected List<SummarizedDifference> summarizedDifferencesOfPaths(List<String[]> diffPaths) {
+        Map<String, SummarizedDifference> summaries = new HashMap<String, SummarizedDifference>();
+
+        // create the initial set of differences
+        for ( int i = 0; i < diffPaths.size(); i++ ) {
+            for ( int j = 0; j <= i; j++ ) {
+                String[] diffPath1 = diffPaths.get(i);
+                String[] diffPath2 = diffPaths.get(j);
+                if ( diffPath1.length == diffPath2.length ) {
+                    int lcp = longestCommonPostfix(diffPath1, diffPath2);
+                    String path = lcp > 0 ? summarizedPath(diffPath2, lcp) : Utils.join(".", diffPath2);
+                    addSummary(summaries, path, true);
+                }
+            }
+        }
+
+        // count differences
+        for ( String[] diffPath : diffPaths ) {
+            for ( SummarizedDifference sumDiff : summaries.values() ) {
+                if ( sumDiff.matches(diffPath) )
+                    addSummary(summaries, sumDiff.getPath(), false);
+            }
+        }
+
+        List<SummarizedDifference> sortedSummaries = new ArrayList<SummarizedDifference>(summaries.values());
+        Collections.sort(sortedSummaries);
+        return sortedSummaries;
+    }
+
+    private static void addSummary(Map<String, SummarizedDifference> summaries, String path, boolean onlyCatalog) {
+        if ( summaries.containsKey(path) ) {
+            if ( ! onlyCatalog )
+                summaries.get(path).incCount();
+        } else {
+            SummarizedDifference sumDiff = new SummarizedDifference(path);
+            summaries.put(sumDiff.getPath(), sumDiff);
+        }
+    }
+
+    protected void printSummaryReport(List<SummarizedDifference> sortedSummaries, SummaryReportParams params ) {
+        GATKReport report = new GATKReport();
+        final String tableName = "diffences";
+        report.addTable(tableName, "Summarized differences between the master and test files.\nSee http://www.broadinstitute.org/gsa/wiki/index.php/DiffObjectsWalker_and_SummarizedDifferences for more information");
+        GATKReportTable table = report.getTable(tableName);
+        table.addPrimaryKey("Difference", true);
+        table.addColumn("NumberOfOccurrences", 0);
+
+        int count = 0, count1 = 0;
+        for ( SummarizedDifference diff : sortedSummaries ) {
+            if ( diff.getCount() < params.minSumDiffToShow )
+                // in order, so break as soon as the count is too low
+                break;
+
+            if ( params.maxItemsToDisplay != 0 && count++ > params.maxItemsToDisplay )
+                break;
+
+            if ( diff.getCount() == 1 ) {
+                count1++;
+                if ( params.maxCountOneItems != 0 && count1 > params.maxCountOneItems )
+                    break;
+            }
+
+            table.set(diff.getPath(), "NumberOfOccurrences", diff.getCount());
+        }
+
+        table.write(params.out);
+    }
+
+    protected static int longestCommonPostfix(String[] diffPath1, String[] diffPath2) {
+        int i = 0;
+        for ( ; i < diffPath1.length; i++ ) {
+            int j = diffPath1.length - i - 1;
+            if ( ! diffPath1[j].equals(diffPath2[j]) )
+                break;
+        }
+        return i;
+    }
+
+    /**
+     * parts is [A B C D]
+     * commonPostfixLength: how many parts are shared at the end, suppose its 2
+     * We want to create a string *.*.C.D
+     *
+     * @param parts
+     * @param commonPostfixLength
+     * @return
+     */
+    protected static String summarizedPath(String[] parts, int commonPostfixLength) {
+        int stop = parts.length - commonPostfixLength;
+        if ( stop > 0 ) parts = parts.clone();
+        for ( int i = 0; i < stop; i++ ) {
+            parts[i] = "*";
+        }
+        return Utils.join(".", parts);
+    }
+
+    /**
+     * TODO -- all of the algorithms above should use SummarizedDifference instead
+     * TODO -- of some SummarizedDifferences and some low-level String[]
+     */
+    public static class SummarizedDifference implements Comparable<SummarizedDifference> {
+        final String path; // X.Y.Z
+        final String[] parts;
+        int count = 0;
+
+        public SummarizedDifference(String path) {
+            this.path = path;
+            this.parts = diffNameToPath(path);
+        }
+
+        public void incCount() { count++; }
+
+        public int getCount() {
+            return count;
+        }
+
+        /**
+         * The fully qualified path object A.B.C etc
+         * @return
+         */
+        public String getPath() {
+            return path;
+        }
+
+        /**
+         * @return the length of the parts of this summary
+         */
+        public int length() {
+            return this.parts.length;
+        }
+
+        /**
+         * Returns true if the string parts matches this summary.  Matches are
+         * must be equal() everywhere where this summary isn't *.
+         * @param otherParts
+         * @return
+         */
+        public boolean matches(String[] otherParts) {
+            if ( otherParts.length != length() )
+                return false;
+
+            // TODO optimization: can start at right most non-star element
+            for ( int i = 0; i < length(); i++ ) {
+                String part = parts[i];
+                if ( ! part.equals("*") && ! part.equals(otherParts[i]) )
+                    return false;
+            }
+
+            return true;
+        }
+
+        @Override
+        public String toString() {
+            return String.format("%s:%d", getPath(), getCount());
+        }
+
+        @Override
+        public int compareTo(SummarizedDifference other) {
+            // sort first highest to lowest count, then by lowest to highest path
+            int countCmp = Integer.valueOf(count).compareTo(other.count);
+            return countCmp != 0 ? -1 * countCmp : path.compareTo(other.path);
+        }
+
+
+    }
+
+    // --------------------------------------------------------------------------------
+    //
+    // plugin manager
+    //
+    // --------------------------------------------------------------------------------
+
+    public void loadDiffableReaders() {
+        List<Class<? extends DiffableReader>> drClasses = new PluginManager<DiffableReader>( DiffableReader.class ).getPlugins();
+
+        logger.info("Loading diffable modules:");
+        for (Class<? extends DiffableReader> drClass : drClasses ) {
+            logger.info("\t" + drClass.getSimpleName());
+
+            try {
+                DiffableReader dr = drClass.newInstance();
+                readers.put(dr.getName(), dr);
+            } catch (InstantiationException e) {
+                throw new ReviewedStingException("Unable to instantiate module '" + drClass.getSimpleName() + "'");
+            } catch (IllegalAccessException e) {
+                throw new ReviewedStingException("Illegal access error when trying to instantiate '" + drClass.getSimpleName() + "'");
+            }
+        }
+    }
+
+    protected Map<String, DiffableReader> getReaders() {
+        return readers;
+    }
+
+    protected DiffableReader getReader(String name) {
+        return readers.get(name);
+    }
+
+    /**
+     * Returns a reader appropriate for this file, or null if no such reader exists
+     * @param file
+     * @return
+     */
+    public DiffableReader findReaderForFile(File file) {
+        for ( DiffableReader reader : readers.values() )
+            if (reader.canRead(file) )
+                return reader;
+
+        return null;
+    }
+
+    /**
+     * Returns true if reader appropriate for this file, or false if no such reader exists
+     * @param file
+     * @return
+     */
+    public boolean canRead(File file) {
+        return findReaderForFile(file) != null;
+    }
+
+    public DiffElement createDiffableFromFile(File file) {
+        DiffableReader reader = findReaderForFile(file);
+        if ( reader == null )
+            throw new UserException("Unsupported file type: " + file);
+        else
+            return reader.readFromFile(file);
+    }
+
+    public static boolean simpleDiffFiles(File masterFile, File testFile, DiffEngine.SummaryReportParams params) {
+        DiffEngine diffEngine = new DiffEngine();
+
+        if ( diffEngine.canRead(masterFile) && diffEngine.canRead(testFile) ) {
+            DiffElement master = diffEngine.createDiffableFromFile(masterFile);
+            DiffElement test = diffEngine.createDiffableFromFile(testFile);
+            List<Difference> diffs = diffEngine.diff(master, test);
+            diffEngine.reportSummarizedDifferences(diffs, params);
+            return true;
+        } else {
+            return false;
+        }
+    }
+
+    public static class SummaryReportParams {
+        PrintStream out = System.out;
+        int maxItemsToDisplay = 0;
+        int maxCountOneItems = 0;
+        int minSumDiffToShow = 0;
+
+        public SummaryReportParams(PrintStream out, int maxItemsToDisplay, int maxCountOneItems, int minSumDiffToShow) {
+            this.out = out;
+            this.maxItemsToDisplay = maxItemsToDisplay;
+            this.maxCountOneItems = maxCountOneItems;
+            this.minSumDiffToShow = minSumDiffToShow;
+        }
+    }
+}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java
new file mode 100644
index 000000000..0720e18c0
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java
@@ -0,0 +1,239 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+import com.google.java.contract.Requires;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+
+import java.util.*;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: depristo
+ * Date: 7/4/11
+ * Time: 12:55 PM
+ *
+ * An interface that must be implemented to allow us to calculate differences
+ * between structured objects
+ */
+public class DiffNode extends DiffValue {
+    private Map<String, DiffElement> getElementMap() {
+        return (Map<String, DiffElement>)super.getValue();
+    }
+    private static Map<String, DiffElement> emptyElements() { return new HashMap<String, DiffElement>(); }
+
+    private DiffNode(Map<String, DiffElement> elements) {
+        super(elements);
+    }
+
+    private DiffNode(DiffElement binding, Map<String, DiffElement> elements) {
+        super(binding, elements);
+    }
+
+    // ---------------------------------------------------------------------------
+    //
+    // constructors
+    //
+    // ---------------------------------------------------------------------------
+
+    public static DiffNode rooted(String name) {
+        return empty(name, DiffElement.ROOT);
+    }
+
+    public static DiffNode empty(String name, DiffElement parent) {
+        DiffNode df = new DiffNode(emptyElements());
+        DiffElement elt = new DiffElement(name, parent, df);
+        df.setBinding(elt);
+        return df;
+    }
+
+    public static DiffNode empty(String name, DiffValue parent) {
+        return empty(name, parent.getBinding());
+    }
+
+    // ---------------------------------------------------------------------------
+    //
+    // accessors
+    //
+    // ---------------------------------------------------------------------------
+
+    @Override
+    public boolean isAtomic() { return false; }
+
+    public Collection<String> getElementNames() {
+        return getElementMap().keySet();
+    }
+
+    public Collection<DiffElement> getElements() {
+        return getElementMap().values();
+    }
+
+    private Collection<DiffElement> getElements(boolean atomicOnly) {
+        List<DiffElement> elts = new ArrayList<DiffElement>();
+        for ( DiffElement elt : getElements() )
+            if ( (atomicOnly && elt.getValue().isAtomic()) || (! atomicOnly && elt.getValue().isCompound()))
+                elts.add(elt);
+        return elts;
+    }
+
+    public Collection<DiffElement> getAtomicElements() {
+        return getElements(true);
+    }
+
+    public Collection<DiffElement> getCompoundElements() {
+        return getElements(false);
+    }
+
+    public DiffElement getElement(String name) {
+        for ( DiffElement elt : getElements() )
+            if ( elt.getName().equals(name) )
+                return elt;
+        return null;
+    }
+
+    /**
+     * Returns true if name is bound in this node
+     * @param name
+     * @return
+     */
+    public boolean hasElement(String name) {
+        return getElement(name) != null;
+    }
+
+    // ---------------------------------------------------------------------------
+    //
+    // add
+    //
+    // ---------------------------------------------------------------------------
+
+    @Requires("elt != null")
+    public void add(DiffElement elt) {
+        if ( getElementMap().containsKey(elt.getName()) )
+            throw new IllegalArgumentException("Attempting to rebind already existing binding: " + elt + " node=" + this);
+        getElementMap().put(elt.getName(), elt);
+    }
+
+    @Requires("elt != null")
+    public void add(DiffValue elt) {
+        add(elt.getBinding());
+    }
+
+    @Requires("elts != null")
+    public void add(Collection<DiffElement> elts) {
+        for ( DiffElement e : elts )
+            add(e);
+    }
+
+    public void add(String name, Object value) {
+        add(new DiffElement(name, this.getBinding(), new DiffValue(value)));
+    }
+
+    // ---------------------------------------------------------------------------
+    //
+    // toString
+    //
+    // ---------------------------------------------------------------------------
+
+    @Override
+    public String toString() {
+        return toString(0);
+    }
+
+    @Override
+    public String toString(int offset) {
+        String off = offset > 0 ? Utils.dupString(' ', offset) : "";
+        StringBuilder b = new StringBuilder();
+
+        b.append("(").append("\n");
+        Collection<DiffElement> atomicElts = getAtomicElements();
+        for ( DiffElement elt : atomicElts ) {
+            b.append(elt.toString(offset + 2)).append('\n');
+        }
+
+        for ( DiffElement elt : getCompoundElements() ) {
+            b.append(elt.toString(offset + 4)).append('\n');
+        }
+        b.append(off).append(")").append("\n");
+
+        return b.toString();
+    }
+
+    @Override
+    public String toOneLineString() {
+        StringBuilder b = new StringBuilder();
+
+        b.append('(');
+        List<String> parts = new ArrayList<String>();
+        for ( DiffElement elt : getElements() )
+            parts.add(elt.toOneLineString());
+        b.append(Utils.join(" ", parts));
+        b.append(')');
+
+        return b.toString();
+    }
+
+    // --------------------------------------------------------------------------------
+    //
+    // fromString and toOneLineString
+    //
+    // --------------------------------------------------------------------------------
+
+    public static DiffElement fromString(String tree) {
+        return fromString(tree, DiffElement.ROOT);
+    }
+
+    /**
+     * Doesn't support full tree structure parsing
+     * @param tree
+     * @param parent
+     * @return
+     */
+    private static DiffElement fromString(String tree, DiffElement parent) {
+        // X=(A=A B=B C=(D=D))
+        String[] parts = tree.split("=", 2);
+        if ( parts.length != 2 )
+            throw new ReviewedStingException("Unexpected tree structure: " + tree + " parts=" + parts);
+        String name = parts[0];
+        String value = parts[1];
+
+        if ( value.length() == 0 )
+            throw new ReviewedStingException("Illegal tree structure: " + value + " at " + tree);
+
+        if ( value.charAt(0) == '(' ) {
+            if ( ! value.endsWith(")") )
+                throw new ReviewedStingException("Illegal tree structure.  Missing ): " + value + " at " + tree);
+            String subtree = value.substring(1, value.length()-1);
+            DiffNode rec = DiffNode.empty(name, parent);
+            String[] subParts = subtree.split(" ");
+            for ( String subPart : subParts ) {
+                rec.add(fromString(subPart, rec.getBinding()));
+            }
+            return rec.getBinding();
+        } else {
+            return new DiffValue(name, parent, value).getBinding();
+        }
+    }
+}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
new file mode 100644
index 000000000..a08108db2
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
@@ -0,0 +1,113 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+import org.apache.xmlbeans.impl.tool.Diff;
+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;
+import org.broadinstitute.sting.gatk.walkers.Requires;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
+
+import java.io.File;
+import java.io.PrintStream;
+import java.util.List;
+
+/**
+ * Compares two record-oriented files, itemizing specific difference between equivalent
+ * records in the two files.  Reports both itemized and summarized differences.
+ * @author Mark DePristo
+ * @version 0.1
+ */
+@Requires(value={})
+public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
+    @Output(doc="File to which results should be written",required=true)
+    protected PrintStream out;
+
+    @Argument(fullName="maxRecords", shortName="M", doc="Max. number of records to process", required=false)
+    int MAX_RECORDS = 0;
+
+    @Argument(fullName="maxCount1Records", shortName="M1", doc="Max. number of records occuring exactly once in the file to process", required=false)
+    int MAX_COUNT1_RECORDS = 0;
+
+    @Argument(fullName="minCountForDiff", shortName="MCFD", doc="Min number of observations for a records to display", required=false)
+    int minCountForDiff = 1;
+
+    @Argument(fullName="showItemizedDifferences", shortName="SID", doc="Should we enumerate all differences between the files?", required=false)
+    boolean showItemizedDifferences = false;
+
+    @Argument(fullName="master", shortName="m", doc="Master file: expected results", required=true)
+    File masterFile;
+
+    @Argument(fullName="test", shortName="t", doc="Test file: new results to compare to the master file", required=true)
+    File testFile;
+
+    final DiffEngine diffEngine = new DiffEngine();
+
+    @Override
+    public void initialize() {
+
+    }
+
+    @Override
+    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        return 0;
+    }
+
+    @Override
+    public Integer reduceInit() {
+        return 0;
+    }
+
+    @Override
+    public Integer reduce(Integer counter, Integer sum) {
+        return counter + sum;
+    }
+
+    @Override
+    public void onTraversalDone(Integer sum) {
+        out.printf("Reading master file %s%n", masterFile);
+        DiffElement master = diffEngine.createDiffableFromFile(masterFile);
+        out.printf("Reading test file %s%n", testFile);
+        DiffElement test = diffEngine.createDiffableFromFile(testFile);
+
+//        out.printf("Master diff objects%n");
+//        out.println(master.toString());
+//        out.printf("Test diff objects%n");
+//        out.println(test.toString());
+
+        List<Difference> diffs = diffEngine.diff(master, test);
+        if ( showItemizedDifferences ) {
+            out.printf("Itemized results%n");
+            for ( Difference diff : diffs )
+                out.printf("DIFF: %s%n", diff.toString());
+        }
+
+        DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(out, MAX_RECORDS, MAX_COUNT1_RECORDS, minCountForDiff);
+        diffEngine.reportSummarizedDifferences(diffs, params);
+    }
+}
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java
new file mode 100644
index 000000000..7245e9e8d
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java
@@ -0,0 +1,90 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+import org.broadinstitute.sting.utils.Utils;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: depristo
+ * Date: 7/4/11
+ * Time: 12:55 PM
+ *
+ * An interface that must be implemented to allow us to calculate differences
+ * between structured objects
+ */
+public class DiffValue {
+    private DiffElement binding = null;
+    final private Object value;
+
+    public DiffValue(Object value) {
+        this.value = value;
+    }
+
+    public DiffValue(DiffElement binding, Object value) {
+        this.binding = binding;
+        this.value = value;
+    }
+
+    public DiffValue(DiffValue parent, Object value) {
+        this(parent.getBinding(), value);
+    }
+
+    public DiffValue(String name, DiffElement parent, Object value) {
+        this.binding = new DiffElement(name, parent, this);
+        this.value = value;
+    }
+
+    public DiffValue(String name, DiffValue parent, Object value) {
+        this(name, parent.getBinding(), value);
+    }
+
+    public DiffElement getBinding() {
+        return binding;
+    }
+
+    protected void setBinding(DiffElement binding) {
+        this.binding = binding;
+    }
+
+    public Object getValue() {
+        return value;
+    }
+
+    public String toString() {
+        return getValue().toString();
+    }
+
+    public String toString(int offset) {
+        return toString();
+    }
+
+    public String toOneLineString() {
+        return getValue().toString();
+    }
+
+    public boolean isAtomic() { return true; }
+    public boolean isCompound() { return ! isAtomic(); }
+}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java
new file mode 100644
index 000000000..84c2eed10
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java
@@ -0,0 +1,50 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+import com.google.java.contract.Ensures;
+import com.google.java.contract.Requires;
+
+import java.io.File;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: depristo
+ * Date: 7/4/11
+ * Time: 1:09 PM
+ *
+ * Interface for readers creating diffable objects from a file
+ */
+public interface DiffableReader {
+    @Ensures("result != null")
+    public String getName();
+
+    @Ensures("result != null")
+    @Requires("file != null")
+    public DiffElement readFromFile(File file);
+
+    @Requires("file != null")
+    public boolean canRead(File file);
+}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java
new file mode 100644
index 000000000..6627a4cc5
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java
@@ -0,0 +1,58 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: depristo
+ * Date: 7/4/11
+ * Time: 12:53 PM
+ *
+ * Represents a specific difference between two specific DiffElements
+ */
+public class Difference {
+    DiffElement master, test;
+
+    public Difference(DiffElement master, DiffElement test) {
+        if ( master == null && test == null ) throw new IllegalArgumentException("Master and test both cannot be null");
+        this.master = master;
+        this.test = test;
+    }
+
+    public String toString() {
+        return String.format("%s:%s!=%s",
+                getFullyQualifiedName(),
+                getOneLineString(master),
+                getOneLineString(test));
+    }
+
+    public String getFullyQualifiedName() {
+        return (master == null ? test : master).fullyQualifiedName();
+    }
+
+    private static String getOneLineString(DiffElement elt) {
+        return elt == null ? "MISSING" : elt.getValue().toOneLineString();
+    }
+}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
new file mode 100644
index 000000000..743178538
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
@@ -0,0 +1,119 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+import org.broad.tribble.readers.AsciiLineReader;
+import org.broad.tribble.readers.LineReader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+import java.io.*;
+import java.util.Arrays;
+import java.util.Map;
+import java.util.zip.GZIPInputStream;
+
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: depristo
+ * Date: 7/4/11
+ * Time: 1:09 PM
+ *
+ * Class implementing diffnode reader for VCF
+ */
+public class VCFDiffableReader implements DiffableReader {
+    @Override
+    public String getName() { return "VCF"; }
+
+    @Override
+    public DiffElement readFromFile(File file) {
+        DiffNode root = DiffNode.rooted(file.getName());
+        try {
+            LineReader lineReader = new AsciiLineReader(new FileInputStream(file));
+            VCFCodec vcfCodec = new VCFCodec();
+            VCFHeader header = (VCFHeader)vcfCodec.readHeader(lineReader);
+
+            String line = lineReader.readLine();
+            while ( line != null ) {
+                VariantContext vc = (VariantContext)vcfCodec.decode(line);
+                String name = vc.getChr() + ":" + vc.getStart();
+                DiffNode vcRoot = DiffNode.empty(name, root);
+
+                // add fields
+                vcRoot.add("CHROM", vc.getChr());
+                vcRoot.add("POS", vc.getStart());
+                vcRoot.add("ID", vc.hasID() ? vc.getID() : VCFConstants.MISSING_VALUE_v4);
+                vcRoot.add("REF", vc.getReference());
+                vcRoot.add("ALT", vc.getAlternateAlleles());
+                vcRoot.add("QUAL", vc.hasNegLog10PError() ? vc.getNegLog10PError() * 10 : VCFConstants.MISSING_VALUE_v4);
+                vcRoot.add("FILTER", vc.getFilters());
+
+                // add info fields
+                for (Map.Entry<String, Object> attribute : vc.getAttributes().entrySet()) {
+                    if ( ! attribute.getKey().startsWith("_") && ! attribute.getKey().equals(VariantContext.ID_KEY))
+                        vcRoot.add(attribute.getKey(), attribute.getValue());
+                }
+
+                for (Genotype g : vc.getGenotypes().values() ) {
+                    DiffNode gRoot = DiffNode.empty(g.getSampleName(), vcRoot);
+                    gRoot.add("GT", g.getGenotypeString());
+                    gRoot.add("GQ", g.hasNegLog10PError() ? g.getNegLog10PError() * 10 : VCFConstants.MISSING_VALUE_v4 );
+
+                    for (Map.Entry<String, Object> attribute : g.getAttributes().entrySet()) {
+                        if ( ! attribute.getKey().startsWith("_") )
+                            gRoot.add(attribute.getKey(), attribute.getValue());
+                    }
+
+                    vcRoot.add(gRoot);
+                }
+
+                root.add(vcRoot);
+                line = lineReader.readLine();
+            }
+
+            lineReader.close();
+        } catch ( IOException e ) {
+            return null;
+        }
+
+        return root.getBinding();
+    }
+
+    @Override
+    public boolean canRead(File file) {
+        try {
+            final String VCF4_HEADER = "##fileformat=VCFv4";
+            char[] buff = new char[VCF4_HEADER.length()];
+            new FileReader(file).read(buff, 0, VCF4_HEADER.length());
+            String firstLine = new String(buff);
+            return firstLine.startsWith(VCF4_HEADER);
+        } catch ( IOException e ) {
+            return false;
+        }
+    }
+}

From d7d15019dd543decffa2169f074b123633fe5984 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 12 Jul 2011 01:16:21 -0400
Subject: [PATCH 083/161] Adding support for other simple header line types
 (e.g. ALT) and cleaning up the interface a bit.

---
 .../walkers/annotator/ChromosomeCounts.java   |  5 +-
 .../walkers/genotyper/UnifiedGenotyper.java   | 17 +++-
 .../utils/codecs/vcf/StandardVCFWriter.java   |  3 +-
 .../utils/codecs/vcf/VCFAltHeaderLine.java    | 28 +++++++
 .../codecs/vcf/VCFCompoundHeaderLine.java     |  3 +
 .../utils/codecs/vcf/VCFFilterHeaderLine.java | 48 +----------
 .../utils/codecs/vcf/VCFFormatHeaderLine.java |  2 +-
 .../utils/codecs/vcf/VCFSimpleHeaderLine.java | 81 +++++++++++++++++++
 .../sting/utils/codecs/vcf/VCFUtils.java      | 15 ----
 9 files changed, 135 insertions(+), 67 deletions(-)
 create mode 100644 public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFAltHeaderLine.java
 create mode 100644 public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFSimpleHeaderLine.java

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
index 143722d7c..ed10d2072 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
@@ -41,8 +42,8 @@ import java.util.*;
 public class ChromosomeCounts implements InfoFieldAnnotation, StandardAnnotation {
 
     private String[] keyNames = { VCFConstants.ALLELE_NUMBER_KEY, VCFConstants.ALLELE_COUNT_KEY, VCFConstants.ALLELE_FREQUENCY_KEY };
-    private VCFInfoHeaderLine[] descriptions = { new VCFInfoHeaderLine(VCFConstants.ALLELE_FREQUENCY_KEY, -1, VCFHeaderLineType.Float, "Allele Frequency, for each ALT allele, in the same order as listed"),
-            new VCFInfoHeaderLine(VCFConstants.ALLELE_COUNT_KEY, -1, VCFHeaderLineType.Integer, "Allele count in genotypes, for each ALT allele, in the same order as listed"),
+    private VCFInfoHeaderLine[] descriptions = { new VCFInfoHeaderLine(VCFConstants.ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Float, "Allele Frequency, for each ALT allele, in the same order as listed"),
+            new VCFInfoHeaderLine(VCFConstants.ALLELE_COUNT_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "Allele count in genotypes, for each ALT allele, in the same order as listed"),
             new VCFInfoHeaderLine(VCFConstants.ALLELE_NUMBER_KEY, 1, VCFHeaderLineType.Integer, "Total number of alleles in called genotypes") };
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 7a765c602..fe0084a19 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -37,7 +37,6 @@ import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import java.util.*;
 import java.io.PrintStream;
@@ -158,7 +157,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
         }
 
         // FORMAT and INFO fields
-        headerInfo.addAll(VCFUtils.getSupportedHeaderStrings());
+        headerInfo.addAll(getSupportedHeaderStrings());
 
         // FILTER fields
         if ( UAC.STANDARD_CONFIDENCE_FOR_EMITTING < UAC.STANDARD_CONFIDENCE_FOR_CALLING )
@@ -167,6 +166,20 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
         return headerInfo;
     }
 
+    /**
+     * return a set of supported format lines; what we currently support for output in the genotype fields of a VCF
+     * @return a set of VCF format lines
+     */
+    private static Set<VCFFormatHeaderLine> getSupportedHeaderStrings() {
+        Set<VCFFormatHeaderLine> result = new HashSet<VCFFormatHeaderLine>();
+        result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype"));
+        result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_QUALITY_KEY, 1, VCFHeaderLineType.Float, "Genotype Quality"));
+        result.add(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Read Depth (only filtered reads used for calling)"));
+        result.add(new VCFFormatHeaderLine(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Float, "Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; if site is not biallelic, number of likelihoods if n*(n+1)/2"));
+
+        return result;
+    }
+
     /**
      * Compute at a given locus.
      *
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
index 230773310..f4996b487 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
@@ -358,9 +358,8 @@ public class StandardVCFWriter implements VCFWriter {
             mWriter.write(key);
 
             if ( !entry.getValue().equals("") ) {
-                int numVals = 1;
                 VCFInfoHeaderLine metaData = mHeader.getInfoHeaderLine(key);
-                if ( metaData != null && (metaData.getCountType() != VCFHeaderLineCount.INTEGER || metaData.getCount() > 0) ) {
+                if ( metaData == null || metaData.getCountType() != VCFHeaderLineCount.INTEGER || metaData.getCount() != 0 ) {
                     mWriter.write("=");
                     mWriter.write(entry.getValue());
                 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFAltHeaderLine.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFAltHeaderLine.java
new file mode 100644
index 000000000..a9de949d8
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFAltHeaderLine.java
@@ -0,0 +1,28 @@
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+/**
+ * @author ebanks
+ * A class representing a key=value entry for ALT fields in the VCF header
+ */
+public class VCFAltHeaderLine extends VCFSimpleHeaderLine  {
+
+    /**
+     * create a VCF filter header line
+     *
+     * @param name         the name for this header line
+     * @param description  the description for this header line
+     */
+    public VCFAltHeaderLine(String name, String description) {
+        super(name, description, SupportedHeaderLineType.ALT);
+    }
+
+    /**
+     * create a VCF info header line
+     *
+     * @param line      the header line
+     * @param version   the vcf header version
+     */
+    protected VCFAltHeaderLine(String line, VCFHeaderVersion version) {
+        super(line, version, SupportedHeaderLineType.ALT);
+    }
+}
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java
index 49f9ab184..bb822f2ed 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java
@@ -89,6 +89,7 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
      * @param count        the count for this header line
      * @param type         the type for this header line
      * @param description  the description for this header line
+     * @param lineType     the header line type
      */
     protected VCFCompoundHeaderLine(String name, int count, VCFHeaderLineType type, String description, SupportedHeaderLineType lineType) {
         super(lineType.toString(), "");
@@ -108,6 +109,7 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
      * @param count        the count type for this header line
      * @param type         the type for this header line
      * @param description  the description for this header line
+     * @param lineType     the header line type
      */
     protected VCFCompoundHeaderLine(String name, VCFHeaderLineCount count, VCFHeaderLineType type, String description, SupportedHeaderLineType lineType) {
         super(lineType.toString(), "");
@@ -124,6 +126,7 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
      *
      * @param line   the header line
      * @param version      the VCF header version
+     * @param lineType     the header line type
      *
      */
     protected VCFCompoundHeaderLine(String line, VCFHeaderVersion version, SupportedHeaderLineType lineType) {
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java
index 9176fc16e..418b80074 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java
@@ -1,19 +1,10 @@
 package org.broadinstitute.sting.utils.codecs.vcf;
 
-import java.util.Arrays;
-import java.util.LinkedHashMap;
-import java.util.Map;
-
-
 /**
  * @author ebanks
  * A class representing a key=value entry for FILTER fields in the VCF header
  */
-public class VCFFilterHeaderLine extends VCFHeaderLine implements VCFNamedHeaderLine  {
-
-    private String name;
-    private String description;
-
+public class VCFFilterHeaderLine extends VCFSimpleHeaderLine  {
 
     /**
      * create a VCF filter header line
@@ -22,12 +13,7 @@ public class VCFFilterHeaderLine extends VCFHeaderLine implements VCFNamedHeader
      * @param description  the description for this header line
      */
     public VCFFilterHeaderLine(String name, String description) {
-        super("FILTER", "");
-        this.name = name;
-        this.description = description;
-
-        if ( name == null || description == null )
-            throw new IllegalArgumentException(String.format("Invalid VCFCompoundHeaderLine: key=%s name=%s desc=%s", super.getKey(), name, description ));
+        super(name, description, SupportedHeaderLineType.FILTER);
     }
 
     /**
@@ -37,34 +23,6 @@ public class VCFFilterHeaderLine extends VCFHeaderLine implements VCFNamedHeader
      * @param version   the vcf header version
      */
     protected VCFFilterHeaderLine(String line, VCFHeaderVersion version) {
-        super("FILTER", "");
-        Map<String,String> mapping = VCFHeaderLineTranslator.parseLine(version,line, Arrays.asList("ID","Description"));
-        name = mapping.get("ID");
-        description = mapping.get("Description");
-        if ( description == null && ALLOW_UNBOUND_DESCRIPTIONS ) // handle the case where there's no description provided 
-            description = UNBOUND_DESCRIPTION;
-    }
-
-    protected String toStringEncoding() {
-        Map<String,Object> map = new LinkedHashMap<String,Object>();
-        map.put("ID", name);
-        map.put("Description", description);
-        return "FILTER=" + VCFHeaderLine.toStringEncoding(map);
-    }
-
-    public boolean equals(Object o) {
-        if ( !(o instanceof VCFFilterHeaderLine) )
-            return false;
-        VCFFilterHeaderLine other = (VCFFilterHeaderLine)o;
-        return name.equals(other.name) &&
-               description.equals(other.description);
-    }
-
-    public String getName() {
-        return name;
-    }
-
-    public String getDescription() {
-        return description;
+        super(line, version, SupportedHeaderLineType.FILTER);
     }
 }
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java
index f68cb670b..474c8dd14 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java
@@ -17,7 +17,7 @@ public class VCFFormatHeaderLine extends VCFCompoundHeaderLine {
     }
 
     public VCFFormatHeaderLine(String name, VCFHeaderLineCount count, VCFHeaderLineType type, String description) {
-        super(name, count, type, description, SupportedHeaderLineType.INFO);
+        super(name, count, type, description, SupportedHeaderLineType.FORMAT);
     }
 
     protected VCFFormatHeaderLine(String line, VCFHeaderVersion version) {
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFSimpleHeaderLine.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFSimpleHeaderLine.java
new file mode 100644
index 000000000..152043f28
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFSimpleHeaderLine.java
@@ -0,0 +1,81 @@
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+import java.util.Arrays;
+import java.util.LinkedHashMap;
+import java.util.Map;
+
+
+/**
+ * @author ebanks
+ * A class representing a key=value entry for simple VCF header types
+ */
+public abstract class VCFSimpleHeaderLine extends VCFHeaderLine implements VCFNamedHeaderLine  {
+
+    public enum SupportedHeaderLineType {
+        FILTER, ALT;
+    }
+
+    private String name;
+    private String description;
+
+    // our type of line, i.e. filter, alt, etc
+    private final SupportedHeaderLineType lineType;
+
+
+    /**
+     * create a VCF filter header line
+     *
+     * @param name         the name for this header line
+     * @param description  the description for this header line
+     * @param lineType     the header line type
+     */
+    public VCFSimpleHeaderLine(String name, String description, SupportedHeaderLineType lineType) {
+        super(lineType.toString(), "");
+        this.lineType = lineType;
+        this.name = name;
+        this.description = description;
+
+        if ( name == null || description == null )
+            throw new IllegalArgumentException(String.format("Invalid VCFSimpleHeaderLine: key=%s name=%s desc=%s", super.getKey(), name, description ));
+    }
+
+    /**
+     * create a VCF info header line
+     *
+     * @param line      the header line
+     * @param version   the vcf header version
+     * @param lineType     the header line type
+     */
+    protected VCFSimpleHeaderLine(String line, VCFHeaderVersion version, SupportedHeaderLineType lineType) {
+        super(lineType.toString(), "");
+        this.lineType = lineType;
+        Map<String,String> mapping = VCFHeaderLineTranslator.parseLine(version,line, Arrays.asList("ID","Description"));
+        name = mapping.get("ID");
+        description = mapping.get("Description");
+        if ( description == null && ALLOW_UNBOUND_DESCRIPTIONS ) // handle the case where there's no description provided 
+            description = UNBOUND_DESCRIPTION;
+    }
+
+    protected String toStringEncoding() {
+        Map<String,Object> map = new LinkedHashMap<String,Object>();
+        map.put("ID", name);
+        map.put("Description", description);
+        return lineType.toString() + "=" + VCFHeaderLine.toStringEncoding(map);
+    }
+
+    public boolean equals(Object o) {
+        if ( !(o instanceof VCFSimpleHeaderLine) )
+            return false;
+        VCFSimpleHeaderLine other = (VCFSimpleHeaderLine)o;
+        return name.equals(other.name) &&
+               description.equals(other.description);
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public String getDescription() {
+        return description;
+    }
+}
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
index ecede068e..4037f75b9 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
@@ -180,19 +180,4 @@ public class VCFUtils {
 
         return new HashSet<VCFHeaderLine>(map.values());
     }
-
-    /**
-     * return a set of supported format lines; what we currently support for output in the genotype fields of a VCF
-     * @return a set of VCF format lines
-     */
-    public static Set<VCFFormatHeaderLine> getSupportedHeaderStrings() {
-        Set<VCFFormatHeaderLine> result = new HashSet<VCFFormatHeaderLine>();
-        result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype"));
-        result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_QUALITY_KEY, 1, VCFHeaderLineType.Float, "Genotype Quality"));
-        result.add(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Read Depth (only filtered reads used for calling)"));
-        result.add(new VCFFormatHeaderLine(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, -1, VCFHeaderLineType.Float, "Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; if site is not biallelic, number of likelihoods if n*(n+1)/2"));
-
-        return result;
-    }
-    
 }
\ No newline at end of file

From f313e14e4ef2c3f933505bb16527313ce09e618c Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Tue, 12 Jul 2011 08:50:58 -0400
Subject: [PATCH 084/161] Now deletes the dump directory on ant clean Moving
 diffengine tests from private to public

---
 build.xml                                     |   1 +
 .../diffengine/DiffEngineUnitTest.java        | 229 ++++++++++++++++
 .../walkers/diffengine/DiffNodeUnitTest.java  | 249 ++++++++++++++++++
 .../diffengine/DiffableReaderUnitTest.java    | 143 ++++++++++
 .../diffengine/DifferenceUnitTest.java        |  95 +++++++
 5 files changed, 717 insertions(+)
 create mode 100644 public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java
 create mode 100644 public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNodeUnitTest.java
 create mode 100644 public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java
 create mode 100644 public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java

diff --git a/build.xml b/build.xml
index 80627fae0..068c69316 100644
--- a/build.xml
+++ b/build.xml
@@ -981,6 +981,7 @@
         <delete dir="out"/>
         <delete dir="${build.dir}"/>
         <delete dir="${lib.dir}"/>
+        <delete dir="dump"/>
         <delete dir="staging"/>
         <delete dir="${dist.dir}"/>
         <delete dir="pipelinetests"/>
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java
new file mode 100644
index 000000000..cd6c3598a
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java
@@ -0,0 +1,229 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+// our package
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+
+// the imports for unit testing.
+
+import org.broadinstitute.sting.BaseTest;
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.*;
+
+/**
+ * Basic unit test for DifferableReaders in reduced reads
+ */
+public class DiffEngineUnitTest extends BaseTest {
+    DiffEngine engine;
+
+    @BeforeClass(enabled = true)
+    public void createDiffEngine() {
+        engine = new DiffEngine();
+    }
+
+    // --------------------------------------------------------------------------------
+    //
+    // Difference testing routines
+    //
+    // --------------------------------------------------------------------------------
+
+    private class DifferenceTest extends TestDataProvider {
+        public DiffElement tree1, tree2;
+        public List<String> differences;
+
+        private DifferenceTest(String tree1, String tree2) {
+            this(tree1, tree2, Collections.<String>emptyList());
+        }
+
+        private DifferenceTest(String tree1, String tree2, String difference) {
+            this(tree1, tree2, Arrays.asList(difference));
+        }
+
+        private DifferenceTest(String tree1, String tree2, List<String> differences) {
+            super(DifferenceTest.class);
+            this.tree1 = DiffNode.fromString(tree1);
+            this.tree2 = DiffNode.fromString(tree2);
+            this.differences = differences;
+        }
+
+        public String toString() {
+            return String.format("tree1=%s tree2=%s diff=%s",
+                    tree1.toOneLineString(), tree2.toOneLineString(), differences);
+        }
+    }
+
+    @DataProvider(name = "trees")
+    public Object[][] createTrees() {
+        new DifferenceTest("A=X", "A=X");
+        new DifferenceTest("A=X", "A=Y", "A:X!=Y");
+        new DifferenceTest("A=X", "B=X", Arrays.asList("A:X!=MISSING", "B:MISSING!=X"));
+        new DifferenceTest("A=(X=1)", "B=(X=1)", Arrays.asList("A:(X=1)!=MISSING", "B:MISSING!=(X=1)"));
+        new DifferenceTest("A=(X=1)", "A=(X=1)");
+        new DifferenceTest("A=(X=1 Y=2)", "A=(X=1 Y=2)");
+        new DifferenceTest("A=(X=1 Y=2 B=(Z=3))", "A=(X=1 Y=2 B=(Z=3))");
+        new DifferenceTest("A=(X=1)", "A=(X=2)", "A.X:1!=2");
+        new DifferenceTest("A=(X=1 Y=2 B=(Z=3))", "A=(X=1 Y=2 B=(Z=4))", "A.B.Z:3!=4");
+        new DifferenceTest("A=(X=1)", "A=(X=1 Y=2)", "A.Y:MISSING!=2");
+        new DifferenceTest("A=(X=1 Y=2 B=(Z=3))", "A=(X=1 Y=2)", "A.B:(Z=3)!=MISSING");
+        return DifferenceTest.getTests(DifferenceTest.class);
+    }
+
+    @Test(enabled = true, dataProvider = "trees")
+    public void testDiffs(DifferenceTest test) {
+        logger.warn("Test tree1: " + test.tree1.toOneLineString());
+        logger.warn("Test tree2: " + test.tree2.toOneLineString());
+
+        List<Difference> diffs = engine.diff(test.tree1, test.tree2);
+        logger.warn("Test expected diff : " + test.differences);
+        logger.warn("Observed diffs     : " + diffs);
+    }
+
+    // --------------------------------------------------------------------------------
+    //
+    // Low-level routines for summarizing differences
+    //
+    // --------------------------------------------------------------------------------
+
+    @Test(enabled = true)
+    public void testLongestCommonPostfix() {
+        testLongestCommonPostfixHelper("A", "A", 1);
+        testLongestCommonPostfixHelper("A", "B", 0);
+        testLongestCommonPostfixHelper("A.B", "A.B", 2);
+        testLongestCommonPostfixHelper("A.B.C", "A.B.C", 3);
+        testLongestCommonPostfixHelper("A.B.C", "X.B.C", 2);
+        testLongestCommonPostfixHelper("A.B.C", "X.Y.C", 1);
+        testLongestCommonPostfixHelper("A.B.C", "X.Y.Z", 0);
+        testLongestCommonPostfixHelper("A.B.C", "A.X.C", 1);
+        testLongestCommonPostfixHelper("A.B.C", "A.X.Z", 0);
+        testLongestCommonPostfixHelper("A.B.C", "A.B.Z", 0);
+    }
+
+    public void testLongestCommonPostfixHelper(String p1, String p2, int expected) {
+        String[] parts1 = p1.split("\\.");
+        String[] parts2 = p2.split("\\.");
+        int obs = DiffEngine.longestCommonPostfix(parts1, parts2);
+        Assert.assertEquals(obs, expected, "p1=" + p1 + " p2=" + p2 + " failed");
+    }
+
+    @Test(enabled = true, dependsOnMethods = "testLongestCommonPostfix")
+    public void testSummarizePath() {
+        testSummarizePathHelper("A", "A", "A");
+        testSummarizePathHelper("A", "B", "*");
+        testSummarizePathHelper("A.B", "A.B", "A.B");
+        testSummarizePathHelper("A.B", "X.B", "*.B");
+        testSummarizePathHelper("A.B", "X.Y", "*.*");
+        testSummarizePathHelper("A.B.C", "A.B.C", "A.B.C");
+        testSummarizePathHelper("A.B.C", "X.B.C", "*.B.C");
+        testSummarizePathHelper("A.B.C", "X.Y.C", "*.*.C");
+        testSummarizePathHelper("A.B.C", "X.Y.Z", "*.*.*");
+        testSummarizePathHelper("A.B.C", "A.X.C", "*.*.C");
+        testSummarizePathHelper("A.B.C", "A.X.Z", "*.*.*");
+        testSummarizePathHelper("A.B.C", "A.B.Z", "*.*.*");
+    }
+
+    public void testSummarizePathHelper(String p1, String p2, String expected) {
+        String[] parts1 = DiffEngine.diffNameToPath(p1);
+        String[] parts2 = DiffEngine.diffNameToPath(p2);
+        int obs = DiffEngine.longestCommonPostfix(parts1, parts2);
+        String path = DiffEngine.summarizedPath(parts2, obs);
+        Assert.assertEquals(path, expected, "p1=" + p1 + " p2=" + p2 + " failed");
+    }
+
+    // --------------------------------------------------------------------------------
+    //
+    // High-level difference summary
+    //
+    // --------------------------------------------------------------------------------
+
+    private class SummarizeDifferenceTest extends TestDataProvider {
+        List<String> diffs = new ArrayList<String>();
+        List<String> expecteds = new ArrayList<String>();
+
+        public SummarizeDifferenceTest() { super(SummarizeDifferenceTest.class); }
+
+        public SummarizeDifferenceTest addDiff(String... diffsToAdd) {
+            diffs.addAll(Arrays.asList(diffsToAdd));
+            return this;
+        }
+
+        public SummarizeDifferenceTest addSummary(String... expectedSummary) {
+            expecteds.addAll(Arrays.asList(expectedSummary));
+            return this;
+        }
+
+        public String toString() {
+            return String.format("diffs=%s => expected=%s", diffs, expecteds);
+        }
+
+        public void test() {
+            List<String[]> diffPaths = new ArrayList<String[]>(diffs.size());
+            for ( String diff : diffs ) { diffPaths.add(DiffEngine.diffNameToPath(diff)); }
+
+            List<DiffEngine.SummarizedDifference> sumDiffs = engine.summarizedDifferencesOfPaths(diffPaths);
+
+            Assert.assertEquals(sumDiffs.size(), expecteds.size(), "Unexpected number of summarized differences: " + sumDiffs);
+
+            for ( int i = 0; i < sumDiffs.size(); i++ ) {
+                DiffEngine.SummarizedDifference sumDiff = sumDiffs.get(i);
+                String expected = expecteds.get(i);
+                String[] pathCount = expected.split(":");
+                String path = pathCount[0];
+                int count = Integer.valueOf(pathCount[1]);
+                Assert.assertEquals(sumDiff.getPath(), path, "Unexpected path at: " + expected + " obs=" + sumDiff + " all=" + sumDiffs);
+                Assert.assertEquals(sumDiff.getCount(), count, "Unexpected counts at: " + expected + " obs=" + sumDiff + " all=" + sumDiffs);
+            }
+        }
+    }
+
+    @DataProvider(name = "summaries")
+    public Object[][] createSummaries() {
+        new SummarizeDifferenceTest().addDiff("A", "A").addSummary("A:2");
+        new SummarizeDifferenceTest().addDiff("A", "B").addSummary("A:1", "B:1");
+        new SummarizeDifferenceTest().addDiff("A", "A", "A").addSummary("A:3");
+        new SummarizeDifferenceTest().addDiff("A", "A", "A", "B").addSummary("A:3", "B:1");
+        new SummarizeDifferenceTest().addDiff("A", "A", "A", "B", "B").addSummary("A:3", "B:2");
+        new SummarizeDifferenceTest().addDiff("A", "A", "A", "B", "B", "C").addSummary("A:3", "B:2", "C:1");
+        new SummarizeDifferenceTest().addDiff("A.X", "A.X").addSummary("A.X:2");
+        new SummarizeDifferenceTest().addDiff("A.X", "A.X", "B.X").addSummary("*.X:3", "A.X:2", "B.X:1");
+        new SummarizeDifferenceTest().addDiff("A.X", "A.X", "B.X", "B.X").addSummary("*.X:4", "A.X:2", "B.X:2");
+        new SummarizeDifferenceTest().addDiff("A.B.C", "X.B.C").addSummary("*.B.C:2", "A.B.C:1", "X.B.C:1");
+        new SummarizeDifferenceTest().addDiff("A.B.C", "X.Y.C", "X.Y.C").addSummary("*.*.C:3", "X.Y.C:2", "A.B.C:1");
+        new SummarizeDifferenceTest().addDiff("A.B.C", "A.X.C", "X.Y.C").addSummary("*.*.C:3", "A.B.C:1", "A.X.C:1", "X.Y.C:1");
+        new SummarizeDifferenceTest().addDiff("A.B.C", "A.X.C", "B.X.C").addSummary("*.*.C:3", "*.X.C:2", "A.B.C:1", "A.X.C:1", "B.X.C:1");
+        new SummarizeDifferenceTest().addDiff("A.B.C", "A.X.C", "B.X.C", "B.X.C").addSummary("*.*.C:4", "*.X.C:3", "B.X.C:2", "A.B.C:1", "A.X.C:1");
+
+        return SummarizeDifferenceTest.getTests(SummarizeDifferenceTest.class);
+    }
+
+
+    @Test(enabled = true, dependsOnMethods = "testSummarizePath", dataProvider = "summaries")
+    public void testSummarizeDifferences(SummarizeDifferenceTest test) {
+        test.test();
+    }
+}
\ No newline at end of file
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNodeUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNodeUnitTest.java
new file mode 100644
index 000000000..534416d29
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNodeUnitTest.java
@@ -0,0 +1,249 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+// our package
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+
+// the imports for unit testing.
+
+
+import org.broadinstitute.sting.BaseTest;
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.*;
+
+/**
+ * Basic unit test for DifferableReaders in reduced reads
+ */
+public class DiffNodeUnitTest extends BaseTest {
+    // Data is:
+    // MY_ROOT
+    //   fields: A=A, B=B
+    //   nodes: C, D
+    //   C: fields: E=E, nodes: none
+    //   D: fields: F=F, G=G, nodes: none
+    static DiffNode MY_ROOT = DiffNode.rooted("MY_ROOT");
+    static DiffValue Value_A = new DiffValue("A", MY_ROOT, "A");
+    static DiffValue Value_B = new DiffValue("B", MY_ROOT, "B");
+    static DiffNode NODE_C = DiffNode.empty("C", MY_ROOT);
+    static DiffNode NODE_D = DiffNode.empty("D", MY_ROOT);
+    static DiffValue Value_E = new DiffValue("E", NODE_C, "E");
+    static DiffValue Value_F = new DiffValue("F", NODE_D, "F");
+    static DiffValue Value_G = new DiffValue("G", NODE_D, "G");
+
+    static {
+        MY_ROOT.add(Value_A);
+        MY_ROOT.add(Value_B);
+        MY_ROOT.add(NODE_C);
+        MY_ROOT.add(NODE_D);
+        NODE_C.add(Value_E);
+        NODE_D.add(Value_F);
+        NODE_D.add(Value_G);
+    }
+
+
+    // --------------------------------------------------------------------------------
+    //
+    // Element testing routines
+    //
+    // --------------------------------------------------------------------------------
+
+    private class ElementTest extends TestDataProvider {
+        public DiffElement elt;
+        public String name;
+        public String fullName;
+        public DiffElement parent;
+
+        private ElementTest(DiffValue elt, DiffValue parent, String name, String fullName) {
+            this(elt.getBinding(), parent.getBinding(), name, fullName);
+        }
+
+        private ElementTest(DiffElement elt, DiffElement parent, String name, String fullName) {
+            super(ElementTest.class);
+            this.elt = elt;
+            this.name = name;
+            this.fullName = fullName;
+            this.parent = parent;
+        }
+
+        public String toString() {
+            return String.format("ElementTest elt=%s name=%s fullName=%s parent=%s",
+                    elt.toOneLineString(), name, fullName, parent.getName());
+        }
+    }
+
+    @DataProvider(name = "elementdata")
+    public Object[][] createElementData() {
+        new ElementTest(MY_ROOT.getBinding(), DiffElement.ROOT, "MY_ROOT", "MY_ROOT");
+        new ElementTest(NODE_C, MY_ROOT, "C", "MY_ROOT.C");
+        new ElementTest(NODE_D, MY_ROOT, "D", "MY_ROOT.D");
+        new ElementTest(Value_A, MY_ROOT, "A", "MY_ROOT.A");
+        new ElementTest(Value_B, MY_ROOT, "B", "MY_ROOT.B");
+        new ElementTest(Value_E, NODE_C, "E", "MY_ROOT.C.E");
+        new ElementTest(Value_F, NODE_D, "F", "MY_ROOT.D.F");
+        new ElementTest(Value_G, NODE_D, "G", "MY_ROOT.D.G");
+        return TestDataProvider.getTests(ElementTest.class);
+    }
+
+    @Test(enabled = true, dataProvider = "elementdata")
+    public void testElementMethods(ElementTest test) {
+        Assert.assertNotNull(test.elt.getName());
+        Assert.assertNotNull(test.elt.getParent());
+        Assert.assertEquals(test.elt.getName(), test.name);
+        Assert.assertEquals(test.elt.getParent(), test.parent);
+        Assert.assertEquals(test.elt.fullyQualifiedName(), test.fullName);
+    }
+
+    // --------------------------------------------------------------------------------
+    //
+    // DiffValue testing routines
+    //
+    // --------------------------------------------------------------------------------
+
+    private class LeafTest extends TestDataProvider {
+        public DiffValue diffvalue;
+        public Object value;
+
+        private LeafTest(DiffValue diffvalue, Object value) {
+            super(LeafTest.class);
+            this.diffvalue = diffvalue;
+            this.value = value;
+        }
+
+        public String toString() {
+            return String.format("LeafTest diffvalue=%s value=%s", diffvalue.toOneLineString(), value);
+        }
+    }
+
+    @DataProvider(name = "leafdata")
+    public Object[][] createLeafData() {
+        new LeafTest(Value_A, "A");
+        new LeafTest(Value_B, "B");
+        new LeafTest(Value_E, "E");
+        new LeafTest(Value_F, "F");
+        new LeafTest(Value_G, "G");
+        return TestDataProvider.getTests(LeafTest.class);
+    }
+
+    @Test(enabled = true, dataProvider = "leafdata")
+    public void testLeafMethods(LeafTest test) {
+        Assert.assertNotNull(test.diffvalue.getValue());
+        Assert.assertEquals(test.diffvalue.getValue(), test.value);
+    }
+
+    // --------------------------------------------------------------------------------
+    //
+    // Node testing routines
+    //
+    // --------------------------------------------------------------------------------
+
+    private class NodeTest extends TestDataProvider {
+        public DiffNode node;
+        public Set<String> fields;
+        public Set<String> subnodes;
+        public Set<String> allNames;
+
+        private NodeTest(DiffNode node, List<String> fields, List<String> subnodes) {
+            super(NodeTest.class);
+            this.node = node;
+            this.fields = new HashSet<String>(fields);
+            this.subnodes = new HashSet<String>(subnodes);
+            this.allNames = new HashSet<String>(fields);
+            allNames.addAll(subnodes);
+        }
+
+        public String toString() {
+            return String.format("NodeTest node=%s fields=%s subnodes=%s",
+                    node.toOneLineString(), fields, subnodes);
+        }
+    }
+
+    @DataProvider(name = "nodedata")
+    public Object[][] createData1() {
+        new NodeTest(MY_ROOT, Arrays.asList("A", "B"), Arrays.asList("C", "D"));
+        new NodeTest(NODE_C, Arrays.asList("E"), Collections.<String>emptyList());
+        new NodeTest(NODE_D, Arrays.asList("F", "G"), Collections.<String>emptyList());
+        return TestDataProvider.getTests(NodeTest.class);
+    }
+
+    @Test(enabled = true, dataProvider = "nodedata")
+    public void testNodeAccessors(NodeTest test) {
+        Assert.assertNotNull(test.node.getElements());
+
+        for ( String name : test.allNames ) {
+            DiffElement elt = test.node.getElement(name);
+            Assert.assertNotNull(elt, "Failed to find field " + elt + " in " + test.node);
+            Assert.assertEquals(elt.getName(), name);
+            Assert.assertEquals(elt.getValue().isAtomic(), test.fields.contains(name), "Failed atomic/compound expectation: " + test.node);
+        }
+    }
+
+    // NOTE: add routines are being implicitly tested by the creation of the data structures
+
+    @Test(enabled = true, dataProvider = "nodedata")
+    public void testCounts(NodeTest test) {
+        Assert.assertEquals(test.node.getElements().size(), test.allNames.size());
+        Assert.assertEquals(test.node.getElementNames(), test.allNames);
+    }
+
+    // --------------------------------------------------------------------------------
+    //
+    // fromString testing routines
+    //
+    // --------------------------------------------------------------------------------
+
+    private class FromStringTest extends TestDataProvider {
+        public String string;
+        public DiffElement expected;
+
+        private FromStringTest(String string, DiffElement expected) {
+            super(FromStringTest.class);
+            this.string = string;
+            this.expected = expected;
+        }
+
+        public String toString() {
+            return String.format("FromStringTest string=%s expected=%s", string, expected.toOneLineString());
+        }
+    }
+
+    @DataProvider(name = "fromstringdata")
+    public Object[][] createFromData() {
+        new FromStringTest("A=A", Value_A.getBinding());
+        new FromStringTest("B=B", Value_B.getBinding());
+        new FromStringTest("C=(E=E)", NODE_C.getBinding());
+        new FromStringTest("D=(F=F G=G)", NODE_D.getBinding());
+        return TestDataProvider.getTests(FromStringTest.class);
+    }
+
+    @Test(enabled = true, dataProvider = "fromstringdata")
+    public void parseFromString(FromStringTest test) {
+        logger.warn("Testing from string: " + test.string);
+        DiffElement elt = DiffNode.fromString(test.string);
+        Assert.assertEquals(elt.toOneLineString(), test.expected.toOneLineString());
+    }
+}
\ No newline at end of file
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java
new file mode 100644
index 000000000..5738b643f
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java
@@ -0,0 +1,143 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+// our package
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+
+// the imports for unit testing.
+
+
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.util.*;
+
+/**
+ * Basic unit test for DifferableReaders in reduced reads
+ */
+public class DiffableReaderUnitTest extends BaseTest {
+    DiffEngine engine;
+
+    File vcfFile = new File(testDir + "diffTestMaster.vcf");
+    File bamFile = new File(testDir + "exampleBAM.bam");
+
+    @BeforeClass(enabled = true)
+    public void createDiffEngine() {
+        engine = new DiffEngine();
+    }
+
+    @Test(enabled = true)
+    public void testPluggableDiffableReaders() {
+        logger.warn("testPluggableDiffableReaders");
+        Map<String, DiffableReader> readers = engine.getReaders();
+        Assert.assertNotNull(readers);
+        Assert.assertTrue(readers.size() > 0);
+        Assert.assertNotNull(readers.get("VCF"));
+        for ( Map.Entry<String, DiffableReader> e : engine.getReaders().entrySet() ) {
+            logger.warn("Found diffable reader: " + e.getKey());
+            Assert.assertEquals(e.getValue().getName(), e.getKey());
+            Assert.assertEquals(e.getValue(), engine.getReader(e.getKey()));
+        }
+    }
+
+    private static void testLeaf(DiffNode rec, String field, Object expected) {
+        DiffElement value = rec.getElement(field);
+        Assert.assertNotNull(value, "Expected to see leaf named " + field + " in rec " + rec);
+        Assert.assertEquals(value.getValue().getValue(), expected, "Expected to leaf named " + field + " to have value " + expected + " in rec " + rec);
+    }
+
+    @Test(enabled = true, dependsOnMethods = "testPluggableDiffableReaders")
+    public void testVCF1() {
+        logger.warn("testVCF1");
+        DiffableReader vcfReader = engine.getReader("VCF");
+        Assert.assertTrue(vcfReader.canRead(vcfFile));
+        Assert.assertFalse(vcfReader.canRead(bamFile));
+
+        DiffElement diff = vcfReader.readFromFile(vcfFile);
+        Assert.assertNotNull(diff);
+
+        Assert.assertEquals(diff.getName(), vcfFile.getName());
+        Assert.assertSame(diff.getParent(), DiffElement.ROOT);
+
+        DiffNode node = diff.getValueAsNode();
+        Assert.assertEquals(node.getElements().size(), 9);
+
+        // chr1    2646    rs62635284      G       A       0.15    PASS    AC=2;AF=1.00;AN=2       GT:AD:DP:GL:GQ  1/1:53,75:3:-12.40,-0.90,-0.00:9.03
+        DiffNode rec1 = node.getElement("chr1:2646").getValueAsNode();
+        testLeaf(rec1, "CHROM", "chr1");
+        testLeaf(rec1, "POS", 2646);
+        testLeaf(rec1, "ID", "rs62635284");
+        testLeaf(rec1, "REF", Allele.create("G", true));
+        testLeaf(rec1, "ALT", new HashSet<Allele>(Arrays.asList(Allele.create("A"))));
+        testLeaf(rec1, "QUAL", 0.15);
+        testLeaf(rec1, "FILTER", Collections.<Object>emptySet());
+        testLeaf(rec1, "AC", "2");
+        testLeaf(rec1, "AF", "1.00");
+        testLeaf(rec1, "AN", "2");
+    }
+
+    @Test(enabled = true, dependsOnMethods = "testPluggableDiffableReaders")
+    public void testBAM() {
+        logger.warn("testBAM");
+        DiffableReader bamReader = engine.getReader("BAM");
+        Assert.assertTrue(bamReader.canRead(bamFile));
+        Assert.assertFalse(bamReader.canRead(vcfFile));
+
+        DiffElement diff = bamReader.readFromFile(bamFile);
+        Assert.assertNotNull(diff);
+
+        Assert.assertEquals(diff.getName(), bamFile.getName());
+        Assert.assertSame(diff.getParent(), DiffElement.ROOT);
+
+        DiffNode node = diff.getValueAsNode();
+        Assert.assertEquals(node.getElements().size(), 33);
+
+        // 30PPJAAXX090125:1:42:512:1817#0 99      chr1    200     0       76M     =
+        // 255     -130    ACCCTAACCCTAACCCTAACCCTAACCATAACCCTAAGACTAACCCTAAACCTAACCCTCATAATCGAAATACAAC
+        // BBBBC@C?AABCBB<63>=B@>+B9-9+)2B8,+@327B5A>90((>-+''3?(/'''A)(''19('7.,**%)3:
+        // PG:Z:0  RG:Z:exampleBAM.bam     SM:Z:exampleBAM.bam
+
+        DiffNode rec1 = node.getElement("30PPJAAXX090125:1:42:512:1817#0_1").getValueAsNode();
+        testLeaf(rec1, "NAME", "30PPJAAXX090125:1:42:512:1817#0");
+        testLeaf(rec1, "FLAGS", 99);
+        testLeaf(rec1, "RNAME", "chr1");
+        testLeaf(rec1, "POS", 200);
+        testLeaf(rec1, "MAPQ", 0);
+        testLeaf(rec1, "CIGAR", "76M");
+        testLeaf(rec1, "RNEXT", "chr1");
+        testLeaf(rec1, "PNEXT", 255);
+        testLeaf(rec1, "TLEN", -130);
+        testLeaf(rec1, "SEQ", "ACCCTAACCCTAACCCTAACCCTAACCATAACCCTAAGACTAACCCTAAACCTAACCCTCATAATCGAAATACAAC");
+        testLeaf(rec1, "QUAL", "BBBBC@C?AABCBB<63>=B@>+B9-9+)2B8,+@327B5A>90((>-+''3?(/'''A)(''19('7.,**%)3:");
+        testLeaf(rec1, "PG", "0");
+        testLeaf(rec1, "RG", "exampleBAM.bam");
+        testLeaf(rec1, "SM", "exampleBAM.bam");
+    }
+}
\ No newline at end of file
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java
new file mode 100644
index 000000000..da272ec30
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java
@@ -0,0 +1,95 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+// our package
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+
+// the imports for unit testing.
+
+
+import org.broadinstitute.sting.BaseTest;
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+
+/**
+ * Basic unit test for DifferableReaders in reduced reads
+ */
+public class DifferenceUnitTest extends BaseTest {
+    // --------------------------------------------------------------------------------
+    //
+    // testing routines
+    //
+    // --------------------------------------------------------------------------------
+
+    private class DifferenceTest extends TestDataProvider {
+        public DiffElement tree1, tree2;
+        public String difference;
+
+        private DifferenceTest(String tree1, String tree2, String difference) {
+            this(DiffNode.fromString(tree1), DiffNode.fromString(tree2), difference);
+        }
+
+        private DifferenceTest(DiffElement tree1, DiffElement tree2, String difference) {
+            super(DifferenceTest.class);
+            this.tree1 = tree1;
+            this.tree2 = tree2;
+            this.difference = difference;
+        }
+
+        public String toString() {
+            return String.format("tree1=%s tree2=%s diff=%s",
+                    tree1 == null ? "null" : tree1.toOneLineString(),
+                    tree2 == null ? "null" : tree2.toOneLineString(),
+                    difference);
+        }
+    }
+
+    @DataProvider(name = "data")
+    public Object[][] createTrees() {
+        new DifferenceTest("A=X", "A=Y", "A:X!=Y");
+        new DifferenceTest("A=Y", "A=X", "A:Y!=X");
+        new DifferenceTest(DiffNode.fromString("A=X"), null, "A:X!=MISSING");
+        new DifferenceTest(null, DiffNode.fromString("A=X"), "A:MISSING!=X");
+        return DifferenceTest.getTests(DifferenceTest.class);
+    }
+
+    @Test(enabled = true, dataProvider = "data")
+    public void testDiffToString(DifferenceTest test) {
+        logger.warn("Test tree1: " + (test.tree1 == null ? "null" : test.tree1.toOneLineString()));
+        logger.warn("Test tree2: " + (test.tree2 == null ? "null" : test.tree2.toOneLineString()));
+        logger.warn("Test expected diff : " + test.difference);
+        Difference diff = new Difference(test.tree1, test.tree2);
+        logger.warn("Observed diffs     : " + diff);
+        Assert.assertEquals(diff.toString(), test.difference, "Observed diff string " + diff + " not equal to expected difference string " + test.difference );
+
+    }
+}
\ No newline at end of file

From 8056a3fe89046d942c4b656ff8138283e0235769 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Tue, 12 Jul 2011 08:52:31 -0400
Subject: [PATCH 085/161] getElement() now uses O(1) get from hash instead of
 linear O(n) search.  Enables us to read large files easily.

---
 .../sting/gatk/walkers/diffengine/DiffNode.java        | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java
index 0720e18c0..3e1be8609 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java
@@ -107,11 +107,13 @@ public class DiffNode extends DiffValue {
         return getElements(false);
     }
 
+    /**
+     * Returns the element bound to name, or null if no such binding exists
+     * @param name
+     * @return
+     */
     public DiffElement getElement(String name) {
-        for ( DiffElement elt : getElements() )
-            if ( elt.getName().equals(name) )
-                return elt;
-        return null;
+        return getElementMap().get(name);
     }
 
     /**

From 05212aea62b2f78f7a739257bac86fd0b16d2c5b Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Tue, 12 Jul 2011 08:53:19 -0400
Subject: [PATCH 086/161] reader now takes an argument for the maximum number
 of elements to read from the file.

---
 .../walkers/diffengine/BAMDiffableReader.java   |  5 ++---
 .../gatk/walkers/diffengine/DiffEngine.java     |  7 ++++++-
 .../walkers/diffengine/DiffObjectsWalker.java   | 17 ++++++++++-------
 .../gatk/walkers/diffengine/DiffableReader.java |  2 +-
 .../walkers/diffengine/VCFDiffableReader.java   | 10 ++++++++--
 .../diffengine/DiffableReaderUnitTest.java      |  4 ++--
 6 files changed, 29 insertions(+), 16 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
index f7a395d9d..a5ebf27bb 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
@@ -51,12 +51,11 @@ import java.util.zip.GZIPInputStream;
  * Class implementing diffnode reader for VCF
  */
 public class BAMDiffableReader implements DiffableReader {
-    private final static int MAX_RECORDS_TO_READ = 1000;
     @Override
     public String getName() { return "BAM"; }
 
     @Override
-    public DiffElement readFromFile(File file) {
+    public DiffElement readFromFile(File file, int maxElementsToRead) {
         final SAMFileReader reader = new SAMFileReader(file, null); // null because we don't want it to look for the index
         reader.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
 
@@ -65,7 +64,7 @@ public class BAMDiffableReader implements DiffableReader {
 
         int count = 0;
         while ( iterator.hasNext() ) {
-            if ( count++ > MAX_RECORDS_TO_READ )
+            if ( count++ > maxElementsToRead && maxElementsToRead != -1)
                 break;
             final SAMRecord record = iterator.next();
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
index ba2713bff..54a7a464d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
@@ -385,12 +385,17 @@ public class DiffEngine {
         return findReaderForFile(file) != null;
     }
 
+
     public DiffElement createDiffableFromFile(File file) {
+        return createDiffableFromFile(file, -1);
+    }
+
+    public DiffElement createDiffableFromFile(File file, int maxElementsToRead) {
         DiffableReader reader = findReaderForFile(file);
         if ( reader == null )
             throw new UserException("Unsupported file type: " + file);
         else
-            return reader.readFromFile(file);
+            return reader.readFromFile(file, maxElementsToRead);
     }
 
     public static boolean simpleDiffFiles(File masterFile, File testFile, DiffEngine.SummaryReportParams params) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
index a08108db2..fe411b195 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
@@ -48,11 +48,14 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
     @Output(doc="File to which results should be written",required=true)
     protected PrintStream out;
 
-    @Argument(fullName="maxRecords", shortName="M", doc="Max. number of records to process", required=false)
-    int MAX_RECORDS = 0;
+    @Argument(fullName="maxObjectsToRead", shortName="motr", doc="Max. number of objects to read from the files.  -1 [default] means unlimited", required=false)
+    int MAX_OBJECTS_TO_READ = -1;
 
-    @Argument(fullName="maxCount1Records", shortName="M1", doc="Max. number of records occuring exactly once in the file to process", required=false)
-    int MAX_COUNT1_RECORDS = 0;
+    @Argument(fullName="maxDiffs", shortName="M", doc="Max. number of diffs to process", required=false)
+    int MAX_DIFFS = 0;
+
+    @Argument(fullName="maxCount1Diffs", shortName="M1", doc="Max. number of diffs occuring exactly once in the file to process", required=false)
+    int MAX_COUNT1_DIFFS = 0;
 
     @Argument(fullName="minCountForDiff", shortName="MCFD", doc="Min number of observations for a records to display", required=false)
     int minCountForDiff = 1;
@@ -91,9 +94,9 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
     @Override
     public void onTraversalDone(Integer sum) {
         out.printf("Reading master file %s%n", masterFile);
-        DiffElement master = diffEngine.createDiffableFromFile(masterFile);
+        DiffElement master = diffEngine.createDiffableFromFile(masterFile, MAX_OBJECTS_TO_READ);
         out.printf("Reading test file %s%n", testFile);
-        DiffElement test = diffEngine.createDiffableFromFile(testFile);
+        DiffElement test = diffEngine.createDiffableFromFile(testFile, MAX_OBJECTS_TO_READ);
 
 //        out.printf("Master diff objects%n");
 //        out.println(master.toString());
@@ -107,7 +110,7 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
                 out.printf("DIFF: %s%n", diff.toString());
         }
 
-        DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(out, MAX_RECORDS, MAX_COUNT1_RECORDS, minCountForDiff);
+        DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(out, MAX_DIFFS, MAX_COUNT1_DIFFS, minCountForDiff);
         diffEngine.reportSummarizedDifferences(diffs, params);
     }
 }
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java
index 84c2eed10..af5771c55 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java
@@ -43,7 +43,7 @@ public interface DiffableReader {
 
     @Ensures("result != null")
     @Requires("file != null")
-    public DiffElement readFromFile(File file);
+    public DiffElement readFromFile(File file, int maxElementsToRead);
 
     @Requires("file != null")
     public boolean canRead(File file);
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
index 743178538..06d14366f 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
@@ -51,15 +51,21 @@ public class VCFDiffableReader implements DiffableReader {
     public String getName() { return "VCF"; }
 
     @Override
-    public DiffElement readFromFile(File file) {
+    public DiffElement readFromFile(File file, int maxElementsToRead) {
         DiffNode root = DiffNode.rooted(file.getName());
         try {
             LineReader lineReader = new AsciiLineReader(new FileInputStream(file));
             VCFCodec vcfCodec = new VCFCodec();
-            VCFHeader header = (VCFHeader)vcfCodec.readHeader(lineReader);
+
+            // must be read as state is stored in reader itself
+            vcfCodec.readHeader(lineReader);
 
             String line = lineReader.readLine();
+            int count = 0;
             while ( line != null ) {
+                if ( count++ > maxElementsToRead && maxElementsToRead != -1)
+                    break;
+
                 VariantContext vc = (VariantContext)vcfCodec.decode(line);
                 String name = vc.getChr() + ":" + vc.getStart();
                 DiffNode vcRoot = DiffNode.empty(name, root);
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java
index 5738b643f..baa2f0383 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java
@@ -80,7 +80,7 @@ public class DiffableReaderUnitTest extends BaseTest {
         Assert.assertTrue(vcfReader.canRead(vcfFile));
         Assert.assertFalse(vcfReader.canRead(bamFile));
 
-        DiffElement diff = vcfReader.readFromFile(vcfFile);
+        DiffElement diff = vcfReader.readFromFile(vcfFile, -1);
         Assert.assertNotNull(diff);
 
         Assert.assertEquals(diff.getName(), vcfFile.getName());
@@ -110,7 +110,7 @@ public class DiffableReaderUnitTest extends BaseTest {
         Assert.assertTrue(bamReader.canRead(bamFile));
         Assert.assertFalse(bamReader.canRead(vcfFile));
 
-        DiffElement diff = bamReader.readFromFile(bamFile);
+        DiffElement diff = bamReader.readFromFile(bamFile, -1);
         Assert.assertNotNull(diff);
 
         Assert.assertEquals(diff.getName(), bamFile.getName());

From cfe43e3971327ff26ef9087e31b4294d4a98d99c Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Tue, 12 Jul 2011 13:43:46 -0400
Subject: [PATCH 088/161] Bug fix for Genotype given alleles: if we are in
 INDEL mode ignore SNPs and MNPs instead of emitting an empty site with
 alleles but no annotations

---
 .../genotyper/UnifiedGenotyperEngine.java      | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index 4c9080884..6fc972b5d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -634,17 +634,27 @@ public class UnifiedGenotyperEngine {
                 if (vcInput == null)
                     return null;
 
-                if (vcInput.isSNP() &&  ( UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH || UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.SNP))
-                    return GenotypeLikelihoodsCalculationModel.Model.SNP;
+                // todo - no support to genotype MNP's yet
+                if  (vcInput.isMNP())
+                    return null;
+
+                if (vcInput.isSNP())  {
+                    if (( UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH || UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.SNP))
+                        return GenotypeLikelihoodsCalculationModel.Model.SNP;
+                    else
+                        // ignore SNP's if user chose INDEL mode
+                        return null;
+                }
                 else if ((vcInput.isIndel() || vcInput.isMixed()) && (UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH || UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.INDEL))
                     return GenotypeLikelihoodsCalculationModel.Model.INDEL;
-            }   else {
+            }
+            else {
                 // todo - this assumes SNP's take priority when BOTH is selected, should do a smarter way once extended events are removed
                 if( UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH || UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.SNP)
                     return GenotypeLikelihoodsCalculationModel.Model.SNP;
                 else if (UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.INDEL)
                     return GenotypeLikelihoodsCalculationModel.Model.INDEL;
-                }
+            }
         }
         return null;
     }

From 73735863b0fbff0e7dc5ee789f2e075ead13f7fa Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Tue, 12 Jul 2011 13:55:21 -0400
Subject: [PATCH 089/161] Fix for the case of requesting genotype for a sample
 that doesn't exist in a VariantContext

---
 .../sting/utils/variantcontext/VariantContext.java           | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
index 5787b591f..da80a3431 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -867,7 +867,10 @@ public class VariantContext implements Feature { // to enable tribble intergrati
 
         for ( String name : sampleNames ) {
             if ( map.containsKey(name) ) throw new IllegalArgumentException("Duplicate names detected in requested samples " + sampleNames);
-            map.put(name, getGenotype(name));
+            final Genotype g = getGenotype(name);
+            if ( g != null ) {
+                map.put(name, g);
+            }
         }
 
         return map;

From a2597e7f00824b37174a648da7c648938f5c4886 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 12 Jul 2011 14:11:53 -0400
Subject: [PATCH 090/161] This commit incorporates several different changes
 that each pretty much break all the VCF-based integration tests, so I bunched
 them all together.  We now officially emit VCF4.1 files (woo hoo), which
 means that the VCF headers are now all different (header version is 4.1 plus
 counts for some of the annotations are 'A' or 'G').  Also, I've added a Read
 Filter for reads with MQ=255 ('unavailable' in the SAM spec) and have applied
 this to the UG and the RMS MQ annotation.

---
 .../MappingQualityUnavailableReadFilter.java  | 43 +++++++++++++++++
 ...java => MappingQualityZeroReadFilter.java} |  5 +-
 .../annotator/AlleleBalanceBySample.java      |  2 +-
 .../walkers/annotator/ChromosomeCounts.java   |  4 +-
 .../annotator/MappingQualityRankSumTest.java  |  7 ++-
 .../gatk/walkers/annotator/NBaseCount.java    |  2 +-
 .../walkers/annotator/RMSMappingQuality.java  |  7 ++-
 .../gatk/walkers/annotator/RankSumTest.java   |  5 +-
 .../walkers/genotyper/UnifiedGenotyper.java   |  5 +-
 .../indels/RealignerTargetCreator.java        |  4 +-
 .../indels/SomaticIndelDetectorWalker.java    |  2 +-
 .../phasing/ReadBackedPhasingWalker.java      |  4 +-
 .../recalibration/CountCovariatesWalker.java  |  4 +-
 .../sting/utils/QualityUtils.java             |  4 ++
 .../utils/codecs/vcf/StandardVCFWriter.java   |  6 +--
 .../VariantAnnotatorIntegrationTest.java      | 28 +++++------
 .../GenomicAnnotatorIntegrationTest.java      |  6 +--
 .../walkers/beagle/BeagleIntegrationTest.java |  6 +--
 .../VariantFiltrationIntegrationTest.java     | 22 ++++-----
 .../UnifiedGenotyperIntegrationTest.java      | 48 +++++++++----------
 .../ReadBackedPhasingIntegrationTest.java     | 12 ++---
 ...ntRecalibrationWalkersIntegrationTest.java |  2 +-
 .../CombineVariantsIntegrationTest.java       | 34 ++++++-------
 .../LiftoverVariantsIntegrationTest.java      |  6 +--
 .../SelectVariantsIntegrationTest.java        |  8 ++--
 .../VCFStreamingIntegrationTest.java          |  2 +-
 .../VariantsToVCFIntegrationTest.java         |  8 ++--
 .../VariantContextIntegrationTest.java        |  2 +-
 28 files changed, 169 insertions(+), 119 deletions(-)
 create mode 100644 public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableReadFilter.java
 rename public/java/src/org/broadinstitute/sting/gatk/filters/{ZeroMappingQualityReadFilter.java => MappingQualityZeroReadFilter.java} (90%)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableReadFilter.java
new file mode 100644
index 000000000..cecbedda8
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableReadFilter.java
@@ -0,0 +1,43 @@
+/*
+ * Copyright (c) 2009 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.filters;
+
+import net.sf.picard.util.QualityUtil;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.QualityUtils;
+
+/**
+ * Filter out mapping quality zero reads.
+ *
+ * @author ebanks
+ * @version 0.1
+ */
+
+public class MappingQualityUnavailableReadFilter extends ReadFilter {
+    public boolean filterOut(SAMRecord rec) {
+        return (rec.getMappingQuality() == QualityUtils.MAPPING_QUALITY_UNAVAILABLE);
+    }
+}
+
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/ZeroMappingQualityReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityZeroReadFilter.java
similarity index 90%
rename from public/java/src/org/broadinstitute/sting/gatk/filters/ZeroMappingQualityReadFilter.java
rename to public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityZeroReadFilter.java
index 7e6fc5e82..e49d4117c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/ZeroMappingQualityReadFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityZeroReadFilter.java
@@ -24,17 +24,16 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 
 /**
- * Filter out zero mapping quality reads.
+ * Filter out mapping quality zero reads.
  *
  * @author hanna
  * @version 0.1
  */
 
-public class ZeroMappingQualityReadFilter extends ReadFilter {
+public class MappingQualityZeroReadFilter extends ReadFilter {
     public boolean filterOut(SAMRecord rec) {
         return (rec.getMappingQuality() == 0);
     }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
index 0be737897..51d290763 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
@@ -62,5 +62,5 @@ public class AlleleBalanceBySample implements GenotypeAnnotation, ExperimentalAn
 
     public List<String> getKeyNames() { return Arrays.asList("AB"); }
 
-    public List<VCFFormatHeaderLine> getDescriptions() { return Arrays.asList(new VCFFormatHeaderLine(getKeyNames().get(0), -1, VCFHeaderLineType.Float, "Allele balance for each het genotype")); }
+    public List<VCFFormatHeaderLine> getDescriptions() { return Arrays.asList(new VCFFormatHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Float, "Allele balance for each het genotype")); }
 }
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
index ed10d2072..f3ec2b1df 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
@@ -42,8 +42,8 @@ import java.util.*;
 public class ChromosomeCounts implements InfoFieldAnnotation, StandardAnnotation {
 
     private String[] keyNames = { VCFConstants.ALLELE_NUMBER_KEY, VCFConstants.ALLELE_COUNT_KEY, VCFConstants.ALLELE_FREQUENCY_KEY };
-    private VCFInfoHeaderLine[] descriptions = { new VCFInfoHeaderLine(VCFConstants.ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Float, "Allele Frequency, for each ALT allele, in the same order as listed"),
-            new VCFInfoHeaderLine(VCFConstants.ALLELE_COUNT_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "Allele count in genotypes, for each ALT allele, in the same order as listed"),
+    private VCFInfoHeaderLine[] descriptions = { new VCFInfoHeaderLine(VCFConstants.ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele Frequency, for each ALT allele, in the same order as listed"),
+            new VCFInfoHeaderLine(VCFConstants.ALLELE_COUNT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Allele count in genotypes, for each ALT allele, in the same order as listed"),
             new VCFInfoHeaderLine(VCFConstants.ALLELE_NUMBER_KEY, 1, VCFHeaderLineType.Integer, "Total number of alleles in called genotypes") };
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
index 11f86b972..8260a5a81 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
@@ -21,7 +22,7 @@ public class MappingQualityRankSumTest extends RankSumTest {
 
     protected void fillQualsFromPileup(byte ref, byte alt, ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals) {
         for ( final PileupElement p : pileup ) {
-            if( isUsableBase(p) && p.getMappingQual() < 254 ) { // 254 and 255 are special mapping qualities used as a code by aligners
+            if ( isUsableBase(p) ) {
                 if ( p.getBase() == ref ) {
                     refQuals.add((double)p.getMappingQual());
                 } else if ( p.getBase() == alt ) {
@@ -34,7 +35,7 @@ public class MappingQualityRankSumTest extends RankSumTest {
         // equivalent is whether indel likelihoods for reads corresponding to ref allele are more likely than reads corresponding to alt allele ?
         HashMap<PileupElement,LinkedHashMap<Allele,Double>> indelLikelihoodMap = IndelGenotypeLikelihoodsCalculationModel.getIndelLikelihoodMap();
         for (final PileupElement p: pileup) {
-            if (indelLikelihoodMap.containsKey(p) && p.getMappingQual() < 254) {
+            if (indelLikelihoodMap.containsKey(p) && p.getMappingQual() != 0 && p.getMappingQual() != QualityUtils.MAPPING_QUALITY_UNAVAILABLE) {
                 // retrieve likelihood information corresponding to this read
                 LinkedHashMap<Allele,Double> el = indelLikelihoodMap.get(p);
                 // by design, first element in LinkedHashMap was ref allele
@@ -54,8 +55,6 @@ public class MappingQualityRankSumTest extends RankSumTest {
                     refQuals.add((double)p.getMappingQual());
                 else if (altLikelihood > refLikelihood + INDEL_LIKELIHOOD_THRESH)
                     altQuals.add((double)p.getMappingQual());
-
-
             }
         }
     }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
index ba3e2cc8b..3b64abfff 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
@@ -47,5 +47,5 @@ public class NBaseCount implements InfoFieldAnnotation {
 
     public List<String> getKeyNames() { return Arrays.asList("PercentNBaseSolid"); }
 
-    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("PercentNBaseSolid", 4, VCFHeaderLineType.Float, "Percentage of N bases in the pileup (counting only SOLiD reads)")); }
+    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("PercentNBaseSolid", 1, VCFHeaderLineType.Float, "Percentage of N bases in the pileup (counting only SOLiD reads)")); }
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
index 6e80c7555..1ef7ccd0b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
@@ -38,8 +39,10 @@ public class RMSMappingQuality implements InfoFieldAnnotation, StandardAnnotatio
                 pileup = context.getBasePileup();
 
             if (pileup != null) {
-                for (PileupElement p : pileup )
-                    qualities[index++] = p.getRead().getMappingQuality();
+                for (PileupElement p : pileup ) {
+                    if ( p.getMappingQual() != QualityUtils.MAPPING_QUALITY_UNAVAILABLE )
+                        qualities[index++] = p.getMappingQual();
+                }
             }
         }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
index 1a967293f..f00abd6a1 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
@@ -106,6 +106,9 @@ public abstract class RankSumTest implements InfoFieldAnnotation, StandardAnnota
     protected abstract void fillIndelQualsFromPileup(ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals);
 
     protected static boolean isUsableBase( final PileupElement p ) {
-        return !( p.isDeletion() || p.getMappingQual() == 0 || ((int)p.getQual()) < 6 ); // need the unBAQed quality score here
+        return !( p.isDeletion() ||
+                  p.getMappingQual() == 0 ||
+                  p.getMappingQual() == QualityUtils.MAPPING_QUALITY_UNAVAILABLE ||
+                  ((int)p.getQual()) < QualityUtils.MIN_USABLE_Q_SCORE ); // need the unBAQed quality score here
     }
 }
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index fe0084a19..fc8a5819a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
+import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableReadFilter;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.gatk.contexts.*;
 import org.broadinstitute.sting.gatk.filters.BadMateFilter;
@@ -47,7 +48,7 @@ import java.io.PrintStream;
  * multi-sample data.  The user can choose from several different incorporated calculation models.
  */
 @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_INPUT)
-@ReadFilters( {BadMateFilter.class} )
+@ReadFilters( {BadMateFilter.class, MappingQualityUnavailableReadFilter.class} )
 @Reference(window=@Window(start=-200,stop=200))
 @By(DataSource.REFERENCE)
 @Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=250)
@@ -175,7 +176,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
         result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype"));
         result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_QUALITY_KEY, 1, VCFHeaderLineType.Float, "Genotype Quality"));
         result.add(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Read Depth (only filtered reads used for calling)"));
-        result.add(new VCFFormatHeaderLine(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Float, "Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; if site is not biallelic, number of likelihoods if n*(n+1)/2"));
+        result.add(new VCFFormatHeaderLine(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"));
 
         return result;
     }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
index 048dbd8cb..3b94989aa 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
@@ -30,7 +30,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.filters.BadCigarFilter;
 import org.broadinstitute.sting.gatk.filters.Platform454Filter;
-import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
+import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
 import org.broadinstitute.sting.gatk.filters.BadMateFilter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
@@ -50,7 +50,7 @@ import java.io.PrintStream;
 /**
  * Emits intervals for the Local Indel Realigner to target for cleaning.  Ignores 454 reads, MQ0 reads, and reads with consecutive indel operators in the CIGAR string.
  */
-@ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class, BadCigarFilter.class})
+@ReadFilters({Platform454Filter.class, MappingQualityZeroReadFilter.class, BadCigarFilter.class})
 @Reference(window=@Window(start=-1,stop=50))
 @Allows(value={DataSource.READS, DataSource.REFERENCE})
 @By(DataSource.REFERENCE)
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
index c2953d1d7..1f05ddaf0 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
@@ -72,7 +72,7 @@ import java.util.*;
  * if first bam has coverage at the site but no indication for an indel. In the --somatic mode, BED output contains
  * only somatic calls, while --verbose output contains all calls annotated with GERMLINE/SOMATIC keywords.
  */
-@ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class, PlatformUnitFilter.class})
+@ReadFilters({Platform454Filter.class, MappingQualityZeroReadFilter.class, PlatformUnitFilter.class})
 public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
 //    @Output
 //    PrintStream out;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
index e59b29502..4833a6cad 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
@@ -32,7 +32,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
-import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
+import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.walkers.*;
@@ -58,7 +58,7 @@ import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFr
 @Requires(value = {DataSource.READS, DataSource.REFERENCE}, referenceMetaData = @RMD(name = "variant", type = ReferenceOrderedDatum.class))
 @By(DataSource.READS)
 
-@ReadFilters({ZeroMappingQualityReadFilter.class})
+@ReadFilters({MappingQualityZeroReadFilter.class})
 // Filter out all reads with zero mapping quality
 
 public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, PhasingStats> {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
index ee504b6e7..6673bec92 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
@@ -34,7 +34,7 @@ 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.datasources.rmd.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
+import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.walkers.*;
@@ -75,7 +75,7 @@ import java.util.Map;
 
 @BAQMode(ApplicationTime = BAQ.ApplicationTime.FORBIDDEN)
 @By( DataSource.READS ) // Only look at covered loci, not every loci of the reference file
-@ReadFilters( {ZeroMappingQualityReadFilter.class} ) // Filter out all reads with zero mapping quality
+@ReadFilters( {MappingQualityZeroReadFilter.class} ) // Filter out all reads with zero mapping quality
 @Requires( {DataSource.READS, DataSource.REFERENCE, DataSource.REFERENCE_BASES} ) // This walker requires both -I input.bam and -R reference.fasta
 @PartitionBy(PartitionType.LOCUS)
 public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.CountedData, CountCovariatesWalker.CountedData> implements TreeReducible<CountCovariatesWalker.CountedData> {
diff --git a/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java b/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java
index 23054e95f..fad2320fc 100755
--- a/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java
@@ -9,9 +9,13 @@ import net.sf.samtools.SAMUtils;
  * @author Kiran Garimella
  */
 public class QualityUtils {
+
     public final static byte MAX_QUAL_SCORE = SAMUtils.MAX_PHRED_SCORE;
     public final static double MIN_REASONABLE_ERROR = 0.0001;
     public final static byte MAX_REASONABLE_Q_SCORE = 40;
+    public final static byte MIN_USABLE_Q_SCORE = 6;
+
+    public final static int MAPPING_QUALITY_UNAVAILABLE = 255;
 
     /**
      * Private constructor.  No instantiating this class!
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
index f4996b487..a8bf74707 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
@@ -123,12 +123,10 @@ public class StandardVCFWriter implements VCFWriter {
         
         try {
             // the file format field needs to be written first
-            mWriter.write(VCFHeader.METADATA_INDICATOR + VCFHeaderVersion.VCF4_0.getFormatString() + "=" + VCFHeaderVersion.VCF4_0.getVersionString() + "\n");
+            mWriter.write(VCFHeader.METADATA_INDICATOR + VCFHeaderVersion.VCF4_1.getFormatString() + "=" + VCFHeaderVersion.VCF4_1.getVersionString() + "\n");
 
             for ( VCFHeaderLine line : mHeader.getMetaData() ) {
-                if ( line.getKey().equals(VCFHeaderVersion.VCF4_0.getFormatString()) ||
-                        line.getKey().equals(VCFHeaderVersion.VCF3_3.getFormatString()) ||
-                        line.getKey().equals(VCFHeaderVersion.VCF3_2.getFormatString()) )
+                if ( VCFHeaderVersion.isFormatString(line.getKey()) )
                     continue;
 
                 // are the records filtered (so we know what to put in the FILTER column of passing records) ?
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
index 6ba6926c6..e6300e6c9 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
@@ -15,7 +15,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsNotAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("4cc077eb3d343e6b7ba12bff86ebe347"));
+                Arrays.asList("8a105fa5eebdfffe7326bc5b3d8ffd1c"));
         executeTest("test file has annotations, not asking for annotations, #1", spec);
     }
 
@@ -23,7 +23,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsNotAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B:variant,VCF3 " + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("1de8e943fbf55246ebd19efa32f22a58"));
+                Arrays.asList("964f1016ec9a3c55333f62dd834c14d6"));
         executeTest("test file has annotations, not asking for annotations, #2", spec);
     }
 
@@ -31,7 +31,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("93c110e45fd4aedb044a8a5501e23336"));
+                Arrays.asList("8e7de435105499cd71ffc099e268a83e"));
         executeTest("test file has annotations, asking for annotations, #1", spec);
     }
 
@@ -39,7 +39,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("f5cb45910ed719f46159f9f71acaecf4"));
+                Arrays.asList("64b6804cb1e27826e3a47089349be581"));
         executeTest("test file has annotations, asking for annotations, #2", spec);
     }
 
@@ -47,7 +47,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsNotAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B:variant,VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("4b48e7d095ef73e3151542ea976ecd89"));
+                Arrays.asList("42ccee09fa9f8c58f4a0d4f1139c094f"));
         executeTest("test file doesn't have annotations, not asking for annotations, #1", spec);
     }
 
@@ -55,7 +55,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsNotAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B:variant,VCF3 " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("28dfbfd178aca071b948cd3dc2365357"));
+                Arrays.asList("f2ddfa8105c290b1f34b7a261a02a1ac"));
         executeTest("test file doesn't have annotations, not asking for annotations, #2", spec);
     }
 
@@ -63,7 +63,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("a330a5bc3ee72a51dbeb7e6c97a0db99"));
+                Arrays.asList("fd1ffb669800c2e07df1e2719aa38e49"));
         executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
     }
 
@@ -71,7 +71,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("3a31d1ef471acfb881a2dec7963fe3f4"));
+                Arrays.asList("09f8e840770a9411ff77508e0ed0837f"));
         executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
     }
 
@@ -79,7 +79,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testOverwritingHeader() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
-                Arrays.asList("a63fd8ff7bafbd46b7f009144a7c2ad1"));
+                Arrays.asList("78d2c19f8107d865970dbaf3e12edd92"));
         executeTest("test overwriting header", spec);
     }
 
@@ -87,7 +87,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoReads() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
-                Arrays.asList("36378f1245bb99d902fbfe147605bc42"));
+                Arrays.asList("16e3a1403fc376320d7c69492cad9345"));
         executeTest("not passing it any reads", spec);
     }
 
@@ -95,7 +95,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testDBTagWithDbsnp() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -D " + GATKDataLocation + "dbsnp_129_b36.rod -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
-                Arrays.asList("0257a1cc3c703535b2d3c5046bf88ab7"));
+                Arrays.asList("3da8ca2b6bdaf6e92d94a8c77a71313d"));
         executeTest("getting DB tag with dbSNP", spec);
     }
 
@@ -103,7 +103,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testDBTagWithHapMap() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B:compH3,VCF " + validationDataLocation + "fakeHM3.vcf -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
-                Arrays.asList("2d7c73489dcf0db433bebdf79a068764"));
+                Arrays.asList("1bc01c5b3bd0b7aef75230310c3ce688"));
         executeTest("getting DB tag with HM3", spec);
     }
 
@@ -111,13 +111,13 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testUsingExpression() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B:foo,VCF " + validationDataLocation + "targetAnnotations.vcf -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -BTI variant", 1,
-                Arrays.asList("2f6efd08d818faa1eb0631844437c64a"));
+                Arrays.asList("e9c0d832dc6b4ed06c955060f830c140"));
         executeTest("using expression", spec);
     }
 
     @Test
     public void testTabixAnnotations() {
-        final String MD5 = "6c7a6a1c0027bf82656542a9b2671a35";
+        final String MD5 = "13269d5a2e16f06fd755cc0fb9271acf";
         for ( String file : Arrays.asList("CEU.exon.2010_03.sites.vcf", "CEU.exon.2010_03.sites.vcf.gz")) {
             WalkerTestSpec spec = new WalkerTestSpec(
                     baseTestString() + " -A HomopolymerRun -B:variant,VCF " + validationDataLocation + "/" + file + " -BTI variant -NO_HEADER", 1,
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotatorIntegrationTest.java
index c4f6d5ebc..c75a5b2dc 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotatorIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotatorIntegrationTest.java
@@ -29,7 +29,7 @@ public class GenomicAnnotatorIntegrationTest extends WalkerTest {
         */
 
 
-        String[] md5WithDashSArg = {"3d3b61a83c1189108eabb2df04218099"};
+        String[] md5WithDashSArg = {"efba4ce1641cfa2ef88a64395f2ebce8"};
         WalkerTestSpec specWithSArg = new WalkerTestSpec(
                 "-T GenomicAnnotator -R " + b36KGReference +
                 " -B:variant,vcf3 /humgen/gsa-hpprojects/GATK/data/Annotations/examples/CEU_hapmap_nogt_23_subset.vcf" +
@@ -58,7 +58,7 @@ public class GenomicAnnotatorIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("caa562160733aa638e1ba413ede209ae")
+                Arrays.asList("772fc3f43b70770ec6c6acbb8bbbd4c0")
         );
         executeTest("testGenomicAnnotatorOnIndels", testOnIndels);
     }
@@ -76,7 +76,7 @@ public class GenomicAnnotatorIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("a4cf76f08fa90284b6988a464b6e0c17")
+                Arrays.asList("081ade7f3d2d3c5f19cb1e8651a626f3")
         );
         executeTest("testGenomicAnnotatorOnSNPsAndIndels", testOnSNPsAndIndels);
     }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java
index 70c34e729..fef1b6e64 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java
@@ -41,7 +41,7 @@ public class BeagleIntegrationTest extends WalkerTest {
                         "-B:beagleR2,BEAGLE " + beagleValidationDataLocation + "inttestbgl.r2 " +
                         "-B:beagleProbs,BEAGLE " + beagleValidationDataLocation + "inttestbgl.gprobs " +
                         "-B:beaglePhased,BEAGLE " + beagleValidationDataLocation + "inttestbgl.phased " +
-                        "-o %s -NO_HEADER", 1, Arrays.asList("6bccee48ad2f06ba5a8c774fed444478"));
+                        "-o %s -NO_HEADER", 1, Arrays.asList("3531451e84208264104040993889aaf4"));
         executeTest("test BeagleOutputToVCF", spec);
     }
    
@@ -60,7 +60,7 @@ public class BeagleIntegrationTest extends WalkerTest {
                 "-T ProduceBeagleInput -B:variant,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/NA12878_HSQ_chr22_14-16m.vcf "+
                         "-B:validation,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/NA12878_OMNI_chr22_14-16m.vcf "+
                         "-L 22:14000000-16000000 -o %s -bvcf %s -bs 0.8 -valp 0.98 -R /humgen/1kg/reference/human_g1k_v37.fasta -NO_HEADER ",2,
-                Arrays.asList("660986891b30cdc937e0f2a3a5743faa","223fb977e8db567dcaf632c6ee51f294"));
+                Arrays.asList("660986891b30cdc937e0f2a3a5743faa","e96ddd51da9f4a797b2aa8c20e404166"));
         executeTest("test BeagleInputWithBootstrap",spec);
     }
 
@@ -72,7 +72,7 @@ public class BeagleIntegrationTest extends WalkerTest {
                 "-B:beagleR2,beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.r2 "+
                 "-B:beagleProbs,beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.gprobs.bgl "+
                 "-B:beaglePhased,beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.phased.bgl "+
-                "-L 20:1-70000 -o %s -NO_HEADER ",1,Arrays.asList("24b88ef8cdf6e347daab491f0256be5a"));
+                "-L 20:1-70000 -o %s -NO_HEADER ",1,Arrays.asList("8dd6ec53994fb46c5c22af8535d22965"));
 
         executeTest("testBeagleChangesSitesToRef",spec);
     }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
index 3d75fdc44..7bec67d2e 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
@@ -16,7 +16,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testNoAction() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("4cc077eb3d343e6b7ba12bff86ebe347"));
+                Arrays.asList("8a105fa5eebdfffe7326bc5b3d8ffd1c"));
         executeTest("test no action", spec);
     }
 
@@ -24,7 +24,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testClusteredSnps() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -window 10 -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("ada5540bb3d9b6eb8f1337ba01e90a94"));
+                Arrays.asList("27b13f179bb4920615dff3a32730d845"));
         executeTest("test clustered SNPs", spec);
     }
 
@@ -32,17 +32,17 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testMasks() {
         WalkerTestSpec spec1 = new WalkerTestSpec(
                 baseTestString() + " -mask foo -B:mask,VCF3 " + validationDataLocation + "vcfexample2.vcf -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("b0fcac4af3526e3b2a37602ab4c0e6ae"));
+                Arrays.asList("578f9e774784c25871678e6464fd212b"));
         executeTest("test mask all", spec1);
 
         WalkerTestSpec spec2 = new WalkerTestSpec(
                 baseTestString() + " -mask foo -B:mask,VCF " + validationDataLocation + "vcfMask.vcf -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("b64baabe905a5d197cc1ab594147d3d5"));
+                Arrays.asList("bfa86a674aefca1b13d341cb14ab3c4f"));
         executeTest("test mask some", spec2);
 
         WalkerTestSpec spec3 = new WalkerTestSpec(
                 baseTestString() + " -mask foo -maskExtend 10 -B:mask,VCF " + validationDataLocation + "vcfMask.vcf -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("0eff92fe72024d535c44b98e1e9e1993"));
+                Arrays.asList("5939f80d14b32d88587373532d7b90e5"));
         executeTest("test mask extend", spec3);
     }
 
@@ -50,7 +50,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testFilter1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("7a40795147cbfa92941489d7239aad92"));
+                Arrays.asList("45219dbcfb6f81bba2ea0c35f5bfd368"));
         executeTest("test filter #1", spec);
     }
 
@@ -58,7 +58,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testFilter2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("e9dd4991b1e325847c77d053dfe8ee54"));
+                Arrays.asList("c95845e817da7352b9b72bc9794f18fb"));
         executeTest("test filter #2", spec);
     }
 
@@ -66,7 +66,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testFilterWithSeparateNames() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --filterName ABF -filter 'AlleleBalance < 0.7' --filterName FSF -filter 'FisherStrand == 1.4' -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("9ded2cce63b8d97550079047051d80a3"));
+                Arrays.asList("b8cdd7f44ff1a395e0a9b06a87e1e530"));
         executeTest("test filter with separate names #2", spec);
     }
 
@@ -74,12 +74,12 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testGenotypeFilters() {
         WalkerTestSpec spec1 = new WalkerTestSpec(
                 baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("6696e3f65a62ce912230d47cdb0c129b"));
+                Arrays.asList("96b61e4543a73fe725e433f007260039"));
         executeTest("test genotype filter #1", spec1);
 
         WalkerTestSpec spec2 = new WalkerTestSpec(
                 baseTestString() + " -G_filter 'AF == 0.04 && isHomVar == 1' -G_filterName foo -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("26e5b4ee954c9e0b5eb044afd4b88ee9"));
+                Arrays.asList("6c8112ab17ce39c8022c891ae73bf38e"));
         executeTest("test genotype filter #2", spec2);
     }
 
@@ -87,7 +87,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testDeletions() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --filterExpression 'QUAL < 100' --filterName foo -B:variant,VCF " + validationDataLocation + "twoDeletions.vcf", 1,
-                Arrays.asList("e63b58be33c9126ad6cc55489aac539b"));
+                Arrays.asList("569546fd798afa0e65c5b61b440d07ac"));
         executeTest("test deletions", spec);
     }
 }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index 20fa7719f..1f23d262e 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -28,7 +28,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultiSamplePilot1() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
-                Arrays.asList("258e1954e6ae55c89abc6a716e19cbe0"));
+                Arrays.asList("c97829259463d04b0159591bb6fb44af"));
         executeTest("test MultiSample Pilot1", spec);
     }
 
@@ -54,12 +54,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testWithAllelesPassedIn() {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
-                Arrays.asList("edeb1db288a24baff59575ceedd94243"));
+                Arrays.asList("2b69667f4770e8c0c894066b7f27e440"));
         executeTest("test MultiSample Pilot2 with alleles passed in", spec1);
 
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
-                Arrays.asList("581990130d90071b084024f4cd7caf91"));
+                Arrays.asList("b77fe007c2a97fcd59dfd5eef94d8b95"));
         executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2);
     }
 
@@ -67,7 +67,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testSingleSamplePilot2() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1,
-                Arrays.asList("d120db27d694a6da32367cc4fb5770fa"));
+                Arrays.asList("ee8a5e63ddd470726a749e69c0c20f60"));
         executeTest("test SingleSample Pilot2", spec);
     }
 
@@ -77,7 +77,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     //
     // --------------------------------------------------------------------------------------------------------------
 
-    private final static String COMPRESSED_OUTPUT_MD5 = "75e5c430ed39f79f24e375037a388dc4";
+    private final static String COMPRESSED_OUTPUT_MD5 = "ef31654a2b85b9b2d3bba4f4a75a17b6";
 
     @Test
     public void testCompressedOutput() {
@@ -107,7 +107,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
         // Note that we need to turn off any randomization for this to work, so no downsampling and no annotations
 
-        String md5 = "a29615dd37222a11b8dadd341b53e43c";
+        String md5 = "46868a9c4134651c54535fb46b408aee";
 
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1,
@@ -138,9 +138,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testCallingParameters() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( "--min_base_quality_score 26", "93e6269e38db9bc1732555e9969e3648" );
-        e.put( "--min_mapping_quality_score 26", "64be99183c100caed4aa5f8bad64c7e9" );
-        e.put( "--p_nonref_model GRID_SEARCH", "0592fe33f705ad8e2f13619fcf157805" );
+        e.put( "--min_base_quality_score 26", "5043c9a101e691602eb7a3f9704bdf20" );
+        e.put( "--min_mapping_quality_score 26", "71a833eb8fd93ee62ae0d5a430f27940" );
+        e.put( "--p_nonref_model GRID_SEARCH", "ddf443e9dcadef367476b26b4d52c134" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@@ -153,9 +153,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testOutputParameter() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( "-sites_only", "1483e637dc0279935a7f90d136d147bb" );
-        e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "adcd91bc7dae8020df8caf1a30060e98" );
-        e.put( "--output_mode EMIT_ALL_SITES", "b708acc2fa40f336bcd2d0c70091e07e" );
+        e.put( "-sites_only", "eaad6ceb71ab94290650a70bea5ab951" );
+        e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "05bf7db8a3d19ef4a3d14772c90b732f" );
+        e.put( "--output_mode EMIT_ALL_SITES", "e4b86740468d7369f0156550855586c7" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@@ -169,12 +169,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testConfidence() {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1,
-                Arrays.asList("64be99183c100caed4aa5f8bad64c7e9"));
+                Arrays.asList("71a833eb8fd93ee62ae0d5a430f27940"));
         executeTest("test confidence 1", spec1);
 
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_emit_conf 10 ", 1,
-                Arrays.asList("e76ca54232d02f0d92730e1affeb804e"));
+                Arrays.asList("79968844dc3ddecb97748c1acf2984c7"));
         executeTest("test confidence 2", spec2);
     }
 
@@ -186,8 +186,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testHeterozyosity() {
         HashMap<Double, String> e = new HashMap<Double, String>();
-        e.put( 0.01, "18d37f7f107853b5e32c757b4e143205" );
-        e.put( 1.0 / 1850, "2bcb90ce2f7542bf590f7612018fae8e" );
+        e.put( 0.01, "4e878664f61d2d800146d3762303fde1" );
+        e.put( 1.0 / 1850, "9204caec095ff5e63ca21a10b6fab453" );
 
         for ( Map.Entry<Double, String> entry : e.entrySet() ) {
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@@ -211,7 +211,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 1:10,000,000-10,100,000",
                 1,
-                Arrays.asList("825f05b31b5bb7e82231a15c7e4e2b0d"));
+                Arrays.asList("1a58ec52df545f946f80cc16c5736a91"));
 
         executeTest(String.format("test multiple technologies"), spec);
     }
@@ -230,7 +230,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -L 1:10,000,000-10,100,000" +
                         " -baq CALCULATE_AS_NECESSARY",
                 1,
-                Arrays.asList("0919ab7e513c377610e23a67d33608fa"));
+                Arrays.asList("62d0f6d9de344ce68ce121c13b1e78b1"));
 
         executeTest(String.format("test calling with BAQ"), spec);
     }
@@ -244,7 +244,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -L 1:10,000,000-10,100,000" +
                         " -baq OFF",
                 1,
-                Arrays.asList("825f05b31b5bb7e82231a15c7e4e2b0d"));
+                Arrays.asList("1a58ec52df545f946f80cc16c5736a91"));
 
         executeTest(String.format("test calling with BAQ OFF"), spec);
     }
@@ -263,7 +263,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 1:10,000,000-10,500,000",
                 1,
-                Arrays.asList("cb37348c41b8181be829912730f747e1"));
+                Arrays.asList("631ae1f1eb6bc4c1a4136b8495250536"));
 
         executeTest(String.format("test indel caller in SLX"), spec);
     }
@@ -278,7 +278,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -minIndelCnt 1" +
                         " -L 1:10,000,000-10,100,000",
                 1,
-                Arrays.asList("ca5b6a5fb53ae401b146cc3044f454f2"));
+                Arrays.asList("fd556585c79e2b892a5976668f45aa43"));
 
         executeTest(String.format("test indel caller in SLX witn low min allele count"), spec);
     }
@@ -291,7 +291,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                          " -o %s" +
                          " -L 1:10,000,000-10,500,000",
                  1,
-                 Arrays.asList("ca4343a4ab6d3cce94ce61d7d1910f81"));
+                 Arrays.asList("9cd56feedd2787919e571383889fde70"));
 
          executeTest(String.format("test indel calling, multiple technologies"), spec);
      }
@@ -301,14 +301,14 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
-                Arrays.asList("3f555b53e9dd14cf7cdf96c24e322364"));
+                Arrays.asList("315e1b78d7a403d7fcbcf0caa8c496b8"));
         executeTest("test MultiSample Pilot2 indels with alleles passed in", spec1);
 
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf "
                         + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
-                Arrays.asList("1b9764b783acf7822edc58e6822eef5b"));
+                Arrays.asList("cf89e0c54f14482a23c105b73a333d8a"));
         executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2);
     }
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java
index 0ed16967a..1bf3e579f 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java
@@ -26,7 +26,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
                         + " -L chr20:332341-382503",
                 1,
-                Arrays.asList("6020a68bbec97fcd87819c10cd4e2470"));
+                Arrays.asList("9568ba0b6624b97ac55a59bdee2d9150"));
         executeTest("MAX 10 het sites [TEST ONE]; require PQ >= 10", spec);
     }
 
@@ -36,7 +36,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
                         + " -L chr20:1232503-1332503",
                 1,
-                Arrays.asList("712c2145df4756c9a15758865d8007b5"));
+                Arrays.asList("ce65194c24fe83b0ec90faa6c8e6109a"));
         executeTest("MAX 10 het sites [TEST TWO]; require PQ >= 10", spec);
     }
 
@@ -46,7 +46,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 2, 30)
                         + " -L chr20:332341-382503",
                 1,
-                Arrays.asList("297e0896e4761529d979f40f5ad694db"));
+                Arrays.asList("02d134fd544613b1e5dd7f7197fc3753"));
         executeTest("MAX 2 het sites [TEST THREE]; require PQ >= 30", spec);
     }
 
@@ -56,7 +56,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 5, 100)
                         + " -L chr20:332341-382503",
                 1,
-                Arrays.asList("52a17f14692d726d3b726cf0ae7f2a09"));
+                Arrays.asList("2f7ec9904fc054c2ba1a7db05eb29334"));
         executeTest("MAX 5 het sites [TEST FOUR]; require PQ >= 100", spec);
     }
 
@@ -66,7 +66,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 1000, 7, 10)
                         + " -L chr20:332341-482503",
                 1,
-                Arrays.asList("af768f7958b8f4599c2374f1cc2fc613"));
+                Arrays.asList("da7a31725f229d1782dd3049848730aa"));
         executeTest("MAX 7 het sites [TEST FIVE]; require PQ >= 10; cacheWindow = 1000", spec);
     }
 
@@ -76,7 +76,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
                         + " -L chr20:652810-681757",
                 1,
-                Arrays.asList("3dd886672f59a47908b94136d0427bb0"));
+                Arrays.asList("e9d35cb88089fb0e8ae6678bfaeeac8c"));
         executeTest("MAX 10 het sites [TEST SIX]; require PQ >= 10; cacheWindow = 20000; has inconsistent sites", spec);
     }
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
index 9600046da..2fec2e70f 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
@@ -27,7 +27,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
     VRTest lowPass = new VRTest("phase1.projectConsensus.chr20.raw.snps.vcf",
             "d33212a84368e821cbedecd4f59756d6",  // tranches
             "4652dca41222bebdf9d9fda343b2a835",  // recal file
-            "5350b1a4c1250cf3b77ca45327c04711"); // cut VCF
+            "243a397a33a935fcaccd5deb6d16f0c0"); // cut VCF
 
     @DataProvider(name = "VRTest")
     public Object[][] createData1() {
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
index 600718aa0..daaab9425 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
@@ -71,24 +71,24 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
     }
 
 
-    @Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "2117fff6e0d182cd20be508e9661829c", true); }
-    @Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "2cfaf7af3dd119df08b8a9c1f72e2f93", " -setKey foo", true); }
-    @Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "1474ac0fde2ce42a3c24f1c97eab333e", " -setKey null", true); }
-    @Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "7fc66df048a0ab08cf507906e1d4a308", false); } // official project VCF files in tabix format
+    @Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "c608b9fc1e36dba6cebb4f259883f9f0", true); }
+    @Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "20caad94411d6ab48153b214de916df8", " -setKey foo", true); }
+    @Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "004f3065cb1bc2ce2f9afd695caf0b48", " -setKey null", true); }
+    @Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "c9c901ff9ef2a982624b203a8086dff0", false); } // official project VCF files in tabix format
 
-    @Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "ec9715f53dbf4531570557c212822f12", false); }
-    @Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "f1072be5f5c6ee810276d9ca6537224d", false); }
+    @Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "7593be578d4274d672fc22fced38012b", false); }
+    @Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "1cd467863c4e948fadd970681552d57e", false); }
 
-    @Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "b77a1eec725201d9d8e74ee0c45638d3", false); } // official project VCF files in tabix format
-    @Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "802977fdfd2f4905b501bb06800f60af", false); } // official project VCF files in tabix format
-    @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "a67157287dd2b24b5cdf7ebf8fcbbe9a", false); }
+    @Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "1d5a021387a8a86554db45a29f66140f", false); } // official project VCF files in tabix format
+    @Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "20163d60f18a46496f6da744ab5cc0f9", false); } // official project VCF files in tabix format
+    @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "5b82f37df1f5ba40f0474d71c94142ec", false); }
 
-    @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "e1f4718a179f1196538a33863da04f53", false); }
+    @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "c58dca482bf97069eac6d9f1a07a2cba", false); }
 
-    @Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "b3783384b7c8e877b971033e90beba48", true); }
+    @Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "89f55abea8f59e39d1effb908440548c", true); }
 
-    @Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "902e541c87caa72134db6293fc46f0ad"); }
-    @Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "f339ad4bb5863b58b9c919ce7d040bb9"); }
+    @Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "4836086891f6cbdd40eebef3076d215a"); }
+    @Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "6a34b5d743efda8b2f3b639f3a2f5de8"); }
 
     @Test public void threeWayWithRefs() {
         WalkerTestSpec spec = new WalkerTestSpec(
@@ -101,7 +101,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
                         " -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" +
                         " -genotypeMergeOptions UNIQUIFY -L 1"),
                 1,
-                Arrays.asList("a07995587b855f3214fb71940bf23c0f"));
+                Arrays.asList("8b78339ccf7a5a5a837f79e88a3a38e5"));
         executeTest("threeWayWithRefs", spec);
     }
 
@@ -120,7 +120,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
     }
 
 //    @Test public void complexTestFull() { combineComplexSites("", "64b991fd3850f83614518f7d71f0532f"); }
-    @Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "0db9ef50fe54b60426474273d7c7fa99"); }
-    @Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "d20acb3d53ba0a02ce92d540ebeda2a9"); }
-    @Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "8d1b3d120515f8b56b5a0d10bc5da713"); }
+    @Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "df96cb3beb2dbb5e02f80abec7d3571e"); }
+    @Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "f72a178137e25dbe0b931934cdc0079d"); }
+    @Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "f704caeaaaed6711943014b847fe381a"); }
 }
\ No newline at end of file
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
index d32ab6282..82c894c6f 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
@@ -40,7 +40,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
          WalkerTestSpec spec = new WalkerTestSpec(
                  "-T LiftoverVariants -o %s -R " + b36KGReference + " -B:variant,vcf3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
                  1,
-                 Arrays.asList("37e23efd7d6471fc0f807b31ccafe0eb"));
+                 Arrays.asList("70aeaca5b74cc7ba8e2da7b71ff0fbfd"));
          executeTest("test b36 to hg19", spec);
     }
 
@@ -49,7 +49,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
          WalkerTestSpec spec = new WalkerTestSpec(
                  "-T LiftoverVariants -o %s -R " + b36KGReference + " -B:variant,vcf3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.unsortedSamples.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
                  1,
-                 Arrays.asList("b6ef4a2f026fd3843aeb9ed764a66921"));
+                 Arrays.asList("3fd7ec2dc4064ef410786276b0dc9d08"));
          executeTest("test b36 to hg19, unsorted samples", spec);
     }
 
@@ -58,7 +58,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
          WalkerTestSpec spec = new WalkerTestSpec(
                  "-T LiftoverVariants -o %s -R " + hg18Reference + " -B:variant,vcf " + validationDataLocation + "liftover_test.vcf -chain " + validationDataLocation + "hg18ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
                  1,
-                 Arrays.asList("3275373b3c44ad14a270b50664b3f8a3"));
+                 Arrays.asList("ab2c6254225d7e2ecf52eee604d5673b"));
          executeTest("test hg18 to hg19, unsorted", spec);
     }
 }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
index e18287a21..b5f41542e 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
@@ -18,7 +18,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
             baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' -B:variant,VCF3 " + testfile + " -NO_HEADER"),
             1,
-            Arrays.asList("1b9d551298dc048c7d36b60440ff4d50")
+            Arrays.asList("d18516c1963802e92cb9e425c0b75fd6")
         );
 
         executeTest("testComplexSelection--" + testfile, spec);
@@ -31,7 +31,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -sn A -sn B -sn C -B:variant,VCF3 " + testfile + " -NO_HEADER"),
                 1,
-                Arrays.asList("5ba7536a0819421b330350a160e4261a")
+                Arrays.asList("b74038779fe6485dbb8734ae48178356")
         );
 
         executeTest("testRepeatedLineSelection--" + testfile, spec);
@@ -44,7 +44,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + hg19Reference + " -sn NA12878 -disc myvar -L 20:1012700-1020000 -B:variant,VCF " + b37hapmapGenotypes + " -B:myvar,VCF " + testFile + " -o %s -NO_HEADER",
                 1,
-                Arrays.asList("97621ae8f29955eedfc4e0be3515fcb9")
+                Arrays.asList("78e6842325f1f1bc9ab30d5e7737ee6e")
         );
 
         executeTest("testDiscordance--" + testFile, spec);
@@ -57,7 +57,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + hg19Reference + " -sn NA12878 -conc hapmap -L 20:1012700-1020000 -B:hapmap,VCF " + b37hapmapGenotypes + " -B:variant,VCF " + testFile + " -o %s -NO_HEADER",
                 1,
-                Arrays.asList("a0ae016fdffcbe7bfb99fd3dbc311407")
+                Arrays.asList("d2ba3ea30a810f6f0fbfb1b643292b6a")
         );
 
         executeTest("testConcordance--" + testFile, spec);
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java
index cf0673ee6..d7efe4212 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java
@@ -60,7 +60,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
                     " --NO_HEADER" +
                     " -o %s",
             1,
-            Arrays.asList("debbbf3e661b6857cc8d99ff7635bb1d")
+            Arrays.asList("658f580f7a294fd334bd897102616fed")
         );
 
         executeTest("testSimpleVCFStreaming", spec);
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
index 64d0db14b..8421076c9 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
@@ -20,7 +20,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
     @Test
     public void testVariantsToVCFUsingGeliInput() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("bd15d98adc76b5798e3bbeff3f936feb");
+        md5.add("815b82fff92aab41c209eedce2d7e7d9");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
@@ -38,7 +38,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
     @Test
     public void testGenotypesToVCFUsingGeliInput() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("acd15d3f85bff5b545bc353e0e23cc6e");
+        md5.add("22336ee9c12aa222ce29c3c5babca7d0");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
@@ -56,7 +56,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
     @Test
     public void testGenotypesToVCFUsingHapMapInput() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("6f34528569f8cf5941cb365fa77288c1");
+        md5.add("9bedaa7670b86a07be5191898c3727cf");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
@@ -73,7 +73,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
     @Test
     public void testGenotypesToVCFUsingVCFInput() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("d8316fc1b9d8e954a58940354119a32e");
+        md5.add("cc215edec9ca28e5c79ab1b67506f9f7");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
index 5d42f8d0c..a344817a0 100755
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
@@ -49,7 +49,7 @@ public class VariantContextIntegrationTest extends WalkerTest {
 
         WalkerTestSpec spec = new WalkerTestSpec( cmdRoot + " -NO_HEADER -B:vcf,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -L 1:1-1000000 -o %s --outputVCF %s",
                 2, // just one output file
-                Arrays.asList("e3c35d0c4b5d4935c84a270f9df0951f", "e6673737acbb6bfabfcd92c4b2268241"));
+                Arrays.asList("e3c35d0c4b5d4935c84a270f9df0951f", "ff91731213fd0bbdc200ab6fd1c93e63"));
          executeTest("testToVCF", spec);
     }
 

From ccedd6ff4c942c20c1a57f6a6bf65c5cb63b6e16 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Tue, 12 Jul 2011 15:20:28 -0400
Subject: [PATCH 091/161] Difference is now the general form -- used to be
 SummarizedDifference.   The old Difference class is now a subclass of
 Difference that includes pointers to specific the master and test
 DiffElements. Added a size() function that calculates the number of elements
 tree from a DiffElement.

---
 .../gatk/walkers/diffengine/DiffElement.java  |   4 +
 .../gatk/walkers/diffengine/DiffEngine.java   | 142 +++++-------------
 .../gatk/walkers/diffengine/DiffNode.java     |   7 +
 .../walkers/diffengine/DiffObjectsWalker.java |   7 +-
 .../gatk/walkers/diffengine/DiffValue.java    |   1 +
 .../gatk/walkers/diffengine/Difference.java   |  83 +++++++---
 .../diffengine/SpecificDifference.java        |  59 ++++++++
 .../diffengine/DiffEngineUnitTest.java        |   6 +-
 .../diffengine/DifferenceUnitTest.java        |   2 +-
 9 files changed, 176 insertions(+), 135 deletions(-)
 create mode 100644 public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/SpecificDifference.java

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java
index eff24bb88..4c3f7bd95 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java
@@ -115,4 +115,8 @@ public class DiffElement {
         else
             throw new ReviewedStingException("Illegal request conversion of a DiffValue into a DiffNode: " + this);
     }
+
+    public int size() {
+        return 1 + getValue().size();
+    }
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
index 54a7a464d..6d85df71d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
@@ -24,11 +24,9 @@
 
 package org.broadinstitute.sting.gatk.walkers.diffengine;
 
-import com.google.java.contract.Requires;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.report.GATKReport;
 import org.broadinstitute.sting.gatk.report.GATKReportTable;
-import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@@ -60,7 +58,7 @@ public class DiffEngine {
     //
     // --------------------------------------------------------------------------------
 
-    public List<Difference> diff(DiffElement master, DiffElement test) {
+    public List<SpecificDifference> diff(DiffElement master, DiffElement test) {
         DiffValue masterValue = master.getValue();
         DiffValue testValue = test.getValue();
 
@@ -70,14 +68,14 @@ public class DiffEngine {
             return diff(masterValue, testValue);
         } else {
             // structural difference in types.  one is node, other is leaf
-            return Arrays.asList(new Difference(master, test));
+            return Arrays.asList(new SpecificDifference(master, test));
         }
     }
 
-    public List<Difference> diff(DiffNode master, DiffNode test) {
+    public List<SpecificDifference> diff(DiffNode master, DiffNode test) {
         Set<String> allNames = new HashSet<String>(master.getElementNames());
         allNames.addAll(test.getElementNames());
-        List<Difference> diffs = new ArrayList<Difference>();
+        List<SpecificDifference> diffs = new ArrayList<SpecificDifference>();
 
         for ( String name : allNames ) {
             DiffElement masterElt = master.getElement(name);
@@ -86,7 +84,7 @@ public class DiffEngine {
                 throw new ReviewedStingException("BUG: unexceptedly got two null elements for field: " + name);
             } else if ( masterElt == null || testElt == null ) { // if either is null, we are missing a value
                 // todo -- should one of these be a special MISSING item?
-                diffs.add(new Difference(masterElt, testElt));
+                diffs.add(new SpecificDifference(masterElt, testElt));
             } else {
                 diffs.addAll(diff(masterElt, testElt));
             }
@@ -95,11 +93,11 @@ public class DiffEngine {
         return diffs;
     }
 
-    public List<Difference> diff(DiffValue master, DiffValue test) {
+    public List<SpecificDifference> diff(DiffValue master, DiffValue test) {
         if ( master.getValue().equals(test.getValue()) ) {
             return Collections.emptyList();
         } else {
-            return Arrays.asList(new Difference(master.getBinding(), test.getBinding()));
+            return Arrays.asList(new SpecificDifference(master.getBinding(), test.getBinding()));
         }
     }
 
@@ -147,64 +145,68 @@ public class DiffEngine {
      * @param params determines how we display the items
      * @param diffs
      */
-    public void reportSummarizedDifferences(List<Difference> diffs, SummaryReportParams params ) {
+    public void reportSummarizedDifferences(List<SpecificDifference> diffs, SummaryReportParams params ) {
         printSummaryReport(summarizeDifferences(diffs), params );
     }
 
-    public List<SummarizedDifference> summarizeDifferences(List<Difference> diffs) {
-        List<String[]> diffPaths = new ArrayList<String[]>(diffs.size());
-
-        for ( Difference diff1 : diffs ) {
-            diffPaths.add(diffNameToPath(diff1.getFullyQualifiedName()));
-        }
-
-        return summarizedDifferencesOfPaths(diffPaths);
+    public List<Difference> summarizeDifferences(List<SpecificDifference> diffs) {
+        return summarizedDifferencesOfPaths(diffs);
     }
 
     final protected static String[] diffNameToPath(String diffName) {
         return diffName.split("\\.");
     }
 
-    protected List<SummarizedDifference> summarizedDifferencesOfPaths(List<String[]> diffPaths) {
-        Map<String, SummarizedDifference> summaries = new HashMap<String, SummarizedDifference>();
+    protected List<Difference> summarizedDifferencesOfPathsFromString(List<String> singletonDiffs) {
+        List<Difference> diffs = new ArrayList<Difference>();
+
+        for ( String diff : singletonDiffs ) {
+            diffs.add(new Difference(diff));
+        }
+
+        return summarizedDifferencesOfPaths(diffs);
+    }
+
+    protected List<Difference> summarizedDifferencesOfPaths(List<? extends Difference> singletonDiffs) {
+        Map<String, Difference> summaries = new HashMap<String, Difference>();
 
         // create the initial set of differences
-        for ( int i = 0; i < diffPaths.size(); i++ ) {
+        for ( int i = 0; i < singletonDiffs.size(); i++ ) {
             for ( int j = 0; j <= i; j++ ) {
-                String[] diffPath1 = diffPaths.get(i);
-                String[] diffPath2 = diffPaths.get(j);
-                if ( diffPath1.length == diffPath2.length ) {
-                    int lcp = longestCommonPostfix(diffPath1, diffPath2);
-                    String path = lcp > 0 ? summarizedPath(diffPath2, lcp) : Utils.join(".", diffPath2);
+                Difference diffPath1 = singletonDiffs.get(i);
+                Difference diffPath2 = singletonDiffs.get(j);
+                if ( diffPath1.length() == diffPath2.length() ) {
+                    int lcp = longestCommonPostfix(diffPath1.getParts(), diffPath2.getParts());
+                    String path = lcp > 0 ? summarizedPath(diffPath2.getParts(), lcp) : diffPath2.getPath();
                     addSummary(summaries, path, true);
                 }
             }
         }
 
         // count differences
-        for ( String[] diffPath : diffPaths ) {
-            for ( SummarizedDifference sumDiff : summaries.values() ) {
-                if ( sumDiff.matches(diffPath) )
+        for ( Difference diffPath : singletonDiffs ) {
+            for ( Difference sumDiff : summaries.values() ) {
+                if ( sumDiff.matches(diffPath.getParts()) )
                     addSummary(summaries, sumDiff.getPath(), false);
             }
         }
 
-        List<SummarizedDifference> sortedSummaries = new ArrayList<SummarizedDifference>(summaries.values());
+        List<Difference> sortedSummaries = new ArrayList<Difference>(summaries.values());
         Collections.sort(sortedSummaries);
         return sortedSummaries;
     }
 
-    private static void addSummary(Map<String, SummarizedDifference> summaries, String path, boolean onlyCatalog) {
+    private static void addSummary(Map<String, Difference> summaries, String path, boolean onlyCatalog) {
         if ( summaries.containsKey(path) ) {
             if ( ! onlyCatalog )
                 summaries.get(path).incCount();
         } else {
-            SummarizedDifference sumDiff = new SummarizedDifference(path);
+            Difference sumDiff = new Difference(path);
             summaries.put(sumDiff.getPath(), sumDiff);
         }
     }
 
-    protected void printSummaryReport(List<SummarizedDifference> sortedSummaries, SummaryReportParams params ) {
+    protected void printSummaryReport(List<Difference> sortedSummaries, SummaryReportParams params ) {
         GATKReport report = new GATKReport();
         final String tableName = "diffences";
         report.addTable(tableName, "Summarized differences between the master and test files.\nSee http://www.broadinstitute.org/gsa/wiki/index.php/DiffObjectsWalker_and_SummarizedDifferences for more information");
@@ -213,7 +215,7 @@ public class DiffEngine {
         table.addColumn("NumberOfOccurrences", 0);
 
         int count = 0, count1 = 0;
-        for ( SummarizedDifference diff : sortedSummaries ) {
+        for ( Difference diff : sortedSummaries ) {
             if ( diff.getCount() < params.minSumDiffToShow )
                 // in order, so break as soon as the count is too low
                 break;
@@ -261,76 +263,6 @@ public class DiffEngine {
         return Utils.join(".", parts);
     }
 
-    /**
-     * TODO -- all of the algorithms above should use SummarizedDifference instead
-     * TODO -- of some SummarizedDifferences and some low-level String[]
-     */
-    public static class SummarizedDifference implements Comparable<SummarizedDifference> {
-        final String path; // X.Y.Z
-        final String[] parts;
-        int count = 0;
-
-        public SummarizedDifference(String path) {
-            this.path = path;
-            this.parts = diffNameToPath(path);
-        }
-
-        public void incCount() { count++; }
-
-        public int getCount() {
-            return count;
-        }
-
-        /**
-         * The fully qualified path object A.B.C etc
-         * @return
-         */
-        public String getPath() {
-            return path;
-        }
-
-        /**
-         * @return the length of the parts of this summary
-         */
-        public int length() {
-            return this.parts.length;
-        }
-
-        /**
-         * Returns true if the string parts matches this summary.  Matches are
-         * must be equal() everywhere where this summary isn't *.
-         * @param otherParts
-         * @return
-         */
-        public boolean matches(String[] otherParts) {
-            if ( otherParts.length != length() )
-                return false;
-
-            // TODO optimization: can start at right most non-star element
-            for ( int i = 0; i < length(); i++ ) {
-                String part = parts[i];
-                if ( ! part.equals("*") && ! part.equals(otherParts[i]) )
-                    return false;
-            }
-
-            return true;
-        }
-
-        @Override
-        public String toString() {
-            return String.format("%s:%d", getPath(), getCount());
-        }
-
-        @Override
-        public int compareTo(SummarizedDifference other) {
-            // sort first highest to lowest count, then by lowest to highest path
-            int countCmp = Integer.valueOf(count).compareTo(other.count);
-            return countCmp != 0 ? -1 * countCmp : path.compareTo(other.path);
-        }
-
-
-    }
-
     // --------------------------------------------------------------------------------
     //
     // plugin manager
@@ -404,7 +336,7 @@ public class DiffEngine {
         if ( diffEngine.canRead(masterFile) && diffEngine.canRead(testFile) ) {
             DiffElement master = diffEngine.createDiffableFromFile(masterFile);
             DiffElement test = diffEngine.createDiffableFromFile(testFile);
-            List<Difference> diffs = diffEngine.diff(master, test);
+            List<SpecificDifference> diffs = diffEngine.diff(master, test);
             diffEngine.reportSummarizedDifferences(diffs, params);
             return true;
         } else {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java
index 3e1be8609..2f48de2d3 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java
@@ -153,6 +153,13 @@ public class DiffNode extends DiffValue {
         add(new DiffElement(name, this.getBinding(), new DiffValue(value)));
     }
 
+    public int size() {
+        int count = 0;
+        for ( DiffElement value : getElements() )
+            count += value.size();
+        return count;
+    }
+
     // ---------------------------------------------------------------------------
     //
     // toString
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
index fe411b195..ecb836af9 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
@@ -24,7 +24,6 @@
 
 package org.broadinstitute.sting.gatk.walkers.diffengine;
 
-import org.apache.xmlbeans.impl.tool.Diff;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -95,18 +94,20 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
     public void onTraversalDone(Integer sum) {
         out.printf("Reading master file %s%n", masterFile);
         DiffElement master = diffEngine.createDiffableFromFile(masterFile, MAX_OBJECTS_TO_READ);
+        out.printf("  Read %d objects%n", master.size());
         out.printf("Reading test file %s%n", testFile);
         DiffElement test = diffEngine.createDiffableFromFile(testFile, MAX_OBJECTS_TO_READ);
+        out.printf("  Read %d objects%n", test.size());
 
 //        out.printf("Master diff objects%n");
 //        out.println(master.toString());
 //        out.printf("Test diff objects%n");
 //        out.println(test.toString());
 
-        List<Difference> diffs = diffEngine.diff(master, test);
+        List<SpecificDifference> diffs = diffEngine.diff(master, test);
         if ( showItemizedDifferences ) {
             out.printf("Itemized results%n");
-            for ( Difference diff : diffs )
+            for ( SpecificDifference diff : diffs )
                 out.printf("DIFF: %s%n", diff.toString());
         }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java
index 7245e9e8d..3750496a1 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java
@@ -87,4 +87,5 @@ public class DiffValue {
 
     public boolean isAtomic() { return true; }
     public boolean isCompound() { return ! isAtomic(); }
+    public int size() { return 1; }
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java
index 6627a4cc5..efc6ef160 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java
@@ -24,35 +24,72 @@
 
 package org.broadinstitute.sting.gatk.walkers.diffengine;
 
-/**
- * Created by IntelliJ IDEA.
- * User: depristo
- * Date: 7/4/11
- * Time: 12:53 PM
- *
- * Represents a specific difference between two specific DiffElements
- */
-public class Difference {
-    DiffElement master, test;
+public class Difference implements Comparable<Difference> {
+    final String path; // X.Y.Z
+    final String[] parts;
+    int count = 0;
 
-    public Difference(DiffElement master, DiffElement test) {
-        if ( master == null && test == null ) throw new IllegalArgumentException("Master and test both cannot be null");
-        this.master = master;
-        this.test = test;
+    public Difference(String path) {
+        this.path = path;
+        this.parts = DiffEngine.diffNameToPath(path);
     }
 
+    public String[] getParts() {
+        return parts;
+    }
+
+    public void incCount() { count++; }
+
+    public int getCount() {
+        return count;
+    }
+
+    /**
+     * The fully qualified path object A.B.C etc
+     * @return
+     */
+    public String getPath() {
+        return path;
+    }
+
+    /**
+     * @return the length of the parts of this summary
+     */
+    public int length() {
+        return this.parts.length;
+    }
+
+    /**
+     * Returns true if the string parts matches this summary.  Matches are
+     * must be equal() everywhere where this summary isn't *.
+     * @param otherParts
+     * @return
+     */
+    public boolean matches(String[] otherParts) {
+        if ( otherParts.length != length() )
+            return false;
+
+        // TODO optimization: can start at right most non-star element
+        for ( int i = 0; i < length(); i++ ) {
+            String part = parts[i];
+            if ( ! part.equals("*") && ! part.equals(otherParts[i]) )
+                return false;
+        }
+
+        return true;
+    }
+
+    @Override
     public String toString() {
-        return String.format("%s:%s!=%s",
-                getFullyQualifiedName(),
-                getOneLineString(master),
-                getOneLineString(test));
+        return String.format("%s:%d", getPath(), getCount());
     }
 
-    public String getFullyQualifiedName() {
-        return (master == null ? test : master).fullyQualifiedName();
+    @Override
+    public int compareTo(Difference other) {
+        // sort first highest to lowest count, then by lowest to highest path
+        int countCmp = Integer.valueOf(count).compareTo(other.count);
+        return countCmp != 0 ? -1 * countCmp : path.compareTo(other.path);
     }
 
-    private static String getOneLineString(DiffElement elt) {
-        return elt == null ? "MISSING" : elt.getValue().toOneLineString();
-    }
+
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/SpecificDifference.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/SpecificDifference.java
new file mode 100644
index 000000000..2fe9b47f8
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/SpecificDifference.java
@@ -0,0 +1,59 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: depristo
+ * Date: 7/4/11
+ * Time: 12:53 PM
+ *
+ * Represents a specific difference between two specific DiffElements
+ */
+public class SpecificDifference extends Difference {
+    DiffElement master, test;
+
+    public SpecificDifference(DiffElement master, DiffElement test) {
+        super(createName(master, test));
+        if ( master == null && test == null ) throw new IllegalArgumentException("Master and test both cannot be null");
+        this.master = master;
+        this.test = test;
+    }
+
+    public String toString() {
+        return String.format("%s:%s!=%s",
+                getPath(),
+                getOneLineString(master),
+                getOneLineString(test));
+    }
+
+    private static String createName(DiffElement master, DiffElement test) {
+        return (master == null ? test : master).fullyQualifiedName();
+    }
+
+    private static String getOneLineString(DiffElement elt) {
+        return elt == null ? "MISSING" : elt.getValue().toOneLineString();
+    }
+}
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java
index cd6c3598a..96dfec6e8 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java
@@ -99,7 +99,7 @@ public class DiffEngineUnitTest extends BaseTest {
         logger.warn("Test tree1: " + test.tree1.toOneLineString());
         logger.warn("Test tree2: " + test.tree2.toOneLineString());
 
-        List<Difference> diffs = engine.diff(test.tree1, test.tree2);
+        List<SpecificDifference> diffs = engine.diff(test.tree1, test.tree2);
         logger.warn("Test expected diff : " + test.differences);
         logger.warn("Observed diffs     : " + diffs);
     }
@@ -185,12 +185,12 @@ public class DiffEngineUnitTest extends BaseTest {
             List<String[]> diffPaths = new ArrayList<String[]>(diffs.size());
             for ( String diff : diffs ) { diffPaths.add(DiffEngine.diffNameToPath(diff)); }
 
-            List<DiffEngine.SummarizedDifference> sumDiffs = engine.summarizedDifferencesOfPaths(diffPaths);
+            List<Difference> sumDiffs = engine.summarizedDifferencesOfPathsFromString(diffs);
 
             Assert.assertEquals(sumDiffs.size(), expecteds.size(), "Unexpected number of summarized differences: " + sumDiffs);
 
             for ( int i = 0; i < sumDiffs.size(); i++ ) {
-                DiffEngine.SummarizedDifference sumDiff = sumDiffs.get(i);
+                Difference sumDiff = sumDiffs.get(i);
                 String expected = expecteds.get(i);
                 String[] pathCount = expected.split(":");
                 String path = pathCount[0];
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java
index da272ec30..64579a01b 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java
@@ -87,7 +87,7 @@ public class DifferenceUnitTest extends BaseTest {
         logger.warn("Test tree1: " + (test.tree1 == null ? "null" : test.tree1.toOneLineString()));
         logger.warn("Test tree2: " + (test.tree2 == null ? "null" : test.tree2.toOneLineString()));
         logger.warn("Test expected diff : " + test.difference);
-        Difference diff = new Difference(test.tree1, test.tree2);
+        SpecificDifference diff = new SpecificDifference(test.tree1, test.tree2);
         logger.warn("Observed diffs     : " + diff);
         Assert.assertEquals(diff.toString(), test.difference, "Observed diff string " + diff + " not equal to expected difference string " + test.difference );
 

From 5077c94d85929bad35fcc00bbeab0b8036aabe4a Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Tue, 12 Jul 2011 15:39:07 -0400
Subject: [PATCH 093/161] Adding MappingQualityUnavailableReadFilter to the SNP
 and indel CountCovariates

---
 .../recalibration/CountCovariatesWalker.java  |  3 +-
 .../RecalibrationWalkersIntegrationTest.java  | 91 +++----------------
 2 files changed, 15 insertions(+), 79 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
index 6673bec92..c21f548b3 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.recalibration;
 
 import org.broad.tribble.bed.BEDCodec;
 import org.broad.tribble.dbsnp.DbSNPCodec;
+import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableReadFilter;
 import org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
 import org.broadinstitute.sting.commandline.Gather;
@@ -75,7 +76,7 @@ import java.util.Map;
 
 @BAQMode(ApplicationTime = BAQ.ApplicationTime.FORBIDDEN)
 @By( DataSource.READS ) // Only look at covered loci, not every loci of the reference file
-@ReadFilters( {MappingQualityZeroReadFilter.class} ) // Filter out all reads with zero mapping quality
+@ReadFilters( {MappingQualityZeroReadFilter.class, MappingQualityUnavailableReadFilter.class} ) // Filter out all reads with zero or unavailable mapping quality
 @Requires( {DataSource.READS, DataSource.REFERENCE, DataSource.REFERENCE_BASES} ) // This walker requires both -I input.bam and -R reference.fasta
 @PartitionBy(PartitionType.LOCUS)
 public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.CountedData, CountCovariatesWalker.CountedData> implements TreeReducible<CountCovariatesWalker.CountedData> {
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
index b0f76229b..129161da3 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
@@ -19,9 +19,9 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     public void testCountCovariates1() {
         HashMap<String, String> e = new HashMap<String, String>();
         e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "7b5832d4b2a23b8ef2bb639eb59bfa88" );
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "f4f8a49bb5764d2a8f61e055f64dcce4");
+        e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "9c006f8e9fb5752b1c139f5a8cc7ea88");
         e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "e6f7b4ab9aa291022e0ba8b7dbe4c77e" );
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "570506533f079d738d70934dfe1c02cd" );
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "e6b98af01c5a08e4954b79ec42db6fc3" );
 
         for ( String parallelism : Arrays.asList("", " -nt 4")) {
             for ( Map.Entry<String, String> entry : e.entrySet() ) {
@@ -53,9 +53,9 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     public void testTableRecalibrator1() {
         HashMap<String, String> e = new HashMap<String, String>();
         e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "0278cce4cfdab869dc0c11d6852a984b" );
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "344d4252143df8c2cce6b568747553a5");
+        e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "6797d7ffa4ef6c48413719ba32696ccf");
         e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "2bb3374dde131791d7638031ae3b3e10" );
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "064c4a7bdd23974c3a9c5f924540df76" );
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "1f9d8944b73169b367cb83b0d22e5432" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -107,7 +107,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testTableRecalibratorMaxQ70() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "344d4252143df8c2cce6b568747553a5" );
+        e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "0278cce4cfdab869dc0c11d6852a984b" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -133,12 +133,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
         }
     }
 
-
-
     @Test
     public void testCountCovariatesSolidIndelsRemoveRefBias() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "0a6cdb9611e5880ea6611205080aa267" );
+        e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "c9ea5f995e1e2b7a5688533e678dcedc" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -164,7 +162,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testTableRecalibratorSolidIndelsRemoveRefBias() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "9bc7e1ad223ba759fe5e8ddb4c07369c" );
+        e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "993fae4270e7e1e15986f270acf247af" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -189,13 +187,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
         }
     }
 
-
-
-
     @Test
     public void testCountCovariatesVCF() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "3700eaf567e4937f442fc777a226d6ad");
+        e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "170f0c3cc4b8d72c539136effeec9a16");
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -219,7 +214,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testCountCovariatesBED() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "6803891a3398821fc8a37e19ea8e5a00");
+        e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "b460478d9683e827784e42bc352db8bb");
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -243,7 +238,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testCountCovariatesVCFPlusDBsnp() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "f224c42fbc4026db973ccc91265ab5c7");
+        e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "a3d892bd60d8f679affda3c1e3af96c1");
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -268,69 +263,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
         }
     }
 
-    @Test
-    public void testCountCovariatesNoReadGroups() {
-        HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "c024e03f019aeceaf364fa58c8295ad8" );
-
-        for ( Map.Entry<String, String> entry : e.entrySet() ) {
-            String bam = entry.getKey();
-            String md5 = entry.getValue();
-
-            WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                    "-R " + b36KGReference +
-                            " --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" +
-                            " -T CountCovariates" +
-                            " -I " + bam +
-                            " -L 1:10,000,000-10,200,000" +
-                            " -cov ReadGroupCovariate" +
-                            " -cov QualityScoreCovariate" +
-                            " -cov CycleCovariate" +
-                            " -cov DinucCovariate" +
-                            " --default_read_group DefaultReadGroup" +
-                            " --default_platform illumina" +
-                            " --solid_recal_mode SET_Q_ZERO" +
-                            " -recalFile %s",
-                    1, // just one output file
-                    Arrays.asList(md5));
-            List<File> result = executeTest("testCountCovariatesNoReadGroups", spec).getFirst();
-            paramsFilesNoReadGroupTest.put(bam, result.get(0).getAbsolutePath());
-        }
-    }
-
-    @Test
-    public void testTableRecalibratorNoReadGroups() {
-        HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "1eefbe7ac0376fc1ed1392d85242171e" );
-
-        for ( Map.Entry<String, String> entry : e.entrySet() ) {
-            String bam = entry.getKey();
-            String md5 = entry.getValue();
-            String paramsFile = paramsFilesNoReadGroupTest.get(bam);
-            System.out.printf("PARAMS FOR %s is %s%n", bam, paramsFile);
-            if ( paramsFile != null ) {
-                WalkerTestSpec spec = new WalkerTestSpec(
-                        "-R " + b36KGReference +
-                                " -T TableRecalibration" +
-                                " -I " + bam +
-                                " -L 1:10,100,000-10,300,000" +
-                                " -o %s" +
-                                " --no_pg_tag" +
-                                " --solid_recal_mode SET_Q_ZERO" +
-                                " --default_read_group DefaultReadGroup" +
-                                " --default_platform illumina" +
-                                " -recalFile " + paramsFile,
-                        1, // just one output file
-                        Arrays.asList(md5));
-                executeTest("testTableRecalibratorNoReadGroups", spec);
-            }
-        }
-    }
-
     @Test
     public void testCountCovariatesNoIndex() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "cfc31bb6f51436d1c3b34f62bb801dc8" );
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "284ccac1f8fe485e52c86333cac7c2d4" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -356,7 +292,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testTableRecalibratorNoIndex() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "83b848a16034c2fb423d1bb0f5be7784" );
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "c167799c2d9cab815d7c9b23337f162e" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -380,11 +316,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
         }
     }
 
-
     @Test
     public void testCountCovariatesFailWithoutDBSNP() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "");
+        e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "");
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();

From 6007eea3ffba2e459ec6bf0a1c66c0a017fe0a62 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 13 Jul 2011 09:56:08 -0400
Subject: [PATCH 099/161] Allowing VCF records without GTs in vf4.1

---
 .../utils/codecs/vcf/StandardVCFWriter.java   | 41 +++++++++++++------
 .../sting/utils/codecs/vcf/VCF3Codec.java     | 13 +++---
 .../sting/utils/codecs/vcf/VCFCodec.java      | 28 ++++++-------
 .../sting/utils/variantcontext/Genotype.java  | 35 +++++++++++++---
 .../utils/variantcontext/VariantContext.java  |  8 ++--
 5 files changed, 83 insertions(+), 42 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
index a8bf74707..f7d09f16d 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
@@ -32,6 +32,7 @@ import org.broad.tribble.index.IndexFactory;
 import org.broad.tribble.util.LittleEndianOutputStream;
 import org.broad.tribble.util.ParsingUtils;
 import org.broad.tribble.util.PositionalStream;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
@@ -300,10 +301,7 @@ public class StandardVCFWriter implements VCFWriter {
             } else {
                 List<String> genotypeAttributeKeys = new ArrayList<String>();
                 if ( vc.hasGenotypes() ) {
-                    genotypeAttributeKeys.add(VCFConstants.GENOTYPE_KEY);
-                    for ( String key : calcVCFGenotypeKeys(vc) ) {
-                        genotypeAttributeKeys.add(key);
-                    }
+                    genotypeAttributeKeys.addAll(calcVCFGenotypeKeys(vc));
                 } else if ( mHeader.hasGenotypingData() ) {
                     // this needs to be done in case all samples are no-calls
                     genotypeAttributeKeys.add(VCFConstants.GENOTYPE_KEY);
@@ -387,16 +385,22 @@ public class StandardVCFWriter implements VCFWriter {
                 continue;
             }
 
-            writeAllele(g.getAllele(0), alleleMap);
-            for (int i = 1; i < g.getPloidy(); i++) {
-                mWriter.write(g.isPhased() ? VCFConstants.PHASED : VCFConstants.UNPHASED);
-                writeAllele(g.getAllele(i), alleleMap);
-            }
-
             List<String> attrs = new ArrayList<String>(genotypeFormatKeys.size());
             for ( String key : genotypeFormatKeys ) {
-                if ( key.equals(VCFConstants.GENOTYPE_KEY) )
+
+                if ( key.equals(VCFConstants.GENOTYPE_KEY) ) {
+                    if ( !g.isAvailable() ) {
+                        throw new ReviewedStingException("GTs cannot be missing for some samples if they are available for others in the record");
+                    }
+
+                    writeAllele(g.getAllele(0), alleleMap);
+                    for (int i = 1; i < g.getPloidy(); i++) {
+                        mWriter.write(g.isPhased() ? VCFConstants.PHASED : VCFConstants.UNPHASED);
+                        writeAllele(g.getAllele(i), alleleMap);
+                    }
+
                     continue;
+                }
 
                 Object val = g.hasAttribute(key) ? g.getAttribute(key) : VCFConstants.MISSING_VALUE_v4;
 
@@ -488,10 +492,13 @@ public class StandardVCFWriter implements VCFWriter {
     private static List<String> calcVCFGenotypeKeys(VariantContext vc) {
         Set<String> keys = new HashSet<String>();
 
+        boolean sawGoodGT = false;
         boolean sawGoodQual = false;
         boolean sawGenotypeFilter = false;
         for ( Genotype g : vc.getGenotypes().values() ) {
             keys.addAll(g.getAttributes().keySet());
+            if ( g.isAvailable() )
+                sawGoodGT = true;
             if ( g.hasNegLog10PError() )
                 sawGoodQual = true;
             if (g.isFiltered() && g.isCalled())
@@ -504,7 +511,17 @@ public class StandardVCFWriter implements VCFWriter {
         if (sawGenotypeFilter)
             keys.add(VCFConstants.GENOTYPE_FILTER_KEY);
 
-        return ParsingUtils.sortList(new ArrayList<String>(keys));
+        List<String> sortedList = ParsingUtils.sortList(new ArrayList<String>(keys));
+
+        // make sure the GT is first
+        if ( sawGoodGT ) {
+            List<String> newList = new ArrayList<String>(sortedList.size()+1);
+            newList.add(VCFConstants.GENOTYPE_KEY);
+            newList.addAll(sortedList);
+            sortedList = newList;
+        }
+
+        return sortedList;
     }
 
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java
index f3c99e963..c29f2ba8b 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java
@@ -141,8 +141,6 @@ public class VCF3Codec extends AbstractVCFCodec {
                     boolean missing = i >= GTValueSplitSize;
 
                     if (gtKey.equals(VCFConstants.GENOTYPE_KEY)) {
-                        if (i != 0)
-                            generateException("Saw GT at position " + i + ", but it must be at the first position for genotypes");
                         genotypeAlleleLocation = i;
                     } else if (gtKey.equals(VCFConstants.GENOTYPE_QUALITY_KEY)) {
                         GTQual = missing ? parseQual(VCFConstants.MISSING_VALUE_v4) : parseQual(GTValueArray[i]);
@@ -156,12 +154,13 @@ public class VCF3Codec extends AbstractVCFCodec {
                 }
             }
 
-            // check to make sure we found a gentoype field
-            if (genotypeAlleleLocation < 0) generateException("Unable to find required field GT for the record; we don't yet support a missing GT field");
+            // check to make sure we found a genotype field
+            if ( genotypeAlleleLocation < 0 )
+                generateException("Unable to find the GT field for the record; the GT field is required");
+            if ( genotypeAlleleLocation > 0 )
+                generateException("Saw GT field at position " + genotypeAlleleLocation + ", but it must be at the first position for genotypes");
 
-            // todo -- assuming allele list length in the single digits is bad.  Fix me.
-            // Check for > 1 for haploid genotypes
-            boolean phased = GTValueArray[genotypeAlleleLocation].length() > 1 && GTValueArray[genotypeAlleleLocation].charAt(1) == '|';
+            boolean phased = GTValueArray[genotypeAlleleLocation].indexOf(VCFConstants.PHASED) != -1;
 
             // add it to the list
             try {
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
index 0fb2940bb..05fff5d9e 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
@@ -145,8 +145,6 @@ public class VCFCodec extends AbstractVCFCodec {
 
                     // todo -- all of these on the fly parsing of the missing value should be static constants
                     if (gtKey.equals(VCFConstants.GENOTYPE_KEY)) {
-                        if (i != 0)
-                            generateException("Saw GT at position " + i + ", but it must be at the first position for genotypes");
                         genotypeAlleleLocation = i;
                     } else if (gtKey.equals(VCFConstants.GENOTYPE_QUALITY_KEY)) {
                         GTQual = missing ? parseQual(VCFConstants.MISSING_VALUE_v4) : parseQual(GTValueArray[i]);
@@ -160,22 +158,24 @@ public class VCFCodec extends AbstractVCFCodec {
                 }
             }
 
-            // check to make sure we found a gentoype field
-            // TODO -- This is no longer required in v4.1
-            if (genotypeAlleleLocation < 0) generateException("Unable to find required field GT for the record; we don't yet support a missing GT field");
+            // check to make sure we found a genotype field if we are a VCF4.0 file
+            if ( version == VCFHeaderVersion.VCF4_0 && genotypeAlleleLocation == -1 )
+                generateException("Unable to find the GT field for the record; the GT field is required in VCF4.0");
+            if ( genotypeAlleleLocation > 0 )
+                generateException("Saw GT field at position " + genotypeAlleleLocation + ", but it must be at the first position for genotypes when present");
 
-            // todo -- assuming allele list length in the single digits is bad.  Fix me.
-            // Check for > 1 for haploid genotypes
-            boolean phased = GTValueArray[genotypeAlleleLocation].length() > 1 && GTValueArray[genotypeAlleleLocation].charAt(1) == '|';
+            List<Allele> GTalleles = (genotypeAlleleLocation == -1 ? null : parseGenotypeAlleles(GTValueArray[genotypeAlleleLocation], alleles, alleleMap));
+            boolean phased = genotypeAlleleLocation != -1 && GTValueArray[genotypeAlleleLocation].indexOf(VCFConstants.PHASED) != -1;
 
             // add it to the list
             try {
-                genotypes.put(sampleName, new Genotype(sampleName,
-                        parseGenotypeAlleles(GTValueArray[genotypeAlleleLocation], alleles, alleleMap),
-                        GTQual,
-                        genotypeFilters,
-                        gtAttributes,
-                        phased));
+                genotypes.put(sampleName,
+                        new Genotype(sampleName,
+                                GTalleles,
+                                GTQual,
+                                genotypeFilters,
+                                gtAttributes,
+                                phased));
             } catch (TribbleException e) {
                 throw new TribbleException.InternalCodecException(e.getMessage() + ", at position " + chr+":"+pos);
             }
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
index 3a87f1196..0b5976c3c 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
@@ -3,6 +3,7 @@ package org.broadinstitute.sting.utils.variantcontext;
 
 import org.broad.tribble.util.ParsingUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.*;
 
@@ -19,12 +20,14 @@ public class Genotype {
     protected InferredGeneticContext commonInfo;
     public final static double NO_NEG_LOG_10PERROR = InferredGeneticContext.NO_NEG_LOG_10PERROR;
     protected List<Allele> alleles = null; // new ArrayList<Allele>();
+    protected Type type = null;
 
     protected boolean isPhased = false;
-    private boolean filtersWereAppliedToContext;
+    protected boolean filtersWereAppliedToContext;
 
     public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes, boolean isPhased) {
-        this.alleles = Collections.unmodifiableList(alleles);
+        if ( alleles != null )
+            this.alleles = Collections.unmodifiableList(alleles);
         commonInfo = new InferredGeneticContext(sampleName, negLog10PError, filters, attributes);
         filtersWereAppliedToContext = filters != null;
         this.isPhased = isPhased;
@@ -66,6 +69,9 @@ public class Genotype {
     }
 
     public List<Allele> getAlleles(Allele allele) {
+        if ( getType() == Type.UNAVAILABLE )
+            throw new ReviewedStingException("Requesting alleles for an UNAVAILABLE genotype");
+
         List<Allele> al = new ArrayList<Allele>();
         for ( Allele a : alleles )
             if ( a.equals(allele) )
@@ -75,6 +81,8 @@ public class Genotype {
     }
 
     public Allele getAllele(int i) {
+        if ( getType() == Type.UNAVAILABLE )
+            throw new ReviewedStingException("Requesting alleles for an UNAVAILABLE genotype");
         return alleles.get(i);
     }
 
@@ -89,10 +97,21 @@ public class Genotype {
         NO_CALL,
         HOM_REF,
         HET,
-        HOM_VAR
+        HOM_VAR,
+        UNAVAILABLE
     }
 
     public Type getType() {
+        if ( type == null ) {
+            type = determineType();
+        }
+        return type;
+    }
+
+    protected Type determineType() {
+        if ( alleles == null )
+            return Type.UNAVAILABLE;
+
         Allele firstAllele = alleles.get(0);
 
         if ( firstAllele.isNoCall() ) {
@@ -122,7 +141,8 @@ public class Genotype {
      * @return true if this genotype is not actually a genotype but a "no call" (e.g. './.' in VCF)
      */
     public boolean isNoCall() { return getType() == Type.NO_CALL; }
-    public boolean isCalled() { return getType() != Type.NO_CALL; }
+    public boolean isCalled() { return getType() != Type.NO_CALL && getType() != Type.UNAVAILABLE; }
+    public boolean isAvailable() { return getType() != Type.UNAVAILABLE; }
 
     //
     // Useful methods for getting genotype likelihoods for a genotype object, if present
@@ -157,8 +177,8 @@ public class Genotype {
     }
 
     public void validate() {
-        if ( alleles == null ) throw new IllegalArgumentException("BUG: alleles cannot be null in setAlleles");
-        if ( alleles.size() == 0) throw new IllegalArgumentException("BUG: alleles cannot be of size 0 in setAlleles");
+        if ( alleles == null ) return;
+        if ( alleles.size() == 0) throw new IllegalArgumentException("BUG: alleles cannot be of size 0");
 
         int nNoCalls = 0;
         for ( Allele allele : alleles ) {
@@ -175,6 +195,9 @@ public class Genotype {
     }
 
     public String getGenotypeString(boolean ignoreRefState) {
+        if ( alleles == null )
+            return null;
+
         // Notes:
         // 1. Make sure to use the appropriate separator depending on whether the genotype is phased
         // 2. If ignoreRefState is true, then we want just the bases of the Alleles (ignoring the '*' indicating a ref Allele)
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
index da80a3431..92c5d648b 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -1206,9 +1206,11 @@ public class VariantContext implements Feature { // to enable tribble intergrati
 
             if ( ! name.equals(g.getSampleName()) ) throw new IllegalStateException("Bound sample name " + name + " does not equal the name of the genotype " + g.getSampleName());
 
-            for ( Allele gAllele : g.getAlleles() ) {
-                if ( ! hasAllele(gAllele) && gAllele.isCalled() )
-                    throw new IllegalStateException("Allele in genotype " + gAllele + " not in the variant context " + alleles);
+            if ( g.isAvailable() ) {
+                for ( Allele gAllele : g.getAlleles() ) {
+                    if ( ! hasAllele(gAllele) && gAllele.isCalled() )
+                        throw new IllegalStateException("Allele in genotype " + gAllele + " not in the variant context " + alleles);
+                }
             }
         }
     }

From 797c50e6894f5e5fd341c3b002610301173c269a Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 13 Jul 2011 10:01:23 -0400
Subject: [PATCH 100/161] Fixing integration tests I broke yesterday; removing
 batch merging test since we don't support that anymore.

---
 .../phasing/MergeMNPsIntegrationTest.java     |  6 +--
 ...gatingAlternateAllelesIntegrationTest.java |  6 +--
 .../BatchMergeIntegrationTest.java            | 46 -------------------
 3 files changed, 6 insertions(+), 52 deletions(-)
 delete mode 100755 public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/BatchMergeIntegrationTest.java

diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsIntegrationTest.java
index 3f87fc1a2..c88eac149 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsIntegrationTest.java
@@ -23,7 +23,7 @@ public class MergeMNPsIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 1)
                         + " -L chr20:556259-756570",
                 1,
-                Arrays.asList("e312b7d3854d5b2834a370659514a813"));
+                Arrays.asList("7f11f7f75d1526077f0173c7ed1fc6c4"));
         executeTest("Merge MNP sites within genomic distance of 1 [TEST ONE]", spec);
     }
 
@@ -33,7 +33,7 @@ public class MergeMNPsIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 10)
                         + " -L chr20:556259-756570",
                 1,
-                Arrays.asList("681f50e45f1d697370d2c355df2e18bc"));
+                Arrays.asList("53dd312468296826bdd3c22387390c88"));
         executeTest("Merge MNP sites within genomic distance of 10 [TEST TWO]", spec);
     }
 
@@ -43,7 +43,7 @@ public class MergeMNPsIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 100)
                         + " -L chr20:556259-756570",
                 1,
-                Arrays.asList("0bccb0ef928a108418246bec01098083"));
+                Arrays.asList("e26f92d2fb9f4eaeac7f9d8ee27410ee"));
         executeTest("Merge MNP sites within genomic distance of 100 [TEST THREE]", spec);
     }
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesIntegrationTest.java
index 009048c10..f855c1dd3 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesIntegrationTest.java
@@ -23,7 +23,7 @@ public class MergeSegregatingAlternateAllelesIntegrationTest extends WalkerTest
                 baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 1)
                         + " -L chr20:556259-756570",
                 1,
-                Arrays.asList("e16f957d888054ae0518e25660295241"));
+                Arrays.asList("af5e1370822551c0c6f50f23447dc627"));
         executeTest("Merge sites within genomic distance of 1 [TEST ONE]", spec);
     }
 
@@ -33,7 +33,7 @@ public class MergeSegregatingAlternateAllelesIntegrationTest extends WalkerTest
                 baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 10)
                         + " -L chr20:556259-756570",
                 1,
-                Arrays.asList("122a482090677c7619c2105d44e00d11"));
+                Arrays.asList("dd8c44ae1ef059a7fe85399467e102eb"));
         executeTest("Merge sites within genomic distance of 10 [TEST TWO]", spec);
     }
 
@@ -43,7 +43,7 @@ public class MergeSegregatingAlternateAllelesIntegrationTest extends WalkerTest
                 baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 100)
                         + " -L chr20:556259-756570",
                 1,
-                Arrays.asList("bc6a8c8a42bb2601db98e88e9ad74748"));
+                Arrays.asList("f81fd72ecaa57b3215406fcea860bcc5"));
         executeTest("Merge sites within genomic distance of 100 [TEST THREE]", spec);
     }
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/BatchMergeIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/BatchMergeIntegrationTest.java
deleted file mode 100755
index 7e1d86105..000000000
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/BatchMergeIntegrationTest.java
+++ /dev/null
@@ -1,46 +0,0 @@
-/*
- * Copyright (c) 2010, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.gatk.walkers.variantutils;
-
-import org.broadinstitute.sting.WalkerTest;
-import org.testng.annotations.Test;
-
-import java.io.File;
-import java.util.Arrays;
-
-public class BatchMergeIntegrationTest extends WalkerTest {
-    @Test
-    public void testBatchMerge1() {
-        String bam = validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.bam";
-        String alleles = validationDataLocation +  "batch.merge.alleles.vcf";
-        WalkerTestSpec spec = new WalkerTestSpec(
-                "-T UnifiedGenotyper -NO_HEADER -BTI alleles -stand_call_conf 0.0 -glm BOTH -G none -nsl -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -o %s -R " + b37KGReference
-                        + " -B:alleles,VCF " + alleles
-                        + " -I " + bam,
-                1,
-                Arrays.asList("f4ed8f4ef2cba96823c06e90e9d0de35"));
-        executeTest("testBatchMerge UG genotype given alleles:" + new File(bam).getName() + " with " + new File(alleles).getName(), spec);
-    }
-}
\ No newline at end of file

From fa3ff5350800f1449b6e4e5f365cf2b745906932 Mon Sep 17 00:00:00 2001
From: Menachem Fromer <fromer@broadinstitute.org>
Date: Wed, 13 Jul 2011 11:58:16 -0400
Subject: [PATCH 104/161] Filters should only be applied to the new VC if the
 old VC had filters applied

---
 .../sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java  | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
index e59b29502..af24035c8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
@@ -220,6 +220,9 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
             }
             else {
                 unprocessedList.add(vc); // Finished with the unprocessed variant, and writer can enforce sorting on-the-fly
+
+                if (DEBUG)
+                    logger.debug("Unprocessed variant = " + VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc));
             }
 
             int numReads = 0;
@@ -1105,7 +1108,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
             this.alleles = vc.getAlleles();
             this.genotypes = new HashMap<String, Genotype>(vc.getGenotypes()); // since vc.getGenotypes() is unmodifiable
             this.negLog10PError = vc.getNegLog10PError();
-            this.filters = vc.getFilters();
+            this.filters = vc.filtersWereApplied() ? vc.getFilters() : null;
             this.attributes = new HashMap<String, Object>(vc.getAttributes());
         }
 

From ff4e31c554f65d9d6ba28a08760409d746602d4a Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Wed, 13 Jul 2011 12:59:18 -0400
Subject: [PATCH 105/161] Changing the file names as per Kris request.

---
 .../queue/qscripts/RecalibrateBaseQualities.scala      | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
index 51de3a7ad..dc9ae0f4b 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
@@ -41,11 +41,11 @@ class RecalibrateBaseQualities extends QScript {
 
     nContigs = getNumberOfContigs(input)
 
-    val recalFile1: File = swapExt(input, ".bam", "recal1.csv")
-    val recalFile2: File = swapExt(input, ".bam", "recal2.csv")
-    val recalBam: File   = swapExt(input, ".bam", "recal.bam")
-    val path1: String    = "before"
-    val path2: String    = "after"
+    val recalFile1: File = swapExt(input, ".bam", ".recal1.csv")
+    val recalFile2: File = swapExt(input, ".bam", ".recal2.csv")
+    val recalBam: File   = swapExt(input, ".bam", ".recal.bam")
+    val path1: String    = input + "before"
+    val path2: String    = input + "after"
     
     add(cov(input, recalFile1),
         recal(input, recalFile1, recalBam),

From 6a431da554634b164635b299e2ef472a35fd0739 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 13 Jul 2011 14:40:01 -0400
Subject: [PATCH 106/161] Don't output source and ref header lines anymore. 
 Short-term motivation for this is that I'd like this tool when run on a VCF
 to emit the exact same VCF.  Long-term motivation is that these tags should
 be output by the VCF writer itself for all tools.

---
 .../walkers/variantutils/VariantsToVCF.java   |  4 +--
 .../utils/codecs/vcf/VCFIntegrationTest.java  | 28 +++++++++++++++++++
 2 files changed, 30 insertions(+), 2 deletions(-)
 create mode 100644 public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
index 7eb49da34..79134b553 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
@@ -199,8 +199,8 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
             // setup the header fields
             Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
             hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
-            hInfo.add(new VCFHeaderLine("source", "VariantsToVCF"));
-            hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
+            //hInfo.add(new VCFHeaderLine("source", "VariantsToVCF"));
+            //hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
 
             allowedGenotypeFormatStrings.add(VCFConstants.GENOTYPE_KEY);
             for ( VCFHeaderLine field : hInfo ) {
diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
new file mode 100644
index 000000000..32ff25c7b
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
@@ -0,0 +1,28 @@
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.util.Arrays;
+import java.util.List;
+
+public class VCFIntegrationTest extends WalkerTest {
+
+    @Test
+    public void testReadingAndWritingWitHNoChanges() {
+
+        String md5ofInputVCF = "a990ba187a69ca44cb9bc2bb44d00447";
+        String testVCF = validationDataLocation + "vcf4.1.example.vcf";
+
+        String baseCommand = "-R " + b37KGReference + " -NO_HEADER -o %s ";
+
+        String test1 = baseCommand + "-T VariantAnnotator -BTI variant -B:variant,vcf " + testVCF;
+        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList(md5ofInputVCF));
+        List<File> result = executeTest("Test Variant Annotator with no changes", spec1).getFirst();
+
+        String test2 = baseCommand + "-T VariantsToVCF -B:variant,vcf " + result.get(0).getAbsolutePath();
+        WalkerTestSpec spec2 = new WalkerTestSpec(test2, 1, Arrays.asList(md5ofInputVCF));
+        executeTest("Test Variants To VCF from new output", spec2);
+    }
+}

From df996a1a738208dac7c42b24645f747304b3de7f Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Wed, 13 Jul 2011 14:53:58 -0400
Subject: [PATCH 107/161] more progress report for the Data Processing
 Pipeline. Bam lists can now have empty lines, comments and whitespaces
 anywhere.

---
 .../qscripts/DataProcessingPipeline.scala     | 19 ++++++++++++++-----
 1 file changed, 14 insertions(+), 5 deletions(-)

diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
index f9369ee3f..d6caabd23 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
@@ -147,13 +147,22 @@ class DataProcessingPipeline extends QScript {
       }
     }
 
+    println("\n\n*** DEBUG ***\n")
     // Creating one file for each sample in the dataset
     val sampleBamFiles = scala.collection.mutable.Map.empty[String, File]
     for ((sample, flist) <- sampleTable) {
+
+      println(sample + ":")
+      for (f <- flist)
+        println (f)
+      println()
+
       val sampleFileName = new File(qscript.outputDir + qscript.projectName + "." + sample + ".bam")
       sampleBamFiles(sample) = sampleFileName
       add(joinBams(flist, sampleFileName))
     }
+    println("*** DEBUG ***\n\n")
+
     return sampleBamFiles.toMap
   }
 
@@ -211,8 +220,10 @@ class DataProcessingPipeline extends QScript {
     if (in.toString.endsWith("bam"))
       return List(in)
     var l: List[File] = List()
-    for (bam <- fromFile(in).getLines)
-      l :+= new File(bam)
+    for (bam <- fromFile(in).getLines) {
+      if (!bam.startsWith("#") && !bam.isEmpty)
+        l :+= new File(bam.trim)
+    }
     return l
   }
 
@@ -234,9 +245,6 @@ class DataProcessingPipeline extends QScript {
     // Generate a BAM file per sample joining all per lane files if necessary
     val sampleBamFiles: Map[String, File] = createSampleFiles(bams, realignedBams)
 
-
-    println("nContigs: " + nContigs)
-
     // Final output list of processed bam files
     var cohortList: List[File] = List()
 
@@ -244,6 +252,7 @@ class DataProcessingPipeline extends QScript {
     println("\nFound the following samples: ")
     for ((sample, file) <- sampleBamFiles)
       println("\t" + sample + " -> " + file)
+    println("\n")
 
     // If this is a 'knowns only' indel realignment run, do it only once for all samples.
     val globalIntervals = new File(outputDir + projectName + ".intervals")

From bb0e3a26fcf2a0c99ee0e70c46fb6359b3720a40 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 13 Jul 2011 14:57:21 -0400
Subject: [PATCH 108/161] Added integration test for VCF writing. Also, bug fix
 for writing the GT-free records.

---
 .../sting/utils/codecs/vcf/StandardVCFWriter.java         | 7 ++++---
 .../variantutils/VariantsToVCFIntegrationTest.java        | 8 ++++----
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
index f7d09f16d..e7ddac185 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
@@ -444,9 +444,10 @@ public class StandardVCFWriter implements VCFWriter {
                     break;
             }
 
-            for (String s : attrs ) {
-                mWriter.write(VCFConstants.GENOTYPE_FIELD_SEPARATOR);
-                mWriter.write(s);
+            for (int i = 0; i < attrs.size(); i++) {
+                if ( i > 0 || genotypeFormatKeys.contains(VCFConstants.GENOTYPE_KEY) )
+                    mWriter.write(VCFConstants.GENOTYPE_FIELD_SEPARATOR);
+                mWriter.write(attrs.get(i));
             }
         }
     }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
index 8421076c9..8c96c1e11 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
@@ -20,7 +20,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
     @Test
     public void testVariantsToVCFUsingGeliInput() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("815b82fff92aab41c209eedce2d7e7d9");
+        md5.add("4accae035d271b35ee2ec58f403c68c6");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
@@ -38,7 +38,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
     @Test
     public void testGenotypesToVCFUsingGeliInput() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("22336ee9c12aa222ce29c3c5babca7d0");
+        md5.add("71e8c98d7c3a73b6287ecc339086fe03");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
@@ -56,7 +56,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
     @Test
     public void testGenotypesToVCFUsingHapMapInput() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("9bedaa7670b86a07be5191898c3727cf");
+        md5.add("f343085305e80c7a2493422e4eaad983");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
@@ -73,7 +73,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
     @Test
     public void testGenotypesToVCFUsingVCFInput() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("cc215edec9ca28e5c79ab1b67506f9f7");
+        md5.add("86f02e2e764ba35854cff2aa05a1fdd8");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +

From 66c652d687ec5b5e15b33255441e31b775d20c3c Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 14 Jul 2011 11:56:10 -0400
Subject: [PATCH 115/161] Added some extra error checks in the VCF codec.  Now
 that we've moved this back into the GATK, changed some of the standard
 exceptions to be USerErrors (instead of TribbleExceptions).

---
 .../utils/codecs/vcf/AbstractVCFCodec.java    | 25 ++++++++++---------
 .../sting/utils/exceptions/UserException.java | 10 ++++++++
 2 files changed, 23 insertions(+), 12 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
index 01344a117..710127f7a 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
@@ -7,6 +7,8 @@ import org.broad.tribble.NameAwareCodec;
 import org.broad.tribble.TribbleException;
 import org.broad.tribble.readers.LineReader;
 import org.broad.tribble.util.ParsingUtils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@@ -96,6 +98,9 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
         for ( String str : headerStrings ) {
             if ( !str.startsWith(VCFHeader.METADATA_INDICATOR) ) {
                 String[] strings = str.substring(1).split(VCFConstants.FIELD_SEPARATOR);
+                if ( strings.length < VCFHeader.HEADER_FIELDS.values().length )
+                    throw new TribbleException.InvalidHeader("there are not enough columns present in the header line: " + str);
+
                 int arrayIndex = 0;
                 for (VCFHeader.HEADER_FIELDS field : VCFHeader.HEADER_FIELDS.values()) {
                     try {
@@ -159,12 +164,11 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
     }
 
     private Feature reallyDecode(String line) {
-        try {
             // the same line reader is not used for parsing the header and parsing lines, if we see a #, we've seen a header line
             if (line.startsWith(VCFHeader.HEADER_INDICATOR)) return null;
 
             // our header cannot be null, we need the genotype sample names and counts
-            if (header == null) throw new IllegalStateException("VCF Header cannot be null when decoding a record");
+            if (header == null) throw new ReviewedStingException("VCF Header cannot be null when decoding a record");
 
             if (parts == null)
                 parts = new String[Math.min(header.getColumnCount(), NUM_STANDARD_FIELDS+1)];
@@ -174,17 +178,18 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
             // if we have don't have a header, or we have a header with no genotyping data check that we have eight columns.  Otherwise check that we have nine (normal colummns + genotyping data)
             if (( (header == null || (header != null && !header.hasGenotypingData())) && nParts != NUM_STANDARD_FIELDS) ||
                  (header != null && header.hasGenotypingData() && nParts != (NUM_STANDARD_FIELDS + 1)) )
-                throw new IllegalArgumentException("There aren't enough columns for line " + line + " (we expected " + (header == null ? NUM_STANDARD_FIELDS : NUM_STANDARD_FIELDS + 1) +
-                        " tokens, and saw " + nParts + " )");
+                throw new UserException.MalformedVCF("there aren't enough columns for line " + line + " (we expected " + (header == null ? NUM_STANDARD_FIELDS : NUM_STANDARD_FIELDS + 1) +
+                        " tokens, and saw " + nParts + " )", lineNo);
 
             return parseVCFLine(parts);
-        } catch (TribbleException e) {
-            throw new TribbleException.InvalidDecodeLine(e.getMessage(), line);
-        }
     }
 
     protected void generateException(String message) {
-        throw new TribbleException.InvalidDecodeLine(message, lineNo);
+        throw new UserException.MalformedVCF(message, lineNo);
+    }
+
+    private static void generateException(String message, int lineNo) {
+        throw new UserException.MalformedVCF(message, lineNo);
     }
 
     /**
@@ -472,10 +477,6 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
         return true;
     }
 
-    private static void generateException(String message, int lineNo) {
-        throw new TribbleException.InvalidDecodeLine(message, lineNo);
-    }
-
     private static int computeForwardClipping(List<Allele> unclippedAlleles, String ref) {
         boolean clipping = true;
         // Note that the computation of forward clipping here is meant only to see whether there is a common
diff --git a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
index 0be4bec91..17c4a7df4 100755
--- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
+++ b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
@@ -154,6 +154,16 @@ public class UserException extends ReviewedStingException {
         }
     }
 
+    public static class MalformedVCF extends UserException {
+        public MalformedVCF(String message, String line) {
+            super(String.format("The provided VCF file is malformed at line %s: %s", line, message));
+        }
+
+        public MalformedVCF(String message, int lineNo) {
+            super(String.format("The provided VCF file is malformed at line nmber %d: %s", lineNo, message));
+        }
+    }
+
     public static class ReadMissingReadGroup extends MalformedBAM {
         public ReadMissingReadGroup(SAMRecord read) {
             super(read, String.format("Read %s is either missing the read group or its read group is not defined in the BAM header, both of which are required by the GATK.  Please use http://www.broadinstitute.org/gsa/wiki/index.php/ReplaceReadGroups to fix this problem", read.getReadName()));

From ed6beae1f3769c247b9a4fc80121985baad6443f Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 14 Jul 2011 13:55:35 -0400
Subject: [PATCH 116/161] Adding headers to diffable reading for VCFs

---
 .../gatk/walkers/diffengine/VCFDiffableReader.java   | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
index 06d14366f..5677574bd 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
@@ -26,16 +26,12 @@ package org.broadinstitute.sting.gatk.walkers.diffengine;
 
 import org.broad.tribble.readers.AsciiLineReader;
 import org.broad.tribble.readers.LineReader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.*;
-import java.util.Arrays;
 import java.util.Map;
-import java.util.zip.GZIPInputStream;
 
 
 /**
@@ -58,7 +54,11 @@ public class VCFDiffableReader implements DiffableReader {
             VCFCodec vcfCodec = new VCFCodec();
 
             // must be read as state is stored in reader itself
-            vcfCodec.readHeader(lineReader);
+            VCFHeader header = (VCFHeader)vcfCodec.readHeader(lineReader);
+            for ( VCFHeaderLine headerLine : header.getMetaData() ) {
+                final String key = (headerLine instanceof VCFNamedHeaderLine ? headerLine.getKey() + "." + ((VCFNamedHeaderLine) headerLine).getName() : headerLine.getKey());
+                root.add(key, headerLine.toString());
+            }
 
             String line = lineReader.readLine();
             int count = 0;

From 9540df69986c16112b5fdd57efebf72846d86424 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 14 Jul 2011 14:00:19 -0400
Subject: [PATCH 117/161] Oops, forgot to update unit test

---
 .../sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java
index baa2f0383..a0cb47770 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java
@@ -87,7 +87,7 @@ public class DiffableReaderUnitTest extends BaseTest {
         Assert.assertSame(diff.getParent(), DiffElement.ROOT);
 
         DiffNode node = diff.getValueAsNode();
-        Assert.assertEquals(node.getElements().size(), 9);
+        Assert.assertEquals(node.getElements().size(), 10);
 
         // chr1    2646    rs62635284      G       A       0.15    PASS    AC=2;AF=1.00;AN=2       GT:AD:DP:GL:GQ  1/1:53,75:3:-12.40,-0.90,-0.00:9.03
         DiffNode rec1 = node.getElement("chr1:2646").getValueAsNode();

From 5ffeddd3b1ac5f83d6018dad0a178ae785a4dc39 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Thu, 14 Jul 2011 14:45:16 -0400
Subject: [PATCH 118/161] better to use _ instead of ., as this is a special
 case later.

---
 .../sting/gatk/walkers/diffengine/VCFDiffableReader.java      | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
index 5677574bd..a812babaf 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
@@ -56,7 +56,9 @@ public class VCFDiffableReader implements DiffableReader {
             // must be read as state is stored in reader itself
             VCFHeader header = (VCFHeader)vcfCodec.readHeader(lineReader);
             for ( VCFHeaderLine headerLine : header.getMetaData() ) {
-                final String key = (headerLine instanceof VCFNamedHeaderLine ? headerLine.getKey() + "." + ((VCFNamedHeaderLine) headerLine).getName() : headerLine.getKey());
+                String key = headerLine.getKey();
+                if ( headerLine instanceof VCFNamedHeaderLine )
+                    key += "_" + ((VCFNamedHeaderLine) headerLine).getName();
                 root.add(key, headerLine.toString());
             }
 

From c0bbeb23ba0200d80f940a395ddc019fdb61f093 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Thu, 14 Jul 2011 15:12:28 -0400
Subject: [PATCH 119/161] Now providing more information when the index on the
 fly isn't equal to the one created by reading the file from disk.

---
 .../test/org/broadinstitute/sting/WalkerTest.java   | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/public/java/test/org/broadinstitute/sting/WalkerTest.java b/public/java/test/org/broadinstitute/sting/WalkerTest.java
index dacaf2738..d65f4ec34 100755
--- a/public/java/test/org/broadinstitute/sting/WalkerTest.java
+++ b/public/java/test/org/broadinstitute/sting/WalkerTest.java
@@ -26,7 +26,9 @@
 package org.broadinstitute.sting;
 
 import org.apache.commons.lang.StringUtils;
+import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.Tribble;
+import org.broad.tribble.index.Index;
 import org.broad.tribble.index.IndexFactory;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
 import org.broadinstitute.sting.gatk.CommandLineExecutable;
@@ -64,10 +66,19 @@ public class WalkerTest extends BaseTest {
             }
 
             System.out.println("Verifying on-the-fly index " + indexFile + " for test " + name + " using file " + resultFile);
-            Assert.assertTrue(IndexFactory.onDiskIndexEqualToNewlyCreatedIndex(resultFile, indexFile, new VCFCodec()), "Index on disk from indexing on the fly not equal to the index created after the run completed");
+            Index indexFromOutputFile = IndexFactory.createIndex(resultFile, new VCFCodec());
+            Index dynamicIndex = IndexFactory.loadIndex(indexFile.getAbsolutePath());
+
+            if ( ! indexFromOutputFile.equals(dynamicIndex) ) {
+                Assert.fail(String.format("Index on disk from indexing on the fly not equal to the index created after the run completed.  FileIndex %s vs. on-the-fly %s%n",
+                        indexFromOutputFile.getProperties(),
+                        dynamicIndex.getProperties()));
+            }
         }
     }
 
+
+
     public List<String> assertMatchingMD5s(final String name, List<File> resultFiles, List<String> expectedMD5s) {
         List<String> md5s = new ArrayList<String>();
         for (int i = 0; i < resultFiles.size(); i++) {

From 9f5180ab053d7116b194f2ef09b5f157dbeb4cca Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Thu, 14 Jul 2011 16:42:17 -0400
Subject: [PATCH 120/161] Recalibrates a list of bam files allowing multiple
 bams to be recalibrated out of a single 'mother' queue job.

---
 .../qscripts/RecalibrateBaseQualities.scala   | 39 +++++++++++++------
 1 file changed, 27 insertions(+), 12 deletions(-)

diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
index dc9ae0f4b..88c7f5ff7 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
@@ -3,6 +3,7 @@ package org.broadinstitute.sting.queue.qscripts
 import org.broadinstitute.sting.queue.QScript
 import org.broadinstitute.sting.queue.extensions.gatk._
 import net.sf.samtools.SAMFileReader
+import io.Source._
 
 /**
  * Created by IntelliJ IDEA.
@@ -37,21 +38,35 @@ class RecalibrateBaseQualities extends QScript {
     return samReader.getFileHeader.getSequenceDictionary.getSequences.size()
   }
 
+  // Reads a BAM LIST file and creates a scala list with all the files
+  def createListFromFile(in: File):List[File] = {
+    if (in.toString.endsWith("bam"))
+      return List(in)
+    var l: List[File] = List()
+    for (bam <- fromFile(in).getLines)
+      l :+= new File(bam)
+    return l
+  }
+
   def script = {
 
-    nContigs = getNumberOfContigs(input)
+    val bamList = createListFromFile(input)
+    nContigs = getNumberOfContigs(bamList(0))
 
-    val recalFile1: File = swapExt(input, ".bam", ".recal1.csv")
-    val recalFile2: File = swapExt(input, ".bam", ".recal2.csv")
-    val recalBam: File   = swapExt(input, ".bam", ".recal.bam")
-    val path1: String    = input + "before"
-    val path2: String    = input + "after"
-    
-    add(cov(input, recalFile1),
-        recal(input, recalFile1, recalBam),
-        cov(recalBam, recalFile2),
-        analyzeCovariates(recalFile1, path1),
-        analyzeCovariates(recalFile2, path2))
+    for (bam <- bamList) {
+
+      val recalFile1: File = swapExt(bam, ".bam", ".recal1.csv")
+      val recalFile2: File = swapExt(bam, ".bam", ".recal2.csv")
+      val recalBam: File   = swapExt(bam, ".bam", ".recal.bam")
+      val path1: String    = bam + "before"
+      val path2: String    = bam + "after"
+
+      add(cov(bam, recalFile1),
+          recal(bam, recalFile1, recalBam),
+          cov(recalBam, recalFile2),
+          analyzeCovariates(recalFile1, path1),
+          analyzeCovariates(recalFile2, path2))
+    }
   }
 
   trait CommandLineGATKArgs extends CommandLineGATK {

From 09ffe277ae7d3418f75510cabe65e6c9a8fa8f25 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Thu, 14 Jul 2011 17:09:35 -0400
Subject: [PATCH 121/161] Added a qscripts util package with some utility
 functions commonly shared across queue scripts. Refactored some of my public
 scripts to use it in an effort to make queue scripts more reusable and
 "supportable".

---
 .../qscripts/DataProcessingPipeline.scala     | 38 ++----------
 .../qscripts/RecalibrateBaseQualities.scala   | 20 +-----
 .../sting/queue/qscripts/utils/Utils.scala    | 62 +++++++++++++++++++
 3 files changed, 71 insertions(+), 49 deletions(-)
 create mode 100644 public/scala/qscript/org/broadinstitute/sting/queue/qscripts/utils/Utils.scala

diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
index f9369ee3f..e62b1b926 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
@@ -4,13 +4,13 @@ import org.broadinstitute.sting.queue.extensions.gatk._
 import org.broadinstitute.sting.queue.QScript
 import org.broadinstitute.sting.queue.function.ListWriterFunction
 
-import scala.io.Source._
 import collection.JavaConversions._
 import org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.ConsensusDeterminationModel
 import org.broadinstitute.sting.queue.extensions.picard._
-import net.sf.samtools.{SAMFileReader, SAMReadGroupRecord}
+import net.sf.samtools.{SAMFileReader}
 import net.sf.samtools.SAMFileHeader.SortOrder
 
+import org.broadinstitute.sting.queue.qscripts.utils.Utils
 
 class DataProcessingPipeline extends QScript {
   qscript =>
@@ -103,18 +103,6 @@ class DataProcessingPipeline extends QScript {
                    val ds: String)
   {}
 
-  // Utility function to check if there are multiple samples in a BAM file (currently we can't deal with that)
-  def hasMultipleSamples(readGroups: java.util.List[SAMReadGroupRecord]): Boolean = {
-    var sample: String = ""
-    for (r <- readGroups) {
-      if (sample.isEmpty)
-        sample = r.getSample
-      else if (sample != r.getSample)
-          return true;
-    }
-    return false
-  }
-
   // Utility function to merge all bam files of similar samples. Generates one BAM file per sample.
   // It uses the sample information on the header of the input BAM files.
   //
@@ -135,7 +123,7 @@ class DataProcessingPipeline extends QScript {
 
       // only allow one sample per file. Bam files with multiple samples would require pre-processing of the file
       // with PrintReads to separate the samples. Tell user to do it himself!
-      assert(!hasMultipleSamples(readGroups), "The pipeline requires that only one sample is present in a BAM file. Please separate the samples in " + bam)
+      assert(!Utils.hasMultipleSamples(readGroups), "The pipeline requires that only one sample is present in a BAM file. Please separate the samples in " + bam)
 
       // Fill out the sample table with the readgroups in this file
       for (rg <- readGroups) {
@@ -157,12 +145,6 @@ class DataProcessingPipeline extends QScript {
     return sampleBamFiles.toMap
   }
 
-  // Checks how many contigs are in the dataset. Uses the BAM file header information.
-  def getNumberOfContigs(bamFile: File): Int = {
-    val samReader = new SAMFileReader(new File(bamFile))
-    return samReader.getFileHeader.getSequenceDictionary.getSequences.size()
-  }
-
   // Rebuilds the Read Group string to give BWA
   def addReadGroups(inBam: File, outBam: File, samReader: SAMFileReader) {
     val readGroups = samReader.getFileHeader.getReadGroups
@@ -206,15 +188,7 @@ class DataProcessingPipeline extends QScript {
     return realignedBams
   }
 
-  // Reads a BAM LIST file and creates a scala list with all the files
-  def createListFromFile(in: File):List[File] = {
-    if (in.toString.endsWith("bam"))
-      return List(in)
-    var l: List[File] = List()
-    for (bam <- fromFile(in).getLines)
-      l :+= new File(bam)
-    return l
-  }
+
 
 
 
@@ -226,8 +200,8 @@ class DataProcessingPipeline extends QScript {
   def script = {
 
     // keep a record of the number of contigs in the first bam file in the list
-    val bams = createListFromFile(input)
-    nContigs = getNumberOfContigs(bams(0))
+    val bams = Utils.createListFromFile(input)
+    nContigs = Utils.getNumberOfContigs(bams(0))
 
     val realignedBams = if (useBWApe || useBWAse) {performAlignment(bams)} else {bams}
 
diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
index 88c7f5ff7..b2960f150 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
@@ -4,6 +4,7 @@ import org.broadinstitute.sting.queue.QScript
 import org.broadinstitute.sting.queue.extensions.gatk._
 import net.sf.samtools.SAMFileReader
 import io.Source._
+import org.broadinstitute.sting.queue.qscripts.utils.Utils
 
 /**
  * Created by IntelliJ IDEA.
@@ -33,25 +34,10 @@ class RecalibrateBaseQualities extends QScript {
   val queueLogDir: String = ".qlog/"
   var nContigs: Int = 0
 
-  def getNumberOfContigs(bamFile: File): Int = {
-    val samReader = new SAMFileReader(new File(bamFile))
-    return samReader.getFileHeader.getSequenceDictionary.getSequences.size()
-  }
-
-  // Reads a BAM LIST file and creates a scala list with all the files
-  def createListFromFile(in: File):List[File] = {
-    if (in.toString.endsWith("bam"))
-      return List(in)
-    var l: List[File] = List()
-    for (bam <- fromFile(in).getLines)
-      l :+= new File(bam)
-    return l
-  }
-
   def script = {
 
-    val bamList = createListFromFile(input)
-    nContigs = getNumberOfContigs(bamList(0))
+    val bamList = Utils.createListFromFile(input)
+    nContigs = Utils.getNumberOfContigs(bamList(0))
 
     for (bam <- bamList) {
 
diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/utils/Utils.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/utils/Utils.scala
new file mode 100644
index 000000000..ff94744ee
--- /dev/null
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/utils/Utils.scala
@@ -0,0 +1,62 @@
+package org.broadinstitute.sting.queue.qscripts.utils
+
+import java.io.File
+import io.Source._
+import net.sf.samtools.{SAMReadGroupRecord, SAMFileReader}
+
+import collection.JavaConversions._
+
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: carneiro
+ * Date: 7/14/11
+ * Time: 4:57 PM
+ * To change this template use File | Settings | File Templates.
+ */
+
+object Utils {
+
+  /**
+   * Takes a bam list file and produces a scala list with each file allowing the bam list
+   * to have empty lines and comment lines (lines starting with #).
+   */
+  def createListFromFile(in: File):List[File] = {
+    // If the file provided ends with .bam, it is not a bam list, we treat it as a single file.
+    // and return a list with only this file.
+    if (in.toString.endsWith(".bam"))
+      return List(in)
+
+    var list: List[File] = List()
+    for (bam <- fromFile(in).getLines)
+      if (!bam.startsWith("#") && !bam.isEmpty )
+        list :+= new File(bam.trim())
+    list
+  }
+
+  /**
+   * Returns the number of contigs in the BAM file header.
+   */
+
+  def getNumberOfContigs(bamFile: File): Int = {
+    val samReader = new SAMFileReader(new File(bamFile))
+    samReader.getFileHeader.getSequenceDictionary.getSequences.size()
+  }
+
+  /**
+   * Check if there are multiple samples in a BAM file
+   */
+
+  def hasMultipleSamples(readGroups: java.util.List[SAMReadGroupRecord]): Boolean = {
+    var sample: String = ""
+    for (r <- readGroups) {
+      if (sample.isEmpty)
+        sample = r.getSample
+      else if (sample != r.getSample)
+          return true;
+    }
+    false
+  }
+
+
+}
\ No newline at end of file

From 43c6a8565bfe77e4c50317a3e8858b754d4afcba Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Thu, 14 Jul 2011 17:10:44 -0400
Subject: [PATCH 122/161] looks better now.

---
 .../org/broadinstitute/sting/queue/qscripts/utils/Utils.scala   | 2 --
 1 file changed, 2 deletions(-)

diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/utils/Utils.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/utils/Utils.scala
index ff94744ee..1189b376c 100644
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/utils/Utils.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/utils/Utils.scala
@@ -37,7 +37,6 @@ object Utils {
   /**
    * Returns the number of contigs in the BAM file header.
    */
-
   def getNumberOfContigs(bamFile: File): Int = {
     val samReader = new SAMFileReader(new File(bamFile))
     samReader.getFileHeader.getSequenceDictionary.getSequences.size()
@@ -46,7 +45,6 @@ object Utils {
   /**
    * Check if there are multiple samples in a BAM file
    */
-
   def hasMultipleSamples(readGroups: java.util.List[SAMReadGroupRecord]): Boolean = {
     var sample: String = ""
     for (r <- readGroups) {

From a670d6420ad586b7138326b994822ce1f6682629 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Fri, 15 Jul 2011 14:31:43 -0400
Subject: [PATCH 125/161] Refactoring Qscript utils into queue general utils
 package.

---
 .../sting/queue/qscripts/DataProcessingPipeline.scala         | 4 ++--
 .../sting/queue/qscripts/RecalibrateBaseQualities.scala       | 4 +---
 .../org/broadinstitute/sting/queue/util}/Utils.scala          | 2 +-
 3 files changed, 4 insertions(+), 6 deletions(-)
 rename public/scala/{qscript/org/broadinstitute/sting/queue/qscripts/utils => src/org/broadinstitute/sting/queue/util}/Utils.scala (96%)

diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
index e62b1b926..40ac43a81 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
@@ -7,10 +7,10 @@ import org.broadinstitute.sting.queue.function.ListWriterFunction
 import collection.JavaConversions._
 import org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.ConsensusDeterminationModel
 import org.broadinstitute.sting.queue.extensions.picard._
-import net.sf.samtools.{SAMFileReader}
+import net.sf.samtools.SAMFileReader
 import net.sf.samtools.SAMFileHeader.SortOrder
 
-import org.broadinstitute.sting.queue.qscripts.utils.Utils
+import org.broadinstitute.sting.queue.util.Utils
 
 class DataProcessingPipeline extends QScript {
   qscript =>
diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
index b2960f150..8ba880291 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
@@ -2,9 +2,7 @@ package org.broadinstitute.sting.queue.qscripts
 
 import org.broadinstitute.sting.queue.QScript
 import org.broadinstitute.sting.queue.extensions.gatk._
-import net.sf.samtools.SAMFileReader
-import io.Source._
-import org.broadinstitute.sting.queue.qscripts.utils.Utils
+import org.broadinstitute.sting.queue.util.Utils
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/utils/Utils.scala b/public/scala/src/org/broadinstitute/sting/queue/util/Utils.scala
similarity index 96%
rename from public/scala/qscript/org/broadinstitute/sting/queue/qscripts/utils/Utils.scala
rename to public/scala/src/org/broadinstitute/sting/queue/util/Utils.scala
index 1189b376c..5b80503a3 100644
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/utils/Utils.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/util/Utils.scala
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.queue.qscripts.utils
+package org.broadinstitute.sting.queue.util
 
 import java.io.File
 import io.Source._

From 7b7d40d5d97461f3b4cf71bf7b6efc0695a97f91 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Fri, 15 Jul 2011 14:34:50 -0400
Subject: [PATCH 126/161] A better name for the qscript utilities. Throw here
 every method you find yourself repeatedly implementing in your qscripts!
 Refactoring appropriately.

---
 .../sting/queue/qscripts/DataProcessingPipeline.scala     | 8 ++++----
 .../sting/queue/qscripts/RecalibrateBaseQualities.scala   | 6 +++---
 .../sting/queue/util/{Utils.scala => QScriptUtils.scala}  | 2 +-
 3 files changed, 8 insertions(+), 8 deletions(-)
 rename public/scala/src/org/broadinstitute/sting/queue/util/{Utils.scala => QScriptUtils.scala} (98%)

diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
index 40ac43a81..050604b4e 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
@@ -10,7 +10,7 @@ import org.broadinstitute.sting.queue.extensions.picard._
 import net.sf.samtools.SAMFileReader
 import net.sf.samtools.SAMFileHeader.SortOrder
 
-import org.broadinstitute.sting.queue.util.Utils
+import org.broadinstitute.sting.queue.util.QScriptUtils
 
 class DataProcessingPipeline extends QScript {
   qscript =>
@@ -123,7 +123,7 @@ class DataProcessingPipeline extends QScript {
 
       // only allow one sample per file. Bam files with multiple samples would require pre-processing of the file
       // with PrintReads to separate the samples. Tell user to do it himself!
-      assert(!Utils.hasMultipleSamples(readGroups), "The pipeline requires that only one sample is present in a BAM file. Please separate the samples in " + bam)
+      assert(!QScriptUtils.hasMultipleSamples(readGroups), "The pipeline requires that only one sample is present in a BAM file. Please separate the samples in " + bam)
 
       // Fill out the sample table with the readgroups in this file
       for (rg <- readGroups) {
@@ -200,8 +200,8 @@ class DataProcessingPipeline extends QScript {
   def script = {
 
     // keep a record of the number of contigs in the first bam file in the list
-    val bams = Utils.createListFromFile(input)
-    nContigs = Utils.getNumberOfContigs(bams(0))
+    val bams = QScriptUtils.createListFromFile(input)
+    nContigs = QScriptUtils.getNumberOfContigs(bams(0))
 
     val realignedBams = if (useBWApe || useBWAse) {performAlignment(bams)} else {bams}
 
diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
index 8ba880291..56ca36925 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
@@ -2,7 +2,7 @@ package org.broadinstitute.sting.queue.qscripts
 
 import org.broadinstitute.sting.queue.QScript
 import org.broadinstitute.sting.queue.extensions.gatk._
-import org.broadinstitute.sting.queue.util.Utils
+import org.broadinstitute.sting.queue.util.QScriptUtils
 
 /**
  * Created by IntelliJ IDEA.
@@ -34,8 +34,8 @@ class RecalibrateBaseQualities extends QScript {
 
   def script = {
 
-    val bamList = Utils.createListFromFile(input)
-    nContigs = Utils.getNumberOfContigs(bamList(0))
+    val bamList = QScriptUtils.createListFromFile(input)
+    nContigs = QScriptUtils.getNumberOfContigs(bamList(0))
 
     for (bam <- bamList) {
 
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/Utils.scala b/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala
similarity index 98%
rename from public/scala/src/org/broadinstitute/sting/queue/util/Utils.scala
rename to public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala
index 5b80503a3..e2f1f1608 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/util/Utils.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala
@@ -15,7 +15,7 @@ import collection.JavaConversions._
  * To change this template use File | Settings | File Templates.
  */
 
-object Utils {
+object QScriptUtils {
 
   /**
    * Takes a bam list file and produces a scala list with each file allowing the bam list

From 224d373997e0f4775207654ad4e246caad6c9aac Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Fri, 15 Jul 2011 15:19:10 -0400
Subject: [PATCH 130/161] No need to double overload the file constructor

---
 .../src/org/broadinstitute/sting/queue/util/QScriptUtils.scala  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala b/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala
index e2f1f1608..9fb4fa30d 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala
@@ -38,7 +38,7 @@ object QScriptUtils {
    * Returns the number of contigs in the BAM file header.
    */
   def getNumberOfContigs(bamFile: File): Int = {
-    val samReader = new SAMFileReader(new File(bamFile))
+    val samReader = new SAMFileReader(bamFile)
     samReader.getFileHeader.getSequenceDictionary.getSequences.size()
   }
 

From 72f4cf9c0ecbd8608d207ee59a5e5bd36a395be8 Mon Sep 17 00:00:00 2001
From: Menachem Fromer <fromer@broadinstitute.org>
Date: Fri, 15 Jul 2011 17:44:31 -0400
Subject: [PATCH 141/161] Walker to perform deterministic annotation of phasing
 by transmission (to be compatible with RBP's definition of consecutive
 pairwise phasing)

---
 .../sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
index 1d9616aac..fbe6e5b5a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
@@ -242,7 +242,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
         return new PhasingStatsAndOutput(phaseStats, completedList);
     }
 
-    private static final Set<String> KEYS_TO_KEEP_IN_REDUCED_VCF = new HashSet<String>(Arrays.asList("PQ"));
+    private static final Set<String> KEYS_TO_KEEP_IN_REDUCED_VCF = new HashSet<String>(Arrays.asList(PQ_KEY));
 
     private VariantContext reduceVCToSamples(VariantContext vc, List<String> samplesToPhase) {
 //        for ( String sample : samplesToPhase )

From 1e4798d5d0303df6b9cd42e9f7f2d30956004668 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Fri, 15 Jul 2011 19:34:14 -0400
Subject: [PATCH 144/161] Added targets to build.xml to re-run only tests that
 have failed (integration, unit, performance or pipeline tests).

This is very useful and easy. After running any test (for example ant integrationtest) and seeing failures, you can rerun ONLY THE TESTS THAT FAILED by using one of the following commands:

ant failed-integration
ant failed-pipeline
ant failed-test
ant failed-performance

obviously matching whatever tests you were running and got failures on.

This should run only the failed tests, and you can keep using this command until you have fixed everything.

(Thanks to David Roazen for major help with ANT)
---
 build.xml | 60 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 60 insertions(+)

diff --git a/build.xml b/build.xml
index 986d89213..91eb1f8e9 100644
--- a/build.xml
+++ b/build.xml
@@ -785,6 +785,50 @@
         </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">
@@ -819,6 +863,22 @@
         <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                             ********* -->
     <!-- ***************************************************************************** -->

From fd1df31ef0ab60ec735ff5692132441224a02659 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Fri, 15 Jul 2011 19:39:42 -0400
Subject: [PATCH 145/161] changing the output directory names for Analyze
 Covariates

---
 .../sting/queue/qscripts/RecalibrateBaseQualities.scala     | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
index 56ca36925..fca420816 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
@@ -42,8 +42,8 @@ class RecalibrateBaseQualities extends QScript {
       val recalFile1: File = swapExt(bam, ".bam", ".recal1.csv")
       val recalFile2: File = swapExt(bam, ".bam", ".recal2.csv")
       val recalBam: File   = swapExt(bam, ".bam", ".recal.bam")
-      val path1: String    = bam + "before"
-      val path2: String    = bam + "after"
+      val path1: String    = bam + ".before"
+      val path2: String    = bam + ".after"
 
       add(cov(bam, recalFile1),
           recal(bam, recalFile1, recalBam),
@@ -83,7 +83,7 @@ class RecalibrateBaseQualities extends QScript {
   case class analyzeCovariates (inRecalFile: File, outPath: String) extends AnalyzeCovariates {
     this.resources = R
     this.recal_file = inRecalFile
-    this.output_dir = outPath.toString
+    this.output_dir = outPath
     this.analysisName = queueLogDir + inRecalFile + ".analyze_covariates"
     this.jobName = queueLogDir + inRecalFile + ".analyze_covariates"
   }

From ed55182a4c5553eb517569567e5193a12eb7e68a Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Sat, 16 Jul 2011 00:09:00 -0400
Subject: [PATCH 146/161] Removing Broad specific paths from parameters and
 making them required. This should make it unambiguous for people inside and
 outside the Broad to use the DataProcessingPipeline (as per request in the
 GetSatisfaction)

---
 .../qscripts/DataProcessingPipeline.scala     | 20 +++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
index 050604b4e..4d4499990 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
@@ -3,10 +3,11 @@ package org.broadinstitute.sting.queue.qscripts
 import org.broadinstitute.sting.queue.extensions.gatk._
 import org.broadinstitute.sting.queue.QScript
 import org.broadinstitute.sting.queue.function.ListWriterFunction
+import org.broadinstitute.sting.queue.extensions.picard._
+import org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.ConsensusDeterminationModel
+import org.broadinstitute.sting.utils.baq.BAQ.CalculationMode
 
 import collection.JavaConversions._
-import org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.ConsensusDeterminationModel
-import org.broadinstitute.sting.queue.extensions.picard._
 import net.sf.samtools.SAMFileReader
 import net.sf.samtools.SAMFileHeader.SortOrder
 
@@ -29,6 +30,11 @@ class DataProcessingPipeline extends QScript {
   @Input(doc="Reference fasta file", fullName="reference", shortName="R", required=true)
   var reference: File = _
 
+  @Input(doc="dbsnp ROD to use (must be in VCF format)", fullName="dbsnp", shortName="D", required=true)
+  var dbSNP: File = _
+
+  @Input(doc="extra VCF files to use as reference indels for Indel Realignment", fullName="extra_indels", shortName="indels", required=true)
+  var indels: File = _
 
 
   /****************************************************************************
@@ -42,12 +48,6 @@ class DataProcessingPipeline extends QScript {
   @Input(doc="The path to the binary of bwa (usually BAM files have already been mapped - but if you want to remap this is the option)", fullName="path_to_bwa", shortName="bwa", required=false)
   var bwaPath: File = _
 
-  @Input(doc="dbsnp ROD to use (must be in VCF format)", fullName="dbsnp", shortName="D", required=false)
-  var dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
-
-  @Input(doc="extra VCF files to use as reference indels for Indel Realignment", fullName="extra_indels", shortName="indels", required=false)
-  var indels: File = new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/AFR+EUR+ASN+1KG.dindel_august_release_merged_pilot1.20110126.sites.vcf")
-
   @Input(doc="the project name determines the final output (BAM file) base name. Example NA12878 yields NA12878.processed.bam", fullName="project", shortName="p", required=false)
   var projectName: String = "project"
 
@@ -295,7 +295,7 @@ class DataProcessingPipeline extends QScript {
     this.targetIntervals = tIntervals
     this.out = outBam
     this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
-    this.rodBind :+= RodBind("indels", "VCF", qscript.indels)
+    this.rodBind :+= RodBind("indels", "VCF", indels)
     this.consensusDeterminationModel =  consensusDeterminationModel
     this.compress = 0
     this.scatterCount = nContigs
@@ -318,7 +318,7 @@ class DataProcessingPipeline extends QScript {
   case class recal (inBam: File, inRecalFile: File, outBam: File) extends TableRecalibration with CommandLineGATKArgs {
     this.input_file :+= inBam
     this.recal_file = inRecalFile
-    this.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY
+    this.baq = CalculationMode.CALCULATE_AS_NECESSARY
     this.out = outBam
     if (!qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString)
     else if (qscript.intervals != null) this.intervals :+= qscript.intervals

From dd92a14b40b6270cf093b38830aab3987b8d0d25 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Sat, 16 Jul 2011 00:23:35 -0400
Subject: [PATCH 147/161] Made extra indel VCF optional but DBSNP mandatory.

---
 .../queue/qscripts/DataProcessingPipeline.scala    | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
index 4d4499990..d55b86d69 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
@@ -33,10 +33,6 @@ class DataProcessingPipeline extends QScript {
   @Input(doc="dbsnp ROD to use (must be in VCF format)", fullName="dbsnp", shortName="D", required=true)
   var dbSNP: File = _
 
-  @Input(doc="extra VCF files to use as reference indels for Indel Realignment", fullName="extra_indels", shortName="indels", required=true)
-  var indels: File = _
-
-
   /****************************************************************************
   * Optional Parameters
   ****************************************************************************/
@@ -45,6 +41,10 @@ class DataProcessingPipeline extends QScript {
 //  @Input(doc="path to Picard's SortSam.jar (if re-aligning a previously processed BAM file)", fullName="path_to_sort_jar", shortName="sort", required=false)
 //  var sortSamJar: File = _
 //
+
+  @Input(doc="extra VCF files to use as reference indels for Indel Realignment", fullName="extra_indels", shortName="indels", required=false)
+  var indels: File = _
+
   @Input(doc="The path to the binary of bwa (usually BAM files have already been mapped - but if you want to remap this is the option)", fullName="path_to_bwa", shortName="bwa", required=false)
   var bwaPath: File = _
 
@@ -284,7 +284,8 @@ class DataProcessingPipeline extends QScript {
     this.out = outIntervals
     this.mismatchFraction = 0.0
     this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
-    this.rodBind :+= RodBind("indels", "VCF", indels)
+    if (!indels.isEmpty)
+      this.rodBind :+= RodBind("indels", "VCF", indels)
     this.scatterCount = nContigs
     this.analysisName = queueLogDir + outIntervals + ".target"
     this.jobName = queueLogDir + outIntervals + ".target"
@@ -295,7 +296,8 @@ class DataProcessingPipeline extends QScript {
     this.targetIntervals = tIntervals
     this.out = outBam
     this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
-    this.rodBind :+= RodBind("indels", "VCF", indels)
+    if (!indels.isEmpty)
+      this.rodBind :+= RodBind("indels", "VCF", indels)
     this.consensusDeterminationModel =  consensusDeterminationModel
     this.compress = 0
     this.scatterCount = nContigs

From 5e7bc862a34d7366c168209261ea5aedb812c790 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Sat, 16 Jul 2011 08:51:21 -0400
Subject: [PATCH 148/161] Rev tribble to include new equal() method that prints
 out details of why two indices are not the same.

---
 .../{tribble-3.jar => tribble-4.jar}          | Bin 258609 -> 286423 bytes
 .../{tribble-3.xml => tribble-4.xml}          |   2 +-
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename settings/repository/org.broad/{tribble-3.jar => tribble-4.jar} (69%)
 rename settings/repository/org.broad/{tribble-3.xml => tribble-4.xml} (58%)

diff --git a/settings/repository/org.broad/tribble-3.jar b/settings/repository/org.broad/tribble-4.jar
similarity index 69%
rename from settings/repository/org.broad/tribble-3.jar
rename to settings/repository/org.broad/tribble-4.jar
index f0ab44a05fb969693b20757be8d29b18f3b611a6..1f82f3cc05b8f02f117506269a8b96110cff591a 100644
GIT binary patch
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diff --git a/settings/repository/org.broad/tribble-3.xml b/settings/repository/org.broad/tribble-4.xml
similarity index 58%
rename from settings/repository/org.broad/tribble-3.xml
rename to settings/repository/org.broad/tribble-4.xml
index c35358331..07235efb0 100644
--- a/settings/repository/org.broad/tribble-3.xml
+++ b/settings/repository/org.broad/tribble-4.xml
@@ -1,4 +1,4 @@
 <ivy-module version="1.0">
-    <info organisation="org.broad" module="tribble" revision="3" 
+    <info organisation="org.broad" module="tribble" revision="4" 
           status="integration" publication="" />
 </ivy-module>

From eacf205f4079e55ed03dd248cbb8c1a41491c01e Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Sat, 16 Jul 2011 09:22:34 -0400
Subject: [PATCH 150/161] Tests needed to be updated to reflect the code reorg
 of tribble.

---
 .../org/broadinstitute/sting/WalkerTest.java  | 21 +++++++++++--------
 .../codecs/vcf/IndexFactoryUnitTest.java      |  3 ++-
 2 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/public/java/test/org/broadinstitute/sting/WalkerTest.java b/public/java/test/org/broadinstitute/sting/WalkerTest.java
index d65f4ec34..a39fa37fe 100755
--- a/public/java/test/org/broadinstitute/sting/WalkerTest.java
+++ b/public/java/test/org/broadinstitute/sting/WalkerTest.java
@@ -65,19 +65,22 @@ public class WalkerTest extends BaseTest {
                 throw new StingException("Found an index created for file " + resultFile + " but we can only validate VCF files.  Extend this code!");
             }
 
-            System.out.println("Verifying on-the-fly index " + indexFile + " for test " + name + " using file " + resultFile);
-            Index indexFromOutputFile = IndexFactory.createIndex(resultFile, new VCFCodec());
-            Index dynamicIndex = IndexFactory.loadIndex(indexFile.getAbsolutePath());
-
-            if ( ! indexFromOutputFile.equals(dynamicIndex) ) {
-                Assert.fail(String.format("Index on disk from indexing on the fly not equal to the index created after the run completed.  FileIndex %s vs. on-the-fly %s%n",
-                        indexFromOutputFile.getProperties(),
-                        dynamicIndex.getProperties()));
-            }
+            assertOnDiskIndexEqualToNewlyCreatedIndex(indexFile, name, resultFile);
         }
     }
 
 
+    public static void assertOnDiskIndexEqualToNewlyCreatedIndex(final File indexFile, final String name, final File resultFile) {
+        System.out.println("Verifying on-the-fly index " + indexFile + " for test " + name + " using file " + resultFile);
+        Index indexFromOutputFile = IndexFactory.createIndex(resultFile, new VCFCodec());
+        Index dynamicIndex = IndexFactory.loadIndex(indexFile.getAbsolutePath());
+
+        if ( ! indexFromOutputFile.equals(dynamicIndex) ) {
+            Assert.fail(String.format("Index on disk from indexing on the fly not equal to the index created after the run completed.  FileIndex %s vs. on-the-fly %s%n",
+                    indexFromOutputFile.getProperties(),
+                    dynamicIndex.getProperties()));
+        }
+    }
 
     public List<String> assertMatchingMD5s(final String name, List<File> resultFiles, List<String> expectedMD5s) {
         List<String> md5s = new ArrayList<String>();
diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java
index 2f6b589f4..68a2ecf8d 100755
--- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java
@@ -4,6 +4,7 @@ import org.broad.tribble.Tribble;
 import org.broad.tribble.index.*;
 import org.broad.tribble.iterators.CloseableTribbleIterator;
 import org.broad.tribble.source.BasicFeatureSource;
+import org.broadinstitute.sting.WalkerTest;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.testng.Assert;
 import org.testng.annotations.Test;
@@ -75,7 +76,7 @@ public class IndexFactoryUnitTest {
 
             // test that the input index is the same as the one created from the identical input file
             // test that the dynamic index is the same as the output index, which is equal to the input index
-            Assert.assertTrue(IndexFactory.onDiskIndexEqualToNewlyCreatedIndex(outputFile, outputFileIndex, new VCFCodec()));
+            WalkerTest.assertOnDiskIndexEqualToNewlyCreatedIndex(outputFileIndex, "unittest", outputFile);
         }
     }
 }

From 07b875c7796972eff2c56c662f198821a5c4e659 Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Sat, 16 Jul 2011 09:57:46 -0400
Subject: [PATCH 151/161] Renaming the updated tribble jar file to match the
 svn revision number.

---
 .../org.broad/{tribble-4.jar => tribble-14.jar}     | Bin
 .../org.broad/{tribble-4.xml => tribble-14.xml}     |   2 +-
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename settings/repository/org.broad/{tribble-4.jar => tribble-14.jar} (100%)
 rename settings/repository/org.broad/{tribble-4.xml => tribble-14.xml} (57%)

diff --git a/settings/repository/org.broad/tribble-4.jar b/settings/repository/org.broad/tribble-14.jar
similarity index 100%
rename from settings/repository/org.broad/tribble-4.jar
rename to settings/repository/org.broad/tribble-14.jar
diff --git a/settings/repository/org.broad/tribble-4.xml b/settings/repository/org.broad/tribble-14.xml
similarity index 57%
rename from settings/repository/org.broad/tribble-4.xml
rename to settings/repository/org.broad/tribble-14.xml
index 07235efb0..f2116324a 100644
--- a/settings/repository/org.broad/tribble-4.xml
+++ b/settings/repository/org.broad/tribble-14.xml
@@ -1,4 +1,4 @@
 <ivy-module version="1.0">
-    <info organisation="org.broad" module="tribble" revision="4" 
+    <info organisation="org.broad" module="tribble" revision="14" 
           status="integration" publication="" />
 </ivy-module>

From 2b55d5b7c0dfca0abd09ab810206d5a437d598ec Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Sat, 16 Jul 2011 16:45:55 -0400
Subject: [PATCH 152/161] Test tribble library where equals() ignores time
 stamps.

---
 settings/repository/org.broad/tribble-14.jar | Bin 286423 -> 286358 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/settings/repository/org.broad/tribble-14.jar b/settings/repository/org.broad/tribble-14.jar
index 1f82f3cc05b8f02f117506269a8b96110cff591a..a0313df326217a5b1820cd7e7d6c029c8129e326 100644
GIT binary patch
delta 6171
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From 92a1c0c278a1d437608bd1b918f702323556e5e1 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Sun, 17 Jul 2011 10:14:23 -0400
Subject: [PATCH 153/161] Moved the varianteval/tags/DataPoint.java and
 varianteval/tags/Analysis.java to varianteval/utils.  This allows rsync to
 see these files with the -C option, as tags is some kind of reserved CVS
 keyword.

---
 .../gatk/walkers/varianteval/VariantEvalWalker.java    |  5 ++---
 .../walkers/varianteval/evaluators/CompOverlap.java    |  4 ++--
 .../walkers/varianteval/evaluators/CountVariants.java  |  4 ++--
 .../varianteval/evaluators/GenotypeConcordance.java    |  4 ++--
 .../evaluators/GenotypePhasingEvaluator.java           |  7 +++----
 .../varianteval/evaluators/IndelLengthHistogram.java   |  4 ++--
 .../varianteval/evaluators/IndelMetricsByAC.java       |  4 ++--
 .../varianteval/evaluators/IndelStatistics.java        |  4 ++--
 .../evaluators/MendelianViolationEvaluator.java        | 10 ++--------
 .../varianteval/evaluators/PrintMissingComp.java       |  4 ++--
 .../varianteval/evaluators/SimpleMetricsByAC.java      |  7 +++----
 .../varianteval/evaluators/ThetaVariantEvaluator.java  |  4 ++--
 .../varianteval/evaluators/TiTvVariantEvaluator.java   |  4 ++--
 .../varianteval/evaluators/ValidationReport.java       |  5 ++---
 .../varianteval/evaluators/VariantQualityScore.java    |  4 ++--
 .../walkers/varianteval/{tags => util}/Analysis.java   |  2 +-
 .../varianteval/util/AnalysisModuleScanner.java        |  2 --
 .../walkers/varianteval/{tags => util}/DataPoint.java  |  2 +-
 .../walkers/varianteval/util/VariantEvalUtils.java     |  3 ---
 19 files changed, 34 insertions(+), 49 deletions(-)
 rename public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/{tags => util}/Analysis.java (80%)
 rename public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/{tags => util}/DataPoint.java (77%)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
index 15d808ebe..c9c5e09a8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
@@ -20,7 +20,7 @@ import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.gatk.walkers.Window;
 import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.*;
 import org.broadinstitute.sting.gatk.walkers.variantrecalibration.Tranche;
 import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator;
@@ -30,10 +30,9 @@ import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
-import net.sf.picard.reference.FastaSequenceFile;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import net.sf.picard.reference.ReferenceSequence;
+
 import java.io.FileNotFoundException;
 
 import java.io.File;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
index 76db330ed..85373baa8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
@@ -1,12 +1,12 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 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.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
 
 /**
  * The Broad Institute
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
index c4277adc9..befb2ff13 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
@@ -1,12 +1,12 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 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.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 @Analysis(description = "Counts different classes of variants in the sample")
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
index 4b56cf130..58803c9d0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
@@ -1,14 +1,14 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
 import org.apache.log4j.Logger;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 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.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java
index 3d14dd0e5..407b71893 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java
@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
 import org.apache.log4j.Logger;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.*;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -9,10 +10,8 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.phasing.AllelePair;
 import org.broadinstitute.sting.gatk.walkers.phasing.ReadBackedPhasingWalker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.NewEvaluationContext;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.MathUtils;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
index 5daf33a9f..f7f9fce0c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
@@ -1,11 +1,11 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 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.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java
index eca6c5193..dd4bb492e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java
@@ -1,12 +1,12 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 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.varianteval.VariantEvalWalker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java
index 48b06d532..1bd420e0a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java
@@ -1,13 +1,13 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 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.varianteval.VariantEvalWalker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
 import org.broadinstitute.sting.utils.IndelUtils;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
index 85e0b5889..16ec74433 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
@@ -1,22 +1,16 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 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.varianteval.VariantEvalWalker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
 import org.broadinstitute.sting.utils.MendelianViolation;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.Arrays;
-import java.util.List;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
 /**
  * Mendelian violation detection and counting
  * <p/>
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java
index 7d54d0df8..e83914ef8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java
@@ -24,12 +24,12 @@
 
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 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.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
 
 @Analysis(name = "PrintMissingComp", description = "the overlap between eval and comp sites")
 public class PrintMissingComp extends VariantEvaluator {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java
index deed05508..395309975 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java
@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.*;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -8,11 +9,9 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.Degeneracy;
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.Sample;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.StateKey;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
 
 import java.util.ArrayList;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java
index 89c67cfe9..f9cda5e0b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java
@@ -1,13 +1,13 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 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.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
 
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.ConcurrentMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java
index 8811dc001..deeafd851 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java
@@ -1,12 +1,12 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
 import org.broadinstitute.sting.utils.BaseUtils;
 
 @Analysis(description = "Ti/Tv Variant Evaluator")
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java
index 405f35635..756427581 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java
@@ -1,14 +1,13 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.*;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java
index 4af14810b..29a61e27a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java
@@ -25,14 +25,14 @@
 
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
 import org.broadinstitute.sting.utils.collections.Pair;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/Analysis.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java
similarity index 80%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/Analysis.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java
index 129d5a95d..2b37ce210 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/Analysis.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.walkers.varianteval.tags;
+package org.broadinstitute.sting.gatk.walkers.varianteval.util;
 
 import java.lang.annotation.Retention;
 import java.lang.annotation.RetentionPolicy;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java
index c8d917040..db44e9e28 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java
@@ -23,8 +23,6 @@
 
 package org.broadinstitute.sting.gatk.walkers.varianteval.util;
 
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.lang.annotation.Annotation;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/DataPoint.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java
similarity index 77%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/DataPoint.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java
index 3ba448049..396843252 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/DataPoint.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.walkers.varianteval.tags;
+package org.broadinstitute.sting.gatk.walkers.varianteval.util;
 
 import java.lang.annotation.Retention;
 import java.lang.annotation.RetentionPolicy;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
index b8e45e462..eabd2e588 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
@@ -7,15 +7,12 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.report.GATKReport;
 import org.broadinstitute.sting.gatk.report.GATKReportTable;
-import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.StandardEval;
 import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.RequiredStratification;
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.StandardStratification;
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;

From a5bfcb1ed9f4ee0f5a94a744bd9e31bbd8d254a2 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Sun, 17 Jul 2011 10:25:34 -0400
Subject: [PATCH 154/161] V15 is broken.  Going up to v16 in a second.

---
 .../{tribble-14.jar => tribble-15.jar}        | Bin 286358 -> 286159 bytes
 .../{tribble-14.xml => tribble-15.xml}        |   2 +-
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename settings/repository/org.broad/{tribble-14.jar => tribble-15.jar} (89%)
 rename settings/repository/org.broad/{tribble-14.xml => tribble-15.xml} (59%)

diff --git a/settings/repository/org.broad/tribble-14.jar b/settings/repository/org.broad/tribble-15.jar
similarity index 89%
rename from settings/repository/org.broad/tribble-14.jar
rename to settings/repository/org.broad/tribble-15.jar
index a0313df326217a5b1820cd7e7d6c029c8129e326..4e89047f49d774453a2ae61d036a21a7d4270d09 100644
GIT binary patch
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diff --git a/settings/repository/org.broad/tribble-14.xml b/settings/repository/org.broad/tribble-15.xml
similarity index 59%
rename from settings/repository/org.broad/tribble-14.xml
rename to settings/repository/org.broad/tribble-15.xml
index f2116324a..e23eec339 100644
--- a/settings/repository/org.broad/tribble-14.xml
+++ b/settings/repository/org.broad/tribble-15.xml
@@ -1,4 +1,4 @@
 <ivy-module version="1.0">
-    <info organisation="org.broad" module="tribble" revision="14" 
+    <info organisation="org.broad" module="tribble" revision="15" 
           status="integration" publication="" />
 </ivy-module>

From 1af76736b9dc41da345df90648ec5d74ade03f70 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Sun, 17 Jul 2011 11:41:34 -0400
Subject: [PATCH 155/161] Guarantees that the list of files will always be in
 the same order.

---
 .../src/org/broadinstitute/sting/queue/util/QScriptUtils.scala  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala b/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala
index 9fb4fa30d..99aaa9474 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala
@@ -31,7 +31,7 @@ object QScriptUtils {
     for (bam <- fromFile(in).getLines)
       if (!bam.startsWith("#") && !bam.isEmpty )
         list :+= new File(bam.trim())
-    list
+    list.sortWith(_.compareTo(_) < 0)
   }
 
   /**

From 4db2b13e9ebd54f832d05f885d7ec8946118fb70 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Sun, 17 Jul 2011 13:05:04 -0400
Subject: [PATCH 156/161] Rev tribble. Just added more documentation for
 diffEngine and pointer to new wiki:

http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine
---
 .../gatk/walkers/diffengine/DiffEngine.java    |   2 +-
 .../walkers/diffengine/DiffableReader.java     |  15 +++++++++++++++
 .../org/broadinstitute/sting/WalkerTest.java   |   2 +-
 settings/repository/org.broad/tribble-15.jar   | Bin 286159 -> 0 bytes
 .../{tribble-15.xml => tribble-16.xml}         |   0
 5 files changed, 17 insertions(+), 2 deletions(-)
 delete mode 100644 settings/repository/org.broad/tribble-15.jar
 rename settings/repository/org.broad/{tribble-15.xml => tribble-16.xml} (100%)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
index 6d85df71d..2f87a900a 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
@@ -209,7 +209,7 @@ public class DiffEngine {
     protected void printSummaryReport(List<Difference> sortedSummaries, SummaryReportParams params ) {
         GATKReport report = new GATKReport();
         final String tableName = "diffences";
-        report.addTable(tableName, "Summarized differences between the master and test files.\nSee http://www.broadinstitute.org/gsa/wiki/index.php/DiffObjectsWalker_and_SummarizedDifferences for more information");
+        report.addTable(tableName, "Summarized differences between the master and test files.\nSee http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine for more information");
         GATKReportTable table = report.getTable(tableName);
         table.addPrimaryKey("Difference", true);
         table.addColumn("NumberOfOccurrences", 0);
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java
index af5771c55..a117206f1 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java
@@ -39,12 +39,27 @@ import java.io.File;
  */
 public interface DiffableReader {
     @Ensures("result != null")
+    /**
+     * Return the name of this DiffableReader type.  For example, the VCF reader returns 'VCF' and the
+     * bam reader 'BAM'
+     */
     public String getName();
 
     @Ensures("result != null")
     @Requires("file != null")
+    /**
+     * Read up to maxElementsToRead DiffElements from file, and return them.
+     */
     public DiffElement readFromFile(File file, int maxElementsToRead);
 
+    /**
+     * Return true if the file can be read into DiffElement objects with this reader. This should
+     * be uniquely true/false for all readers, as the system will use the first reader that can read the
+     * file.  This routine should never throw an exception.  The VCF reader, for example, looks at the
+     * first line of the file for the ##format=VCF4.1 header, and the BAM reader for the BAM_MAGIC value
+     * @param file
+     * @return
+     */
     @Requires("file != null")
     public boolean canRead(File file);
 }
diff --git a/public/java/test/org/broadinstitute/sting/WalkerTest.java b/public/java/test/org/broadinstitute/sting/WalkerTest.java
index a39fa37fe..22635dfa3 100755
--- a/public/java/test/org/broadinstitute/sting/WalkerTest.java
+++ b/public/java/test/org/broadinstitute/sting/WalkerTest.java
@@ -75,7 +75,7 @@ public class WalkerTest extends BaseTest {
         Index indexFromOutputFile = IndexFactory.createIndex(resultFile, new VCFCodec());
         Index dynamicIndex = IndexFactory.loadIndex(indexFile.getAbsolutePath());
 
-        if ( ! indexFromOutputFile.equals(dynamicIndex) ) {
+        if ( ! indexFromOutputFile.equalsIgnoreTimestamp(dynamicIndex) ) {
             Assert.fail(String.format("Index on disk from indexing on the fly not equal to the index created after the run completed.  FileIndex %s vs. on-the-fly %s%n",
                     indexFromOutputFile.getProperties(),
                     dynamicIndex.getProperties()));
diff --git a/settings/repository/org.broad/tribble-15.jar b/settings/repository/org.broad/tribble-15.jar
deleted file mode 100644
index 4e89047f49d774453a2ae61d036a21a7d4270d09..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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diff --git a/settings/repository/org.broad/tribble-15.xml b/settings/repository/org.broad/tribble-16.xml
similarity index 100%
rename from settings/repository/org.broad/tribble-15.xml
rename to settings/repository/org.broad/tribble-16.xml

From 35ec82a467b3e739c98bc700c4765d9f0a0be17a Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Sun, 17 Jul 2011 13:08:08 -0400
Subject: [PATCH 157/161] Oops, need this

---
 settings/repository/org.broad/tribble-16.jar | Bin 0 -> 286215 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 settings/repository/org.broad/tribble-16.jar

diff --git a/settings/repository/org.broad/tribble-16.jar b/settings/repository/org.broad/tribble-16.jar
new file mode 100644
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literal 0
HcmV?d00001


From 9ca9cf52aca2fe7bc47c6cc5d7eb527a77c488a6 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Sun, 17 Jul 2011 15:38:33 -0400
Subject: [PATCH 158/161] Uncommenting a stray commented test.

---
 .../walkers/variantutils/CombineVariantsIntegrationTest.java    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
index daaab9425..fb18c6c33 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
@@ -119,7 +119,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
         executeTest("combineComplexSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec);
     }
 
-//    @Test public void complexTestFull() { combineComplexSites("", "64b991fd3850f83614518f7d71f0532f"); }
+    @Test public void complexTestFull() { combineComplexSites("", "64b991fd3850f83614518f7d71f0532f"); }
     @Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "df96cb3beb2dbb5e02f80abec7d3571e"); }
     @Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "f72a178137e25dbe0b931934cdc0079d"); }
     @Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "f704caeaaaed6711943014b847fe381a"); }

From 9992c373be8bda5fd4e5999ac3cac36c35e9bb96 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Sun, 17 Jul 2011 20:29:58 -0400
Subject: [PATCH 159/161] Optimize imports run on the whole project, public and
 private.  I just got too tired of all of the unused imports floating around. 
 Confirmed that the system builds after the changes.

---
 .../analyzecovariates/AnalyzeCovariates.java  | 11 +++--
 .../sting/commandline/Argument.java           |  7 +--
 .../commandline/ArgumentDefinitionGroup.java  |  4 +-
 .../commandline/ArgumentDefinitions.java      |  4 +-
 .../commandline/ArgumentTypeDescriptor.java   |  6 +--
 .../sting/commandline/CommandLineProgram.java | 10 +++-
 .../sting/commandline/CommandLineUtils.java   | 10 +++-
 .../MissingArgumentValueException.java        |  2 -
 .../sting/commandline/ParsingEngine.java      | 10 ++--
 .../sting/commandline/ParsingMethod.java      |  4 +-
 .../sting/gatk/CommandLineExecutable.java     | 21 +++------
 .../sting/gatk/CommandLineGATK.java           | 10 ++--
 .../sting/gatk/GenomeAnalysisEngine.java      | 15 ++----
 .../sting/gatk/ReadMetrics.java               |  9 ++--
 .../sting/gatk/ReadProperties.java            |  1 -
 .../sting/gatk/WalkerManager.java             |  7 ++-
 .../arguments/GATKArgumentCollection.java     | 11 ++---
 .../sting/gatk/contexts/AlignmentContext.java |  6 +--
 .../gatk/contexts/AlignmentContextUtils.java  |  2 +-
 .../sting/gatk/contexts/ReferenceContext.java |  9 ++--
 .../datasources/providers/AllLocusView.java   | 16 +++----
 .../providers/LocusReferenceView.java         | 11 ++---
 .../providers/LocusShardDataProvider.java     |  9 ++--
 .../gatk/datasources/providers/LocusView.java |  2 +-
 .../ManagingReferenceOrderedView.java         |  2 +-
 .../providers/ReadReferenceView.java          |  3 +-
 .../providers/ReadShardDataProvider.java      |  7 ++-
 .../gatk/datasources/providers/ReadView.java  |  5 +-
 .../datasources/providers/ReferenceView.java  | 18 ++++----
 .../datasources/providers/RodLocusView.java   |  4 +-
 .../providers/ShardDataProvider.java          |  5 +-
 .../reads/BAMBlockStartIterator.java          |  5 --
 .../gatk/datasources/reads/BAMSchedule.java   |  7 +--
 .../gatk/datasources/reads/BAMScheduler.java  | 12 +----
 .../gatk/datasources/reads/FilePointer.java   | 10 +---
 .../gatk/datasources/reads/GATKBAMIndex.java  | 14 ++----
 .../datasources/reads/GATKBAMIndexData.java   |  6 +--
 .../datasources/reads/IntervalSharder.java    | 11 +----
 .../gatk/datasources/reads/LocusShard.java    |  3 +-
 .../datasources/reads/LocusShardStrategy.java | 17 +++----
 .../datasources/reads/MonolithicShard.java    |  2 +-
 .../reads/MonolithicShardStrategy.java        |  2 +-
 .../gatk/datasources/reads/ReadShard.java     | 14 +++---
 .../datasources/reads/ReadShardStrategy.java  |  5 +-
 .../gatk/datasources/reads/SAMDataSource.java | 14 +++---
 .../sting/gatk/datasources/reads/Shard.java   |  8 +---
 .../reads/ShardStrategyFactory.java           |  4 +-
 .../reads/utilities/BAMFileStat.java          |  8 ++--
 .../reads/utilities/BAMTagRenamer.java        |  8 ++--
 .../reads/utilities/PrintBGZFBounds.java      |  1 -
 .../reference/ReferenceDataSource.java        | 11 ++---
 .../gatk/datasources/rmd/ResourcePool.java    |  6 +--
 .../datasources/sample/SampleDataSource.java  |  5 +-
 .../sting/gatk/examples/CoverageBySample.java | 17 ++++---
 .../gatk/examples/GATKPaperGenotyper.java     |  4 +-
 .../sting/gatk/executive/Accumulator.java     | 12 ++---
 .../executive/HierarchicalMicroScheduler.java | 18 ++++----
 .../gatk/executive/LinearMicroScheduler.java  | 11 ++---
 .../sting/gatk/executive/MicroScheduler.java  | 25 +++++-----
 .../sting/gatk/executive/OutputMergeTask.java |  3 +-
 .../sting/gatk/executive/ReduceTree.java      |  4 +-
 .../sting/gatk/executive/ShardTraverser.java  |  6 +--
 .../sting/gatk/executive/TreeReducer.java     |  2 +-
 .../sting/gatk/executive/WindowMaker.java     | 19 ++++----
 .../sting/gatk/filters/BadCigarFilter.java    |  6 ++-
 .../sting/gatk/filters/BadMateFilter.java     |  1 -
 .../filters/CountingFilteringIterator.java    | 13 +++---
 .../gatk/filters/DuplicateReadFilter.java     |  1 -
 .../FailsVendorQualityCheckReadFilter.java    |  1 -
 .../sting/gatk/filters/FilterManager.java     |  3 --
 .../gatk/filters/MalformedReadFilter.java     |  2 +-
 .../filters/MappingQualityReadFilter.java     |  1 -
 .../MappingQualityUnavailableReadFilter.java  |  1 -
 .../gatk/filters/MaxInsertSizeFilter.java     |  1 -
 .../gatk/filters/MaxReadLengthFilter.java     |  1 -
 .../gatk/filters/MissingReadGroupFilter.java  |  1 -
 .../NoOriginalQualityScoresFilter.java        |  1 -
 .../NotPrimaryAlignmentReadFilter.java        |  1 -
 .../sting/gatk/filters/Platform454Filter.java |  2 -
 .../sting/gatk/filters/PlatformFilter.java    |  4 +-
 .../gatk/filters/PlatformUnitFilter.java      | 10 ++--
 .../sting/gatk/filters/ReadFilter.java        |  1 -
 .../filters/ReadGroupBlackListFilter.java     | 13 +++---
 .../sting/gatk/filters/ReadStrandFilter.java  |  1 -
 .../sting/gatk/filters/SampleFilter.java      |  3 +-
 .../gatk/filters/SingleReadGroupFilter.java   |  3 +-
 .../gatk/filters/UnmappedReadFilter.java      |  1 -
 .../sting/gatk/io/DirectOutputTracker.java    |  4 +-
 .../sting/gatk/io/OutputTracker.java          | 16 +++----
 .../sting/gatk/io/StingSAMFileWriter.java     |  2 +-
 .../gatk/io/ThreadLocalOutputTracker.java     |  9 ++--
 .../gatk/io/storage/OutputStreamStorage.java  |  4 +-
 .../gatk/io/storage/SAMFileWriterStorage.java |  9 ++--
 .../sting/gatk/io/storage/StorageFactory.java |  2 +-
 .../gatk/io/storage/VCFWriterStorage.java     | 19 +++++---
 .../OutputStreamArgumentTypeDescriptor.java   |  2 +-
 .../sting/gatk/io/stubs/OutputStreamStub.java |  4 +-
 .../SAMFileReaderArgumentTypeDescriptor.java  |  8 ++--
 .../SAMFileWriterArgumentTypeDescriptor.java  |  9 ++--
 .../gatk/io/stubs/SAMFileWriterStub.java      | 15 +++---
 .../VCFWriterArgumentTypeDescriptor.java      |  7 ++-
 .../sting/gatk/io/stubs/VCFWriterStub.java    | 18 ++++----
 .../gatk/iterators/BoundedReadIterator.java   |  4 +-
 .../gatk/iterators/BufferingReadIterator.java |  5 +-
 .../gatk/iterators/DownsampleIterator.java    |  3 +-
 .../gatk/iterators/GenomeLocusIterator.java   |  2 +-
 .../sting/gatk/iterators/LocusIterator.java   |  3 +-
 .../gatk/iterators/LocusIteratorByState.java  | 20 +++++---
 .../sting/gatk/iterators/NullSAMIterator.java |  1 -
 .../iterators/PositionTrackingIterator.java   |  1 -
 .../iterators/ReadFormattingIterator.java     |  7 +--
 .../gatk/iterators/StingSAMIterator.java      |  1 -
 .../sting/gatk/phonehome/GATKRunReport.java   |  5 +-
 .../sting/gatk/refdata/RODRecordIterator.java | 10 ++--
 .../sting/gatk/refdata/RODRecordListImpl.java |  2 +-
 .../gatk/refdata/RefMetaDataTracker.java      |  4 +-
 .../gatk/refdata/SeekableRODIterator.java     |  2 +-
 .../gatk/refdata/VariantContextAdaptors.java  | 12 ++---
 .../annotator/AnnotatorInputTableCodec.java   | 12 ++---
 .../annotator/AnnotatorInputTableFeature.java |  4 +-
 .../refdata/features/beagle/BeagleCodec.java  | 10 ++--
 .../features/beagle/BeagleFeature.java        |  5 +-
 .../features/refseq/RefSeqFeature.java        |  3 +-
 .../features/sampileup/SAMPileupCodec.java    |  4 +-
 .../features/sampileup/SAMPileupFeature.java  |  3 +-
 .../features/samread/SAMReadCodec.java        |  6 +--
 .../refdata/features/table/BedTableCodec.java |  5 --
 .../refdata/features/table/TableCodec.java    |  6 +--
 .../refdata/features/table/TableFeature.java  |  2 +-
 .../gatk/refdata/indexer/RMDIndexer.java      |  1 -
 .../gatk/refdata/tracks/QueryableTrack.java   |  1 -
 .../sting/gatk/refdata/tracks/RMDTrack.java   |  2 -
 .../tracks/builders/RMDTrackBuilder.java      |  8 ++--
 .../utils/FeatureToGATKFeatureIterator.java   |  2 -
 .../sting/gatk/refdata/utils/GATKFeature.java |  2 -
 .../LocationAwareSeekableRODIterator.java     |  4 --
 .../StringToGenomeLocIteratorAdapter.java     |  2 +-
 .../refdata/utils/helpers/DbSNPHelper.java    |  2 +-
 .../gatk/traversals/TraversalEngine.java      |  9 ++--
 .../gatk/traversals/TraverseDuplicates.java   |  3 +-
 .../sting/gatk/traversals/TraverseLoci.java   |  1 -
 .../gatk/traversals/TraverseReadPairs.java    | 16 ++++---
 .../sting/gatk/traversals/TraverseReads.java  |  8 ++--
 .../sting/gatk/walkers/Allows.java            |  7 +--
 .../sting/gatk/walkers/BAQMode.java           |  7 +--
 .../broadinstitute/sting/gatk/walkers/By.java |  7 +--
 .../sting/gatk/walkers/ClipReadsWalker.java   | 26 +++++------
 .../sting/gatk/walkers/DuplicateWalker.java   |  7 +--
 .../walkers/FindReadsWithNamesWalker.java     |  1 -
 .../sting/gatk/walkers/FlagStatWalker.java    |  6 +--
 .../walkers/GCContentByIntervalWalker.java    |  3 +-
 .../sting/gatk/walkers/LocusWalker.java       |  7 ++-
 .../sting/gatk/walkers/PileupWalker.java      |  8 ++--
 .../sting/gatk/walkers/PrintRODsWalker.java   |  4 +-
 .../sting/gatk/walkers/PrintReadsWalker.java  |  6 +--
 .../sting/gatk/walkers/ReadWalker.java        |  2 +-
 .../sting/gatk/walkers/Requires.java          |  7 +--
 .../gatk/walkers/SplitSamFileWalker.java      | 18 +++++---
 .../sting/gatk/walkers/Walker.java            |  6 +--
 .../sting/gatk/walkers/WalkerName.java        |  6 +--
 .../sting/gatk/walkers/Window.java            |  5 +-
 .../gatk/walkers/annotator/AlleleBalance.java | 16 +++----
 .../annotator/AlleleBalanceBySample.java      | 14 ++++--
 .../walkers/annotator/AnnotationByDepth.java  |  3 +-
 .../gatk/walkers/annotator/BaseCounts.java    | 12 ++---
 .../annotator/BaseQualityRankSumTest.java     |  8 ++--
 .../walkers/annotator/ChromosomeCounts.java   | 20 ++++----
 .../walkers/annotator/DepthOfCoverage.java    | 15 +++---
 .../annotator/DepthPerAlleleBySample.java     | 19 ++++----
 .../gatk/walkers/annotator/FisherStrand.java  | 14 +++---
 .../gatk/walkers/annotator/GCContent.java     | 13 +++---
 .../sting/gatk/walkers/annotator/GLstats.java | 15 +++---
 .../walkers/annotator/HaplotypeScore.java     | 32 +++++++------
 .../gatk/walkers/annotator/HardyWeinberg.java | 15 +++---
 .../walkers/annotator/HomopolymerRun.java     | 10 ++--
 .../gatk/walkers/annotator/IndelType.java     |  6 +--
 .../sting/gatk/walkers/annotator/LowMQ.java   | 12 ++---
 .../annotator/MappingQualityRankSumTest.java  |  8 ++--
 .../walkers/annotator/MappingQualityZero.java |  8 ++--
 .../annotator/MappingQualityZeroBySample.java | 20 ++++----
 .../annotator/MappingQualityZeroFraction.java |  6 +--
 .../gatk/walkers/annotator/NBaseCount.java    |  6 +--
 .../gatk/walkers/annotator/QualByDepth.java   | 12 ++---
 .../walkers/annotator/RMSMappingQuality.java  | 15 +++---
 .../gatk/walkers/annotator/RankSumTest.java   | 15 +++---
 .../ReadDepthAndAllelicFractionBySample.java  | 21 ++++-----
 .../walkers/annotator/ReadPosRankSumTest.java | 11 +++--
 .../gatk/walkers/annotator/SBByDepth.java     | 10 ++--
 .../gatk/walkers/annotator/SampleList.java    | 10 ++--
 .../walkers/annotator/SpanningDeletions.java  |  6 +--
 .../annotator/TechnologyComposition.java      |  6 ++-
 .../walkers/annotator/VariantAnnotator.java   | 13 +++---
 .../annotator/VariantAnnotatorEngine.java     | 31 ++++++-------
 .../genomicannotator/GenomicAnnotation.java   | 14 +++---
 .../genomicannotator/GenomicAnnotator.java    | 22 ++++-----
 .../annotator/genomicannotator/JoinTable.java |  6 +--
 .../genomicannotator/JoinTableParser.java     |  8 ++--
 .../TranscriptToGenomicInfo.java              | 15 ++----
 .../interfaces/GenotypeAnnotation.java        | 10 ++--
 .../interfaces/InfoFieldAnnotation.java       |  8 ++--
 .../beagle/BeagleOutputToVCFWalker.java       | 14 +++---
 .../beagle/ProduceBeagleInputWalker.java      | 13 +++---
 .../VariantsToBeagleUnphasedWalker.java       | 19 ++++----
 .../walkers/coverage/CallableLociWalker.java  |  6 +--
 .../coverage/CoarseCoverageWalker.java        |  7 ++-
 .../coverage/CompareCallableLociWalker.java   | 10 ++--
 .../gatk/walkers/coverage/CoverageUtils.java  |  4 +-
 .../coverage/DepthOfCoverageWalker.java       | 11 +++--
 .../walkers/diffengine/BAMDiffableReader.java | 13 ++----
 .../gatk/walkers/diffengine/DiffElement.java  |  4 +-
 .../gatk/walkers/diffengine/DiffValue.java    |  2 -
 .../walkers/diffengine/VCFDiffableReader.java |  5 +-
 .../fasta/FastaAlternateReferenceWalker.java  |  2 +-
 .../walkers/fasta/FastaReferenceWalker.java   |  5 +-
 .../gatk/walkers/filters/ClusteredSnps.java   |  2 +-
 .../walkers/filters/FiltrationContext.java    |  2 +-
 .../filters/FiltrationContextWindow.java      |  4 +-
 .../filters/VariantFiltrationWalker.java      | 13 +++---
 .../AlleleFrequencyCalculationModel.java      |  7 +--
 .../genotyper/DiploidIndelGenotypePriors.java |  2 -
 .../DiploidSNPGenotypeLikelihoods.java        | 11 +++--
 .../genotyper/ExactAFCalculationModel.java    | 15 ++++--
 .../GenotypeLikelihoodsCalculationModel.java  |  2 +-
 .../genotyper/GridSearchAFEstimation.java     | 10 ++--
 ...elGenotypeLikelihoodsCalculationModel.java | 11 ++---
 .../MultiallelicGenotypeLikelihoods.java      |  2 +-
 ...NPGenotypeLikelihoodsCalculationModel.java | 18 ++++----
 .../walkers/genotyper/UGCalcLikelihoods.java  |  8 ++--
 .../walkers/genotyper/UGCallVariants.java     |  8 ++--
 .../genotyper/UnifiedArgumentCollection.java  |  1 -
 .../walkers/genotyper/UnifiedGenotyper.java   | 19 ++++----
 .../genotyper/UnifiedGenotyperEngine.java     | 16 ++++---
 .../indels/ConstrainedMateFixingManager.java  |  6 ++-
 .../indels/HaplotypeIndelErrorModel.java      |  7 +--
 .../gatk/walkers/indels/IndelRealigner.java   | 38 +++++++--------
 .../gatk/walkers/indels/LeftAlignIndels.java  |  6 ++-
 .../indels/PairHMMIndelErrorModel.java        | 27 +++++------
 .../walkers/indels/RealignedReadCounter.java  | 24 ++++++----
 .../indels/RealignerTargetCreator.java        | 12 ++---
 ...CoordinateComparatorWithUnmappedReads.java |  3 +-
 .../indels/SomaticIndelDetectorWalker.java    | 46 +++++++++++--------
 .../gatk/walkers/phasing/AllelePair.java      |  2 +-
 .../walkers/phasing/AnnotateMNPsWalker.java   |  9 ++--
 .../gatk/walkers/phasing/MergeMNPsWalker.java |  8 ++--
 ...eSegregatingAlternateAllelesVCFWriter.java | 15 +++---
 ...ergeSegregatingAlternateAllelesWalker.java | 10 ++--
 .../phasing/ReadBackedPhasingWalker.java      | 21 +++++----
 .../gatk/walkers/phasing/SNPallelePair.java   |  4 +-
 .../sting/gatk/walkers/phasing/WriteVCF.java  |  2 +-
 .../sting/gatk/walkers/qc/CountIntervals.java |  4 +-
 .../gatk/walkers/qc/CountLociWalker.java      |  1 -
 .../gatk/walkers/qc/CountPairsWalker.java     |  6 +--
 .../gatk/walkers/qc/CountReadsWalker.java     |  4 +-
 .../gatk/walkers/qc/CountRodByRefWalker.java  |  2 +-
 .../sting/gatk/walkers/qc/CountRodWalker.java | 11 +++--
 .../gatk/walkers/qc/CycleQualityWalker.java   | 24 +++++-----
 .../walkers/qc/PrintLocusContextWalker.java   | 12 ++---
 .../walkers/qc/ReadClippingStatsWalker.java   | 27 ++++++-----
 .../gatk/walkers/qc/ReadValidationWalker.java |  8 ++--
 .../walkers/qc/RodSystemValidationWalker.java |  6 ++-
 .../walkers/qc/ValidatingPileupWalker.java    |  8 ++--
 .../CountCovariatesGatherer.java              |  1 -
 .../recalibration/CountCovariatesWalker.java  | 13 +++---
 .../walkers/recalibration/CycleCovariate.java |  1 -
 .../walkers/recalibration/DinucCovariate.java |  5 +-
 .../recalibration/RecalDataManager.java       | 18 ++++----
 .../recalibration/RecalDatumOptimized.java    |  2 +-
 .../TableRecalibrationWalker.java             | 30 ++++++------
 .../walkers/sequenom/CreateSequenomMask.java  |  4 +-
 .../walkers/sequenom/PickSequenomProbes.java  | 18 ++++----
 .../varianteval/VariantEvalWalker.java        | 17 +++----
 .../evaluators/CompEvalGenotypes.java         |  2 +-
 .../varianteval/evaluators/CompOverlap.java   |  6 +--
 .../varianteval/evaluators/CountVariants.java |  8 ++--
 .../evaluators/GenotypeConcordance.java       | 12 ++---
 .../evaluators/GenotypePhasingEvaluator.java  |  7 +--
 .../evaluators/IndelLengthHistogram.java      |  8 ++--
 .../evaluators/IndelMetricsByAC.java          |  6 +--
 .../evaluators/IndelStatistics.java           |  8 ++--
 .../MendelianViolationEvaluator.java          |  8 ++--
 .../evaluators/PrintMissingComp.java          |  6 +--
 .../evaluators/SamplePreviousGenotypes.java   |  2 +-
 .../evaluators/SimpleMetricsByAC.java         |  7 +--
 .../evaluators/ThetaVariantEvaluator.java     |  6 +--
 .../evaluators/TiTvVariantEvaluator.java      |  8 ++--
 .../evaluators/ValidationReport.java          | 12 ++---
 .../evaluators/VariantEvaluator.java          |  2 +-
 .../evaluators/VariantQualityScore.java       | 10 ++--
 .../stratifications/AlleleCount.java          |  5 +-
 .../stratifications/AlleleFrequency.java      |  2 +-
 .../varianteval/stratifications/CompRod.java  |  2 +-
 .../varianteval/stratifications/Contig.java   |  2 +-
 .../varianteval/stratifications/CpG.java      |  2 +-
 .../stratifications/Degeneracy.java           |  4 +-
 .../varianteval/stratifications/EvalRod.java  |  2 +-
 .../varianteval/stratifications/Filter.java   |  2 +-
 .../stratifications/FunctionalClass.java      |  2 +-
 .../stratifications/JexlExpression.java       |  4 +-
 .../varianteval/stratifications/Novelty.java  |  2 +-
 .../varianteval/stratifications/Sample.java   |  2 +-
 .../stratifications/VariantStratifier.java    |  3 +-
 .../util/NewEvaluationContext.java            |  2 +-
 .../util/SortableJexlVCMatchExp.java          |  2 +-
 .../varianteval/util/VariantEvalUtils.java    |  4 +-
 .../ApplyRecalibration.java                   | 12 ++---
 .../walkers/variantrecalibration/Tranche.java |  7 ++-
 .../VQSRCalibrationCurve.java                 |  2 +-
 .../VariantDataManager.java                   |  6 ++-
 .../VariantRecalibrator.java                  |  4 +-
 .../walkers/variantutils/CombineVariants.java | 13 +++---
 .../variantutils/FilterLiftedVariants.java    | 19 ++++----
 .../variantutils/LeftAlignVariants.java       | 12 ++---
 .../variantutils/LiftoverVariants.java        | 32 ++++++-------
 .../variantutils/RandomlySplitVariants.java   | 13 +++---
 .../walkers/variantutils/SelectVariants.java  | 19 ++++----
 .../variantutils/ValidateVariants.java        | 21 +++++----
 .../VariantValidationAssessor.java            | 13 +++---
 .../walkers/variantutils/VariantsToTable.java |  5 +-
 .../walkers/variantutils/VariantsToVCF.java   | 24 +++++-----
 .../sting/jna/clibrary/LibC.java              |  5 +-
 .../sting/jna/lsf/v7_0_6/LibLsf.java          |  2 +-
 .../gatk/ArgumentDefinitionField.java         |  7 ++-
 .../queue/extensions/gatk/ArgumentField.java  |  5 +-
 .../gatk/GATKExtensionsGenerator.java         |  7 ++-
 .../sting/utils/DisjointSet.java              |  4 +-
 .../broadinstitute/sting/utils/GenomeLoc.java |  1 -
 .../sting/utils/GenomeLocParser.java          |  6 ++-
 .../sting/utils/IndelUtils.java               |  2 +-
 .../broadinstitute/sting/utils/MathUtils.java |  9 ++--
 .../sting/utils/MendelianViolation.java       |  7 +--
 .../broadinstitute/sting/utils/PathUtils.java |  4 +-
 .../sting/utils/ReservoirDownsampler.java     |  4 +-
 .../sting/utils/SWPairwiseAlignment.java      |  7 ++-
 .../sting/utils/SampleUtils.java              |  6 +--
 .../sting/utils/SimpleTimer.java              |  5 +-
 .../org/broadinstitute/sting/utils/Utils.java |  5 +-
 .../broadinstitute/sting/utils/baq/BAQ.java   |  6 +--
 .../sting/utils/baq/BAQSamIterator.java       |  5 +-
 .../sting/utils/bed/BedParser.java            |  5 +-
 .../sting/utils/classloader/JVMUtils.java     |  2 +-
 .../sting/utils/clipreads/ClippingOp.java     |  3 --
 .../sting/utils/clipreads/ReadClipper.java    |  1 -
 .../codecs/completegenomics/CGVarCodec.java   |  1 -
 .../utils/codecs/soapsnp/SoapSNPCodec.java    |  6 +--
 .../utils/codecs/vcf/StandardVCFWriter.java   |  4 +-
 .../sting/utils/codecs/vcf/VCFParser.java     |  4 +-
 .../sting/utils/codecs/vcf/VCFUtils.java      |  4 +-
 .../utils/collections/NestedHashMap.java      |  3 +-
 .../utils/collections/RODMergingIterator.java |  7 ++-
 .../sting/utils/duplicates/DupUtils.java      |  9 ++--
 .../sting/utils/exceptions/UserException.java |  3 +-
 .../CachingIndexedFastaSequenceFile.java      |  7 +--
 .../sting/utils/genotype/DiploidGenotype.java |  1 -
 .../sting/utils/genotype/Haplotype.java       |  8 ++--
 .../sting/utils/help/ApplicationDetails.java  |  8 ++--
 .../sting/utils/help/DescriptionTaglet.java   |  1 -
 .../sting/utils/help/DisplayNameTaglet.java   |  1 -
 .../sting/utils/help/HelpFormatter.java       | 12 ++---
 .../sting/utils/help/HelpTaglet.java          |  4 +-
 .../help/ResourceBundleExtractorDoclet.java   | 14 +++---
 .../sting/utils/help/SummaryTaglet.java       |  1 -
 .../sting/utils/instrumentation/Sizeof.java   |  2 +-
 .../interval/IntervalFileMergingIterator.java |  6 +--
 .../sting/utils/interval/IntervalUtils.java   |  4 +-
 .../interval/NwayIntervalMergingIterator.java |  3 +-
 .../interval/OverlappingIntervalIterator.java |  3 +-
 .../pileup/AbstractReadBackedPileup.java      | 11 ++---
 .../pileup/ExtendedEventPileupElement.java    |  3 --
 .../sting/utils/pileup/FragmentPileup.java    |  5 +-
 .../pileup/MergingPileupElementIterator.java  |  2 +-
 .../sting/utils/pileup/PileupElement.java     |  5 +-
 .../pileup/ReadBackedExtendedEventPileup.java |  6 +--
 .../ReadBackedExtendedEventPileupImpl.java    |  5 +-
 .../sting/utils/pileup/ReadBackedPileup.java  |  5 +-
 .../utils/pileup/ReadBackedPileupImpl.java    |  2 +-
 .../sting/utils/sam/AlignmentUtils.java       |  9 ++--
 .../utils/sam/ArtificialReadsTraversal.java   | 16 +++----
 .../utils/sam/ArtificialSAMFileReader.java    | 16 ++++---
 .../utils/sam/ArtificialSAMIterator.java      |  5 +-
 .../utils/sam/ArtificialSAMQueryIterator.java |  5 +-
 .../sting/utils/sam/ComparableSAMRecord.java  |  2 -
 .../utils/sam/GATKSAMReadGroupRecord.java     |  2 +-
 .../sting/utils/sam/GATKSAMRecord.java        |  8 ++--
 .../sting/utils/sam/ReadUtils.java            |  5 +-
 .../sting/utils/sam/SAMFileReaderBuilder.java |  3 +-
 .../utils/sam/SimplifyingSAMFileWriter.java   |  7 ---
 .../sting/utils/text/ListFileUtils.java       |  1 -
 .../sting/utils/text/TextFormattingUtils.java |  8 ++--
 .../sting/utils/text/XReadLines.java          |  6 +--
 .../FileBackedGenomeLocProcessingTracker.java |  4 --
 .../NoOpGenomeLocProcessingTracker.java       |  4 --
 .../sting/utils/threading/SharedFileLock.java |  3 --
 .../threading/SharedFileThreadSafeLock.java   |  5 --
 .../sting/utils/variantcontext/Allele.java    |  4 +-
 .../variantcontext/GenotypeLikelihoods.java   |  2 +-
 .../variantcontext/MutableVariantContext.java |  5 +-
 .../utils/variantcontext/VariantContext.java  |  2 +-
 .../variantcontext/VariantContextUtils.java   | 19 +++++---
 .../variantcontext/VariantJEXLContext.java    |  5 +-
 .../sting/utils/wiggle/WiggleWriter.java      |  2 +-
 400 files changed, 1480 insertions(+), 1602 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java b/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
index f8e298d88..b9e380295 100755
--- a/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
+++ b/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.
diff --git a/public/java/src/org/broadinstitute/sting/commandline/Argument.java b/public/java/src/org/broadinstitute/sting/commandline/Argument.java
index b2ee9d1fc..33592287d 100755
--- a/public/java/src/org/broadinstitute/sting/commandline/Argument.java
+++ b/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.
diff --git a/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java b/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java
index c36a8e04f..b47677b08 100644
--- a/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java
+++ b/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.
diff --git a/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java b/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java
index 39e698ca3..9f92df6e0 100755
--- a/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java
+++ b/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.
diff --git a/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
index 6c50e1784..9c33e084d 100644
--- a/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
+++ b/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;
diff --git a/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java b/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java
index d404a2b6e..aba4fc109 100644
--- a/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java
+++ b/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 {
 
diff --git a/public/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java b/public/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java
index 99608f167..bd2006388 100644
--- a/public/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java
+++ b/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.
diff --git a/public/java/src/org/broadinstitute/sting/commandline/MissingArgumentValueException.java b/public/java/src/org/broadinstitute/sting/commandline/MissingArgumentValueException.java
index 8029db7b3..4e6c3a16f 100644
--- a/public/java/src/org/broadinstitute/sting/commandline/MissingArgumentValueException.java
+++ b/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.
  */
diff --git a/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java b/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
index 717c5c522..8423bb2f2 100755
--- a/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
+++ b/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.*;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java b/public/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java
index d1cda3ed9..a070cb5a1 100755
--- a/public/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java
+++ b/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.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
index fd7e749c3..a080ab439 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
+++ b/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
diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
index 7982f61e2..da2be74bf 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
+++ b/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.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index f8527c33b..918bc1251 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/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.*;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java b/public/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java
index 27a86ab3f..7cb615f7f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java
+++ b/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.
  */
diff --git a/public/java/src/org/broadinstitute/sting/gatk/ReadProperties.java b/public/java/src/org/broadinstitute/sting/gatk/ReadProperties.java
index 1a361029a..93fa2d146 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/ReadProperties.java
+++ b/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;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java b/public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
index 9553f651e..cf190835e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
+++ b/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.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
index 93638f21d..ee2e85025 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
+++ b/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;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java b/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
index 337c2664c..17e4a0743 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
+++ b/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
diff --git a/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java b/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java
index 6a0d30837..1f9a7d705 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java
+++ b/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.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java b/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
index 760b3a7bc..376064cdb 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
+++ b/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
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java
index b36c59a2c..e92599494 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java
+++ b/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
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java
index 330a9e4f7..ff312bcac 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java
+++ b/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
  *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java
index 72b962522..55304da34 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java
+++ b/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.
  *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java
index b467a2ab5..f9ed0cb74 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java
+++ b/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;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java
index a91e169c1..223659a46 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java
+++ b/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
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java
index d2c097f5d..3d62faf49 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java
+++ b/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
  *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java
index 5a672b09f..7843e7518 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java
+++ b/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.
  *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java
index 0c4b78a7c..e809092d4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java
+++ b/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
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java
index d6c938f36..efb92235f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java
+++ b/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
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java
index feed2ab85..39c632539 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java
+++ b/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;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java
index a0ea32f9b..803bd885b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java
+++ b/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
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMBlockStartIterator.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMBlockStartIterator.java
index a9e04e357..de938e845 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMBlockStartIterator.java
+++ b/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.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java
index 34693d501..521bcd5a3 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java
+++ b/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.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java
index 266232c0f..467aebac5 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java
+++ b/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.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java
index c014c1995..e4141f61c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java
+++ b/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.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
index 8ebb8b1a8..5d0c38b78 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
+++ b/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.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java
index f9b998a60..daf1b77e3 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java
+++ b/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;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java
index fc3f76ab7..4ddf28dce 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java
+++ b/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.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java
index 26af890b4..19d33aa6b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java
+++ b/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
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShardStrategy.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShardStrategy.java
index 950d67428..a5ca07853 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShardStrategy.java
+++ b/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.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShard.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShard.java
index 7579c22f6..278eeb898 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShard.java
+++ b/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;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShardStrategy.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShardStrategy.java
index 10228ecd7..28b737f28 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShardStrategy.java
+++ b/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).
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java
index 9aecd7779..4d9c9092d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java
+++ b/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
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShardStrategy.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShardStrategy.java
index da70a615b..c2235ec73 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShardStrategy.java
+++ b/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.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
index c2aa5f18e..6064806f3 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
+++ b/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;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/Shard.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/Shard.java
index 418f5d3ee..f8d941784 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/Shard.java
+++ b/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;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardStrategyFactory.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardStrategyFactory.java
index fa733ce12..780b41ef7 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardStrategyFactory.java
+++ b/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;
 
 /**
  *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMFileStat.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMFileStat.java
index ae0f1cf43..07c13a76e 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMFileStat.java
+++ b/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;
 
 /**
  *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java
index f03e2a44f..54de04379 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java
+++ b/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;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBGZFBounds.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBGZFBounds.java
index df7dccaa9..773541d11 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBGZFBounds.java
+++ b/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;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java
index c2d64ddd8..ef69a8e5f 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java
+++ b/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;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ResourcePool.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ResourcePool.java
index 934f4f997..21f58d480 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ResourcePool.java
+++ b/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.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java
index 0a5981a1b..067bf3f72 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java
+++ b/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;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java b/public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java
index a1419ba70..5dbd90405 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java
+++ b/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.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java
index b96d0ffbf..26205a203 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java
+++ b/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;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java b/public/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java
index 3e335733d..b23782563 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java
+++ b/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
  */
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
index 8a27e008c..59fb4aa9e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
+++ b/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.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
index 4cb571c45..9466fdf75 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
+++ b/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 {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
index cfe0f8187..23e5769f1 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
+++ b/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;
 
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/OutputMergeTask.java b/public/java/src/org/broadinstitute/sting/gatk/executive/OutputMergeTask.java
index 76e0c1c8a..7be37a616 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/OutputMergeTask.java
+++ b/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
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/ReduceTree.java b/public/java/src/org/broadinstitute/sting/gatk/executive/ReduceTree.java
index 151a1ba26..7aac70b47 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/ReduceTree.java
+++ b/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
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java b/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
index b78a4edc9..6136bd68d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
+++ b/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;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java b/public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java
index 8fb4adb5d..d36a3b576 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java
+++ b/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
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java b/public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java
index 5c341bb02..cfbce58ee 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java
+++ b/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
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java
index b8a3ee977..0987c5d74 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java
+++ b/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.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/BadMateFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/BadMateFilter.java
index 3b988c8fb..8596e18eb 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/BadMateFilter.java
+++ b/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;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java b/public/java/src/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java
index 84390c173..03fc2063b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java
+++ b/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.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java
index fb3c38582..589910fc7 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java
+++ b/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;
 
 /*
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckReadFilter.java
index b7806524a..cd77a9e7e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckReadFilter.java
+++ b/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;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java b/public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java
index cda08fb66..67f82235d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java
+++ b/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;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
index 4deeb09ee..74deace9a 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
+++ b/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;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java
index bcd473b15..75369b306 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java
+++ b/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;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableReadFilter.java
index cecbedda8..1afec36d1 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableReadFilter.java
+++ b/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;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java
index 584783d34..7bcee033f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java
@@ -1,6 +1,5 @@
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.commandline.Argument;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MaxReadLengthFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MaxReadLengthFilter.java
index 8a2fd5af3..cd31da61a 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/MaxReadLengthFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/MaxReadLengthFilter.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;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java
index d5d40ec38..490a55040 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java
@@ -24,7 +24,6 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java
index fc21538e8..29738e499 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java
@@ -1,6 +1,5 @@
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 
 /*
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentReadFilter.java
index cfbba0383..31c2144ce 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentReadFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentReadFilter.java
@@ -24,7 +24,6 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java
index dcddebd55..8ad91ac1c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java
@@ -25,9 +25,7 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
-
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java
index 691fd95f0..30b2f828d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java
@@ -25,11 +25,9 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
-
-import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 /**
  * Filter out PL matching reads.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java
index 4ef88402d..81044b888 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java
@@ -1,14 +1,12 @@
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
-import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMReadGroupRecord;
-
-import java.util.Set;
-import java.util.HashSet;
-
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
+import java.util.HashSet;
+import java.util.Set;
+
 /**
  * Created by IntelliJ IDEA.
  * User: asivache
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java
index 1d74ee20e..227637761 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.gatk.filters;
 
 import net.sf.picard.filter.SamRecordFilter;
-import net.sf.samtools.SAMFileHeader;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java
index 69ebc8b04..0e5e8800c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java
@@ -25,17 +25,16 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import java.util.*;
-import java.util.Map.Entry;
-import java.io.File;
-import java.io.FileNotFoundException;
-
-import net.sf.picard.filter.SamRecordFilter;
-import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMReadGroupRecord;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
 
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.util.*;
+import java.util.Map.Entry;
+
 /**
  * Removes records matching the read group tag and exact match string.
  * For example, this filter value:
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java
index 1b2a77f45..16eeed3cc 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.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;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java
index 682b22b1f..99d6bc154 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java
@@ -25,9 +25,8 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
-import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMReadGroupRecord;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.commandline.Argument;
 
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java
index 05b472036..2f93cbcae 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java
@@ -25,9 +25,8 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMReadGroupRecord;
-import net.sf.picard.filter.SamRecordFilter;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.commandline.Argument;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java
index ac4f4853a..e7ee345d2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java
@@ -24,7 +24,6 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/DirectOutputTracker.java b/public/java/src/org/broadinstitute/sting/gatk/io/DirectOutputTracker.java
index 865528688..658a28fbd 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/DirectOutputTracker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/DirectOutputTracker.java
@@ -25,9 +25,9 @@
 
 package org.broadinstitute.sting.gatk.io;
 
-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.StorageFactory;
+import org.broadinstitute.sting.gatk.io.stubs.Stub;
 
 /**
  * Maps creation of storage directly to output streams in parent.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java b/public/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
index b68013aa4..f39ba2d8d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
@@ -26,20 +26,20 @@
 package org.broadinstitute.sting.gatk.io;
 
 import net.sf.samtools.SAMFileReader;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.commandline.ArgumentSource;
-import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder;
-import org.broadinstitute.sting.gatk.walkers.Walker;
+import org.broadinstitute.sting.gatk.io.storage.Storage;
+import org.broadinstitute.sting.gatk.io.storage.StorageFactory;
 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.walkers.Walker;
+import org.broadinstitute.sting.utils.classloader.JVMUtils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder;
 
-import java.io.*;
+import java.io.OutputStream;
 import java.lang.reflect.Field;
-import java.util.Map;
 import java.util.HashMap;
+import java.util.Map;
 
 /**
  * Manages the output and err streams that are created specifically for walker
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java b/public/java/src/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java
index 8701ecf3c..a9a74925d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.io;
 
-import net.sf.samtools.SAMFileWriter;
 import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMFileWriter;
 
 /**
  * A writer that will allow unsorted BAM files to be written
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java b/public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java
index 36960246a..999deddd1 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java
@@ -25,15 +25,16 @@
 
 package org.broadinstitute.sting.gatk.io;
 
-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.executive.OutputMergeTask;
+import org.broadinstitute.sting.gatk.io.storage.Storage;
+import org.broadinstitute.sting.gatk.io.storage.StorageFactory;
+import org.broadinstitute.sting.gatk.io.stubs.Stub;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
-import java.util.*;
 import java.io.File;
 import java.io.IOException;
+import java.util.HashMap;
+import java.util.Map;
 
 /**
  * An output tracker that can either track its output per-thread or directly,
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java
index 4dc976289..56c9c0465 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java
@@ -25,14 +25,14 @@
 
 package org.broadinstitute.sting.gatk.io.storage;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.io.*;
+import java.nio.channels.Channels;
 import java.nio.channels.FileChannel;
 import java.nio.channels.WritableByteChannel;
-import java.nio.channels.Channels;
 
 public class OutputStreamStorage extends OutputStream implements Storage<OutputStream> {
     /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
index 610db1d76..cb8786be1 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
@@ -27,17 +27,16 @@ package org.broadinstitute.sting.gatk.io.storage;
 
 import net.sf.samtools.*;
 import net.sf.samtools.util.CloseableIterator;
-
-import java.io.*;
-import java.lang.reflect.InvocationTargetException;
-import java.lang.reflect.Method;
-
 import net.sf.samtools.util.RuntimeIOException;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.sam.SimplifyingSAMFileWriter;
 
+import java.io.File;
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
+
 /**
  * Provides temporary storage for SAMFileWriters.
  *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java
index ee5c56524..66907dd6b 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java
@@ -25,9 +25,9 @@
 
 package org.broadinstitute.sting.gatk.io.storage;
 
-import org.broadinstitute.sting.gatk.io.stubs.Stub;
 import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub;
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub;
+import org.broadinstitute.sting.gatk.io.stubs.Stub;
 import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
index 74176ec35..1da03e9c2 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
@@ -1,16 +1,21 @@
 package org.broadinstitute.sting.gatk.io.storage;
 
+import net.sf.samtools.util.BlockCompressedOutputStream;
 import org.apache.log4j.Logger;
 import org.broad.tribble.source.BasicFeatureSource;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
-
-import java.io.*;
-
-import net.sf.samtools.util.BlockCompressedOutputStream;
+import org.broadinstitute.sting.utils.codecs.vcf.StandardVCFWriter;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.PrintStream;
 
 /**
  * Provides temporary and permanent storage for genotypes in VCF format.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java
index 00e78f391..8bc97c886 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java
@@ -30,8 +30,8 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.io.OutputStream;
 import java.io.File;
+import java.io.OutputStream;
 import java.lang.reflect.Constructor;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java
index 5cf84c5a2..27bcb8a1c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java
@@ -27,9 +27,9 @@ package org.broadinstitute.sting.gatk.io.stubs;
 
 import org.broadinstitute.sting.gatk.io.OutputTracker;
 
-import java.io.OutputStream;
-import java.io.IOException;
 import java.io.File;
+import java.io.IOException;
+import java.io.OutputStream;
 
 /**
  * A stub for routing and management of anything backed by an OutputStream.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java
index d847015ed..f124c2302 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java
@@ -24,14 +24,14 @@
 
 package org.broadinstitute.sting.gatk.io.stubs;
 
-import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
-import org.broadinstitute.sting.commandline.ArgumentSource;
+import net.sf.samtools.SAMFileReader;
 import org.broadinstitute.sting.commandline.ArgumentMatches;
+import org.broadinstitute.sting.commandline.ArgumentSource;
+import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
 import org.broadinstitute.sting.commandline.ParsingEngine;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import net.sf.samtools.SAMFileReader;
 
 import java.io.File;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
index a9a272220..38640eda0 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
@@ -25,18 +25,17 @@
 
 package org.broadinstitute.sting.gatk.io.stubs;
 
+import net.sf.samtools.SAMFileWriter;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
-import net.sf.samtools.SAMFileWriter;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
 
-import java.lang.annotation.Annotation;
-import java.util.List;
-import java.util.Arrays;
 import java.io.File;
 import java.io.OutputStream;
+import java.lang.annotation.Annotation;
+import java.util.Arrays;
+import java.util.List;
 
 /**
  * Insert a SAMFileWriterStub  instead of a full-fledged concrete OutputStream implementations.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java
index f5c1e0efc..d8e59a3dd 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java
@@ -25,20 +25,19 @@
 
 package org.broadinstitute.sting.gatk.io.stubs;
 
+import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMFileWriter;
 import net.sf.samtools.SAMRecord;
-import net.sf.samtools.SAMFileHeader;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.gatk.io.OutputTracker;
+import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
+import org.broadinstitute.sting.utils.baq.BAQ;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.io.File;
 import java.io.OutputStream;
 
-import org.broadinstitute.sting.gatk.io.OutputTracker;
-import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.baq.BAQ;
-
 /**
  * A stub for routing and management of SAM file reading and writing.
  *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java
index 7521e754d..615841f02 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java
@@ -25,14 +25,17 @@
 
 package org.broadinstitute.sting.gatk.io.stubs;
 
-import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.File;
 import java.io.OutputStream;
-import java.util.*;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
 
 /**
  * Injects new command-line arguments into the system providing support for the genotype writer.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java
index 1a79d2785..bb84f9457 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java
@@ -25,19 +25,19 @@
 
 package org.broadinstitute.sting.gatk.io.stubs;
 
-import java.io.File;
-import java.io.PrintStream;
-import java.io.OutputStream;
-import java.util.Collection;
-
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.gatk.CommandLineExecutable;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.io.OutputTracker;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+import java.io.File;
+import java.io.OutputStream;
+import java.io.PrintStream;
+import java.util.Collection;
 
 /**
  * A stub for routing and management of genotype reading and writing.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/BoundedReadIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/BoundedReadIterator.java
index b5643f834..478675f9d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/iterators/BoundedReadIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/BoundedReadIterator.java
@@ -1,13 +1,11 @@
 package org.broadinstitute.sting.gatk.iterators;
 
+import net.sf.picard.sam.MergingSamRecordIterator;
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMRecord;
-import net.sf.picard.sam.MergingSamRecordIterator;
 
 import java.util.Iterator;
 
-import org.broadinstitute.sting.gatk.ReadProperties;
-
 /*
  * Copyright (c) 2009 The Broad Institute
  *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java
index f3a060be1..7eaf4be41 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java
@@ -26,12 +26,11 @@ package org.broadinstitute.sting.gatk.iterators;
 
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.util.CloseableIterator;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.Queue;
 import java.util.LinkedList;
 import java.util.NoSuchElementException;
-
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import java.util.Queue;
 
 /**
  * Buffers access to a large stream of reads, replenishing the buffer only when the reads  
diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/DownsampleIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/DownsampleIterator.java
index 1342f11fd..835748ff0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/iterators/DownsampleIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/DownsampleIterator.java
@@ -1,11 +1,10 @@
 package org.broadinstitute.sting.gatk.iterators;
 
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 
 import java.util.Iterator;
 
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-
 
 public class DownsampleIterator implements StingSAMIterator {
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/GenomeLocusIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/GenomeLocusIterator.java
index aa376a12a..240564d34 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/iterators/GenomeLocusIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/GenomeLocusIterator.java
@@ -3,8 +3,8 @@ package org.broadinstitute.sting.gatk.iterators;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 
-import java.util.NoSuchElementException;
 import java.util.Iterator;
+import java.util.NoSuchElementException;
 /**
  * User: hanna
  * Date: May 12, 2009
diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIterator.java
index 30c1cf512..e177984ca 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIterator.java
@@ -1,11 +1,10 @@
 package org.broadinstitute.sting.gatk.iterators;
 
 import net.sf.samtools.util.CloseableIterator;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 
 import java.util.Iterator;
 
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-
 /**
  * Iterator that traverses a SAM File, accumulating information on a per-locus basis
  */
diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
index 4e58813f5..e13c5a764 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
@@ -25,19 +25,27 @@
 
 package org.broadinstitute.sting.gatk.iterators;
 
-import net.sf.samtools.*;
 import net.sf.picard.util.PeekableIterator;
+import net.sf.samtools.Cigar;
+import net.sf.samtools.CigarElement;
+import net.sf.samtools.CigarOperator;
+import net.sf.samtools.SAMRecord;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.gatk.ReadProperties;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.DownsamplingMethod;
 import org.broadinstitute.sting.gatk.DownsampleType;
+import org.broadinstitute.sting.gatk.DownsamplingMethod;
+import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
 import org.broadinstitute.sting.gatk.datasources.sample.SampleDataSource;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.ReservoirDownsampler;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.pileup.*;
+import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileupImpl;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 import java.util.*;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/NullSAMIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/NullSAMIterator.java
index ff458467f..21b71c9e6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/iterators/NullSAMIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/NullSAMIterator.java
@@ -1,6 +1,5 @@
 package org.broadinstitute.sting.gatk.iterators;
 
-import org.broadinstitute.sting.gatk.ReadProperties;
 import net.sf.samtools.SAMRecord;
 
 import java.util.Iterator;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/PositionTrackingIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/PositionTrackingIterator.java
index c2d3976ea..cc499b247 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/iterators/PositionTrackingIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/PositionTrackingIterator.java
@@ -25,7 +25,6 @@
 
 package org.broadinstitute.sting.gatk.iterators;
 
-import org.broadinstitute.sting.gatk.ReadProperties;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.util.CloseableIterator;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java
index 239392eec..2f30d12a8 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java
@@ -1,13 +1,8 @@
 package org.broadinstitute.sting.gatk.iterators;
 
 import net.sf.samtools.SAMRecord;
-import net.sf.samtools.SAMTag;
-import net.sf.samtools.SAMReadGroupRecord;
-import org.broadinstitute.sting.gatk.ReadProperties;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.apache.log4j.Logger;
-
-import java.util.List;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 /**
  * An iterator which does post-processing of a read, including potentially wrapping
diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIterator.java
index d294993d4..1b248d097 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIterator.java
@@ -2,7 +2,6 @@ package org.broadinstitute.sting.gatk.iterators;
 
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.util.CloseableIterator;
-import org.broadinstitute.sting.gatk.ReadProperties;
 /**
  *
  * User: aaron
diff --git a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java b/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
index a51ca9292..69c0b3e0a 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
@@ -26,19 +26,16 @@ package org.broadinstitute.sting.gatk.phonehome;
 
 import org.apache.log4j.Level;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.commandline.CommandLineUtils;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 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.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.exceptions.StingException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.jets3t.service.S3Service;
 import org.jets3t.service.S3ServiceException;
 import org.jets3t.service.impl.rest.httpclient.RestS3Service;
-import org.jets3t.service.model.S3Bucket;
 import org.jets3t.service.model.S3Object;
 import org.jets3t.service.security.AWSCredentials;
 import org.simpleframework.xml.Element;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java
index fa0c323b5..ce924fd87 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java
@@ -25,17 +25,17 @@
 
 package org.broadinstitute.sting.gatk.refdata;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
 
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.lang.reflect.Constructor;
 import java.util.Iterator;
 import java.util.regex.Pattern;
-import java.io.FileNotFoundException;
-import java.io.File;
-import java.lang.reflect.Constructor;
 
 /**
  * This is a low-level iterator designed to provide system-wide generic support for reading record-oriented data
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java
index cff97e4ee..59b273d38 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java
@@ -2,9 +2,9 @@ package org.broadinstitute.sting.gatk.refdata;
 
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
+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 java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
index 43bf6f8e0..d03b122e2 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
@@ -1,13 +1,13 @@
 package org.broadinstitute.sting.gatk.refdata;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
-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.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java
index b3cb22a03..b7437e6e8 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java
@@ -6,9 +6,9 @@ import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.util.Iterator;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
index c7c0468e7..1d622e2c7 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
@@ -3,17 +3,13 @@ package org.broadinstitute.sting.gatk.refdata;
 import org.broad.tribble.Feature;
 import org.broad.tribble.dbsnp.DbSNPFeature;
 import org.broad.tribble.gelitext.GeliTextFeature;
-import org.broadinstitute.sting.utils.codecs.hapmap.HapMapFeature;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.MutableGenotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.codecs.hapmap.HapMapFeature;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.*;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java
index 59cd14a22..6bba754be 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java
@@ -25,12 +25,6 @@
 
 package org.broadinstitute.sting.gatk.refdata.features.annotator;
 
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.StringTokenizer;
-
 import org.apache.log4j.Logger;
 import org.broad.tribble.Feature;
 import org.broad.tribble.exception.CodecLineParsingException;
@@ -41,6 +35,12 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.Utils;
 
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.StringTokenizer;
+
 public class AnnotatorInputTableCodec implements ReferenceDependentFeatureCodec<AnnotatorInputTableFeature> {
 
     private static Logger logger = Logger.getLogger(AnnotatorInputTableCodec.class);
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableFeature.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableFeature.java
index d97e378fb..d12badd28 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableFeature.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableFeature.java
@@ -25,13 +25,13 @@
 
 package org.broadinstitute.sting.gatk.refdata.features.annotator;
 
+import org.broad.tribble.Feature;
+
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.Map;
 
-import org.broad.tribble.Feature;
-
 /**
  * This class represents a single record in an AnnotatorInputTable.
  */
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleCodec.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleCodec.java
index 7f97451cf..5e536d4c1 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleCodec.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleCodec.java
@@ -26,19 +26,19 @@ package org.broadinstitute.sting.gatk.refdata.features.beagle;
 
 
 import org.broad.tribble.Feature;
+import org.broad.tribble.exception.CodecLineParsingException;
 import org.broad.tribble.readers.AsciiLineReader;
 import org.broad.tribble.readers.LineReader;
+import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.HashMap;
-import java.util.regex.Matcher;
 import java.util.regex.Pattern;
-import org.broad.tribble.exception.CodecLineParsingException;
-import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 
 public class BeagleCodec implements ReferenceDependentFeatureCodec<BeagleFeature> {
     private String[] header;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java
index c7bf86569..e6832754d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java
@@ -25,14 +25,11 @@
 package org.broadinstitute.sting.gatk.refdata.features.beagle;
 
 import org.broad.tribble.Feature;
-
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 
 import java.util.ArrayList;
 import java.util.Map;
 
-import net.sf.samtools.util.StringUtil;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-
 public class BeagleFeature implements Feature {
 
     private String chr;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java
index 4648efd1e..d12114f9a 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java
@@ -4,9 +4,8 @@ import org.broad.tribble.Feature;
 import org.broadinstitute.sting.gatk.refdata.Transcript;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.ArrayList;
 import java.util.List;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java
index 00b7c45d9..43e2c3ff5 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java
@@ -25,15 +25,15 @@
 
 package org.broadinstitute.sting.gatk.refdata.features.sampileup;
 
-import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.Feature;
+import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.exception.CodecLineParsingException;
 import org.broad.tribble.readers.LineReader;
 import org.broad.tribble.util.ParsingUtils;
 
 import java.util.ArrayList;
-import java.util.regex.Pattern;
 import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 import static org.broadinstitute.sting.gatk.refdata.features.sampileup.SAMPileupFeature.VariantType;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupFeature.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupFeature.java
index a794c2704..378f26934 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupFeature.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupFeature.java
@@ -25,12 +25,11 @@
 
 package org.broadinstitute.sting.gatk.refdata.features.sampileup;
 
+import net.sf.samtools.util.StringUtil;
 import org.broad.tribble.Feature;
 
 import java.util.List;
 
-import net.sf.samtools.util.StringUtil;
-
 /**
  * A tribble feature representing a SAM pileup.
  *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadCodec.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadCodec.java
index 15f559d46..039b8adde 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadCodec.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadCodec.java
@@ -24,14 +24,14 @@
 
 package org.broadinstitute.sting.gatk.refdata.features.samread;
 
+import net.sf.samtools.Cigar;
+import net.sf.samtools.TextCigarCodec;
+import net.sf.samtools.util.StringUtil;
 import org.broad.tribble.Feature;
 import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.exception.CodecLineParsingException;
 import org.broad.tribble.readers.LineReader;
 import org.broad.tribble.util.ParsingUtils;
-import net.sf.samtools.util.StringUtil;
-import net.sf.samtools.TextCigarCodec;
-import net.sf.samtools.Cigar;
 
 /**
  * Decodes a simple SAM text string.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/BedTableCodec.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/BedTableCodec.java
index b831606a3..745ccdd9f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/BedTableCodec.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/BedTableCodec.java
@@ -1,13 +1,8 @@
 package org.broadinstitute.sting.gatk.refdata.features.table;
 
 import org.broad.tribble.Feature;
-import org.broad.tribble.readers.LineReader;
 import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.exceptions.UserException;
 
-import java.io.IOException;
-import java.util.ArrayList;
 import java.util.Arrays;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java
index 6f0a712bf..ab1ac59d8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java
@@ -1,16 +1,14 @@
 package org.broadinstitute.sting.gatk.refdata.features.table;
 
 import org.broad.tribble.Feature;
-import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.readers.LineReader;
 import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
-import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.interval.IntervalUtils;
 
 import java.io.IOException;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
 
 /**
  * implementation of a simple table (tab or comma delimited format) input files
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java
index 4b4ebe450..ca73ee960 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java
@@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.refdata.features.table;
 import org.broad.tribble.Feature;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
-import java.util.*;
+import java.util.List;
 
 /**
  * A feature representing a single row out of a text table
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/indexer/RMDIndexer.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/indexer/RMDIndexer.java
index 5bb65f9a2..085d6b5b3 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/indexer/RMDIndexer.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/indexer/RMDIndexer.java
@@ -10,7 +10,6 @@ import org.broad.tribble.util.LittleEndianOutputStream;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.CommandLineProgram;
 import org.broadinstitute.sting.commandline.Input;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
 import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/QueryableTrack.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/QueryableTrack.java
index 19050ae11..731df997d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/QueryableTrack.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/QueryableTrack.java
@@ -28,7 +28,6 @@ import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
 import java.io.IOException;
-import java.util.Iterator;
 
 /**
  * @author aaron
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java
index 3b9f8243f..ba1ca674e 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java
@@ -35,8 +35,6 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.io.File;
 import java.io.IOException;
-import java.lang.reflect.Type;
-import java.util.Iterator;
 
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java
index c2057ad5e..19c91be1b 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java
@@ -42,15 +42,17 @@ import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
 import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.SequenceDictionaryUtils;
-import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+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.file.FSLockWithShared;
 import org.broadinstitute.sting.utils.file.FileSystemInabilityToLockException;
 import org.broadinstitute.sting.utils.instrumentation.Sizeof;
 
-import java.io.*;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
 import java.util.*;
 
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java
index 462bf98df..104ba87b5 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java
@@ -28,8 +28,6 @@ import org.broad.tribble.Feature;
 import org.broad.tribble.iterators.CloseableTribbleIterator;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 
-import java.util.Iterator;
-
 
 /**
  * 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java
index 1553402a5..59e8471a3 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java
@@ -28,8 +28,6 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 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 org.broadinstitute.sting.utils.exceptions.UserException;
 
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/LocationAwareSeekableRODIterator.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/LocationAwareSeekableRODIterator.java
index 83aa5f056..96086598a 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/LocationAwareSeekableRODIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/LocationAwareSeekableRODIterator.java
@@ -2,12 +2,8 @@ package org.broadinstitute.sting.gatk.refdata.utils;
 
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.util.CloseableIterator;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
-import java.util.Iterator;
-import java.util.List;
-
 /**
  * @author aaron
  *         <p/>
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/StringToGenomeLocIteratorAdapter.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/StringToGenomeLocIteratorAdapter.java
index 101784d97..fc7f7c58f 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/StringToGenomeLocIteratorAdapter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/StringToGenomeLocIteratorAdapter.java
@@ -25,10 +25,10 @@
 
 package org.broadinstitute.sting.gatk.refdata.utils;
 
+import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.bed.BedParser;
-import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
 
 import java.util.Iterator;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java
index 75e7c1a32..3201769e0 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java
@@ -3,8 +3,8 @@ package org.broadinstitute.sting.gatk.refdata.utils.helpers;
 import net.sf.samtools.util.SequenceUtil;
 import org.broad.tribble.annotation.Strand;
 import org.broad.tribble.dbsnp.DbSNPFeature;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Arrays;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
index e1085c6b2..89a179d0e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
@@ -25,11 +25,11 @@
 package org.broadinstitute.sting.gatk.traversals;
 
 import org.apache.log4j.Logger;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.gatk.ReadMetrics;
 import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
 import org.broadinstitute.sting.gatk.datasources.reads.Shard;
 import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.ReadMetrics;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -38,7 +38,10 @@ import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.PrintStream;
-import java.util.*;
+import java.util.Arrays;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
 
 public abstract class TraversalEngine<M,T,WalkerType extends Walker<M,T>,ProviderType extends ShardDataProvider> {
     // Time in milliseconds since we initialized this engine
diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java
index 89ff688a7..1ba48ca5f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java
@@ -28,12 +28,11 @@ package org.broadinstitute.sting.gatk.traversals;
 import net.sf.samtools.SAMRecord;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.datasources.providers.ReadView;
 import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider;
+import org.broadinstitute.sting.gatk.datasources.providers.ReadView;
 import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
 import org.broadinstitute.sting.gatk.walkers.DuplicateWalker;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
 
 import java.util.*;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java
index 240176f2f..232989fb0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java
@@ -10,7 +10,6 @@ import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java
index f15a20cd3..196d54036 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java
@@ -1,16 +1,18 @@
 package org.broadinstitute.sting.gatk.traversals;
 
-import org.broadinstitute.sting.gatk.walkers.Requires;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.ReadPairWalker;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMRecordCoordinateComparator;
+import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider;
 import org.broadinstitute.sting.gatk.datasources.providers.ReadView;
 import org.broadinstitute.sting.gatk.datasources.reads.Shard;
-import org.apache.log4j.Logger;
-import net.sf.samtools.SAMRecord;
-import net.sf.samtools.SAMRecordCoordinateComparator;
+import org.broadinstitute.sting.gatk.walkers.DataSource;
+import org.broadinstitute.sting.gatk.walkers.ReadPairWalker;
+import org.broadinstitute.sting.gatk.walkers.Requires;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
 
 /**
  * Traverse over a collection of read pairs, assuming that a given shard will contain all pairs.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java
index 670676b48..06e4539c4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java
@@ -2,14 +2,16 @@ package org.broadinstitute.sting.gatk.traversals;
 
 import net.sf.samtools.SAMRecord;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.gatk.WalkerManager;
 import org.broadinstitute.sting.gatk.ReadMetrics;
+import org.broadinstitute.sting.gatk.WalkerManager;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.datasources.providers.*;
+import org.broadinstitute.sting.gatk.datasources.providers.ReadBasedReferenceOrderedView;
+import org.broadinstitute.sting.gatk.datasources.providers.ReadReferenceView;
+import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider;
+import org.broadinstitute.sting.gatk.datasources.providers.ReadView;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
 /*
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/Allows.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/Allows.java
index a29e51189..2541921e9 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/Allows.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/Allows.java
@@ -1,11 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers;
 
-import java.lang.annotation.Documented;
-import java.lang.annotation.Inherited;
-import java.lang.annotation.Retention;
-import java.lang.annotation.RetentionPolicy;
-import java.lang.annotation.Target;
-import java.lang.annotation.ElementType;
+import java.lang.annotation.*;
 /**
  * User: hanna
  * Date: May 19, 2009
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/BAQMode.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/BAQMode.java
index 99dd46cbe..03097887d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/BAQMode.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/BAQMode.java
@@ -1,11 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers;
 
-import java.lang.annotation.Documented;
-import java.lang.annotation.Inherited;
-import java.lang.annotation.Retention;
-import java.lang.annotation.RetentionPolicy;
-import java.lang.annotation.Target;
-import java.lang.annotation.ElementType;
+import java.lang.annotation.*;
 
 /**
  * User: hanna
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/By.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/By.java
index 25455b587..8fa6a4c1b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/By.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/By.java
@@ -1,11 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers;
 
-import java.lang.annotation.Documented;
-import java.lang.annotation.Inherited;
-import java.lang.annotation.Retention;
-import java.lang.annotation.RetentionPolicy;
-import java.lang.annotation.Target;
-import java.lang.annotation.ElementType;
+import java.lang.annotation.*;
 /**
  * User: hanna
  * Date: May 14, 2009
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
index 1a3f87a7a..ca4e3f5e3 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
@@ -25,29 +25,29 @@
 
 package org.broadinstitute.sting.gatk.walkers;
 
-import net.sf.samtools.*;
-import net.sf.picard.reference.ReferenceSequenceFileFactory;
-import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.picard.reference.ReferenceSequence;
-import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import net.sf.picard.reference.ReferenceSequenceFile;
+import net.sf.picard.reference.ReferenceSequenceFileFactory;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.util.StringUtil;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.utils.*;
+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.utils.BaseUtils;
+import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.clipreads.ClippingOp;
 import org.broadinstitute.sting.utils.clipreads.ClippingRepresentation;
 import org.broadinstitute.sting.utils.clipreads.ReadClipper;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.utils.sam.ReadUtils;
 
-import java.util.*;
-import java.util.regex.Pattern;
-import java.util.regex.Matcher;
 import java.io.File;
 import java.io.PrintStream;
-
-import net.sf.samtools.util.StringUtil;
-import org.broadinstitute.sting.utils.sam.ReadUtils;
+import java.util.*;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 /**
  * This ReadWalker provides simple, yet powerful read clipping capabilities.  It allows the user to clip bases in reads
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/DuplicateWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/DuplicateWalker.java
index 1fc606f07..4bfedb672 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/DuplicateWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/DuplicateWalker.java
@@ -1,16 +1,13 @@
 package org.broadinstitute.sting.gatk.walkers;
 
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter;
 import org.broadinstitute.sting.gatk.filters.NotPrimaryAlignmentReadFilter;
+import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
 import java.util.List;
 import java.util.Set;
-import java.util.Arrays;
-
-import net.sf.samtools.SAMRecord;
-import net.sf.picard.filter.SamRecordFilter;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNamesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNamesWalker.java
index a272150c7..56287df31 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNamesWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNamesWalker.java
@@ -26,7 +26,6 @@
 package org.broadinstitute.sting.gatk.walkers;
 
 import net.sf.samtools.SAMFileWriter;
-import net.sf.samtools.SAMReadGroupRecord;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java
index 13a55eaac..fcfcb81b5 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java
@@ -1,13 +1,13 @@
 package org.broadinstitute.sting.gatk.walkers;
 
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 
+import java.io.PrintStream;
 import java.text.DecimalFormat;
 import java.text.NumberFormat;
-import java.io.PrintStream;
 
 
 /*
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/GCContentByIntervalWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/GCContentByIntervalWalker.java
index c0f469973..68bea4dba 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/GCContentByIntervalWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/GCContentByIntervalWalker.java
@@ -28,13 +28,12 @@ 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.*;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
 
 import java.io.PrintStream;
-import java.util.*;
+import java.util.List;
 
 /**
  * Walks along reference and calculates the GC content for each interval.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java
index fc4b403c5..b0b2687f4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java
@@ -1,9 +1,12 @@
 package org.broadinstitute.sting.gatk.walkers;
 
-import org.broadinstitute.sting.gatk.filters.*;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.filters.DuplicateReadFilter;
+import org.broadinstitute.sting.gatk.filters.FailsVendorQualityCheckReadFilter;
+import org.broadinstitute.sting.gatk.filters.NotPrimaryAlignmentReadFilter;
+import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
index 84d868c1a..508d1f6ee 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
@@ -26,22 +26,22 @@
 package org.broadinstitute.sting.gatk.walkers;
 
 import org.broad.tribble.dbsnp.DbSNPFeature;
+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;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
-import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
+import java.io.PrintStream;
 import java.util.ArrayList;
 import java.util.List;
-import java.io.PrintStream;
 
 /**
  * Prints the alignment in the pileup format. In the pileup format, each line represents a genomic position,
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java
index 9ac3fc0e6..158992a22 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java
@@ -25,15 +25,15 @@
 
 package org.broadinstitute.sting.gatk.walkers;
 
+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.refdata.VariantContextAdaptors;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
-import org.broadinstitute.sting.commandline.Output;
 
-import java.util.Iterator;
 import java.io.PrintStream;
+import java.util.Iterator;
 
 /**
  * Prints out all of the RODs in the input data set. Data is rendered using the toString() method
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
index 07938d322..a189c00b5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
@@ -28,14 +28,12 @@ package org.broadinstitute.sting.gatk.walkers;
 import net.sf.samtools.SAMFileWriter;
 import net.sf.samtools.SAMReadGroupRecord;
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.utils.baq.BAQ;
 
-import java.io.PrintStream;
-
 /**
  * Renders, in SAM/BAM format, all reads from the input data set in the order in which they appear
  * in the input file.  It can dynamically merge the contents of multiple input BAM files, resulting
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java
index a5486fd9a..db2038aa3 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.gatk.walkers;
 
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/Requires.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/Requires.java
index 6c1e64c4e..e9a381a85 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/Requires.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/Requires.java
@@ -1,11 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers;
 
-import java.lang.annotation.Documented;
-import java.lang.annotation.Inherited;
-import java.lang.annotation.Retention;
-import java.lang.annotation.RetentionPolicy;
-import java.lang.annotation.Target;
-import java.lang.annotation.ElementType;
+import java.lang.annotation.*;
 /**
  * User: hanna
  * Date: May 19, 2009
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java
index 014acff9c..486d233b7 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java
@@ -25,14 +25,20 @@
 
 package org.broadinstitute.sting.gatk.walkers;
 
-import net.sf.samtools.*;
-import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.utils.sam.ReadUtils;
+import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMFileWriter;
+import net.sf.samtools.SAMReadGroupRecord;
+import net.sf.samtools.SAMRecord;
 import org.apache.log4j.Logger;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.utils.sam.ReadUtils;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 /**
  * Divides the input data set into separate BAM files, one for each sample in the input data set.  The split
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
index f0ba8bb46..384742302 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
@@ -25,14 +25,14 @@
 
 package org.broadinstitute.sting.gatk.walkers;
 
-import java.util.List;
-
+import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.filters.MalformedReadFilter;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.apache.log4j.Logger;
+
+import java.util.List;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/WalkerName.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/WalkerName.java
index 0e4d40675..4d46607e5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/WalkerName.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/WalkerName.java
@@ -1,10 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers;
 
-import java.lang.annotation.Documented;
-import java.lang.annotation.ElementType;
-import java.lang.annotation.Retention;
-import java.lang.annotation.RetentionPolicy;
-import java.lang.annotation.Target;
+import java.lang.annotation.*;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/Window.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/Window.java
index 0b718071d..9827fdf09 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/Window.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/Window.java
@@ -25,7 +25,10 @@
 
 package org.broadinstitute.sting.gatk.walkers;
 
-import java.lang.annotation.*;
+import java.lang.annotation.Documented;
+import java.lang.annotation.Inherited;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
 
 /**
  * Describes the size of the window into the genome.  Has differing semantics based on
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
index b02dcd8e2..3144098a8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
@@ -25,21 +25,21 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 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.annotator.interfaces.*;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Map;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Arrays;
+import java.util.Map;
 
 
 public class AlleleBalance implements InfoFieldAnnotation {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
index 51d290763..a99f87a70 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
@@ -1,12 +1,16 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+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.annotator.interfaces.ExperimentalAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
+import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.gatk.contexts.*;
-import org.broadinstitute.sting.utils.variantcontext.*;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java
index 51b5381dc..6c14e7445 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java
@@ -1,8 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+
 import java.util.Map;
 
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
index 244627154..66416ce11 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
@@ -31,19 +31,19 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 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.annotator.interfaces.*;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Map;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Arrays;
+import java.util.Map;
 
 
 public class BaseCounts implements InfoFieldAnnotation {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
index ff916bedd..2a5c996f7 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
@@ -1,16 +1,16 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
-import java.util.Arrays;
 
 
 public class BaseQualityRankSumTest extends RankSumTest {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
index f3ec2b1df..74f7f9d80 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
@@ -25,18 +25,22 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
-import java.util.*;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 
 public class ChromosomeCounts implements InfoFieldAnnotation, StandardAnnotation {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
index e56825dbe..c384e0d09 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
@@ -1,18 +1,19 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 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.annotator.interfaces.*;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Map;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Arrays;
+import java.util.Map;
 
 
 public class DepthOfCoverage implements InfoFieldAnnotation, StandardAnnotation {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
index ee66b50ee..e3e8bc258 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
@@ -1,21 +1,20 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFCompoundHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 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.annotator.interfaces.GenotypeAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
index 2115526a6..97ed221e7 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
@@ -24,20 +24,20 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import cern.jet.math.Arithmetic;
 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.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
-import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import cern.jet.math.Arithmetic;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
index 5eaa30bf3..48677bbe5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
@@ -1,18 +1,19 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 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.annotator.interfaces.*;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Map;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Arrays;
+import java.util.Map;
 
 
 public class GCContent implements InfoFieldAnnotation, ExperimentalAnnotation {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GLstats.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GLstats.java
index 3a5db2884..cca0ad4bc 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GLstats.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GLstats.java
@@ -1,19 +1,20 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 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.annotator.interfaces.*;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Map;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Arrays;
+import java.util.Map;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
index bd8c51a41..b175579f1 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
@@ -24,25 +24,29 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
+import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.QualityUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.genotype.Haplotype;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
-import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
-import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.genotype.Haplotype;
-import org.broadinstitute.sting.utils.pileup.*;
 
 import java.util.*;
-import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 
 public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
     private final static boolean DEBUG = false;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
index ecebfbbd2..d86728d5e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
@@ -1,20 +1,21 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broad.tribble.util.popgen.HardyWeinbergCalculation;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 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.annotator.interfaces.*;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.WorkInProgressAnnotation;
 import org.broadinstitute.sting.utils.QualityUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Map;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Arrays;
+import java.util.Map;
 
 
 public class HardyWeinberg implements InfoFieldAnnotation, WorkInProgressAnnotation {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
index 099780fa7..02efd854c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
@@ -1,19 +1,19 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 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.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Map;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Arrays;
+import java.util.Map;
 
 
 public class HomopolymerRun implements InfoFieldAnnotation, StandardAnnotation {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java
index ee8b01d7d..12b48473d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java
@@ -1,14 +1,14 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 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.annotator.interfaces.ExperimentalAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.IndelUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
index f23433bb5..1d999c531 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
@@ -1,19 +1,19 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 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.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Map;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Arrays;
+import java.util.Map;
 
 
 public class LowMQ implements InfoFieldAnnotation {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
index 8260a5a81..cc62580a9 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
@@ -1,17 +1,17 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
 import org.broadinstitute.sting.utils.QualityUtils;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
-import java.util.Arrays;
 
 
 public class MappingQualityRankSumTest extends RankSumTest {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
index 25a7b286d..f240d02bc 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
@@ -1,16 +1,16 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 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.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
index 00cc30309..0ca53adf2 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
@@ -25,22 +25,22 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Map;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Arrays;
+import java.util.Map;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
index dc4934ade..08a25a7e3 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
@@ -1,15 +1,15 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 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.annotator.interfaces.ExperimentalAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
index 3b64abfff..1c70a1b33 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
@@ -1,14 +1,14 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 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.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
index 720984835..2175d39e6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
@@ -1,19 +1,19 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 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.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Map;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Arrays;
+import java.util.Map;
 
 
 public class QualByDepth extends AnnotationByDepth implements InfoFieldAnnotation, StandardAnnotation {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
index 1ef7ccd0b..d52f07b58 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
@@ -1,20 +1,23 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.QualityUtils;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 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.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.QualityUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.*;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 
 public class RMSMappingQuality implements InfoFieldAnnotation, StandardAnnotation {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
index f00abd6a1..5466828f6 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
@@ -1,22 +1,23 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 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.annotator.interfaces.*;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.MannWhitneyU;
+import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.List;
 import java.util.ArrayList;
-import java.util.Map;
 import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java
index a670532af..c56e2622d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java
@@ -26,25 +26,24 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
-import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFCompoundHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Map;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Arrays;
+import java.util.Map;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
index 727904a3b..aabfb2970 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
@@ -1,14 +1,17 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import net.sf.samtools.Cigar;
+import net.sf.samtools.CigarElement;
+import net.sf.samtools.CigarOperator;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
 import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
-import net.sf.samtools.*;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java
index fc769ac54..a5ebd8db2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java
@@ -1,13 +1,13 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 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.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
index e2fd2a3d4..ff9092a71 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
@@ -25,15 +25,15 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 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.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
index 0b6cbcc2e..a4668eeb6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
@@ -1,14 +1,14 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 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.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java
index 351117809..b46d82d8b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java
@@ -5,7 +5,6 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.utils.IndelUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
@@ -13,7 +12,10 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.*;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
index cd5b6694b..acbeee3b2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
@@ -25,24 +25,23 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Hidden;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationType;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.classloader.PluginManager;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
index 54c8be73a..fdf498a3d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
@@ -25,30 +25,27 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.LinkedHashMap;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.Map.Entry;
-
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
-import org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator.*;
+import org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator.GenomicAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator.JoinTable;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationInterfaceManager;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+import java.util.*;
+import java.util.Map.Entry;
 
 
 public class VariantAnnotatorEngine {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java
index e02c62baf..05c1b3c52 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java
@@ -25,13 +25,6 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator;
 
-import java.util.*;
-import java.util.Map.Entry;
-
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -39,7 +32,14 @@ import org.broadinstitute.sting.gatk.refdata.features.annotator.AnnotatorInputTa
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+import java.util.*;
+import java.util.Map.Entry;
 
 /**
  * This plugin for {@link VariantAnnotatorEngine} serves as the core
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java
index 69a35a584..b42310780 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java
@@ -26,28 +26,28 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator;
 
-import java.io.File;
-import java.io.IOException;
-import java.util.*;
-import java.util.Map.Entry;
-
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 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.AlignmentContextUtils;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.features.annotator.AnnotatorInputTableCodec;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.*;
+import java.util.Map.Entry;
 
 /**
  * Annotates variant calls with information from user-specified tabular files.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java
index c57aacb5b..714f374cf 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java
@@ -25,6 +25,9 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator;
 
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileReader;
@@ -33,9 +36,6 @@ import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-
 /**
  * This is a container that holds all data corresponding to a single join table as specified by one -J arg (ex: -J bindingName1,/path/to/file,bindingName1.columnName=bindingName2.columnName2).
  * Some terminology:
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java
index d3fcfd42a..3b6c87f90 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java
@@ -25,16 +25,16 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator;
 
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-
 /**
  * Used to parse files passed to the GenomicAnnotator via the -J arg.
  * The files must be tab-delimited, and the first non-empty/non-commented line
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java
index 0ed61fc48..0bbfa51b4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java
@@ -24,9 +24,6 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator;
 
-import java.io.*;
-import java.util.*;
-
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -36,17 +33,15 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.features.annotator.AnnotatorInputTableCodec;
 import org.broadinstitute.sting.gatk.refdata.features.annotator.AnnotatorInputTableFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
-import org.broadinstitute.sting.gatk.walkers.By;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.RMD;
-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.*;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
+import java.io.IOException;
+import java.io.PrintStream;
+import java.util.*;
+
 /**
  *  Takes a table of transcripts (eg. UCSC refGene, knownGene, and CCDS tables) and generates the big table which contains
  *  annotations for each possible variant at each transcript position (eg. 4 variants at each genomic position).
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
index 29b256479..57bc44ab8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
@@ -1,14 +1,14 @@
 package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
 
+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.utils.codecs.vcf.VCFFormatHeaderLine;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 
-import java.util.Map;
 import java.util.List;
+import java.util.Map;
 
 public interface GenotypeAnnotation {
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
index 5b33395b5..4e850d01b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
@@ -1,13 +1,13 @@
 package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Map;
 import java.util.List;
+import java.util.Map;
 
 public interface InfoFieldAnnotation {
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
index aa23abc67..21c8ec430 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
@@ -25,26 +25,26 @@
 
 package org.broadinstitute.sting.gatk.walkers.beagle;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 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.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.gatk.refdata.features.beagle.BeagleFeature;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.sting.gatk.refdata.features.beagle.BeagleFeature;
 import org.broadinstitute.sting.gatk.walkers.RMD;
 import org.broadinstitute.sting.gatk.walkers.Requires;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.util.*;
+
 import static java.lang.Math.log10;
 
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
index 93ee0b085..3eed12992 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
@@ -25,10 +25,6 @@
 
 package org.broadinstitute.sting.gatk.walkers.beagle;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.commandline.Input;
@@ -36,17 +32,20 @@ import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.RMD;
 import org.broadinstitute.sting.gatk.walkers.Requires;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VQSRCalibrationCurve;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.StingException;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.io.File;
 import java.io.PrintStream;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java
index 18aa3e257..f6cd1d636 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java
@@ -25,28 +25,29 @@
 
 package org.broadinstitute.sting.gatk.walkers.beagle;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 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.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RMD;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.io.PrintStream;
-import java.util.*;
+import java.util.Arrays;
+import java.util.Set;
 
 /**
  * Produces an input file to Beagle imputation engine, listing unphased, hard-called genotypes for a single sample
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java
index 2c67265d6..90e6fcd77 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java
@@ -22,6 +22,8 @@
 
 package org.broadinstitute.sting.gatk.walkers.coverage;
 
+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;
@@ -31,12 +33,10 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
 
 import java.io.File;
-import java.io.PrintStream;
 import java.io.FileNotFoundException;
+import java.io.PrintStream;
 
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java
index ae947eac1..405a44c29 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java
@@ -26,12 +26,11 @@
 package org.broadinstitute.sting.gatk.walkers.coverage;
 
 import net.sf.samtools.SAMRecord;
-
-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.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 
 import java.io.PrintStream;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java
index 5a9c62b7f..6b91b0198 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java
@@ -22,19 +22,19 @@
 
 package org.broadinstitute.sting.gatk.walkers.coverage;
 
+import org.broad.tribble.bed.FullBEDFeature;
+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;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
-import org.broad.tribble.bed.FullBEDFeature;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
-import java.util.*;
 import java.io.PrintStream;
+import java.util.Arrays;
+import java.util.List;
 
 /**
  * Test routine for new VariantContext object
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
index 298aa90b9..a41e55166 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
@@ -8,7 +8,9 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 
-import java.util.*;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Map;
 
 /**
  * IF THERE IS NO JAVADOC RIGHT HERE, YELL AT chartl
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
index 91ae81cd5..c1956f1d7 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
@@ -26,6 +26,8 @@
 package org.broadinstitute.sting.gatk.walkers.coverage;
 
 import net.sf.samtools.SAMReadGroupRecord;
+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;
@@ -34,12 +36,13 @@ import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqCodec;
 import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
-import org.broadinstitute.sting.gatk.refdata.utils.*;
+import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
+import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
+import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
index a5ebf27bb..15b16ca6b 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
@@ -24,22 +24,15 @@
 
 package org.broadinstitute.sting.gatk.walkers.diffengine;
 
-import net.sf.samtools.*;
+import net.sf.samtools.SAMFileReader;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMRecordIterator;
 import net.sf.samtools.util.BlockCompressedInputStream;
-import org.broad.tribble.readers.AsciiLineReader;
-import org.broad.tribble.readers.LineReader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.io.DataInputStream;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.util.Arrays;
-import java.util.Map;
-import java.util.zip.GZIPInputStream;
 
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java
index 4c3f7bd95..eb8a71c2c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java
@@ -24,7 +24,9 @@
 
 package org.broadinstitute.sting.gatk.walkers.diffengine;
 
-import com.google.java.contract.*;
+import com.google.java.contract.Ensures;
+import com.google.java.contract.Invariant;
+import com.google.java.contract.Requires;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java
index 3750496a1..963191446 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java
@@ -24,8 +24,6 @@
 
 package org.broadinstitute.sting.gatk.walkers.diffengine;
 
-import org.broadinstitute.sting.utils.Utils;
-
 /**
  * Created by IntelliJ IDEA.
  * User: depristo
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
index a812babaf..4e44578c7 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
@@ -30,7 +30,10 @@ import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.io.*;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileReader;
+import java.io.IOException;
 import java.util.Map;
 
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
index 828d39717..efc101618 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
@@ -25,13 +25,13 @@
 
 package org.broadinstitute.sting.gatk.walkers.fasta;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 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.*;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.Collection;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java
index 6be2336c0..2dbfc76ff 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java
@@ -25,16 +25,15 @@
 
 package org.broadinstitute.sting.gatk.walkers.fasta;
 
+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;
 import org.broadinstitute.sting.gatk.walkers.RefWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
 
 import java.io.PrintStream;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java
index b31526987..2c009f7f2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.filters;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 public class ClusteredSnps {
     private GenomeLocParser genomeLocParser;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java
index c3849e240..ede19746a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java
@@ -25,8 +25,8 @@
 
 package org.broadinstitute.sting.gatk.walkers.filters;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 
 public class FiltrationContext {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java
index 225cdecc3..d7c0dd4d5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java
@@ -27,7 +27,9 @@ package org.broadinstitute.sting.gatk.walkers.filters;
 
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.*;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.ListIterator;
 
 /**
  * A window of variants surrounding the current variant being investigated
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
index 884d0ac24..6c023573a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
@@ -25,21 +25,20 @@
 
 package org.broadinstitute.sting.gatk.walkers.filters;
 
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.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.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
index 47be7e6fe..83a8ce7d7 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
@@ -26,14 +26,15 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.PrintStream;
-import java.util.*;
+import java.util.Map;
+import java.util.Set;
 
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidIndelGenotypePriors.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidIndelGenotypePriors.java
index 22c9dcf91..696a74de8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidIndelGenotypePriors.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidIndelGenotypePriors.java
@@ -4,8 +4,6 @@ import org.broadinstitute.sting.gatk.walkers.indels.HaplotypeIndelErrorModel;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
 
-import java.util.Arrays;
-
 /**
  * Created by IntelliJ IDEA.
  * User: delangel
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
index ab075eaf2..2014801e4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
@@ -26,13 +26,14 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import net.sf.samtools.SAMUtils;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.pileup.FragmentPileup;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
-import org.broadinstitute.sting.utils.sam.ReadUtils;
+import org.broadinstitute.sting.utils.pileup.FragmentPileup;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
 import static java.lang.Math.log10;
 import static java.lang.Math.pow;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
index 89504b371..5c27bc943 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
@@ -26,17 +26,22 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.apache.log4j.Logger;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.SimpleTimer;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.exceptions.UserException;
 import sun.reflect.generics.reflectiveObjects.NotImplementedException;
 
-import java.util.*;
 import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
 
 public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
     //
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
index 3902a0b7f..8261cd588 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
@@ -30,11 +30,11 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 
 import java.util.Map;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GridSearchAFEstimation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GridSearchAFEstimation.java
index c4e315f68..10b646d63 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GridSearchAFEstimation.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GridSearchAFEstimation.java
@@ -26,18 +26,18 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.*;
 import java.io.PrintStream;
+import java.util.*;
 
 public class GridSearchAFEstimation extends AlleleFrequencyCalculationModel {
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
index 1f430548b..be2039780 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
@@ -25,16 +25,14 @@
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
-import net.sf.samtools.SAMRecord;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.indels.HaplotypeIndelErrorModel;
 import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
-import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.genotype.Haplotype;
@@ -42,11 +40,10 @@ import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/MultiallelicGenotypeLikelihoods.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/MultiallelicGenotypeLikelihoods.java
index 2cf149fd0..3652763de 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/MultiallelicGenotypeLikelihoods.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/MultiallelicGenotypeLikelihoods.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.exceptions.StingException;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 
 import java.util.ArrayList;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
index 9f4d4182f..3e3cd128b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
@@ -25,23 +25,25 @@
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.apache.log4j.Logger;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
 
 public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsCalculationModel {
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java
index cf1c57a05..22c3081a3 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java
@@ -25,8 +25,6 @@
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.ArgumentCollection;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.DownsampleType;
@@ -36,8 +34,12 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.*;
+import java.util.HashSet;
+import java.util.Set;
+import java.util.TreeSet;
 
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java
index 1533e8777..68d8f9b54 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java
@@ -24,19 +24,19 @@
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.ArgumentCollection;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
index 055eb0b97..2b25df4aa 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
@@ -27,7 +27,6 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Hidden;
-import org.broadinstitute.sting.commandline.Input;
 
 import java.io.File;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index fc8a5819a..2a0338bca 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -25,22 +25,25 @@
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
-import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableReadFilter;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.gatk.contexts.*;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.ArgumentCollection;
+import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.DownsampleType;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.filters.BadMateFilter;
+import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableReadFilter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
-import org.broadinstitute.sting.gatk.DownsampleType;
-import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
-import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 
-import java.util.*;
 import java.io.PrintStream;
+import java.util.*;
 
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index 6fc972b5d..a10897172 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -25,22 +25,24 @@
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
+import com.google.java.contract.Requires;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.baq.BAQ;
-import org.broadinstitute.sting.utils.pileup.*;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import com.google.java.contract.*;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.PrintStream;
 import java.util.*;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
index df1f4f908..adb7c4c38 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
@@ -1,11 +1,13 @@
 package org.broadinstitute.sting.gatk.walkers.indels;
 
 import net.sf.picard.sam.SamPairUtil;
-import net.sf.samtools.*;
+import net.sf.samtools.SAMFileWriter;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMRecordComparator;
+import net.sf.samtools.SAMRecordCoordinateComparator;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.util.*;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
index 7617aa9de..e68aa31e0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
@@ -25,21 +25,16 @@
 
 package org.broadinstitute.sting.gatk.walkers.indels;
 
-import net.sf.samtools.AlignmentBlock;
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.gatk.walkers.genotyper.ExactAFCalculationModel;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.QualityUtils;
-import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.genotype.Haplotype;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 
 import java.util.Arrays;
 import java.util.HashMap;
-import java.util.List;
 
 public class HaplotypeIndelErrorModel {
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index a53665d64..61f21c488 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -25,39 +25,41 @@
 
 package org.broadinstitute.sting.gatk.walkers.indels;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.samtools.*;
 import net.sf.samtools.util.RuntimeIOException;
-import net.sf.samtools.util.StringUtil;
 import net.sf.samtools.util.SequenceUtil;
-import net.sf.picard.reference.IndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.commandline.*;
+import net.sf.samtools.util.StringUtil;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Hidden;
+import org.broadinstitute.sting.commandline.Input;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
-import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
-import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.exceptions.StingException;
-import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
-import org.broadinstitute.sting.utils.interval.IntervalUtils;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.*;
-import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.walkers.BAQMode;
 import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
+import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
+import org.broadinstitute.sting.gatk.walkers.BAQMode;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.baq.BAQ;
+import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.StingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.interval.IntervalFileMergingIterator;
+import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
+import org.broadinstitute.sting.utils.interval.IntervalUtils;
 import org.broadinstitute.sting.utils.interval.NwayIntervalMergingIterator;
+import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.sam.NWaySAMFileWriter;
+import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.utils.sam.AlignmentUtils;
-import org.broadinstitute.sting.utils.sam.ReadUtils;
-import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
 import java.io.FileNotFoundException;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
index 010e0cf6f..af8051334 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
@@ -25,8 +25,10 @@
 
 package org.broadinstitute.sting.gatk.walkers.indels;
 
-import net.sf.samtools.*;
-import org.broadinstitute.sting.commandline.*;
+import net.sf.samtools.Cigar;
+import net.sf.samtools.SAMRecord;
+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;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
index ab7ae4184..60262d6f4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
@@ -28,30 +28,25 @@ package org.broadinstitute.sting.gatk.walkers.indels;
 import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
 import net.sf.samtools.CigarOperator;
-import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-/*import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.Covariate;
-import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalDataManager;
-import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalDatum;
-import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalibrationArgumentCollection;
-*/import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.QualityUtils;
-import org.broadinstitute.sting.utils.classloader.PluginManager;
-import org.broadinstitute.sting.utils.collections.NestedHashMap;
-import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.genotype.Haplotype;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
-import org.broadinstitute.sting.utils.text.XReadLines;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 
 import java.io.File;
-import java.io.FileNotFoundException;
-import java.util.*;
-import java.util.regex.Pattern;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+
+/*import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.Covariate;
+import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalDataManager;
+import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalDatum;
+import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalibrationArgumentCollection;
+*/
 
 
 public class PairHMMIndelErrorModel {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignedReadCounter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignedReadCounter.java
index fc196e712..2c89b907b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignedReadCounter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignedReadCounter.java
@@ -25,19 +25,23 @@
 
 package org.broadinstitute.sting.gatk.walkers.indels;
 
-import net.sf.samtools.*;
-import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.*;
-import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.gatk.filters.BadMateFilter;
-import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.interval.IntervalFileMergingIterator;
-import org.broadinstitute.sting.utils.sam.ReadUtils;
+import net.sf.samtools.CigarElement;
+import net.sf.samtools.CigarOperator;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.filters.BadMateFilter;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.By;
+import org.broadinstitute.sting.gatk.walkers.DataSource;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.interval.IntervalFileMergingIterator;
+import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
+import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 import java.io.File;
-import java.util.*;
+import java.util.Iterator;
 
 @By(DataSource.READS)
 // walker to count realigned reads
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
index 3b94989aa..488e37f26 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
@@ -25,27 +25,27 @@
 
 package org.broadinstitute.sting.gatk.walkers.indels;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+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.filters.BadCigarFilter;
-import org.broadinstitute.sting.gatk.filters.Platform454Filter;
-import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
 import org.broadinstitute.sting.gatk.filters.BadMateFilter;
+import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
+import org.broadinstitute.sting.gatk.filters.Platform454Filter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.baq.BAQ;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.ArrayList;
 import java.io.PrintStream;
+import java.util.ArrayList;
 
 /**
  * Emits intervals for the Local Indel Realigner to target for cleaning.  Ignores 454 reads, MQ0 reads, and reads with consecutive indel operators in the CIGAR string.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SAMRecordCoordinateComparatorWithUnmappedReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SAMRecordCoordinateComparatorWithUnmappedReads.java
index 1fe3fdd04..3854a4a8c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SAMRecordCoordinateComparatorWithUnmappedReads.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SAMRecordCoordinateComparatorWithUnmappedReads.java
@@ -23,7 +23,8 @@
  */
 package org.broadinstitute.sting.gatk.walkers.indels;
 
-import net.sf.samtools.*;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMRecordCoordinateComparator;
 
 /**
  * Extends Picard's Comparator for sorting SAMRecords by coordinate.  This one actually deals with unmapped reads
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
index 1f05ddaf0..443e6e9f2 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
@@ -25,15 +25,21 @@
 
 package org.broadinstitute.sting.gatk.walkers.indels;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import net.sf.samtools.*;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Hidden;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.commandline.Tags;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
 import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource;
-import org.broadinstitute.sting.gatk.filters.*;
-import org.broadinstitute.sting.gatk.refdata.*;
+import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
+import org.broadinstitute.sting.gatk.filters.Platform454Filter;
+import org.broadinstitute.sting.gatk.filters.PlatformUnitFilter;
+import org.broadinstitute.sting.gatk.filters.PlatformUnitFilterHelper;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.refdata.SeekableRODIterator;
+import org.broadinstitute.sting.gatk.refdata.Transcript;
 import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqCodec;
 import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
@@ -42,22 +48,22 @@ import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODItera
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.gatk.walkers.ReadFilters;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.interval.IntervalUtils;
-import org.broadinstitute.sting.utils.interval.IntervalFileMergingIterator;
-import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
-import org.broadinstitute.sting.utils.interval.OverlappingIntervalIterator;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.exceptions.StingException;
-import org.broadinstitute.sting.utils.sam.AlignmentUtils;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocSortedSet;
+import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.collections.CircularArray;
 import org.broadinstitute.sting.utils.collections.PrimitivePair;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.commandline.Hidden;
-
-import net.sf.samtools.*;
+import org.broadinstitute.sting.utils.exceptions.StingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.interval.IntervalFileMergingIterator;
+import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
+import org.broadinstitute.sting.utils.interval.IntervalUtils;
+import org.broadinstitute.sting.utils.interval.OverlappingIntervalIterator;
+import org.broadinstitute.sting.utils.sam.AlignmentUtils;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.*;
 import java.util.*;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
index 869edf784..cb123c868 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
@@ -23,9 +23,9 @@
  */
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.ArrayList;
 import java.util.List;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java
index 81d9b4ddb..9aa370d3f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java
@@ -24,14 +24,10 @@
 
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.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.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.features.annotator.AnnotatorInputTableFeature;
@@ -41,9 +37,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator.AminoAci
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java
index 709bc44ce..5bd438605 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java
@@ -24,10 +24,6 @@
 
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -35,7 +31,11 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
index abced442e..b0491a281 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
@@ -24,20 +24,19 @@
 
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
-import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.picard.reference.ReferenceSequenceFile;
 import org.apache.log4j.Logger;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
+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.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.File;
 import java.io.FileNotFoundException;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java
index ec6f5c648..be15d4541 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java
@@ -24,20 +24,22 @@
 
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
index fbe6e5b5a..9702fd18c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
@@ -23,27 +23,28 @@
  */
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Hidden;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
 import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.DisjointSet;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.HasGenomeLocation;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.codecs.vcf.SortingVCFWriter;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.io.*;
 import java.util.*;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
index db1f888a1..153c4a23f 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
@@ -23,10 +23,10 @@
  */
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
 
 public class SNPallelePair extends AllelePair {
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/WriteVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/WriteVCF.java
index f82e48abd..2851ace0d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/WriteVCF.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/WriteVCF.java
@@ -24,9 +24,9 @@
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
 import org.apache.log4j.Logger;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 
 public class WriteVCF {
     public static void writeVCF(VariantContext vc, VCFWriter writer, Logger logger) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java
index feb5f62af..2bdd4558f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java
@@ -6,14 +6,12 @@ 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.refdata.utils.GATKFeature;
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.walkers.RefWalker;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
 
-import java.util.List;
 import java.io.PrintStream;
+import java.util.List;
 
 /**
  * Counts the number of contiguous regions the walker traverses over. Slower than it needs to be, but
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java
index ef6ff04f2..0d68c8493 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java
@@ -1,6 +1,5 @@
 package org.broadinstitute.sting.gatk.walkers.qc;
 
-import net.sf.samtools.SAMFileWriter;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountPairsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountPairsWalker.java
index cece04fcf..df89efe6d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountPairsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountPairsWalker.java
@@ -25,14 +25,14 @@
 
 package org.broadinstitute.sting.gatk.walkers.qc;
 
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.walkers.ReadPairWalker;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
-import org.broadinstitute.sting.commandline.Output;
-import net.sf.samtools.SAMRecord;
 
+import java.io.PrintStream;
 import java.util.Collection;
 import java.util.List;
-import java.io.PrintStream;
 
 /**
  * Counts the number of read pairs encountered in a file sorted in
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java
index 74f63aa2f..87c0409b9 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java
@@ -1,11 +1,11 @@
 package org.broadinstitute.sting.gatk.walkers.qc;
 
 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.Requires;
 import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.walkers.Requires;
 
 /**
  * Walks over the input data set, calculating the number of reads seen for diagnostic purposes.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java
index a4e80138f..d1545f159 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java
@@ -25,13 +25,13 @@
 
 package org.broadinstitute.sting.gatk.walkers.qc;
 
+import org.broadinstitute.sting.commandline.Argument;
 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.RefWalker;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.commandline.Argument;
 
 /**
  * Prints out counts of the number of reference ordered data objects are
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java
index 92867e1a9..8a03dea44 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java
@@ -27,23 +27,24 @@ package org.broadinstitute.sting.gatk.walkers.qc;
 
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.SAMSequenceRecord;
+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;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
 
+import java.io.PrintStream;
 import java.util.ArrayList;
-import java.util.List;
 import java.util.Collection;
 import java.util.LinkedList;
-import java.io.PrintStream;
+import java.util.List;
 
 /**
  * Prints out counts of the number of reference ordered data objects are
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java
index 5ae35416a..b5f5442cd 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java
@@ -25,22 +25,22 @@
 
 package org.broadinstitute.sting.gatk.walkers.qc;
 
-import org.broadinstitute.sting.gatk.walkers.Requires;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.collections.PrimitivePair;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.sam.AlignmentUtils;
+import net.sf.samtools.SAMReadGroupRecord;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
-import net.sf.samtools.SAMRecord;
-import net.sf.samtools.SAMReadGroupRecord;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.DataSource;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.walkers.Requires;
+import org.broadinstitute.sting.utils.collections.PrimitivePair;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 
-import java.util.*;
 import java.io.*;
+import java.util.*;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java
index 39b69ba29..d3b992cb5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java
@@ -1,16 +1,16 @@
 package org.broadinstitute.sting.gatk.walkers.qc;
 
+import net.sf.samtools.SAMRecord;
+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.*;
-import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 
-import java.util.List;
-import java.util.Arrays;
 import java.io.PrintStream;
-
-import net.sf.samtools.SAMRecord;
+import java.util.Arrays;
+import java.util.List;
 
 /**
  * At each locus in the input data set, prints the reference base, genomic location, and
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java
index 2f1773d01..908e389a8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java
@@ -22,21 +22,24 @@
 
 package org.broadinstitute.sting.gatk.walkers.qc;
 
-import org.broadinstitute.sting.gatk.walkers.Requires;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.sam.AlignmentUtils;
+import net.sf.samtools.CigarElement;
+import net.sf.samtools.CigarOperator;
+import net.sf.samtools.SAMReadGroupRecord;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
-import net.sf.samtools.*;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.DataSource;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.walkers.Requires;
+import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 
-import java.util.*;
-import java.io.*;
+import java.io.PrintStream;
+import java.util.Arrays;
 
 /**
  * User: depristo
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java
index 6ad0340a4..fa1bb4d55 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java
@@ -1,16 +1,16 @@
 package org.broadinstitute.sting.gatk.walkers.qc;
 
+import net.sf.samtools.SAMFileWriter;
+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 org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import net.sf.samtools.SAMRecord;
-import net.sf.samtools.SAMFileWriter;
 
 import java.security.MessageDigest;
 import java.security.NoSuchAlgorithmException;
-import java.util.List;
 import java.util.ArrayList;
+import java.util.List;
 
 
 /*
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java
index 9cb715507..170630b77 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java
@@ -1,6 +1,5 @@
 package org.broadinstitute.sting.gatk.walkers.qc;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -8,8 +7,11 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 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.gatk.walkers.Reference;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.sting.gatk.walkers.Window;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.*;
 import java.math.BigInteger;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java
index bc68be592..e1e6c4b69 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java
@@ -25,20 +25,20 @@
 
 package org.broadinstitute.sting.gatk.walkers.qc;
 
+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;
 import org.broadinstitute.sting.gatk.refdata.features.sampileup.SAMPileupFeature;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
+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.ReadBackedPileup;
 
-import java.util.Arrays;
 import java.io.PrintStream;
+import java.util.Arrays;
 
 /**
  * At every locus in the input set, compares the pileup data (reference base, aligned base from
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesGatherer.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesGatherer.java
index 568e1b638..fc6b3daee 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesGatherer.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesGatherer.java
@@ -7,7 +7,6 @@ import org.broadinstitute.sting.utils.text.XReadLines;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.PrintStream;
-import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.regex.Pattern;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
index c21f548b3..8c6539f8d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
@@ -27,24 +27,25 @@ package org.broadinstitute.sting.gatk.walkers.recalibration;
 
 import org.broad.tribble.bed.BEDCodec;
 import org.broad.tribble.dbsnp.DbSNPCodec;
-import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableReadFilter;
-import org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.ArgumentCollection;
 import org.broadinstitute.sting.commandline.Gather;
 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.datasources.rmd.ReferenceOrderedDataSource;
+import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableReadFilter;
 import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
 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.*;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
+import org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
 import org.broadinstitute.sting.utils.collections.NestedHashMap;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.ArgumentCollection;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
index 64e0864c0..945d02837 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
 import net.sf.samtools.SAMRecord;
-
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java
index 0de6897d0..a7717161a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java
@@ -1,11 +1,10 @@
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
-import java.util.HashMap;
-
 import net.sf.samtools.SAMRecord;
-
 import org.broadinstitute.sting.utils.BaseUtils;
 
+import java.util.HashMap;
+
 /*
  * Copyright (c) 2009 The Broad Institute
  *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
index fdbeb6a31..e6d0b306c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
@@ -25,19 +25,21 @@
 
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
+import net.sf.samtools.SAMReadGroupRecord;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMUtils;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.collections.NestedHashMap;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
-import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.collections.NestedHashMap;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
-import java.util.*;
-
-import net.sf.samtools.SAMRecord;
-import net.sf.samtools.SAMReadGroupRecord;
-import net.sf.samtools.SAMUtils;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDatumOptimized.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDatumOptimized.java
index 7ba441ccc..f04989fa5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDatumOptimized.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDatumOptimized.java
@@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.recalibration;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.QualityUtils;
 
-import java.util.*;
+import java.util.List;
 
 /*
  * Copyright (c) 2010 The Broad Institute
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
index 0eaa1245e..0277fda0d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -25,31 +25,33 @@
 
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.util.*;
-import java.util.regex.Pattern;
-
 import net.sf.samtools.*;
 import net.sf.samtools.util.SequenceUtil;
-
+import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.classloader.PluginManager;
-import org.broadinstitute.sting.utils.collections.NestedHashMap;
 import org.broadinstitute.sting.utils.QualityUtils;
-import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.baq.BAQ;
-import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.utils.classloader.PluginManager;
+import org.broadinstitute.sting.utils.collections.NestedHashMap;
+import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.sting.utils.text.TextFormattingUtils;
+import org.broadinstitute.sting.utils.text.XReadLines;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.MissingResourceException;
+import java.util.ResourceBundle;
+import java.util.regex.Pattern;
 
 /**
  * This walker is designed to work as the second pass in a two-pass processing step, doing a by-read traversal.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java
index c1c17bda5..b3b63bb96 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java
@@ -1,12 +1,12 @@
 package org.broadinstitute.sting.gatk.walkers.sequenom;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+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.RodWalker;
-import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.PrintStream;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
index fde233b5d..b877ff70b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
@@ -25,29 +25,27 @@
 
 package org.broadinstitute.sting.gatk.walkers.sequenom;
 
-import net.sf.samtools.util.CloseableIterator;
 import org.broad.tribble.bed.BEDCodec;
-import org.broad.tribble.dbsnp.DbSNPCodec;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+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.*;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
+import org.broadinstitute.sting.gatk.refdata.SeekableRODIterator;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
-import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
-import java.util.*;
 import java.io.PrintStream;
+import java.util.*;
 
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
index c9c5e09a8..fe3173506 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
@@ -1,14 +1,12 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.samtools.SAMSequenceRecord;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 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.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
@@ -20,22 +18,21 @@ import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.gatk.walkers.Window;
 import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.*;
 import org.broadinstitute.sting.gatk.walkers.variantrecalibration.Tranche;
 import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
-import net.sf.picard.reference.IndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-
-import java.io.FileNotFoundException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.io.File;
+import java.io.FileNotFoundException;
 import java.io.PrintStream;
 import java.lang.reflect.Field;
 import java.util.*;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompEvalGenotypes.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompEvalGenotypes.java
index 787dbe9af..925bff9c0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompEvalGenotypes.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompEvalGenotypes.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
 
 class NewCompEvalGenotypes {
     private GenomeLoc loc;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
index 85373baa8..255a54737 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
@@ -1,12 +1,12 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
+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.varianteval.util.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 
 /**
  * The Broad Institute
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
index befb2ff13..8c281b2f8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
@@ -1,13 +1,13 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 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.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 @Analysis(description = "Counts different classes of variants in the sample")
 public class CountVariants extends VariantEvaluator implements StandardEval {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
index 58803c9d0..bbd3f5f54 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
@@ -1,18 +1,18 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 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.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java
index 407b71893..a476a2680 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java
@@ -1,9 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.*;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -12,8 +9,12 @@ import org.broadinstitute.sting.gatk.walkers.phasing.ReadBackedPhasingWalker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.NewEvaluationContext;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.HashMap;
 import java.util.HashSet;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
index f7f9fce0c..77def0f30 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
@@ -1,13 +1,13 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 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.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 /**
  * IF THERE IS NO JAVADOC RIGHT HERE, YELL AT chartl
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java
index dd4bb492e..6e1b76acd 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java
@@ -1,14 +1,14 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 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.varianteval.VariantEvalWalker;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java
index 1bd420e0a..d99196ecf 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java
@@ -1,15 +1,15 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 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.varianteval.VariantEvalWalker;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
 import org.broadinstitute.sting.utils.IndelUtils;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
index 16ec74433..a0cc393d9 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
@@ -1,15 +1,15 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 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.varianteval.VariantEvalWalker;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.MendelianViolation;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 /**
  * Mendelian violation detection and counting
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java
index e83914ef8..b209ee13d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java
@@ -24,12 +24,12 @@
 
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 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.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 @Analysis(name = "PrintMissingComp", description = "the overlap between eval and comp sites")
 public class PrintMissingComp extends VariantEvaluator {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java
index 5f3e6b0fa..751f61a97 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
 
 import java.util.HashMap;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java
index 395309975..d466645ea 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java
@@ -1,17 +1,18 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.*;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.Degeneracy;
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.Sample;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.StateKey;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.util.ArrayList;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java
index f9cda5e0b..ec43cbd55 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java
@@ -1,13 +1,13 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
+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.varianteval.util.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.ConcurrentMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java
index deeafd851..be957abd7 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java
@@ -1,13 +1,13 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 @Analysis(description = "Ti/Tv Variant Evaluator")
 public class TiTvVariantEvaluator extends VariantEvaluator implements StandardEval {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java
index 756427581..9c331b577 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java
@@ -1,16 +1,16 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 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.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.*;
+import java.util.Set;
 
 /**
  * The Broad Institute
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java
index 6017ecca3..e29e7ed50 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java
@@ -1,12 +1,12 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 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.varianteval.VariantEvalWalker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.NewEvaluationContext;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.StateKey;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 public abstract class VariantEvaluator {
     public void initialize(VariantEvalWalker walker) {}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java
index 29a61e27a..b6ad55b18 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java
@@ -25,16 +25,16 @@
 
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
 import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.util.ArrayList;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
index 2cbc66e31..411493d4f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
@@ -1,12 +1,11 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
-import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java
index 48b4ffa91..2ffc7716c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java
@@ -1,10 +1,10 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
 import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java
index 9942ba8d6..c6975808f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java
index 1a9d31085..c14355035 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java
index 15b1d41c1..3e8a6ed17 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java
index 65af6090c..155a66186 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java
@@ -1,14 +1,14 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.HashMap;
-import java.util.Set;
 import java.util.HashSet;
+import java.util.Set;
 
 public class Degeneracy extends VariantStratifier {
     private ArrayList<String> states;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java
index 7bd15a974..40f952fd2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java
index 8d8782ab7..3b7a419f2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java
index fd724d6d1..c6c094f8e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java
index a7ccd3182..76efedbf4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java
@@ -1,10 +1,10 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.util.ArrayList;
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java
index 39d2e6b4d..a0973a088 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Collection;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java
index f909de4f3..a2a3eb3fb 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java
index 218cb23ca..2c4b8bc46 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java
@@ -1,11 +1,10 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java
index 3208c26bb..8112ae97f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java
@@ -1,6 +1,5 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.util;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -9,6 +8,7 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvalu
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.StingException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.HashMap;
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java
index 0281653af..38f7a7f40 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.util;
 
-import org.apache.commons.jexl2.*;
+import org.apache.commons.jexl2.Expression;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 public class SortableJexlVCMatchExp extends VariantContextUtils.JexlVCMatchExp implements Comparable<SortableJexlVCMatchExp> {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
index eabd2e588..0a915db37 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
@@ -1,9 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.util;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.report.GATKReport;
 import org.broadinstitute.sting.gatk.report.GATKReportTable;
@@ -16,6 +14,8 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.Variant
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.lang.reflect.Field;
 import java.util.*;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
index d4e07dccf..403c67d3e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
@@ -25,23 +25,23 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Input;
+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.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.collections.NestedHashMap;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
 import java.io.FileNotFoundException;
-import java.lang.Double;
 import java.util.*;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java
index 64fe36637..15424f0f7 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java
@@ -25,11 +25,14 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
-import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
 
-import java.io.*;
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.PrintStream;
 import java.util.*;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java
index 5deb5d8c2..bc7252ec2 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java
@@ -26,10 +26,10 @@
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
 import java.io.FileNotFoundException;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
index ddeda1699..67d54a408 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -26,7 +26,6 @@
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -34,9 +33,12 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.PrintStream;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index 2d0355d7d..8179463eb 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -25,14 +25,12 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.ArgumentCollection;
 import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
@@ -42,6 +40,8 @@ import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.io.File;
 import java.io.FileNotFoundException;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
index 597a54dc1..837f352f8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
@@ -25,12 +25,12 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Hidden;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.Reference;
 import org.broadinstitute.sting.gatk.walkers.Requires;
@@ -38,11 +38,10 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.Window;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
-import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
index ba6f5e513..b45ee1b67 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
@@ -24,18 +24,21 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
-import org.broadinstitute.sting.utils.SampleUtils;
+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.*;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.*;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Map;
+import java.util.Set;
 
 /**
  * Filters a lifted-over VCF file for ref bases that have been changed.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
index d9dd85f0c..2ebd183f4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
@@ -28,21 +28,17 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
 import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
 import net.sf.samtools.CigarOperator;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.SortingVCFWriter;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 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.*;
 import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
index 7eda54387..4f05c8aac 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
@@ -24,27 +24,27 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
-
-import java.io.File;
-import java.util.*;
-
 import net.sf.picard.PicardException;
 import net.sf.picard.liftover.LiftOver;
 import net.sf.picard.util.Interval;
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMFileReader;
+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;
+import org.broadinstitute.sting.gatk.walkers.RMD;
+import org.broadinstitute.sting.gatk.walkers.Requires;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+
+import java.io.File;
+import java.util.*;
 
 /**
  * Lifts a VCF file over from one build to another.  Note that the resulting VCF could be mis-sorted.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
index 0c41a9728..f0756d884 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
@@ -24,11 +24,6 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.StandardVCFWriter;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
@@ -39,11 +34,15 @@ import org.broadinstitute.sting.gatk.walkers.RMD;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
 
 /**
  * Takes a VCF file, randomly splits variants into two different sets, and outputs 2 new VCFs with the results.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index cbac54326..1db692e9f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -24,27 +24,26 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broadinstitute.sting.commandline.Hidden;
-import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.utils.variantcontext.*;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.MendelianViolation;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RMD;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.MendelianViolation;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.apache.log4j.Logger;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.io.File;
-import java.lang.annotation.AnnotationFormatError;
 import java.util.*;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
index 1bd73414c..0644c669b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
@@ -25,22 +25,25 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broad.tribble.dbsnp.DbSNPFeature;
 import org.broad.tribble.TribbleException;
+import org.broad.tribble.dbsnp.DbSNPFeature;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Hidden;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Hidden;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.*;
 import java.io.File;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
 
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
index 482679593..86bb3b0e8 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
@@ -25,20 +25,19 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.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.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
index 71dd5df3f..8d90af65a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
@@ -24,18 +24,17 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 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.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.io.PrintStream;
 import java.util.*;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
index 79134b553..aa0e5987f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
@@ -28,26 +28,26 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
 import net.sf.samtools.util.CloseableIterator;
 import org.broad.tribble.dbsnp.DbSNPCodec;
 import org.broad.tribble.dbsnp.DbSNPFeature;
-import org.broadinstitute.sting.utils.codecs.hapmap.HapMapFeature;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
-import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.gatk.refdata.*;
 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.datasources.rmd.ReferenceOrderedDataSource;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
 import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.codecs.hapmap.HapMapFeature;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/jna/clibrary/LibC.java b/public/java/src/org/broadinstitute/sting/jna/clibrary/LibC.java
index b01533ee6..b5efcc153 100644
--- a/public/java/src/org/broadinstitute/sting/jna/clibrary/LibC.java
+++ b/public/java/src/org/broadinstitute/sting/jna/clibrary/LibC.java
@@ -24,7 +24,10 @@
 
 package org.broadinstitute.sting.jna.clibrary;
 
-import com.sun.jna.*;
+import com.sun.jna.LastErrorException;
+import com.sun.jna.Native;
+import com.sun.jna.NativeLong;
+import com.sun.jna.Structure;
 import com.sun.jna.ptr.NativeLongByReference;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/jna/lsf/v7_0_6/LibLsf.java b/public/java/src/org/broadinstitute/sting/jna/lsf/v7_0_6/LibLsf.java
index 0c0579d6f..c7b3de6cf 100644
--- a/public/java/src/org/broadinstitute/sting/jna/lsf/v7_0_6/LibLsf.java
+++ b/public/java/src/org/broadinstitute/sting/jna/lsf/v7_0_6/LibLsf.java
@@ -29,7 +29,7 @@ import com.sun.jna.ptr.FloatByReference;
 import com.sun.jna.ptr.IntByReference;
 import com.sun.jna.ptr.PointerByReference;
 import org.broadinstitute.sting.jna.clibrary.JNAUtils;
-import org.broadinstitute.sting.jna.clibrary.LibC.*;
+import org.broadinstitute.sting.jna.clibrary.LibC.timeval;
 
 /*
   NOTE: This library uses Pointer for some Struct.ByReference members going
diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
index fe6758e76..c09c4037e 100644
--- a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
+++ b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
@@ -27,13 +27,16 @@ package org.broadinstitute.sting.queue.extensions.gatk;
 import net.sf.samtools.BAMIndex;
 import net.sf.samtools.SAMFileWriter;
 import org.broad.tribble.Tribble;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 
 import java.io.File;
 import java.lang.annotation.Annotation;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
 
 public abstract class ArgumentDefinitionField extends ArgumentField {
 
diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java
index 2da427d44..e90933504 100644
--- a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java
+++ b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java
@@ -35,7 +35,10 @@ import java.io.File;
 import java.io.InputStream;
 import java.io.OutputStream;
 import java.lang.annotation.Annotation;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.List;
 
 public abstract class ArgumentField {
 
diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
index 21fb44733..5095bd6e5 100644
--- a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
+++ b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
@@ -27,17 +27,20 @@ package org.broadinstitute.sting.queue.extensions.gatk;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang.StringUtils;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
+import org.broadinstitute.sting.commandline.CommandLineProgram;
+import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.commandline.ParsingEngine;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.WalkerManager;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.filters.FilterManager;
 import org.broadinstitute.sting.gatk.filters.ReadFilter;
-import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor;
 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.refdata.tracks.builders.RMDTrackBuilder;
 import org.broadinstitute.sting.gatk.walkers.PartitionBy;
 import org.broadinstitute.sting.gatk.walkers.PartitionType;
diff --git a/public/java/src/org/broadinstitute/sting/utils/DisjointSet.java b/public/java/src/org/broadinstitute/sting/utils/DisjointSet.java
index 5f68d3414..52c18e6d6 100644
--- a/public/java/src/org/broadinstitute/sting/utils/DisjointSet.java
+++ b/public/java/src/org/broadinstitute/sting/utils/DisjointSet.java
@@ -23,7 +23,9 @@
  */
 package org.broadinstitute.sting.utils;
 
-import java.util.*;
+import java.util.Collection;
+import java.util.Set;
+import java.util.TreeSet;
 
 public class DisjointSet {
     private ItemNode[] nodes;
diff --git a/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
index 1f8800542..b96923589 100644
--- a/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
+++ b/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
@@ -2,7 +2,6 @@ package org.broadinstitute.sting.utils;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
-import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.Serializable;
diff --git a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
index 18a1e7ffd..a5c6e0537 100644
--- a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
+++ b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
@@ -25,12 +25,14 @@
 
 package org.broadinstitute.sting.utils;
 
-import com.google.java.contract.*;
+import com.google.java.contract.Ensures;
+import com.google.java.contract.Invariant;
+import com.google.java.contract.Requires;
+import com.google.java.contract.ThrowEnsures;
 import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.SAMSequenceRecord;
-
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
diff --git a/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java b/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java
index 30e1a3f5b..af69ebca6 100755
--- a/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.utils;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Arrays;
diff --git a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
index 50aa0f707..36ed506aa 100755
--- a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
@@ -25,17 +25,14 @@
 
 package org.broadinstitute.sting.utils;
 
-import cern.jet.math.Arithmetic;
-
-import java.math.BigDecimal;
-import java.util.*;
-
 import com.google.java.contract.Requires;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.collections.PrimitivePair;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
+import java.math.BigDecimal;
+import java.util.*;
+
 /**
  * MathUtils is a static class (no instantiation allowed!) with some useful math methods.
  *
diff --git a/public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java b/public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java
index a8089ffe8..c6a07b5ce 100755
--- a/public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java
+++ b/public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java
@@ -1,12 +1,13 @@
 package org.broadinstitute.sting.utils;
 
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.*;
+import java.util.Collection;
+import java.util.List;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/PathUtils.java b/public/java/src/org/broadinstitute/sting/utils/PathUtils.java
index 47466be20..822d04dfd 100755
--- a/public/java/src/org/broadinstitute/sting/utils/PathUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/PathUtils.java
@@ -2,10 +2,10 @@ package org.broadinstitute.sting.utils;
 
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.List;
-import java.util.ArrayList;
 import java.io.File;
 import java.io.FilenameFilter;
+import java.util.ArrayList;
+import java.util.List;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/utils/ReservoirDownsampler.java b/public/java/src/org/broadinstitute/sting/utils/ReservoirDownsampler.java
index 30257d967..a758df431 100644
--- a/public/java/src/org/broadinstitute/sting/utils/ReservoirDownsampler.java
+++ b/public/java/src/org/broadinstitute/sting/utils/ReservoirDownsampler.java
@@ -3,7 +3,9 @@ package org.broadinstitute.sting.utils;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Iterator;
 
 /**
  * Randomly downsample from a stream of elements.  This algorithm is a direct,
diff --git a/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java b/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java
index 4b7fa3e41..92d73a5ce 100755
--- a/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java
+++ b/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java
@@ -24,15 +24,14 @@
 
 package org.broadinstitute.sting.utils;
 
+import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
 import net.sf.samtools.CigarOperator;
-import net.sf.samtools.Cigar;
-
-import java.util.*;
-
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 
+import java.util.*;
+
 /**
  * Created by IntelliJ IDEA.
  * User: asivache
diff --git a/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java b/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java
index c0370064d..f9997bfd8 100755
--- a/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java
@@ -27,12 +27,12 @@ package org.broadinstitute.sting.utils;
 
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMReadGroupRecord;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.io.File;
 import java.io.FileNotFoundException;
diff --git a/public/java/src/org/broadinstitute/sting/utils/SimpleTimer.java b/public/java/src/org/broadinstitute/sting/utils/SimpleTimer.java
index a59c5134a..342087b41 100644
--- a/public/java/src/org/broadinstitute/sting/utils/SimpleTimer.java
+++ b/public/java/src/org/broadinstitute/sting/utils/SimpleTimer.java
@@ -1,7 +1,10 @@
 package org.broadinstitute.sting.utils;
 
+import com.google.java.contract.Ensures;
+import com.google.java.contract.Invariant;
+import com.google.java.contract.Requires;
+
 import java.io.PrintStream;
-import com.google.java.contract.*;
 
 /**
  * A useful simple system for timing code.  This code is not thread safe!
diff --git a/public/java/src/org/broadinstitute/sting/utils/Utils.java b/public/java/src/org/broadinstitute/sting/utils/Utils.java
index 4c13d8b18..6a50badce 100755
--- a/public/java/src/org/broadinstitute/sting/utils/Utils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/Utils.java
@@ -25,13 +25,12 @@
 
 package org.broadinstitute.sting.utils;
 
-import java.util.*;
-
 import net.sf.samtools.util.StringUtil;
-
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.collections.Pair;
 
+import java.util.*;
+
 /**
  * Created by IntelliJ IDEA.
  * User: depristo
diff --git a/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java b/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java
index 456f0fa0f..ef7cf751e 100644
--- a/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java
+++ b/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java
@@ -1,10 +1,10 @@
 package org.broadinstitute.sting.utils.baq;
 
-import net.sf.samtools.SAMRecord;
-import net.sf.samtools.CigarElement;
-import net.sf.samtools.CigarOperator;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.picard.reference.ReferenceSequence;
+import net.sf.samtools.CigarElement;
+import net.sf.samtools.CigarOperator;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
diff --git a/public/java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java b/public/java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java
index 24d4152a5..26356a4a4 100644
--- a/public/java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java
+++ b/public/java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java
@@ -2,11 +2,10 @@ package org.broadinstitute.sting.utils.baq;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
-import net.sf.samtools.SAMRecord;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.baq.BAQ;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.Iterator;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/bed/BedParser.java b/public/java/src/org/broadinstitute/sting/utils/bed/BedParser.java
index abcae066f..b95165841 100644
--- a/public/java/src/org/broadinstitute/sting/utils/bed/BedParser.java
+++ b/public/java/src/org/broadinstitute/sting/utils/bed/BedParser.java
@@ -1,11 +1,12 @@
 package org.broadinstitute.sting.utils.bed;
 
-import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.io.*;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.List;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java b/public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java
index 404bd80b6..e65b8f921 100755
--- a/public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java
@@ -29,9 +29,9 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.reflections.util.ClasspathHelper;
 
-import java.lang.reflect.*;
 import java.io.File;
 import java.io.IOException;
+import java.lang.reflect.*;
 import java.net.URL;
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java b/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java
index 95f3e160c..5449906b2 100644
--- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java
+++ b/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java
@@ -4,9 +4,6 @@ import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
 import net.sf.samtools.CigarOperator;
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.walkers.ClipReadsWalker;
-import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 import java.util.Vector;
diff --git a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
index 031467ed9..988d297f6 100644
--- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
+++ b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.utils.clipreads;
 
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.walkers.ClipReadsWalker;
 
 import java.util.ArrayList;
 import java.util.List;
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java
index a286ce789..fef6c4ea0 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java
@@ -30,7 +30,6 @@ import org.broad.tribble.readers.LineReader;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.io.IOException;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.regex.Matcher;
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java
index 618d9ce79..e169dbdfc 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java
@@ -4,11 +4,11 @@ import org.broad.tribble.Feature;
 import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.NameAwareCodec;
 import org.broad.tribble.TribbleException;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broad.tribble.exception.CodecLineParsingException;
 import org.broad.tribble.readers.LineReader;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
index e7ddac185..b7f4be39a 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
@@ -33,13 +33,13 @@ import org.broad.tribble.util.LittleEndianOutputStream;
 import org.broad.tribble.util.ParsingUtils;
 import org.broad.tribble.util.PositionalStream;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.*;
-import java.util.*;
 import java.lang.reflect.Array;
+import java.util.*;
 
 /**
  * this class writes VCF files
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFParser.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFParser.java
index dac996494..1dba351e2 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFParser.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFParser.java
@@ -2,7 +2,9 @@ package org.broadinstitute.sting.utils.codecs.vcf;
 
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import java.util.*;
+
+import java.util.List;
+import java.util.Map;
 
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
index 4037f75b9..f43891e77 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
@@ -25,10 +25,10 @@
 
 package org.broadinstitute.sting.utils.codecs.vcf;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
-import org.apache.log4j.Logger;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/collections/NestedHashMap.java b/public/java/src/org/broadinstitute/sting/utils/collections/NestedHashMap.java
index a36ed9ac6..d280ac804 100755
--- a/public/java/src/org/broadinstitute/sting/utils/collections/NestedHashMap.java
+++ b/public/java/src/org/broadinstitute/sting/utils/collections/NestedHashMap.java
@@ -25,7 +25,8 @@
 
 package org.broadinstitute.sting.utils.collections;
 
-import java.util.*;
+import java.util.HashMap;
+import java.util.Map;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/utils/collections/RODMergingIterator.java b/public/java/src/org/broadinstitute/sting/utils/collections/RODMergingIterator.java
index 3a731c2fd..6d6cb8272 100644
--- a/public/java/src/org/broadinstitute/sting/utils/collections/RODMergingIterator.java
+++ b/public/java/src/org/broadinstitute/sting/utils/collections/RODMergingIterator.java
@@ -27,10 +27,13 @@ package org.broadinstitute.sting.utils.collections;
 
 import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.*;
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.PriorityQueue;
 
 public class RODMergingIterator implements Iterator<RODRecordList>, Iterable<RODRecordList> {
     PriorityQueue<Element> queue = new PriorityQueue<Element>();
diff --git a/public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java b/public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java
index 41de5ef96..bba47c76c 100644
--- a/public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java
@@ -26,15 +26,18 @@
 package org.broadinstitute.sting.utils.duplicates;
 
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
 
-import java.util.List;
 import java.util.Arrays;
+import java.util.List;
 
 public class DupUtils {
     private static SAMRecord tmpCopyRead(SAMRecord read) {
diff --git a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
index 17c4a7df4..7eab6f6c9 100755
--- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
+++ b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
@@ -28,9 +28,8 @@ import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.SAMSequenceRecord;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
 import java.util.Arrays;
diff --git a/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java b/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java
index 0c5085cc7..43ef4aa74 100644
--- a/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java
+++ b/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java
@@ -25,15 +25,16 @@
 package org.broadinstitute.sting.utils.fasta;
 
 import net.sf.picard.PicardException;
-import net.sf.picard.reference.*;
+import net.sf.picard.reference.FastaSequenceIndex;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import net.sf.picard.reference.ReferenceSequence;
 import net.sf.samtools.SAMSequenceRecord;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.util.Arrays;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-
 /**
  * A caching version of the IndexedFastaSequenceFile that avoids going to disk as often as the raw indexer.
  *
diff --git a/public/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java b/public/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java
index cbfba848c..1c2cfe2e1 100755
--- a/public/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java
+++ b/public/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java
@@ -26,7 +26,6 @@
 package org.broadinstitute.sting.utils.genotype;
 
 import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.MathUtils;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java b/public/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java
index 31791e805..a17e81461 100755
--- a/public/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java
+++ b/public/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java
@@ -24,14 +24,14 @@
 
 package org.broadinstitute.sting.utils.genotype;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 
-import java.util.*;
+import java.util.Arrays;
+import java.util.LinkedHashMap;
+import java.util.List;
 
 public class Haplotype {
     protected byte[] bases = null;
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java b/public/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java
index d9e74640f..483c874dc 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java
@@ -25,13 +25,13 @@
 
 package org.broadinstitute.sting.utils.help;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.commandline.CommandLineProgram;
+import org.broadinstitute.sting.utils.classloader.JVMUtils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.List;
-import java.util.Collections;
 import java.io.IOException;
+import java.util.Collections;
+import java.util.List;
 
 /**
  * Contains details additional details that the program can
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/DescriptionTaglet.java b/public/java/src/org/broadinstitute/sting/utils/help/DescriptionTaglet.java
index 68633a2b3..65c332048 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/DescriptionTaglet.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/DescriptionTaglet.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.utils.help;
 
 import com.sun.tools.doclets.Taglet;
-import com.sun.javadoc.Tag;
 
 import java.util.Map;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/DisplayNameTaglet.java b/public/java/src/org/broadinstitute/sting/utils/help/DisplayNameTaglet.java
index be6f7f3eb..6c6dad736 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/DisplayNameTaglet.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/DisplayNameTaglet.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.utils.help;
 
 import com.sun.tools.doclets.Taglet;
-import com.sun.javadoc.Tag;
 
 import java.util.Map;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/HelpFormatter.java b/public/java/src/org/broadinstitute/sting/utils/help/HelpFormatter.java
index 493f26e76..a9d71ef98 100755
--- a/public/java/src/org/broadinstitute/sting/utils/help/HelpFormatter.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/HelpFormatter.java
@@ -25,22 +25,16 @@
 
 package org.broadinstitute.sting.utils.help;
 
+import org.apache.log4j.Logger;
 import org.broadinstitute.sting.commandline.ArgumentDefinition;
 import org.broadinstitute.sting.commandline.ArgumentDefinitionGroup;
 import org.broadinstitute.sting.commandline.ArgumentDefinitions;
-import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 import org.broadinstitute.sting.utils.Utils;
-import org.apache.log4j.Logger;
+import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 
-import java.util.Formatter;
-import java.util.List;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.Comparator;
-import java.util.Collection;
-import java.util.Collections;
 import java.text.DateFormat;
 import java.text.SimpleDateFormat;
+import java.util.*;
 /**
  * Print out help for Sting command-line applications.
  */
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/HelpTaglet.java b/public/java/src/org/broadinstitute/sting/utils/help/HelpTaglet.java
index b962664eb..b350b1a29 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/HelpTaglet.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/HelpTaglet.java
@@ -1,9 +1,7 @@
 package org.broadinstitute.sting.utils.help;
 
-import com.sun.tools.doclets.Taglet;
 import com.sun.javadoc.Tag;
-
-import java.util.Map;
+import com.sun.tools.doclets.Taglet;
 
 /**
  * Basic functionality for the help taglet.
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java b/public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
index 4afac69c3..6ee12d42e 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
@@ -26,14 +26,16 @@
 package org.broadinstitute.sting.utils.help;
 
 import com.sun.javadoc.*;
+import org.broadinstitute.sting.gatk.walkers.Walker;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.classloader.JVMUtils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.*;
-import java.util.*;
-
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.classloader.JVMUtils;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.gatk.walkers.Walker;
+import java.util.HashSet;
+import java.util.Properties;
+import java.util.Scanner;
+import java.util.Set;
 
 /**
  * Extracts certain types of javadoc (specifically package and class descriptions) and makes them available
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/SummaryTaglet.java b/public/java/src/org/broadinstitute/sting/utils/help/SummaryTaglet.java
index 036bbec4f..db8b55940 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/SummaryTaglet.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/SummaryTaglet.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.utils.help;
 
 import com.sun.tools.doclets.Taglet;
-import com.sun.javadoc.Tag;
 
 import java.util.Map;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java b/public/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java
index 3420c9876..73a29ba4f 100644
--- a/public/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java
+++ b/public/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java
@@ -27,9 +27,9 @@ package org.broadinstitute.sting.utils.instrumentation;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.lang.instrument.Instrumentation;
+import java.lang.reflect.Array;
 import java.lang.reflect.Field;
 import java.lang.reflect.Modifier;
-import java.lang.reflect.Array;
 import java.util.IdentityHashMap;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/utils/interval/IntervalFileMergingIterator.java b/public/java/src/org/broadinstitute/sting/utils/interval/IntervalFileMergingIterator.java
index e722ac196..988240ef9 100644
--- a/public/java/src/org/broadinstitute/sting/utils/interval/IntervalFileMergingIterator.java
+++ b/public/java/src/org/broadinstitute/sting/utils/interval/IntervalFileMergingIterator.java
@@ -25,16 +25,16 @@
 
 package org.broadinstitute.sting.utils.interval;
 
+import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
+import org.broadinstitute.sting.gatk.refdata.utils.StringToGenomeLocIteratorAdapter;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
-import org.broadinstitute.sting.gatk.refdata.utils.StringToGenomeLocIteratorAdapter;
 
-import java.util.Iterator;
 import java.io.File;
 import java.io.FileNotFoundException;
+import java.util.Iterator;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java b/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
index 80dc35455..f551e1368 100644
--- a/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
@@ -5,17 +5,17 @@ import net.sf.picard.util.IntervalList;
 import net.sf.samtools.SAMFileHeader;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource;
-import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 import org.broadinstitute.sting.utils.bed.BedParser;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
 
+import java.io.File;
 import java.io.IOException;
 import java.util.*;
-import java.io.File;
 
 /**
  * Parse text representations of interval strings that
diff --git a/public/java/src/org/broadinstitute/sting/utils/interval/NwayIntervalMergingIterator.java b/public/java/src/org/broadinstitute/sting/utils/interval/NwayIntervalMergingIterator.java
index 31a2f41fb..7e87ce8b5 100644
--- a/public/java/src/org/broadinstitute/sting/utils/interval/NwayIntervalMergingIterator.java
+++ b/public/java/src/org/broadinstitute/sting/utils/interval/NwayIntervalMergingIterator.java
@@ -26,11 +26,10 @@
 package org.broadinstitute.sting.utils.interval;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
-import java.util.PriorityQueue;
 import java.util.Iterator;
+import java.util.PriorityQueue;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/utils/interval/OverlappingIntervalIterator.java b/public/java/src/org/broadinstitute/sting/utils/interval/OverlappingIntervalIterator.java
index 0b63d582e..29ffb13e4 100755
--- a/public/java/src/org/broadinstitute/sting/utils/interval/OverlappingIntervalIterator.java
+++ b/public/java/src/org/broadinstitute/sting/utils/interval/OverlappingIntervalIterator.java
@@ -25,9 +25,8 @@
 
 package org.broadinstitute.sting.utils.interval;
 
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
+import org.broadinstitute.sting.utils.GenomeLoc;
 
 import java.util.Iterator;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java b/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
index 543302446..3821c9c8a 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
@@ -24,19 +24,16 @@
 
 package org.broadinstitute.sting.utils.pileup;
 
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
-import org.broadinstitute.sting.utils.HasGenomeLocation;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.gatk.iterators.IterableIterator;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.StingException;
 
 import java.util.*;
 
-import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.exceptions.StingException;
-
 /**
  * A generic implementation of read-backed pileups.
  *
diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/ExtendedEventPileupElement.java b/public/java/src/org/broadinstitute/sting/utils/pileup/ExtendedEventPileupElement.java
index b6f3e9f09..26e66014c 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/ExtendedEventPileupElement.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/ExtendedEventPileupElement.java
@@ -1,8 +1,5 @@
 package org.broadinstitute.sting.utils.pileup;
 
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.BaseUtils;
 import net.sf.samtools.SAMRecord;
 
 import java.util.Arrays;
diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/FragmentPileup.java b/public/java/src/org/broadinstitute/sting/utils/pileup/FragmentPileup.java
index 6c855c1c7..f7d237401 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/FragmentPileup.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/FragmentPileup.java
@@ -1,6 +1,9 @@
 package org.broadinstitute.sting.utils.pileup;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Map;
 
 /**
  * An easy to access fragment-based pileup, which contains two separate pileups.  The first
diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/MergingPileupElementIterator.java b/public/java/src/org/broadinstitute/sting/utils/pileup/MergingPileupElementIterator.java
index d8af2ea8f..7005cf869 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/MergingPileupElementIterator.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/MergingPileupElementIterator.java
@@ -27,9 +27,9 @@ package org.broadinstitute.sting.utils.pileup;
 import net.sf.picard.util.PeekableIterator;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
 
-import java.util.PriorityQueue;
 import java.util.Comparator;
 import java.util.Iterator;
+import java.util.PriorityQueue;
 
 /**
  * Merges multiple pileups broken down by sample.
diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
index 51e02bf74..66e1afecb 100755
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
@@ -1,9 +1,10 @@
 package org.broadinstitute.sting.utils.pileup;
 
-import org.broadinstitute.sting.utils.*;
+import com.google.java.contract.Ensures;
+import com.google.java.contract.Requires;
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
-import com.google.java.contract.*;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java
index a32aa5645..8d43a368a 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java
@@ -24,15 +24,13 @@
 
 package org.broadinstitute.sting.utils.pileup;
 
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
 
-import java.util.Iterator;
-import java.util.List;
 import java.util.Collection;
-
-import net.sf.samtools.SAMRecord;
+import java.util.List;
 
 /**
  * A clean interface for working with extended event pileups.
diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java
index a1a08c95f..31d29430a 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java
@@ -23,15 +23,14 @@
  */
 package org.broadinstitute.sting.utils.pileup;
 
+import net.sf.samtools.SAMRecord;
 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.collections.Pair;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.*;
 
-import net.sf.samtools.SAMRecord;
-
 public class ReadBackedExtendedEventPileupImpl extends AbstractReadBackedPileup<ReadBackedExtendedEventPileupImpl,ExtendedEventPileupElement> implements ReadBackedExtendedEventPileup {
     private int nInsertions;
     private int maxDeletionLength;      // cached value of the length of the longest deletion observed at the site
diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java
index c52cc0b52..36b8a8c65 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java
@@ -24,14 +24,13 @@
 
 package org.broadinstitute.sting.utils.pileup;
 
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.gatk.iterators.IterableIterator;
-import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.HasGenomeLocation;
 
-import java.util.List;
 import java.util.Collection;
+import java.util.List;
 
 /**
  * A data retrieval interface for accessing parts of the pileup.
diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java
index 70eba577c..e5b054961 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java
@@ -23,9 +23,9 @@
  */
 package org.broadinstitute.sting.utils.pileup;
 
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import net.sf.samtools.SAMRecord;
 
 import java.util.List;
 import java.util.Map;
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
index 4e4294b20..344eccb83 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
@@ -25,15 +25,16 @@
 
 package org.broadinstitute.sting.utils.sam;
 
-import net.sf.samtools.CigarOperator;
-import net.sf.samtools.SAMRecord;
 import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
+import net.sf.samtools.CigarOperator;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.pileup.*;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
 import java.util.ArrayList;
 import java.util.Arrays;
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java
index 5812c9aec..5f7db458a 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java
@@ -1,15 +1,13 @@
 package org.broadinstitute.sting.utils.sam;
 
-import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
-import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.apache.log4j.Logger;
-
-import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMRecord;
+import org.apache.log4j.Logger;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
+import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.walkers.Walker;
 
 
 /*
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java
index ce6ca570c..adf60b16b 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java
@@ -1,15 +1,17 @@
 package org.broadinstitute.sting.utils.sam;
 
 import net.sf.samtools.*;
-
-import java.io.InputStream;
-import java.io.ByteArrayInputStream;
-import java.io.UnsupportedEncodingException;
-import java.util.*;
-
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.io.UnsupportedEncodingException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Iterator;
+import java.util.List;
 /**
  * User: hanna
  * Date: Jun 11, 2009
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java
index b683f5247..62e371bc0 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java
@@ -1,9 +1,8 @@
 package org.broadinstitute.sting.utils.sam;
 
-import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
-import org.broadinstitute.sting.gatk.ReadProperties;
-import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
 
 import java.util.Iterator;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java
index 4f5dcca61..2b359fe6a 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java
@@ -1,13 +1,12 @@
 package org.broadinstitute.sting.utils.sam;
 
 import net.sf.samtools.SAMFileHeader;
-import net.sf.samtools.SAMSequenceRecord;
 import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMSequenceRecord;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.List;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-
 
 /*
  * Copyright (c) 2009 The Broad Institute
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ComparableSAMRecord.java b/public/java/src/org/broadinstitute/sting/utils/sam/ComparableSAMRecord.java
index 01f1dfe96..31deb7535 100755
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ComparableSAMRecord.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ComparableSAMRecord.java
@@ -26,8 +26,6 @@
 package org.broadinstitute.sting.utils.sam;
 
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 
 public class ComparableSAMRecord implements Comparable<ComparableSAMRecord> {
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java
index 2b8ac387c..c7ffcab0c 100755
--- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.utils.sam;
 
-import net.sf.samtools.*;
+import net.sf.samtools.SAMReadGroupRecord;
 
 /**
  * @author ebanks
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
index f3d9edab9..517f9f75d 100755
--- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
@@ -1,12 +1,14 @@
 package org.broadinstitute.sting.utils.sam;
 
-import java.lang.reflect.Method;
-import java.util.*;
-
 import net.sf.samtools.*;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
+import java.lang.reflect.Method;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
 /**
  * @author ebanks
  * GATKSAMRecord
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
index 080762039..6c15910b1 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
@@ -25,13 +25,14 @@
 
 package org.broadinstitute.sting.utils.sam;
 
-import com.google.java.contract.*;
+import com.google.java.contract.Ensures;
+import com.google.java.contract.Requires;
 import net.sf.samtools.*;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.*;
 import java.io.File;
+import java.util.*;
 
 /**
  * A miscellaneous collection of utilities for working with SAM files, headers, etc.
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java b/public/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java
index f8a0ca6a7..bb9db5d98 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java
@@ -26,11 +26,10 @@
 package org.broadinstitute.sting.utils.sam;
 
 import net.sf.samtools.SAMFileReader;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.File;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-
 /**
  * Allows the user to steadily accumulate information about what
  * components go into a SAM file writer, ultimately using this
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/SimplifyingSAMFileWriter.java b/public/java/src/org/broadinstitute/sting/utils/sam/SimplifyingSAMFileWriter.java
index df2010e8b..60e1d9948 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/SimplifyingSAMFileWriter.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/SimplifyingSAMFileWriter.java
@@ -3,13 +3,6 @@ package org.broadinstitute.sting.utils.sam;
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMFileWriter;
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-
-import java.util.Iterator;
-import java.util.NoSuchElementException;
 
 /**
  * XXX
diff --git a/public/java/src/org/broadinstitute/sting/utils/text/ListFileUtils.java b/public/java/src/org/broadinstitute/sting/utils/text/ListFileUtils.java
index 9beb7895b..f6aa882ad 100644
--- a/public/java/src/org/broadinstitute/sting/utils/text/ListFileUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/text/ListFileUtils.java
@@ -26,7 +26,6 @@ package org.broadinstitute.sting.utils.text;
 
 import org.broadinstitute.sting.commandline.ParsingEngine;
 import org.broadinstitute.sting.commandline.Tags;
-import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
 import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
 import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
diff --git a/public/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java b/public/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java
index 803d6ac0f..1d4251542 100644
--- a/public/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java
@@ -28,11 +28,11 @@ package org.broadinstitute.sting.utils.text;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.*;
-import java.util.regex.Pattern;
-import java.util.regex.Matcher;
-import java.io.StringReader;
 import java.io.IOException;
+import java.io.StringReader;
+import java.util.*;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 /**
  * Common utilities for dealing with text formatting.
diff --git a/public/java/src/org/broadinstitute/sting/utils/text/XReadLines.java b/public/java/src/org/broadinstitute/sting/utils/text/XReadLines.java
index 064256388..52b6f3b01 100644
--- a/public/java/src/org/broadinstitute/sting/utils/text/XReadLines.java
+++ b/public/java/src/org/broadinstitute/sting/utils/text/XReadLines.java
@@ -25,10 +25,10 @@
 
 package org.broadinstitute.sting.utils.text;
 
-import java.util.Iterator;
-import java.util.List;
-import java.util.LinkedList;
 import java.io.*;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
 
 /**
  * Support for Python-like xreadlines() function as a class.  This is an iterator and iterable over
diff --git a/public/java/src/org/broadinstitute/sting/utils/threading/FileBackedGenomeLocProcessingTracker.java b/public/java/src/org/broadinstitute/sting/utils/threading/FileBackedGenomeLocProcessingTracker.java
index cae099eeb..3763ec67d 100644
--- a/public/java/src/org/broadinstitute/sting/utils/threading/FileBackedGenomeLocProcessingTracker.java
+++ b/public/java/src/org/broadinstitute/sting/utils/threading/FileBackedGenomeLocProcessingTracker.java
@@ -1,18 +1,14 @@
 package org.broadinstitute.sting.utils.threading;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.io.*;
-import java.nio.ByteBuffer;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.Collection;
 import java.util.List;
-import java.util.concurrent.locks.ReentrantLock;
 
 /**
  * Keeps a copy of the processing locks in a file
diff --git a/public/java/src/org/broadinstitute/sting/utils/threading/NoOpGenomeLocProcessingTracker.java b/public/java/src/org/broadinstitute/sting/utils/threading/NoOpGenomeLocProcessingTracker.java
index 4e61ef9e1..ad2a6d31b 100644
--- a/public/java/src/org/broadinstitute/sting/utils/threading/NoOpGenomeLocProcessingTracker.java
+++ b/public/java/src/org/broadinstitute/sting/utils/threading/NoOpGenomeLocProcessingTracker.java
@@ -1,9 +1,5 @@
 package org.broadinstitute.sting.utils.threading;
 
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-
-import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.List;
diff --git a/public/java/src/org/broadinstitute/sting/utils/threading/SharedFileLock.java b/public/java/src/org/broadinstitute/sting/utils/threading/SharedFileLock.java
index 3eb2be96b..0f47da413 100644
--- a/public/java/src/org/broadinstitute/sting/utils/threading/SharedFileLock.java
+++ b/public/java/src/org/broadinstitute/sting/utils/threading/SharedFileLock.java
@@ -6,10 +6,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.io.File;
-import java.io.FileNotFoundException;
 import java.io.IOException;
-import java.io.RandomAccessFile;
-import java.nio.channels.*;
 
 /**
  * User: depristo
diff --git a/public/java/src/org/broadinstitute/sting/utils/threading/SharedFileThreadSafeLock.java b/public/java/src/org/broadinstitute/sting/utils/threading/SharedFileThreadSafeLock.java
index dec69f7c2..d70879a0a 100644
--- a/public/java/src/org/broadinstitute/sting/utils/threading/SharedFileThreadSafeLock.java
+++ b/public/java/src/org/broadinstitute/sting/utils/threading/SharedFileThreadSafeLock.java
@@ -2,13 +2,8 @@ package org.broadinstitute.sting.utils.threading;
 
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.RandomAccessFile;
-import java.nio.channels.*;
 
 /**
  * User: depristo
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java
index 901de6fae..c3f437f11 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.utils.variantcontext;
 
-import java.util.Arrays;
-import java.util.List;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collection;
+import java.util.List;
 
 /**
  * Immutable representation of an allele
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
index 3feaf5e1c..dba16cf86 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
@@ -24,8 +24,8 @@
 
 package org.broadinstitute.sting.utils.variantcontext;
 
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broad.tribble.TribbleException;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 
 public class GenotypeLikelihoods {
     public static final boolean CAP_PLS = false;
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/MutableVariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/MutableVariantContext.java
index 4efba8825..a191670a4 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/MutableVariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/MutableVariantContext.java
@@ -1,7 +1,10 @@
 package org.broadinstitute.sting.utils.variantcontext;
 
 
-import java.util.*;
+import java.util.Collection;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeMap;
 
 /**
  * Mutable version of VariantContext
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
index 92c5d648b..eab392c4d 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -2,8 +2,8 @@ package org.broadinstitute.sting.utils.variantcontext;
 
 import org.broad.tribble.Feature;
 import org.broad.tribble.TribbleException;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broad.tribble.util.ParsingUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFParser;
 
 import java.util.*;
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
index 5d58954aa..5a5671056 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
@@ -23,21 +23,26 @@
 
 package org.broadinstitute.sting.utils.variantcontext;
 
-import java.io.Serializable;
-import java.util.*;
-
-import com.google.java.contract.*;
+import com.google.java.contract.Ensures;
+import com.google.java.contract.Requires;
 import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.samtools.util.StringUtil;
-import org.apache.commons.jexl2.*;
+import org.apache.commons.jexl2.Expression;
+import org.apache.commons.jexl2.JexlEngine;
 import org.broad.tribble.util.popgen.HardyWeinbergCalculation;
-import org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec;
 import org.broadinstitute.sting.gatk.walkers.phasing.ReadBackedPhasingWalker;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
+import java.io.Serializable;
+import java.util.*;
+
 public class VariantContextUtils {
     final public static JexlEngine engine = new JexlEngine();
     static {
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java
index c5a3b6f2a..a59ed7abe 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java
@@ -29,7 +29,10 @@ import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
-import java.util.*;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
 
 /**
  *
diff --git a/public/java/src/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java b/public/java/src/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java
index ab91d0e2e..5782c2704 100755
--- a/public/java/src/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java
+++ b/public/java/src/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.utils.wiggle;
 
-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 java.io.*;

From 0a0363aef23e25f876034928eae7e4b3fff08623 Mon Sep 17 00:00:00 2001
From: Matt Hanna <hanna@broadinstitute.org>
Date: Sun, 17 Jul 2011 20:43:35 -0400
Subject: [PATCH 160/161] Revving Picard to get a parser that works with the
 latest metrics file formats we're starting to see.

---
 ...1941.jar => picard-private-parts-1954.jar} | Bin 36047 -> 36047 bytes
 .../picard-private-parts-1954.xml             |   3 +++
 ...941.xml => picard-private-parts-1954.xml~} |   0
 ...icard-1.47.869.jar => picard-1.48.889.jar} | Bin 1084255 -> 1106870 bytes
 .../repository/net.sf/picard-1.48.889.xml     |   3 +++
 ...card-1.47.869.xml => picard-1.48.889.xml~} |   0
 settings/repository/net.sf/sam-1.47.869.xml   |   3 ---
 .../{sam-1.47.869.jar => sam-1.48.889.jar}    | Bin 535562 -> 536180 bytes
 settings/repository/net.sf/sam-1.48.889.xml   |   3 +++
 9 files changed, 9 insertions(+), 3 deletions(-)
 rename settings/repository/edu.mit.broad/{picard-private-parts-1941.jar => picard-private-parts-1954.jar} (88%)
 create mode 100644 settings/repository/edu.mit.broad/picard-private-parts-1954.xml
 rename settings/repository/edu.mit.broad/{picard-private-parts-1941.xml => picard-private-parts-1954.xml~} (100%)
 rename settings/repository/net.sf/{picard-1.47.869.jar => picard-1.48.889.jar} (87%)
 create mode 100644 settings/repository/net.sf/picard-1.48.889.xml
 rename settings/repository/net.sf/{picard-1.47.869.xml => picard-1.48.889.xml~} (100%)
 delete mode 100644 settings/repository/net.sf/sam-1.47.869.xml
 rename settings/repository/net.sf/{sam-1.47.869.jar => sam-1.48.889.jar} (91%)
 create mode 100644 settings/repository/net.sf/sam-1.48.889.xml

diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1941.jar b/settings/repository/edu.mit.broad/picard-private-parts-1954.jar
similarity index 88%
rename from settings/repository/edu.mit.broad/picard-private-parts-1941.jar
rename to settings/repository/edu.mit.broad/picard-private-parts-1954.jar
index 760db5cb8e7fbcd12b9cd90049ff2ff9ba037b11..67637d3d9311d10767c5758006471a628c5a8a88 100644
GIT binary patch
delta 633
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SKesy?O#kjq0jp2y$prxRP5Jr&

delta 633
zcmX><lj;0SCf)#VW)?061`Y-Wq1ba1c{P{?ft1A@=IWSp6R*pIsh`RqYO*||CP;F!
zH=_ZVu4A+UiErM`D9;WSxXWP)Rw&8o3YJLZoXrSk{O4-t0W&(q|FM9TcFEX*1y0NO
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Me|M)q)b->70E2e^Pyhe`

diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1954.xml b/settings/repository/edu.mit.broad/picard-private-parts-1954.xml
new file mode 100644
index 000000000..c702fd6e5
--- /dev/null
+++ b/settings/repository/edu.mit.broad/picard-private-parts-1954.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1954" status="integration" publication="20110712113100" />
+</ivy-module>
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1941.xml b/settings/repository/edu.mit.broad/picard-private-parts-1954.xml~
similarity index 100%
rename from settings/repository/edu.mit.broad/picard-private-parts-1941.xml
rename to settings/repository/edu.mit.broad/picard-private-parts-1954.xml~
diff --git a/settings/repository/net.sf/picard-1.47.869.jar b/settings/repository/net.sf/picard-1.48.889.jar
similarity index 87%
rename from settings/repository/net.sf/picard-1.47.869.jar
rename to settings/repository/net.sf/picard-1.48.889.jar
index d277fd2177e994cf602f728bfad82c7abc7f885e..1b725dde5da26bac05010bc371775cdb890c323c 100644
GIT binary patch
delta 67365
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diff --git a/settings/repository/net.sf/picard-1.48.889.xml b/settings/repository/net.sf/picard-1.48.889.xml
new file mode 100644
index 000000000..877687930
--- /dev/null
+++ b/settings/repository/net.sf/picard-1.48.889.xml
@@ -0,0 +1,3 @@
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+    <info organisation="net.sf" module="picard" revision="1.48.889" status="release" />
+</ivy-module>
diff --git a/settings/repository/net.sf/picard-1.47.869.xml b/settings/repository/net.sf/picard-1.48.889.xml~
similarity index 100%
rename from settings/repository/net.sf/picard-1.47.869.xml
rename to settings/repository/net.sf/picard-1.48.889.xml~
diff --git a/settings/repository/net.sf/sam-1.47.869.xml b/settings/repository/net.sf/sam-1.47.869.xml
deleted file mode 100644
index 1b76fe2f9..000000000
--- a/settings/repository/net.sf/sam-1.47.869.xml
+++ /dev/null
@@ -1,3 +0,0 @@
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diff --git a/settings/repository/net.sf/sam-1.47.869.jar b/settings/repository/net.sf/sam-1.48.889.jar
similarity index 91%
rename from settings/repository/net.sf/sam-1.47.869.jar
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diff --git a/settings/repository/net.sf/sam-1.48.889.xml b/settings/repository/net.sf/sam-1.48.889.xml
new file mode 100644
index 000000000..8046a0c02
--- /dev/null
+++ b/settings/repository/net.sf/sam-1.48.889.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.48.889" status="release" />
+</ivy-module>

From 00b650a35dad72cc79ce962ba6e1f6f01299cf3f Mon Sep 17 00:00:00 2001
From: Matt Hanna <hanna@broadinstitute.org>
Date: Sun, 17 Jul 2011 20:52:46 -0400
Subject: [PATCH 161/161] Get rid of accidental commit of emacs backup '~'
 file.

---
 settings/repository/net.sf/picard-1.48.889.xml~ | 3 ---
 1 file changed, 3 deletions(-)
 delete mode 100644 settings/repository/net.sf/picard-1.48.889.xml~

diff --git a/settings/repository/net.sf/picard-1.48.889.xml~ b/settings/repository/net.sf/picard-1.48.889.xml~
deleted file mode 100644
index 86d07d4fa..000000000
--- a/settings/repository/net.sf/picard-1.48.889.xml~
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.47.869" status="release" />
-</ivy-module>