From ed465cd2a506a623a0efbcc5d8477ebeb925726a Mon Sep 17 00:00:00 2001
From: Geraldine Van der Auwera <vdauwera@broadinstitute.org>
Date: Mon, 26 Aug 2013 17:33:17 -0400
Subject: [PATCH 01/77] Fixed a few typos and clarified some doc points.

---
 .../VariantDataManager.java                   |  2 +-
 .../VariantRecalibrator.java                  | 31 ++++++++++++-------
 2 files changed, 20 insertions(+), 13 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
index 9752ab5f5..65b1c2322 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -264,7 +264,7 @@ public class VariantDataManager {
         Collections.sort( data, new VariantDatum.VariantDatumLODComparator() );
         final int numToAdd = minimumNumber - trainingData.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 --numBadVariants arugment but this is unsafe." );
+            throw new UserException.BadInput( "Error during negative model training. Minimum number of variants to use in training is larger than the whole call set. You can try lowering the --numBadVariants argument but this is unsafe." );
         }
         int index = 0, numAdded = 0;
         while( numAdded < numToAdd && index < data.size() ) {
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index 1c56f7fff..5a8debc72 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -79,14 +79,14 @@ import java.util.*;
  * Create a Gaussian mixture model by looking at the annotations values over a high quality subset of the input call set and then evaluate all input variants.
  *
  * <p>
- * This walker is the first pass in a two-stage processing step. This walker is designed to be used in conjunction with ApplyRecalibration walker.
+ * This walker is the first pass in a two-stage processing step. This walker is designed to be used in conjunction with the ApplyRecalibration walker.
  *</p>
  *
  * <p>
  * The purpose of the variant recalibrator is to assign a well-calibrated probability to each variant call in a call set.
- * One can then create highly accurate call sets by filtering based on this single estimate for the accuracy of each call.
+ * You can then create highly accurate call sets by filtering based on this single estimate for the accuracy of each call.
  * The approach taken by variant quality score recalibration is to develop a continuous, covarying estimate of the relationship
- * between SNP call annotations (QD, MQ, HaplotypeScore, and ReadPosRankSum, for example) and the the probability that a SNP is a true genetic
+ * between SNP call annotations (QD, MQ, HaplotypeScore, and ReadPosRankSum, for example) and the probability that a SNP is a true genetic
  * variant versus a sequencing or data processing artifact. This model is determined adaptively based on "true sites" provided
  * as input, typically HapMap 3 sites and those sites found to be polymorphic on the Omni 2.5M SNP chip array. This adaptive
  * error model can then be applied to both known and novel variation discovered in the call set of interest to evaluate the
@@ -94,12 +94,7 @@ import java.util.*;
  * the log odds ratio of being a true variant versus being false under the trained Gaussian mixture model.
  * </p>
  *
- * <p>
- * NOTE: In order to create the model reporting plots Rscript needs to be in your environment PATH (this is the scripting version of R, not the interactive version).
- * See <a target="r-project" href="http://www.r-project.org">http://www.r-project.org</a> for more info on how to download and install R.
- * </p>
- *
- * <h3>Input</h3>
+ * <h3>Inputs</h3>
  * <p>
  * The input raw variants to be recalibrated.
  * <p>
@@ -127,6 +122,17 @@ import java.util.*;
  *   -rscriptFile path/to/output.plots.R
  * </pre>
  *
+ * <h3>Caveat</h3>
+ *
+ * <ul>
+ * <li>The values used in the example above are only meant to show how the command lines are composed.
+ * They are not meant to be taken as specific recommendations of values to use in your own work, and they may be
+ * different from the values cited elsewhere in our documentation. For the latest and greatest recommendations on
+ * how to set parameter values for you own analyses, please read the Best Practices section of the documentation.</li>
+ *
+ * <li>In order to create the model reporting plots Rscript needs to be in your environment PATH (this is the scripting version of R, not the interactive version).
+ * See <a target="r-project" href="http://www.r-project.org">http://www.r-project.org</a> for more info on how to download and install R.</li>
+ * </ul>
  */
 
 @DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARDISC, extraDocs = {CommandLineGATK.class} )
@@ -155,7 +161,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
      * Training - Input variants which are found to overlap with these training sites are used to build the Gaussian mixture model.
      * Truth - When deciding where to set the cutoff in VQSLOD sensitivity to these truth sites is used.
      * Known - The known / novel status of a variant isn't used by the algorithm itself and is only used for reporting / display purposes.
-     * Bad - In addition to using the worst 3% of variants as compared to the Gaussian mixture model, we can also supplement the list with a database of known bad variants.
+     * Bad - In addition to using the set of worst ranked variants as compared to the Gaussian mixture model (see -numBad argument), we can also supplement the list with a database of known bad variants.
      */
     @Input(fullName="resource", shortName = "resource", doc="A list of sites for which to apply a prior probability of being correct but which aren't used by the algorithm (training and truth sets are required to run)", required=true)
     public List<RodBinding<VariantContext>> resource = Collections.emptyList();
@@ -175,7 +181,8 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     /**
      * The expected transition / transversion ratio of true novel variants in your targeted region (whole genome, exome, specific
      * genes), which varies greatly by the CpG and GC content of the region. See expected Ti/Tv ratios section of the GATK best
-     * practices documentation (http://www.broadinstitute.org/gatk/guide/topic?name=best-practices) for more information. Normal whole genome values are 2.15 and for whole exome 3.2. Note
+     * practices documentation (http://www.broadinstitute.org/gatk/guide/topic?name=best-practices) for more information.
+     * Normal values are 2.15 for human whole genome values and 3.2 for human whole exomes. Note
      * that this parameter is used for display purposes only and isn't used anywhere in the algorithm!
      */
     @Argument(fullName="target_titv", shortName="titv", doc="The expected novel Ti/Tv ratio to use when calculating FDR tranches and for display on the optimization curve output figures. (approx 2.15 for whole genome experiments). ONLY USED FOR PLOTTING PURPOSES!", required=false)
@@ -335,7 +342,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         engine.evaluateData( dataManager.getData(), badModel, true );
 
         if( badModel.failedToConverge || goodModel.failedToConverge ) {
-            throw new UserException("NaN LOD value assigned. Clustering with this few variants and these annotations is unsafe. Please consider " + (badModel.failedToConverge ? "raising the number of variants used to train the negative model (via --numBad 3000, for example)." : "lowering the maximum number of Gaussians allowed for use in the model (via --maxGaussians 4, for example).") );
+            throw new UserException("NaN LOD value assigned. Clustering with this few variants and these annotations is unsafe. Please consider " + (badModel.failedToConverge ? "raising the number of variants used to train the negative model (via --numBadVariants 3000, for example)." : "lowering the maximum number of Gaussians allowed for use in the model (via --maxGaussians 4, for example).") );
         }
 
         engine.calculateWorstPerformingAnnotation( dataManager.getData(), goodModel, badModel );

From 3671e41b0c19c188a09fdbfca9b07cfc42a6fc64 Mon Sep 17 00:00:00 2001
From: bradtaylor <bradt@broadinstitute.org>
Date: Tue, 11 Jun 2013 17:04:19 -0400
Subject: [PATCH 02/77] Add Array Logless PairHMM

A new PairHMM implementation for read/haplotype likelihood calculations. Output is the same as the LOGLESS_CACHING version.

Instead of allocating an entire (read x haplotype) matrix for each HMM state, this version stores sub-computations in 1D arrays. It also accesses intersections of the (read x haplotype) alignment in a different order, proceeding over "diagonals" if we think of the alignment as a matrix.

This implementation makes use of haplotype caching. Because arrays are overwritten, it has to explicitly store mid-process information. Knowing where to capture this info requires us to look ahead at the subsequent haplotype to be analyzed. This necessitated a signature change in the primary method for all pairHMM implementations.

We also had to adjust the classes that employ the pairHMM:
LikelihoodCalculationEngine (used by HaplotypeCaller)
PairHMMIndelErrorModel (used by indel genotyping classes)

Made the array version the default in the HaplotypeCaller and the UnifiedArgumentCollection.
The latter affects classes:
ErrorModel
GeneralPloidyIndelGenotypeLikelihoodsCalculationModel
IndelGenotypeLikelihoodsCalculationModel
... all of which use the pairHMM via PairHMMIndelErrorModel
---
 .../genotyper/UnifiedArgumentCollection.java  |   2 +-
 .../haplotypecaller/HaplotypeCaller.java      |   2 +-
 .../LikelihoodCalculationEngine.java          |  11 +-
 .../indels/PairHMMIndelErrorModel.java        |  58 ++-
 .../utils/pairhmm/ArrayLoglessPairHMM.java    | 359 ++++++++++++++++++
 .../sting/utils/pairhmm/CnyPairHMM.java       |   3 +-
 .../sting/utils/pairhmm/LoglessPairHMM.java   |   3 +-
 .../sting/utils/pairhmm/PairHMMTestData.java  |  58 ++-
 .../sting/utils/pairhmm/PairHMMUnitTest.java  | 113 ++++--
 .../sting/utils/pairhmm/Log10PairHMM.java     |   3 +-
 .../sting/utils/pairhmm/N2MemoryPairHMM.java  |   4 -
 .../sting/utils/pairhmm/PairHMM.java          |  25 +-
 12 files changed, 560 insertions(+), 81 deletions(-)
 create mode 100644 protected/java/src/org/broadinstitute/sting/utils/pairhmm/ArrayLoglessPairHMM.java

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
index 4fae3d6e3..ff6bc5407 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
@@ -85,7 +85,7 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection
      * The PairHMM implementation to use for -glm INDEL genotype likelihood calculations. The various implementations balance a tradeoff of accuracy and runtime.
      */
     @Argument(fullName = "pair_hmm_implementation", shortName = "pairHMM", doc = "The PairHMM implementation to use for -glm INDEL genotype likelihood calculations", required = false)
-    public PairHMM.HMM_IMPLEMENTATION pairHMM = PairHMM.HMM_IMPLEMENTATION.LOGLESS_CACHING;
+    public PairHMM.HMM_IMPLEMENTATION pairHMM = PairHMM.HMM_IMPLEMENTATION.ARRAY_LOGLESS;
 
     /**
      * The minimum confidence needed in a given base for it to be used in variant calling.  Note that the base quality of a base
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
index 0b95ed07e..7edf55fed 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
@@ -387,7 +387,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
      */
     @Hidden
     @Argument(fullName = "pair_hmm_implementation", shortName = "pairHMM", doc = "The PairHMM implementation to use for genotype likelihood calculations", required = false)
-    public PairHMM.HMM_IMPLEMENTATION pairHMM = PairHMM.HMM_IMPLEMENTATION.LOGLESS_CACHING;
+    public PairHMM.HMM_IMPLEMENTATION pairHMM = PairHMM.HMM_IMPLEMENTATION.ARRAY_LOGLESS;
 
     @Hidden
     @Argument(fullName="keepRG", shortName="keepRG", doc="Only use read from this read group when making calls (but use all reads to build the assembly)", required = false)
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
index e6e76ba90..0d55797bc 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
@@ -58,6 +58,7 @@ import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.haplotype.Haplotype;
 import org.broadinstitute.sting.utils.haplotype.HaplotypeScoreComparator;
+import org.broadinstitute.sting.utils.pairhmm.ArrayLoglessPairHMM;
 import org.broadinstitute.sting.utils.pairhmm.Log10PairHMM;
 import org.broadinstitute.sting.utils.pairhmm.LoglessPairHMM;
 import org.broadinstitute.sting.utils.pairhmm.CnyPairHMM;
@@ -98,8 +99,13 @@ public class LikelihoodCalculationEngine {
                         return new LoglessPairHMM();
                     else
                         return new CnyPairHMM();
+                case ARRAY_LOGLESS:
+                    if (noFpga || !CnyPairHMM.isAvailable())
+                        return new ArrayLoglessPairHMM();
+                    else
+                        return new CnyPairHMM();
                 default:
-                    throw new UserException.BadArgumentValue("pairHMM", "Specified pairHMM implementation is unrecognized or incompatible with the HaplotypeCaller. Acceptable options are ORIGINAL, EXACT, CACHING, and LOGLESS_CACHING.");
+                    throw new UserException.BadArgumentValue("pairHMM", "Specified pairHMM implementation is unrecognized or incompatible with the HaplotypeCaller. Acceptable options are ORIGINAL, EXACT, CACHING, LOGLESS_CACHING, and ARRAY_LOGLESS.");
             }
         }
     };
@@ -258,9 +264,10 @@ public class LikelihoodCalculationEngine {
             // iterate over all haplotypes, calculating the likelihood of the read for each haplotype
             for( int jjj = 0; jjj < numHaplotypes; jjj++ ) {
                 final Haplotype haplotype = haplotypes.get(jjj);
+                final byte[] nextHaplotypeBases = (jjj == numHaplotypes - 1) ? null : haplotypes.get(jjj+1).getBases();
                 final boolean isFirstHaplotype = jjj == 0;
                 final double log10l = pairHMM.get().computeReadLikelihoodGivenHaplotypeLog10(haplotype.getBases(),
-                        readBases, readQuals, readInsQuals, readDelQuals, overallGCP, isFirstHaplotype);
+                        readBases, readQuals, readInsQuals, readDelQuals, overallGCP, isFirstHaplotype, nextHaplotypeBases);
 
                 if ( WRITE_LIKELIHOODS_TO_FILE ) {
                     likelihoodsStream.printf("%s %s %s %s %s %s %f%n",
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
index c77557da6..3c6e409b9 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
@@ -53,6 +53,7 @@ import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.clipping.ReadClipper;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.pairhmm.ArrayLoglessPairHMM;
 import org.broadinstitute.sting.utils.pairhmm.Log10PairHMM;
 import org.broadinstitute.sting.utils.pairhmm.LoglessPairHMM;
 import org.broadinstitute.sting.utils.pairhmm.PairHMM;
@@ -120,8 +121,11 @@ public class PairHMMIndelErrorModel {
             case LOGLESS_CACHING:
                 pairHMM = new LoglessPairHMM();
                 break;
+            case ARRAY_LOGLESS:
+                pairHMM = new ArrayLoglessPairHMM();
+                break;
             default:
-                throw new UserException.BadArgumentValue("pairHMM", "Specified pairHMM implementation is unrecognized or incompatible with the UnifiedGenotyper. Acceptable options are ORIGINAL, EXACT or LOGLESS_CACHING.");
+                throw new UserException.BadArgumentValue("pairHMM", "Specified pairHMM implementation is unrecognized or incompatible with the UnifiedGenotyper. Acceptable options are ORIGINAL, EXACT, LOGLESS_CACHING, or ARRAY_LOGLESS.");
         }
 
         // fill gap penalty table, affine naive model:
@@ -365,7 +369,10 @@ public class PairHMMIndelErrorModel {
                         baseDeletionQualities = contextLogGapOpenProbabilities;
                     }
 
+                    byte[] currentHaplotypeBases = null;
                     boolean firstHap = true;
+                    double readLikelihood;
+                    Allele currentAllele = null;
                     for (Allele a: haplotypeMap.keySet()) {
 
                         Haplotype haplotype = haplotypeMap.get(a);
@@ -381,34 +388,65 @@ public class PairHMMIndelErrorModel {
                         final long indStart = startLocationInRefForHaplotypes - haplotype.getStartPosition();
                         final long indStop =  stopLocationInRefForHaplotypes - haplotype.getStartPosition();
 
-                        double readLikelihood;
+
                         if (DEBUG)
                             System.out.format("indStart: %d indStop: %d WinStart:%d WinStop:%d start: %d stop: %d readLength: %d C:%s\n",
                                     indStart, indStop, ref.getWindow().getStart(), ref.getWindow().getStop(), startLocationInRefForHaplotypes, stopLocationInRefForHaplotypes, read.getReadLength(), read.getCigar().toString());
 
-                        final byte[] haplotypeBases = Arrays.copyOfRange(haplotype.getBases(), (int)indStart, (int)indStop);
+                        // peak at the next haplotype in the list
+                        final byte[] nextHaplotypeBases = Arrays.copyOfRange(haplotype.getBases(), (int)indStart, (int)indStop);
+                        // process the current haplotype in the list
+                        if (currentHaplotypeBases != null) {
+                            // it's possible that the indel starts at the last base of the haplotypes
+                            if ( currentHaplotypeBases.length == 0 ) {
+                                readLikelihood = -Double.MAX_VALUE;
+                            } else {
+                                if (firstHap) {
+                                    //no need to reallocate arrays for each new haplotype, as length won't change
+                                    pairHMM.initialize(readBases.length, currentHaplotypeBases.length);
+                                    firstHap = false;
+                                }
 
+                                readLikelihood = pairHMM.computeReadLikelihoodGivenHaplotypeLog10(currentHaplotypeBases, readBases, readQuals,
+                                        baseInsertionQualities, baseDeletionQualities, contextLogGapContinuationProbabilities, firstHap, nextHaplotypeBases);
+                            }
+
+                            if (DEBUG) {
+                                System.out.println("H:"+new String(currentHaplotypeBases));
+                                System.out.println("R:"+new String(readBases));
+                                System.out.format("L:%4.2f\n",readLikelihood);
+                            }
+
+                            perReadAlleleLikelihoodMap.add(p, currentAllele, readLikelihood);
+                            readLikelihoods[readIdx][j++] = readLikelihood;
+                        }
+                        // update the current haplotype
+                        currentHaplotypeBases = nextHaplotypeBases;
+                        currentAllele = a;
+                    }
+                    // process the final haplotype
+                    if (currentHaplotypeBases != null) {
                         // it's possible that the indel starts at the last base of the haplotypes
-                        if ( haplotypeBases.length == 0 ) {
+                        if ( currentHaplotypeBases.length == 0 ) {
                             readLikelihood = -Double.MAX_VALUE;
                         } else {
                             if (firstHap) {
                                 //no need to reallocate arrays for each new haplotype, as length won't change
-                                pairHMM.initialize(readBases.length, haplotypeBases.length);
+                                pairHMM.initialize(readBases.length, currentHaplotypeBases.length);
                                 firstHap = false;
                             }
-
-                            readLikelihood = pairHMM.computeReadLikelihoodGivenHaplotypeLog10(haplotypeBases, readBases, readQuals,
-                                    baseInsertionQualities, baseDeletionQualities, contextLogGapContinuationProbabilities, firstHap);
+                            // there is no next haplotype, so pass null for nextHaplotypeBases.
+                            readLikelihood = pairHMM.computeReadLikelihoodGivenHaplotypeLog10(currentHaplotypeBases, readBases, readQuals,
+                                    baseInsertionQualities, baseDeletionQualities, contextLogGapContinuationProbabilities, firstHap, null);
                         }
 
                         if (DEBUG) {
-                            System.out.println("H:"+new String(haplotypeBases));
+                            System.out.println("H:"+new String(currentHaplotypeBases));
                             System.out.println("R:"+new String(readBases));
                             System.out.format("L:%4.2f\n",readLikelihood);
                         }
 
-                        perReadAlleleLikelihoodMap.add(p, a, readLikelihood);
+                        perReadAlleleLikelihoodMap.add(p, currentAllele, readLikelihood);
                         readLikelihoods[readIdx][j++] = readLikelihood;
                     }
                 }
diff --git a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/ArrayLoglessPairHMM.java b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/ArrayLoglessPairHMM.java
new file mode 100644
index 000000000..26eb745bd
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/ArrayLoglessPairHMM.java
@@ -0,0 +1,359 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+*
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*
+*  4. INDEMNIFICATION
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+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.sting.utils.pairhmm;
+
+import com.google.java.contract.Ensures;
+import com.google.java.contract.Requires;
+import org.broadinstitute.sting.utils.QualityUtils;
+import java.util.Arrays;
+
+/**
+ * Created with IntelliJ IDEA.
+ * User: bradt
+ * Date: 6/11/13
+ */
+public class ArrayLoglessPairHMM extends PairHMM {
+    private static final double INITIAL_CONDITION = Math.pow(2, 1020);
+    private static final double INITIAL_CONDITION_LOG10 = Math.log10(INITIAL_CONDITION);
+
+    // we divide e by 3 because the observed base could have come from any of the non-observed alleles
+    protected static final double TRISTATE_CORRECTION = 3.0;
+
+    private static final int matchToMatch = 0;
+    private static final int indelToMatch = 1;
+    private static final int matchToInsertion = 2;
+    private static final int insertionToInsertion = 3;
+    private static final int matchToDeletion = 4;
+    private static final int deletionToDeletion = 5;
+
+    protected double[][] transition = null; // The transition probabilities cache
+    protected double[][] prior = null;      // The prior probabilities cache
+
+    // Array declarations for arrays implementation
+    private double[] currentMatchArray = null;
+    private double[] currentDeleteArray = null;
+    private double[] currentInsertArray = null;
+    private double[] parentMatchArray = null;
+    private double[] parentDeleteArray = null;
+    private double[] parentInsertArray = null;
+    private double[] grandparentMatchArray = null;
+    private double[] grandparentDeleteArray = null;
+    private double[] grandparentInsertArray = null;
+
+    // When successive haplotypes have a common prefix, these arrays store cached info from the previous haplotype; for reading
+    private double[] matchCacheArray = null;
+    private double[] deleteCacheArray = null;
+    private double[] insertCacheArray = null;
+
+    // These arrays store cache info for use with the next haplotype; for writing
+    private double[] nextMatchCacheArray = null;
+    private double[] nextDeleteCacheArray = null;
+    private double[] nextInsertCacheArray = null;
+
+    // Used when caching to store our intermediate sum at point of first difference bw successive haplotypes
+    private double partialSum;
+
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public void initialize(final int readMaxLength, final int haplotypeMaxLength ) {
+        super.initialize(readMaxLength, haplotypeMaxLength);
+
+        transition = new double[paddedMaxReadLength][6];
+        prior = new double[paddedMaxReadLength][paddedMaxHaplotypeLength];
+
+        // Initialize all arrays
+        // Final Cell of array is a padding cell, initialized to zero.
+        currentMatchArray = new double[paddedMaxReadLength];
+        currentDeleteArray = new double[paddedMaxReadLength];
+        currentInsertArray = new double[paddedMaxReadLength];
+
+        parentMatchArray = new double[paddedMaxReadLength];
+        parentDeleteArray = new double[paddedMaxReadLength];
+        parentInsertArray = new double[paddedMaxReadLength];
+
+        grandparentMatchArray = new double[paddedMaxReadLength];
+        grandparentDeleteArray = new double[paddedMaxReadLength];
+        grandparentInsertArray = new double[paddedMaxReadLength];
+
+        // Initialize the special arrays used for caching when successive haplotypes have a common prefix
+        matchCacheArray = new double[paddedMaxReadLength];
+        deleteCacheArray = new double[paddedMaxReadLength];
+        insertCacheArray = new double[paddedMaxReadLength];
+
+        nextMatchCacheArray = new double[paddedMaxReadLength];
+        nextDeleteCacheArray = new double[paddedMaxReadLength];
+        nextInsertCacheArray = new double [paddedMaxReadLength];
+    }
+
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public double subComputeReadLikelihoodGivenHaplotypeLog10( final byte[] haplotypeBases,
+                                                               final byte[] readBases,
+                                                               final byte[] readQuals,
+                                                               final byte[] insertionGOP,
+                                                               final byte[] deletionGOP,
+                                                               final byte[] overallGCP,
+                                                               int hapStartIndex,
+                                                               final boolean recacheReadValues,
+                                                               final int nextHapStartIndex) {
+
+        if ( ! constantsAreInitialized) {
+            initializeProbabilities(transition, insertionGOP, deletionGOP, overallGCP);
+
+            // note that we initialized the constants
+            constantsAreInitialized = true;
+        }
+        initializePriors(haplotypeBases, readBases, readQuals, hapStartIndex);
+
+        // Some housekeeping to be done if we are starting a new read
+        if (recacheReadValues) {
+            hapStartIndex = 0;
+
+            initializeProbabilities(transition, insertionGOP, deletionGOP, overallGCP);
+            // note that we initialized the constants
+            constantsAreInitialized = true;
+
+            // Pad the ends of the Match and Insert arrays with 0. Analogous to the first row in the Match, Insert matrices of N2MemoryPairHMM
+            grandparentMatchArray[readBases.length] = 0;
+            grandparentInsertArray[readBases.length] = 0;
+            parentMatchArray[readBases.length] = 0;
+            parentInsertArray[readBases.length] = 0;
+            currentMatchArray[readBases.length] = 0;
+            currentInsertArray[readBases.length] = 0;
+            matchCacheArray[readBases.length] = 0;
+            insertCacheArray[readBases.length] = 0;
+            nextMatchCacheArray[readBases.length] = 0;
+            nextInsertCacheArray[readBases.length] = 0;
+        }
+        // if we have not cached from prev haplotype, clear any info we may have accumulated in a previous HMM iteration
+        if (hapStartIndex == 0) {
+            Arrays.fill(matchCacheArray, 0, readBases.length, 0);
+            Arrays.fill(deleteCacheArray, 0, readBases.length, 0);
+            Arrays.fill(insertCacheArray, 0, readBases.length, 0);
+
+            partialSum = 0;
+
+            // Padding value for the deletion arrays. Let's us have free deletions at the beginning
+            // Needs to be reset when starting a new read or when hap length changes (ie when hapStartIndex is 0)
+            final double initialValue = INITIAL_CONDITION / haplotypeBases.length;
+            // Pad the deletion arrays. Akin to padding the first row in the deletion matrix
+            parentDeleteArray[readBases.length] = initialValue;
+            grandparentDeleteArray[readBases.length] = initialValue;
+            currentDeleteArray[readBases.length] = initialValue;
+            deleteCacheArray[readBases.length] = initialValue;
+            nextDeleteCacheArray[readBases.length] = initialValue;
+        }
+        // We build up our solution by looking at position [0] in the match, insert arrays. Need to set to 0 before we start.
+        grandparentMatchArray[0] = 0;
+        grandparentInsertArray[0] = 0;
+        parentMatchArray[0] = 0;
+        parentInsertArray[0] = 0;
+        currentMatchArray[0] = 0;
+        currentInsertArray[0] = 0;
+
+        // Array implementation. Start by initializing some array parameters
+        // Number of diagonals for a matrix  = rows + cols - 1;
+        final int maxDiagonals = readBases.length + haplotypeBases.length - hapStartIndex - 1;
+        // The array indices we want to fill will be between these values
+        int startFill;
+        int endFill;
+        // The position of the arrays to be updated
+        int arrayIndex;
+        // The coordinate in our priors and transition matrices corresponding to a given position in the read/haplotype alignment
+        int matrixRow;
+        int matrixCol;
+        // The final answer prior to log10 correction
+        double finalArraySumProbabilities = partialSum;
+        // This array will contain the partial sum to cache for the next haplotype
+        final int cacheSumIndex = nextHapStartIndex - hapStartIndex + readBases.length - 1;
+
+        // Perform dynamic programming using arrays, as if over diagonals of a hypothetical read/haplotype alignment matrix
+        for (int i = 1; i <= maxDiagonals; i++) {
+            // set the bounds for cells we wish to fill in the arrays
+            startFill = Math.max(readBases.length - i, 0);
+            endFill = Math.min(maxDiagonals - i + 1, readBases.length);
+
+            // apply any previously cached array information
+            if (i <= readBases.length) {
+                // apply caching info necessary for calculating current DELETE array values
+                parentMatchArray[startFill] = matchCacheArray[startFill];
+                parentDeleteArray[startFill] = deleteCacheArray[startFill];
+                // apply caching info necessary for calculating current MATCH array values
+                grandparentMatchArray[startFill + 1] = matchCacheArray[startFill + 1];
+                grandparentDeleteArray[startFill + 1] = deleteCacheArray[startFill + 1];
+                grandparentInsertArray[startFill + 1] = insertCacheArray[startFill + 1];
+            }
+
+            // fill in the cells for our arrays
+            for (arrayIndex = startFill; arrayIndex < endFill; arrayIndex++) {
+
+                // translate the array position into a row, column in the priors and transition matrices
+                matrixRow = readBases.length - arrayIndex - 1;
+                matrixCol = i - matrixRow - 1 + hapStartIndex;
+
+                // update cell for each of our new arrays. Prior, transition matrices are padded +1 row,col
+                updateArrayCell(arrayIndex, prior[matrixRow+1][matrixCol+1], transition[matrixRow+1]);
+
+                // Set up caching for the next haplotype
+                // At the position of the final similar base between this haplotype and the next one, remember the mid-array values
+                if (matrixCol == nextHapStartIndex - 1) {
+                    nextMatchCacheArray[arrayIndex] = currentMatchArray[arrayIndex];
+                    nextDeleteCacheArray[arrayIndex] = currentDeleteArray[arrayIndex];
+                    nextInsertCacheArray[arrayIndex] = currentInsertArray[arrayIndex];
+                }
+            }
+
+            // final probability is the log10 sum of the last element in the Match and Insertion state arrays
+            // this way we ignore all paths that ended in deletions! (huge)
+            // but we have to sum all the paths ending in the M and I arrays, because they're no longer extended.
+            // Where i > readBases.length, array[0] corresponds to bottom row of a [read] x [haplotype] matrix. Before this, they carries the 0's we set above.
+            finalArraySumProbabilities += currentInsertArray[0] + currentMatchArray[0];
+
+            // Partial sum for caching the next haplotype:
+            // At the position of the last similar base between this haplotype and the next one...
+            // ...remember the partial sum, so that we can start here on the next hap.
+            if (i == cacheSumIndex)
+                partialSum = finalArraySumProbabilities;
+
+            // rotate array references
+            double[] tempMatchArray = grandparentMatchArray;
+            double[] tempDeleteArray = grandparentDeleteArray;
+            double[] tempInsertArray = grandparentInsertArray;
+
+            grandparentMatchArray = parentMatchArray;
+            grandparentDeleteArray = parentDeleteArray;
+            grandparentInsertArray = parentInsertArray;
+
+            parentMatchArray = currentMatchArray;
+            parentDeleteArray = currentDeleteArray;
+            parentInsertArray = currentInsertArray;
+
+            currentMatchArray = tempMatchArray;
+            currentDeleteArray = tempDeleteArray;
+            currentInsertArray = tempInsertArray;
+        }
+        // The cache arrays we wrote for this haplotype will be read for the next haplotype.
+        matchCacheArray = nextMatchCacheArray.clone();
+        deleteCacheArray = nextDeleteCacheArray.clone();
+        insertCacheArray = nextInsertCacheArray.clone();
+
+        //return result
+        return Math.log10(finalArraySumProbabilities) - INITIAL_CONDITION_LOG10;
+    }
+
+    /**
+     * Initializes the matrix that holds all the constants related to the editing
+     * distance between the read and the haplotype.
+     *
+     * @param haplotypeBases the bases of the haplotype
+     * @param readBases      the bases of the read
+     * @param readQuals      the base quality scores of the read
+     * @param startIndex     where to start updating the distanceMatrix (in case this read is similar to the previous read)
+     */
+    public void initializePriors(final byte[] haplotypeBases, final byte[] readBases, final byte[] readQuals, final int startIndex) {
+
+        // initialize the pBaseReadLog10 matrix for all combinations of read x haplotype bases
+        // Abusing the fact that java initializes arrays with 0.0, so no need to fill in rows and columns below 2.
+
+        for (int i = 0; i < readBases.length; i++) {
+            final byte x = readBases[i];
+            final byte qual = readQuals[i];
+            for (int j = startIndex; j < haplotypeBases.length; j++) {
+                final byte y = haplotypeBases[j];
+                prior[i+1][j+1] = ( x == y || x == (byte) 'N' || y == (byte) 'N' ?
+                        QualityUtils.qualToProb(qual) : (QualityUtils.qualToErrorProb(qual) / (doNotUseTristateCorrection ? 1.0 : TRISTATE_CORRECTION)) );
+            }
+        }
+    }
+
+    /**
+     * Initializes the matrix that holds all the constants related to quality scores.
+     *
+     * @param insertionGOP   insertion quality scores of the read
+     * @param deletionGOP    deletion quality scores of the read
+     * @param overallGCP     overall gap continuation penalty
+     */
+    @Requires({
+            "insertionGOP != null",
+            "deletionGOP != null",
+            "overallGCP != null"
+    })
+    @Ensures("constantsAreInitialized")
+    protected static void initializeProbabilities(final double[][] transition, final byte[] insertionGOP, final byte[] deletionGOP, final byte[] overallGCP) {
+        for (int i = 0; i < insertionGOP.length; i++) {
+            final int qualIndexGOP = Math.min(insertionGOP[i] + deletionGOP[i], Byte.MAX_VALUE);
+            transition[i+1][matchToMatch] = QualityUtils.qualToProb((byte) qualIndexGOP);
+            transition[i+1][indelToMatch] = QualityUtils.qualToProb(overallGCP[i]);
+            transition[i+1][matchToInsertion] = QualityUtils.qualToErrorProb(insertionGOP[i]);
+            transition[i+1][insertionToInsertion] = QualityUtils.qualToErrorProb(overallGCP[i]);
+            transition[i+1][matchToDeletion] = QualityUtils.qualToErrorProb(deletionGOP[i]);
+            transition[i+1][deletionToDeletion] = QualityUtils.qualToErrorProb(overallGCP[i]);
+        }
+    }
+
+    /**
+     * Updates a cell in the HMM arrays
+     *
+     * @param indK             index in the arrays to update
+     * @param prior            the likelihood editing distance matrix for the read x haplotype
+     * @param transition       an array with the six transition relevant to this location
+     */
+    private void updateArrayCell( final int indK, final double prior, final double[] transition) {
+        currentMatchArray[indK] = prior * ( grandparentMatchArray[indK + 1] * transition[matchToMatch] +
+                grandparentInsertArray[indK + 1] * transition[indelToMatch] +
+                grandparentDeleteArray[indK + 1] * transition[indelToMatch] );
+        currentInsertArray[indK] = parentMatchArray[indK + 1] * transition[matchToInsertion] + parentInsertArray[indK + 1] * transition[insertionToInsertion];
+        currentDeleteArray[indK] = parentMatchArray[indK] * transition[matchToDeletion] + parentDeleteArray[indK] * transition[deletionToDeletion];
+    }
+
+}
diff --git a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/CnyPairHMM.java b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/CnyPairHMM.java
index 0afd4afe2..d92b918ba 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/CnyPairHMM.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/CnyPairHMM.java
@@ -191,7 +191,8 @@ public final class CnyPairHMM extends PairHMM implements BatchPairHMM {
                                                                   final byte[] deletionGOP,
                                                                   final byte[] overallGCP,
                                                                   final int hapStartIndex,
-                                                                  final boolean recacheReadValues ) {
+                                                                  final boolean recacheReadValues,
+                                                                  final int nextHapStartIndex) {
         return 0.0;
     }
 
diff --git a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/LoglessPairHMM.java b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/LoglessPairHMM.java
index 49148c152..e745ca1f5 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/LoglessPairHMM.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/LoglessPairHMM.java
@@ -92,7 +92,8 @@ public final class LoglessPairHMM extends N2MemoryPairHMM {
                                                                final byte[] deletionGOP,
                                                                final byte[] overallGCP,
                                                                final int hapStartIndex,
-                                                               final boolean recacheReadValues ) {
+                                                               final boolean recacheReadValues,
+                                                               final int nextHapStartIndex) {
 
         if (previousHaplotypeBases == null || previousHaplotypeBases.length != haplotypeBases.length) {
             final double initialValue = INITIAL_CONDITION / haplotypeBases.length;
diff --git a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/PairHMMTestData.java b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/PairHMMTestData.java
index 3d8137ecf..7fef514d9 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/PairHMMTestData.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/PairHMMTestData.java
@@ -67,12 +67,14 @@ import java.util.zip.GZIPInputStream;
  */
 public class PairHMMTestData {
     public final String ref;
+    public final String nextRef;
     private final String read;
     public final byte[] baseQuals, insQuals, delQuals, gcp;
     public final double log10l;
 
-    PairHMMTestData(String ref, String read, byte[] baseQuals, byte[] insQuals, byte[] delQuals, byte[] gcp, double log10l) {
+    PairHMMTestData(String ref, String nextRef, String read, byte[] baseQuals, byte[] insQuals, byte[] delQuals, byte[] gcp, double log10l) {
         this.ref = ref;
+        this.nextRef = nextRef;
         this.read = read;
         this.baseQuals = baseQuals;
         this.insQuals = insQuals;
@@ -81,8 +83,9 @@ public class PairHMMTestData {
         this.log10l = log10l;
     }
 
-    PairHMMTestData(String ref, String read, final byte qual) {
+    PairHMMTestData(String ref, String nextRef, String read, final byte qual) {
         this.ref = ref;
+        this.nextRef = nextRef;
         this.read = read;
         this.baseQuals = this.insQuals = this.delQuals =  Utils.dupBytes(qual, read.length());
         this.gcp =  Utils.dupBytes((byte)10, read.length());
@@ -92,13 +95,14 @@ public class PairHMMTestData {
     public double runHMM(final PairHMM hmm) {
         hmm.initialize(getRead().length(), ref.length());
         return hmm.computeReadLikelihoodGivenHaplotypeLog10(ref.getBytes(), getRead().getBytes(),
-                baseQuals, insQuals, delQuals, gcp, true);
+                baseQuals, insQuals, delQuals, gcp, true, null);
     }
 
     @Override
     public String toString() {
         return "Info{" +
                 "ref='" + ref + '\'' +
+                ", nextRef=" + nextRef + '\'' +
                 ", read='" + getRead() + '\'' +
                 ", log10l=" + log10l +
                 '}';
@@ -115,7 +119,7 @@ public class PairHMMTestData {
             hmm.initialize(first.getRead().length(), maxHaplotypeLen);
             for ( final PairHMMTestData datum : data ) {
                 hmm.computeReadLikelihoodGivenHaplotypeLog10(datum.ref.getBytes(), datum.getRead().getBytes(),
-                        datum.baseQuals, datum.insQuals, datum.delQuals, datum.gcp, false);
+                        datum.baseQuals, datum.insQuals, datum.delQuals, datum.gcp, false, datum.nextRef.getBytes());
 
             }
         }
@@ -136,22 +140,44 @@ public class PairHMMTestData {
             in = new GZIPInputStream(in);
         }
 
+        String[] nextEntry;
+        String[] thisEntry = null;
         for ( final String line : new XReadLines(in) ) {
-            final String[] parts = line.split(" ");
-            final PairHMMTestData info = new PairHMMTestData(
-                    parts[0], parts[1],
-                    SAMUtils.fastqToPhred(parts[2]),
-                    SAMUtils.fastqToPhred(parts[3]),
-                    SAMUtils.fastqToPhred(parts[4]),
-                    SAMUtils.fastqToPhred(parts[5]),
-                    Double.parseDouble(parts[6]));
+            // peak at the next entry (to get the haplotype bases)
+            nextEntry = line.split(" ");
+            // process the current entry
+            if (thisEntry != null) {
+                final PairHMMTestData info = new PairHMMTestData(
+                        thisEntry[0], nextEntry[0], thisEntry[1],
+                        SAMUtils.fastqToPhred(thisEntry[2]),
+                        SAMUtils.fastqToPhred(thisEntry[3]),
+                        SAMUtils.fastqToPhred(thisEntry[4]),
+                        SAMUtils.fastqToPhred(thisEntry[5]),
+                        Double.parseDouble(thisEntry[6]));
 
-            if ( ! results.containsKey(info.read) )  {
-                results.put(info.read, new LinkedList<PairHMMTestData>());
+                if ( ! results.containsKey(info.read) )  {
+                    results.put(info.read, new LinkedList<PairHMMTestData>());
+                }
+                final List<PairHMMTestData> byHap = results.get(info.read);
+                byHap.add(info);
             }
-            final List<PairHMMTestData> byHap = results.get(info.read);
-            byHap.add(info);
+            // update the current entry
+            thisEntry = nextEntry;
         }
+        // process the final entry
+        final PairHMMTestData info = new PairHMMTestData(
+                thisEntry[0], null, thisEntry[1],
+                SAMUtils.fastqToPhred(thisEntry[2]),
+                SAMUtils.fastqToPhred(thisEntry[3]),
+                SAMUtils.fastqToPhred(thisEntry[4]),
+                SAMUtils.fastqToPhred(thisEntry[5]),
+                Double.parseDouble(thisEntry[6]));
+
+        if ( ! results.containsKey(info.read) )  {
+            results.put(info.read, new LinkedList<PairHMMTestData>());
+        }
+        final List<PairHMMTestData> byHap = results.get(info.read);
+        byHap.add(info);
 
         return results;
     }
diff --git a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java
index 7334eec3f..b235f95c8 100644
--- a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java
@@ -72,16 +72,18 @@ public class PairHMMUnitTest extends BaseTest {
     final N2MemoryPairHMM exactHMM = new Log10PairHMM(true); // the log truth implementation
     final N2MemoryPairHMM originalHMM = new Log10PairHMM(false); // the reference implementation
     final N2MemoryPairHMM loglessHMM = new LoglessPairHMM();
+    final PairHMM arrayHMM = new ArrayLoglessPairHMM();
 
     @BeforeClass
     public void initialize() {
         exactHMM.doNotUseTristateCorrection();
         originalHMM.doNotUseTristateCorrection();
         loglessHMM.doNotUseTristateCorrection();
+        arrayHMM.doNotUseTristateCorrection();
     }
 
-    private List<N2MemoryPairHMM> getHMMs() {
-        return Arrays.asList(exactHMM, originalHMM, loglessHMM);
+    private List<PairHMM> getHMMs() {
+        return Arrays.asList(exactHMM, originalHMM, loglessHMM, arrayHMM);
     }
 
     // --------------------------------------------------------------------------------
@@ -91,8 +93,8 @@ public class PairHMMUnitTest extends BaseTest {
     // --------------------------------------------------------------------------------
 
     private class BasicLikelihoodTestProvider {
-        final String ref, read;
-        final byte[] refBasesWithContext, readBasesWithContext;
+        final String ref, nextRef, read;
+        final byte[] refBasesWithContext, nextRefBasesWithContext, readBasesWithContext;
         final int baseQual, insQual, delQual, gcp;
         final int expectedQual;
         final boolean left, right;
@@ -100,28 +102,30 @@ public class PairHMMUnitTest extends BaseTest {
         final static String LEFT_FLANK = "GATTTATCATCGAGTCTGC";
         final static String RIGHT_FLANK = "CATGGATCGTTATCAGCTATCTCGAGGGATTCACTTAACAGTTTTA";
 
-        public BasicLikelihoodTestProvider(final String ref, final String read, final int baseQual, final int insQual, final int delQual, final int expectedQual, final int gcp ) {
-            this(ref, read, baseQual, insQual, delQual, expectedQual, gcp, false, false);
+        public BasicLikelihoodTestProvider(final String ref, final String nextRef, final String read, final int baseQual, final int insQual, final int delQual, final int expectedQual, final int gcp ) {
+            this(ref, nextRef, read, baseQual, insQual, delQual, expectedQual, gcp, false, false);
         }
 
-        public BasicLikelihoodTestProvider(final String ref, final String read, final int baseQual, final int insQual, final int delQual, final int expectedQual, final int gcp, final boolean left, final boolean right) {
+        public BasicLikelihoodTestProvider(final String ref, final String nextRef, final String read, final int baseQual, final int insQual, final int delQual, final int expectedQual, final int gcp, final boolean left, final boolean right) {
             this.baseQual = baseQual;
             this.delQual = delQual;
             this.insQual = insQual;
             this.gcp = gcp;
             this.read = read;
             this.ref = ref;
+            this.nextRef = nextRef;
             this.expectedQual = expectedQual;
             this.left = left;
             this.right = right;
 
             refBasesWithContext = asBytes(ref, left, right);
+            nextRefBasesWithContext = asBytes(nextRef, left, right);
             readBasesWithContext = asBytes(read, false, false);
         }
 
         @Override
         public String toString() {
-            return String.format("ref=%s read=%s b/i/d/c quals = %d/%d/%d/%d l/r flank = %b/%b e[qual]=%d", ref, read, baseQual, insQual, delQual, gcp, left, right, expectedQual);
+            return String.format("ref=%s nextRef=%s read=%s b/i/d/c quals = %d/%d/%d/%d l/r flank = %b/%b e[qual]=%d", ref, nextRef, read, baseQual, insQual, delQual, gcp, left, right, expectedQual);
         }
 
         public double expectedLogL() {
@@ -129,7 +133,7 @@ public class PairHMMUnitTest extends BaseTest {
         }
 
         public double getTolerance(final PairHMM hmm) {
-            if ( hmm instanceof LoglessPairHMM)
+            if ( hmm instanceof LoglessPairHMM || hmm instanceof ArrayLoglessPairHMM)
                 return toleranceFromExact();
             if ( hmm instanceof Log10PairHMM ) {
                 return ((Log10PairHMM)hmm).isDoingExactLog10Calculations() ? toleranceFromExact() : toleranceFromReference();
@@ -154,11 +158,14 @@ public class PairHMMUnitTest extends BaseTest {
             return pairHMM.computeReadLikelihoodGivenHaplotypeLog10(
                     refBasesWithContext, readBasesWithContext,
                     qualAsBytes(baseQual, false, anchorIndel), qualAsBytes(insQual, true, anchorIndel), qualAsBytes(delQual, true, anchorIndel),
-                    qualAsBytes(gcp, false, anchorIndel), true);
+                    qualAsBytes(gcp, false, anchorIndel), true, nextRefBasesWithContext);
         }
 
         private byte[] asBytes(final String bases, final boolean left, final boolean right) {
-            return ( (left ? LEFT_FLANK : "") + CONTEXT + bases + CONTEXT + (right ? RIGHT_FLANK : "")).getBytes();
+            if(bases == null)
+                return null;
+            else
+                return ( (left ? LEFT_FLANK : "") + CONTEXT + bases + CONTEXT + (right ? RIGHT_FLANK : "")).getBytes();
         }
 
         private byte[] qualAsBytes(final int phredQual, final boolean doGOP, final boolean anchorIndel) {
@@ -204,7 +211,8 @@ public class PairHMMUnitTest extends BaseTest {
                             final String ref  = new String(new byte[]{refBase});
                             final String read = new String(new byte[]{readBase});
                             final int expected = refBase == readBase ? 0 : baseQual;
-                            tests.add(new Object[]{new BasicLikelihoodTestProvider(ref, read, baseQual, indelQual, indelQual, expected, gcp)});
+                            // runBasicLikelihoodTests uses calcLogL(), which runs HMM with recacheReads=true. Since we will not cache, should pass null in place of a nextRef
+                            tests.add(new Object[]{new BasicLikelihoodTestProvider(ref, null, read, baseQual, indelQual, indelQual, expected, gcp)});
                         }
                     }
 
@@ -220,10 +228,11 @@ public class PairHMMUnitTest extends BaseTest {
                                 final String ref = insertionP ? small : big;
                                 final String read = insertionP ? big : small;
 
-                                tests.add(new Object[]{new BasicLikelihoodTestProvider(ref, read, baseQual, indelQual, indelQual, expected, gcp)});
-                                tests.add(new Object[]{new BasicLikelihoodTestProvider(ref, read, baseQual, indelQual, indelQual, expected, gcp, true, false)});
-                                tests.add(new Object[]{new BasicLikelihoodTestProvider(ref, read, baseQual, indelQual, indelQual, expected, gcp, false, true)});
-                                tests.add(new Object[]{new BasicLikelihoodTestProvider(ref, read, baseQual, indelQual, indelQual, expected, gcp, true, true)});
+                                // runBasicLikelihoodTests uses calcLogL(), which runs HMM with recacheReads=true. Since we will not cache, should pass null in place of a nextRef
+                                tests.add(new Object[]{new BasicLikelihoodTestProvider(ref, null, read, baseQual, indelQual, indelQual, expected, gcp)});
+                                tests.add(new Object[]{new BasicLikelihoodTestProvider(ref, null, read, baseQual, indelQual, indelQual, expected, gcp, true, false)});
+                                tests.add(new Object[]{new BasicLikelihoodTestProvider(ref, null, read, baseQual, indelQual, indelQual, expected, gcp, false, true)});
+                                tests.add(new Object[]{new BasicLikelihoodTestProvider(ref, null, read, baseQual, indelQual, indelQual, expected, gcp, true, true)});
                             }
                         }
                     }
@@ -261,7 +270,8 @@ public class PairHMMUnitTest extends BaseTest {
 
                             for ( final boolean leftFlank : Arrays.asList(true, false) )
                                 for ( final boolean rightFlank : Arrays.asList(true, false) )
-                                    tests.add(new Object[]{new BasicLikelihoodTestProvider(ref, read, baseQual, indelQual, indelQual, -0, gcp, leftFlank, rightFlank)});
+                                    // runOptimizedLikelihoodTests uses calcLogL(), which runs HMM with recacheReads=true. Since we will not cache, should pass null in place of a nextRef
+                                    tests.add(new Object[]{new BasicLikelihoodTestProvider(ref, null, read, baseQual, indelQual, indelQual, -0, gcp, leftFlank, rightFlank)});
                         }
                     }
                 }
@@ -302,6 +312,7 @@ public class PairHMMUnitTest extends BaseTest {
         }
     }
 
+
     @Test(enabled = !DEBUG)
     public void testMismatchInEveryPositionInTheReadWithCenteredHaplotype() {
         final byte[] haplotype1 = "TTCTCTTCTGTTGTGGCTGGTT".getBytes();
@@ -323,7 +334,7 @@ public class PairHMMUnitTest extends BaseTest {
             final byte[] mread = Arrays.copyOfRange(haplotype1,offset,haplotype1.length-offset);
             // change single base at position k to C. If it's a C, change to T
             mread[k] = ( mread[k] == (byte)'C' ? (byte)'T' : (byte)'C');
-            final double res1 = loglessHMM.computeReadLikelihoodGivenHaplotypeLog10(haplotype1, mread, quals, gop, gop, gcp, false);
+            final double res1 = loglessHMM.computeReadLikelihoodGivenHaplotypeLog10(haplotype1, mread, quals, gop, gop, gcp, true, null);
             final double expected = Math.log10(1.0/haplotype1.length * Math.pow(QualityUtils.qualToProb(matchQual), mread.length-1) * QualityUtils.qualToErrorProb(mismatchQual));
             Assert.assertEquals(res1, expected, 1e-2);
         }
@@ -351,7 +362,7 @@ public class PairHMMUnitTest extends BaseTest {
             final byte[] mread = Arrays.copyOfRange(haplotype1,offset,haplotype1.length);
             // change single base at position k to C. If it's a C, change to T
             mread[k] = ( mread[k] == (byte)'C' ? (byte)'T' : (byte)'C');
-            final double res1 = loglessHMM.computeReadLikelihoodGivenHaplotypeLog10(haplotype1, mread, quals, gop, gop, gcp, false);
+            final double res1 = loglessHMM.computeReadLikelihoodGivenHaplotypeLog10(haplotype1, mread, quals, gop, gop, gcp, true , null);
             final double expected = Math.log10(1.0/haplotype1.length * Math.pow(QualityUtils.qualToProb(matchQual), mread.length-1) * QualityUtils.qualToErrorProb(mismatchQual));
             Assert.assertEquals(res1, expected, 1e-2);
         }
@@ -382,11 +393,12 @@ public class PairHMMUnitTest extends BaseTest {
         final byte delQual = 37;
         final byte gcp = 10;
         hmm.initialize(readBases.length, refBases.length);
+        // running HMM with no haplotype caching. Should therefore pass null in place of nextRef bases
         final double d = hmm.computeReadLikelihoodGivenHaplotypeLog10( refBases, readBases,
                 Utils.dupBytes(baseQual, readBases.length),
                 Utils.dupBytes(insQual, readBases.length),
                 Utils.dupBytes(delQual, readBases.length),
-                Utils.dupBytes(gcp, readBases.length), true);
+                Utils.dupBytes(gcp, readBases.length), true, null);
         Assert.assertTrue(d <= 0.0, "Likelihoods should be <= 0 but got "+ d);
     }
 
@@ -399,11 +411,12 @@ public class PairHMMUnitTest extends BaseTest {
         final byte delQual = 100;
         final byte gcp = 100;
         hmm.initialize(readBases.length, refBases.length);
+        // running HMM with no haplotype caching. Should therefore pass null in place of nextRef bases
         double d = hmm.computeReadLikelihoodGivenHaplotypeLog10( refBases, readBases,
                 Utils.dupBytes(baseQual, readBases.length),
                 Utils.dupBytes(insQual, readBases.length),
                 Utils.dupBytes(delQual, readBases.length),
-                Utils.dupBytes(gcp, readBases.length), true);
+                Utils.dupBytes(gcp, readBases.length), true, null);
         double expected =  0;
         final double initialCondition = ((double) Math.abs(refBases.length-readBases.length+1))/refBases.length;
         if (readBases.length < refBases.length) {
@@ -445,11 +458,12 @@ public class PairHMMUnitTest extends BaseTest {
         final byte delQual = 40;
         final byte gcp = 10;
         hmm.initialize(readBases.length, refBases.length);
+        // running HMM with no haplotype caching. Should therefore pass null in place of nextRef bases
         hmm.computeReadLikelihoodGivenHaplotypeLog10( refBases, readBases,
                 Utils.dupBytes(baseQual, readBases.length),
                 Utils.dupBytes(insQual, readBases.length),
                 Utils.dupBytes(delQual, readBases.length),
-                Utils.dupBytes(gcp, readBases.length), true);
+                Utils.dupBytes(gcp, readBases.length), true, null);
     }
 
     @Test(enabled = !DEBUG)
@@ -460,20 +474,27 @@ public class PairHMMUnitTest extends BaseTest {
         final byte insQual = 40;
         final byte delQual = 40;
         final byte gcp = 10;
-
+        // running HMMs with no haplotype caching. Should therefore pass null in place of nextRef bases
         exactHMM.initialize(readBases.length, refBases.length);
         exactHMM.computeReadLikelihoodGivenHaplotypeLog10( refBases, readBases,
                 Utils.dupBytes(baseQual, readBases.length),
                 Utils.dupBytes(insQual, readBases.length),
                 Utils.dupBytes(delQual, readBases.length),
-                Utils.dupBytes(gcp, readBases.length), true);
+                Utils.dupBytes(gcp, readBases.length), true, null);
 
         loglessHMM.initialize(readBases.length, refBases.length);
         loglessHMM.computeReadLikelihoodGivenHaplotypeLog10( refBases, readBases,
                 Utils.dupBytes(baseQual, readBases.length),
                 Utils.dupBytes(insQual, readBases.length),
                 Utils.dupBytes(delQual, readBases.length),
-                Utils.dupBytes(gcp, readBases.length), true);
+                Utils.dupBytes(gcp, readBases.length), true, null);
+
+        arrayHMM.initialize(readBases.length, refBases.length);
+        arrayHMM.computeReadLikelihoodGivenHaplotypeLog10( refBases, readBases,
+                Utils.dupBytes(baseQual, readBases.length),
+                Utils.dupBytes(insQual, readBases.length),
+                Utils.dupBytes(delQual, readBases.length),
+                Utils.dupBytes(gcp, readBases.length), true, null);
     }
 
     @DataProvider(name = "JustHMMProvider")
@@ -498,7 +519,8 @@ public class PairHMMUnitTest extends BaseTest {
         final byte[] gcp = Utils.dupBytes((byte) 10, delQual.length);
         hmm.initialize(readBases.length + 100, refBases.length + 100);
         for ( int nExtraMaxSize = 0; nExtraMaxSize < 100; nExtraMaxSize++ ) {
-            hmm.computeReadLikelihoodGivenHaplotypeLog10( refBases, readBases, quals, insQual, delQual, gcp, true);
+            // running HMM with no haplotype caching. Should therefore pass null in place of nextRef bases
+            hmm.computeReadLikelihoodGivenHaplotypeLog10( refBases, readBases, quals, insQual, delQual, gcp, true, null);
         }
     }
 
@@ -506,10 +528,12 @@ public class PairHMMUnitTest extends BaseTest {
     public Object[][] makeHaplotypeIndexingProvider() {
         List<Object[]> tests = new ArrayList<Object[]>();
 
+        // First difference (root2, root3) is the base position immediately following first difference (root1, root2)
         final String root1    = "ACGTGTCAAACCGGGTT";
-        final String root2    = "ACGTGTCACACTGGGTT"; // differs in two locations
+        final String root2    = "ACGTGTCACACTGGGTT"; // differs in two locations from root1
+        final String root3    = "ACGTGTCACTCCGCGTT"; // differs in two locations from root2
 
-        final String read1    = "ACGTGTCACACTGGATT"; // 1 diff from 2, 2 diff from root1
+        final String read1    = "ACGTGTCACACTGGATT"; // 1 diff from 2, 2 diff from root1, 2 diff from root3
         final String read2    = root1; // same as root1
         final String read3    = root2; // same as root2
         final String read4    = "ACGTGTCACACTGGATTCGAT";
@@ -521,7 +545,7 @@ public class PairHMMUnitTest extends BaseTest {
 //                int readLength = read.length(); {
                 for ( int readLength = 10; readLength < read.length(); readLength++ ) {
                     final String myRead = read.substring(0, readLength);
-                    tests.add(new Object[]{hmm, root1, root2, myRead});
+                    tests.add(new Object[]{hmm, root1, root2, root3, myRead});
                 }
             }
         }
@@ -530,7 +554,7 @@ public class PairHMMUnitTest extends BaseTest {
     }
 
     @Test(enabled = !DEBUG, dataProvider = "HaplotypeIndexingProvider")
-    void testHaplotypeIndexing(final PairHMM hmm, final String root1, final String root2, final String read) {
+    void testHaplotypeIndexing(final PairHMM hmm, final String root1, final String root2, final String root3, final String read) {
         final double TOLERANCE = 1e-9;
         final String prefix   = "AACCGGTTTTTGGGCCCAAACGTACGTACAGTTGGTCAACATCGATCAGGTTCCGGAGTAC";
 
@@ -544,24 +568,30 @@ public class PairHMMUnitTest extends BaseTest {
             final String myPrefix = prefix.substring(prefixStart, prefix.length());
             final String hap1 = myPrefix + root1;
             final String hap2 = myPrefix + root2;
+            final String hap3 = myPrefix + root3;
 
             final int hapStart = PairHMM.findFirstPositionWhereHaplotypesDiffer(hap1.getBytes(), hap2.getBytes());
 
-            final double actual1 = testHaplotypeIndexingCalc(hmm, hap1, read, 0, true);
-            final double actual2 = testHaplotypeIndexingCalc(hmm, hap2, read, hapStart, false);
-            final double expected2 = testHaplotypeIndexingCalc(hmm, hap2, read, 0, true);
-            Assert.assertEquals(actual2, expected2, TOLERANCE, "Caching calculation failed for read " + read + " against haplotype with prefix '" + myPrefix
+            // Run the HMM on the first haplotype, peaking ahead the second, to set up caching
+            // Then run on the second haplotype in both cached and uncached mode, and verify that results are the same
+            // When evaluating actual2, it is important that we both apply old caching from hap1 and set up new caching for hap3, to ensure read/write operations do not cause conflicts
+            final double actual1 = testHaplotypeIndexingCalc(hmm, hap1, hap2, read, 0, true);
+            final double actual2 = testHaplotypeIndexingCalc(hmm, hap2, hap3, read, hapStart, false);
+            final double expected2 = testHaplotypeIndexingCalc(hmm, hap2, null, read, 0, true);
+            Assert.assertEquals(actual2, expected2, TOLERANCE, "HMM " + hmm.getClass() + " Caching calculation failed for read " + read + " against haplotype with prefix '" + myPrefix
                     + "' expected " + expected2 + " but got " + actual2 + " with hapStart of " + hapStart);
         }
     }
 
-    private double testHaplotypeIndexingCalc(final PairHMM hmm, final String hap, final String read, final int hapStart, final boolean recache) {
+    private double testHaplotypeIndexingCalc(final PairHMM hmm, final String hap, final String nextHap, final String read, final int hapStart, final boolean recache) {
         final byte[] readBases = read.getBytes();
+        // if not peaking ahead to capture info for a future cache run, the next haplotype will be null, and this should be passed to HMM
+        final byte[] nextHapBases = nextHap == null ? null : nextHap.getBytes();
         final byte[] baseQuals = Utils.dupBytes((byte)30, readBases.length);
         final byte[] insQuals = Utils.dupBytes((byte)45, readBases.length);
         final byte[] delQuals = Utils.dupBytes((byte)40, readBases.length);
         final byte[] gcp = Utils.dupBytes((byte)10, readBases.length);
-        double d = hmm.computeReadLikelihoodGivenHaplotypeLog10(hap.getBytes(), readBases, baseQuals, insQuals, delQuals, gcp, recache);
+        double d = hmm.computeReadLikelihoodGivenHaplotypeLog10(hap.getBytes(), readBases, baseQuals, insQuals, delQuals, gcp, recache, nextHapBases);
         Assert.assertTrue(MathUtils.goodLog10Probability(d), "Likelihoods = " + d + " was bad for read " + read + " and ref " + hap + " with hapStart " + hapStart);
         return d;
     }
@@ -576,7 +606,6 @@ public class PairHMMUnitTest extends BaseTest {
                     for ( final boolean oneIsDiff : Arrays.asList(true, false) ) {
                         final byte[] hap1 = Utils.dupBytes((byte)'A', haplotypeSize1);
                         final byte[] hap2 = Utils.dupBytes((byte)'A', haplotypeSize2);
-
                         final int expected = oneIsDiff
                                 ? makeDiff(hap1, differingSite, minLength)
                                 : makeDiff(hap2, differingSite, minLength);
@@ -604,6 +633,10 @@ public class PairHMMUnitTest extends BaseTest {
         myLoglessPairHMM.doNotUseTristateCorrection();
         tests.add(new Object[]{myLoglessPairHMM});
 
+        final ArrayLoglessPairHMM myArrayLoglessPairHMM = new ArrayLoglessPairHMM();
+        myArrayLoglessPairHMM.doNotUseTristateCorrection();
+        tests.add(new Object[]{myArrayLoglessPairHMM});
+
         final Log10PairHMM myLog10PairHMM = new Log10PairHMM(true);
         myLog10PairHMM.doNotUseTristateCorrection();
         tests.add(new Object[]{myLog10PairHMM});
@@ -619,7 +652,7 @@ public class PairHMMUnitTest extends BaseTest {
 
         // didn't call initialize => should exception out
         double d = hmm.computeReadLikelihoodGivenHaplotypeLog10( refBases, readBases,
-                baseQuals, baseQuals, baseQuals, baseQuals, true);
+                baseQuals, baseQuals, baseQuals, baseQuals, true, null);
     }
 
     @Test(enabled = true, expectedExceptions = IllegalArgumentException.class, dataProvider = "JustHMMProvider")
@@ -630,7 +663,7 @@ public class PairHMMUnitTest extends BaseTest {
 
         hmm.initialize(3, 3);
         double d = hmm.computeReadLikelihoodGivenHaplotypeLog10( refBases, readBases,
-                baseQuals, baseQuals, baseQuals, baseQuals, true);
+                baseQuals, baseQuals, baseQuals, baseQuals, true, null);
     }
 
     @Test(enabled = true, expectedExceptions = IllegalArgumentException.class, dataProvider = "JustHMMProvider")
@@ -641,6 +674,6 @@ public class PairHMMUnitTest extends BaseTest {
 
         hmm.initialize(2, 3);
         double d = hmm.computeReadLikelihoodGivenHaplotypeLog10( refBases, readBases,
-                baseQuals, baseQuals, baseQuals, baseQuals, true);
+                baseQuals, baseQuals, baseQuals, baseQuals, true, null);
     }
 }
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/utils/pairhmm/Log10PairHMM.java b/public/java/src/org/broadinstitute/sting/utils/pairhmm/Log10PairHMM.java
index a75c9426c..e7bc5cb56 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pairhmm/Log10PairHMM.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pairhmm/Log10PairHMM.java
@@ -101,7 +101,8 @@ public final class Log10PairHMM extends N2MemoryPairHMM {
                                                                final byte[] deletionGOP,
                                                                final byte[] overallGCP,
                                                                final int hapStartIndex,
-                                                               final boolean recacheReadValues ) {
+                                                               final boolean recacheReadValues,
+                                                               final int nextHapStartIndex) {
 
         if (previousHaplotypeBases == null || previousHaplotypeBases.length != haplotypeBases.length) {
             // set the initial value (free deletions in the beginning) for the first row in the deletion matrix
diff --git a/public/java/src/org/broadinstitute/sting/utils/pairhmm/N2MemoryPairHMM.java b/public/java/src/org/broadinstitute/sting/utils/pairhmm/N2MemoryPairHMM.java
index 1b277d3d8..a091a0716 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pairhmm/N2MemoryPairHMM.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pairhmm/N2MemoryPairHMM.java
@@ -44,10 +44,6 @@ abstract class N2MemoryPairHMM extends PairHMM {
     protected double[][] insertionMatrix = null;
     protected double[][] deletionMatrix = null;
 
-    // only used for debugging purposes
-    protected boolean doNotUseTristateCorrection = false;
-    protected void doNotUseTristateCorrection() { doNotUseTristateCorrection = true; }
-
     /**
      * Initialize this PairHMM, making it suitable to run against a read and haplotype with given lengths
      *
diff --git a/public/java/src/org/broadinstitute/sting/utils/pairhmm/PairHMM.java b/public/java/src/org/broadinstitute/sting/utils/pairhmm/PairHMM.java
index f4f70ac63..eb52f4a85 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pairhmm/PairHMM.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pairhmm/PairHMM.java
@@ -43,6 +43,7 @@ public abstract class PairHMM {
     protected boolean constantsAreInitialized = false;
 
     protected byte[] previousHaplotypeBases;
+    protected int hapStartIndex;
 
     public enum HMM_IMPLEMENTATION {
         /* Very slow implementation which uses very accurate log10 sum functions. Only meant to be used as a reference test implementation */
@@ -51,6 +52,8 @@ public abstract class PairHMM {
         ORIGINAL,
         /* Optimized version of the PairHMM which caches per-read computations and operations in real space to avoid costly sums of log10'ed likelihoods */
         LOGLESS_CACHING,
+        /* Logless caching PairHMM that stores computations in 1D arrays instead of matrices, and which proceeds diagonally over the (read x haplotype) intersection matrix */
+        ARRAY_LOGLESS
     }
 
     protected int maxHaplotypeLength, maxReadLength;
@@ -58,6 +61,10 @@ public abstract class PairHMM {
     protected int paddedReadLength, paddedHaplotypeLength;
     private boolean initialized = false;
 
+    // only used for debugging purposes
+    protected boolean doNotUseTristateCorrection = false;
+    protected void doNotUseTristateCorrection() { doNotUseTristateCorrection = true; }
+
     /**
      * Initialize this PairHMM, making it suitable to run against a read and haplotype with given lengths
      *
@@ -109,7 +116,8 @@ public abstract class PairHMM {
                                                                   final byte[] insertionGOP,
                                                                   final byte[] deletionGOP,
                                                                   final byte[] overallGCP,
-                                                                  final boolean recacheReadValues ) {
+                                                                  final boolean recacheReadValues,
+                                                                  final byte[] nextHaploytpeBases) {
         if ( ! initialized ) throw new IllegalStateException("Must call initialize before calling computeReadLikelihoodGivenHaplotypeLog10");
         if ( haplotypeBases == null ) throw new IllegalArgumentException("haplotypeBases cannot be null");
         if ( haplotypeBases.length > maxHaplotypeLength ) throw new IllegalArgumentException("Haplotype bases is too long, got " + haplotypeBases.length + " but max is " + maxHaplotypeLength);
@@ -123,9 +131,13 @@ public abstract class PairHMM {
         paddedReadLength = readBases.length + 1;
         paddedHaplotypeLength = haplotypeBases.length + 1;
 
-        final int hapStartIndex =  (previousHaplotypeBases == null || haplotypeBases.length != previousHaplotypeBases.length || recacheReadValues) ? 0 : findFirstPositionWhereHaplotypesDiffer(haplotypeBases, previousHaplotypeBases);
+        hapStartIndex =  (recacheReadValues) ? 0 : hapStartIndex;
 
-        double result = subComputeReadLikelihoodGivenHaplotypeLog10(haplotypeBases, readBases, readQuals, insertionGOP, deletionGOP, overallGCP, hapStartIndex, recacheReadValues);
+        // Pre-compute the difference between the current haplotype and the next one to be run
+        // Looking ahead is necessary for the ArrayLoglessPairHMM implementation
+        final int nextHapStartIndex =  (nextHaploytpeBases == null || haplotypeBases.length != nextHaploytpeBases.length) ? 0 : findFirstPositionWhereHaplotypesDiffer(haplotypeBases, nextHaploytpeBases);
+
+        double result = subComputeReadLikelihoodGivenHaplotypeLog10(haplotypeBases, readBases, readQuals, insertionGOP, deletionGOP, overallGCP, hapStartIndex, recacheReadValues, nextHapStartIndex);
 
         if ( ! MathUtils.goodLog10Probability(result) )
             throw new IllegalStateException("PairHMM Log Probability cannot be greater than 0: " + String.format("haplotype: %s, read: %s, result: %f", Arrays.toString(haplotypeBases), Arrays.toString(readBases), result));
@@ -134,6 +146,10 @@ public abstract class PairHMM {
         // Warning: This assumes no downstream modification of the haplotype bases (saves us from copying the array). It is okay for the haplotype caller and the Unified Genotyper.
         previousHaplotypeBases = haplotypeBases;
 
+        // For the next iteration, the hapStartIndex for the next haploytpe becomes the index for the current haplotype
+        // The array implementation has to look ahead to the next haplotype to store caching info. It cannot do this if nextHapStart is before hapStart
+        hapStartIndex = (nextHapStartIndex < hapStartIndex) ? 0: nextHapStartIndex;
+
         return result;
     }
 
@@ -149,7 +165,8 @@ public abstract class PairHMM {
                                                                            final byte[] deletionGOP,
                                                                            final byte[] overallGCP,
                                                                            final int hapStartIndex,
-                                                                           final boolean recacheReadValues );
+                                                                           final boolean recacheReadValues,
+                                                                           final int nextHapStartIndex);
 
     /**
      * Compute the first position at which two haplotypes differ

From 86fe9fae76e81b13fb801223aad37d7451fd7d1c Mon Sep 17 00:00:00 2001
From: bradtaylor <bradt@broadinstitute.org>
Date: Wed, 7 Aug 2013 18:27:30 -0400
Subject: [PATCH 03/77] Changes to Array PairHMM to address review comments

Returned Logless Caching implementation to the default in all cases. Changing to the array version will await performance benchmarking

Refactored many pieces of functionality in ArrayLoglessPairHMM into their own methods.
---
 .../genotyper/UnifiedArgumentCollection.java  |   2 +-
 .../haplotypecaller/HaplotypeCaller.java      |   2 +-
 .../utils/pairhmm/ArrayLoglessPairHMM.java    | 278 ++++++++++++------
 3 files changed, 186 insertions(+), 96 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
index ff6bc5407..4fae3d6e3 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
@@ -85,7 +85,7 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection
      * The PairHMM implementation to use for -glm INDEL genotype likelihood calculations. The various implementations balance a tradeoff of accuracy and runtime.
      */
     @Argument(fullName = "pair_hmm_implementation", shortName = "pairHMM", doc = "The PairHMM implementation to use for -glm INDEL genotype likelihood calculations", required = false)
-    public PairHMM.HMM_IMPLEMENTATION pairHMM = PairHMM.HMM_IMPLEMENTATION.ARRAY_LOGLESS;
+    public PairHMM.HMM_IMPLEMENTATION pairHMM = PairHMM.HMM_IMPLEMENTATION.LOGLESS_CACHING;
 
     /**
      * The minimum confidence needed in a given base for it to be used in variant calling.  Note that the base quality of a base
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
index 7edf55fed..0b95ed07e 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
@@ -387,7 +387,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
      */
     @Hidden
     @Argument(fullName = "pair_hmm_implementation", shortName = "pairHMM", doc = "The PairHMM implementation to use for genotype likelihood calculations", required = false)
-    public PairHMM.HMM_IMPLEMENTATION pairHMM = PairHMM.HMM_IMPLEMENTATION.ARRAY_LOGLESS;
+    public PairHMM.HMM_IMPLEMENTATION pairHMM = PairHMM.HMM_IMPLEMENTATION.LOGLESS_CACHING;
 
     @Hidden
     @Argument(fullName="keepRG", shortName="keepRG", doc="Only use read from this read group when making calls (but use all reads to build the assembly)", required = false)
diff --git a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/ArrayLoglessPairHMM.java b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/ArrayLoglessPairHMM.java
index 26eb745bd..4b996e770 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/ArrayLoglessPairHMM.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/ArrayLoglessPairHMM.java
@@ -130,6 +130,7 @@ public class ArrayLoglessPairHMM extends PairHMM {
         nextMatchCacheArray = new double[paddedMaxReadLength];
         nextDeleteCacheArray = new double[paddedMaxReadLength];
         nextInsertCacheArray = new double [paddedMaxReadLength];
+
     }
 
 
@@ -163,59 +164,27 @@ public class ArrayLoglessPairHMM extends PairHMM {
             // note that we initialized the constants
             constantsAreInitialized = true;
 
-            // Pad the ends of the Match and Insert arrays with 0. Analogous to the first row in the Match, Insert matrices of N2MemoryPairHMM
-            grandparentMatchArray[readBases.length] = 0;
-            grandparentInsertArray[readBases.length] = 0;
-            parentMatchArray[readBases.length] = 0;
-            parentInsertArray[readBases.length] = 0;
-            currentMatchArray[readBases.length] = 0;
-            currentInsertArray[readBases.length] = 0;
-            matchCacheArray[readBases.length] = 0;
-            insertCacheArray[readBases.length] = 0;
-            nextMatchCacheArray[readBases.length] = 0;
-            nextInsertCacheArray[readBases.length] = 0;
+            // Read length may have changed, so we need to set zero-value padding at the appropriate position.
+            padMatchAndInsertArrays(readBases.length);
         }
-        // if we have not cached from prev haplotype, clear any info we may have accumulated in a previous HMM iteration
+
+        // if we have not cached from a previous haplotype, clear any info we may have accumulated in a previous HMM iteration
         if (hapStartIndex == 0) {
-            Arrays.fill(matchCacheArray, 0, readBases.length, 0);
-            Arrays.fill(deleteCacheArray, 0, readBases.length, 0);
-            Arrays.fill(insertCacheArray, 0, readBases.length, 0);
+            clearPreviouslyCachedInfo(readBases.length);
 
-            partialSum = 0;
-
-            // Padding value for the deletion arrays. Let's us have free deletions at the beginning
-            // Needs to be reset when starting a new read or when hap length changes (ie when hapStartIndex is 0)
-            final double initialValue = INITIAL_CONDITION / haplotypeBases.length;
-            // Pad the deletion arrays. Akin to padding the first row in the deletion matrix
-            parentDeleteArray[readBases.length] = initialValue;
-            grandparentDeleteArray[readBases.length] = initialValue;
-            currentDeleteArray[readBases.length] = initialValue;
-            deleteCacheArray[readBases.length] = initialValue;
-            nextDeleteCacheArray[readBases.length] = initialValue;
+            // Haplotype length may have changed, so we need to set initial-value padding at the appropriate position.
+            padDeleteArrays(haplotypeBases.length, readBases.length);
         }
-        // We build up our solution by looking at position [0] in the match, insert arrays. Need to set to 0 before we start.
-        grandparentMatchArray[0] = 0;
-        grandparentInsertArray[0] = 0;
-        parentMatchArray[0] = 0;
-        parentInsertArray[0] = 0;
-        currentMatchArray[0] = 0;
-        currentInsertArray[0] = 0;
 
-        // Array implementation. Start by initializing some array parameters
-        // Number of diagonals for a matrix  = rows + cols - 1;
-        final int maxDiagonals = readBases.length + haplotypeBases.length - hapStartIndex - 1;
-        // The array indices we want to fill will be between these values
-        int startFill;
-        int endFill;
-        // The position of the arrays to be updated
-        int arrayIndex;
-        // The coordinate in our priors and transition matrices corresponding to a given position in the read/haplotype alignment
-        int matrixRow;
-        int matrixCol;
-        // The final answer prior to log10 correction
-        double finalArraySumProbabilities = partialSum;
-        // This array will contain the partial sum to cache for the next haplotype
-        final int cacheSumIndex = nextHapStartIndex - hapStartIndex + readBases.length - 1;
+        // We build up our solution by looking at position [0] in the match, insert arrays. Need to set these to 0 before we start.
+        clearArraySolutionPosition();
+
+        // Some parameters to control behavior during the dynamic programming loop
+        final int maxDiagonals = readBases.length + haplotypeBases.length - hapStartIndex - 1;   // Number of diagonals for a matrix  = rows + cols - 1;
+        int startFill;                                                                           // The lower bound of the array indices we want to over-write
+        int endFill;                                                                             // The upper bound of the array indices we want to over-write
+        final int cacheSumIndex = nextHapStartIndex - hapStartIndex + readBases.length - 1;      // This array will contain the partial sum to cache for the next haplotype
+        double finalArraySumProbabilities = partialSum;                                          // The final answer prior to log10 correction
 
         // Perform dynamic programming using arrays, as if over diagonals of a hypothetical read/haplotype alignment matrix
         for (int i = 1; i <= maxDiagonals; i++) {
@@ -224,34 +193,11 @@ public class ArrayLoglessPairHMM extends PairHMM {
             endFill = Math.min(maxDiagonals - i + 1, readBases.length);
 
             // apply any previously cached array information
-            if (i <= readBases.length) {
-                // apply caching info necessary for calculating current DELETE array values
-                parentMatchArray[startFill] = matchCacheArray[startFill];
-                parentDeleteArray[startFill] = deleteCacheArray[startFill];
-                // apply caching info necessary for calculating current MATCH array values
-                grandparentMatchArray[startFill + 1] = matchCacheArray[startFill + 1];
-                grandparentDeleteArray[startFill + 1] = deleteCacheArray[startFill + 1];
-                grandparentInsertArray[startFill + 1] = insertCacheArray[startFill + 1];
-            }
+            if (i <= readBases.length)
+                applyPreviouslyCachedInfo(startFill);
 
-            // fill in the cells for our arrays
-            for (arrayIndex = startFill; arrayIndex < endFill; arrayIndex++) {
-
-                // translate the array position into a row, column in the priors and transition matrices
-                matrixRow = readBases.length - arrayIndex - 1;
-                matrixCol = i - matrixRow - 1 + hapStartIndex;
-
-                // update cell for each of our new arrays. Prior, transition matrices are padded +1 row,col
-                updateArrayCell(arrayIndex, prior[matrixRow+1][matrixCol+1], transition[matrixRow+1]);
-
-                // Set up caching for the next haplotype
-                // At the position of the final similar base between this haplotype and the next one, remember the mid-array values
-                if (matrixCol == nextHapStartIndex - 1) {
-                    nextMatchCacheArray[arrayIndex] = currentMatchArray[arrayIndex];
-                    nextDeleteCacheArray[arrayIndex] = currentDeleteArray[arrayIndex];
-                    nextInsertCacheArray[arrayIndex] = currentInsertArray[arrayIndex];
-                }
-            }
+            // fill in the cells for our current arrays
+            updateArrays(readBases.length, hapStartIndex, nextHapStartIndex, startFill, endFill, i);
 
             // final probability is the log10 sum of the last element in the Match and Insertion state arrays
             // this way we ignore all paths that ended in deletions! (huge)
@@ -265,27 +211,10 @@ public class ArrayLoglessPairHMM extends PairHMM {
             if (i == cacheSumIndex)
                 partialSum = finalArraySumProbabilities;
 
-            // rotate array references
-            double[] tempMatchArray = grandparentMatchArray;
-            double[] tempDeleteArray = grandparentDeleteArray;
-            double[] tempInsertArray = grandparentInsertArray;
-
-            grandparentMatchArray = parentMatchArray;
-            grandparentDeleteArray = parentDeleteArray;
-            grandparentInsertArray = parentInsertArray;
-
-            parentMatchArray = currentMatchArray;
-            parentDeleteArray = currentDeleteArray;
-            parentInsertArray = currentInsertArray;
-
-            currentMatchArray = tempMatchArray;
-            currentDeleteArray = tempDeleteArray;
-            currentInsertArray = tempInsertArray;
+            rotateArrayReferences();
         }
         // The cache arrays we wrote for this haplotype will be read for the next haplotype.
-        matchCacheArray = nextMatchCacheArray.clone();
-        deleteCacheArray = nextDeleteCacheArray.clone();
-        insertCacheArray = nextInsertCacheArray.clone();
+        rotateCacheArrays();
 
         //return result
         return Math.log10(finalArraySumProbabilities) - INITIAL_CONDITION_LOG10;
@@ -341,6 +270,136 @@ public class ArrayLoglessPairHMM extends PairHMM {
         }
     }
 
+    /**
+     * Pad the ends of the Match and Insert arrays with 0.
+     * Analogous to setting zeros in the first row in the Match, Insert matrices of N2MemoryPairHMM.
+     *
+     * @param padPosition Which index in the arrays we wish to pad
+     */
+    private void padMatchAndInsertArrays(final int padPosition) {
+        grandparentMatchArray[padPosition] = 0;
+        grandparentInsertArray[padPosition] = 0;
+        parentMatchArray[padPosition] = 0;
+        parentInsertArray[padPosition] = 0;
+        currentMatchArray[padPosition] = 0;
+        currentInsertArray[padPosition] = 0;
+        matchCacheArray[padPosition] = 0;
+        insertCacheArray[padPosition] = 0;
+        nextMatchCacheArray[padPosition] = 0;
+        nextInsertCacheArray[padPosition] = 0;
+    }
+
+    /**
+     * Pad the Delete arrays with an intial value. Let's us have free deletions at the beginning of the alignment.
+     * Analogous to padding the first row of the Delete matrix of N2MemoryPairHMM.
+     *
+     * @param haplotypeLength   The length of the present haplotype. Necessary for calculating initial padding value
+     * @param padPosition       Which index in the arrays we wish to pad
+     */
+    private void padDeleteArrays(final int haplotypeLength, final int padPosition) {
+        final double initialValue = INITIAL_CONDITION / haplotypeLength;
+
+        // Pad the deletion arrays. Akin to padding the first row in the deletion matrix
+        parentDeleteArray[padPosition] = initialValue;
+        grandparentDeleteArray[padPosition] = initialValue;
+        currentDeleteArray[padPosition] = initialValue;
+        deleteCacheArray[padPosition] = initialValue;
+        nextDeleteCacheArray[padPosition] = initialValue;
+    }
+
+    /**
+     * We build up our solution by looking at position [0] in the match, insert arrays. Need to set these to 0 before we start.
+     *
+     */
+    private void clearArraySolutionPosition() {
+        grandparentMatchArray[0] = 0;
+        grandparentInsertArray[0] = 0;
+        parentMatchArray[0] = 0;
+        parentInsertArray[0] = 0;
+        currentMatchArray[0] = 0;
+        currentInsertArray[0] = 0;
+    }
+
+    /**
+     * Clears cached information saved from the last haplotype,
+     * allowing us to start at the beginning of the present haplotype with intitial values of 0.
+     *
+     * @param fillLength How much of the cache arrays do we need to zero
+     */
+    private void clearPreviouslyCachedInfo(final int fillLength) {
+        Arrays.fill(matchCacheArray, 0, fillLength, 0);
+        Arrays.fill(deleteCacheArray, 0, fillLength, 0);
+        Arrays.fill(insertCacheArray, 0, fillLength, 0);
+
+        partialSum = 0;
+    }
+
+    /**
+     * Applies cached information saved from the last haplotype,
+     * allowing us to start in the middle of the present haplotype.
+     *
+     * @param indK the index in the arrays we wish to update with cached info
+     */
+    private void applyPreviouslyCachedInfo(int indK) {
+        // apply caching info necessary for calculating current DELETE array values
+        parentMatchArray[indK] = matchCacheArray[indK];
+        parentDeleteArray[indK] = deleteCacheArray[indK];
+
+        // apply caching info necessary for calculating current MATCH array values
+        grandparentMatchArray[indK + 1] = matchCacheArray[indK + 1];
+        grandparentDeleteArray[indK + 1] = deleteCacheArray[indK + 1];
+        grandparentInsertArray[indK + 1] = insertCacheArray[indK + 1];
+    }
+
+    /**
+     * Records the mid-process state of one location in the read/haplotype alignment.
+     * Writes new cache information for use with the next haplotype we see.
+     *
+     * @param indK the index in the cache arrays we wish to store information in
+     */
+    private void recordNewCacheInfo(int indK) {
+        nextMatchCacheArray[indK] = currentMatchArray[indK];
+        nextDeleteCacheArray[indK] = currentDeleteArray[indK];
+        nextInsertCacheArray[indK] = currentInsertArray[indK];
+    }
+
+    /**
+     * Update the HMM arrays for the current diagonal.
+     *
+     * @param readLength        The length of the read
+     * @param hapStartIndex     An offset that tells us if we are starting in the middle of the present haplotype
+     * @param nextHapStartIndex An offset that tells us which base in the NEXT haplotype we need to look at to record new caching info
+     * @param startFill         The lower bound of the array indices we want to over-write
+     * @param endFill           The upper bound of the array indices we want to over-write
+     * @param iii               The index indicating which diagonal of the read/haplotype alignment we are working on
+     */
+    private void updateArrays(final int readLength,
+                              final int hapStartIndex,
+                              final int nextHapStartIndex,
+                              final int startFill,
+                              final int endFill,
+                              final int iii) {
+
+        // The coordinate in our priors and transition matrices corresponding to a given position in the read/haplotype alignment
+        int matrixRow;
+        int matrixCol;
+
+        int arrayIndex;
+        for (arrayIndex = startFill; arrayIndex < endFill; arrayIndex++) {
+            // translate the array position into a row, column in the priors and transition matrices
+            matrixRow = readLength - arrayIndex - 1;
+            matrixCol = iii - matrixRow - 1 + hapStartIndex;
+
+            // update cell for each of our current arrays. Prior, transition matrices are padded +1 row,col
+            updateArrayCell(arrayIndex, prior[matrixRow+1][matrixCol+1], transition[matrixRow+1]);
+
+            // Set up caching for the next haplotype
+            // At the position of the final similar base between this haplotype and the next one, remember the mid-array values
+            if (matrixCol == nextHapStartIndex - 1)
+                recordNewCacheInfo(arrayIndex);
+        }
+    }
+
     /**
      * Updates a cell in the HMM arrays
      *
@@ -356,4 +415,35 @@ public class ArrayLoglessPairHMM extends PairHMM {
         currentDeleteArray[indK] = parentMatchArray[indK] * transition[matchToDeletion] + parentDeleteArray[indK] * transition[deletionToDeletion];
     }
 
+    /**
+     * To prepare for the next diagonal in our loop, each array must be bumped to an older generation
+     *
+     */
+    private void rotateArrayReferences() {
+        double[] tempMatchArray = grandparentMatchArray;
+        double[] tempDeleteArray = grandparentDeleteArray;
+        double[] tempInsertArray = grandparentInsertArray;
+
+        grandparentMatchArray = parentMatchArray;
+        grandparentDeleteArray = parentDeleteArray;
+        grandparentInsertArray = parentInsertArray;
+
+        parentMatchArray = currentMatchArray;
+        parentDeleteArray = currentDeleteArray;
+        parentInsertArray = currentInsertArray;
+
+        currentMatchArray = tempMatchArray;
+        currentDeleteArray = tempDeleteArray;
+        currentInsertArray = tempInsertArray;
+    }
+
+    /**
+     * To prepare for the next haplotype, the caching info we wrote is copied into the cach-read arrays
+     *
+     */
+    private void rotateCacheArrays() {
+        matchCacheArray = nextMatchCacheArray.clone();
+        deleteCacheArray = nextDeleteCacheArray.clone();
+        insertCacheArray = nextInsertCacheArray.clone();
+    }
 }

From 0435bbe38fda417ba6a88b99bc0c5b515bcaca1e Mon Sep 17 00:00:00 2001
From: bradtaylor <bradt@broadinstitute.org>
Date: Sun, 18 Aug 2013 21:24:58 -0400
Subject: [PATCH 04/77] Retreived PairHMM benchmarks from archive and made
 improvements

PairHMMSyntheticBenchmark and PairHMMEmpirical benchmark were written to test the banded pairHMM, and were archived along with it. I returned them to the test directory for use in benchmarking the ArrayLoglessPairHMM. I commented out references to the banded pairHMM (which was left in archive), rather than removing those references entirely.

Renamed PairHMMEmpiricalBenchmark to PairHMMBandedEmpiricalBenchmark and returned it to the archive. It has a few problems for use as a general benchmark, including initializing the HMM too frequently and doing too much setup work in the 'time' method. However, since the size selection and debug printing are useful for testing the banded implementation, I decided to keep it as-is and archive it alongside with the other banded pairHMM classes. I did fix one bug that was causing the selectWorkingData function to return prematurely. As a result, the benchmark was only evaluating 4-40 pairHMM calls instead of the desired "maxRecords".

I wrote a new PairHMMEmpiricalBenchmark that simply works through a list of data, with setup work and hmm-initialization moved to its own function. This involved writing a new data read-in function in PairHMMTestData. The original was not maintaining the input data in order, the end result of which would be an over-estimate of how much caching we are able to do. The new benchmark class more closely mirrors real-world operation over large data.

It might be cleaner to fix some of the issues with the BandedEmpiricalBenchmark and use one read-in function. However, this would involve more extensive changes to:
PairHMMBandedEmpiricalBenchmark
PairHMMTestData
BandedLoglessPairHMMUnitTest

I decided against this as the banded benchmark and unit test are archived.
---
 .../pairhmm/PairHMMEmpiricalBenchmark.java    | 115 ++++++++++++++++
 .../pairhmm/PairHMMSyntheticBenchmark.java    | 127 ++++++++++++++++++
 .../sting/utils/pairhmm/PairHMMTestData.java  |  84 ++++++++++--
 3 files changed, 318 insertions(+), 8 deletions(-)
 create mode 100644 protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMEmpiricalBenchmark.java
 create mode 100644 protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMSyntheticBenchmark.java
 rename protected/java/{src => test}/org/broadinstitute/sting/utils/pairhmm/PairHMMTestData.java (80%)

diff --git a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMEmpiricalBenchmark.java b/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMEmpiricalBenchmark.java
new file mode 100644
index 000000000..151097aad
--- /dev/null
+++ b/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMEmpiricalBenchmark.java
@@ -0,0 +1,115 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*  
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*  
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*  
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*  
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*  
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. 
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.  
+*  
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY 
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*  
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*  
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*  
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*  
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt. 
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. 
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.sting.utils.pairhmm;
+
+import com.google.caliper.Param;
+import com.google.caliper.SimpleBenchmark;
+
+import java.io.File;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.lang.Math;
+
+/**
+ * Caliper microbenchmark for empirical test data for PairHMM
+ */
+public class PairHMMEmpiricalBenchmark extends SimpleBenchmark {
+    @Param ({"array_logless", "logless"})
+    String algorithm;
+
+    @Param({"likelihoods_NA12878_HiSeqWGS_chr20_1mb.txt"})
+    String likelihoodsFile;
+
+    @Param({"1000","10000","70000"})
+    int records;
+
+    PairHMM hmm =null;
+
+    List<PairHMMTestData> empiricalData = new LinkedList<>();
+    List<PairHMMTestData> workingData = new LinkedList<>();
+
+
+    @Override
+    protected void setUp() throws Exception {
+        empiricalData = PairHMMTestData.readLikelihoodsInOrder(new File(likelihoodsFile));
+        records = Math.min(records, empiricalData.size());
+        workingData = empiricalData.subList(0,records);
+
+        int maxReadLength = PairHMMTestData.calcMaxReadLen(workingData);
+        int maxHaplotypeLength = PairHMMTestData.calcMaxHaplotypeLen(workingData);
+
+        hmm = getHmm();
+        hmm.initialize(maxReadLength,maxHaplotypeLength);
+    }
+
+    private PairHMM getHmm() {
+        switch (algorithm) {
+            case "logless": return new LoglessPairHMM();
+            case "array_logless": return new ArrayLoglessPairHMM();
+            default: throw new IllegalStateException("Unexpected algorithm " + algorithm);
+        }
+    }
+
+    public double timeHMM(int rep){
+        double result = 0;
+        for (int i = 0; i < rep; i++) {
+            for (final PairHMMTestData datum : workingData){
+                result += hmm.computeReadLikelihoodGivenHaplotypeLog10(datum.ref.getBytes(),
+                                                                       datum.getRead().getBytes(),
+                                                                       datum.baseQuals,
+                                                                       datum.insQuals,
+                                                                       datum.delQuals,
+                                                                       datum.gcp,
+                                                                       datum.newRead,
+                                                                       datum.nextRef.getBytes());
+
+            }
+        }
+        return result;
+    }
+}
diff --git a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMSyntheticBenchmark.java b/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMSyntheticBenchmark.java
new file mode 100644
index 000000000..9706c0e9d
--- /dev/null
+++ b/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMSyntheticBenchmark.java
@@ -0,0 +1,127 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*  
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*  
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*  
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*  
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*  
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. 
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.  
+*  
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY 
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*  
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*  
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*  
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*  
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt. 
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. 
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.sting.utils.pairhmm;
+
+import com.google.caliper.Param;
+import com.google.caliper.SimpleBenchmark;
+import net.sf.samtools.Cigar;
+import net.sf.samtools.CigarElement;
+import net.sf.samtools.TextCigarCodec;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.sam.AlignmentUtils;
+
+import java.util.*;
+
+/**
+ * Caliper microbenchmark for synthetic test data for PairHMM
+ */
+public class PairHMMSyntheticBenchmark extends SimpleBenchmark {
+    @Param ({"array_logless", "logless"})
+//    @Param({"logless", "array_logless"})
+//    @Param({"logless", "banded_w5_mle10", "banded_w5_mle20"})
+//    @Param({"logless", "banded_w10_mle20", "banded_w5_mle20", "banded_w5_mle10"})
+    String algorithm;
+
+//    @Param({"40", "100", "200", "300", "500"})
+    @Param({"40", "300"})
+//    @Param({"300"})
+    int refLength;
+
+//    @Param({"200"})
+    @Param({"40", "101", "200"})
+//    @Param({"40", "100", "200", "300", "500"})
+    int readLength;
+
+    private PairHMM hmm;
+    private PairHMMTestData testData;
+
+
+    @Override
+    protected void setUp() throws Exception {
+        hmm = getHmm();
+        final String ref = generateSeq(refLength);
+        final String nextRef = generateSeq(refLength);
+        final String read = generateSeq(readLength);
+        testData = new PairHMMTestData(ref, nextRef, read, (byte)30);
+        System.out.println(testData.toString());
+    }
+
+    private PairHMM getHmm() {
+        switch (algorithm) {
+            case "logless": return new LoglessPairHMM();
+            case "array_logless": return new ArrayLoglessPairHMM();
+//            case "banded_w10_mle20": return new BandedLoglessPairHMM(10, 1e-20);
+//            case "banded_w5_mle20":  return new BandedLoglessPairHMM(5, 1e-20);
+//            case "banded_w5_mle10":  return new BandedLoglessPairHMM(5, 1e-10);
+            default: throw new IllegalStateException("Unexpected algorithm " + algorithm);
+        }
+    }
+
+    private String generateSeq(final int len) {
+        final List<String> root = Arrays.asList("A", "C", "G", "T");
+
+        String seq = "";
+        for ( int i = 0; true; i++ ) {
+            final String base = root.get(i % root.size());
+            final int copies = i / root.size() + 1;
+            seq += Utils.dupString(base, copies);
+            if ( seq.length() >= len )
+                return seq.substring(0, len);
+        }
+    }
+
+    public void timePairHMM(int rep) {
+        for ( int i = 0; i < rep; i++ ) {
+            testData.runHMM(hmm);
+        }
+//        if ( hmm instanceof BandedLoglessPairHMM ) {
+//            final BandedLoglessPairHMM banded = (BandedLoglessPairHMM)hmm;
+//            System.out.printf("Banded n cells possible  : %d%n", banded.nCellsOverall);
+//            System.out.printf("Banded n cells evaluated : %d%n", banded.nCellsEvaluated);
+//        }
+    }
+}
diff --git a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/PairHMMTestData.java b/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMTestData.java
similarity index 80%
rename from protected/java/src/org/broadinstitute/sting/utils/pairhmm/PairHMMTestData.java
rename to protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMTestData.java
index 7fef514d9..e6c8e1e61 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/PairHMMTestData.java
+++ b/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMTestData.java
@@ -71,8 +71,9 @@ public class PairHMMTestData {
     private final String read;
     public final byte[] baseQuals, insQuals, delQuals, gcp;
     public final double log10l;
+    public final boolean newRead;
 
-    PairHMMTestData(String ref, String nextRef, String read, byte[] baseQuals, byte[] insQuals, byte[] delQuals, byte[] gcp, double log10l) {
+    PairHMMTestData(String ref, String nextRef, String read, byte[] baseQuals, byte[] insQuals, byte[] delQuals, byte[] gcp, double log10l, boolean newRead) {
         this.ref = ref;
         this.nextRef = nextRef;
         this.read = read;
@@ -81,6 +82,7 @@ public class PairHMMTestData {
         this.delQuals = delQuals;
         this.gcp = gcp;
         this.log10l = log10l;
+        this.newRead = newRead;
     }
 
     PairHMMTestData(String ref, String nextRef, String read, final byte qual) {
@@ -90,6 +92,7 @@ public class PairHMMTestData {
         this.baseQuals = this.insQuals = this.delQuals =  Utils.dupBytes(qual, read.length());
         this.gcp =  Utils.dupBytes((byte)10, read.length());
         this.log10l = -1;
+        this.newRead = true;
     }
 
     public double runHMM(final PairHMM hmm) {
@@ -104,25 +107,28 @@ public class PairHMMTestData {
                 "ref='" + ref + '\'' +
                 ", nextRef=" + nextRef + '\'' +
                 ", read='" + getRead() + '\'' +
-                ", log10l=" + log10l +
+                ", log10l=" + log10l + '\'' +
+                ", newRead=" + newRead +
                 '}';
     }
 
-    public static void runHMMs(final PairHMM hmm, final List<PairHMMTestData> data, final boolean runSingly) {
+    public static double runHMMs(final PairHMM hmm, final List<PairHMMTestData> data, final boolean runSingly) {
+        double result = 0;
         if ( runSingly ) {
             for ( final PairHMMTestData datum : data )
-                datum.runHMM(hmm);
+                result += datum.runHMM(hmm);
         } else {
             // running in batch mode
             final PairHMMTestData first = data.get(0);
             int maxHaplotypeLen = calcMaxHaplotypeLen(data);
             hmm.initialize(first.getRead().length(), maxHaplotypeLen);
             for ( final PairHMMTestData datum : data ) {
-                hmm.computeReadLikelihoodGivenHaplotypeLog10(datum.ref.getBytes(), datum.getRead().getBytes(),
-                        datum.baseQuals, datum.insQuals, datum.delQuals, datum.gcp, false, datum.nextRef.getBytes());
+                result += hmm.computeReadLikelihoodGivenHaplotypeLog10(datum.ref.getBytes(), datum.getRead().getBytes(),
+                        datum.baseQuals, datum.insQuals, datum.delQuals, datum.gcp, datum.newRead, datum.nextRef.getBytes());
 
             }
         }
+        return result;
     }
 
     public static int calcMaxHaplotypeLen(final List<PairHMMTestData> data) {
@@ -132,6 +138,13 @@ public class PairHMMTestData {
         return maxHaplotypeLen;
     }
 
+    public static int calcMaxReadLen(final List<PairHMMTestData> data) {
+        int maxReadLen = 0;
+        for ( final PairHMMTestData datum : data )
+            maxReadLen = Math.max(maxReadLen, datum.getRead().length());
+        return maxReadLen;
+    }
+
     public static Map<String, List<PairHMMTestData>> readLikelihoods(final File file) throws IOException {
         final Map<String, List<PairHMMTestData>> results = new LinkedHashMap<>();
 
@@ -153,7 +166,8 @@ public class PairHMMTestData {
                         SAMUtils.fastqToPhred(thisEntry[3]),
                         SAMUtils.fastqToPhred(thisEntry[4]),
                         SAMUtils.fastqToPhred(thisEntry[5]),
-                        Double.parseDouble(thisEntry[6]));
+                        Double.parseDouble(thisEntry[6]),
+                        ! results.containsKey(thisEntry[1]));
 
                 if ( ! results.containsKey(info.read) )  {
                     results.put(info.read, new LinkedList<PairHMMTestData>());
@@ -171,7 +185,8 @@ public class PairHMMTestData {
                 SAMUtils.fastqToPhred(thisEntry[3]),
                 SAMUtils.fastqToPhred(thisEntry[4]),
                 SAMUtils.fastqToPhred(thisEntry[5]),
-                Double.parseDouble(thisEntry[6]));
+                Double.parseDouble(thisEntry[6]),
+                ! results.containsKey(thisEntry[1]));
 
         if ( ! results.containsKey(info.read) )  {
             results.put(info.read, new LinkedList<PairHMMTestData>());
@@ -182,6 +197,59 @@ public class PairHMMTestData {
         return results;
     }
 
+
+    /*
+     * simplified likelihoods file reader that returns a list instead of a map
+     *
+     * readLikelihoods() method was reordering inputs, with the result that caching would be more efficient
+     * This method simply returns a list of read/haplotype pairs in their original order, providing a more realistic caching scenario
+     */
+    public static List<PairHMMTestData> readLikelihoodsInOrder(final File file) throws IOException {
+        final List<PairHMMTestData> results = new LinkedList<>();
+
+        InputStream in = new FileInputStream(file);
+        if ( file.getName().endsWith(".gz") ) {
+            in = new GZIPInputStream(in);
+        }
+
+        String previousRead = null;
+        String[] nextEntry;
+        String[] thisEntry = null;
+        for ( final String line : new XReadLines(in) ) {
+            // peak at the next entry (to get the haplotype bases)
+            nextEntry = line.split(" ");
+            // process the current entry
+            if (thisEntry != null) {
+                final PairHMMTestData info = new PairHMMTestData(
+                        thisEntry[0], nextEntry[0], thisEntry[1],
+                        SAMUtils.fastqToPhred(thisEntry[2]),
+                        SAMUtils.fastqToPhred(thisEntry[3]),
+                        SAMUtils.fastqToPhred(thisEntry[4]),
+                        SAMUtils.fastqToPhred(thisEntry[5]),
+                        Double.parseDouble(thisEntry[6]),
+                        !(thisEntry[1].equals(previousRead)));
+
+                results.add(info);
+                previousRead = info.getRead();
+            }
+            // update the current entry
+            thisEntry = nextEntry;
+        }
+        // process the final entry
+        final PairHMMTestData info = new PairHMMTestData(
+                thisEntry[0], null, thisEntry[1],
+                SAMUtils.fastqToPhred(thisEntry[2]),
+                SAMUtils.fastqToPhred(thisEntry[3]),
+                SAMUtils.fastqToPhred(thisEntry[4]),
+                SAMUtils.fastqToPhred(thisEntry[5]),
+                Double.parseDouble(thisEntry[6]),
+                !(thisEntry[1].equals(previousRead)));
+
+        results.add(info);
+
+        return results;
+    }
+
     public String getRead() {
         return read;
     }

From 4473b0065e10e66b106ae03243c6e1770055ba46 Mon Sep 17 00:00:00 2001
From: Louis Bergelson <louisb@broadinstitute.org>
Date: Thu, 29 Aug 2013 11:23:47 -0400
Subject: [PATCH 05/77] adding a check for the UNAVAILABLE case of GenotypeType
 in CountVariants

---
 .../varianteval/VariantEvalIntegrationTest.java | 17 ++++++++++++++++-
 .../varianteval/evaluators/CountVariants.java   |  2 ++
 2 files changed, 18 insertions(+), 1 deletion(-)

diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
index d695f2d13..9b5290dee 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
@@ -48,8 +48,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval;
 
 import org.broadinstitute.sting.WalkerTest;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.testng.annotations.Test;
 import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -376,6 +376,21 @@ public class VariantEvalIntegrationTest extends WalkerTest {
         executeTestParallel("testEvalTrackWithoutGenotypes",spec);
     }
 
+    @Test
+    public void testEvalTrackWithoutGenotypesWithSampleFields() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                buildCommandLine(
+                        "-T VariantEval",
+                        "-R " + b37KGReference,
+                        "-eval " + variantEvalTestDataRoot + "noGenotypes.vcf",
+                        "-o %s"
+                ),
+                1,
+                Arrays.asList("")); //There is no md5 because we only care that this completes without an exception.
+        executeTest("testEvalTrackWithoutGenotypesWithSampleFields", spec);
+
+    }
+
     @Test
     public void testMultipleEvalTracksWithoutGenotypes() {
         String extraArgs = "-T VariantEval -R " + b37KGReference +
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 33a5a9fc9..63c34586e 100644
--- 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
@@ -197,6 +197,8 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
                     break;
                 case MIXED:
                     break;
+                case UNAVAILABLE:
+                    break;
                 default:
                     throw new ReviewedStingException("BUG: Unexpected genotype type: " + g);
             }

From ea0deb1bb23951966a9b9b33ce741c32aa05a390 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Fri, 30 Aug 2013 12:18:19 -0400
Subject: [PATCH 06/77] Changed the error for the record size mismatch in the
 genotyping engine to be a user error since it is possible to reach this state
 with input VCFs that contain the same event multiple times (and it's not
 something we want to handle in the code).

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

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
index 82029b872..cb3b9b65f 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
@@ -58,6 +58,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.collections.DefaultHashMap;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.haplotype.EventMap;
 import org.broadinstitute.sting.utils.haplotype.Haplotype;
@@ -186,7 +187,8 @@ public class GenotypingEngine {
                 if( mergedVC == null ) { continue; }
 
                 if( eventsAtThisLoc.size() != mergedVC.getAlternateAlleles().size() ) {
-                    throw new ReviewedStingException("Record size mismatch! Something went wrong in the merging of alleles.");
+                    // this is possible in GGA mode when the same event is represented in multiple input records
+                    throw new UserException("The same event (although possibly represented differently) is present in multiple input records at location " + loc + " and this is not something we can handle at this time.  You will need to remove one of the records in order to proceed with your input file(s).");
                 }
                 final Map<VariantContext, Allele> mergeMap = new LinkedHashMap<>();
                 mergeMap.put(null, mergedVC.getReference()); // the reference event (null) --> the reference allele

From b6c3ed0295395cc07dda28a02c05a619ae1983d8 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Fri, 6 Sep 2013 09:30:01 -0400
Subject: [PATCH 07/77] Added REVERT SOFTCLIPPED bases to ClipReads

---
 .../sting/gatk/walkers/readutils/ClipReads.java               | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java
index 879022299..dfc36954b 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java
@@ -305,7 +305,7 @@ public class ClipReads extends ReadWalker<ClipReads.ReadClipperWithData, ClipRea
      */
     public ReadClipperWithData map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker) {
         if ( onlyDoRead == null || read.getReadName().equals(onlyDoRead) ) {
-            if ( clippingRepresentation == ClippingRepresentation.HARDCLIP_BASES )
+            if ( clippingRepresentation == ClippingRepresentation.HARDCLIP_BASES || clippingRepresentation == ClippingRepresentation.REVERT_SOFTCLIPPED_BASES )
                 read = ReadClipper.revertSoftClippedBases(read);
             ReadClipperWithData clipper = new ReadClipperWithData(read, sequencesToClip);
 
@@ -600,4 +600,4 @@ public class ClipReads extends ReadWalker<ClipReads.ReadClipperWithData, ClipRea
     }
 
 
-}
\ No newline at end of file
+}

From 3503050a39b8f8a402729f667b1268e471cf4582 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Thu, 8 Aug 2013 15:09:38 -0400
Subject: [PATCH 08/77] Created a single sample calling pipeline which
 leverages the reference model calculation mode of the HaplotypeCaller

-- Adding changes to CombineVariants to work with the Reference Model mode of the HaplotypeCaller.
-- Added -combineAnnotations mode to CombineVariants to merge the info field annotations by taking the median
-- Added new StrandBiasBySample genotype annotation for use in computing strand bias from single sample input vcfs
-- Bug fixes to calcGenotypeLikelihoodsOfRefVsAny, used in isActive() as well as the reference model
-- Added active region trimming capabilities to the reference model mode, not perfect yet, turn off with --dontTrimActiveRegions
-- We only realign reads in the reference model if there are non-reference haplotypes, a big time savings
-- We only realign reads in the reference model if the read is informative for a particular haplotype over another
-- GVCF blocks will now track and output the minimum PLs over the block

-- MD5 changes!
-- HC tests: from bug fixes in calcGenotypeLikelihoodsOfRefVsAny
-- GVCF tests: from HC changes above and adding in active region trimming
---
 .../annotator/DepthPerAlleleBySample.java     |  12 +-
 .../gatk/walkers/annotator/FisherStrand.java  |  96 ++++++-
 .../walkers/annotator/InbreedingCoeff.java    |  18 +-
 .../walkers/annotator/StrandBiasBySample.java | 100 +++++++
 .../genotyper/ConsensusAlleleCounter.java     |   7 +-
 ...elGenotypeLikelihoodsCalculationModel.java |   2 +-
 ...elGenotypeLikelihoodsCalculationModel.java |   8 +-
 .../haplotypecaller/ActiveRegionTrimmer.java  |  10 +-
 .../haplotypecaller/GenotypingEngine.java     |   2 +-
 .../haplotypecaller/HaplotypeCaller.java      |  25 +-
 .../haplotypecaller/RefVsAnyResult.java       |  10 +-
 .../ReferenceConfidenceModel.java             |  93 ++++--
 .../sting/utils/gvcf/GVCFWriter.java          |   1 +
 .../sting/utils/gvcf/HomRefBlock.java         |  23 +-
 .../CalledHaplotypeBAMWriter.java             |   1 -
 .../HaplotypeBAMWriter.java                   |  28 +-
 .../VariantAnnotatorIntegrationTest.java      |  55 ++++
 .../IndelGenotypeLikelihoodsUnitTest.java     |   2 +-
 .../HaplotypeCallerGVCFIntegrationTest.java   |  10 +-
 .../HaplotypeCallerIntegrationTest.java       |  12 +-
 ...aplotypeCallerParallelIntegrationTest.java |   4 +-
 .../ReferenceConfidenceModelUnitTest.java     |   7 +-
 .../CombineVariantsIntegrationTest.java       |  19 +-
 .../sting/utils/gvcf/GVCFWriterUnitTest.java  |  14 +-
 .../sting/utils/gvcf/HomRefBlockUnitTest.java |  22 +-
 .../traversals/TraverseActiveRegions.java     |   2 +-
 .../walkers/annotator/VariantAnnotator.java   |  24 +-
 .../annotator/VariantAnnotatorEngine.java     |  56 ++--
 .../walkers/variantutils/CombineVariants.java |  48 ++--
 .../broadinstitute/sting/utils/MathUtils.java |  20 +-
 .../sting/utils/pileup/PileupElement.java     |   2 +-
 .../utils/smithwaterman/SmithWaterman.java    |   2 +-
 .../variant/GATKVariantContextUtils.java      | 267 ++++++++++++------
 .../sting/utils/MathUtilsUnitTest.java        |  10 +-
 .../GATKVariantContextUtilsUnitTest.java      |  46 ++-
 .../variant/VariantContextBenchmark.java      |  10 +-
 36 files changed, 781 insertions(+), 287 deletions(-)
 create mode 100644 protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasBySample.java

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
index b22ea7931..0da865a85 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
@@ -112,18 +112,18 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
 
     private void annotateWithPileup(final AlignmentContext stratifiedContext, final VariantContext vc, final GenotypeBuilder gb) {
 
-        HashMap<Byte, Integer> alleleCounts = new HashMap<Byte, Integer>();
-        for ( Allele allele : vc.getAlleles() )
+        final HashMap<Byte, Integer> alleleCounts = new HashMap<>();
+        for ( final Allele allele : vc.getAlleles() )
             alleleCounts.put(allele.getBases()[0], 0);
 
-        ReadBackedPileup pileup = stratifiedContext.getBasePileup();
-        for ( PileupElement p : pileup ) {
+        final ReadBackedPileup pileup = stratifiedContext.getBasePileup();
+        for ( final PileupElement p : pileup ) {
             if ( alleleCounts.containsKey(p.getBase()) )
                 alleleCounts.put(p.getBase(), alleleCounts.get(p.getBase())+p.getRepresentativeCount());
         }
 
         // we need to add counts in the correct order
-        int[] counts = new int[alleleCounts.size()];
+        final int[] counts = new int[alleleCounts.size()];
         counts[0] = alleleCounts.get(vc.getReference().getBases()[0]);
         for (int i = 0; i < vc.getAlternateAlleles().size(); i++)
             counts[i+1] = alleleCounts.get(vc.getAlternateAllele(i).getBases()[0]);
@@ -141,7 +141,7 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
         final HashMap<Allele, Integer> alleleCounts = new HashMap<>();
         for ( final Allele allele : vc.getAlleles() ) { alleleCounts.put(allele, 0); }
 
-        for (Map.Entry<GATKSAMRecord,Map<Allele,Double>> el : perReadAlleleLikelihoodMap.getLikelihoodReadMap().entrySet()) {
+        for ( final Map.Entry<GATKSAMRecord,Map<Allele,Double>> el : perReadAlleleLikelihoodMap.getLikelihoodReadMap().entrySet()) {
             final MostLikelyAllele a = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue(), alleles);
             if (! a.isInformative() ) continue; // read is non-informative
             final GATKSAMRecord read = el.getKey();
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
index cdbd43a7a..95be967a2 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
@@ -58,6 +58,8 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnota
 import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.QualityUtils;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.GenotypesContext;
 import org.broadinstitute.variant.vcf.VCFHeaderLineType;
 import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
@@ -97,6 +99,13 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
         if ( !vc.isVariant() )
             return null;
 
+        if ( vc.hasGenotypes() ) {
+            final int[][] tableFromPerSampleAnnotations = getTableFromSamples( vc.getGenotypes() );
+            if ( tableFromPerSampleAnnotations != null ) {
+              return pValueForBestTable(tableFromPerSampleAnnotations, null);
+            }
+        }
+
         if (vc.isSNP() && stratifiedContexts != null) {
             final int[][] tableNoFiltering = getSNPContingencyTable(stratifiedContexts, vc.getReference(), vc.getAltAlleleWithHighestAlleleCount(), -1);
             final int[][] tableFiltering = getSNPContingencyTable(stratifiedContexts, vc.getReference(), vc.getAltAlleleWithHighestAlleleCount(), MIN_QUAL_FOR_FILTERED_TEST);
@@ -117,6 +126,32 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
             return null;
     }
 
+    /**
+     * Create the FisherStrand table by retrieving the per-sample strand bias annotation and adding them together
+     * @param genotypes the genotypes from which to pull out the per-sample strand bias annotation
+     * @return the table used for the FisherStrand p-value calculation, will be null if none of the genotypes contain the per-sample SB annotation
+     */
+    private int[][] getTableFromSamples( final GenotypesContext genotypes ) {
+        if( genotypes == null ) { throw new IllegalArgumentException("Genotypes cannot be null."); }
+
+        final int[] sbArray = {0,0,0,0}; // forward-reverse -by- alternate-reference
+        boolean foundData = false;
+
+        for( final Genotype g : genotypes ) {
+            if( g.isNoCall() || ! g.hasAnyAttribute(StrandBiasBySample.STRAND_BIAS_BY_SAMPLE_KEY_NAME) )
+                continue;
+
+            foundData = true;
+            final String sbbsString = (String) g.getAnyAttribute(StrandBiasBySample.STRAND_BIAS_BY_SAMPLE_KEY_NAME);
+            final int[] data = encodeSBBS(sbbsString);
+            for( int index = 0; index < sbArray.length; index++ ) {
+                sbArray[index] += data[index];
+            }
+        }
+
+        return ( foundData ? decodeSBBS(sbArray) : null );
+    }
+
     /**
      * Create an annotation for the highest (i.e., least significant) p-value of table1 and table2
      *
@@ -148,12 +183,56 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
     }
 
     public List<String> getKeyNames() {
-        return Arrays.asList(FS);
+        return Collections.singletonList(FS);
     }
 
     public List<VCFInfoHeaderLine> getDescriptions() {
-        return Arrays.asList(
-                new VCFInfoHeaderLine(FS, 1, VCFHeaderLineType.Float, "Phred-scaled p-value using Fisher's exact test to detect strand bias"));
+        return Collections.singletonList(new VCFInfoHeaderLine(FS, 1, VCFHeaderLineType.Float, "Phred-scaled p-value using Fisher's exact test to detect strand bias"));
+    }
+
+    /**
+     * Helper function to turn the FisherStrand table into the SB annotation array
+     * @param table the table used by the FisherStrand annotation
+     * @return the array used by the per-sample Strand Bias annotation
+     */
+    public static int[] getContingencyArray( final int[][] table ) {
+        if(table.length != 2) { throw new IllegalArgumentException("Expecting a 2x2 strand bias table."); }
+        if(table[0].length != 2) { throw new IllegalArgumentException("Expecting a 2x2 strand bias table."); }
+        final int[] array = new int[4]; // TODO - if we ever want to do something clever with multi-allelic sites this will need to change
+        array[0] = table[0][0];
+        array[1] = table[0][1];
+        array[2] = table[1][0];
+        array[3] = table[1][1];
+        return array;
+    }
+
+    /**
+     * Helper function to parse the genotype annotation into the SB annotation array
+     * @param string the string that is returned by genotype.getAnnotation("SB")
+     * @return the array used by the per-sample Strand Bias annotation
+     */
+    private static int[] encodeSBBS( final String string ) {
+        final int[] array = new int[4];
+        final StringTokenizer tokenizer = new StringTokenizer(string, ",", false);
+        for( int index = 0; index < 4; index++ ) {
+            array[index] = Integer.parseInt(tokenizer.nextToken());
+        }
+        return array;
+    }
+
+    /**
+     * Helper function to turn the  SB annotation array into the FisherStrand table
+     * @param array the array used by the per-sample Strand Bias annotation
+     * @return the table used by the FisherStrand annotation
+     */
+    private static int[][] decodeSBBS( final int[] array ) {
+        if(array.length != 4) { throw new IllegalArgumentException("Expecting a length = 4 strand bias array."); }
+        final int[][] table = new int[2][2];
+        table[0][0] = array[0];
+        table[0][1] = array[1];
+        table[1][0] = array[2];
+        table[1][1] = array[3];
+        return table;
     }
 
     private Double pValueForContingencyTable(int[][] originalTable) {
@@ -284,13 +363,16 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
      *   allele2   #       #
      * @return a 2x2 contingency table
      */
-    private static int[][] getContingencyTable( final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap, final VariantContext vc) {
+    public static int[][] getContingencyTable( final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap, final VariantContext vc) {
+        if( stratifiedPerReadAlleleLikelihoodMap == null ) { throw new IllegalArgumentException("stratifiedPerReadAlleleLikelihoodMap cannot be null"); }
+        if( vc == null ) { throw new IllegalArgumentException("input vc cannot be null"); }
+
         final Allele ref = vc.getReference();
         final Allele alt = vc.getAltAlleleWithHighestAlleleCount();
-        int[][] table = new int[2][2];
+        final int[][] table = new int[2][2];
 
-        for (PerReadAlleleLikelihoodMap maps : stratifiedPerReadAlleleLikelihoodMap.values() ) {
-            for (Map.Entry<GATKSAMRecord,Map<Allele,Double>> el : maps.getLikelihoodReadMap().entrySet()) {
+        for (final PerReadAlleleLikelihoodMap maps : stratifiedPerReadAlleleLikelihoodMap.values() ) {
+            for (final Map.Entry<GATKSAMRecord,Map<Allele,Double>> el : maps.getLikelihoodReadMap().entrySet()) {
                 final MostLikelyAllele mostLikelyAllele = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue());
                 final GATKSAMRecord read = el.getKey();
                 final int representativeCount = read.isReducedRead() ? read.getReducedCount(ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(read, vc.getStart(), ReadUtils.ClippingTail.RIGHT_TAIL)) : 1;
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
index bdf37df71..da2143ec1 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
@@ -76,8 +76,10 @@ import java.util.*;
 public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
 
     private static final int MIN_SAMPLES = 10;
+    private static final String INBREEDING_COEFFICIENT_KEY_NAME = "InbreedingCoeff";
     private Set<String> founderIds;
 
+    @Override
     public Map<String, Object> annotate(final RefMetaDataTracker tracker,
                                         final AnnotatorCompatible walker,
                                         final ReferenceContext ref,
@@ -92,15 +94,15 @@ public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnno
 
     private Map<String, Object> calculateIC(final VariantContext vc) {
         final GenotypesContext genotypes = (founderIds == null || founderIds.isEmpty()) ? vc.getGenotypes() : vc.getGenotypes(founderIds);
-        if ( genotypes == null || genotypes.size() < MIN_SAMPLES || !vc.isVariant())
+        if (genotypes == null || genotypes.size() < MIN_SAMPLES || !vc.isVariant())
             return null;
 
         int idxAA = 0, idxAB = 1, idxBB = 2;
 
         if (!vc.isBiallelic()) {
             // for non-bliallelic case, do test with most common alt allele.
-            // Get then corresponding indeces in GL vectors to retrieve GL of AA,AB and BB.
-            int[] idxVector = vc.getGLIndecesOfAlternateAllele(vc.getAltAlleleWithHighestAlleleCount());
+            // Get then corresponding indices in GL vectors to retrieve GL of AA,AB and BB.
+            final int[] idxVector = vc.getGLIndecesOfAlternateAllele(vc.getAltAlleleWithHighestAlleleCount());
             idxAA = idxVector[0];
             idxAB = idxVector[1];
             idxBB = idxVector[2];
@@ -132,12 +134,12 @@ public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnno
         final double q = 1.0 - p; // expected alternative allele frequency
         final double F = 1.0 - ( hetCount / ( 2.0 * p * q * (double)N ) ); // inbreeding coefficient
 
-        Map<String, Object> map = new HashMap<String, Object>();
-        map.put(getKeyNames().get(0), String.format("%.4f", F));
-        return map;
+        return Collections.singletonMap(getKeyNames().get(0), (Object)String.format("%.4f", F));
     }
 
-    public List<String> getKeyNames() { return Arrays.asList("InbreedingCoeff"); }
+    @Override
+    public List<String> getKeyNames() { return Collections.singletonList(INBREEDING_COEFFICIENT_KEY_NAME); }
 
-    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("InbreedingCoeff", 1, VCFHeaderLineType.Float, "Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation")); }
+    @Override
+    public List<VCFInfoHeaderLine> getDescriptions() { return Collections.singletonList(new VCFInfoHeaderLine(INBREEDING_COEFFICIENT_KEY_NAME, 1, VCFHeaderLineType.Float, "Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation")); }
 }
\ No newline at end of file
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasBySample.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasBySample.java
new file mode 100644
index 000000000..fde344e9f
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasBySample.java
@@ -0,0 +1,100 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+*
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+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.AnnotatorCompatible;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.vcf.VCFFormatHeaderLine;
+import org.broadinstitute.variant.vcf.VCFHeaderLineType;
+
+import java.util.*;
+
+/**
+ * Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias
+ * User: rpoplin
+ * Date: 8/28/13
+ */
+
+public class StrandBiasBySample extends GenotypeAnnotation implements ExperimentalAnnotation {
+
+    public final static String STRAND_BIAS_BY_SAMPLE_KEY_NAME = "SB";
+
+    @Override
+    public void annotate(final RefMetaDataTracker tracker,
+                         final AnnotatorCompatible walker,
+                         final ReferenceContext ref,
+                         final AlignmentContext stratifiedContext,
+                         final VariantContext vc,
+                         final Genotype g,
+                         final GenotypeBuilder gb,
+                         final PerReadAlleleLikelihoodMap alleleLikelihoodMap) {
+        if ( g == null || !g.isCalled() || ( stratifiedContext == null && alleleLikelihoodMap == null) )
+            return;
+
+        if (alleleLikelihoodMap == null )
+            throw new IllegalStateException("StrandBiasBySample can only be used with likelihood based annotations in the HaplotypeCaller");
+
+        final int[][] table = FisherStrand.getContingencyTable(Collections.singletonMap(g.getSampleName(), alleleLikelihoodMap), vc);
+
+        gb.attribute(STRAND_BIAS_BY_SAMPLE_KEY_NAME, FisherStrand.getContingencyArray(table));
+    }
+
+    @Override
+    public List<String> getKeyNames() { return Collections.singletonList(STRAND_BIAS_BY_SAMPLE_KEY_NAME); }
+
+    @Override
+    public List<VCFFormatHeaderLine> getDescriptions() { return Collections.singletonList(new VCFFormatHeaderLine(getKeyNames().get(0), 4, VCFHeaderLineType.Integer, "Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.")); }
+
+}
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
index ddf47805f..6f16a704f 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
@@ -76,16 +76,13 @@ public class ConsensusAlleleCounter {
     private final int minIndelCountForGenotyping;
     private final boolean doMultiAllelicCalls;
     private final double minFractionInOneSample;
-    private final GenomeLocParser locParser;
 
-    public ConsensusAlleleCounter(final GenomeLocParser locParser,
-                                  final boolean doMultiAllelicCalls,
+    public ConsensusAlleleCounter(final boolean doMultiAllelicCalls,
                                   final int minIndelCountForGenotyping,
                                   final double minFractionInOneSample) {
         this.minIndelCountForGenotyping = minIndelCountForGenotyping;
         this.doMultiAllelicCalls = doMultiAllelicCalls;
         this.minFractionInOneSample = minFractionInOneSample;
-        this.locParser = locParser;
     }
 
     /**
@@ -289,7 +286,7 @@ public class ConsensusAlleleCounter {
         if (vcs.isEmpty())
             return Collections.emptyList(); // nothing else to do, no alleles passed minimum count criterion
 
-        final VariantContext mergedVC = GATKVariantContextUtils.simpleMerge(vcs, null, GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, GATKVariantContextUtils.GenotypeMergeType.UNSORTED, false, false, null, false, false);
+        final VariantContext mergedVC = GATKVariantContextUtils.simpleMerge(vcs, null, GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, GATKVariantContextUtils.GenotypeMergeType.UNSORTED, false, false, null, false, false, false);
         return mergedVC.getAlleles();
     }
 }
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java
index 9c4694955..3cee8f2d8 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java
@@ -108,7 +108,7 @@ public class GeneralPloidyIndelGenotypeLikelihoodsCalculationModel extends Gener
                                                   final List<Allele> allAllelesToUse){
 
 
-        List<Allele> alleles = IndelGenotypeLikelihoodsCalculationModel.getInitialAlleleList(tracker, ref, contexts, contextType, locParser, UAC,true);
+        List<Allele> alleles = IndelGenotypeLikelihoodsCalculationModel.getInitialAlleleList(tracker, ref, contexts, contextType, UAC,true);
 
         if (alleles.size() > MAX_NUM_ALLELES_TO_GENOTYPE)
             alleles = alleles.subList(0,MAX_NUM_ALLELES_TO_GENOTYPE);
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
index 0f3f7739d..4a3231b3e 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
@@ -89,9 +89,8 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
     protected static List<Allele> computeConsensusAlleles(final ReferenceContext ref,
                                                  final Map<String, AlignmentContext> contexts,
                                                  final AlignmentContextUtils.ReadOrientation contextType,
-                                                 final GenomeLocParser locParser,
                                                  final UnifiedArgumentCollection UAC) {
-        ConsensusAlleleCounter counter = new ConsensusAlleleCounter(locParser, true, UAC.MIN_INDEL_COUNT_FOR_GENOTYPING, UAC.MIN_INDEL_FRACTION_PER_SAMPLE);
+        ConsensusAlleleCounter counter = new ConsensusAlleleCounter(true, UAC.MIN_INDEL_COUNT_FOR_GENOTYPING, UAC.MIN_INDEL_FRACTION_PER_SAMPLE);
         return counter.computeConsensusAlleles(ref, contexts, contextType);
     }
 
@@ -113,7 +112,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
             // starting a new site: clear allele list
             haplotypeMap.clear();
             perReadAlleleLikelihoodMap.clear(); // clean mapping sample-> per read, per allele likelihoods
-            alleleList = getInitialAlleleList(tracker, ref, contexts, contextType, locParser, UAC, ignoreSNPAllelesWhenGenotypingIndels);
+            alleleList = getInitialAlleleList(tracker, ref, contexts, contextType, UAC, ignoreSNPAllelesWhenGenotypingIndels);
             if (alleleList.isEmpty())
                 return null;
         }
@@ -212,7 +211,6 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
                                                     final ReferenceContext ref,
                                                     final Map<String, AlignmentContext> contexts,
                                                     final AlignmentContextUtils.ReadOrientation contextType,
-                                                    final GenomeLocParser locParser,
                                                     final UnifiedArgumentCollection UAC,
                                                     final boolean ignoreSNPAllelesWhenGenotypingIndels) {
 
@@ -244,7 +242,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
             }
 
         } else {
-            alleles = computeConsensusAlleles(ref, contexts, contextType, locParser, UAC);
+            alleles = computeConsensusAlleles(ref, contexts, contextType, UAC);
         }
         return alleles;
     }
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTrimmer.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTrimmer.java
index 063e3b218..4de90b337 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTrimmer.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTrimmer.java
@@ -101,24 +101,26 @@ class ActiveRegionTrimmer {
      *
      * @param region our full active region
      * @param allVariantsWithinExtendedRegion all of the variants found in the entire region, sorted by their start position
+     * @param emitReferenceConfidence are we going to estimate the reference confidence with this active region?
      * @return a new ActiveRegion trimmed down to just what's needed for genotyping, or null if we couldn't do this successfully
      */
-    public ActiveRegion trimRegion(final ActiveRegion region, final TreeSet<VariantContext> allVariantsWithinExtendedRegion) {
+    public ActiveRegion trimRegion(final ActiveRegion region, final TreeSet<VariantContext> allVariantsWithinExtendedRegion, final boolean emitReferenceConfidence) {
         if ( allVariantsWithinExtendedRegion.isEmpty() ) // no variants, so just return the current region
             return null;
 
-        final List<VariantContext> withinActiveRegion = new LinkedList<VariantContext>();
-        int pad = snpPadding;
+        final List<VariantContext> withinActiveRegion = new LinkedList<>();
+        boolean foundNonSnp = false;
         GenomeLoc trimLoc = null;
         for ( final VariantContext vc : allVariantsWithinExtendedRegion ) {
             final GenomeLoc vcLoc = parser.createGenomeLoc(vc);
             if ( region.getLocation().overlapsP(vcLoc) ) {
                 if ( ! vc.isSNP() ) // if anything isn't a SNP use the bigger padding
-                    pad = nonSnpPadding;
+                    foundNonSnp = true;
                 trimLoc = trimLoc == null ? vcLoc : trimLoc.endpointSpan(vcLoc);
                 withinActiveRegion.add(vc);
             }
         }
+        final int pad = ( emitReferenceConfidence || foundNonSnp ? nonSnpPadding : snpPadding );
 
         // we don't actually have anything in the region after removing variants that don't overlap the region's full location
         if ( trimLoc == null ) return null;
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
index cb3b9b65f..cc89792d5 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
@@ -183,7 +183,7 @@ public class GenotypingEngine {
                 final List<String> priorityList = makePriorityList(eventsAtThisLoc);
 
                 // Merge the event to find a common reference representation
-                final VariantContext mergedVC = GATKVariantContextUtils.simpleMerge(eventsAtThisLoc, priorityList, GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, GATKVariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, null, false, false);
+                final VariantContext mergedVC = GATKVariantContextUtils.simpleMerge(eventsAtThisLoc, priorityList, GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, GATKVariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, null, false, false, false);
                 if( mergedVC == null ) { continue; }
 
                 if( eventsAtThisLoc.size() != mergedVC.getAlternateAlleles().size() ) {
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
index 0b95ed07e..8776a5e4b 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
@@ -290,7 +290,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
      * B <= X < C
      * X >= C
      *
-     * The default bands give the following GQ blocks:
+     * The default bands with (1, 10, 20, 30, 40, 50) give the following GQ blocks:
      *
      * [0, 0]
      * (0, 10]
@@ -304,7 +304,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
      */
     @Advanced
     @Argument(fullName="GVCFGQBands", shortName="GQB", doc="Emit experimental reference confidence scores", required = false)
-    protected List<Integer> GVCFGQBands = Arrays.asList(1, 10, 20, 30, 40, 50);
+    protected List<Integer> GVCFGQBands = Arrays.asList(5, 20, 60);
 
     /**
      * This parameter determines the maximum size of an indel considered as potentially segregating in the
@@ -541,7 +541,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
         samplesList.addAll( samples );
         // initialize the UnifiedGenotyper Engine which is used to call into the exact model
         final UnifiedArgumentCollection UAC = new UnifiedArgumentCollection( SCAC ); // this adapter is used so that the full set of unused UG arguments aren't exposed to the HC user
-        // HC GGA mode depends critically on EMIT_ALL_SITES being set for the UG engine // TODO -- why is this?
+        // HC GGA mode depends critically on EMIT_ALL_SITES being set for the UG engine
         UAC.OutputMode = SCAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES
                 ? UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES : UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_VARIANTS_ONLY;
         UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, GATKVariantContextUtils.DEFAULT_PLOIDY);
@@ -553,11 +553,11 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
         simpleUAC.STANDARD_CONFIDENCE_FOR_CALLING = Math.min( 4.0, UAC.STANDARD_CONFIDENCE_FOR_CALLING ); // low values used for isActive determination only, default/user-specified values used for actual calling
         simpleUAC.STANDARD_CONFIDENCE_FOR_EMITTING = Math.min( 4.0, UAC.STANDARD_CONFIDENCE_FOR_EMITTING ); // low values used for isActive determination only, default/user-specified values used for actual calling
         simpleUAC.CONTAMINATION_FRACTION = 0.0;
-        simpleUAC.CONTAMINATION_FRACTION_FILE=null;
+        simpleUAC.CONTAMINATION_FRACTION_FILE = null;
         simpleUAC.exactCallsLog = null;
         UG_engine_simple_genotyper = new UnifiedGenotyperEngine(getToolkit(), simpleUAC, logger, null, null, samples, GATKVariantContextUtils.DEFAULT_PLOIDY);
 
-        if( UAC.CONTAMINATION_FRACTION_FILE !=null) {
+        if( UAC.CONTAMINATION_FRACTION_FILE != null ) {
             UAC.setSampleContamination(AlleleBiasedDownsamplingUtils.loadContaminationFile(UAC.CONTAMINATION_FRACTION_FILE, UAC.CONTAMINATION_FRACTION, samples, logger));
         }
 
@@ -867,17 +867,17 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
         // Create ReadErrorCorrector object if requested - will be used within assembly engine.
         ReadErrorCorrector readErrorCorrector = null;
         if (errorCorrectReads)
-            readErrorCorrector = new ReadErrorCorrector(kmerLengthForReadErrorCorrection, MIN_TAIL_QUALITY_WITH_ERROR_CORRECTION, minObservationsForKmerToBeSolid, DEBUG,fullReferenceWithPadding);
+            readErrorCorrector = new ReadErrorCorrector(kmerLengthForReadErrorCorrection, MIN_TAIL_QUALITY_WITH_ERROR_CORRECTION, minObservationsForKmerToBeSolid, DEBUG, fullReferenceWithPadding);
 
         try {
-            final List<Haplotype> haplotypes = assemblyEngine.runLocalAssembly( activeRegion, referenceHaplotype, fullReferenceWithPadding, paddedReferenceLoc, activeAllelesToGenotype,readErrorCorrector );
-            if ( ! emitReferenceConfidence() && ! dontTrimActiveRegions ) {
+            final List<Haplotype> haplotypes = assemblyEngine.runLocalAssembly( activeRegion, referenceHaplotype, fullReferenceWithPadding, paddedReferenceLoc, activeAllelesToGenotype, readErrorCorrector );
+            if ( ! dontTrimActiveRegions ) {
                 return trimActiveRegion(activeRegion, haplotypes, activeAllelesToGenotype, fullReferenceWithPadding, paddedReferenceLoc);
             } else {
                 // we don't want to trim active regions, so go ahead and use the old one
                 return new AssemblyResult(haplotypes, activeRegion, fullReferenceWithPadding, paddedReferenceLoc, true);
             }
-        } catch ( Exception e ) {
+        } catch ( final Exception e ) {
             // Capture any exception that might be thrown, and write out the assembly failure BAM if requested
             if ( captureAssemblyFailureBAM ) {
                 final SAMFileWriter writer = ReadUtils.createSAMFileWriterWithCompression(getToolkit().getSAMFileHeader(), true, "assemblyFailure.bam", 5);
@@ -969,7 +969,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
         EventMap.buildEventMapsForHaplotypes(haplotypes, fullReferenceWithPadding, paddedReferenceLoc, DEBUG);
         final TreeSet<VariantContext> allVariantsWithinFullActiveRegion = EventMap.getAllVariantContexts(haplotypes);
         allVariantsWithinFullActiveRegion.addAll(activeAllelesToGenotype);
-        final ActiveRegion trimmedActiveRegion = trimmer.trimRegion(originalActiveRegion, allVariantsWithinFullActiveRegion);
+        final ActiveRegion trimmedActiveRegion = trimmer.trimRegion(originalActiveRegion, allVariantsWithinFullActiveRegion, false); // TODO -- should pass emitReferenceConfidence()
 
         if ( trimmedActiveRegion == null ) {
             // there were no variants found within the active region itself, so just return null
@@ -1001,7 +1001,6 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
             }
         }
 
-
         // trim down the reads and add them to the trimmed active region
         final List<GATKSAMRecord> trimmedReads = new ArrayList<>(originalActiveRegion.getReads().size());
         for( final GATKSAMRecord read : originalActiveRegion.getReads() ) {
@@ -1096,7 +1095,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
         activeRegion.addAll(downsampledReads);
     }
 
-    private Set<GATKSAMRecord> filterNonPassingReads( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion ) {
+    private Set<GATKSAMRecord> filterNonPassingReads( final ActiveRegion activeRegion ) {
         final Set<GATKSAMRecord> readsToRemove = new LinkedHashSet<>();
         for( final GATKSAMRecord rec : activeRegion.getReads() ) {
             if( rec.getReadLength() < MIN_READ_LENGTH || rec.getMappingQuality() < 20 || BadMateFilter.hasBadMate(rec) || (keepRG != null && !rec.getReadGroup().getId().equals(keepRG)) ) {
@@ -1107,7 +1106,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
         return readsToRemove;
     }
 
-    private GenomeLoc getPaddedLoc( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion ) {
+    private GenomeLoc getPaddedLoc( final ActiveRegion activeRegion ) {
         final int padLeft = Math.max(activeRegion.getExtendedLoc().getStart()-REFERENCE_PADDING, 1);
         final int padRight = Math.min(activeRegion.getExtendedLoc().getStop()+REFERENCE_PADDING, referenceReader.getSequenceDictionary().getSequence(activeRegion.getExtendedLoc().getContig()).getSequenceLength());
         return getToolkit().getGenomeLocParser().createGenomeLoc(activeRegion.getExtendedLoc().getContig(), padLeft, padRight);
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RefVsAnyResult.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RefVsAnyResult.java
index ee7565282..8fb7afec7 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RefVsAnyResult.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RefVsAnyResult.java
@@ -68,5 +68,13 @@ final class RefVsAnyResult {
     /**
      * @return Get the DP (sum of AD values)
      */
-    public int getDP() { return AD_Ref_Any[0] + AD_Ref_Any[1]; }
+    protected int getDP() { return AD_Ref_Any[0] + AD_Ref_Any[1]; }
+
+    /**
+     * Cap the het and hom var likelihood values by the hom ref likelihood.
+     */
+    protected void capByHomRefLikelihood() {
+        genotypeLikelihoods[1] = Math.min(genotypeLikelihoods[0], genotypeLikelihoods[1]);
+        genotypeLikelihoods[2] = Math.min(genotypeLikelihoods[0], genotypeLikelihoods[2]);
+    }
 }
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModel.java
index 98264d4c2..2c123880d 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModel.java
@@ -61,6 +61,7 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
 import org.broadinstitute.variant.variantcontext.*;
 import org.broadinstitute.variant.vcf.VCFFormatHeaderLine;
 import org.broadinstitute.variant.vcf.VCFHeaderLine;
@@ -81,10 +82,9 @@ import java.util.*;
  * Time: 12:52 PM
  */
 public class ReferenceConfidenceModel {
-    public final static String NON_REF_SYMBOLIC_ALLELE_NAME = "NON_REF";
-    public final static Allele NON_REF_SYMBOLIC_ALLELE = Allele.create("<"+NON_REF_SYMBOLIC_ALLELE_NAME+">", false); // represents any possible non-ref allele at this site
 
-    public final static String INDEL_INFORMATIVE_DEPTH = "CD";
+    //public final static String INDEL_INFORMATIVE_DEPTH = "CD"; // temporarily taking this extra genotype level information out for now
+    public final static String ALTERNATE_ALLELE_STRING = "ALT"; // arbitrary alternate allele
 
     private final GenomeLocParser genomeLocParser;
     private final Set<String> samples;
@@ -94,6 +94,8 @@ public class ReferenceConfidenceModel {
     private final static boolean WRITE_DEBUGGING_BAM = false;
     private final SAMFileWriter debuggingWriter;
 
+    private final static byte REF_MODEL_DELETION_QUAL = (byte) 30;
+
     /**
      * Create a new ReferenceConfidenceModel
      *
@@ -124,6 +126,8 @@ public class ReferenceConfidenceModel {
         } else {
             debuggingWriter = null;
         }
+
+        initializeIndelPLCache();
     }
 
     /**
@@ -132,8 +136,9 @@ public class ReferenceConfidenceModel {
      */
     public Set<VCFHeaderLine> getVCFHeaderLines() {
         final Set<VCFHeaderLine> headerLines = new LinkedHashSet<>();
-        headerLines.add(new VCFSimpleHeaderLine("ALT", NON_REF_SYMBOLIC_ALLELE_NAME, "Represents any possible alternative allele at this location"));
-        headerLines.add(new VCFFormatHeaderLine(INDEL_INFORMATIVE_DEPTH, 1, VCFHeaderLineType.Integer, "Number of reads at locus that are informative about an indel of size <= " + indelInformativeDepthIndelSize));
+        // TODO - do we need a new kind of VCF Header subclass for specifying arbitrary alternate alleles?
+        headerLines.add(new VCFSimpleHeaderLine(ALTERNATE_ALLELE_STRING, GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE_NAME, "Represents any possible alternative allele at this location"));
+        //headerLines.add(new VCFFormatHeaderLine(INDEL_INFORMATIVE_DEPTH, 1, VCFHeaderLineType.Integer, "Number of reads at locus that are informative about an indel of size <= " + indelInformativeDepthIndelSize));
         return headerLines;
     }
 
@@ -161,7 +166,7 @@ public class ReferenceConfidenceModel {
      * @param stratifiedReadMap a map from a single sample to its PerReadAlleleLikelihoodMap for each haplotype in calledHaplotypes
      * @param variantCalls calls made in this region.  The return result will contain any variant call in this list in the
      *                     correct order by genomic position, and any variant in this list will stop us emitting a ref confidence
-     *                     under any position is covers (for snps that 1 bp, but for deletion its the entire ref span)
+     *                     under any position it covers (for snps and insertions that is 1 bp, but for deletions its the entire ref span)
      * @return an ordered list of variant contexts that spans activeRegion.getLoc() and includes both reference confidence
      *         contexts as well as calls from variantCalls if any were provided
      */
@@ -181,7 +186,7 @@ public class ReferenceConfidenceModel {
         if ( refHaplotype.length() != activeRegion.getExtendedLoc().size() ) throw new IllegalArgumentException("refHaplotype " + refHaplotype.length() + " and activeRegion location size " + activeRegion.getLocation().size() + " are different");
 
         final GenomeLoc refSpan = activeRegion.getLocation();
-        final List<ReadBackedPileup> refPileups = getPileupsOverReference(refHaplotype, calledHaplotypes, paddedReferenceLoc, refSpan, stratifiedReadMap);
+        final List<ReadBackedPileup> refPileups = getPileupsOverReference(refHaplotype, calledHaplotypes, paddedReferenceLoc, activeRegion, refSpan, stratifiedReadMap);
         final byte[] ref = refHaplotype.getBases();
         final List<VariantContext> results = new ArrayList<>(refSpan.size());
         final String sampleName = stratifiedReadMap.keySet().iterator().next();
@@ -201,9 +206,10 @@ public class ReferenceConfidenceModel {
                 final int refOffset = offset + globalRefOffset;
                 final byte refBase = ref[refOffset];
                 final RefVsAnyResult homRefCalc = calcGenotypeLikelihoodsOfRefVsAny(pileup, refBase, (byte)6, null);
+                homRefCalc.capByHomRefLikelihood();
 
                 final Allele refAllele = Allele.create(refBase, true);
-                final List<Allele> refSiteAlleles = Arrays.asList(refAllele, NON_REF_SYMBOLIC_ALLELE);
+                final List<Allele> refSiteAlleles = Arrays.asList(refAllele, GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE);
                 final VariantContextBuilder vcb = new VariantContextBuilder("HC", curPos.getContig(), curPos.getStart(), curPos.getStart(), refSiteAlleles);
                 final GenotypeBuilder gb = new GenotypeBuilder(sampleName, Arrays.asList(refAllele, refAllele));
                 gb.AD(homRefCalc.AD_Ref_Any);
@@ -224,7 +230,7 @@ public class ReferenceConfidenceModel {
 
                 gb.GQ((int) (-10 * leastConfidenceGLs.getLog10GQ(GenotypeType.HOM_REF)));
                 gb.PL(leastConfidenceGLs.getAsPLs());
-                gb.attribute(INDEL_INFORMATIVE_DEPTH, nIndelInformativeReads);
+                //gb.attribute(INDEL_INFORMATIVE_DEPTH, nIndelInformativeReads);
 
                 vcb.genotypes(gb.make());
                 results.add(vcb.make());
@@ -252,14 +258,21 @@ public class ReferenceConfidenceModel {
      * @return non-null GenotypeLikelihoods given N
      */
     protected final GenotypeLikelihoods getIndelPLs(final int nInformativeReads) {
-        // TODO -- optimization -- this could easily be optimized with some caching
-        final double homRef = 0.0;
-        final double het    = - LOG10_2 * nInformativeReads;
-        final double homVar = INDEL_ERROR_RATE * nInformativeReads;
-        return GenotypeLikelihoods.fromLog10Likelihoods(new double[]{homRef, het, homVar});
+        return indelPLCache[nInformativeReads > MAX_N_INDEL_INFORMATIVE_READS ? MAX_N_INDEL_INFORMATIVE_READS : nInformativeReads];
+    }
+
+    protected static final int MAX_N_INDEL_INFORMATIVE_READS = 40; // more than this is overkill because GQs are capped at 99 anyway
+    private static final GenotypeLikelihoods[] indelPLCache = new GenotypeLikelihoods[MAX_N_INDEL_INFORMATIVE_READS + 1];
+    private static final double INDEL_ERROR_RATE = -4.5; // 10^-4.5 indel errors per bp
+
+    private void initializeIndelPLCache() {
+        for( int nInformativeReads = 0; nInformativeReads <= MAX_N_INDEL_INFORMATIVE_READS; nInformativeReads++ ) {
+            final double homRef = 0.0;
+            final double het    = MathUtils.LOG_ONE_HALF * nInformativeReads;
+            final double homVar = INDEL_ERROR_RATE * nInformativeReads;
+            indelPLCache[nInformativeReads] = GenotypeLikelihoods.fromLog10Likelihoods(new double[]{homRef, het, homVar});
+        }
     }
-    private final static double LOG10_2 = Math.log10(2);
-    private final static double INDEL_ERROR_RATE = -4.5; // 10^-4.5 indel errors per bp
 
     /**
      * Calculate the genotype likelihoods for the sample in pileup for being hom-ref contrasted with being ref vs. alt
@@ -274,8 +287,8 @@ public class ReferenceConfidenceModel {
         final RefVsAnyResult result = new RefVsAnyResult();
 
         for( final PileupElement p : pileup ) {
-            final byte qual = p.getQual();
-            if( p.isDeletion() || qual > minBaseQual) {
+            final byte qual = (p.isDeletion() ? REF_MODEL_DELETION_QUAL : p.getQual());
+            if( p.isDeletion() || qual > minBaseQual ) {
                 int AA = 0; final int AB = 1; int BB = 2;
                 if( p.getBase() != refBase || p.isDeletion() || p.isBeforeDeletionStart() || p.isAfterDeletionEnd() || p.isBeforeInsertion() || p.isAfterInsertion() || p.isNextToSoftClip() ) {
                     AA = 2;
@@ -302,20 +315,37 @@ public class ReferenceConfidenceModel {
     private List<ReadBackedPileup> getPileupsOverReference(final Haplotype refHaplotype,
                                                            final Collection<Haplotype> calledHaplotypes,
                                                            final GenomeLoc paddedReferenceLoc,
+                                                           final ActiveRegion activeRegion,
                                                            final GenomeLoc activeRegionSpan,
                                                            final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap) {
-        final ReadDestination.ToList realignedReadsDest = new ReadDestination.ToList(header, "FOO");
-        final HaplotypeBAMWriter writer = HaplotypeBAMWriter.create(HaplotypeBAMWriter.Type.CALLED_HAPLOTYPES, realignedReadsDest);
-        writer.setWriteHaplotypesAsWell(false); // don't write out reads for the haplotypes, as we only want the realigned reads themselves
-        writer.writeReadsAlignedToHaplotypes(calledHaplotypes.isEmpty() ? Collections.singleton(refHaplotype) : calledHaplotypes, paddedReferenceLoc, stratifiedReadMap);
-        final List<GATKSAMRecord> realignedReads = ReadUtils.sortReadsByCoordinate(realignedReadsDest.getReads());
+
+        if ( refHaplotype == null ) throw new IllegalArgumentException("refHaplotype cannot be null");
+        if ( calledHaplotypes == null ) throw new IllegalArgumentException("calledHaplotypes cannot be null");
+        if ( !calledHaplotypes.contains(refHaplotype)) throw new IllegalArgumentException("calledHaplotypes must contain the refHaplotype");
+        if ( paddedReferenceLoc == null ) throw new IllegalArgumentException("paddedReferenceLoc cannot be null");
+        if ( activeRegion == null ) throw new IllegalArgumentException("activeRegion cannot be null");
+        if ( stratifiedReadMap == null ) throw new IllegalArgumentException("stratifiedReadMap cannot be null");
+        if ( stratifiedReadMap.size() != 1 ) throw new IllegalArgumentException("stratifiedReadMap must contain exactly one sample but it contained " + stratifiedReadMap.size());
+
+        List<GATKSAMRecord> realignedReads;
+
+        if( calledHaplotypes.size() == 1 ) { // only contains ref haplotype so an optimization is to just trust the alignments to the reference haplotype as provided by the aligner
+            realignedReads = activeRegion.getReads();
+        } else {
+            final ReadDestination.ToList realignedReadsDest = new ReadDestination.ToList(header, "FOO");
+            final HaplotypeBAMWriter writer = HaplotypeBAMWriter.create(HaplotypeBAMWriter.Type.CALLED_HAPLOTYPES, realignedReadsDest);
+            writer.setWriteHaplotypesAsWell(false); // don't write out reads for the haplotypes, as we only want the realigned reads themselves
+            writer.setOnlyRealignInformativeReads(true);
+            writer.writeReadsAlignedToHaplotypes(calledHaplotypes, paddedReferenceLoc, stratifiedReadMap);
+            realignedReads = ReadUtils.sortReadsByCoordinate(realignedReadsDest.getReads());
+        }
 
         if ( debuggingWriter != null )
             for ( final GATKSAMRecord read : realignedReads )
                 debuggingWriter.addAlignment(read);
 
         final LocusIteratorByState libs = new LocusIteratorByState(realignedReads.iterator(), LocusIteratorByState.NO_DOWNSAMPLING,
-                false, genomeLocParser, samples, false);
+                true, genomeLocParser, samples, false);
 
         final List<ReadBackedPileup> pileups = new LinkedList<>();
         final int startPos = activeRegionSpan.getStart();
@@ -378,7 +408,7 @@ public class ReferenceConfidenceModel {
             final byte refBase  = refBases[refStart + i];
             if ( readBase != refBase ) {
                 sum += readQuals[readStart + i];
-                if ( sum > maxSum )
+                if ( sum > maxSum ) // abort early
                     return sum;
             }
         }
@@ -403,7 +433,10 @@ public class ReferenceConfidenceModel {
                                                          final byte[] refBases,
                                                          final int refStart,
                                                          final int maxIndelSize) {
-        // todo -- fast exit when n bases left < maxIndelSize
+        // fast exit when n bases left < maxIndelSize
+        if( readBases.length - readStart < maxIndelSize || refBases.length - refStart < maxIndelSize ) {
+            return false;
+        }
 
         final int baselineMMSum = sumMismatchingQualities(readBases, readQuals, readStart, refBases, refStart, Integer.MAX_VALUE);
 
@@ -445,12 +478,16 @@ public class ReferenceConfidenceModel {
             final int offset = p.getOffset();
 
             // doesn't count as evidence
-            if ( p.isBeforeDeletionStart() || p.isBeforeInsertion() )
+            if ( p.isBeforeDeletionStart() || p.isBeforeInsertion() || p.isDeletion() )
                 continue;
 
             // todo -- this code really should handle CIGARs directly instead of relying on the above tests
-            if ( isReadInformativeAboutIndelsOfSize(read.getReadBases(), read.getBaseQualities(), offset, ref, pileupOffsetIntoRef, maxIndelSize))
+            if ( isReadInformativeAboutIndelsOfSize(read.getReadBases(), read.getBaseQualities(), offset, ref, pileupOffsetIntoRef, maxIndelSize) ) {
                 nInformative++;
+                if( nInformative > MAX_N_INDEL_INFORMATIVE_READS ) {
+                    return MAX_N_INDEL_INFORMATIVE_READS;
+                }
+            }
         }
         return nInformative;
     }
diff --git a/protected/java/src/org/broadinstitute/sting/utils/gvcf/GVCFWriter.java b/protected/java/src/org/broadinstitute/sting/utils/gvcf/GVCFWriter.java
index 8f509b36b..8ee3c166c 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/gvcf/GVCFWriter.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/gvcf/GVCFWriter.java
@@ -230,6 +230,7 @@ public class GVCFWriter implements VariantContextWriter {
         gb.DP(block.getMedianDP());
         gb.attribute(MIN_DP_FORMAT_FIELD, block.getMinDP());
         gb.attribute(MIN_GQ_FORMAT_FIELD, block.getMinGQ());
+        gb.PL(block.getMinPLs());
 
         return vcb.genotypes(gb.make()).make();
     }
diff --git a/protected/java/src/org/broadinstitute/sting/utils/gvcf/HomRefBlock.java b/protected/java/src/org/broadinstitute/sting/utils/gvcf/HomRefBlock.java
index 282e49217..ebd167a31 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/gvcf/HomRefBlock.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/gvcf/HomRefBlock.java
@@ -69,10 +69,11 @@ import java.util.List;
  */
 final class HomRefBlock {
     private final VariantContext startingVC;
-    int stop;
+    private int stop;
     private final int minGQ, maxGQ;
-    private List<Integer> GQs = new ArrayList<>(100);
-    private List<Integer> DPs = new ArrayList<>(100);
+    private int[] minPLs = null;
+    final private List<Integer> GQs = new ArrayList<>(100);
+    final private List<Integer> DPs = new ArrayList<>(100);
     private final Allele ref;
 
     /**
@@ -116,9 +117,23 @@ final class HomRefBlock {
     public void add(final int pos, final Genotype g) {
         if ( g == null ) throw new IllegalArgumentException("g cannot be null");
         if ( ! g.hasGQ() ) throw new IllegalArgumentException("g must have GQ field");
+        if ( ! g.hasPL() ) throw new IllegalArgumentException("g must have PL field");
         if ( ! g.hasDP() ) throw new IllegalArgumentException("g must have DP field");
         if ( pos != stop + 1 ) throw new IllegalArgumentException("adding genotype at pos " + pos + " isn't contiguous with previous stop " + stop);
 
+        if( minPLs == null ) { // if the minPLs vector has not been set yet, create it here by copying the provided genotype's PLs
+            final int[] PL = g.getPL();
+            if( PL.length == 3 ) {
+                minPLs = PL.clone();
+            }
+        } else { // otherwise take the min with the provided genotype's PLs
+            final int[] PL = g.getPL();
+            if( PL.length == 3 ) {
+                minPLs[0] = Math.min(minPLs[0], PL[0]);
+                minPLs[1] = Math.min(minPLs[1], PL[1]);
+                minPLs[2] = Math.min(minPLs[2], PL[2]);
+            }
+        }
         stop = pos;
         GQs.add(Math.min(g.getGQ(), 99)); // cap the GQs by the max. of 99 emission
         DPs.add(g.getDP());
@@ -141,6 +156,8 @@ final class HomRefBlock {
     public int getMinDP() { return MathUtils.arrayMin(DPs); }
     /** Get the median DP observed within this band */
     public int getMedianDP() { return MathUtils.median(DPs); }
+    /** Get the min PLs observed within this band, can be null if no PLs have yet been observed */
+    public int[] getMinPLs() { return minPLs; }
 
     protected int getGQUpperBound() { return maxGQ; }
     protected int getGQLowerBound() { return minGQ; }
diff --git a/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java b/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java
index c298485f6..1e6d7c13c 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java
@@ -46,7 +46,6 @@
 
 package org.broadinstitute.sting.utils.haplotypeBAMWriter;
 
-import net.sf.samtools.SAMFileWriter;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.haplotype.Haplotype;
 import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele;
diff --git a/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java b/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java
index 509399fd9..df523b74d 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java
@@ -77,8 +77,9 @@ public abstract class HaplotypeBAMWriter {
     protected final static String READ_GROUP_ID = "ArtificialHaplotype";
     protected final static String HAPLOTYPE_TAG = "HC";
 
-    final ReadDestination output;
-    boolean writeHaplotypesAsWell = true;
+    private final ReadDestination output;
+    private boolean writeHaplotypesAsWell = true;
+    private boolean onlyRealignInformativeReads = false;
 
     /**
      * Possible modes for writing haplotypes to BAMs
@@ -181,9 +182,16 @@ public abstract class HaplotypeBAMWriter {
                                              final Haplotype haplotype,
                                              final int referenceStart,
                                              final boolean isInformative) {
-        final GATKSAMRecord alignedToRef = createReadAlignedToRef(originalRead, haplotype, referenceStart, isInformative);
-        if ( alignedToRef != null )
-            output.add(alignedToRef);
+        if( onlyRealignInformativeReads && !isInformative ) {
+            if( originalRead != null ) {
+                output.add(originalRead);
+            }
+        } else {
+            final GATKSAMRecord alignedToRef = createReadAlignedToRef(originalRead, haplotype, referenceStart, isInformative);
+            if ( alignedToRef != null ) {
+                output.add(alignedToRef);
+            }
+        }
     }
 
     /**
@@ -305,7 +313,15 @@ public abstract class HaplotypeBAMWriter {
         return writeHaplotypesAsWell;
     }
 
-    public void setWriteHaplotypesAsWell(boolean writeHaplotypesAsWell) {
+    public void setWriteHaplotypesAsWell(final boolean writeHaplotypesAsWell) {
         this.writeHaplotypesAsWell = writeHaplotypesAsWell;
     }
+
+    public boolean getOnlyRealignInformativeReads() {
+        return onlyRealignInformativeReads;
+    }
+
+    public void setOnlyRealignInformativeReads(final boolean onlyRealignInformativeReads) {
+        this.onlyRealignInformativeReads = onlyRealignInformativeReads;
+    }
 }
\ No newline at end of file
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
index 37dc7adba..9f8b72c1d 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
@@ -46,14 +46,25 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.readers.LineIterator;
+import org.broad.tribble.readers.PositionalBufferedStream;
 import org.broadinstitute.sting.WalkerTest;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.vcf.VCFCodec;
+import org.testng.Assert;
 import org.testng.annotations.Test;
 
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
 import java.util.Arrays;
 
 public class VariantAnnotatorIntegrationTest extends WalkerTest {
 
+    final static String REF = b37KGReference;
+    final static String CEUTRIO_BAM = validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam";
+
     public static String baseTestString() {
         return "-T VariantAnnotator -R " + b36KGReference + " --no_cmdline_in_header -o %s";
     }
@@ -290,4 +301,48 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
         executeTest("Testing InbreedingCoeff annotation with PED file", spec);
     }
 
+    @Test
+    public void testStrandBiasBySample() throws IOException {
+        final String base = String.format("-T HaplotypeCaller --disableDithering -R %s -I %s", REF, CEUTRIO_BAM) + " --no_cmdline_in_header -o %s -L 20:10130000-10134800";
+        final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList(""));
+        final File outputVCF = executeTest("testStrandBiasBySample", spec).getFirst().get(0);
+
+        final String baseNoFS = String.format("-T HaplotypeCaller --disableDithering -R %s -I %s", REF, CEUTRIO_BAM) + " --no_cmdline_in_header -o %s -L 20:10130000-10134800 -XA FisherStrand -A StrandBiasBySample";
+        final WalkerTestSpec specNoFS = new WalkerTestSpec(baseNoFS, 1, Arrays.asList(""));
+        specNoFS.disableShadowBCF();
+        final File outputVCFNoFS = executeTest("testStrandBiasBySample component stand bias annotation", specNoFS).getFirst().get(0);
+
+        final String baseAnn = String.format("-T VariantAnnotator -R %s -V %s", REF, outputVCFNoFS.getAbsolutePath()) + " --no_cmdline_in_header -o %s -L 20:10130000-10134800 -A FisherStrand";
+        final WalkerTestSpec specAnn = new WalkerTestSpec(baseAnn, 1, Arrays.asList(""));
+        specAnn.disableShadowBCF();
+        final File outputVCFAnn = executeTest("testStrandBiasBySample re-annotation of FisherStrand", specAnn).getFirst().get(0);
+
+        // confirm that the FisherStrand values are identical for the two pipelines
+        final VCFCodec codec = new VCFCodec();
+        final FileInputStream s = new FileInputStream(outputVCF);
+        final LineIterator lineIterator = codec.makeSourceFromStream(new PositionalBufferedStream(s));
+        codec.readHeader(lineIterator);
+
+        final VCFCodec codecAnn = new VCFCodec();
+        final FileInputStream sAnn = new FileInputStream(outputVCFAnn);
+        final LineIterator lineIteratorAnn = codecAnn.makeSourceFromStream(new PositionalBufferedStream(sAnn));
+        codecAnn.readHeader(lineIteratorAnn);
+
+        while( lineIterator.hasNext() && lineIteratorAnn.hasNext() ) {
+            final String line = lineIterator.next();
+            Assert.assertFalse(line == null);
+            final VariantContext vc = codec.decode(line);
+
+            final String lineAnn = lineIteratorAnn.next();
+            Assert.assertFalse(lineAnn == null);
+            final VariantContext vcAnn = codecAnn.decode(lineAnn);
+
+            Assert.assertTrue(vc.hasAttribute("FS"));
+            Assert.assertTrue(vcAnn.hasAttribute("FS"));
+            Assert.assertEquals(vc.getAttributeAsDouble("FS", 0.0), vcAnn.getAttributeAsDouble("FS", -1.0));
+        }
+
+        Assert.assertFalse(lineIterator.hasNext());
+        Assert.assertFalse(lineIteratorAnn.hasNext());
+    }
 }
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java
index 355a47cbc..445864380 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java
@@ -129,7 +129,7 @@ public class IndelGenotypeLikelihoodsUnitTest extends BaseTest {
     }
     
     private List<Allele> getConsensusAlleles(int eventLength, boolean isInsertion, int minCnt, double minFraction, String altBases) {
-        final ConsensusAlleleCounter counter = new ConsensusAlleleCounter(pileupProvider.genomeLocParser, true, minCnt, minFraction);
+        final ConsensusAlleleCounter counter = new ConsensusAlleleCounter(true, minCnt, minFraction);
         return counter.computeConsensusAlleles(pileupProvider.referenceContext,
                 pileupProvider.getAlignmentContextFromAlleles(isInsertion?eventLength:-eventLength,altBases,numReadsPerAllele),
                 AlignmentContextUtils.ReadOrientation.COMPLETE);
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
index e73c04d2c..e430cd8d1 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
@@ -57,18 +57,18 @@ import java.util.List;
 public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
     @DataProvider(name = "MyDataProvider")
     public Object[][] makeMyDataProvider() {
-        List<Object[]> tests = new ArrayList<Object[]>();
+        List<Object[]> tests = new ArrayList<>();
 
         final String PCRFreeIntervals = "-L 20:10,000,000-10,010,000";
         final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
 
         // this functionality can be adapted to provide input data for whatever you might want in your data
         tests.add(new Object[]{NA12878_PCRFREE, HaplotypeCaller.ReferenceConfidenceMode.NONE, PCRFreeIntervals, "3ce9c42e7e97a45a82315523dbd77fcf"});
-        tests.add(new Object[]{NA12878_PCRFREE, HaplotypeCaller.ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "e32b7fc4de29ed141dcafc0d789d5ed6"});
-        tests.add(new Object[]{NA12878_PCRFREE, HaplotypeCaller.ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "ecac86e8ef4856e6dfa306c436e9b545"});
+        tests.add(new Object[]{NA12878_PCRFREE, HaplotypeCaller.ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "c5a55196e10680a02c833a8a44733306"});
+        tests.add(new Object[]{NA12878_PCRFREE, HaplotypeCaller.ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "9b9923ef41bfc7346c905fdecf918f92"});
         tests.add(new Object[]{NA12878_WEx, HaplotypeCaller.ReferenceConfidenceMode.NONE, WExIntervals, "7cb1e431119df00ec243a6a115fa74b8"});
-        tests.add(new Object[]{NA12878_WEx, HaplotypeCaller.ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "7828256b82df377cc3a26a55dbf68f91"});
-        tests.add(new Object[]{NA12878_WEx, HaplotypeCaller.ReferenceConfidenceMode.GVCF, WExIntervals, "e41e0acf172a994e938a150390badd39"});
+        tests.add(new Object[]{NA12878_WEx, HaplotypeCaller.ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "90e22230149e6c32d1115d0e2f03cab1"});
+        tests.add(new Object[]{NA12878_WEx, HaplotypeCaller.ReferenceConfidenceMode.GVCF, WExIntervals, "b39a4bc19a0acfbade22a011cd229262"});
 
 
         return tests.toArray(new Object[][]{});
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index 5824e905f..f7056ef58 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -136,16 +136,16 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     }
 
     private boolean containsDuplicateRecord( final File vcf, final GenomeLocParser parser ) {
-        final List<Pair<GenomeLoc, GenotypingEngine.Event>> VCs = new ArrayList<Pair<GenomeLoc, GenotypingEngine.Event>>();
+        final List<Pair<GenomeLoc, GenotypingEngine.Event>> VCs = new ArrayList<>();
         try {
             for( final VariantContext vc :  GATKVCFUtils.readVCF(vcf).getSecond() ) {
-                VCs.add(new Pair<GenomeLoc, GenotypingEngine.Event>(parser.createGenomeLoc(vc), new GenotypingEngine.Event(vc)));
+                VCs.add(new Pair<>(parser.createGenomeLoc(vc), new GenotypingEngine.Event(vc)));
             }
         } catch( IOException e ) {
             throw new IllegalStateException("Somehow the temporary VCF from the integration test could not be read.");
         }
 
-        final Set<Pair<GenomeLoc, GenotypingEngine.Event>> VCsAsSet = new HashSet<Pair<GenomeLoc, GenotypingEngine.Event>>(VCs);
+        final Set<Pair<GenomeLoc, GenotypingEngine.Event>> VCsAsSet = new HashSet<>(VCs);
         return VCsAsSet.size() != VCs.size(); // The set will remove duplicate Events.
     }
 
@@ -233,7 +233,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void HCTestDBSNPAnnotationWGS() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-10,100,000 -D " + b37dbSNP132, 1,
-                Arrays.asList("f3e636d64042e766cc6515987e85a968"));
+                Arrays.asList("a43d6226a51eb525f0774f88e3778189"));
         executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
     }
 
@@ -256,7 +256,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void HCTestAggressivePcrIndelModelWGS() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller --disableDithering --pcr_indel_model AGGRESSIVE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,000,000-10,300,000", 1,
-                Arrays.asList("ab49f80783e5db5f9ab6b13ba2ad00cb"));
+                Arrays.asList("19c2992541ede7407192660fdc1fadbf"));
         executeTest("HC calling with aggressive indel error modeling on WGS intervals", spec);
     }
 
@@ -264,7 +264,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void HCTestConservativePcrIndelModelWGS() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller --disableDithering --pcr_indel_model CONSERVATIVE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,000,000-10,300,000", 1,
-                Arrays.asList("16f7ffa063511c70bad795639a1c2638"));
+                Arrays.asList("f4ab037915db3a40ba26e9ee30d40e16"));
         executeTest("HC calling with conservative indel error modeling on WGS intervals", spec);
     }
 }
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java
index 3402b73f0..21648b2b9 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java
@@ -58,10 +58,10 @@ import java.util.List;
 public class HaplotypeCallerParallelIntegrationTest extends WalkerTest {
     @DataProvider(name = "NCTDataProvider")
     public Object[][] makeNCTDataProvider() {
-        List<Object[]> tests = new ArrayList<Object[]>();
+        List<Object[]> tests = new ArrayList<>();
 
         for ( final int nct : Arrays.asList(1, 2, 4) ) {
-            tests.add(new Object[]{nct, "e4bf389676fa090c95980349310ba5ca"});
+            tests.add(new Object[]{nct, "29cb04cca87f42b4762c34dfea5d15b7"});
         }
 
         return tests.toArray(new Object[][]{});
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java
index 3a4ed7e59..5c6ae93e5 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java
@@ -99,7 +99,7 @@ public class ReferenceConfidenceModelUnitTest extends BaseTest {
 
     @DataProvider(name = "CalcNIndelInformativeReadsData")
     public Object[][] makeMyDataProvider() {
-        List<Object[]> tests = new ArrayList<Object[]>();
+        List<Object[]> tests = new ArrayList<>();
 
         { // very basic testing
             final String ref  = "ACGT";
@@ -187,7 +187,7 @@ public class ReferenceConfidenceModelUnitTest extends BaseTest {
         Assert.assertEquals(prev.getAsPLs(), new int[]{0, 0, 0});
         Assert.assertEquals(-10 * prev.getLog10GQ(GenotypeType.HOM_REF), 0.0);
 
-        for ( int i = 1; i < 10000; i++ ) {
+        for ( int i = 1; i <= ReferenceConfidenceModel.MAX_N_INDEL_INFORMATIVE_READS; i++ ) {
             final GenotypeLikelihoods current = model.getIndelPLs(i);
             final double prevGQ = -10 * prev.getLog10GQ(GenotypeType.HOM_REF);
             final double currGQ = -10 * current.getLog10GQ(GenotypeType.HOM_REF);
@@ -379,7 +379,7 @@ public class ReferenceConfidenceModelUnitTest extends BaseTest {
                 Assert.assertEquals(refModel.getEnd(), loc.getStart() + i);
                 Assert.assertFalse(refModel.hasLog10PError());
                 Assert.assertEquals(refModel.getAlternateAlleles().size(), 1);
-                Assert.assertEquals(refModel.getAlternateAllele(0), ReferenceConfidenceModel.NON_REF_SYMBOLIC_ALLELE);
+                Assert.assertEquals(refModel.getAlternateAllele(0), GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE);
                 Assert.assertTrue(refModel.hasGenotype(sample));
 
                 final Genotype g = refModel.getGenotype(sample);
@@ -388,7 +388,6 @@ public class ReferenceConfidenceModelUnitTest extends BaseTest {
                 Assert.assertEquals(g.getDP(), expectedDP);
                 Assert.assertTrue(g.hasGQ());
                 Assert.assertTrue(g.hasPL());
-                Assert.assertTrue(g.hasExtendedAttribute(ReferenceConfidenceModel.INDEL_INFORMATIVE_DEPTH));
             }
 
             final VariantContext vc = call == null ? refModel : call;
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
index 917cbd542..66bc74caa 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
@@ -67,7 +67,11 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
     // TODO TODO TODO TODO TODO TODO TODO TODO
     //
     private static String baseTestString(String args) {
-        return "-T CombineVariants --no_cmdline_in_header -L 1:1-50,000,000 -o %s -R " + b36KGReference + args;
+        return baseTestString(args, b36KGReference);
+    }
+
+    private static String baseTestString(String args, String ref) {
+        return "-T CombineVariants --no_cmdline_in_header -L 1:1-50,000,000 -o %s -R " + ref + args;
         //return "-T CombineVariants --no_cmdline_in_header -L 1:1-50,000,000 -o %s -U LENIENT_VCF_PROCESSING -R " + b36KGReference + args;
     }
 
@@ -181,6 +185,19 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
     @Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "46bbbbb8fc9ae6467a4f8fe35b8d7d14"); }
     @Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "46bbbbb8fc9ae6467a4f8fe35b8d7d14"); }
 
+    @Test public void combineSingleSamplePipelineGVCF() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString(" -V:sample1 " + privateTestDir + "combine.single.sample.pipeline.1.vcf" +
+                        " -V:sample2 " + privateTestDir + "combine.single.sample.pipeline.2.vcf" +
+                        " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
+                        " -multipleAllelesMergeType MIX_TYPES" +
+                        " --excludeNonVariants -combineAnnotations -setKey null" +
+                        " -L 20:10,000,000-10,001,000", b37KGReference),
+                1,
+                Arrays.asList("2e15db35359144683f1e58e147362679"));
+        cvExecuteTest("combineSingleSamplePipelineGVCF", spec, true);
+    }
+
     @Test
     public void combineDBSNPDuplicateSites() {
          WalkerTestSpec spec = new WalkerTestSpec(
diff --git a/protected/java/test/org/broadinstitute/sting/utils/gvcf/GVCFWriterUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/gvcf/GVCFWriterUnitTest.java
index ffbc3c43f..e353739e5 100644
--- a/protected/java/test/org/broadinstitute/sting/utils/gvcf/GVCFWriterUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/utils/gvcf/GVCFWriterUnitTest.java
@@ -49,7 +49,6 @@ package org.broadinstitute.sting.utils.gvcf;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.walkers.haplotypecaller.ReferenceConfidenceModel;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
 import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
 import org.broadinstitute.variant.variantcontext.*;
 import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
@@ -91,7 +90,7 @@ public class GVCFWriterUnitTest extends BaseTest {
     private List<Integer> standardPartition = Arrays.asList(1, 10, 20);
     private Allele REF = Allele.create("N", true);
     private Allele ALT = Allele.create("A");
-    private List<Allele> ALLELES = Arrays.asList(REF, ReferenceConfidenceModel.NON_REF_SYMBOLIC_ALLELE);
+    private List<Allele> ALLELES = Arrays.asList(REF, GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE);
     private final String SAMPLE_NAME = "XXYYZZ";
 
     @BeforeMethod
@@ -223,10 +222,10 @@ public class GVCFWriterUnitTest extends BaseTest {
         Assert.assertEquals(vc.getStart(), start);
         Assert.assertEquals(vc.getEnd(), stop);
         if ( nonRef ) {
-            Assert.assertNotEquals(vc.getAlternateAllele(0), ReferenceConfidenceModel.NON_REF_SYMBOLIC_ALLELE);
+            Assert.assertNotEquals(vc.getAlternateAllele(0), GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE);
         } else {
             Assert.assertEquals(vc.getNAlleles(), 2);
-            Assert.assertEquals(vc.getAlternateAllele(0), ReferenceConfidenceModel.NON_REF_SYMBOLIC_ALLELE);
+            Assert.assertEquals(vc.getAlternateAllele(0), GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE);
             Assert.assertEquals(vc.getAttributeAsInt(GVCFWriter.BLOCK_SIZE_INFO_FIELD, -1), stop - start + 1);
             Assert.assertEquals(vc.getAttributeAsInt(VCFConstants.END_KEY, -1), stop);
             Assert.assertTrue(vc.hasGenotypes());
@@ -234,8 +233,9 @@ public class GVCFWriterUnitTest extends BaseTest {
             Assert.assertEquals(vc.getGenotypes().size(), 1);
             final Genotype g = vc.getGenotype(SAMPLE_NAME);
             Assert.assertEquals(g.hasAD(), false);
-            Assert.assertEquals(g.hasLikelihoods(), false);
-            Assert.assertEquals(g.hasPL(), false);
+            Assert.assertEquals(g.hasLikelihoods(), true);
+            Assert.assertEquals(g.hasPL(), true);
+            Assert.assertEquals(g.getPL().length == 3, true);
             Assert.assertEquals(g.hasDP(), true);
             Assert.assertEquals(g.hasGQ(), true);
         }
@@ -307,7 +307,7 @@ public class GVCFWriterUnitTest extends BaseTest {
 
     @DataProvider(name = "BandPartitionData")
     public Object[][] makeBandPartitionData() {
-        List<Object[]> tests = new ArrayList<Object[]>();
+        List<Object[]> tests = new ArrayList<>();
 
         tests.add(new Object[]{null, false});
         tests.add(new Object[]{Collections.emptyList(), false});
diff --git a/protected/java/test/org/broadinstitute/sting/utils/gvcf/HomRefBlockUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/gvcf/HomRefBlockUnitTest.java
index 239aa93b5..ec4797f3d 100644
--- a/protected/java/test/org/broadinstitute/sting/utils/gvcf/HomRefBlockUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/utils/gvcf/HomRefBlockUnitTest.java
@@ -85,32 +85,34 @@ public class HomRefBlockUnitTest extends BaseTest {
 
     @Test
     public void testMinMedian() {
+        //TODO - might be better to make this test use a data provider?
         final HomRefBlock band = new HomRefBlock(vc, 10, 20);
         final GenotypeBuilder gb = new GenotypeBuilder("NA12878");
 
         int pos = vc.getStart();
-        band.add(pos++, gb.DP(10).GQ(11).make());
+        band.add(pos++, gb.DP(10).GQ(11).PL(new int[]{0,11,100}).make());
         Assert.assertEquals(band.getStop(), pos - 1);
         assertValues(band, 10, 10, 11, 11);
 
-        band.add(pos++, gb.DP(11).GQ(10).make());
+        band.add(pos++, gb.DP(11).GQ(10).PL(new int[]{0,10,100}).make());
         Assert.assertEquals(band.getStop(), pos - 1);
         assertValues(band, 10, 11, 10, 11);
 
-        band.add(pos++, gb.DP(12).GQ(12).make());
+        band.add(pos++, gb.DP(12).GQ(12).PL(new int[]{0,12,100}).make());
         Assert.assertEquals(band.getStop(), pos - 1);
         assertValues(band, 10, 11, 10, 11);
 
-        band.add(pos++, gb.DP(13).GQ(15).make());
+        band.add(pos++, gb.DP(13).GQ(15).PL(new int[]{0,15,100}).make());
         Assert.assertEquals(band.getStop(), pos - 1);
-        band.add(pos++, gb.DP(14).GQ(16).make());
+        band.add(pos++, gb.DP(14).GQ(16).PL(new int[]{0,16,100}).make());
         Assert.assertEquals(band.getStop(), pos - 1);
-        band.add(pos++, gb.DP(15).GQ(17).make());
+        band.add(pos++, gb.DP(15).GQ(17).PL(new int[]{0,17,100}).make());
         Assert.assertEquals(band.getStop(), pos - 1);
-        band.add(pos++, gb.DP(16).GQ(18).make());
+        band.add(pos++, gb.DP(16).GQ(18).PL(new int[]{0,18,100}).make());
         Assert.assertEquals(band.getStop(), pos - 1);
         assertValues(band, 10, 13, 10, 15);
         Assert.assertEquals(band.getSize(), pos - vc.getStart());
+        Assert.assertTrue(Arrays.equals(band.getMinPLs(), new int[]{0,10,100}));
     }
 
     @Test
@@ -118,7 +120,7 @@ public class HomRefBlockUnitTest extends BaseTest {
         final HomRefBlock band = new HomRefBlock(vc, 10, 20);
         final GenotypeBuilder gb = new GenotypeBuilder("NA12878");
 
-        band.add(vc.getStart(), gb.DP(1000).GQ(1000).make());
+        band.add(vc.getStart(), gb.DP(1000).GQ(1000).PL(new int[]{0,10,100}).make());
         assertValues(band, 1000, 1000, 99, 99);
     }
 
@@ -127,7 +129,7 @@ public class HomRefBlockUnitTest extends BaseTest {
         final HomRefBlock band = new HomRefBlock(vc, 10, 20);
         final GenotypeBuilder gb = new GenotypeBuilder("NA12878");
 
-        band.add(vc.getStart() + 10, gb.DP(10).GQ(11).make());
+        band.add(vc.getStart() + 10, gb.DP(10).GQ(11).PL(new int[]{0,10,100}).make());
     }
 
     private void assertValues(final HomRefBlock band, final int minDP, final int medianDP, final int minGQ, final int medianGQ) {
@@ -140,7 +142,7 @@ public class HomRefBlockUnitTest extends BaseTest {
 
     @DataProvider(name = "ContiguousData")
     public Object[][] makeContiguousData() {
-        List<Object[]> tests = new ArrayList<Object[]>();
+        List<Object[]> tests = new ArrayList<>();
 
         for ( final String chrMod : Arrays.asList("", ".mismatch") ) {
             for ( final int offset : Arrays.asList(-10, -1, 0, 1, 10) ) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
index b85365366..f8628bb78 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
@@ -86,7 +86,7 @@ public final class TraverseActiveRegions<M, T> extends TraversalEngine<M,T,Activ
     private int maxRegionSize = -1;
     private int minRegionSize = -1;
 
-    private final LinkedList<ActiveRegion> workQueue = new LinkedList<ActiveRegion>();
+    private final LinkedList<ActiveRegion> workQueue = new LinkedList<>();
 
     private TAROrderedReadCache myReads = null;
 
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 10ba4ca17..f2f808cad 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
@@ -32,6 +32,7 @@ import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgume
 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.downsampling.DownsampleType;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
@@ -83,6 +84,7 @@ import java.util.*;
 @Requires(value={})
 @Allows(value={DataSource.READS, DataSource.REFERENCE})
 @Reference(window=@Window(start=-50,stop=50))
+@Downsample(by= DownsampleType.BY_SAMPLE, toCoverage=250)
 @By(DataSource.REFERENCE)
 public class VariantAnnotator extends RodWalker<Integer, Integer> implements AnnotatorCompatible, TreeReducible<Integer> {
 
@@ -132,21 +134,21 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
      * See the -list argument to view available annotations.
      */
     @Argument(fullName="annotation", shortName="A", doc="One or more specific annotations to apply to variant calls", required=false)
-    protected List<String> annotationsToUse = new ArrayList<String>();
+    protected List<String> annotationsToUse = new ArrayList<>();
 
     /**
      * Note that this argument has higher priority than the -A or -G arguments,
      * so annotations will be excluded even if they are explicitly included with the other options.
      */
     @Argument(fullName="excludeAnnotation", shortName="XA", doc="One or more specific annotations to exclude", required=false)
-    protected List<String> annotationsToExclude = new ArrayList<String>();
+    protected List<String> annotationsToExclude = new ArrayList<>();
 
     /**
      * If specified, all available annotations in the group will be applied. See the VariantAnnotator -list argument to view available groups.
      * Keep in mind that RODRequiringAnnotations are not intended to be used as a group, because they require specific ROD inputs.
      */
     @Argument(fullName="group", shortName="G", doc="One or more classes/groups of annotations to apply to variant calls", required=false)
-    protected List<String> annotationGroupsToUse = new ArrayList<String>();
+    protected List<String> annotationGroupsToUse = new ArrayList<>();
 
     /**
      * This option enables you to add annotations from one VCF to another.
@@ -193,8 +195,8 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
         }
 
         // get the list of all sample names from the variant VCF input rod, if applicable
-        List<String> rodName = Arrays.asList(variantCollection.variants.getName());
-        Set<String> samples = SampleUtils.getUniqueSamplesFromRods(getToolkit(), rodName);
+        final List<String> rodName = Arrays.asList(variantCollection.variants.getName());
+        final Set<String> samples = SampleUtils.getUniqueSamplesFromRods(getToolkit(), rodName);
 
         if ( USE_ALL_ANNOTATIONS )
             engine = new VariantAnnotatorEngine(annotationsToExclude, this, getToolkit());
@@ -204,23 +206,23 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
 
         // setup the header fields
         // note that if any of the definitions conflict with our new ones, then we want to overwrite the old ones
-        Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
+        final Set<VCFHeaderLine> hInfo = new HashSet<>();
         hInfo.addAll(engine.getVCFAnnotationDescriptions());
-        for ( VCFHeaderLine line : GATKVCFUtils.getHeaderFields(getToolkit(), Arrays.asList(variantCollection.variants.getName())) ) {
+        for ( final VCFHeaderLine line : GATKVCFUtils.getHeaderFields(getToolkit(), Arrays.asList(variantCollection.variants.getName())) ) {
             if ( isUniqueHeaderLine(line, hInfo) )
                 hInfo.add(line);
         }
         // for the expressions, pull the info header line from the header of the resource rod
-        for ( VariantAnnotatorEngine.VAExpression expression : engine.getRequestedExpressions() ) {
+        for ( final VariantAnnotatorEngine.VAExpression expression : engine.getRequestedExpressions() ) {
             // special case the ID field
             if ( expression.fieldName.equals("ID") ) {
                 hInfo.add(new VCFInfoHeaderLine(expression.fullName, 1, VCFHeaderLineType.String, "ID field transferred from external VCF resource"));
                 continue;
             }
             VCFInfoHeaderLine targetHeaderLine = null;
-            for ( VCFHeaderLine line : GATKVCFUtils.getHeaderFields(getToolkit(), Arrays.asList(expression.binding.getName())) ) {
+            for ( final VCFHeaderLine line : GATKVCFUtils.getHeaderFields(getToolkit(), Arrays.asList(expression.binding.getName())) ) {
                 if ( line instanceof VCFInfoHeaderLine ) {
-                    VCFInfoHeaderLine infoline = (VCFInfoHeaderLine)line;
+                    final VCFInfoHeaderLine infoline = (VCFInfoHeaderLine)line;
                     if ( infoline.getID().equals(expression.fieldName) ) {
                         targetHeaderLine = infoline;
                         break;
@@ -285,7 +287,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
         Map<String, AlignmentContext> stratifiedContexts;
         if ( BaseUtils.simpleBaseToBaseIndex(ref.getBase()) != -1 ) {
             stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(context.getBasePileup());
-            annotatedVCs = new ArrayList<VariantContext>(VCs.size());
+            annotatedVCs = new ArrayList<>(VCs.size());
             for ( VariantContext vc : VCs )
                 annotatedVCs.add(engine.annotateContext(tracker, ref, stratifiedContexts, vc));
         }
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 078a36dd9..25e683c2f 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
@@ -58,15 +58,15 @@ public class VariantAnnotatorEngine {
         public RodBinding<VariantContext> binding;
 
         public VAExpression(String fullExpression, List<RodBinding<VariantContext>> bindings) {
-            int indexOfDot = fullExpression.lastIndexOf(".");
+            final int indexOfDot = fullExpression.lastIndexOf(".");
             if ( indexOfDot == -1 )
                 throw new UserException.BadArgumentValue(fullExpression, "it should be in rodname.value format");
 
             fullName = fullExpression;
             fieldName = fullExpression.substring(indexOfDot+1);
 
-            String bindingName = fullExpression.substring(0, indexOfDot);
-            for ( RodBinding<VariantContext> rod : bindings ) {
+            final String bindingName = fullExpression.substring(0, indexOfDot);
+            for ( final RodBinding<VariantContext> rod : bindings ) {
                 if ( rod.getName().equals(bindingName) ) {
                     binding = rod;
                     break;
@@ -96,7 +96,7 @@ public class VariantAnnotatorEngine {
     // select specific expressions to use
     public void initializeExpressions(Set<String> expressionsToUse) {
         // set up the expressions
-        for ( String expression : expressionsToUse )
+        for ( final String expression : expressionsToUse )
             requestedExpressions.add(new VAExpression(expression, walker.getResourceRodBindings()));
     }
 
@@ -113,15 +113,15 @@ public class VariantAnnotatorEngine {
         if ( annotationsToExclude.size() == 0 )
             return;
 
-        List<InfoFieldAnnotation> tempRequestedInfoAnnotations = new ArrayList<InfoFieldAnnotation>(requestedInfoAnnotations.size());
-        for ( InfoFieldAnnotation annotation : requestedInfoAnnotations ) {
+        final List<InfoFieldAnnotation> tempRequestedInfoAnnotations = new ArrayList<>(requestedInfoAnnotations.size());
+        for ( final InfoFieldAnnotation annotation : requestedInfoAnnotations ) {
             if ( !annotationsToExclude.contains(annotation.getClass().getSimpleName()) )
                 tempRequestedInfoAnnotations.add(annotation);
         }
         requestedInfoAnnotations = tempRequestedInfoAnnotations;
 
-        List<GenotypeAnnotation> tempRequestedGenotypeAnnotations = new ArrayList<GenotypeAnnotation>(requestedGenotypeAnnotations.size());
-        for ( GenotypeAnnotation annotation : requestedGenotypeAnnotations ) {
+        final List<GenotypeAnnotation> tempRequestedGenotypeAnnotations = new ArrayList<>(requestedGenotypeAnnotations.size());
+        for ( final GenotypeAnnotation annotation : requestedGenotypeAnnotations ) {
             if ( !annotationsToExclude.contains(annotation.getClass().getSimpleName()) )
                 tempRequestedGenotypeAnnotations.add(annotation);
         }
@@ -143,24 +143,24 @@ public class VariantAnnotatorEngine {
         variantOverlapAnnotator = new VariantOverlapAnnotator(dbSNPBinding, overlapBindings, engine.getGenomeLocParser());
     }
 
-    public void invokeAnnotationInitializationMethods( Set<VCFHeaderLine> headerLines ) {
-        for ( VariantAnnotatorAnnotation annotation : requestedInfoAnnotations ) {
+    public void invokeAnnotationInitializationMethods( final Set<VCFHeaderLine> headerLines ) {
+        for ( final VariantAnnotatorAnnotation annotation : requestedInfoAnnotations ) {
             annotation.initialize(walker, toolkit, headerLines);
         }
 
-        for ( VariantAnnotatorAnnotation annotation : requestedGenotypeAnnotations ) {
+        for ( final VariantAnnotatorAnnotation annotation : requestedGenotypeAnnotations ) {
             annotation.initialize(walker, toolkit, headerLines);
         }
     }
 
     public Set<VCFHeaderLine> getVCFAnnotationDescriptions() {
-        Set<VCFHeaderLine> descriptions = new HashSet<VCFHeaderLine>();
+        final Set<VCFHeaderLine> descriptions = new HashSet<>();
 
-        for ( InfoFieldAnnotation annotation : requestedInfoAnnotations )
+        for ( final InfoFieldAnnotation annotation : requestedInfoAnnotations )
             descriptions.addAll(annotation.getDescriptions());
-        for ( GenotypeAnnotation annotation : requestedGenotypeAnnotations )
+        for ( final GenotypeAnnotation annotation : requestedGenotypeAnnotations )
             descriptions.addAll(annotation.getDescriptions());
-        for ( String db : variantOverlapAnnotator.getOverlapNames() ) {
+        for ( final String db : variantOverlapAnnotator.getOverlapNames() ) {
             if ( VCFStandardHeaderLines.getInfoLine(db, false) != null )
                 descriptions.add(VCFStandardHeaderLines.getInfoLine(db));
             else
@@ -170,10 +170,10 @@ public class VariantAnnotatorEngine {
         return descriptions;
     }
 
-    public  VariantContext annotateContext(final RefMetaDataTracker tracker,
-                                           final ReferenceContext ref,
-                                           final Map<String, AlignmentContext> stratifiedContexts,
-                                           VariantContext vc) {
+    public VariantContext annotateContext(final RefMetaDataTracker tracker,
+                                          final ReferenceContext ref,
+                                          final Map<String, AlignmentContext> stratifiedContexts,
+                                          final VariantContext vc) {
         return annotateContext(tracker, ref, stratifiedContexts, vc, null);
     }
 
@@ -182,20 +182,20 @@ public class VariantAnnotatorEngine {
                                           final Map<String, AlignmentContext> stratifiedContexts,
                                           final VariantContext vc,
                                           final Map<String,PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
-        Map<String, Object> infoAnnotations = new LinkedHashMap<String, Object>(vc.getAttributes());
+        final Map<String, Object> infoAnnotations = new LinkedHashMap<>(vc.getAttributes());
 
         // annotate expressions where available
         annotateExpressions(tracker, ref.getLocus(), infoAnnotations);
 
         // go through all the requested info annotationTypes
-        for ( InfoFieldAnnotation annotationType : requestedInfoAnnotations ) {
-            Map<String, Object> annotationsFromCurrentType = annotationType.annotate(tracker, walker, ref, stratifiedContexts, vc, perReadAlleleLikelihoodMap);
+        for ( final InfoFieldAnnotation annotationType : requestedInfoAnnotations ) {
+            final Map<String, Object> annotationsFromCurrentType = annotationType.annotate(tracker, walker, ref, stratifiedContexts, vc, perReadAlleleLikelihoodMap);
             if ( annotationsFromCurrentType != null )
                 infoAnnotations.putAll(annotationsFromCurrentType);
         }
 
         // generate a new annotated VC
-        VariantContextBuilder builder = new VariantContextBuilder(vc).attributes(infoAnnotations);
+        final VariantContextBuilder builder = new VariantContextBuilder(vc).attributes(infoAnnotations);
 
         // annotate genotypes, creating another new VC in the process
         final VariantContext annotated = builder.genotypes(annotateGenotypes(tracker, ref, stratifiedContexts, vc, perReadAlleleLikelihoodMap)).make();
@@ -210,11 +210,11 @@ public class VariantAnnotatorEngine {
         final Map<String, Object> infoAnnotations = new LinkedHashMap<>(vc.getAttributes());
 
         // go through all the requested info annotationTypes
-        for ( InfoFieldAnnotation annotationType : requestedInfoAnnotations ) {
+        for ( final InfoFieldAnnotation annotationType : requestedInfoAnnotations ) {
             if ( !(annotationType instanceof ActiveRegionBasedAnnotation) )
                 continue;
 
-            Map<String, Object> annotationsFromCurrentType = annotationType.annotate(perReadAlleleLikelihoodMap, vc);
+            final Map<String, Object> annotationsFromCurrentType = annotationType.annotate(perReadAlleleLikelihoodMap, vc);
             if ( annotationsFromCurrentType != null ) {
                 infoAnnotations.putAll(annotationsFromCurrentType);
             }
@@ -244,12 +244,12 @@ public class VariantAnnotatorEngine {
     }
 
     private void annotateExpressions(final RefMetaDataTracker tracker, final GenomeLoc loc, final Map<String, Object> infoAnnotations) {
-        for ( VAExpression expression : requestedExpressions ) {
-            Collection<VariantContext> VCs = tracker.getValues(expression.binding, loc);
+        for ( final VAExpression expression : requestedExpressions ) {
+            final Collection<VariantContext> VCs = tracker.getValues(expression.binding, loc);
             if ( VCs.size() == 0 )
                 continue;
 
-            VariantContext vc = VCs.iterator().next();
+            final VariantContext vc = VCs.iterator().next();
             // special-case the ID field
             if ( expression.fieldName.equals("ID") ) {
                 if ( vc.hasID() )
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 45dbc937d..396d5686b 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
@@ -164,6 +164,9 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
     @Argument(fullName="minimalVCF", shortName="minimalVCF", doc="If true, then the output VCF will contain no INFO or genotype FORMAT fields", required=false)
     public boolean minimalVCF = false;
 
+    @Argument(fullName="excludeNonVariants", shortName="env", doc="Don't include loci found to be non-variant after the combining procedure", required=false)
+    public boolean EXCLUDE_NON_VARIANTS = false;
+
     /**
      * Set to 'null' if you don't want the set field emitted.
      */
@@ -171,7 +174,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
     public String SET_KEY = "set";
 
     /**
-     * This option allows the user to perform a simple merge (concatenation) to combine the VCFs, drastically reducing the runtime..
+     * This option allows the user to perform a simple merge (concatenation) to combine the VCFs, drastically reducing the runtime.
      */
     @Argument(fullName="assumeIdenticalSamples", shortName="assumeIdenticalSamples", doc="If true, assume input VCFs have identical sample sets and disjoint calls", required=false)
     public boolean ASSUME_IDENTICAL_SAMPLES = false;
@@ -188,6 +191,9 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
     @Argument(fullName="mergeInfoWithMaxAC", shortName="mergeInfoWithMaxAC", doc="If true, when VCF records overlap the info field is taken from the one with the max AC instead of only taking the fields which are identical across the overlapping records.", required=false)
     public boolean MERGE_INFO_WITH_MAX_AC = false;
 
+    @Argument(fullName="combineAnnotations", shortName="combineAnnotations", doc="If true, combine the annotation values in some straightforward manner assuming the input callsets are i.i.d.", required=false)
+    public boolean COMBINE_ANNOTATIONS = false;
+
     private List<String> priority = null;
 
     /** Optimization to strip out genotypes before merging if we are doing a sites_only output */
@@ -238,7 +244,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
             throw new UserException.MissingArgument("rod_priority_list", "Priority string must be provided if you want to prioritize genotypes");
 
         if ( PRIORITY_STRING != null){
-            priority = new ArrayList<String>(Arrays.asList(PRIORITY_STRING.split(",")));
+            priority = new ArrayList<>(Arrays.asList(PRIORITY_STRING.split(",")));
             if ( rodNames.size() != priority.size() )
                 throw new UserException.BadArgumentValue("rod_priority_list", "The priority list must contain exactly one rod binding per ROD provided to the GATK: rodNames=" + rodNames + " priority=" + priority);
 
@@ -252,13 +258,16 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
         if ( tracker == null ) // RodWalkers can make funky map calls
             return 0;
 
-        Set<String> rodNames = SampleUtils.getRodNamesWithVCFHeader(getToolkit(), null);
+        final Set<String> rodNames = SampleUtils.getRodNamesWithVCFHeader(getToolkit(), null);
         // get all of the vcf rods at this locus
         // Need to provide reference bases to simpleMerge starting at current locus
         Collection<VariantContext> vcs = tracker.getValues(variants, context.getLocation());
+        Collection<VariantContext> potentialRefVCs = tracker.getValues(variants);
+        potentialRefVCs.removeAll(vcs);
 
         if ( sitesOnlyVCF ) {
             vcs = VariantContextUtils.sitesOnlyVariantContexts(vcs);
+            potentialRefVCs = VariantContextUtils.sitesOnlyVariantContexts(potentialRefVCs);
         }
 
         if ( ASSUME_IDENTICAL_SAMPLES ) {
@@ -270,7 +279,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
         }
 
         int numFilteredRecords = 0;
-        for (VariantContext vc : vcs) {
+        for (final VariantContext vc : vcs) {
             if (vc.filtersWereApplied() && vc.isFiltered())
                 numFilteredRecords++;
         }
@@ -278,16 +287,16 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
         if (minimumN > 1 && (vcs.size() - numFilteredRecords < minimumN))
             return 0;
 
-        List<VariantContext> mergedVCs = new ArrayList<VariantContext>();
+        final List<VariantContext> mergedVCs = new ArrayList<>();
 
         if (multipleAllelesMergeType == GATKVariantContextUtils.MultipleAllelesMergeType.BY_TYPE) {
-            Map<VariantContext.Type, List<VariantContext>> VCsByType = GATKVariantContextUtils.separateVariantContextsByType(vcs);
+            final Map<VariantContext.Type, List<VariantContext>> VCsByType = GATKVariantContextUtils.separateVariantContextsByType(vcs);
 
             // TODO -- clean this up in a refactoring
             // merge NO_VARIATION into another type of variant (based on the ordering in VariantContext.Type)
             if ( VCsByType.containsKey(VariantContext.Type.NO_VARIATION) && VCsByType.size() > 1 ) {
                 final List<VariantContext> refs = VCsByType.remove(VariantContext.Type.NO_VARIATION);
-                for ( VariantContext.Type type : VariantContext.Type.values() ) {
+                for ( final VariantContext.Type type : VariantContext.Type.values() ) {
                     if ( VCsByType.containsKey(type) ) {
                         VCsByType.get(type).addAll(refs);
                         break;
@@ -296,23 +305,27 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
             }
 
             // iterate over the types so that it's deterministic
-            for (VariantContext.Type type : VariantContext.Type.values()) {
-                if (VCsByType.containsKey(type))
-                    mergedVCs.add(GATKVariantContextUtils.simpleMerge(VCsByType.get(type),
-                            priority, rodNames.size(), filteredRecordsMergeType, genotypeMergeOption, true, printComplexMerges,
-                            SET_KEY, filteredAreUncalled, MERGE_INFO_WITH_MAX_AC));
+            for (final VariantContext.Type type : VariantContext.Type.values()) {
+                // make sure that it is a variant or in case it is not, that we want to include the sites with no variants
+                if (!EXCLUDE_NON_VARIANTS || !type.equals(VariantContext.Type.NO_VARIATION)) {
+                    if (VCsByType.containsKey(type)) {
+                        mergedVCs.add(GATKVariantContextUtils.simpleMerge(VCsByType.get(type), potentialRefVCs,
+                                priority, rodNames.size(), filteredRecordsMergeType, genotypeMergeOption, true, printComplexMerges,
+                                SET_KEY, filteredAreUncalled, MERGE_INFO_WITH_MAX_AC, COMBINE_ANNOTATIONS));
+                    }
+                }
             }
         }
         else if (multipleAllelesMergeType == GATKVariantContextUtils.MultipleAllelesMergeType.MIX_TYPES) {
-            mergedVCs.add(GATKVariantContextUtils.simpleMerge(vcs,
+            mergedVCs.add(GATKVariantContextUtils.simpleMerge(vcs, potentialRefVCs,
                     priority, rodNames.size(), filteredRecordsMergeType, genotypeMergeOption, true, printComplexMerges,
-                    SET_KEY, filteredAreUncalled, MERGE_INFO_WITH_MAX_AC));
+                    SET_KEY, filteredAreUncalled, MERGE_INFO_WITH_MAX_AC, COMBINE_ANNOTATIONS));
         }
         else {
             logger.warn("Ignoring all records at site " + ref.getLocus());
         }
 
-        for ( VariantContext mergedVC : mergedVCs ) {
+        for ( final VariantContext mergedVC : mergedVCs ) {
             // only operate at the start of events
             if ( mergedVC == null )
                 continue;
@@ -320,9 +333,12 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
             final VariantContextBuilder builder = new VariantContextBuilder(mergedVC);
             // re-compute chromosome counts
             VariantContextUtils.calculateChromosomeCounts(builder, false);
+
             if ( minimalVCF )
                 GATKVariantContextUtils.pruneVariantContext(builder, Arrays.asList(SET_KEY));
-            vcfWriter.add(builder.make());
+            final VariantContext vc = builder.make();
+            if( !EXCLUDE_NON_VARIANTS || vc.isPolymorphicInSamples() )
+                vcfWriter.add(builder.make());
         }
 
         return vcs.isEmpty() ? 0 : 1;
diff --git a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
index 3af71eabb..bfae7e94c 100644
--- a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
@@ -845,17 +845,29 @@ public class MathUtils {
     }
 
     /**
-     * Compute the median element of the array of integers
+     * Compute the median element of the list of integers
      * @param array a list of integers
      * @return the median element
      */
-    public static int median(final List<Integer> array) {
+    public static <T extends Comparable<? super T>> T median(final List<T> array) {
+         /* TODO -- from Valentin
+        the current implementation is not the usual median when the input is of even length. More concretely it returns the ith element of the list where i = floor(input.size() / 2).
+
+        But actually that is not the "usual" definition of a median, as it is supposed to return the average of the two middle values when the sample length is an even number (i.e. median(1,2,3,4,5,6) == 3.5). [Sources: R and wikipedia]
+
+        My suggestion for a solution is then:
+
+        unify median and medianDoubles to public static <T extends Number> T median(Collection<T>)
+        check on null elements and throw an exception if there are any or perhaps return a null; documented in the javadoc.
+        relocate, rename and refactor MathUtils.median(X) to Utils.ithElement(X,X.size()/2)
+        In addition, the current median implementation sorts the whole input list witch is O(n log n). However find out the ith element (thus calculate the median) can be done in O(n)
+        */
         if ( array == null ) throw new IllegalArgumentException("Array must be non-null");
         final int size = array.size();
         if ( size == 0 ) throw new IllegalArgumentException("Array cannot have size 0");
         else if ( size == 1 ) return array.get(0);
         else {
-            final ArrayList<Integer> sorted = new ArrayList<>(array);
+            final ArrayList<T> sorted = new ArrayList<>(array);
             Collections.sort(sorted);
             return sorted.get(size / 2);
         }
@@ -1405,7 +1417,7 @@ public class MathUtils {
      * @return
      */
     public static List<Integer> log10LinearRange(final int start, final int stop, final double eps) {
-        final LinkedList<Integer> values = new LinkedList<Integer>();
+        final LinkedList<Integer> values = new LinkedList<>();
         final double log10range = Math.log10(stop - start);
 
         if ( start == 0 )
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 f4c673e61..8a034dde0 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
@@ -46,7 +46,7 @@ import java.util.List;
  * Time: 8:54:05 AM
  */
 public class PileupElement implements Comparable<PileupElement> {
-    private final static LinkedList<CigarElement> EMPTY_LINKED_LIST = new LinkedList<CigarElement>();
+    private final static LinkedList<CigarElement> EMPTY_LINKED_LIST = new LinkedList<>();
 
     private final static EnumSet<CigarOperator> ON_GENOME_OPERATORS =
             EnumSet.of(CigarOperator.M, CigarOperator.EQ, CigarOperator.X, CigarOperator.D);
diff --git a/public/java/src/org/broadinstitute/sting/utils/smithwaterman/SmithWaterman.java b/public/java/src/org/broadinstitute/sting/utils/smithwaterman/SmithWaterman.java
index 3a8afca8c..4cf39d6be 100644
--- a/public/java/src/org/broadinstitute/sting/utils/smithwaterman/SmithWaterman.java
+++ b/public/java/src/org/broadinstitute/sting/utils/smithwaterman/SmithWaterman.java
@@ -30,7 +30,7 @@ import net.sf.samtools.Cigar;
 /**
  * Generic interface for SmithWaterman calculations
  *
- * This interface allows clients to use a generic SmithWaterman variable, without propogating the specific
+ * This interface allows clients to use a generic SmithWaterman variable, without propagating the specific
  * implementation of SmithWaterman throughout their code:
  *
  * SmithWaterman sw = new SpecificSmithWatermanImplementation(ref, read, params)
diff --git a/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
index 3bc5da82f..e8c438a53 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
@@ -45,7 +45,11 @@ public class GATKVariantContextUtils {
 
     public static final int DEFAULT_PLOIDY = 2;
     public static final double SUM_GL_THRESH_NOCALL = -0.1; // if sum(gl) is bigger than this threshold, we treat GL's as non-informative and will force a no-call.
-    protected static final List<Allele> NO_CALL_ALLELES = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL);
+
+    public final static List<Allele> NO_CALL_ALLELES = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL);
+    public final static String NON_REF_SYMBOLIC_ALLELE_NAME = "NON_REF";
+    public final static Allele NON_REF_SYMBOLIC_ALLELE = Allele.create("<"+NON_REF_SYMBOLIC_ALLELE_NAME+">", false); // represents any possible non-ref allele at this site
+
     public final static String MERGE_FILTER_PREFIX = "filterIn";
     public final static String MERGE_REF_IN_ALL = "ReferenceInAll";
     public final static String MERGE_FILTER_IN_ALL = "FilteredInAll";
@@ -108,7 +112,7 @@ public class GATKVariantContextUtils {
             int averageLengthNum = 0;
             int averageLengthDenom = 0;
             int refLength = vc.getReference().length();
-            for ( Allele a : vc.getAlternateAlleles() ) {
+            for ( final Allele a : vc.getAlternateAlleles() ) {
                 int numAllele = vc.getCalledChrCount(a);
                 int alleleSize;
                 if ( a.length() == refLength ) {
@@ -182,8 +186,8 @@ public class GATKVariantContextUtils {
      */
     public static VariantContext reverseComplement(VariantContext vc) {
         // create a mapping from original allele to reverse complemented allele
-        HashMap<Allele, Allele> alleleMap = new HashMap<Allele, Allele>(vc.getAlleles().size());
-        for ( Allele originalAllele : vc.getAlleles() ) {
+        HashMap<Allele, Allele> alleleMap = new HashMap<>(vc.getAlleles().size());
+        for ( final Allele originalAllele : vc.getAlleles() ) {
             Allele newAllele;
             if ( originalAllele.isNoCall() )
                 newAllele = originalAllele;
@@ -195,8 +199,8 @@ public class GATKVariantContextUtils {
         // create new Genotype objects
         GenotypesContext newGenotypes = GenotypesContext.create(vc.getNSamples());
         for ( final Genotype genotype : vc.getGenotypes() ) {
-            List<Allele> newAlleles = new ArrayList<Allele>();
-            for ( Allele allele : genotype.getAlleles() ) {
+            List<Allele> newAlleles = new ArrayList<>();
+            for ( final Allele allele : genotype.getAlleles() ) {
                 Allele newAllele = alleleMap.get(allele);
                 if ( newAllele == null )
                     newAllele = Allele.NO_CALL;
@@ -267,7 +271,7 @@ public class GATKVariantContextUtils {
         final byte[] refAlleleBases = Arrays.copyOfRange(refAllele.getBases(), 1, refAllele.length());
 
         byte[] repeatUnit = null;
-        final ArrayList<Integer> lengths = new ArrayList<Integer>();
+        final ArrayList<Integer> lengths = new ArrayList<>();
 
         for ( final Allele allele : vc.getAlternateAlleles() ) {
             Pair<int[],byte[]> result = getNumTandemRepeatUnits(refAlleleBases, Arrays.copyOfRange(allele.getBases(), 1, allele.length()), refBasesStartingAtVCWithoutPad.getBytes());
@@ -317,7 +321,7 @@ public class GATKVariantContextUtils {
         repetitionCount[0] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(refBases, remainingRefContext), true)-repetitionsInRef;
         repetitionCount[1] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(altBases, remainingRefContext), true)-repetitionsInRef;
 
-        return new Pair<int[], byte[]>(repetitionCount, repeatUnit);
+        return new Pair<>(repetitionCount, repeatUnit);
 
     }
 
@@ -528,7 +532,7 @@ public class GATKVariantContextUtils {
                 } else {
                     newLikelihoods = new double[likelihoodIndexesToUse.size()];
                     int newIndex = 0;
-                    for ( int oldIndex : likelihoodIndexesToUse )
+                    for ( final int oldIndex : likelihoodIndexesToUse )
                         newLikelihoods[newIndex++] = originalLikelihoods[oldIndex];
 
                     // might need to re-normalize
@@ -718,6 +722,7 @@ public class GATKVariantContextUtils {
      * @param setKey                    the key name of the set
      * @param filteredAreUncalled       are filtered records uncalled?
      * @param mergeInfoWithMaxAC        should we merge in info from the VC with maximum allele count?
+     * @param combineAnnotations        should we merge info field annotations by assuming the incoming VCs are i.i.d.
      * @return new VariantContext       representing the merge of unsortedVCs
      */
     public static VariantContext simpleMerge(final Collection<VariantContext> unsortedVCs,
@@ -728,9 +733,10 @@ public class GATKVariantContextUtils {
                                              final boolean printMessages,
                                              final String setKey,
                                              final boolean filteredAreUncalled,
-                                             final boolean mergeInfoWithMaxAC ) {
+                                             final boolean mergeInfoWithMaxAC,
+                                             final boolean combineAnnotations ) {
         int originalNumOfVCs = priorityListOfVCs == null ? 0 : priorityListOfVCs.size();
-        return simpleMerge(unsortedVCs, priorityListOfVCs, originalNumOfVCs, filteredRecordMergeType, genotypeMergeOptions, annotateOrigin, printMessages, setKey, filteredAreUncalled, mergeInfoWithMaxAC);
+        return simpleMerge(unsortedVCs, Collections.<VariantContext>emptyList(), priorityListOfVCs, originalNumOfVCs, filteredRecordMergeType, genotypeMergeOptions, annotateOrigin, printMessages, setKey, filteredAreUncalled, mergeInfoWithMaxAC, combineAnnotations);
     }
 
     /**
@@ -738,11 +744,12 @@ public class GATKVariantContextUtils {
      * If uniquifySamples is true, the priority order is ignored and names are created by concatenating the VC name with
      * the sample name.
      * simpleMerge does not verify any more unique sample names EVEN if genotypeMergeOptions == GenotypeMergeType.REQUIRE_UNIQUE. One should use
-     * SampleUtils.verifyUniqueSamplesNames to check that before using sempleMerge.
+     * SampleUtils.verifyUniqueSamplesNames to check that before using simpleMerge.
      *
      * For more information on this method see: http://www.thedistractionnetwork.com/programmer-problem/
      *
      * @param unsortedVCs               collection of unsorted VCs
+     * @param potentialRefVCs           collection of unsorted VCs that overlap this locus which should only be searched for potential reference records
      * @param priorityListOfVCs         priority list detailing the order in which we should grab the VCs
      * @param filteredRecordMergeType   merge type for filtered records
      * @param genotypeMergeOptions      merge option for genotypes
@@ -751,9 +758,11 @@ public class GATKVariantContextUtils {
      * @param setKey                    the key name of the set
      * @param filteredAreUncalled       are filtered records uncalled?
      * @param mergeInfoWithMaxAC        should we merge in info from the VC with maximum allele count?
+     * @param combineAnnotations        should we merge info field annotations by assuming the incoming VCs are i.i.d.
      * @return new VariantContext       representing the merge of unsortedVCs
      */
     public static VariantContext simpleMerge(final Collection<VariantContext> unsortedVCs,
+                                             final Collection<VariantContext> potentialRefVCs,
                                              final List<String> priorityListOfVCs,
                                              final int originalNumOfVCs,
                                              final FilteredRecordMergeType filteredRecordMergeType,
@@ -762,7 +771,8 @@ public class GATKVariantContextUtils {
                                              final boolean printMessages,
                                              final String setKey,
                                              final boolean filteredAreUncalled,
-                                             final boolean mergeInfoWithMaxAC ) {
+                                             final boolean mergeInfoWithMaxAC,
+                                             final boolean combineAnnotations ) {
 
         if ( unsortedVCs == null || unsortedVCs.size() == 0 )
             return null;
@@ -775,12 +785,16 @@ public class GATKVariantContextUtils {
 
         final List<VariantContext> preFilteredVCs = sortVariantContextsByPriority(unsortedVCs, priorityListOfVCs, genotypeMergeOptions);
         // Make sure all variant contexts are padded with reference base in case of indels if necessary
-        final List<VariantContext> VCs = new ArrayList<VariantContext>();
+        List<VariantContext> VCs = new ArrayList<>();
 
         for (final VariantContext vc : preFilteredVCs) {
             if ( ! filteredAreUncalled || vc.isNotFiltered() )
                 VCs.add(vc);
         }
+
+        // cycle through and fill in NON_REF_SYMBOLIC_ALLELEs with the actual alternate allele if possible
+        VCs = fillInNonRefSymbolicAlleles(VCs, potentialRefVCs);
+
         if ( VCs.size() == 0 ) // everything is filtered out and we're filteredAreUncalled
             return null;
 
@@ -789,17 +803,18 @@ public class GATKVariantContextUtils {
         final String name = first.getSource();
         final Allele refAllele = determineReferenceAllele(VCs);
 
-        final Set<Allele> alleles = new LinkedHashSet<Allele>();
-        final Set<String> filters = new HashSet<String>();
-        final Map<String, Object> attributes = new LinkedHashMap<String, Object>();
-        final Set<String> inconsistentAttributes = new HashSet<String>();
-        final Set<String> variantSources = new HashSet<String>(); // contains the set of sources we found in our set of VCs that are variant
-        final Set<String> rsIDs = new LinkedHashSet<String>(1); // most of the time there's one id
+        final Set<Allele> alleles = new LinkedHashSet<>();
+        final Set<String> filters = new HashSet<>();
+        final Map<String, Object> attributes = new LinkedHashMap<>();
+        final Set<String> inconsistentAttributes = new HashSet<>();
+        final Set<String> variantSources = new HashSet<>(); // contains the set of sources we found in our set of VCs that are variant
+        final Set<String> rsIDs = new LinkedHashSet<>(1); // most of the time there's one id
 
         VariantContext longestVC = first;
         int depth = 0;
         int maxAC = -1;
-        final Map<String, Object> attributesWithMaxAC = new LinkedHashMap<String, Object>();
+        final Map<String, Object> attributesWithMaxAC = new LinkedHashMap<>();
+        final Map<String, List<Comparable>> annotationMap = new LinkedHashMap<>();
         double log10PError = CommonInfo.NO_LOG10_PERROR;
         boolean anyVCHadFiltersApplied = false;
         VariantContext vcWithMaxAC = null;
@@ -811,7 +826,6 @@ public class GATKVariantContextUtils {
         boolean remapped = false;
 
         // cycle through and add info from the other VCs, making sure the loc/reference matches
-
         for ( final VariantContext vc : VCs ) {
             if ( longestVC.getStart() != vc.getStart() )
                 throw new IllegalStateException("BUG: attempting to merge VariantContexts with different start sites: first="+ first.toString() + " second=" + vc.toString());
@@ -846,10 +860,10 @@ public class GATKVariantContextUtils {
             if ( vc.hasID() ) rsIDs.add(vc.getID());
             if (mergeInfoWithMaxAC && vc.hasAttribute(VCFConstants.ALLELE_COUNT_KEY)) {
                 String rawAlleleCounts = vc.getAttributeAsString(VCFConstants.ALLELE_COUNT_KEY, null);
-                // lets see if the string contains a , separator
+                // lets see if the string contains a "," separator
                 if (rawAlleleCounts.contains(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR)) {
-                    List<String> alleleCountArray = Arrays.asList(rawAlleleCounts.substring(1, rawAlleleCounts.length() - 1).split(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR));
-                    for (String alleleCount : alleleCountArray) {
+                    final List<String> alleleCountArray = Arrays.asList(rawAlleleCounts.substring(1, rawAlleleCounts.length() - 1).split(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR));
+                    for (final String alleleCount : alleleCountArray) {
                         final int ac = Integer.valueOf(alleleCount.trim());
                         if (ac > maxAC) {
                             maxAC = ac;
@@ -866,21 +880,36 @@ public class GATKVariantContextUtils {
             }
 
             for (final Map.Entry<String, Object> p : vc.getAttributes().entrySet()) {
-                String key = p.getKey();
-                // if we don't like the key already, don't go anywhere
-                if ( ! inconsistentAttributes.contains(key) ) {
-                    final boolean alreadyFound = attributes.containsKey(key);
-                    final Object boundValue = attributes.get(key);
-                    final boolean boundIsMissingValue = alreadyFound && boundValue.equals(VCFConstants.MISSING_VALUE_v4);
+                final String key = p.getKey();
+                final Object value = p.getValue();
+                boolean badAnnotation = false;
+                if ( combineAnnotations ) { // add the annotation values to a list for combining later
+                    List<Comparable> values = annotationMap.get(key);
+                    if( values == null ) {
+                        values = new ArrayList<>();
+                        annotationMap.put(key, values);
+                    }
+                    try {
+                        final String stringValue = value.toString();
+                        values.add(stringValue.contains(".") ? Double.parseDouble(stringValue) : Integer.parseInt(stringValue));
+                    } catch (NumberFormatException e) {
+                        badAnnotation = true;
+                    }
+                }
+                if ( ! combineAnnotations || badAnnotation ) { // only output annotations that have the same value in every input VC
+                    // if we don't like the key already, don't go anywhere
+                    if ( ! inconsistentAttributes.contains(key) ) {
+                        final boolean alreadyFound = attributes.containsKey(key);
+                        final Object boundValue = attributes.get(key);
+                        final boolean boundIsMissingValue = alreadyFound && boundValue.equals(VCFConstants.MISSING_VALUE_v4);
 
-                    if ( alreadyFound && ! boundValue.equals(p.getValue()) && ! boundIsMissingValue ) {
-                        // we found the value but we're inconsistent, put it in the exclude list
-                        //System.out.printf("Inconsistent INFO values: %s => %s and %s%n", key, boundValue, p.getValue());
-                        inconsistentAttributes.add(key);
-                        attributes.remove(key);
-                    } else if ( ! alreadyFound || boundIsMissingValue )  { // no value
-                        //if ( vc != first ) System.out.printf("Adding key %s => %s%n", p.getKey(), p.getValue());
-                        attributes.put(key, p.getValue());
+                        if ( alreadyFound && ! boundValue.equals(value) && ! boundIsMissingValue ) {
+                            // we found the value but we're inconsistent, put it in the exclude list
+                            inconsistentAttributes.add(key);
+                            attributes.remove(key);
+                        } else if ( ! alreadyFound || boundIsMissingValue )  { // no value
+                            attributes.put(key, value);
+                        }
                     }
                 }
             }
@@ -906,6 +935,12 @@ public class GATKVariantContextUtils {
         // take the VC with the maxAC and pull the attributes into a modifiable map
         if ( mergeInfoWithMaxAC && vcWithMaxAC != null ) {
             attributesWithMaxAC.putAll(vcWithMaxAC.getAttributes());
+        } else if ( combineAnnotations ) { // when combining annotations use the median value from all input VCs which had annotations provided
+            for ( final Map.Entry<String, List<Comparable>> p : annotationMap.entrySet() ) {
+                if ( ! p.getValue().isEmpty() ) {
+                    attributes.put(p.getKey(), combineAnnotationValues(p.getValue()));
+                }
+            }
         }
 
         // if at least one record was unfiltered and we want a union, clear all of the filters
@@ -922,7 +957,7 @@ public class GATKVariantContextUtils {
             else if ( variantSources.isEmpty() )    // everyone was reference
                 setValue = MERGE_REF_IN_ALL;
             else {
-                final LinkedHashSet<String> s = new LinkedHashSet<String>();
+                final LinkedHashSet<String> s = new LinkedHashSet<>();
                 for ( final VariantContext vc : VCs )
                     if ( vc.isVariant() )
                         s.add( vc.isFiltered() ? MERGE_FILTER_PREFIX + vc.getSource() : vc.getSource() );
@@ -950,7 +985,12 @@ public class GATKVariantContextUtils {
         if ( anyVCHadFiltersApplied ) {
             builder.filters(filters.isEmpty() ? filters : new TreeSet<>(filters));
         }
-        builder.attributes(new TreeMap<String, Object>(mergeInfoWithMaxAC ? attributesWithMaxAC : attributes));
+        builder.attributes(new TreeMap<>(mergeInfoWithMaxAC ? attributesWithMaxAC : attributes));
+        if( combineAnnotations ) {
+            // unfortunately some attributes are just too dangerous to try to combine together
+            builder.rmAttribute(VCFConstants.MLE_ALLELE_COUNT_KEY);
+            builder.rmAttribute(VCFConstants.MLE_ALLELE_FREQUENCY_KEY);
+        }
 
         // Trim the padded bases of all alleles if necessary
         final VariantContext merged = builder.make();
@@ -958,6 +998,68 @@ public class GATKVariantContextUtils {
         return merged;
     }
 
+    private static final Comparable combineAnnotationValues( final List<Comparable> array ) {
+        return MathUtils.median(array); // right now we take the median but other options could be explored
+    }
+
+    /**
+     * cycle through and fill in NON_REF_SYMBOLIC_ALLELEs with the actual alternate allele if possible
+     * @param VCs the list of VCs in which to fill in symbolic alleles
+     * @param potentialRefVCs the list of VCs which are overlapping the current locus-- need to look for reference blocks and fill in with alternate alleles
+     * @return the list of VCs to merge in which all the NON_REF_SYMBOLIC_ALLELEs have been replaced with the correct alternate allele
+     */
+    protected static final List<VariantContext> fillInNonRefSymbolicAlleles( final List<VariantContext> VCs, final Collection<VariantContext> potentialRefVCs ) {
+        if( VCs == null ) { throw new IllegalArgumentException("VCs cannot be null"); }
+        if( potentialRefVCs == null ) { throw new IllegalArgumentException("potentialRefVCs cannot be null"); }
+
+        final List<VariantContext> VCsToReturn = new ArrayList<>(VCs.size());
+        boolean containsNonRefSymbolicAllele = false;
+        VariantContext nonRefVC = null;
+        for( final VariantContext vc : VCs ) {
+            if( vc.hasAllele(NON_REF_SYMBOLIC_ALLELE) ) {
+                containsNonRefSymbolicAllele = true;
+            } else if ( nonRefVC == null ) {
+                nonRefVC = vc;
+            }
+            if( nonRefVC != null && containsNonRefSymbolicAllele == true ) {
+                break; // break out so that we don't run over the whole list unnecessarily
+            }
+        }
+        for( final VariantContext vc : potentialRefVCs ) {
+            if( vc.hasAllele(NON_REF_SYMBOLIC_ALLELE) ) {
+                containsNonRefSymbolicAllele = true;
+                VCs.add(vc); // add the overlapping non-ref symbolic records to the VCs list in order to be filled in below
+            }
+        }
+
+        if( !containsNonRefSymbolicAllele ) {
+            return VCs;
+        }
+
+        for( final VariantContext vc : VCs ) {
+            if( vc.hasAllele(NON_REF_SYMBOLIC_ALLELE) ) { // create a new record based on the current record but instead has the symbolic allele replaced by the alternate allele for this site
+                if( nonRefVC != null ) {
+                    final GenotypesContext genotypes = GenotypesContext.create(vc.getSampleNames().size());
+                    int depth = 0;
+                    for( final String sample : vc.getSampleNames() ) {
+                        final Genotype gt = vc.getGenotype(sample);
+                        final ArrayList<Allele> refAlleles = new ArrayList<>(2);
+                        refAlleles.add(nonRefVC.getReference());
+                        refAlleles.add(nonRefVC.getReference());
+                        final int[] pl = ( nonRefVC.isBiallelic() ? gt.getPL() : null ); // PLs only works for biallelic sites for now
+                        depth += ( gt.hasDP() ? gt.getDP() : Integer.parseInt((String)gt.getAnyAttribute("MIN_DP")) ); // DP is special-cased in CombineVariants so fill it in here
+                        genotypes.add(new GenotypeBuilder(gt).alleles(refAlleles).PL(pl).make());
+                    }
+                    VCsToReturn.add(new VariantContextBuilder(nonRefVC).attributes(null).attribute("DP", depth).genotypes(genotypes).make());
+                }
+            } else {
+                VCsToReturn.add(vc);
+            }
+        }
+
+        return VCsToReturn;
+    }
+
     private static final boolean hasPLIncompatibleAlleles(final Collection<Allele> alleleSet1, final Collection<Allele> alleleSet2) {
         final Iterator<Allele> it1 = alleleSet1.iterator();
         final Iterator<Allele> it2 = alleleSet2.iterator();
@@ -989,8 +1091,8 @@ public class GATKVariantContextUtils {
     static private Allele determineReferenceAllele(List<VariantContext> VCs) {
         Allele ref = null;
 
-        for ( VariantContext vc : VCs ) {
-            Allele myRef = vc.getReference();
+        for ( final VariantContext vc : VCs ) {
+            final Allele myRef = vc.getReference();
             if ( ref == null || ref.length() < myRef.length() )
                 ref = myRef;
             else if ( ref.length() == myRef.length() && ! ref.equals(myRef) )
@@ -1024,13 +1126,13 @@ public class GATKVariantContextUtils {
 //            System.out.printf("myref %s%n", myRef );
 //            System.out.printf("extrabases %s%n", new String(extraBases));
 
-            Map<Allele, Allele> map = new HashMap<Allele, Allele>();
-            for ( Allele a : vc.getAlleles() ) {
+            Map<Allele, Allele> map = new HashMap<>();
+            for ( final Allele a : vc.getAlleles() ) {
                 if ( a.isReference() )
                     map.put(a, refAllele);
                 else {
                     Allele extended = Allele.extend(a, extraBases);
-                    for ( Allele b : allAlleles )
+                    for ( final Allele b : allAlleles )
                         if ( extended.equals(b) )
                             extended = b;
 //                    System.out.printf("  Extending %s => %s%n", a, extended);
@@ -1050,23 +1152,23 @@ public class GATKVariantContextUtils {
             throw new IllegalArgumentException("Cannot merge calls by priority with a null priority list");
 
         if ( priorityListOfVCs == null || mergeOption == GenotypeMergeType.UNSORTED )
-            return new ArrayList<VariantContext>(unsortedVCs);
+            return new ArrayList<>(unsortedVCs);
         else {
-            ArrayList<VariantContext> sorted = new ArrayList<VariantContext>(unsortedVCs);
+            ArrayList<VariantContext> sorted = new ArrayList<>(unsortedVCs);
             Collections.sort(sorted, new CompareByPriority(priorityListOfVCs));
             return sorted;
         }
     }
 
-    private static void mergeGenotypes(GenotypesContext mergedGenotypes, VariantContext oneVC, AlleleMapper alleleMapping, boolean uniqifySamples) {
+    private static void mergeGenotypes(GenotypesContext mergedGenotypes, VariantContext oneVC, AlleleMapper alleleMapping, boolean uniquifySamples) {
         //TODO: should we add a check for cases when the genotypeMergeOption is REQUIRE_UNIQUE
-        for ( Genotype g : oneVC.getGenotypes() ) {
-            String name = mergedSampleName(oneVC.getSource(), g.getSampleName(), uniqifySamples);
+        for ( final Genotype g : oneVC.getGenotypes() ) {
+            final String name = mergedSampleName(oneVC.getSource(), g.getSampleName(), uniquifySamples);
             if ( ! mergedGenotypes.containsSample(name) ) {
                 // only add if the name is new
                 Genotype newG = g;
 
-                if ( uniqifySamples || alleleMapping.needsRemapping() ) {
+                if ( uniquifySamples || alleleMapping.needsRemapping() ) {
                     final List<Allele> alleles = alleleMapping.needsRemapping() ? alleleMapping.remap(g.getAlleles()) : g.getAlleles();
                     newG = new GenotypeBuilder(g).name(name).alleles(alleles).make();
                 }
@@ -1076,8 +1178,8 @@ public class GATKVariantContextUtils {
         }
     }
 
-    public static String mergedSampleName(String trackName, String sampleName, boolean uniqify ) {
-        return uniqify ? sampleName + "." + trackName : sampleName;
+    public static String mergedSampleName(String trackName, String sampleName, boolean uniquify ) {
+        return uniquify ? sampleName + "." + trackName : sampleName;
     }
 
     /**
@@ -1104,8 +1206,8 @@ public class GATKVariantContextUtils {
      * Trim the alleles in inputVC forward and reverse, as requested
      *
      * @param inputVC a non-null input VC whose alleles might need a haircut
-     * @param trimForward should we trim up the alleles from the foward direction?
-     * @param trimReverse shold we trim up the alleles from the reverse direction?
+     * @param trimForward should we trim up the alleles from the forward direction?
+     * @param trimReverse should we trim up the alleles from the reverse direction?
      * @return a non-null VariantContext (may be == to inputVC) with trimmed up alleles
      */
     @Ensures("result != null")
@@ -1140,8 +1242,8 @@ public class GATKVariantContextUtils {
         if( fwdTrimEnd == -1 && revTrim == 0 ) // nothing to do, so just return inputVC unmodified
             return inputVC;
 
-        final List<Allele> alleles = new LinkedList<Allele>();
-        final Map<Allele, Allele> originalToTrimmedAlleleMap = new HashMap<Allele, Allele>();
+        final List<Allele> alleles = new LinkedList<>();
+        final Map<Allele, Allele> originalToTrimmedAlleleMap = new HashMap<>();
 
         for (final Allele a : inputVC.getAlleles()) {
             if (a.isSymbolic()) {
@@ -1300,7 +1402,7 @@ public class GATKVariantContextUtils {
     }
 
     private final static Map<String, Object> subsetAttributes(final CommonInfo igc, final Collection<String> keysToPreserve) {
-        Map<String, Object> attributes = new HashMap<String, Object>(keysToPreserve.size());
+        Map<String, Object> attributes = new HashMap<>(keysToPreserve.size());
         for ( final String key : keysToPreserve  ) {
             if ( igc.hasAttribute(key) )
                 attributes.put(key, igc.getAttribute(key));
@@ -1343,7 +1445,7 @@ public class GATKVariantContextUtils {
         if (!vc1.getReference().equals(vc2.getReference()))
             return false;
 
-        for (Allele a :vc1.getAlternateAlleles()) {
+        for (final Allele a :vc1.getAlternateAlleles()) {
             if (!vc2.getAlternateAlleles().contains(a))
                 return false;
         }
@@ -1351,17 +1453,24 @@ public class GATKVariantContextUtils {
         return true;
     }
 
-    public static Map<VariantContext.Type, List<VariantContext>> separateVariantContextsByType(Collection<VariantContext> VCs) {
-        HashMap<VariantContext.Type, List<VariantContext>> mappedVCs = new HashMap<VariantContext.Type, List<VariantContext>>();
-        for ( VariantContext vc : VCs ) {
+    public static Map<VariantContext.Type, List<VariantContext>> separateVariantContextsByType( final Collection<VariantContext> VCs ) {
+        if( VCs == null ) { throw new IllegalArgumentException("VCs cannot be null."); }
+
+        final HashMap<VariantContext.Type, List<VariantContext>> mappedVCs = new HashMap<>();
+        for ( final VariantContext vc : VCs ) {
+            VariantContext.Type vcType = vc.getType();
+            if( vc.hasAllele(NON_REF_SYMBOLIC_ALLELE) ) {
+                if( vc.getAlternateAlleles().size() > 1 ) { throw new IllegalStateException("Reference records should not have more than one alternate allele"); }
+                vcType = VariantContext.Type.NO_VARIATION;
+            }
 
             // look at previous variant contexts of different type. If:
             // a) otherVC has alleles which are subset of vc, remove otherVC from its list and add otherVC to vc's list
             // b) vc has alleles which are subset of otherVC. Then, add vc to otherVC's type list (rather, do nothing since vc will be added automatically to its list)
             // c) neither: do nothing, just add vc to its own list
             boolean addtoOwnList = true;
-            for (VariantContext.Type type : VariantContext.Type.values()) {
-                if (type.equals(vc.getType()))
+            for (final VariantContext.Type type : VariantContext.Type.values()) {
+                if (type.equals(vcType))
                     continue;
 
                 if (!mappedVCs.containsKey(type))
@@ -1376,9 +1485,9 @@ public class GATKVariantContextUtils {
                         // avoid having empty lists
                         if (vcList.size() == 0)
                             mappedVCs.remove(type);
-                        if ( !mappedVCs.containsKey(vc.getType()) )
-                            mappedVCs.put(vc.getType(), new ArrayList<VariantContext>());
-                        mappedVCs.get(vc.getType()).add(otherVC);
+                        if ( !mappedVCs.containsKey(vcType) )
+                            mappedVCs.put(vcType, new ArrayList<VariantContext>());
+                        mappedVCs.get(vcType).add(otherVC);
                         break;
                     }
                     else if (allelesAreSubset(vc,otherVC)) {
@@ -1390,9 +1499,9 @@ public class GATKVariantContextUtils {
                 }
             }
             if (addtoOwnList) {
-                if ( !mappedVCs.containsKey(vc.getType()) )
-                    mappedVCs.put(vc.getType(), new ArrayList<VariantContext>());
-                mappedVCs.get(vc.getType()).add(vc);
+                if ( !mappedVCs.containsKey(vcType) )
+                    mappedVCs.put(vcType, new ArrayList<VariantContext>());
+                mappedVCs.get(vcType).add(vc);
             }
         }
 
@@ -1403,10 +1512,10 @@ public class GATKVariantContextUtils {
         if ( allowedAttributes == null )
             return vc;
 
-        GenotypesContext newGenotypes = GenotypesContext.create(vc.getNSamples());
+        final GenotypesContext newGenotypes = GenotypesContext.create(vc.getNSamples());
         for ( final Genotype genotype : vc.getGenotypes() ) {
-            Map<String, Object> attrs = new HashMap<String, Object>();
-            for ( Map.Entry<String, Object> attr : genotype.getExtendedAttributes().entrySet() ) {
+            final Map<String, Object> attrs = new HashMap<>();
+            for ( final Map.Entry<String, Object> attr : genotype.getExtendedAttributes().entrySet() ) {
                 if ( allowedAttributes.contains(attr.getKey()) )
                     attrs.put(attr.getKey(), attr.getValue());
             }
@@ -1427,8 +1536,8 @@ public class GATKVariantContextUtils {
         public Allele remap(Allele a)                   { return map != null && map.containsKey(a) ? map.get(a) : a; }
 
         public List<Allele> remap(List<Allele> as) {
-            List<Allele> newAs = new ArrayList<Allele>();
-            for ( Allele a : as ) {
+            List<Allele> newAs = new ArrayList<>();
+            for ( final Allele a : as ) {
                 //System.out.printf("  Remapping %s => %s%n", a, remap(a));
                 newAs.add(remap(a));
             }
@@ -1467,7 +1576,7 @@ public class GATKVariantContextUtils {
         if ( alleleStrings == null || alleleStrings.isEmpty() )
             throw new IllegalArgumentException("alleleStrings must be non-empty, non-null list");
 
-        final List<Allele> alleles = new LinkedList<Allele>();
+        final List<Allele> alleles = new LinkedList<>();
         final int length = alleleStrings.get(0).length();
 
         boolean first = true;
@@ -1503,7 +1612,7 @@ public class GATKVariantContextUtils {
         if ( ref.length != alt.length )
             throw new IllegalStateException("ref and alt alleles for MNP have different lengths");
 
-        final List<VariantContext> result = new ArrayList<VariantContext>(ref.length);
+        final List<VariantContext> result = new ArrayList<>(ref.length);
 
         for ( int i = 0; i < ref.length; i++ ) {
 
@@ -1518,7 +1627,7 @@ public class GATKVariantContextUtils {
                 final VariantContextBuilder newVC = new VariantContextBuilder(vc).start(vc.getStart() + i).stop(vc.getStart() + i).alleles(Arrays.asList(newRefAllele, newAltAllele));
 
                 // create new genotypes with updated alleles
-                final Map<Allele, Allele> alleleMap = new HashMap<Allele, Allele>();
+                final Map<Allele, Allele> alleleMap = new HashMap<>();
                 alleleMap.put(vc.getReference(), newRefAllele);
                 alleleMap.put(vc.getAlternateAllele(0), newAltAllele);
                 final GenotypesContext newGenotypes = updateGenotypesWithMappedAlleles(vc.getGenotypes(), new AlleleMapper(alleleMap));
diff --git a/public/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java
index f2718fb8c..a13797523 100644
--- a/public/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java
@@ -500,7 +500,7 @@ public class MathUtilsUnitTest extends BaseTest {
 
     @DataProvider(name = "MedianData")
     public Object[][] makeMedianData() {
-        List<Object[]> tests = new ArrayList<Object[]>();
+        final List<Object[]> tests = new ArrayList<>();
 
         // this functionality can be adapted to provide input data for whatever you might want in your data
         tests.add(new Object[]{Arrays.asList(10), 10});
@@ -510,12 +510,16 @@ public class MathUtilsUnitTest extends BaseTest {
             tests.add(new Object[]{values, 1});
         }
 
+        for ( final List<Double> values : Utils.makePermutations(Arrays.asList(1.1,2.1,-3.1), 3, false) ) {
+            tests.add(new Object[]{values, 1.1});
+        }
+
         return tests.toArray(new Object[][]{});
     }
 
     @Test(dataProvider = "MedianData")
-    public void testMedian(final List<Integer> values, final int expected) {
-        final int actual = MathUtils.median(values);
+    public void testMedian(final List<Comparable> values, final Comparable expected) {
+        final Comparable actual = MathUtils.median(values);
         Assert.assertEquals(actual, expected, "Failed with " + values);
     }
 }
diff --git a/public/java/test/org/broadinstitute/sting/utils/variant/GATKVariantContextUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variant/GATKVariantContextUtilsUnitTest.java
index 937698d82..220e64f7d 100644
--- a/public/java/test/org/broadinstitute/sting/utils/variant/GATKVariantContextUtilsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variant/GATKVariantContextUtilsUnitTest.java
@@ -107,7 +107,7 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
 
         private MergeAllelesTest(List<Allele>... arg) {
             super(MergeAllelesTest.class);
-            LinkedList<List<Allele>> all = new LinkedList<List<Allele>>(Arrays.asList(arg));
+            LinkedList<List<Allele>> all = new LinkedList<>(Arrays.asList(arg));
             expected = all.pollLast();
             inputs = all;
         }
@@ -185,7 +185,7 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
         final VariantContext merged = GATKVariantContextUtils.simpleMerge(
                 inputs, priority,
                 GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
-                GATKVariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, "set", false, false);
+                GATKVariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, "set", false, false, false);
 
         Assert.assertEquals(merged.getAlleles(), cfg.expected);
     }
@@ -243,7 +243,7 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
         final VariantContext merged = GATKVariantContextUtils.simpleMerge(
                 inputs, null,
                 GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
-                GATKVariantContextUtils.GenotypeMergeType.UNSORTED, false, false, "set", false, false);
+                GATKVariantContextUtils.GenotypeMergeType.UNSORTED, false, false, "set", false, false, false);
         Assert.assertEquals(merged.getID(), cfg.expected);
     }
 
@@ -358,7 +358,7 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
     public void testMergeFiltered(MergeFilteredTest cfg) {
         final List<String> priority = vcs2priority(cfg.inputs);
         final VariantContext merged = GATKVariantContextUtils.simpleMerge(
-                cfg.inputs, priority, cfg.type, GATKVariantContextUtils.GenotypeMergeType.PRIORITIZE, true, false, "set", false, false);
+                cfg.inputs, priority, cfg.type, GATKVariantContextUtils.GenotypeMergeType.PRIORITIZE, true, false, "set", false, false, false);
 
         // test alleles are equal
         Assert.assertEquals(merged.getAlleles(), cfg.expected.getAlleles());
@@ -485,7 +485,7 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
     public void testMergeGenotypes(MergeGenotypesTest cfg) {
         final VariantContext merged = GATKVariantContextUtils.simpleMerge(
                 cfg.inputs, cfg.priority, GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
-                GATKVariantContextUtils.GenotypeMergeType.PRIORITIZE, true, false, "set", false, false);
+                GATKVariantContextUtils.GenotypeMergeType.PRIORITIZE, true, false, "set", false, false, false);
 
         // test alleles are equal
         Assert.assertEquals(merged.getAlleles(), cfg.expected.getAlleles());
@@ -526,10 +526,10 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
 
         final VariantContext merged = GATKVariantContextUtils.simpleMerge(
                 Arrays.asList(vc1, vc2), null, GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
-                GATKVariantContextUtils.GenotypeMergeType.UNIQUIFY, false, false, "set", false, false);
+                GATKVariantContextUtils.GenotypeMergeType.UNIQUIFY, false, false, "set", false, false, false);
 
         // test genotypes
-        Assert.assertEquals(merged.getSampleNames(), new HashSet<String>(Arrays.asList("s1.1", "s1.2")));
+        Assert.assertEquals(merged.getSampleNames(), new HashSet<>(Arrays.asList("s1.1", "s1.2")));
     }
 
 // TODO: remove after testing
@@ -540,7 +540,7 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
 //
 //        final VariantContext merged = VariantContextUtils.simpleMerge(
 //                Arrays.asList(vc1, vc2), null, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
-//                VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE, false, false, "set", false, false);
+//                VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE, false, false, "set", false, false, false);
 //    }
 
     // --------------------------------------------------------------------------------
@@ -559,7 +559,7 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
 
                 final VariantContext merged = GATKVariantContextUtils.simpleMerge(
                         Arrays.asList(vc1, vc2), priority, GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
-                        GATKVariantContextUtils.GenotypeMergeType.PRIORITIZE, annotate, false, set, false, false);
+                        GATKVariantContextUtils.GenotypeMergeType.PRIORITIZE, annotate, false, set, false, false, false);
 
                 if ( annotate )
                     Assert.assertEquals(merged.getAttribute(set), GATKVariantContextUtils.MERGE_INTERSECTION);
@@ -570,7 +570,7 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
     }
 
     private static final List<String> vcs2priority(final Collection<VariantContext> vcs) {
-        final List<String> priority = new ArrayList<String>();
+        final List<String> priority = new ArrayList<>();
 
         for ( final VariantContext vc : vcs ) {
             priority.add(vc.getSource());
@@ -997,7 +997,7 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
 
     @DataProvider(name = "PrimitiveAlleleSplittingData")
     public Object[][] makePrimitiveAlleleSplittingData() {
-        List<Object[]> tests = new ArrayList<Object[]>();
+        List<Object[]> tests = new ArrayList<>();
 
         // no split
         tests.add(new Object[]{"A", "C", 0, null});
@@ -1039,6 +1039,26 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
         }
     }
 
+    @Test(enabled = !DEBUG)
+    public void testFillInNonRefSymbolicAlleles() {
+        final int start = 10;
+        final String ref = "A";
+        final String alt = "C";
+        final VariantContext vcAlt = GATKVariantContextUtils.makeFromAlleles("test", "20", start, Arrays.asList(ref, alt));
+        final VariantContext vcRef = GATKVariantContextUtils.makeFromAlleles("test", "20", start, Arrays.asList(ref, "<"+GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE_NAME+">"));
+
+        List<VariantContext> VCs = Arrays.asList(vcAlt, vcRef);
+        VCs = GATKVariantContextUtils.fillInNonRefSymbolicAlleles(VCs, Collections.<VariantContext>emptyList());
+
+        // make sure the non ref symbolic alleles have all been filled in with the appropriate alternate allele
+        for( final VariantContext vc : VCs ) {
+            Assert.assertTrue(vc.getAlternateAlleles().size() == 1);
+            Assert.assertTrue(vc.getAlternateAllele(0).isNonReference());
+            Assert.assertTrue(!vc.getReference().isSymbolic());
+            Assert.assertTrue(!vc.getAlternateAllele(0).isSymbolic());
+        }
+    }
+
     // --------------------------------------------------------------------------------
     //
     // test allele remapping
@@ -1047,7 +1067,7 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
 
     @DataProvider(name = "AlleleRemappingData")
     public Object[][] makeAlleleRemappingData() {
-        List<Object[]> tests = new ArrayList<Object[]>();
+        List<Object[]> tests = new ArrayList<>();
 
         final Allele originalBase1 = Allele.create((byte)'A');
         final Allele originalBase2 = Allele.create((byte)'T');
@@ -1055,7 +1075,7 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
         for ( final byte base1 : BaseUtils.BASES ) {
             for ( final byte base2 : BaseUtils.BASES ) {
                 for ( final int numGenotypes : Arrays.asList(0, 1, 2, 5) ) {
-                    Map<Allele, Allele> map = new HashMap<Allele, Allele>(2);
+                    Map<Allele, Allele> map = new HashMap<>(2);
                     map.put(originalBase1, Allele.create(base1));
                     map.put(originalBase2, Allele.create(base2));
 
diff --git a/public/java/test/org/broadinstitute/sting/utils/variant/VariantContextBenchmark.java b/public/java/test/org/broadinstitute/sting/utils/variant/VariantContextBenchmark.java
index 381b282e0..a1b75a3f1 100644
--- a/public/java/test/org/broadinstitute/sting/utils/variant/VariantContextBenchmark.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variant/VariantContextBenchmark.java
@@ -147,7 +147,7 @@ public class VariantContextBenchmark extends SimpleBenchmark {
                     Set<String> samples;
                     public void run(final VariantContext vc) {
                         if ( samples == null )
-                            samples = new HashSet<String>(new ArrayList<String>(vc.getSampleNames()).subList(0, nSamplesToTake));
+                            samples = new HashSet<>(new ArrayList<>(vc.getSampleNames()).subList(0, nSamplesToTake));
                         VariantContext sub = vc.subContextFromSamples(samples);
                         sub.getNSamples();
                     }
@@ -176,7 +176,7 @@ public class VariantContextBenchmark extends SimpleBenchmark {
                     Set<String> samples;
                     public void run(final VariantContext vc) {
                         if ( samples == null )
-                            samples = new HashSet<String>(new ArrayList<String>(vc.getSampleNames()).subList(0, nSamplesToTake));
+                            samples = new HashSet<>(new ArrayList<>(vc.getSampleNames()).subList(0, nSamplesToTake));
                         vc.getGenotypes(samples).size();
                     }
                 };
@@ -221,7 +221,7 @@ public class VariantContextBenchmark extends SimpleBenchmark {
             case MERGE:
                 return new FunctionToBenchmark<VariantContext>() {
                     public void run(final VariantContext vc) {
-                        List<VariantContext> toMerge = new ArrayList<VariantContext>();
+                        List<VariantContext> toMerge = new ArrayList<>();
 
                         for ( int i = 0; i < dupsToMerge; i++ ) {
                             GenotypesContext gc = GenotypesContext.create(vc.getNSamples());
@@ -234,7 +234,7 @@ public class VariantContextBenchmark extends SimpleBenchmark {
                         GATKVariantContextUtils.simpleMerge(toMerge, null,
                                 GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
                                 GATKVariantContextUtils.GenotypeMergeType.UNSORTED,
-                                true, false, "set", false, true);
+                                true, false, "set", false, true, false);
                     }
                 };
 
@@ -363,7 +363,7 @@ public class VariantContextBenchmark extends SimpleBenchmark {
 //                                toMerge, null,
 //                                org.broadinstitute.variant.variantcontext.v13.VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
 //                                org.broadinstitute.variant.variantcontext.v13.VariantContextUtils.GenotypeMergeType.UNSORTED,
-//                                true, false, "set", false, true);
+//                                true, false, "set", false, true, false);
 //                    }
 //                };
 //

From 8b829255e7526ed27ec8c2318288ae9789ab8c92 Mon Sep 17 00:00:00 2001
From: Geraldine Van der Auwera <vdauwera@broadinstitute.org>
Date: Mon, 9 Sep 2013 19:40:03 -0400
Subject: [PATCH 10/77] Clarified docs on using clipping options

---
 .../gatk/walkers/readutils/ClipReads.java     | 54 ++++++++++---------
 1 file changed, 29 insertions(+), 25 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java
index dfc36954b..78029eb85 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java
@@ -57,36 +57,34 @@ import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
 /**
- * This tool provides simple, powerful read clipping capabilities to remove low quality strings of bases, sections of reads, and reads containing user-provided sequences.
+ * Read clipping based on quality, position or sequence matching
  *
+ * <p>This tool provides simple, powerful read clipping capabilities that allow you to remove low quality strings of bases, sections of reads, and reads containing user-provided sequences.</p> 
  *
- * <p>
- * It allows the user to clip bases in reads with poor quality scores, that match particular
- * sequences, or that were generated by particular machine cycles.
+ * <p>There are three options for clipping (quality, position and sequence), which can be used alone or in combination. In addition, you can also specify a clipping representation, which determines exactly how ClipReads applies clips to the reads (soft clips, writing Q0 base quality scores, etc.). Please note that you MUST specify at least one of the three clipping options, and specifying a clipping representation is not sufficient. If you do not specify a clipping option, the program will run but it will not do anything to your reads.</p>
  *
  * <dl>
  *     <dt>Quality score based clipping</dt>
  *     <dd>
  *         Clip bases from the read in clipper from
- *         <br>argmax_x{ \sum{i = x + 1}^l (qTrimmingThreshold - qual)</br>
- *         to the end of the read.  This is blatantly stolen from BWA.
+ *         <pre>argmax_x{ \sum{i = x + 1}^l (qTrimmingThreshold - qual)</pre>
+ *         to the end of the read.  This is copied from BWA.
  *
  *         Walk through the read from the end (in machine cycle order) to the beginning, calculating the
  *         running sum of qTrimmingThreshold - qual.  While we do this, we track the maximum value of this
  *         sum where the delta > 0.  After the loop, clipPoint is either -1 (don't do anything) or the
  *         clipping index in the read (from the end).
- *     </dd>
+ *     </dd><br />
  *     <dt>Cycle based clipping</dt>
  *     <dd>Clips machine cycles from the read. Accepts a string of ranges of the form start1-end1,start2-end2, etc.
  *     For each start/end pair, removes bases in machine cycles from start to end, inclusive. These are 1-based values (positions).
  *     For example, 1-5,10-12 clips the first 5 bases, and then three bases at cycles 10, 11, and 12.
- *     </dd>
+ *     </dd><br />
  *     <dt>Sequence matching</dt>
  *     <dd>Clips bases from that exactly match one of a number of base sequences. This employs an exact match algorithm,
  *     filtering only bases whose sequence exactly matches SEQ.</dd>
  * </dl>
  *
- * </p>
  *
  * <h3>Input</h3>
  * <p>
@@ -99,7 +97,7 @@ import java.util.regex.Pattern;
  *     operation applied to each read.
  * </p>
  * <p>
- *     <h3>Summary output</h3>
+ *     <h4>Summary output (console)</h4>
  *     <pre>
  *     Number of examined reads              13
  *     Number of clipped reads               13
@@ -113,16 +111,29 @@ import java.util.regex.Pattern;
  *     </pre>
  * </p>
  *
- * <p>
- *     <h3>Example clipping</h3>
- *     Suppose we are given this read:
+ * <h3>Example</h3>
+ * <pre>
+ *   java -jar GenomeAnalysisTK.jar \
+ *     -T ClipReads \
+ *     -R reference.fasta \
+ *     -I original.bam \
+ *     -o clipped.bam \
+ *     -XF seqsToClip.fasta \
+ *     -X CCCCC \
+ *     -CT "1-5,11-15" \
+ *     -QT 10
+ * </pre>
+ * <p>The command line shown above will apply all three options in combination. See the detailed examples below to see how the choice of clipping representation affects the output.</p>
+ *
+ *     <h4>Detailed clipping examples</h4>
+ *     <p>Suppose we are given this read:</p>
  *     <pre>
  *     314KGAAXX090507:1:19:1420:1123#0        16      chrM    3116    29      76M     *       *       *
  *          TAGGACCCGGGCCCCCCTCCCCAATCCTCCAACGCATATAGCGGCCGCGCCTTCCCCCGTAAATGATATCATCTCA
  *          #################4?6/?2135;;;'1/=/<'B9;12;68?A79@,@==@9?=AAA3;A@B;A?B54;?ABA
  *     </pre>
  *
- *     If we are clipping reads with -QT 10 and -CR WRITE_NS, we get:
+ *     <p>If we are clipping reads with -QT 10 and -CR WRITE_NS, we get:</p>
  *
  *     <pre>
  *     314KGAAXX090507:1:19:1420:1123#0        16      chrM    3116    29      76M     *       *       *
@@ -130,26 +141,20 @@ import java.util.regex.Pattern;
  *          #################4?6/?2135;;;'1/=/<'B9;12;68?A79@,@==@9?=AAA3;A@B;A?B54;?ABA
  *     </pre>
  *
- *     Whereas with -CR WRITE_Q0S:
+ *     <p>Whereas with -QT 10 -CR WRITE_Q0S:</p>
  *     <pre>
  *     314KGAAXX090507:1:19:1420:1123#0        16      chrM    3116    29      76M     *       *       *
  *          TAGGACCCGGGCCCCCCTCCCCAATCCTCCAACGCATATAGCGGCCGCGCCTTCCCCCGTAAATGATATCATCTCA
  *          !!!!!!!!!!!!!!!!!4?6/?2135;;;'1/=/<'B9;12;68?A79@,@==@9?=AAA3;A@B;A?B54;?ABA
  *     </pre>
  *
- *     Or -CR SOFTCLIP_BASES:
+ *     <p>Or -QT 10 -CR SOFTCLIP_BASES:</p>
  *     <pre>
  *     314KGAAXX090507:1:19:1420:1123#0        16      chrM    3133    29      17S59M  *       *       *
  *          TAGGACCCGGGCCCCCCTCCCCAATCCTCCAACGCATATAGCGGCCGCGCCTTCCCCCGTAAATGATATCATCTCA
  *          #################4?6/?2135;;;'1/=/<'B9;12;68?A79@,@==@9?=AAA3;A@B;A?B54;?ABA
  *     </pre>
- * </p>
  *
- * <h3>Examples</h3>
- * <pre>
- *     -T ClipReads -I my.bam -I your.bam -o my_and_your.clipped.bam -R Homo_sapiens_assembly18.fasta \
- *     -XF seqsToClip.fasta -X CCCCC -CT "1-5,11-15" -QT 10
- * </pre>
 
  * @author Mark DePristo
  * @since 2010
@@ -158,10 +163,9 @@ import java.util.regex.Pattern;
 @Requires({DataSource.READS})
 public class ClipReads extends ReadWalker<ClipReads.ReadClipperWithData, ClipReads.ClippingData> {
     /**
-     * If provided, ClipReads will write summary statistics about the clipping operations applied
-     * to the reads to this file.
+     * If provided, ClipReads will write summary statistics about the clipping operations applied to the reads in this file.
      */
-    @Output(fullName = "outputStatistics", shortName = "os", doc = "Write output statistics to this file", required = false, defaultToStdout = false)
+    @Output(fullName = "outputStatistics", shortName = "os", doc = "File to output statistics", required = false, defaultToStdout = false)
     PrintStream out = null;
 
     /**

From 2f5064dd1d1e1d8e5b8071bfca3c29b4cc174df1 Mon Sep 17 00:00:00 2001
From: chapmanb <chapmanb@50mail.com>
Date: Mon, 12 Aug 2013 14:36:57 -0400
Subject: [PATCH 11/77] Provide close methods to clean up resources used while
 creating AlignmentContexts from BAM file regions. Allows utilization of
 CoveredLocusView via the API

Signed-off-by: David Roazen <droazen@broadinstitute.org>
---
 .../sting/gatk/datasources/reads/BAMScheduler.java        | 8 ++++++++
 .../sting/gatk/datasources/reads/IntervalSharder.java     | 3 +++
 .../sting/gatk/datasources/reads/SAMDataSource.java       | 8 ++++++++
 .../sting/gatk/datasources/reads/ShardBalancer.java       | 3 +++
 4 files changed, 22 insertions(+)

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 adb668ff9..2f03edb68 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
@@ -246,6 +246,14 @@ public class BAMScheduler implements Iterator<FilePointer> {
      */
     private PeekableIterator<BAMScheduleEntry> bamScheduleIterator = null;
 
+    /**
+     * Clean up underlying BAMSchedule file handles.
+     */
+    public void close() {
+        if(bamScheduleIterator != null)
+            bamScheduleIterator.close();
+    }
+
     /**
      * Get the next overlapping tree of bins associated with the given BAM file.
      * @param currentLocus The actual locus for which to check overlap.
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 048ce17f5..b476945ce 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
@@ -62,6 +62,9 @@ public class IntervalSharder implements Iterator<FilePointer> {
         wrappedIterator = new PeekableIterator<FilePointer>(scheduler);
         this.parser = parser;
     }
+    public void close() {
+      wrappedIterator.close();
+    }
 
     public boolean hasNext() {
         return wrappedIterator.hasNext();
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 ac2ed4a4c..9dc9734a5 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
@@ -352,6 +352,14 @@ public class SAMDataSource {
         resourcePool.releaseReaders(readers);
     }
 
+    public void close() {
+        SAMReaders readers = resourcePool.getAvailableReaders();
+        for(SAMReaderID readerID: readerIDs) {
+            SAMFileReader reader = readers.getReader(readerID);
+            reader.close();
+        }
+    }
+
     /**
      * Returns Reads data structure containing information about the reads data sources placed in this pool as well as
      * information about how they are downsampled, sorted, and filtered
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardBalancer.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardBalancer.java
index ff0fa1127..37f1bcfac 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardBalancer.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardBalancer.java
@@ -43,4 +43,7 @@ public abstract class ShardBalancer implements Iterable<Shard> {
         this.filePointers = new PeekableIterator<FilePointer>(filePointers);
         this.parser = parser;
     }
+    public void close() {
+      this.filePointers.close();
+    }
 }

From 74639463b948c660f232fd53cf6728881ad717b1 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Thu, 19 Sep 2013 23:07:20 -0400
Subject: [PATCH 12/77] Updating excessive coverage default parameter

most people don't care about excessive coverage (unless you're very
particular about your analysis). Therefore the best possible default
value for this is Integer.maxValue so it doesn't get in the way.

Itemized Changes:
   * change maximumCoverage threshold to Integer.maxValue

[delivers #57353620]
---
 .../gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java
index a6cbc1da3..c330b3f02 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java
@@ -77,7 +77,7 @@ final class ThresHolder {
      * If at any locus, a sample has more coverage than this, it will be reported as EXCESSIVE_COVERAGE
      */
     @Argument(fullName = "maximum_coverage", shortName = "max", doc = "The maximum allowable coverage, used for calling EXCESSIVE_COVERAGE", required = false)
-    public int maximumCoverage = 700;
+    public int maximumCoverage = Integer.MAX_VALUE;
 
     /**
      * If any sample has a paired read whose distance between alignment starts (between the pairs) is greater than this, it will be reported as BAD_MATE

From 5e2ffc74fccf6c6485ddaab1bdb7c9a6007cccb7 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Fri, 20 Sep 2013 16:47:12 -0400
Subject: [PATCH 13/77] Automated interpretation for QualifyMissingIntervals

   * add a new column to do what I have been doing manually for every project, understand why we got no usable coverage in that interval
   * add unit tests -- this tool is now public, we need tests.
   * slightly better docs -- in an effort to produce better docs for this tool
---
 .../walkers/diagnostics/missing/Metrics.java  | 35 +++----
 .../missing/QualifyMissingIntervals.java      | 94 +++++++++++++++++-
 .../QualifyMissingIntervalsUnitTest.java      | 95 +++++++++++++++++++
 3 files changed, 199 insertions(+), 25 deletions(-)
 create mode 100644 protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/Metrics.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/Metrics.java
index 9296cc89b..63c35fd65 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/Metrics.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/Metrics.java
@@ -47,29 +47,7 @@
 package org.broadinstitute.sting.gatk.walkers.diagnostics.missing;
 
 /**
- * Short one line description of the walker.
- * <p/>
- * <p>
- * [Long description of the walker]
- * </p>
- * <p/>
- * <p/>
- * <h2>Input</h2>
- * <p>
- * [Description of the Input]
- * </p>
- * <p/>
- * <h2>Output</h2>
- * <p>
- * [Description of the Output]
- * </p>
- * <p/>
- * <h2>Examples</h2>
- * <pre>
- *    java
- *      -jar GenomeAnalysisTK.jar
- *      -T [walker name]
- *  </pre>
+ * Metrics class for the QualifyMissingInterval walker
  *
  * @author Mauricio Carneiro
  * @since 5/1/13
@@ -81,6 +59,8 @@ final class Metrics {
     private int reads;
     private int refs;
 
+    public Metrics() {}
+
     void reads(int reads) {this.reads = reads;}
     void refs(int refs) {this.refs = refs;}
 
@@ -108,4 +88,13 @@ final class Metrics {
 
         return this;
     }
+
+    // Test related constructor and methods
+    protected Metrics(double gccontent, double baseQual, double mapQual, int reads, int refs) {
+        this.gccontent = gccontent;
+        this.baseQual = baseQual;
+        this.mapQual = mapQual;
+        this.reads = reads;
+        this.refs = refs;
+    }
 }
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
index eabcf20c1..8cc7bb8f3 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
@@ -117,6 +117,56 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
     @Argument(shortName = "cds", required = false)
     public String cdsFile = null;
 
+    /**
+     * This value will be used to determine whether or not an interval had too high or too low GC content to be
+     * sequenced. This is only applied if there was not enough data in the interval.
+     */
+    @Argument(doc = "upper and lower bound for an interval to be considered high/low GC content",
+            shortName = "gc", required = false)
+    public double gcThreshold = 0.3;
+
+    /**
+     * The coverage of a missing interval may determine whether or not an interval is sequenceable. A low coverage will
+     * trigger gc content, mapping, base qualities and other checks to figure out why this interval was deemed
+     * unsequenceable.
+     */
+    @Argument(doc = "minimum coverage to be considered sequenceable",
+            shortName = "cov", required = false)
+    public int coverageThreshold = 20;
+
+    /**
+     * An average mapping quality above this value will determine the interval to be mappable.
+     */
+    @Argument(doc = "minimum mapping quality for it to be considered usable",
+            shortName = "mmq", required = false)
+    public byte mappingThreshold = 20;
+
+    /**
+     * An average base quality above this value will rule out the possibility of context specific problems with the
+     * sequencer.
+     */
+    @Argument(doc = "minimum base quality for it to be considered usable",
+            shortName = "mbq", required = false)
+    public byte qualThreshold = 20;
+
+    /**
+     * Intervals that are too small generate biased analysis. For example an interval of size 1 will have GC content
+     * 1 or 0. To avoid misinterpreting small intervals, all intervals below this threshold will be ignored in the
+     * interpretation.
+     */
+    @Argument(doc = "minimum interval length to be considered",
+            shortName = "size", required = false)
+    public byte intervalSizeThreshold = 10;
+
+    enum Interpretation {
+        UNKNOWN,
+        UNMAPPABLE,
+        UNSEQUENCEABLE,
+        GCCONTENT,
+        NO_DATA,
+        SMALL_INTERVAL
+    }
+
     GATKReport simpleReport;
     GenomeLocSortedSet target;
     GenomeLocSortedSet cds;
@@ -130,7 +180,7 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
         if (cdsFile == null)
             cdsFile = targetsFile;
 
-        simpleReport = GATKReport.newSimpleReport("QualifyMissingIntervals", "IN", "GC", "BQ", "MQ", "DP", "TP", "CD", "LN");
+        simpleReport = GATKReport.newSimpleReport("QualifyMissingIntervals", "IN", "GC", "BQ", "MQ", "DP", "TP", "CD", "LN", "DS");
         final GenomeLocParser parser = getToolkit().getGenomeLocParser();
         target = new GenomeLocSortedSet(parser, IntervalUtils.intervalFileToList(parser, targetsFile));
         cds = new GenomeLocSortedSet(parser, IntervalUtils.intervalFileToList(parser, cdsFile));
@@ -184,7 +234,8 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
                     metrics.depth(),
                     getPositionInTarget(interval),
                     cds.overlaps(interval),
-                    interval.size()
+                    interval.size(),
+                    interpret(metrics, interval)
             );
         }
         simpleReport.print(out);
@@ -199,4 +250,43 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
         }
         return result;
     }
+
+    String interpret(final Metrics metrics, final GenomeLoc interval) {
+        if (interval.size() < intervalSizeThreshold) {
+            return Interpretation.SMALL_INTERVAL.toString();
+        }
+        else if (metrics.depth() == 0.0) {
+            return Interpretation.NO_DATA.toString();
+        }
+        return trim(checkMappability(metrics) + checkGCContent(metrics) + checkContext(metrics));
+    }
+
+    String checkMappability(Metrics metrics) {
+        return metrics.depth() >= coverageThreshold && metrics.mapQual() < mappingThreshold ?
+                Interpretation.UNMAPPABLE + ", " : "";
+    }
+
+    String checkGCContent(Metrics metrics) {
+        return metrics.depth() < coverageThreshold && (metrics.gccontent() < gcThreshold || metrics.gccontent() > 1.0-gcThreshold) ?
+                Interpretation.GCCONTENT + ", " : "";
+    }
+
+    String checkContext(Metrics metrics) {
+        return metrics.depth() < coverageThreshold && metrics.baseQual() < qualThreshold ?
+                Interpretation.UNSEQUENCEABLE + ", " : "";
+    }
+
+    String trim (String s) {
+        if (s.isEmpty())
+            return Interpretation.UNKNOWN.toString();
+
+        s = s.trim();
+        if (s.endsWith(","))
+            s = s.substring(0, s.length() - 1);
+        return s;
+    }
+
+
+
+
 }
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java
new file mode 100644
index 000000000..7d6d05736
--- /dev/null
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java
@@ -0,0 +1,95 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*  
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*  
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*  
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*  
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*  
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. 
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.  
+*  
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY 
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*  
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*  
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*  
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*  
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt. 
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. 
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.sting.gatk.walkers.diagnostics.missing;
+
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.UnvalidatingGenomeLoc;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+/**
+ * Created with IntelliJ IDEA.
+ * User: carneiro
+ * Date: 9/20/13
+ * Time: 3:59 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class QualifyMissingIntervalsUnitTest extends BaseTest {
+    @Test(enabled = true)
+    public void testInterpretation() {
+        final QualifyMissingIntervals tool = new QualifyMissingIntervals();
+
+        final Metrics unmappable = new Metrics(0.5, 7500.0, 0.0, 2500, 20);
+        final Metrics highGC = new Metrics(0.99, 0.0, 0.0, 0, 20);
+        final Metrics lowGC = new Metrics(0.09, 0.0, 0.0, 0, 20);
+        final Metrics unsequenceable = new Metrics(0.5, 3.0, 1200.0, 10, 20);
+        final Metrics noData = new Metrics(0.5, 0.0, 0.0, 0, 20);
+        final Metrics unknown = new Metrics(0.5, 30.0, 120000.0, 2500, 20);
+
+        final Metrics[] array = {unmappable, highGC, lowGC, unsequenceable, noData, unknown};
+
+        final GenomeLoc testInterval = new UnvalidatingGenomeLoc("chr1", 0, 10000, 20000);
+        final GenomeLoc smallInterval = new UnvalidatingGenomeLoc("chr1", 0, 1, 4);
+
+
+        Assert.assertNotEquals(tool.checkMappability(unmappable), "");
+        Assert.assertNotEquals(tool.checkGCContent(highGC), "");
+        Assert.assertNotEquals(tool.checkGCContent(lowGC), "");
+        Assert.assertNotEquals(tool.checkContext(unsequenceable), "");
+
+        Assert.assertEquals(tool.interpret(unmappable, testInterval), QualifyMissingIntervals.Interpretation.UNMAPPABLE.toString());
+        Assert.assertEquals(tool.interpret(noData, testInterval), QualifyMissingIntervals.Interpretation.NO_DATA.toString());
+        Assert.assertEquals(tool.interpret(noData, testInterval), QualifyMissingIntervals.Interpretation.NO_DATA.toString());
+        Assert.assertEquals(tool.interpret(noData, testInterval), QualifyMissingIntervals.Interpretation.NO_DATA.toString());
+        Assert.assertEquals(tool.interpret(noData, testInterval), QualifyMissingIntervals.Interpretation.NO_DATA.toString());
+        Assert.assertEquals(tool.interpret(unknown, testInterval), QualifyMissingIntervals.Interpretation.UNKNOWN.toString());
+
+        for (Metrics m : array)
+            Assert.assertEquals(tool.interpret(m, smallInterval), QualifyMissingIntervals.Interpretation.SMALL_INTERVAL.toString());
+    }
+}

From 5bbad75402424c80789aef5496ea5004c5d26c93 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Fri, 20 Sep 2013 18:54:01 -0400
Subject: [PATCH 14/77] Changing max coverage threshold

Because Integer.maxValue is not unit testable
---
 .../gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java
index c330b3f02..b088951e5 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java
@@ -77,7 +77,7 @@ final class ThresHolder {
      * If at any locus, a sample has more coverage than this, it will be reported as EXCESSIVE_COVERAGE
      */
     @Argument(fullName = "maximum_coverage", shortName = "max", doc = "The maximum allowable coverage, used for calling EXCESSIVE_COVERAGE", required = false)
-    public int maximumCoverage = Integer.MAX_VALUE;
+    public int maximumCoverage = Integer.MAX_VALUE / 2;
 
     /**
      * If any sample has a paired read whose distance between alignment starts (between the pairs) is greater than this, it will be reported as BAD_MATE

From b32ad99d3f63d1341ff7429f9bb203367e8937fd Mon Sep 17 00:00:00 2001
From: Louis Bergelson <louisb@broadinstitute.org>
Date: Tue, 27 Aug 2013 15:56:30 -0400
Subject: [PATCH 15/77] Changing from scala 2.9.2 to 2.10.2. --modified ivy
 dependencies --modified scala classpath in build.xml to include scala-reflect

--changed imports to point to the new scala scala.reflect.internal.util

--set the bootclasspath in QScriptManager as well as the classpath variable.

--removing Set[File] <-> Set[String] conversions
----Set is invariant now and the conversions broke
--removing unit tests for Set[File] <-> Set[String] conversions
---
 build.xml                                     |  1 +
 ivy.xml                                       |  4 +-
 .../sting/queue/QScriptManager.scala          |  8 +-
 .../queue/util/StringFileConversions.scala    | 22 ------
 .../util/StringFileConversionsUnitTest.scala  | 75 -------------------
 5 files changed, 8 insertions(+), 102 deletions(-)

diff --git a/build.xml b/build.xml
index 0844717dd..47472d33e 100644
--- a/build.xml
+++ b/build.xml
@@ -526,6 +526,7 @@
             <fileset dir="${lib.dir}">
                 <include name="scala-compiler-*.jar"/>
                 <include name="scala-library-*.jar"/>
+                <include name="scala-reflect-*.jar"/>
             </fileset>
         </path>
         <taskdef resource="scala/tools/ant/antlib.xml">
diff --git a/ivy.xml b/ivy.xml
index ed13af1c2..2e45247ab 100644
--- a/ivy.xml
+++ b/ivy.xml
@@ -82,8 +82,8 @@
         <dependency org="net.sf.gridscheduler" name="drmaa" rev="latest.integration"/>
 
         <!-- Scala dependancies -->
-        <dependency org="org.scala-lang" name="scala-compiler" rev="2.9.2"/>
-        <dependency org="org.scala-lang" name="scala-library" rev="2.9.2"/>
+        <dependency org="org.scala-lang" name="scala-compiler" rev="2.10.2"/>
+        <dependency org="org.scala-lang" name="scala-library" rev="2.10.2"/>
 
         <!-- testing and evaluation dependencies -->
         <dependency org="org.testng" name="testng" rev="6.8"/>
diff --git a/public/scala/src/org/broadinstitute/sting/queue/QScriptManager.scala b/public/scala/src/org/broadinstitute/sting/queue/QScriptManager.scala
index 37c4a5bbe..c6b8eff13 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/QScriptManager.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/QScriptManager.scala
@@ -33,10 +33,9 @@ import java.io.File
 import scala.tools.nsc.reporters.AbstractReporter
 import java.lang.String
 import org.apache.log4j.Level
-import scala.tools.nsc.util.{FakePos, NoPosition, Position}
 import org.broadinstitute.sting.queue.util.TextFormatUtils._
 import org.broadinstitute.sting.utils.classloader.JVMUtils
-import tools.util.StringOps
+import scala.reflect.internal.util.{FakePos, NoPosition, Position, StringOps}
 
 /**
  * Plugin manager for QScripts which loads QScripts into the current class loader.
@@ -53,7 +52,10 @@ class QScriptManager() extends Logging {
       settings.outdir.value = tempDir.getPath
 
       // Set the classpath to the current class path.
-      JVMUtils.getClasspathURLs.foreach(url => settings.classpath.append(url.getPath))
+      JVMUtils.getClasspathURLs.foreach(url => {
+          settings.bootclasspath.append(url.getPath)
+          settings.classpath.append(url.getPath)
+      })
 
       val reporter = new QScriptManager.Log4JReporter(settings)
 
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/StringFileConversions.scala b/public/scala/src/org/broadinstitute/sting/queue/util/StringFileConversions.scala
index 35f872848..8e8a87abe 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/util/StringFileConversions.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/util/StringFileConversions.scala
@@ -77,21 +77,6 @@ object StringFileConversions {
     })
   }
 
-  implicit def stringsAsFiles(x: Set[Comparable[_ >: File with String <: Comparable[_ >: File with String <: Comparable[_ >: File with String <: Serializable] with Serializable] with Serializable] with Serializable]): Set[File] = {
-    x.map(_ match {
-      case string: String => stringAsFile(string)
-      case file: File => file
-      case null => null
-    })
-  }
-
-  implicit def filesAsStrings(x: Set[Comparable[_ >: String with File <: Comparable[_ >: String with File <: Comparable[_ >: String with File <: Serializable] with Serializable] with Serializable] with Serializable]): Set[String] = {
-    x.map(_ match {
-      case file: File => fileAsString(file)
-      case string: String => string
-      case null => null
-    })
-  }
 }
 
 /**
@@ -124,11 +109,4 @@ trait StringFileConversions {
     StringFileConversions.filesAsStringsList(x)
   }
 
-  implicit def stringsAsFiles(x: Set[Comparable[_ >: File with String <: Comparable[_ >: File with String <: Comparable[_ >: File with String <: Serializable] with Serializable] with Serializable] with Serializable]): Set[File] = {
-    StringFileConversions.stringsAsFiles(x)
-  }
-
-  implicit def filesAsStrings(x: Set[Comparable[_ >: String with File <: Comparable[_ >: String with File <: Comparable[_ >: String with File <: Serializable] with Serializable] with Serializable] with Serializable]): Set[String] = {
-    StringFileConversions.filesAsStrings(x)
-  }
 }
diff --git a/public/scala/test/org/broadinstitute/sting/queue/util/StringFileConversionsUnitTest.scala b/public/scala/test/org/broadinstitute/sting/queue/util/StringFileConversionsUnitTest.scala
index 22a7a8a04..5ee02b8bc 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/util/StringFileConversionsUnitTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/util/StringFileConversionsUnitTest.scala
@@ -87,44 +87,6 @@ class StringFileConversionsUnitTest {
     Assert.assertEquals(strings, Seq(null, null))
   }
 
-  @Test
-  def testStringToFileSet() {
-    var files = Set(new File("foo"))
-    files += "bar"
-    Assert.assertEquals(files, Set(new File("foo"), new File("bar")))
-
-    files = Set(new File("foo"))
-    files += null.asInstanceOf[String]
-    Assert.assertEquals(files, Set(new File("foo"), null))
-
-    files = Set[File](null)
-    files += "foo"
-    Assert.assertEquals(files, Set(new File("foo"), null))
-
-    files = Set[File](null)
-    files += null.asInstanceOf[String]
-    Assert.assertEquals(files, Set(null))
-  }
-
-  @Test
-  def testFileToStringSet() {
-    var strings = Set("foo")
-    strings += new File("bar")
-    Assert.assertEquals(strings, Set("foo", "bar"))
-
-    strings = Set("foo")
-    strings += null.asInstanceOf[File]
-    Assert.assertEquals(strings, Set("foo", null))
-
-    strings = Set[String](null)
-    strings += new File("foo")
-    Assert.assertEquals(strings, Set("foo", null))
-
-    strings = Set[String](null)
-    strings += null.asInstanceOf[File]
-    Assert.assertEquals(strings, Set(null))
-  }
-
   @Test
   def testStringListToFileList() {
     var files = Seq(new File("foo"))
@@ -163,41 +125,4 @@ class StringFileConversionsUnitTest {
     Assert.assertEquals(strings, Seq(null, null))
   }
 
-  @Test
-  def testStringSetToFileSet() {
-    var files = Set(new File("foo"))
-    files ++= Set("bar")
-    Assert.assertEquals(files, Set(new File("foo"), new File("bar")))
-
-    files = Set(new File("foo"))
-    files ++= Set[String](null)
-    Assert.assertEquals(files, Set(new File("foo"), null))
-
-    files = Set[File](null)
-    files ++= Set("foo")
-    Assert.assertEquals(files, Set(new File("foo"), null))
-
-    files = Set[File](null)
-    files ++= Set[String](null)
-    Assert.assertEquals(files, Set(null))
-  }
-
-  @Test
-  def testFileSetToStringSet() {
-    var strings = Set("foo")
-    strings ++= Set(new File("bar"))
-    Assert.assertEquals(strings, Set("foo", "bar"))
-
-    strings = Set("foo")
-    strings ++= Set[File](null)
-    Assert.assertEquals(strings, Set("foo", null))
-
-    strings = Set[String](null)
-    strings ++= Set(new File("foo"))
-    Assert.assertEquals(strings, Set("foo", null))
-
-    strings = Set[String](null)
-    strings ++= Set[File](null)
-    Assert.assertEquals(strings, Set(null))
-  }
 }

From c05208ecec01bdc969d2b2a0bb547dad9999b77e Mon Sep 17 00:00:00 2001
From: Louis Bergelson <louisb@broadinstitute.org>
Date: Fri, 30 Aug 2013 16:43:21 -0400
Subject: [PATCH 16/77] Resolving warnings --specifying exception types in
 cases where none was already specified ----mostly changed to catch Exception
 instead of Throwable ----EmailMessage has a point where it should only be
 expecting a RetryException but was catching everything

--changing build.xml so that it prints scala feature warning details

--added necessary imports needed to remove feature warnings

--updating a newly deprecated enum declaration to match the new syntax
---
 build.xml                                                     | 4 ++--
 .../sting/queue/engine/drmaa/DrmaaJobRunner.scala             | 2 +-
 .../sting/queue/engine/lsf/Lsf706JobRunner.scala              | 2 +-
 .../sting/queue/engine/shell/ShellJobRunner.scala             | 4 ++--
 .../org/broadinstitute/sting/queue/function/QFunction.scala   | 1 +
 .../sting/queue/library/ipf/vcf/VCFExtractSamples.scala       | 2 +-
 .../org/broadinstitute/sting/queue/util/EmailMessage.scala    | 4 ++--
 .../sting/queue/util/PrimitiveOptionConversions.scala         | 2 ++
 .../scala/src/org/broadinstitute/sting/queue/util/Retry.scala | 2 +-
 .../sting/queue/util/StringFileConversions.scala              | 1 +
 .../broadinstitute/sting/queue/pipeline/PipelineTest.scala    | 4 ++--
 11 files changed, 16 insertions(+), 12 deletions(-)

diff --git a/build.xml b/build.xml
index 47472d33e..16cfa9a61 100644
--- a/build.xml
+++ b/build.xml
@@ -538,7 +538,7 @@
     <target name="scala.compile" depends="init,resolve,gatk.compile,queue-extensions.generate,init.scala.compile" if="include.scala">
         <mkdir dir="${scala.classes}"/>
         <echo>Building Scala...</echo>
-        <scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.classes}" classpathref="scala.dependencies" deprecation="yes" unchecked="yes">
+        <scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.classes}" classpathref="scala.dependencies" deprecation="yes" unchecked="yes" addparams="-feature">
             <src refid="scala.source.path" />
             <src path="${queue-extensions.source.dir}" />
             <include name="**/*.scala" />
@@ -1219,7 +1219,7 @@
 
     <target name="test.scala.compile" depends="test.java.compile,scala.compile" if="include.scala">
         <echo message="Scala: Compiling test cases!"/>
-        <scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.test.classes}" deprecation="yes" unchecked="yes">
+        <scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.test.classes}" deprecation="yes" unchecked="yes" addparams="-feature">
 	        <src refid="scala.test.source.path" />
             <classpath>
                 <path refid="build.results"/>
diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala b/public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala
index 9cfd69247..79fc8589f 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala
@@ -160,7 +160,7 @@ class DrmaaJobRunner(val session: Session, val function: CommandLineFunction) ex
           // resource of the designated queue to SIGTERM
           session.control(jobId, Session.TERMINATE)
         } catch {
-          case e =>
+          case e: Exception =>
             logger.error("Unable to kill job " + jobId, e)
         }
       }
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 1140c4945..ead29bbf5 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
@@ -361,7 +361,7 @@ object Lsf706JobRunner extends Logging {
           if (LibBat.lsb_signaljob(runner.jobId, SIGTERM) < 0)
             logger.error(LibBat.lsb_sperror("Unable to kill job " + runner.jobId))
         } catch {
-          case e =>
+          case e: Exception=>
             logger.error("Unable to kill job " + runner.jobId, e)
         }
       }
diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/shell/ShellJobRunner.scala b/public/scala/src/org/broadinstitute/sting/queue/engine/shell/ShellJobRunner.scala
index 13b3c7cb3..e3528f54f 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/engine/shell/ShellJobRunner.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/engine/shell/ShellJobRunner.scala
@@ -83,8 +83,8 @@ class ShellJobRunner(val function: CommandLineFunction) extends CommandLineJobRu
       try {
         controller.tryDestroy()
       } catch {
-        case e =>
-          logger.error("Unable to kill shell job: " + function.description)
+        case e: Exception =>
+          logger.error("Unable to kill shell job: " + function.description, e)
       }
     }
   }
diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala b/public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala
index 81c76dd29..abbb63271 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala
@@ -32,6 +32,7 @@ import org.broadinstitute.sting.queue.{QException, QSettings}
 import java.lang.IllegalStateException
 import org.broadinstitute.sting.queue.util._
 import org.broadinstitute.sting.utils.io.IOUtils
+import scala.language.reflectiveCalls
 
 /**
  * The base interface for all functions in Queue.
diff --git a/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSamples.scala b/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSamples.scala
index 6dcc69854..ddff95f21 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSamples.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSamples.scala
@@ -39,7 +39,7 @@ class VCFExtractSamples(inVCF: File, outVCF: File, samples: List[String]) extend
   @Argument(doc="The samples to extract from the VCF") var extractSamples : List[String] = samples
 
   var out : PrintWriter = _
-  var columns : List[Int] = 0 to 8 toList
+  var columns : List[Int] = (0 to 8).toList
 
   def run = {
     out = new PrintWriter(new PrintStream(outputVCF))
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/EmailMessage.scala b/public/scala/src/org/broadinstitute/sting/queue/util/EmailMessage.scala
index 4d3bf719c..96a5973be 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/util/EmailMessage.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/util/EmailMessage.scala
@@ -26,7 +26,7 @@
 package org.broadinstitute.sting.queue.util
 
 import org.apache.commons.mail.{MultiPartEmail, EmailAttachment}
-import java.io.{FileReader, File}
+import java.io.{IOException, FileReader, File}
 import javax.mail.internet.InternetAddress
 import scala.collection.JavaConversions._
 
@@ -105,7 +105,7 @@ class EmailMessage extends Logging {
     try {
       Retry.attempt(() => send(settings), .5)
     } catch {
-      case e => logger.error("Error sending message: %n%s".format(this.toString), e)
+      case e: RetryException=> logger.error("Error sending message: %n%s".format(this.toString), e)
     }
   }
 
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/PrimitiveOptionConversions.scala b/public/scala/src/org/broadinstitute/sting/queue/util/PrimitiveOptionConversions.scala
index 4acd27497..cb7b95b76 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/util/PrimitiveOptionConversions.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/util/PrimitiveOptionConversions.scala
@@ -25,6 +25,8 @@
 
 package org.broadinstitute.sting.queue.util
 
+import scala.language.implicitConversions
+
 /**
  * An importable object that provides automatic primitive to option conversion.
  */
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/Retry.scala b/public/scala/src/org/broadinstitute/sting/queue/util/Retry.scala
index b112ed9a3..5b9e42a1e 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/util/Retry.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/util/Retry.scala
@@ -49,7 +49,7 @@ object Retry extends Logging {
         result = f()
         success = true
       } catch {
-        case e => {
+        case e: Exception=> {
           count += 1
           if (count < tries) {
             val minutes = wait(count-1)
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/StringFileConversions.scala b/public/scala/src/org/broadinstitute/sting/queue/util/StringFileConversions.scala
index 8e8a87abe..ff99cb346 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/util/StringFileConversions.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/util/StringFileConversions.scala
@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.queue.util
 
 import java.io.{Serializable, File}
+import scala.language.implicitConversions
 
 /**
  * Converts String to/from File
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 e9a288117..251b1c511 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala
@@ -182,7 +182,7 @@ object PipelineTest extends BaseTest with Logging {
       println("Executing test %s with Queue arguments: %s".format(name, Utils.join(" ",command)))
       CommandLineProgram.start(instance, command)
     } catch {
-      case e =>
+      case e: Exception =>
         gotAnException = true
         if (expectedException != null) {
           // we expect an exception
@@ -224,7 +224,7 @@ object PipelineTest extends BaseTest with Logging {
         try {
           commandLine.shutdown()
         } catch {
-          case _ => /* ignore */
+          case _: Throwable => /* ignore */
         })
     }
   })

From d6992d12632c0cfc6b3bdf5b88872fb2d4625e41 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 23 Sep 2013 15:48:47 -0400
Subject: [PATCH 17/77] Updated docs to tell users not to use PCR indel error
 modeling for PCR free data.

---
 .../sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java      | 1 +
 1 file changed, 1 insertion(+)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
index 8776a5e4b..360d0979f 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
@@ -475,6 +475,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
     /**
      * Which PCR indel error model should we use when calculating likelihoods?  If NONE is selected, then the default base
      * insertion/deletion qualities will be used (or taken from the read if generated through the BaseRecalibrator).
+     * VERY IMPORTANT: when using PCR-free sequencing data we definitely recommend setting this argument to NONE.
      */
     @Advanced
     @Argument(fullName = "pcr_indel_model", shortName = "pcrModel", doc = "The PCR indel model to use", required = false)

From 2783c84c6b68b289d31ae16549492db92a8927a4 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 24 Sep 2013 22:32:19 -0400
Subject: [PATCH 18/77] Updated docs for DepthPerSampleHC to deliver PT
 #54237024.

---
 .../gatk/walkers/annotator/DepthPerSampleHC.java  | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerSampleHC.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerSampleHC.java
index 9bd641011..21325e6f1 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerSampleHC.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerSampleHC.java
@@ -51,7 +51,6 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@@ -68,11 +67,15 @@ import java.util.*;
 
 
 /**
- * The depth of coverage of each allele per sample
+ * The depth of coverage for informative reads for each sample.
  *
- * the depth for the HC is the sum of the informative alleles at this site.  It's not perfect (as we cannot
- * differentiate between reads that align over the event but aren't informative vs. those that aren't even
- * close) but it's a pretty good proxy and it matches with the AD field (i.e., sum(AD) = DP).
+ * An informative read is defined as one from which the allele it carries can be easily distinguished.  An example of a
+ * case where a read might be uninformative is where it only partially overlaps a short tandem repeat and it is not clear
+ * whether the read contains the reference allele or e.g. an extra repeat.
+ * The depth here is the sum of the informative reads at this site as determined by the Haplotype Caller; as such it can
+ * only be calculated and generated through the Haplotype Caller (it will not work when run through the Variant Annotator).
+ * This calculation is not perfect but it is a pretty good proxy for depth and it does match the values in the AD field
+ * (i.e., sum(AD) = DP).
  */
 public class DepthPerSampleHC extends GenotypeAnnotation {
     public void annotate(final RefMetaDataTracker tracker,
@@ -121,6 +124,6 @@ public class DepthPerSampleHC extends GenotypeAnnotation {
     }
 
     public List<VCFFormatHeaderLine> getDescriptions() {
-        return Collections.singletonList(VCFStandardHeaderLines.getFormatLine(getKeyNames().get(0)));
+        return Collections.singletonList(VCFStandardHeaderLines.getFormatLine(VCFConstants.DEPTH_KEY));
     }
 }
\ No newline at end of file

From 5113e21437b9a69f99bdea49fa80854d8ab090e7 Mon Sep 17 00:00:00 2001
From: Michael McCowan <mccowan@broadinstitute.org>
Date: Mon, 23 Sep 2013 14:26:24 -0400
Subject: [PATCH 20/77] Bug fix: annotation values ar parsed as Doubles when
 they should be parsed as Integers due to implicit conversion. * Updated
 expected test data in which an integer annotation (MQ0) was formatted as a
 double.

---
 .../variantutils/CombineVariantsIntegrationTest.java        | 2 +-
 .../sting/utils/variant/GATKVariantContextUtils.java        | 6 +++++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
index 66bc74caa..2eeb9221e 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
@@ -194,7 +194,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
                         " --excludeNonVariants -combineAnnotations -setKey null" +
                         " -L 20:10,000,000-10,001,000", b37KGReference),
                 1,
-                Arrays.asList("2e15db35359144683f1e58e147362679"));
+                Arrays.asList("0413f0725fc5ec3a4f1ee246f6cb3a2a"));
         cvExecuteTest("combineSingleSamplePipelineGVCF", spec, true);
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
index e8c438a53..11cd27a9f 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
@@ -891,7 +891,11 @@ public class GATKVariantContextUtils {
                     }
                     try {
                         final String stringValue = value.toString();
-                        values.add(stringValue.contains(".") ? Double.parseDouble(stringValue) : Integer.parseInt(stringValue));
+                        // Branch to avoid unintentional, implicit type conversions that occur with the ? operator.
+                        if (stringValue.contains("."))
+                            values.add(Double.parseDouble(stringValue));
+                        else 
+                            values.add(Integer.parseInt(stringValue));
                     } catch (NumberFormatException e) {
                         badAnnotation = true;
                     }

From 27808d336af0745500f050b4f8150eb2c9e4b3d2 Mon Sep 17 00:00:00 2001
From: Geraldine Van der Auwera <vdauwera@broadinstitute.org>
Date: Thu, 26 Sep 2013 13:13:53 -0400
Subject: [PATCH 21/77] Minor clarifications regarding ignoreFilter argument

---
 .../walkers/variantrecalibration/ApplyRecalibration.java     | 5 ++++-
 .../walkers/variantrecalibration/VariantRecalibrator.java    | 5 ++++-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
index 3ae68edab..314efe2a2 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
@@ -136,7 +136,10 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> implements T
     /////////////////////////////
     @Argument(fullName="ts_filter_level", shortName="ts_filter_level", doc="The truth sensitivity level at which to start filtering", required=false)
     protected double TS_FILTER_LEVEL = 99.0;
-    @Argument(fullName="ignore_filter", shortName="ignoreFilter", doc="If specified the variant recalibrator will use variants even if the specified filter name is marked in the input VCF file", required=false)
+    /**
+     * For this to work properly, the -ignoreFilter argument should also be applied to the VariantRecalibration command.
+     */
+    @Argument(fullName="ignore_filter", shortName="ignoreFilter", doc="If specified, the recalibration will be applied to variants marked as filtered by the specified filter name in the input VCF file", required=false)
     private String[] IGNORE_INPUT_FILTERS = null;
     @Argument(fullName="excludeFiltered", shortName="ef", doc="Don't output filtered loci after applying the recalibration", required=false)
     protected boolean EXCLUDE_FILTERED = false;
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index 5a8debc72..1ee02d10d 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -201,7 +201,10 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
      */
     @Argument(fullName="TStranche", shortName="tranche", doc="The levels of novel false discovery rate (FDR, implied by ti/tv) at which to slice the data. (in percent, that is 1.0 for 1 percent)", required=false)
     private double[] TS_TRANCHES = new double[] {100.0, 99.9, 99.0, 90.0};
-    @Argument(fullName="ignore_filter", shortName="ignoreFilter", doc="If specified the variant recalibrator will use variants even if the specified filter name is marked in the input VCF file", required=false)
+    /**
+     * For this to work properly, the -ignoreFilter argument should also be applied to the ApplyRecalibration command.
+     */
+    @Argument(fullName="ignore_filter", shortName="ignoreFilter", doc="If specified, the variant recalibrator will also use variants marked as filtered by the specified filter name in the input VCF file", required=false)
     private String[] IGNORE_INPUT_FILTERS = null;
     @Output(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, defaultToStdout=false)
     private File RSCRIPT_FILE = null;

From 66d0235efcd858dbc915f59960bf8acd9fb1659f Mon Sep 17 00:00:00 2001
From: Geraldine Van der Auwera <vdauwera@broadinstitute.org>
Date: Thu, 26 Sep 2013 14:28:22 -0400
Subject: [PATCH 22/77] Minor clarifications & formatting tweaks for dcov docs

---
 .../arguments/GATKArgumentCollection.java     | 26 ++++++++++++-------
 1 file changed, 17 insertions(+), 9 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
index 174e434fe..e1620c938 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
@@ -119,21 +119,29 @@ public class GATKArgumentCollection {
     // Downsampling Arguments
     //
     // --------------------------------------------------------------------------------------------------------------
-    @Argument(fullName = "downsampling_type", shortName="dt", doc="Type of reads downsampling to employ at a given locus.  Reads will be selected randomly to be removed from the pile based on the method described here", required = false)
+    /**
+     * Reads will be selected randomly to be removed from the pile based on the method described here.
+     */
+    @Argument(fullName = "downsampling_type", shortName="dt", doc="Type of reads downsampling to employ at a given locus", required = false)
     public DownsampleType downsamplingType = null;
 
     @Argument(fullName = "downsample_to_fraction", shortName = "dfrac", doc = "Fraction [0.0-1.0] of reads to downsample to", required = false)
     public Double downsampleFraction = null;
 
+    /**
+     * For locus-based traversals (eg., LocusWalkers and ActiveRegionWalkers), downsample_to_coverage controls the
+     * maximum depth of coverage at each locus. For non-locus-based traversals (eg., ReadWalkers), this controls the
+     * maximum number of reads sharing the same alignment start position. Note that for ReadWalkers, since -dcov controls
+     * the maximum number of reads sharing the same alignment start position, you will typically need to use much lower
+     * dcov values than you would with LocusWalkers to see an effect. Note also that this downsampling option does NOT
+     * produce an unbiased random sampling from all available reads at each locus: instead, the primary goal of the
+     * to-coverage downsampler is to maintain an even representation of reads from all alignment start positions when
+     * removing excess coverage. For a true across-the-board unbiased random sampling of reads, use -dfrac instead. Also
+     * note that the coverage target is an approximate goal that is not guaranteed to be met exactly: the downsampling
+     * algorithm will under some circumstances retain slightly more coverage than requested.
+     */
     @Argument(fullName = "downsample_to_coverage", shortName = "dcov",
-              doc = "Coverage [integer] to downsample to. For locus-based traversals (eg., LocusWalkers and ActiveRegionWalkers)," +
-                    "this controls the maximum depth of coverage at each locus. For non-locus-based traversals (eg., ReadWalkers), " +
-                    "this controls the maximum number of reads sharing the same alignment start position. Note that this downsampling " +
-                    "option does NOT produce an unbiased random sampling from all available reads at each locus: instead, the primary goal of " +
-                    "the to-coverage downsampler is to maintain an even representation of reads from all alignment start positions " +
-                    "when removing excess coverage. For a true across-the-board unbiased random sampling of reads, use -dfrac instead. " +
-                    "Also note that the coverage target is an approximate goal that is not guaranteed to be met exactly: the downsampling " +
-                    "algorithm will under some circumstances retain slightly more coverage than requested.",
+              doc = "Coverage [integer] to downsample to",
               required = false)
     public Integer downsampleCoverage = null;
 

From 511948890a4b72f7a9a6c33579f2c66555c46ae6 Mon Sep 17 00:00:00 2001
From: Geraldine Van der Auwera <vdauwera@broadinstitute.org>
Date: Thu, 26 Sep 2013 14:50:32 -0400
Subject: [PATCH 23/77] Modify gatkdoc template to handle downsampling info
 better

---
 settings/helpTemplates/generic.template.html | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/settings/helpTemplates/generic.template.html b/settings/helpTemplates/generic.template.html
index 098d294cb..b78bba48c 100644
--- a/settings/helpTemplates/generic.template.html
+++ b/settings/helpTemplates/generic.template.html
@@ -174,11 +174,16 @@
 		</#if>
 		<#if downsampling?size != 0>
 			<h3>Downsampling settings</h3>
-			<p>This tool overrides the engine's default downsampling settings.</p>
-			<ul>
-				<li>Mode: <b>${downsampling.by}</b></li>
-				<li>To coverage: <b>${downsampling.to_cov}</b></li>
-			</ul>
+			<#if downsampling.by == "NONE">
+				<p>This tool does not apply any downsampling by default.</p>
+			</#if>
+			<#if downsampling.by != "NONE">
+				<p>This tool applies the following downsampling settings by default.</p>
+				<ul>
+					<li>Mode: <b>${downsampling.by}</b></li>
+					<li>To coverage: <b>${downsampling.to_cov}</b></li>
+				</ul>
+			</#if>
 		</#if>
 		<#if refwindow?size != 0>
 			<h3>Window size</h3>

From ef1d58b7ff42d8fb340bb16487f127d0f8b1c26f Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Fri, 27 Sep 2013 11:24:35 -0400
Subject: [PATCH 24/77] Bugfix for hom ref records that aren't GVCF blocks.

---
 .../genotyper/UnifiedGenotyperEngine.java     |  2 +-
 .../sting/utils/gvcf/GVCFWriter.java          |  5 +++-
 .../sting/utils/gvcf/GVCFWriterUnitTest.java  | 29 +++++++++++++++++++
 3 files changed, 34 insertions(+), 2 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index ec31e1f2f..5c6e9dc01 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -374,7 +374,7 @@ public class UnifiedGenotyperEngine {
                                                  final VariantContext vc,
                                                  final GenotypeLikelihoodsCalculationModel.Model model,
                                                  final Map<String, org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
-        return calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model, false,perReadAlleleLikelihoodMap);
+        return calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model, false, perReadAlleleLikelihoodMap);
     }
 
     /**
diff --git a/protected/java/src/org/broadinstitute/sting/utils/gvcf/GVCFWriter.java b/protected/java/src/org/broadinstitute/sting/utils/gvcf/GVCFWriter.java
index 8ee3c166c..98aedf786 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/gvcf/GVCFWriter.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/gvcf/GVCFWriter.java
@@ -46,6 +46,9 @@
 
 package org.broadinstitute.sting.utils.gvcf;
 
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.ReferenceConfidenceModel;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
 import org.broadinstitute.variant.variantcontext.Genotype;
 import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
 import org.broadinstitute.variant.variantcontext.VariantContext;
@@ -284,7 +287,7 @@ public class GVCFWriter implements VariantContextWriter {
             }
 
             final Genotype g = vc.getGenotype(0);
-            if ( g.isHomRef() ) {
+            if ( g.isHomRef() && vc.hasAlternateAllele(GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE) ) {
                 // create bands
                 final VariantContext maybeCompletedBand = addHomRefSite(vc, g);
                 if ( maybeCompletedBand != null ) underlyingWriter.add(maybeCompletedBand);
diff --git a/protected/java/test/org/broadinstitute/sting/utils/gvcf/GVCFWriterUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/gvcf/GVCFWriterUnitTest.java
index e353739e5..5c14c490e 100644
--- a/protected/java/test/org/broadinstitute/sting/utils/gvcf/GVCFWriterUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/utils/gvcf/GVCFWriterUnitTest.java
@@ -129,6 +129,16 @@ public class GVCFWriterUnitTest extends BaseTest {
         return vcb.genotypes(gb.make()).make();
     }
 
+    private VariantContext makeHomRefAlt(final String contig, final int start, final int GQ) {
+        final VariantContextBuilder vcb = new VariantContextBuilder("test", contig, start, start, Arrays.asList(REF, ALT));
+        final GenotypeBuilder gb = new GenotypeBuilder(SAMPLE_NAME, Arrays.asList(REF, REF));
+        gb.GQ(GQ);
+        gb.DP(10);
+        gb.AD(new int[]{1, 2});
+        gb.PL(new int[]{0, 10, 100});
+        return vcb.genotypes(gb.make()).make();
+    }
+
     private VariantContext makeNonRef(final String contig, final int start, final int GQ) {
         final VariantContextBuilder vcb = new VariantContextBuilder("test", contig, start, start, Arrays.asList(REF, ALT));
         final GenotypeBuilder gb = new GenotypeBuilder(SAMPLE_NAME, Arrays.asList(REF, ALT));
@@ -305,6 +315,25 @@ public class GVCFWriterUnitTest extends BaseTest {
         assertGoodVC(mockWriter.emitted.get(2), "20", 6, 7, false);
     }
 
+    @Test
+    public void testHomRefAlt() {
+        final GVCFWriter writer = new GVCFWriter(mockWriter, standardPartition);
+
+        writer.add(makeHomRef("20", 1, 0));
+        writer.add(makeHomRef("20", 2, 0));
+        writer.add(makeHomRefAlt("20", 3, 0));
+        writer.add(makeHomRef("20", 4, 0));
+        writer.add(makeHomRef("20", 5, 0));
+        writer.add(makeHomRef("20", 6, 0));
+        writer.add(makeHomRef("20", 7, 0));
+        writer.close();
+        Assert.assertEquals(mockWriter.emitted.size(), 3);
+        assertGoodVC(mockWriter.emitted.get(0), "20", 1, 2, false);
+        Assert.assertFalse(mockWriter.emitted.get(1).hasAttribute("END"));
+        Assert.assertFalse(mockWriter.emitted.get(1).hasAttribute("BLOCK_SIZE"));
+        assertGoodVC(mockWriter.emitted.get(2), "20", 4, 7, false);
+    }
+
     @DataProvider(name = "BandPartitionData")
     public Object[][] makeBandPartitionData() {
         List<Object[]> tests = new ArrayList<>();

From 9f7fa247f67e3cd33f26c3e1cf2848c35bd479e3 Mon Sep 17 00:00:00 2001
From: Geraldine Van der Auwera <vdauwera@broadinstitute.org>
Date: Thu, 26 Sep 2013 16:04:08 -0400
Subject: [PATCH 25/77] Disable VQSR tranche plots in INDEL mode

---
 .../VariantRecalibrator.java                  | 21 ++++++++++++-------
 1 file changed, 13 insertions(+), 8 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index 1ee02d10d..c3f575022 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -181,7 +181,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     /**
      * The expected transition / transversion ratio of true novel variants in your targeted region (whole genome, exome, specific
      * genes), which varies greatly by the CpG and GC content of the region. See expected Ti/Tv ratios section of the GATK best
-     * practices documentation (http://www.broadinstitute.org/gatk/guide/topic?name=best-practices) for more information.
+     * practices documentation (http://www.broadinstitute.org/gatk/guide/best-practices) for more information.
      * Normal values are 2.15 for human whole genome values and 3.2 for human whole exomes. Note
      * that this parameter is used for display purposes only and isn't used anywhere in the algorithm!
      */
@@ -371,13 +371,18 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
             createVisualizationScript( dataManager.getRandomDataForPlotting( 6000 ), goodModel, badModel, lodCutoff, dataManager.getAnnotationKeys().toArray(new String[USE_ANNOTATIONS.length]) );
         }
 
-        // Execute the RScript command to plot the table of truth values
-        RScriptExecutor executor = new RScriptExecutor();
-        executor.addScript(new Resource(PLOT_TRANCHES_RSCRIPT, VariantRecalibrator.class));
-        executor.addArgs(TRANCHES_FILE.getAbsoluteFile(), TARGET_TITV);
-        // Print out the command line to make it clear to the user what is being executed and how one might modify it
-        logger.info("Executing: " + executor.getApproximateCommandLine());
-        executor.exec();
+        if(VRAC.MODE == VariantRecalibratorArgumentCollection.Mode.INDEL) {
+            // Print out an info message to make it clear why the tranches plot is not generated
+            logger.info("Tranches plot will not be generated since we are running in INDEL mode");
+        } else {
+            // Execute the RScript command to plot the table of truth values
+            RScriptExecutor executor = new RScriptExecutor();
+            executor.addScript(new Resource(PLOT_TRANCHES_RSCRIPT, VariantRecalibrator.class));
+            executor.addArgs(TRANCHES_FILE.getAbsoluteFile(), TARGET_TITV);
+            // Print out the command line to make it clear to the user what is being executed and how one might modify it
+            logger.info("Executing: " + executor.getApproximateCommandLine());
+            executor.exec();
+        }
     }
 
     private void createVisualizationScript( final ExpandingArrayList<VariantDatum> randomData, final GaussianMixtureModel goodModel, final GaussianMixtureModel badModel, final double lodCutoff, final String[] annotationKeys ) {

From 839b918f58fdc31a03d59d40f161ddbe30c3d4e7 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Mon, 9 Sep 2013 16:10:39 -0400
Subject: [PATCH 26/77] Length metric updates to QualifyMissingIntervals

   * add a length of the overlaping interval metric as per CSER request
   * standardized the distance metrics to be positive when fully  overlapping and the longest off-target tail (as a negative number)  when not overlapping
   * add gatkdocs to the tool (finally!)
---
 .../missing/QualifyMissingIntervals.java      | 64 +++++++++++++++----
 1 file changed, 51 insertions(+), 13 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
index 8cc7bb8f3..9fabd6a37 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
@@ -76,10 +76,12 @@ import java.util.List;
  * <ul>
  *     <li>Average Base Quality</li>
  *     <li>Average Mapping Quality</li>
+ *     <li>Average Depth</li>
  *     <li>GC Content</li>
- *     <li>Position in the target</li>
- *     <li>Coding Sequence / Intron</li>
- *     <li>Length of the uncovered area</li>
+ *     <li>Position in the target (Integer.MIN_VALUE if no overlap)</li>
+ *     <li>Length of the overlapping target (zero if no overlap)</li>
+ *     <li>Coding Sequence / Intron (optional)</li>
+ *     <li>Length of the uncovered interval</li>
  * </ul>
  *
  * <h3>Input</h3>
@@ -89,7 +91,7 @@ import java.util.List;
  *
  * <h3>Output</h3>
  * <p>
- *  GC content calculations per interval.
+ *  GC content, distance from the end of the target, coding sequence intersection, mapping and base quality averages and average depth per "missing" interval.
  * </p>
  *
  * <h3>Example</h3>
@@ -108,12 +110,24 @@ import java.util.List;
 @DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
 @By(DataSource.REFERENCE)
 public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics> implements NanoSchedulable {
+    /**
+     * A single GATKReport table with the qualifications on why the intervals passed by the -L argument were missing.
+     */
     @Output
     protected PrintStream out;
 
+    /**
+     * List of targets used in the experiment. This file will be used to calculate the distance your missing
+     * intervals are to the targets (usually exons). Typically this is your hybrid selection targets file
+     * (e.g. Agilent exome target list)
+     */
     @Argument(shortName = "targets", required = true)
     public String targetsFile;
 
+    /**
+     * List of coding sequence intervals (exons) if different from the targets file, to distinguish intervals
+     * that overlap the cds and intervals that don't.
+     */
     @Argument(shortName = "cds", required = false)
     public String cdsFile = null;
 
@@ -224,15 +238,18 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
 
     public void onTraversalDone(List<Pair<GenomeLoc, Metrics>> results) {
         for (Pair<GenomeLoc, Metrics> r : results) {
-            GenomeLoc interval = r.getFirst();
-            Metrics metrics = r.getSecond();
+            final GenomeLoc interval = r.getFirst();
+            final Metrics metrics = r.getSecond();
+            final List<GenomeLoc> overlappingIntervals = target.getOverlapping(interval);
+
             simpleReport.addRow(
                     interval.toString(),
                     metrics.gccontent(),
                     metrics.baseQual(),
                     metrics.mapQual(),
                     metrics.depth(),
-                    getPositionInTarget(interval),
+                    getPositionInTarget(interval, overlappingIntervals),
+                    getTargetSize(overlappingIntervals),
                     cds.overlaps(interval),
                     interval.size(),
                     interpret(metrics, interval)
@@ -242,13 +259,34 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
         out.close();
     }
 
-    private int getPositionInTarget(GenomeLoc interval) {
-        final List<GenomeLoc> hits = target.getOverlapping(interval);
-        int result = 0;
-        for (GenomeLoc hit : hits) {
-            result = interval.getStart() - hit.getStart(); // if there are multiple hits, we'll get the last one.
+    private int getPositionInTarget(final GenomeLoc interval, final List<GenomeLoc> hits) {
+        if (hits.size() > 0) {
+            final GenomeLoc hit = hits.get(0);
+
+            // interval is larger on both ends than the target -- return the maximum distance to either side as a negative number. (min of 2 negative numbers)
+            if (interval.getStart() < hit.getStart() && interval.getStop() > hit.getStop())
+                return Math.min(interval.getStart() - hit.getStart(),
+                                interval.getStop() - hit.getStop());
+
+            // interval is a left overlap -- return a negative number representing the distance between the two starts
+            else if (interval.getStart() < hit.getStart())
+                return hit.getStart() - interval.getStart();
+
+            // interval is a right overlap -- return a negative number representing the distance between the two stops
+            else if (interval.getStop() > hit.getStop())
+                return hit.getStop() - interval.getStop();
+
+            // interval is fully contained -- return the smallest distance to the edge of the target (left or right) as a positive number
+            else
+                return Math.min(Math.abs(hit.getStart() - interval.getStart()),
+                                Math.abs(hit.getStop() - interval.getStop()));
         }
-        return result;
+        // if there is no overlapping interval, return int min value.
+        return Integer.MIN_VALUE;
+    }
+
+    private int getTargetSize(final List<GenomeLoc> overlappingIntervals) {
+        return overlappingIntervals.size() > 0 ? overlappingIntervals.get(0).size() : -1;
     }
 
     String interpret(final Metrics metrics, final GenomeLoc interval) {

From 63ace685c90d4973c6cb144095db8502e8f602e9 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Tue, 10 Sep 2013 10:59:27 -0400
Subject: [PATCH 27/77] add unit tests

---
 .../missing/QualifyMissingIntervals.java      | 23 +++++------
 .../QualifyMissingIntervalsUnitTest.java      | 38 ++++++++++++++++++-
 2 files changed, 47 insertions(+), 14 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
index 9fabd6a37..014ed6dcb 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
@@ -259,27 +259,24 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
         out.close();
     }
 
-    private int getPositionInTarget(final GenomeLoc interval, final List<GenomeLoc> hits) {
-        if (hits.size() > 0) {
-            final GenomeLoc hit = hits.get(0);
+    protected static int getPositionInTarget(final GenomeLoc interval, final List<GenomeLoc> targets) {
+        if (targets.size() > 0) {
+            final GenomeLoc target = targets.get(0);
 
             // interval is larger on both ends than the target -- return the maximum distance to either side as a negative number. (min of 2 negative numbers)
-            if (interval.getStart() < hit.getStart() && interval.getStop() > hit.getStop())
-                return Math.min(interval.getStart() - hit.getStart(),
-                                interval.getStop() - hit.getStop());
+            if (interval.getStart() < target.getStart() && interval.getStop() > target.getStop())
+                return Math.min(target.getStart() - interval.getStart(), target.getStop() - interval.getStop());
 
             // interval is a left overlap -- return a negative number representing the distance between the two starts
-            else if (interval.getStart() < hit.getStart())
-                return hit.getStart() - interval.getStart();
+            else if (interval.getStart() < target.getStart())
+                return interval.getStart() - target.getStart();
 
             // interval is a right overlap -- return a negative number representing the distance between the two stops
-            else if (interval.getStop() > hit.getStop())
-                return hit.getStop() - interval.getStop();
+            else if (interval.getStop() > target.getStop())
+                return target.getStop() - interval.getStop();
 
             // interval is fully contained -- return the smallest distance to the edge of the target (left or right) as a positive number
-            else
-                return Math.min(Math.abs(hit.getStart() - interval.getStart()),
-                                Math.abs(hit.getStop() - interval.getStop()));
+            return Math.min(interval.getStart() - target.getStart(), target.getStop() - interval.getStop());
         }
         // if there is no overlapping interval, return int min value.
         return Integer.MIN_VALUE;
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java
index 7d6d05736..7ab891bd0 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java
@@ -46,6 +46,8 @@
 
 package org.broadinstitute.sting.gatk.walkers.diagnostics.missing;
 
+import it.unimi.dsi.fastutil.objects.ObjectArrayList;
+import java.util.List;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.UnvalidatingGenomeLoc;
@@ -57,7 +59,6 @@ import org.testng.annotations.Test;
  * User: carneiro
  * Date: 9/20/13
  * Time: 3:59 PM
- * To change this template use File | Settings | File Templates.
  */
 public class QualifyMissingIntervalsUnitTest extends BaseTest {
     @Test(enabled = true)
@@ -92,4 +93,39 @@ public class QualifyMissingIntervalsUnitTest extends BaseTest {
         for (Metrics m : array)
             Assert.assertEquals(tool.interpret(m, smallInterval), QualifyMissingIntervals.Interpretation.SMALL_INTERVAL.toString());
     }
+
+    @Test(enabled = true)
+    void testGetPositionInTarget () {
+        final UnvalidatingGenomeLoc target = new UnvalidatingGenomeLoc("a", 0, 30, 50);
+        final List<GenomeLoc> targets = new ObjectArrayList<>(1);
+        targets.add(target);
+
+        // left overlap
+        UnvalidatingGenomeLoc interval = new UnvalidatingGenomeLoc("a", 0, 10, 50);
+        Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, targets), -20);
+
+        // right overlap
+        interval = new UnvalidatingGenomeLoc("a", 0, 40, 60);
+        Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, targets), -10);
+
+        // interval > target with short right tail
+        interval = new UnvalidatingGenomeLoc("a", 0, 10, 60);
+        Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, targets), -10);
+
+        // interval > target with short left tail
+        interval = new UnvalidatingGenomeLoc("a", 0, 10, 80);
+        Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, targets), -30);
+
+        // interval < target with short right tail
+        interval = new UnvalidatingGenomeLoc("a", 0, 32, 40);
+        Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, targets), 2);
+
+        // interval < target with short left tail
+        interval = new UnvalidatingGenomeLoc("a", 0, 40, 42);
+        Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, targets), 8);
+
+        // no overlap
+        interval = new UnvalidatingGenomeLoc("a", 0, 40, 42);
+        Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, new ObjectArrayList<GenomeLoc>()), Integer.MIN_VALUE);
+    }
 }

From 5d6421494b201d903881590a17211a028e42c704 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Wed, 9 Oct 2013 14:38:15 -0400
Subject: [PATCH 32/77] Fix mismatching number of columns in report

Quick fix the missing column header in the QualifyMissingIntervals
report.

Adding a QScript for the tool as well as a few minor updates to the
GATKReportGatherer.
---
 .../diagnostics/missing/QualifyMissingIntervals.java  | 11 ++++++-----
 .../sting/gatk/report/GATKReportGatherer.java         |  8 +++-----
 2 files changed, 9 insertions(+), 10 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
index 014ed6dcb..52a92d9ff 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
@@ -47,16 +47,15 @@
 package org.broadinstitute.sting.gatk.walkers.diagnostics.missing;
 
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Gather;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 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.report.GATKReport;
-import org.broadinstitute.sting.gatk.walkers.By;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.gatk.walkers.NanoSchedulable;
+import org.broadinstitute.sting.gatk.report.GATKReportGatherer;
+import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
@@ -109,10 +108,12 @@ import java.util.List;
  */
 @DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
 @By(DataSource.REFERENCE)
+@PartitionBy(PartitionType.INTERVAL)
 public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics> implements NanoSchedulable {
     /**
      * A single GATKReport table with the qualifications on why the intervals passed by the -L argument were missing.
      */
+    @Gather(GATKReportGatherer.class)
     @Output
     protected PrintStream out;
 
@@ -194,7 +195,7 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
         if (cdsFile == null)
             cdsFile = targetsFile;
 
-        simpleReport = GATKReport.newSimpleReport("QualifyMissingIntervals", "IN", "GC", "BQ", "MQ", "DP", "TP", "CD", "LN", "DS");
+        simpleReport = GATKReport.newSimpleReport("QualifyMissingIntervals", "IN", "GC", "BQ", "MQ", "DP", "TP", "TS", "CD", "LN", "DS");
         final GenomeLocParser parser = getToolkit().getGenomeLocParser();
         target = new GenomeLocSortedSet(parser, IntervalUtils.intervalFileToList(parser, targetsFile));
         cds = new GenomeLocSortedSet(parser, IntervalUtils.intervalFileToList(parser, cdsFile));
diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportGatherer.java b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportGatherer.java
index e9ccebf34..5e7c3ec86 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportGatherer.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportGatherer.java
@@ -42,23 +42,21 @@ public class GATKReportGatherer extends Gatherer {
         try {
             o = new PrintStream(output);
         } catch (FileNotFoundException e) {
-            throw new UserException("File to be output by CoverageByRG Gather function was not found");
+            throw new UserException(String.format("File %s to be output by GATKReportGatherer function was not found", output));
         }
 
         GATKReport current = new GATKReport();
         boolean isFirst = true;
         for (File input : inputs) {
-
-            // If the table is empty
             if (isFirst) {
                 current = new GATKReport(input);
                 isFirst = false;
             } else {
-                GATKReport toAdd = new GATKReport(input);
-                current.concat(toAdd);
+                current.concat(new GATKReport(input));
             }
         }
 
         current.print(o);
+        o.close();
     }
 }

From efbfdb64fed48c27bd052812ecec483124946945 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Mon, 19 Aug 2013 23:52:23 -0400
Subject: [PATCH 33/77] Qscript to Downsample and analyze an exome BAM

this script downsamples an exome BAM several times and makes a coverage distribution
analysis (of bases that pass filters) as well as haplotype caller calls with a NA12878
Knowledge Base assessment with comparison against multi-sample calling
with the UG.

This script was used for the "downsampling the exome" presentation
---
 .../sting/queue/util/QScriptUtils.scala         | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 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 7b0e5d1be..b078bcd4f 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala
@@ -79,8 +79,23 @@ object QScriptUtils {
       if (sample.isEmpty)
         sample = r.getSample
       else if (sample != r.getSample)
-          return true;
+          return true
     }
     false
   }
+
+  /**
+   * Returns all distinct samples in the BAM file
+   *
+   * @param bam the bam file
+   * @return    a set with all distinct samples (in no particular order)
+   */
+  def getSamplesFromBAM(bam: File) : Set[String] = {
+    val reader = new SAMFileReader(bam)
+    var samples: Set[String] = Set()
+    for (rg <- reader.getFileHeader.getReadGroups) {
+      samples += rg.getSample
+    }
+    samples
+  }
 }

From 5a2ef37ead2360bb87f4d74feb225cdffae54e1f Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Wed, 16 Oct 2013 15:24:33 -0400
Subject: [PATCH 36/77] Tweak dcov documentation to help prevent user confusion

Geraldine-approved!
---
 .../arguments/GATKArgumentCollection.java     | 19 +++++++++----------
 1 file changed, 9 insertions(+), 10 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
index e1620c938..17849749e 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
@@ -129,19 +129,18 @@ public class GATKArgumentCollection {
     public Double downsampleFraction = null;
 
     /**
-     * For locus-based traversals (eg., LocusWalkers and ActiveRegionWalkers), downsample_to_coverage controls the
-     * maximum depth of coverage at each locus. For non-locus-based traversals (eg., ReadWalkers), this controls the
-     * maximum number of reads sharing the same alignment start position. Note that for ReadWalkers, since -dcov controls
-     * the maximum number of reads sharing the same alignment start position, you will typically need to use much lower
-     * dcov values than you would with LocusWalkers to see an effect. Note also that this downsampling option does NOT
-     * produce an unbiased random sampling from all available reads at each locus: instead, the primary goal of the
+     * For locus-based traversals (LocusWalkers and ActiveRegionWalkers), downsample_to_coverage controls the
+     * maximum depth of coverage at each locus. For read-based traversals (ReadWalkers), it controls the
+     * maximum number of reads sharing the same alignment start position. For ReadWalkers you will typically need to use
+     * much lower dcov values than you would with LocusWalkers to see an effect. Note that this downsampling option does
+     * not produce an unbiased random sampling from all available reads at each locus: instead, the primary goal of the
      * to-coverage downsampler is to maintain an even representation of reads from all alignment start positions when
-     * removing excess coverage. For a true across-the-board unbiased random sampling of reads, use -dfrac instead. Also
-     * note that the coverage target is an approximate goal that is not guaranteed to be met exactly: the downsampling
-     * algorithm will under some circumstances retain slightly more coverage than requested.
+     * removing excess coverage. For a truly unbiased random sampling of reads, use -dfrac instead. Also note
+     * that the coverage target is an approximate goal that is not guaranteed to be met exactly: the downsampling
+     * algorithm will under some circumstances retain slightly more or less coverage than requested.
      */
     @Argument(fullName = "downsample_to_coverage", shortName = "dcov",
-              doc = "Coverage [integer] to downsample to",
+              doc = "Coverage [integer] to downsample to per locus (for locus walkers) or per alignment start position (for read walkers)",
               required = false)
     public Integer downsampleCoverage = null;
 

From 9498950b1c02cd77a2ab4a539f76a8f2ce2724c3 Mon Sep 17 00:00:00 2001
From: Louis Bergelson <louisb@broadinstitute.org>
Date: Thu, 3 Oct 2013 16:52:48 -0400
Subject: [PATCH 37/77] Adding more specific error message when one of the
 scripts doesn't exist. --Previously it gave a cryptic message: ----IO error
 while decoding blarg.script with UTF-8 ----Please try specifying another one
 using the -encoding option

---
 .../src/org/broadinstitute/sting/queue/QScriptManager.scala | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/public/scala/src/org/broadinstitute/sting/queue/QScriptManager.scala b/public/scala/src/org/broadinstitute/sting/queue/QScriptManager.scala
index c6b8eff13..80dd53302 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/QScriptManager.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/QScriptManager.scala
@@ -36,6 +36,7 @@ import org.apache.log4j.Level
 import org.broadinstitute.sting.queue.util.TextFormatUtils._
 import org.broadinstitute.sting.utils.classloader.JVMUtils
 import scala.reflect.internal.util.{FakePos, NoPosition, Position, StringOps}
+import org.broadinstitute.sting.utils.exceptions.UserException
 
 /**
  * Plugin manager for QScripts which loads QScripts into the current class loader.
@@ -46,6 +47,11 @@ class QScriptManager() extends Logging {
    * Heavily based on scala/src/compiler/scala/tools/ant/Scalac.scala
    */
   def loadScripts(scripts: Seq[File], tempDir: File) {
+    // Make sure the scripts actually exist.
+    scripts.foreach{
+        file => if( !file.exists()) throw new UserException.CouldNotReadInputFile(file, "it does not exist.")
+    }
+
     if (scripts.size > 0) {
       val settings = new Settings((error: String) => logger.error(error))
       settings.deprecation.value = true

From 5ed47988b83de0c17cc9b1065522a4aa14f8818b Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Thu, 24 Oct 2013 17:13:25 -0400
Subject: [PATCH 38/77] Changed the parameter names from cds to baits

Making the usage more clear since the parameter is being used over and over to define baited
regions. Updated the headers accordingly and made it more readable.
---
 .../missing/QualifyMissingIntervals.java      | 25 +++++++++----------
 1 file changed, 12 insertions(+), 13 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
index 52a92d9ff..54fc6e97e 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
@@ -126,11 +126,10 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
     public String targetsFile;
 
     /**
-     * List of coding sequence intervals (exons) if different from the targets file, to distinguish intervals
-     * that overlap the cds and intervals that don't.
+     * List of baits to distinguish untargeted intervals from those that are targeted but not covered
      */
-    @Argument(shortName = "cds", required = false)
-    public String cdsFile = null;
+    @Argument(shortName = "baits", required = false)
+    public String baitsFile = null;
 
     /**
      * This value will be used to determine whether or not an interval had too high or too low GC content to be
@@ -183,8 +182,8 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
     }
 
     GATKReport simpleReport;
-    GenomeLocSortedSet target;
-    GenomeLocSortedSet cds;
+    GenomeLocSortedSet targets;
+    GenomeLocSortedSet baits;
 
     public boolean isReduceByInterval() {
         return true;
@@ -192,13 +191,13 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
 
     public void initialize() {
         // if cds file is not provided, just use the targets file (no harm done)
-        if (cdsFile == null)
-            cdsFile = targetsFile;
+        if (baitsFile == null)
+            baitsFile = targetsFile;
 
-        simpleReport = GATKReport.newSimpleReport("QualifyMissingIntervals", "IN", "GC", "BQ", "MQ", "DP", "TP", "TS", "CD", "LN", "DS");
+        simpleReport = GATKReport.newSimpleReport("QualifyMissingIntervals", "INTERVAL", "GC", "BQ", "MQ", "DP", "POS_IN_TARGET", "TARGET_SIZE", "BAITED", "MISSING_SIZE", "INTERPRETATION");
         final GenomeLocParser parser = getToolkit().getGenomeLocParser();
-        target = new GenomeLocSortedSet(parser, IntervalUtils.intervalFileToList(parser, targetsFile));
-        cds = new GenomeLocSortedSet(parser, IntervalUtils.intervalFileToList(parser, cdsFile));
+        targets = new GenomeLocSortedSet(parser, IntervalUtils.intervalFileToList(parser, targetsFile));
+        baits = new GenomeLocSortedSet(parser, IntervalUtils.intervalFileToList(parser, baitsFile));
     }
 
     public Metrics reduceInit() {
@@ -241,7 +240,7 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
         for (Pair<GenomeLoc, Metrics> r : results) {
             final GenomeLoc interval = r.getFirst();
             final Metrics metrics = r.getSecond();
-            final List<GenomeLoc> overlappingIntervals = target.getOverlapping(interval);
+            final List<GenomeLoc> overlappingIntervals = targets.getOverlapping(interval);
 
             simpleReport.addRow(
                     interval.toString(),
@@ -251,7 +250,7 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
                     metrics.depth(),
                     getPositionInTarget(interval, overlappingIntervals),
                     getTargetSize(overlappingIntervals),
-                    cds.overlaps(interval),
+                    baits.overlaps(interval),
                     interval.size(),
                     interpret(metrics, interval)
             );

From 209f2a61aa7e8f1e2903c0e25261edcee948507a Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 29 Oct 2013 10:33:51 -0400
Subject: [PATCH 39/77] Updated the GATK bundle script to:

1. Include exome target list for b37
2. Not delete the 'current' link unless -run is applied to the command line!  (sorry, Ryan)
---
 .../queue/qscripts/GATKResourcesBundle.scala   | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
index 1736adc17..d3e94d306 100644
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
@@ -95,6 +95,7 @@ class GATKResourcesBundle extends QScript {
   def isBAM(file: File) = file.getName.endsWith(".bam")
   def isOUT(file: File) = file.getName.endsWith(".out")
   def isFASTA(file: File) = file.getName.endsWith(".fasta")
+  def isIntervalList(file: File) = file.getName.endsWith(".interval_list")
 
   var RESOURCES: List[Resource] = Nil
   def addResource(comp: Resource) { RESOURCES = comp :: RESOURCES }
@@ -180,11 +181,17 @@ class GATKResourcesBundle extends QScript {
       "NA12878.HiSeq.WGS.bwa.cleaned.raw.subset", b37, true, true))
 
     //
-    // Test BAM file, specific to each reference
+    // Test BAM file, only for the b37 reference
     //
     addResource(new Resource("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.b37.NA12878.bam",
       "IGNORE", b37, false, false))
 
+    //
+    // Exome targets file, only for the b37 reference
+    //
+    addResource(new Resource("/seq/references/HybSelOligos/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",
+      "Broad.human.exome", b37, true, false, false))
+
     //
     // refGene files specific to each reference
     //
@@ -217,7 +224,7 @@ class GATKResourcesBundle extends QScript {
 
     val currentLink = new File(BUNDLE_ROOT + "/current")
 
-    if ( currentLink.exists ) currentLink.delete()
+    if ( currentLink.exists ) add(new deleteLink(currentLink))
 
     add(new linkFile(bundleDir, currentLink))
   }
@@ -275,6 +282,9 @@ class GATKResourcesBundle extends QScript {
               }
             }
           }
+        } else if ( isIntervalList(resource.file) ) {
+            val out = destFile(BUNDLE_DIR, resource.ref, resource.destname(resource.ref))
+            add(new cpFile(resource.file, out))
         } else {
           //throw new ReviewedStingException("Unknown file type: " + resource)
         }
@@ -354,6 +364,10 @@ class GATKResourcesBundle extends QScript {
     def commandLine = "cp %s %s".format(in.getAbsolutePath, out.getAbsolutePath)
   }
 
+  class deleteLink(@Input val in: File) extends CommandLineFunction {
+    def commandLine = "rm %s".format(in.getAbsolutePath)
+  }
+
   class linkFile(@Input val in: File, @Output val out: File) extends CommandLineFunction {
     def commandLine = "ln -s %s %s".format(in.getAbsolutePath, out.getAbsolutePath)
   }

From b22c9c2cb46b3218f1121e0adcb3b3525ec0191b Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Mon, 30 Sep 2013 10:17:43 -0400
Subject: [PATCH 40/77] Improvements to the reference model pipeline.

-- We use the RegenotypeVariants walker to recompute the qual field. (instead of the discussed idea of adding this functionality to CombineVariants)
-- QualByDepth will now be recomputed even if the stratified contexts are missing. This greatly improves the QD estimate for this pipeline. Doesn't work for multi-allelics since the qual can't be recomputed.
---
 .../gatk/walkers/annotator/QualByDepth.java   | 15 +++---
 .../gatk/walkers/annotator/RankSumTest.java   |  2 +-
 .../VariantAnnotatorIntegrationTest.java      | 48 +++++++++++++++++++
 .../walkers/variantutils/CombineVariants.java |  2 -
 4 files changed, 58 insertions(+), 9 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
index a3fbcc439..906cfa021 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
@@ -54,6 +54,8 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBa
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
+import org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverage;
+import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
 import org.broadinstitute.variant.vcf.VCFHeaderLineType;
@@ -94,19 +96,20 @@ public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotati
             if ( !genotype.isHet() && !genotype.isHomVar() )
                 continue;
 
-            if (stratifiedContexts!= null) {
-                AlignmentContext context = stratifiedContexts.get(genotype.getSampleName());
+            if (stratifiedContexts!= null && !stratifiedContexts.isEmpty()) {
+                final AlignmentContext context = stratifiedContexts.get(genotype.getSampleName());
                 if ( context == null )
                     continue;
                 depth += context.getBasePileup().depthOfCoverage();
 
-            }
-            else if (perReadAlleleLikelihoodMap != null) {
-                PerReadAlleleLikelihoodMap perReadAlleleLikelihoods = perReadAlleleLikelihoodMap.get(genotype.getSampleName());
+            } else if (perReadAlleleLikelihoodMap != null) {
+                final PerReadAlleleLikelihoodMap perReadAlleleLikelihoods = perReadAlleleLikelihoodMap.get(genotype.getSampleName());
                 if (perReadAlleleLikelihoods == null || perReadAlleleLikelihoods.isEmpty())
                     continue;
 
                 depth += perReadAlleleLikelihoods.getNumberOfStoredElements();
+            } else if (genotype.hasDP() && vc.isBiallelic()) { // TODO -- this currently only works with biallelic variants for now because multiallelics have had their PLs stripped out and therefore their qual score can't be recomputed
+                depth += genotype.getDP();
             }
         }
 
@@ -116,7 +119,7 @@ public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotati
         final double altAlleleLength = GATKVariantContextUtils.getMeanAltAlleleLength(vc);
         double QD = -10.0 * vc.getLog10PError() / ((double)depth * altAlleleLength);
         QD = fixTooHighQD(QD);
-        Map<String, Object> map = new HashMap<String, Object>();
+        Map<String, Object> map = new HashMap<>();
         map.put(getKeyNames().get(0), String.format("%.2f", QD));
         return map;
     }
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
index 1ba13afa1..ab5a40145 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
@@ -83,7 +83,7 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements ActiveR
                                         final Map<String, AlignmentContext> stratifiedContexts,
                                         final VariantContext vc,
                                         final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
-        // either stratifiedContexts or  stratifiedPerReadAlleleLikelihoodMap has to be non-null
+        // either stratifiedContexts or stratifiedPerReadAlleleLikelihoodMap has to be non-null
 
         final GenotypesContext genotypes = vc.getGenotypes();
         if (genotypes == null || genotypes.size() == 0)
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
index 9f8b72c1d..58c3bb9bd 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
@@ -345,4 +345,52 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
         Assert.assertFalse(lineIterator.hasNext());
         Assert.assertFalse(lineIteratorAnn.hasNext());
     }
+
+    @Test
+    public void testQualByDepth() throws IOException {
+        final String base = String.format("-T HaplotypeCaller --disableDithering -R %s -I %s", REF, CEUTRIO_BAM) + " --no_cmdline_in_header -o %s -L 20:10130000-10134800";
+        final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList(""));
+        final File outputVCF = executeTest("testQualByDepth", spec).getFirst().get(0);
+
+        final String baseNoQD = String.format("-T HaplotypeCaller --disableDithering -R %s -I %s", REF, CEUTRIO_BAM) + " --no_cmdline_in_header -o %s -L 20:10130000-10134800 -XA QualByDepth";
+        final WalkerTestSpec specNoQD = new WalkerTestSpec(baseNoQD, 1, Arrays.asList(""));
+        specNoQD.disableShadowBCF();
+        final File outputVCFNoQD = executeTest("testQualByDepth calling without QD", specNoQD).getFirst().get(0);
+
+        final String baseAnn = String.format("-T VariantAnnotator -R %s -V %s", REF, outputVCFNoQD.getAbsolutePath()) + " --no_cmdline_in_header -o %s -L 20:10130000-10134800 -A QualByDepth";
+        final WalkerTestSpec specAnn = new WalkerTestSpec(baseAnn, 1, Arrays.asList("139a4384f5a7c1f49ada67f416642249"));
+        specAnn.disableShadowBCF();
+        final File outputVCFAnn = executeTest("testQualByDepth re-annotation of QD", specAnn).getFirst().get(0);
+
+        // confirm that the QD values are present in the new file for all biallelic variants
+        // QD values won't be identical because some filtered reads are missing during re-annotation
+
+        final VCFCodec codec = new VCFCodec();
+        final FileInputStream s = new FileInputStream(outputVCF);
+        final LineIterator lineIterator = codec.makeSourceFromStream(new PositionalBufferedStream(s));
+        codec.readHeader(lineIterator);
+
+        final VCFCodec codecAnn = new VCFCodec();
+        final FileInputStream sAnn = new FileInputStream(outputVCFAnn);
+        final LineIterator lineIteratorAnn = codecAnn.makeSourceFromStream(new PositionalBufferedStream(sAnn));
+        codecAnn.readHeader(lineIteratorAnn);
+
+        while( lineIterator.hasNext() && lineIteratorAnn.hasNext() ) {
+            final String line = lineIterator.next();
+            Assert.assertFalse(line == null);
+            final VariantContext vc = codec.decode(line);
+
+            final String lineAnn = lineIteratorAnn.next();
+            Assert.assertFalse(lineAnn == null);
+            final VariantContext vcAnn = codecAnn.decode(lineAnn);
+
+            if( vc.isBiallelic() ) {
+                Assert.assertTrue(vc.hasAttribute("QD"));
+                Assert.assertTrue(vcAnn.hasAttribute("QD"));
+            }
+        }
+
+        Assert.assertFalse(lineIterator.hasNext());
+        Assert.assertFalse(lineIteratorAnn.hasNext());
+    }
 }
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 396d5686b..1362b109e 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
@@ -235,8 +235,6 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
         vcfWriter.writeHeader(vcfHeader);
     }
 
-
-
     private void validateAnnotateUnionArguments() {
         Set<String> rodNames = SampleUtils.getRodNamesWithVCFHeader(getToolkit(), null);
 

From 96024403bf9dbcb32de249d448363f4163a49e66 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 4 Nov 2013 10:01:22 -0500
Subject: [PATCH 41/77] Update the dbsnp version in the bundle from 137 to 138;
 resolves PT #59771004.

---
 .../sting/queue/qscripts/GATKResourcesBundle.scala            | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
index d3e94d306..307ce171f 100644
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
@@ -149,8 +149,8 @@ class GATKResourcesBundle extends QScript {
     //
     // standard VCF files.  Will be lifted to each reference
     //
-    addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_137_b37.leftAligned.vcf",
-      "dbsnp_137", b37, true, false))
+    addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_138_b37.leftAligned.vcf",
+      "dbsnp_138", b37, true, false))
 
     addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Omni2.5_chip/Omni25_sites_2141_samples.b37.vcf",
       "1000G_omni2.5", b37, true, false))

From 2fc40a0aedd95086043c69bf1ea7b5eee38b03c4 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 7 Nov 2013 09:02:17 -0500
Subject: [PATCH 43/77] Fixing the liftover script to not require strict VCF
 header validation.

Apparently no one has used the liftover script for a while (which I guess is a good thing)...
---
 .../sting/gatk/walkers/variantutils/LiftoverVariants.java     | 3 ++-
 public/perl/liftOverVCF.pl                                    | 4 ++--
 2 files changed, 4 insertions(+), 3 deletions(-)

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 379b1c2a3..478a2a351 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
@@ -42,6 +42,7 @@ import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.help.HelpConstants;
 import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
 import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.variant.variantcontext.writer.Options;
 import org.broadinstitute.variant.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
@@ -118,7 +119,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
 
 
         final VCFHeader vcfHeader = new VCFHeader(metaData, samples);
-        writer = VariantContextWriterFactory.create(file, getMasterSequenceDictionary(), VariantContextWriterFactory.NO_OPTIONS);
+        writer = VariantContextWriterFactory.create(file, getMasterSequenceDictionary(), EnumSet.of(Options.ALLOW_MISSING_FIELDS_IN_HEADER));
         writer.writeHeader(vcfHeader);
     }
 
diff --git a/public/perl/liftOverVCF.pl b/public/perl/liftOverVCF.pl
index ba4198292..a942145d7 100755
--- a/public/perl/liftOverVCF.pl
+++ b/public/perl/liftOverVCF.pl
@@ -36,7 +36,7 @@ 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 -V:variant $in -o $unsorted_vcf -chain $chain -dict $newRef.dict";
+my $cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T LiftoverVariants -R $oldRef.fasta -V:variant $in -o $unsorted_vcf -chain $chain -dict $newRef.dict -U LENIENT_VCF_PROCESSING";
 if ($recordOriginalLocation) {
   $cmd .= " -recordOriginalLocation";
 }
@@ -66,7 +66,7 @@ system($cmd) == 0 or quit("The sorting step failed.  Please correct the necessar
 
 # Filter the VCF for bad records
 print "\nFixing/removing bad records...\n";
-$cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T FilterLiftedVariants -R $newRef.fasta -V:variant $sorted_vcf -o $out";
+$cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T FilterLiftedVariants -R $newRef.fasta -V:variant $sorted_vcf -o $out -U LENIENT_VCF_PROCESSING";
 system($cmd) == 0 or quit("The filtering step failed.  Please correct the necessary errors before retrying.");
 
 # clean up

From 725656ae7e613e1d610029909c3615408d2e8733 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Thu, 22 Aug 2013 22:18:47 -0400
Subject: [PATCH 45/77] Generalizing the FullProcessingPipeline Qscript

We have generalized the processing script to be able to handle multiple scenarios. Originally it was
designed for PCR free data only, we added all the steps necessary to start from fastq and process
RNA-seq as well as non-human data. This is our go to script in TechDev.

   * add optional "starting from fastq" path to the pipeline
   * add mark duplicates (optionally) to the pipeline
   * add an option to run with the mouse data (without dbsnp and with single ended fastq)
   * add option to process RNA-seq data from topHat (add RG and reassign mapping quality if necessary)
   * add option to filter or include reads with N in the cigar string
   * add parameter to allow keeping the intermediate files
---
 .../sting/queue/extensions/gatk/GATKExtensionsGenerator.java    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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 ced0809f7..bf675503b 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
@@ -325,7 +325,7 @@ public class GATKExtensionsGenerator extends CommandLineProgram {
      * @throws IOException If the file cannot be written.
      */
     private void writeFile(String fullClassName, String content) throws IOException {
-        File outputFile = new File(outputDirectory, fullClassName.replace(".", "/") + ".scala");
+        File outputFile = new File(outputDirectory, fullClassName.replace(".", "/") + "MoleculoPipeline.scala");
         if (outputFile.exists()) {
             String existingContent = FileUtils.readFileToString(outputFile);
             if (StringUtils.equals(content, existingContent))

From 296bcc7fb14369f2ec3e40229e47273798e220aa Mon Sep 17 00:00:00 2001
From: Phillip Dexheimer <phillip.dexheimer@cchmc.org>
Date: Tue, 12 Nov 2013 11:42:09 -0500
Subject: [PATCH 46/77] Changed name of jobs submitted to cluster job runners

-- Added 'jobRunnerJobName' definition to QFunction, defaults to value of shortDescription
-- Edited Lsf and Drmaa JobRunners to use this string instead of description for naming jobs in the scheduler

Signed-off-by: Joel Thibault <thibault@broadinstitute.org>
---
 .../sting/queue/engine/drmaa/DrmaaJobRunner.scala            | 2 +-
 .../sting/queue/engine/lsf/Lsf706JobRunner.scala             | 2 +-
 .../org/broadinstitute/sting/queue/function/QFunction.scala  | 5 +++++
 3 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala b/public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala
index 79fc8589f..b405c91a2 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala
@@ -50,7 +50,7 @@ class DrmaaJobRunner(val session: Session, val function: CommandLineFunction) ex
     session.synchronized {
       val drmaaJob: JobTemplate = session.createJobTemplate
 
-      drmaaJob.setJobName(function.description.take(jobNameLength).replaceAll(jobNameFilter, "_"))
+      drmaaJob.setJobName(function.jobRunnerJobName.take(jobNameLength).replaceAll(jobNameFilter, "_"))
 
       // Set the current working directory
       drmaaJob.setWorkingDirectory(function.commandDirectory.getPath)
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 ead29bbf5..e9f141880 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
@@ -71,7 +71,7 @@ class Lsf706JobRunner(val function: CommandLineFunction) extends CommandLineJobR
       for (i <- 0 until LibLsf.LSF_RLIM_NLIMITS)
         request.rLimits(i) = LibLsf.DEFAULT_RLIMIT;
 
-      request.jobName = function.description.take(LibBat.MAX_JOB_NAME_LEN)
+      request.jobName = function.jobRunnerJobName.take(LibBat.MAX_JOB_NAME_LEN)
       request.options |= LibBat.SUB_JOB_NAME
 
       // Set the output file for stdout
diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala b/public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala
index abbb63271..3afd289af 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala
@@ -150,6 +150,11 @@ trait QFunction extends Logging with QJobReport {
       case _ => analysisName
     }
   }
+  
+  /**
+   * The name of the job as submitted to the job runner
+   */
+  def jobRunnerJobName = shortDescription
 
   /**
    * Returns true if the function is done.

From dac3dbc997cb6778b0eb88e87f7be9c15afdb46b Mon Sep 17 00:00:00 2001
From: Geraldine Van der Auwera <vdauwera@broadinstitute.org>
Date: Fri, 11 Oct 2013 10:23:38 -0400
Subject: [PATCH 47/77] Improved gatkdocs for InbreedingCoefficient,
 ReduceReads, ErrorRatePerCycle

Clarified caveat for InbreedingCoefficient
Cleaned up docstrings for ReduceReads
Brushed up doc for ErrorRatePerCycle
---
 .../walkers/annotator/InbreedingCoeff.java    |  4 +-
 .../compression/reducereads/ReduceReads.java  | 80 +++++++++----------
 .../diagnostics/ErrorRatePerCycle.java        | 23 +++---
 3 files changed, 54 insertions(+), 53 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
index da2143ec1..3f815346d 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
@@ -70,8 +70,8 @@ import java.util.*;
  *
  * A continuous generalization of the Hardy-Weinberg test for disequilibrium that works
  * well with limited coverage per sample.  See the 1000 Genomes Phase I release for
- * more information.  Note that the Inbreeding Coefficient will not be calculated for files
- * with fewer than a minimum (generally 10) number of samples.
+ * more information.  Note that the Inbreeding Coefficient can only be calculated for
+ * cohorts containing at least 10 founder samples.
  */
 public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
 
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
index 31fe7e380..383ba5ee9 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
@@ -84,10 +84,10 @@ import java.util.List;
  * Reduces the BAM file using read based compression that keeps only essential information for variant calling
  *
  * <p>
- * This walker will generated reduced versions of the BAM files that still follow the BAM spec
- * and contain all the information necessary for the GSA variant calling pipeline. Some options
- * allow you to tune in how much compression you want to achieve. The default values have been
- * shown to reduce a typical whole exome BAM file 100x. The higher the coverage, the bigger the
+ * This tool will generate reduced versions of the BAM files that still follow the BAM specification
+ * and contain all the information necessary to call variants according to the GATK Best Practices recommendations.
+ * Some options allow you to tune how much compression you want to achieve. The default values have been
+ * shown to reduce a typical whole exome BAM file by 100x. The higher the coverage, the bigger the
  * savings in file size and performance of the downstream tools.
  *
  * <h3>Input</h3>
@@ -121,25 +121,25 @@ public class ReduceReads extends ReadWalker<ObjectArrayList<GATKSAMRecord>, Redu
     private SAMFileWriter writerToUse = null;
 
     /**
-     * The number of bases to keep around mismatches (potential variation)
+     *
      */
-    @Argument(fullName = "context_size", shortName = "cs", doc = "", required = false)
+    @Argument(fullName = "context_size", shortName = "cs", doc = "The number of bases to keep around mismatches (potential variation)", required = false)
     public int contextSize = 10;
 
     /**
-     * The minimum mapping quality to be considered for the consensus synthetic read. Reads that have
+     * Reads that have
      * mapping quality below this threshold will not be counted towards consensus, but are still counted
      * towards variable regions.
      */
-    @Argument(fullName = "minimum_mapping_quality", shortName = "minmap", doc = "", required = false)
+    @Argument(fullName = "minimum_mapping_quality", shortName = "minmap", doc = "The minimum mapping quality to be considered for the consensus synthetic read", required = false)
     public int minMappingQuality = 20;
 
     /**
-     * The minimum base quality to be considered for the consensus synthetic read. Reads that have
+     * Reads that have
      * base quality below this threshold will not be counted towards consensus, but are still counted
      * towards variable regions.
      */
-    @Argument(fullName = "minimum_base_quality_to_consider", shortName = "minqual", doc = "", required = false)
+    @Argument(fullName = "minimum_base_quality_to_consider", shortName = "minqual", doc = "The minimum base quality to be considered for the consensus synthetic read", required = false)
     public byte minBaseQual = 15;
 
     /**
@@ -160,81 +160,77 @@ public class ReduceReads extends ReadWalker<ObjectArrayList<GATKSAMRecord>, Redu
     public List<RodBinding<VariantContext>> known = Collections.emptyList();
 
     /**
-     * Do not simplify read (strip away all extra information of the read -- anything other than bases, quals
-     * and read group).
+     * This strips away all extra information of the read -- anything other than bases, quals
+     * and read group.
      */
-    @Argument(fullName = "dont_simplify_reads", shortName = "nosimplify", doc = "", required = false)
+    @Argument(fullName = "dont_simplify_reads", shortName = "nosimplify", doc = "Do not simplify read", required = false)
     public boolean DONT_SIMPLIFY_READS = false;
 
     /**
-     * Do not hard clip adaptor sequences. Note: You don't have to turn this on for reads that are not mate paired.
-     * The program will behave correctly in those cases.
+     * Note that it is not necessary to turn this on for reads that are not mate paired.
+     * The program will behave correctly by default in those cases.
      */
-    @Argument(fullName = "dont_hardclip_adaptor_sequences", shortName = "noclip_ad", doc = "", required = false)
+    @Argument(fullName = "dont_hardclip_adaptor_sequences", shortName = "noclip_ad", doc = "Do not hard clip adaptor sequences", required = false)
     public boolean DONT_CLIP_ADAPTOR_SEQUENCES = false;
 
     /**
-     * Do not hard clip the low quality tails of the reads. This option overrides the argument of minimum tail
+     * This option overrides the argument of minimum tail
      * quality.
      */
-    @Argument(fullName = "dont_hardclip_low_qual_tails", shortName = "noclip_tail", doc = "", required = false)
+    @Argument(fullName = "dont_hardclip_low_qual_tails", shortName = "noclip_tail", doc = "Do not hard clip the low quality tails of the reads", required = false)
     public boolean DONT_CLIP_LOW_QUAL_TAILS = false;
 
     /**
-     * Do not use high quality soft-clipped bases. By default, ReduceReads will hard clip away any low quality soft clipped
+     * By default, ReduceReads will hard clip away any low quality soft clipped
      * base left by the aligner and use the high quality soft clipped bases in it's traversal algorithm to identify variant
      * regions. The minimum quality for soft clipped bases is the same as the minimum base quality to consider (minqual)
      */
-    @Argument(fullName = "dont_use_softclipped_bases", shortName = "no_soft", doc = "", required = false)
+    @Argument(fullName = "dont_use_softclipped_bases", shortName = "no_soft", doc = "Do not use high quality soft-clipped bases", required = false)
     public boolean DONT_USE_SOFTCLIPPED_BASES = false;
 
     /**
-     * Do not compress read names. By default, ReduceReads will compress read names to numbers and guarantee 
+     * By default, ReduceReads will compress read names to numbers and guarantee
      * uniqueness and reads with similar name will still have similar compressed names. Note: If you scatter/gather
      * there is no guarantee that read name uniqueness will be maintained -- in this case we recommend not compressing. 
      */
-    @Argument(fullName = "dont_compress_read_names", shortName = "nocmp_names", doc = "", required = false)
+    @Argument(fullName = "dont_compress_read_names", shortName = "nocmp_names", doc = "Do not compress read names", required = false)
     public boolean DONT_COMPRESS_READ_NAMES = false;
 
     /**
-     * Optionally hard clip all incoming reads to the desired intervals. The hard clips will happen exactly at the interval
-     * border.
+     * The hard clips will happen exactly at the interval border.
      */
-    @Argument(fullName = "hard_clip_to_interval", shortName = "clip_int", doc = "", required = false)
+    @Argument(fullName = "hard_clip_to_interval", shortName = "clip_int", doc = "Hard clip all incoming reads to the desired intervals", required = false)
     public boolean HARD_CLIP_TO_INTERVAL = false;
 
     /**
-     * Minimum proportion of mismatches in a site to trigger a variant region. Anything below this will be
+     * Anything below this will be
      * considered consensus and reduced (otherwise we will try to trigger polyploid compression).  Note that
      * this value is used only regions with high coverage.
      */
     @Advanced
-    @Argument(fullName = "minimum_alt_proportion_to_trigger_variant", shortName = "minvar", doc = "", required = false)
+    @Argument(fullName = "minimum_alt_proportion_to_trigger_variant", shortName = "minvar", doc = "Minimum proportion of mismatches in a site to trigger a variant region", required = false)
     public double minAltProportionToTriggerVariant = 0.05;
 
     /**
-     * Minimum p-value from binomial distribution of mismatches in a site to trigger a variant region.
      * Any site with a value falling below this will be considered consensus and reduced (otherwise we will try to
      * trigger polyploid compression).  Note that this value is used only regions with low coverage.
      */
     @Advanced
-    @Argument(fullName = "minimum_alt_pvalue_to_trigger_variant", shortName = "min_pvalue", doc = "", required = false)
+    @Argument(fullName = "minimum_alt_pvalue_to_trigger_variant", shortName = "min_pvalue", doc = "Minimum p-value from binomial distribution of mismatches in a site to trigger a variant region", required = false)
     public double minAltPValueToTriggerVariant = 0.01;
 
     /**
-     * Minimum proportion of indels in a site to trigger a variant region. Anything below this will be
-     * considered consensus.
+     * Anything below this will be considered consensus.
      */
-    @Argument(fullName = "minimum_del_proportion_to_trigger_variant", shortName = "mindel", doc = "", required = false)
+    @Argument(fullName = "minimum_del_proportion_to_trigger_variant", shortName = "mindel", doc = "Minimum proportion of indels in a site to trigger a variant region", required = false)
     public double minIndelProportionToTriggerVariant = 0.05;
 
     /**
-     * The number of reads emitted per sample in a variant region can be downsampled for better compression.
      * This level of downsampling only happens after the region has been evaluated, therefore it can
      * be combined with the engine level downsampling.
      * A value of 0 turns downsampling off.
      */
-    @Argument(fullName = "downsample_coverage", shortName = "ds", doc = "", required = false)
+    @Argument(fullName = "downsample_coverage", shortName = "ds", doc = "Downsample the number of reads emitted per sample in a variant region for better compression", required = false)
     public int downsampleCoverage = 250;
 
     /**
@@ -243,27 +239,27 @@ public class ReduceReads extends ReadWalker<ObjectArrayList<GATKSAMRecord>, Redu
      * To prevent users from unintentionally running the tool in a less than ideal manner, we require them
      * to explicitly enable multi-sample analysis with this argument.
      */
-    @Argument(fullName = "cancer_mode", shortName = "cancer_mode", doc = "enable multi-samples reduction for cancer analysis", required = false)
+    @Argument(fullName = "cancer_mode", shortName = "cancer_mode", doc = "Enable multi-sample reduction for cancer analysis", required = false)
     public boolean ALLOW_MULTIPLE_SAMPLES = false;
 
     @Hidden
-    @Argument(fullName = "nwayout", shortName = "nw", doc = "", required = false)
+    @Argument(fullName = "nwayout", shortName = "nw", doc = "Generate separate output files per input file", required = false)
     public boolean nwayout = false;
 
     @Hidden
-    @Argument(fullName = "", shortName = "dl", doc = "", required = false)
+    @Argument(fullName = "", shortName = "dl", doc = "Debug level", required = false)
     public int debugLevel = 0;
 
     @Hidden
-    @Argument(fullName = "", shortName = "dr", doc = "", required = false)
+    @Argument(fullName = "", shortName = "dr", doc = "Debug read", required = false)
     public String debugRead = "";
 
     @Hidden
-    @Argument(fullName = "downsample_strategy", shortName = "dm", doc = "", required = false)
+    @Argument(fullName = "downsample_strategy", shortName = "dm", doc = "Downsampling strategy", required = false)
     public DownsampleStrategy downsampleStrategy = DownsampleStrategy.Normal;
     
     @Hidden 
-    @Argument(fullName = "no_pg_tag", shortName = "npt", doc ="", required = false)
+    @Argument(fullName = "no_pg_tag", shortName = "npt", doc ="Discard program tags", required = false)
     public boolean NO_PG_TAG = false;
 
     public enum DownsampleStrategy {
@@ -297,7 +293,7 @@ public class ReduceReads extends ReadWalker<ObjectArrayList<GATKSAMRecord>, Redu
             throw new UserException.MissingArgument("out", "the output must be provided and is optional only for certain debugging modes");
 
         if ( nwayout && out != null )
-            throw new UserException.CommandLineException("--out and --nwayout can not be used simultaneously; please use one or the other");
+            throw new UserException.CommandLineException("--out and --nwayout cannot be used simultaneously; please use one or the other");
 
         if ( minAltPValueToTriggerVariant < 0.0 || minAltPValueToTriggerVariant > 1.0 )
             throw new UserException.BadArgumentValue("--minimum_alt_pvalue_to_trigger_variant", "must be a value between 0 and 1 (inclusive)");
@@ -306,7 +302,7 @@ public class ReduceReads extends ReadWalker<ObjectArrayList<GATKSAMRecord>, Redu
             throw new UserException.BadArgumentValue("--minimum_alt_proportion_to_trigger_variant", "must be a value between 0 and 1 (inclusive)");
 
         if ( SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader()).size() > 1 && !ALLOW_MULTIPLE_SAMPLES )
-            throw new UserException.BadInput("Reduce Reads is not meant to be run for more than 1 sample at a time except for the specific case of tumor/normal pairs in cancer analysis");
+            throw new UserException.BadInput("Reduce Reads is not meant to be run for more than 1 sample at a time except for the specific case of tumor/normal pairs in cancer analysis. If that is what you want to do, use the -cancer_mode flag.");
 
         if ( known.isEmpty() )
             knownSnpPositions = null;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java
index 86676ca54..42e3ae0c0 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java
@@ -44,10 +44,11 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import java.io.PrintStream;
 
 /**
- * Computes the read error rate per position in read (in the original 5'->3' orientation that the read had coming off the machine)
+ * Compute the read error rate per position
  *
- * Emits a GATKReport containing readgroup, cycle, mismatches, counts, qual, and error rate for each read
- * group in the input BAMs FOR ONLY THE FIRST OF PAIR READS.
+ * <p>This tool computes the read error rate per position in sequence reads. It does this in the original 5'->3'
+ * orientation that the read had coming off the machine. It then emits a GATKReport containing readgroup, cycle,
+ * mismatches, counts, qual, and error rate for each read group in the input BAMs.</p>
  *
  * <h3>Input</h3>
  *  <p>
@@ -56,9 +57,9 @@ import java.io.PrintStream;
  *
  * <h3>Output</h3>
  *  <p>
- *      GATKReport containing readgroup, cycle, mismatches, counts, qual, and error rate.
+ *      A GATKReport containing readgroup, cycle, mismatches, counts, qual, and error rate.
  *
- *      For example, running this tool on the NA12878 data sets:
+ *      For example, running this tool on the NA12878 data sets yields the following table:
  *
  *      <pre>
  *      ##:GATKReport.v0.2 ErrorRatePerCycle : The error rate per sequenced position in the reads
@@ -82,16 +83,20 @@ import java.io.PrintStream;
  *      </pre>
  *  </p>
  *
- * <h3>Examples</h3>
+ * <h3>Example</h3>
  *  <pre>
  *    java
  *      -jar GenomeAnalysisTK.jar
  *      -T ErrorRatePerCycle
- *      -I bundle/current/b37/NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam
- *      -R bundle/current/b37/human_g1k_v37.fasta
- *      -o example.gatkreport.txt
+ *      -R human_g1k_v37.fasta
+ *      -I my_sequence_reads.bam
+ *      -o error_rates.gatkreport.txt
  *  </pre>
  *
+ * <h3>Caveat</h3>
+ *
+ * <p>Note that when it is run on paired-end sequence data, this tool only uses the first read in a pair.</p>
+ *
  * @author Kiran Garimella, Mark DePristo
  */
 @DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )

From e40a07bb586752f23da345d3f0be69357fb8289b Mon Sep 17 00:00:00 2001
From: bradtaylor <bradt@broadinstitute.org>
Date: Mon, 21 Oct 2013 14:08:03 -0400
Subject: [PATCH 48/77] Improve the PairHMM API for better FPGA integration

Motivation:
The API was different between the regular PairHMM and the FPGA-implementation
via CnyPairHMM. As a result, the LikelihoodCalculationEngine had
to use account for this. The goal is to change the API to be the same
for all implementations, and make it easier to access.

PairHMM
PairHMM now accepts a list of reads and a map of alleles/haplotpes and returns a PerReadAlleleLikelihoodMap.
Added a new primary method that loops the reads and haplotypes, extracts qualities,
and passes them to the computeReadLikelihoodGivenHaplotypeLog10 method.
Did not alter that method, or its subcompute method, at all.
PairHMM also now handles its own (re)initialization, so users don't have to worry about that.

CnyPairHMM
Added that same new primary access method to this FPGA class.
Method overrides the default implementation in PairHMM. Walks through a list of reads.
Individual-read quals and the full haplotype list are fed to batchAdd(), as before.
However, instead of waiting for every read to get added, and then walking through the reads
again to extract results, we just get the haplotype-results array for each read as soon as it
is generated, and pack it into a perReadAlleleLikelihoodMap for return.
The main access method is now the same no matter whether the FPGA CnyPairHMM is used or not.

LikelihoodCalculationEngine
The functionality to loop through the reads and haplotypes and get individual log10-likelihoods
was moved to the PairHMM, and so removed from here. However, this class does need to retain
the ability to pre-process the reads, and post-process the resulting likelihoods map.
Those features were separated from running the HMM and refactored into their own methods
Commented out the (unused) system for finding best N haplotypes for genotyping.

PairHMMIndelErrorModel
Similar changes were made as to the LCE. However, in this case the haplotypes are modified
based on each individual read, so the read-list we feed into the HMM only has one read.
---
 .../LikelihoodCalculationEngine.java          | 546 +++++++++---------
 .../indels/PairHMMIndelErrorModel.java        | 150 +++--
 .../utils/pairhmm/ArrayLoglessPairHMM.java    |   1 +
 .../sting/utils/pairhmm/CnyPairHMM.java       |  67 ++-
 .../sting/utils/pairhmm/LoglessPairHMM.java   |  11 -
 .../genotyper/PerReadAlleleLikelihoodMap.java |  25 +-
 .../sting/utils/pairhmm/Log10PairHMM.java     |   3 -
 .../sting/utils/pairhmm/N2MemoryPairHMM.java  |   7 +-
 .../sting/utils/pairhmm/PairHMM.java          |  87 ++-
 .../sting/utils/sam/GATKSAMRecord.java        |  51 +-
 10 files changed, 547 insertions(+), 401 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
index 0d55797bc..4eb728390 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
@@ -52,18 +52,10 @@ import net.sf.samtools.SAMUtils;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.QualityUtils;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.haplotype.Haplotype;
-import org.broadinstitute.sting.utils.haplotype.HaplotypeScoreComparator;
-import org.broadinstitute.sting.utils.pairhmm.ArrayLoglessPairHMM;
-import org.broadinstitute.sting.utils.pairhmm.Log10PairHMM;
-import org.broadinstitute.sting.utils.pairhmm.LoglessPairHMM;
-import org.broadinstitute.sting.utils.pairhmm.CnyPairHMM;
-import org.broadinstitute.sting.utils.pairhmm.BatchPairHMM;
-import org.broadinstitute.sting.utils.pairhmm.PairHMM;
+import org.broadinstitute.sting.utils.pairhmm.*;
 import org.broadinstitute.sting.utils.recalibration.covariates.RepeatCovariate;
 import org.broadinstitute.sting.utils.recalibration.covariates.RepeatLengthCovariate;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@@ -88,7 +80,7 @@ public class LikelihoodCalculationEngine {
     private final PairHMM.HMM_IMPLEMENTATION hmmType;
     private final boolean noFpga;
 
-    private final ThreadLocal<PairHMM> pairHMM = new ThreadLocal<PairHMM>() {
+    private final ThreadLocal<PairHMM> pairHMMThreadLocal = new ThreadLocal<PairHMM>() {
         @Override
         protected PairHMM initialValue() {
             switch (hmmType) {
@@ -109,6 +101,8 @@ public class LikelihoodCalculationEngine {
             }
         }
     };
+//    Attempted to do as below, to avoid calling pairHMMThreadLocal.get() later on, but it resulted in a NullPointerException
+//    private final PairHMM pairHMM = pairHMMThreadLocal.get();
 
     private final static boolean WRITE_LIKELIHOODS_TO_FILE = false;
     private final static String LIKELIHOODS_FILENAME = "likelihoods.txt";
@@ -173,36 +167,145 @@ public class LikelihoodCalculationEngine {
         if ( likelihoodsStream != null ) likelihoodsStream.close();
     }
 
-    /**
-     * Initialize our pairHMM with parameters appropriate to the haplotypes and reads we're going to evaluate
-     *
-     * After calling this routine the PairHMM will be configured to best evaluate all reads in the samples
-     * against the set of haplotypes
-     *
-     * @param haplotypes a non-null list of haplotypes
-     * @param perSampleReadList a mapping from sample -> reads
-     */
-    private void initializePairHMM(final List<Haplotype> haplotypes, final Map<String, List<GATKSAMRecord>> perSampleReadList) {
-        int X_METRIC_LENGTH = 0;
-        for( final Map.Entry<String, List<GATKSAMRecord>> sample : perSampleReadList.entrySet() ) {
-            for( final GATKSAMRecord read : sample.getValue() ) {
-                final int readLength = read.getReadLength();
-                if( readLength > X_METRIC_LENGTH ) { X_METRIC_LENGTH = readLength; }
-            }
+    private void writeDebugLikelihoods(final GATKSAMRecord processedRead, final Haplotype haplotype, final double log10l){
+        if ( WRITE_LIKELIHOODS_TO_FILE ) {
+            likelihoodsStream.printf("%s %s %s %s %s %s %f%n",
+                    haplotype.getBaseString(),
+                    new String(processedRead.getReadBases() ),
+                    SAMUtils.phredToFastq(processedRead.getBaseQualities() ),
+                    SAMUtils.phredToFastq(processedRead.getBaseInsertionQualities() ),
+                    SAMUtils.phredToFastq(processedRead.getBaseDeletionQualities() ),
+                    SAMUtils.phredToFastq(constantGCP),
+                    log10l);
         }
-        int Y_METRIC_LENGTH = 0;
-        for( final Haplotype h : haplotypes ) {
-            final int haplotypeLength = h.getBases().length;
-            if( haplotypeLength > Y_METRIC_LENGTH ) { Y_METRIC_LENGTH = haplotypeLength; }
-        }
-
-        // initialize arrays to hold the probabilities of being in the match, insertion and deletion cases
-        pairHMM.get().initialize(X_METRIC_LENGTH, Y_METRIC_LENGTH);
     }
 
+    private Map<Allele, Haplotype> createAlleleMap(List<Haplotype> haplotypes){
+        final int numHaplotypes = haplotypes.size();
+        final Map<Allele, Haplotype> alleleMap = new LinkedHashMap<>(numHaplotypes);
+        for ( final Haplotype haplotype : haplotypes ) {
+            final Allele allele = Allele.create(haplotype, true);
+            alleleMap.put(allele, haplotype);
+        }
+        return alleleMap;
+    }
+
+    private Map<GATKSAMRecord, byte[]> fillGCPArrays(List<GATKSAMRecord> reads){
+        final Map<GATKSAMRecord, byte []> GCPArrayMap = new LinkedHashMap<>();
+        for (GATKSAMRecord read: reads){
+            byte [] GCPArray = new byte[read.getReadBases().length];
+            Arrays.fill( GCPArray, constantGCP ); // Is there a way to derive empirical estimates for this from the data?
+            GCPArrayMap.put(read, GCPArray);
+        }
+        return GCPArrayMap;
+    }
+
+    private void capMinimumReadQualities(GATKSAMRecord read, byte[] readQuals, byte[] readInsQuals, byte[] readDelQuals) {
+        for( int kkk = 0; kkk < readQuals.length; kkk++ ) {
+            readQuals[kkk] = (byte) Math.min( 0xff & readQuals[kkk], read.getMappingQuality()); // cap base quality by mapping quality, as in UG
+            readQuals[kkk] = ( readQuals[kkk] < BASE_QUALITY_SCORE_THRESHOLD ? QualityUtils.MIN_USABLE_Q_SCORE : readQuals[kkk] );
+            readInsQuals[kkk] = ( readInsQuals[kkk] < QualityUtils.MIN_USABLE_Q_SCORE ? QualityUtils.MIN_USABLE_Q_SCORE : readInsQuals[kkk] );
+            readDelQuals[kkk] = ( readDelQuals[kkk] < QualityUtils.MIN_USABLE_Q_SCORE ? QualityUtils.MIN_USABLE_Q_SCORE : readDelQuals[kkk] );
+        }
+    }
+
+    /**
+     * Pre-processing of the reads to be evaluated at the current location from the current sample.
+     * We apply the PCR Error Model, and cap the minimum base, insertion, and deletion qualities of each read.
+     * Modified copies of reads are packed into a new list, while original reads are retained for downstream use
+     *
+     * @param reads The original list of unmodified reads
+     * @return processedReads. A new list of reads, in the same order, whose qualities have been altered by PCR error model and minimal quality thresholding
+     */
+    private List<GATKSAMRecord> modifyReadQualities(final List<GATKSAMRecord> reads) {
+        List<GATKSAMRecord> processedReads = new LinkedList<>();
+        for ( GATKSAMRecord read : reads ) {
+
+            final byte[] readBases = read.getReadBases();
+
+            // NOTE -- must clone anything that gets modified here so we don't screw up future uses of the read
+            final byte[] readQuals = read.getBaseQualities().clone();
+            final byte[] readInsQuals = read.getBaseInsertionQualities().clone();
+            final byte[] readDelQuals = read.getBaseDeletionQualities().clone();
+
+            applyPCRErrorModel(readBases, readInsQuals, readDelQuals);
+            capMinimumReadQualities(read, readQuals, readInsQuals, readDelQuals);
+
+            // Create a new copy of the read and sets its base qualities to the modified versions.
+            // Pack this into a new list for return
+            final GATKSAMRecord processedRead = GATKSAMRecord.createQualityModifiedRead(read, readBases, readQuals, readInsQuals, readDelQuals);
+            processedReads.add(processedRead);
+        }
+        return processedReads;
+    }
+
+    /**
+     * Post-processing of the read/allele likelihoods.
+     *
+     * We send quality-capped reads to the pairHMM for evaluation, and it returns a map containing these capped reads.
+     * We wish to return a map containing the original, unmodified reads.
+     *
+     * At the same time, we want to effectively set a lower cap on the reference score, based on the global mis-mapping rate.
+     * This protects us from the case where the assembly has produced haplotypes
+     * that are very divergent from reference, but are supported by only one read.  In effect
+     * we capping how badly scoring the reference can be for any read by the chance that the read
+     * itself just doesn't belong here
+     *
+     * @param perReadAlleleLikelihoodMap the original map returned by the PairHMM. Contains the processed reads, the haplotype Alleles, and their log10ls
+     * @param reads Our original, unmodified reads
+     * @param processedReads Reads whose minimum base,insertion,deletion qualities have been capped; these were actually used to derive log10ls
+     * @param alleleHaplotypeMap The map associating the Allele and Haplotype versions of each haplotype
+     *
+     * @return processedReadAlleleLikelihoodMap; a new PRALM containing the original reads, and their haplotype log10ls including capped reference log10ls
+     */
+    private PerReadAlleleLikelihoodMap capReferenceHaplotypeLikelihoods(PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap, List<GATKSAMRecord> reads, List<GATKSAMRecord> processedReads, Map<Allele, Haplotype> alleleHaplotypeMap){
+
+        // a new read/allele map, to contain the uncapped reads, haplotypes, and potentially the capped reference log10ls
+        final PerReadAlleleLikelihoodMap processedReadAlleleLikelihoodMap = new PerReadAlleleLikelihoodMap();
+
+        Allele refAllele = null;
+        final int numReads = reads.size();
+        for (int readIndex = 0; readIndex < numReads; readIndex++) {
+
+            // Get the original and quality-modified read from their respective lists
+            // Note that this requires both lists to have reads in the same order
+            final GATKSAMRecord originalRead = reads.get(readIndex);
+            final GATKSAMRecord processedRead = processedReads.get(readIndex);
+
+            // keep track of the reference likelihood and the best non-ref likelihood
+            double refLog10l = Double.NEGATIVE_INFINITY;
+            double bestNonReflog10L = Double.NEGATIVE_INFINITY;
+
+            for ( Allele allele : alleleHaplotypeMap.keySet() ) {
+                final double log10l = perReadAlleleLikelihoodMap.getLikelihoodAssociatedWithReadAndAllele(processedRead, allele);
+                final Haplotype haplotype = alleleHaplotypeMap.get(allele);
+                if ( haplotype.isNonReference() )
+                    bestNonReflog10L = Math.max(bestNonReflog10L, log10l);
+                else {
+                    refAllele = allele;
+                    refLog10l = log10l;
+                }
+                writeDebugLikelihoods(processedRead, haplotype, log10l);
+
+                // add the ORIGINAL (non-capped) read to the final map, along with the current haplotype and associated log10l
+                processedReadAlleleLikelihoodMap.add(originalRead, allele, log10l);
+            }
+
+            // ensure that the reference haplotype is no worse than the best non-ref haplotype minus the global
+            // mismapping rate.  This protects us from the case where the assembly has produced haplotypes
+            // that are very divergent from reference, but are supported by only one read.  In effect
+            // we capping how badly scoring the reference can be for any read by the chance that the read
+            // itself just doesn't belong here
+            final double worstRefLog10Allowed = bestNonReflog10L + log10globalReadMismappingRate;
+            if ( refLog10l < (worstRefLog10Allowed) ) {
+                processedReadAlleleLikelihoodMap.add(originalRead, refAllele, worstRefLog10Allowed);
+            }
+        }
+        return processedReadAlleleLikelihoodMap;
+    }
+
+
     public Map<String, PerReadAlleleLikelihoodMap> computeReadLikelihoods( final List<Haplotype> haplotypes, final Map<String, List<GATKSAMRecord>> perSampleReadList ) {
-        // configure the HMM
-        initializePairHMM(haplotypes, perSampleReadList);
 
         // Add likelihoods for each sample's reads to our stratifiedReadMap
         final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap = new LinkedHashMap<>();
@@ -218,137 +321,22 @@ public class LikelihoodCalculationEngine {
     }
 
     private PerReadAlleleLikelihoodMap computeReadLikelihoods( final List<Haplotype> haplotypes, final List<GATKSAMRecord> reads) {
-        // first, a little set up to get copies of the Haplotypes that are Alleles (more efficient than creating them each time)
-        final BatchPairHMM batchPairHMM = (pairHMM.get() instanceof BatchPairHMM) ? (BatchPairHMM)pairHMM.get() : null;
-        final Vector<GATKSAMRecord> batchedReads = new Vector<GATKSAMRecord>(reads.size());
-        final int numHaplotypes = haplotypes.size();
-        final Map<Haplotype, Allele> alleleVersions = new LinkedHashMap<>(numHaplotypes);
-        Allele refAllele = null;
-        for ( final Haplotype haplotype : haplotypes ) {
-            final Allele allele = Allele.create(haplotype, true);
-            alleleVersions.put(haplotype, allele);
-            if ( haplotype.isReference() ) refAllele = allele;
-        }
 
-        final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = new PerReadAlleleLikelihoodMap();
-        for( final GATKSAMRecord read : reads ) {
+        // Modify the read qualities by applying the PCR error model and capping the minimum base,insertion,deletion qualities
+        List<GATKSAMRecord> processedReads = modifyReadQualities(reads);
 
-            final byte[] readBases = read.getReadBases();
-            final byte[] overallGCP = new byte[read.getReadLength()];
-            Arrays.fill( overallGCP, constantGCP ); // Is there a way to derive empirical estimates for this from the data?
+        // Get alleles corresponding to our haplotypees
+        Map<Allele, Haplotype> alleleHaplotypeMap = createAlleleMap(haplotypes);
 
-            // NOTE -- must clone anything that gets modified here so we don't screw up future uses of the read
-            final byte[] readQuals = read.getBaseQualities().clone();
-            final byte[] readInsQuals = read.getBaseInsertionQualities().clone();
-            final byte[] readDelQuals = read.getBaseDeletionQualities().clone();
+        // Get an array containing the constantGCP for each read in our modified read list
+        Map<GATKSAMRecord,byte[]> GCPArrayMap = fillGCPArrays(processedReads);
 
-            applyPCRErrorModel(readBases, readInsQuals, readDelQuals);
+        // Run the PairHMM to calculate the log10 likelihood of each (processed) reads' arising from each haplotype
+        PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = pairHMMThreadLocal.get().computeLikelihoods(processedReads, alleleHaplotypeMap, GCPArrayMap);
 
-            for( int kkk = 0; kkk < readQuals.length; kkk++ ) {
-                readQuals[kkk] = (byte) Math.min( 0xff & readQuals[kkk], read.getMappingQuality()); // cap base quality by mapping quality, as in UG
-                readQuals[kkk] = ( readQuals[kkk] < BASE_QUALITY_SCORE_THRESHOLD ? QualityUtils.MIN_USABLE_Q_SCORE : readQuals[kkk] );
-                readInsQuals[kkk] = ( readInsQuals[kkk] < QualityUtils.MIN_USABLE_Q_SCORE ? QualityUtils.MIN_USABLE_Q_SCORE : readInsQuals[kkk] );
-                readDelQuals[kkk] = ( readDelQuals[kkk] < QualityUtils.MIN_USABLE_Q_SCORE ? QualityUtils.MIN_USABLE_Q_SCORE : readDelQuals[kkk] );
-            }
+        // Generate a new map containing the original, unmodified reads, and with minimal reference haplotype log10ls determined from the global mis-mapping rate
 
-            if ( batchPairHMM != null ) {
-                batchPairHMM.batchAdd(haplotypes, readBases, readQuals, readInsQuals, readDelQuals, overallGCP);
-                batchedReads.add(read);
-                continue;
-            }
-
-            // keep track of the reference likelihood and the best non-ref likelihood
-            double refLog10l = Double.NEGATIVE_INFINITY;
-            double bestNonReflog10L = Double.NEGATIVE_INFINITY;
-
-            // iterate over all haplotypes, calculating the likelihood of the read for each haplotype
-            for( int jjj = 0; jjj < numHaplotypes; jjj++ ) {
-                final Haplotype haplotype = haplotypes.get(jjj);
-                final byte[] nextHaplotypeBases = (jjj == numHaplotypes - 1) ? null : haplotypes.get(jjj+1).getBases();
-                final boolean isFirstHaplotype = jjj == 0;
-                final double log10l = pairHMM.get().computeReadLikelihoodGivenHaplotypeLog10(haplotype.getBases(),
-                        readBases, readQuals, readInsQuals, readDelQuals, overallGCP, isFirstHaplotype, nextHaplotypeBases);
-
-                if ( WRITE_LIKELIHOODS_TO_FILE ) {
-                    likelihoodsStream.printf("%s %s %s %s %s %s %f%n",
-                            haplotype.getBaseString(),
-                            new String(readBases),
-                            SAMUtils.phredToFastq(readQuals),
-                            SAMUtils.phredToFastq(readInsQuals),
-                            SAMUtils.phredToFastq(readDelQuals),
-                            SAMUtils.phredToFastq(overallGCP),
-                            log10l);
-                }
-
-                if ( haplotype.isNonReference() )
-                    bestNonReflog10L = Math.max(bestNonReflog10L, log10l);
-                else
-                    refLog10l = log10l;
-
-                perReadAlleleLikelihoodMap.add(read, alleleVersions.get(haplotype), log10l);
-            }
-
-            // ensure that the reference haplotype is no worse than the best non-ref haplotype minus the global
-            // mismapping rate.  This protects us from the case where the assembly has produced haplotypes
-            // that are very divergent from reference, but are supported by only one read.  In effect
-            // we capping how badly scoring the reference can be for any read by the chance that the read
-            // itself just doesn't belong here
-            final double worstRefLog10Allowed = bestNonReflog10L + log10globalReadMismappingRate;
-            if ( refLog10l < (worstRefLog10Allowed) ) {
-                perReadAlleleLikelihoodMap.add(read, refAllele, worstRefLog10Allowed);
-            }
-        }
-
-        if ( batchPairHMM != null ) {
-            for( final GATKSAMRecord read : batchedReads ) {
-                double refLog10l = Double.NEGATIVE_INFINITY;
-                double bestNonReflog10L = Double.NEGATIVE_INFINITY;
-                final double[] likelihoods = batchPairHMM.batchGetResult();
-                for( int jjj = 0; jjj < numHaplotypes; jjj++ ) {
-                    final Haplotype haplotype = haplotypes.get(jjj);
-                    final double log10l = likelihoods[jjj];
-
-                    if ( WRITE_LIKELIHOODS_TO_FILE ) {
-                        final byte[] overallGCP = new byte[read.getReadLength()];
-                        Arrays.fill( overallGCP, constantGCP ); // Is there a way to derive empirical estimates for this from the data?
-                        // NOTE -- must clone anything that gets modified here so we don't screw up future uses of the read
-                        final byte[] readQuals = read.getBaseQualities().clone();
-                        final byte[] readInsQuals = read.getBaseInsertionQualities();
-                        final byte[] readDelQuals = read.getBaseDeletionQualities();
-                        for( int kkk = 0; kkk < readQuals.length; kkk++ ) {
-                            readQuals[kkk] = (byte) Math.min( 0xff & readQuals[kkk], read.getMappingQuality()); // cap base quality by mapping quality, as in UG
-                            //readQuals[kkk] = ( readQuals[kkk] > readInsQuals[kkk] ? readInsQuals[kkk] : readQuals[kkk] ); // cap base quality by base insertion quality, needs to be evaluated
-                            //readQuals[kkk] = ( readQuals[kkk] > readDelQuals[kkk] ? readDelQuals[kkk] : readQuals[kkk] ); // cap base quality by base deletion quality, needs to be evaluated
-                            // TODO -- why is Q18 hard-coded here???
-                            readQuals[kkk] = ( readQuals[kkk] < (byte) 18 ? QualityUtils.MIN_USABLE_Q_SCORE : readQuals[kkk] );
-                        }
-                        likelihoodsStream.printf("%s %s %s %s %s %s %f%n",
-                                haplotype.getBaseString(),
-                                new String(read.getReadBases()),
-                                SAMUtils.phredToFastq(readQuals),
-                                SAMUtils.phredToFastq(readInsQuals),
-                                SAMUtils.phredToFastq(readDelQuals),
-                                SAMUtils.phredToFastq(overallGCP),
-                                log10l);
-                    }
-
-                    if ( haplotype.isNonReference() )
-                        bestNonReflog10L = Math.max(bestNonReflog10L, log10l);
-                    else
-                        refLog10l = log10l;
-
-
-                    perReadAlleleLikelihoodMap.add(read, alleleVersions.get(haplotype), log10l);
-                }
-
-                final double worstRefLog10Allowed = bestNonReflog10L + log10globalReadMismappingRate;
-                if ( refLog10l < (worstRefLog10Allowed) ) {
-                    perReadAlleleLikelihoodMap.add(read, refAllele, worstRefLog10Allowed);
-                }
-            }
-        }
-
-        return perReadAlleleLikelihoodMap;
+        return capReferenceHaplotypeLikelihoods(perReadAlleleLikelihoodMap, reads, processedReads, alleleHaplotypeMap);
     }
 
     @Requires({"alleleOrdering.size() > 0"})
@@ -421,125 +409,125 @@ public class LikelihoodCalculationEngine {
     // System to compute the best N haplotypes for genotyping
     //
     // --------------------------------------------------------------------------------
-
-    /**
-     * Helper function for selectBestHaplotypesFromEachSample that updates the score of haplotype haplotypeAsAllele
-     * @param map an annoying map object that moves us between the allele and haplotype representation
-     * @param haplotypeAsAllele the allele version of the haplotype
-     * @return the haplotype version, with its score incremented by 1 if its non-reference
-     */
-    private Haplotype updateSelectHaplotype(final Map<Allele, Haplotype> map, final Allele haplotypeAsAllele) {
-        final Haplotype h = map.get(haplotypeAsAllele); // TODO -- fixme when haplotypes are properly generic
-        if ( h.isNonReference() ) h.setScore(h.getScore() + 1); // ref is already at max value
-        return h;
-    }
-
-    /**
-     * Take the best N haplotypes and return them as a list
-     *
-     * Only considers the haplotypes selectedHaplotypes that were actually selected by at least one sample
-     * as it's preferred haplotype.  Takes the best N haplotypes from selectedHaplotypes in decreasing
-     * order of score (so higher score haplotypes are preferred).  The N we take is determined by
-     *
-     * N = min(2 * nSamples + 1, maxNumHaplotypesInPopulation)
-     *
-     * where 2 * nSamples is the number of chromosomes in 2 samples including the reference, and our workload is
-     * bounded by maxNumHaplotypesInPopulation as that number can grow without bound
-     *
-     * @param selectedHaplotypes a non-null set of haplotypes with scores >= 1
-     * @param nSamples the number of samples used to select the haplotypes
-     * @param maxNumHaplotypesInPopulation the maximum number of haplotypes we're allowed to take, regardless of nSamples
-     * @return a list of N or fewer haplotypes, with the reference haplotype first
-     */
-    private List<Haplotype> selectBestHaplotypesAccordingToScore(final Set<Haplotype> selectedHaplotypes, final int nSamples, final int maxNumHaplotypesInPopulation) {
-        final List<Haplotype> selectedHaplotypesList = new ArrayList<Haplotype>(selectedHaplotypes);
-        Collections.sort(selectedHaplotypesList, new HaplotypeScoreComparator());
-        final int numChromosomesInSamplesPlusRef = 2 * nSamples + 1;
-        final int haplotypesToKeep = Math.min(numChromosomesInSamplesPlusRef, maxNumHaplotypesInPopulation);
-        final List<Haplotype> bestHaplotypes = selectedHaplotypesList.size() <= haplotypesToKeep ? selectedHaplotypesList : selectedHaplotypesList.subList(0, haplotypesToKeep);
-        if ( bestHaplotypes.get(0).isNonReference()) throw new IllegalStateException("BUG: reference haplotype should be first in list");
-        return bestHaplotypes;
-    }
-
-    /**
-     * Select the best haplotypes for genotyping the samples in stratifiedReadMap
-     *
-     * Selects these haplotypes by counting up how often each haplotype is selected as one of the most likely
-     * haplotypes per sample.  What this means is that each sample computes the diploid genotype likelihoods for
-     * all possible pairs of haplotypes, and the pair with the highest likelihood has each haplotype each get
-     * one extra count for each haplotype (so hom-var haplotypes get two counts).  After performing this calculation
-     * the best N haplotypes are selected (@see #selectBestHaplotypesAccordingToScore) and a list of the
-     * haplotypes in order of score are returned, ensuring that at least one of the haplotypes is reference.
-     *
-     * @param haplotypes a list of all haplotypes we're considering
-     * @param stratifiedReadMap a map from sample -> read likelihoods per haplotype
-     * @param maxNumHaplotypesInPopulation the max. number of haplotypes we can select from haplotypes
-     * @return a list of selected haplotypes with size <= maxNumHaplotypesInPopulation
-     */
-    public List<Haplotype> selectBestHaplotypesFromEachSample(final List<Haplotype> haplotypes, final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap, final int maxNumHaplotypesInPopulation) {
-        if ( haplotypes.size() < 2 ) throw new IllegalArgumentException("Must have at least 2 haplotypes to consider but only have " + haplotypes);
-
-        if ( haplotypes.size() == 2 ) return haplotypes; // fast path -- we'll always want to use 2 haplotypes
-
-        // all of the haplotypes that at least one sample called as one of the most likely
-        final Set<Haplotype> selectedHaplotypes = new HashSet<>();
-        selectedHaplotypes.add(findReferenceHaplotype(haplotypes)); // ref is always one of the selected
-
-        // our annoying map from allele -> haplotype
-        final Map<Allele, Haplotype> allele2Haplotype = new HashMap<>();
-        for ( final Haplotype h : haplotypes ) {
-            h.setScore(h.isReference() ? Double.MAX_VALUE : 0.0); // set all of the scores to 0 (lowest value) for all non-ref haplotypes
-            allele2Haplotype.put(Allele.create(h, h.isReference()), h);
-        }
-
-        // for each sample, compute the most likely pair of haplotypes
-        for ( final Map.Entry<String, PerReadAlleleLikelihoodMap> entry : stratifiedReadMap.entrySet() ) {
-            // get the two most likely haplotypes under a diploid model for this sample
-            final MostLikelyAllele mla = entry.getValue().getMostLikelyDiploidAlleles();
-
-            if ( mla != null ) { // there was something to evaluate in this sample
-                // note that there must be at least 2 haplotypes
-                final Haplotype best = updateSelectHaplotype(allele2Haplotype, mla.getMostLikelyAllele());
-                final Haplotype second = updateSelectHaplotype(allele2Haplotype, mla.getSecondMostLikelyAllele());
-
-//            if ( DEBUG ) {
-//                logger.info("Chose haplotypes " + best + " " + best.getCigar() + " and " + second + " " + second.getCigar() + " for sample " + entry.getKey());
+//
+//    /**
+//     * Helper function for selectBestHaplotypesFromEachSample that updates the score of haplotype haplotypeAsAllele
+//     * @param map an annoying map object that moves us between the allele and haplotype representation
+//     * @param haplotypeAsAllele the allele version of the haplotype
+//     * @return the haplotype version, with its score incremented by 1 if its non-reference
+//     */
+//    private Haplotype updateSelectHaplotype(final Map<Allele, Haplotype> map, final Allele haplotypeAsAllele) {
+//        final Haplotype h = map.get(haplotypeAsAllele); // TODO -- fixme when haplotypes are properly generic
+//        if ( h.isNonReference() ) h.setScore(h.getScore() + 1); // ref is already at max value
+//        return h;
+//    }
+//
+//    /**
+//     * Take the best N haplotypes and return them as a list
+//     *
+//     * Only considers the haplotypes selectedHaplotypes that were actually selected by at least one sample
+//     * as it's preferred haplotype.  Takes the best N haplotypes from selectedHaplotypes in decreasing
+//     * order of score (so higher score haplotypes are preferred).  The N we take is determined by
+//     *
+//     * N = min(2 * nSamples + 1, maxNumHaplotypesInPopulation)
+//     *
+//     * where 2 * nSamples is the number of chromosomes in 2 samples including the reference, and our workload is
+//     * bounded by maxNumHaplotypesInPopulation as that number can grow without bound
+//     *
+//     * @param selectedHaplotypes a non-null set of haplotypes with scores >= 1
+//     * @param nSamples the number of samples used to select the haplotypes
+//     * @param maxNumHaplotypesInPopulation the maximum number of haplotypes we're allowed to take, regardless of nSamples
+//     * @return a list of N or fewer haplotypes, with the reference haplotype first
+//     */
+//    private List<Haplotype> selectBestHaplotypesAccordingToScore(final Set<Haplotype> selectedHaplotypes, final int nSamples, final int maxNumHaplotypesInPopulation) {
+//        final List<Haplotype> selectedHaplotypesList = new ArrayList<>(selectedHaplotypes);
+//        Collections.sort(selectedHaplotypesList, new HaplotypeScoreComparator());
+//        final int numChromosomesInSamplesPlusRef = 2 * nSamples + 1;
+//        final int haplotypesToKeep = Math.min(numChromosomesInSamplesPlusRef, maxNumHaplotypesInPopulation);
+//        final List<Haplotype> bestHaplotypes = selectedHaplotypesList.size() <= haplotypesToKeep ? selectedHaplotypesList : selectedHaplotypesList.subList(0, haplotypesToKeep);
+//        if ( bestHaplotypes.get(0).isNonReference()) throw new IllegalStateException("BUG: reference haplotype should be first in list");
+//        return bestHaplotypes;
+//    }
+//
+//    /**
+//     * Select the best haplotypes for genotyping the samples in stratifiedReadMap
+//     *
+//     * Selects these haplotypes by counting up how often each haplotype is selected as one of the most likely
+//     * haplotypes per sample.  What this means is that each sample computes the diploid genotype likelihoods for
+//     * all possible pairs of haplotypes, and the pair with the highest likelihood has each haplotype each get
+//     * one extra count for each haplotype (so hom-var haplotypes get two counts).  After performing this calculation
+//     * the best N haplotypes are selected (@see #selectBestHaplotypesAccordingToScore) and a list of the
+//     * haplotypes in order of score are returned, ensuring that at least one of the haplotypes is reference.
+//     *
+//     * @param haplotypes a list of all haplotypes we're considering
+//     * @param stratifiedReadMap a map from sample -> read likelihoods per haplotype
+//     * @param maxNumHaplotypesInPopulation the max. number of haplotypes we can select from haplotypes
+//     * @return a list of selected haplotypes with size <= maxNumHaplotypesInPopulation
+//     */
+//    public List<Haplotype> selectBestHaplotypesFromEachSample(final List<Haplotype> haplotypes, final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap, final int maxNumHaplotypesInPopulation) {
+//        if ( haplotypes.size() < 2 ) throw new IllegalArgumentException("Must have at least 2 haplotypes to consider but only have " + haplotypes);
+//
+//        if ( haplotypes.size() == 2 ) return haplotypes; // fast path -- we'll always want to use 2 haplotypes
+//
+//        // all of the haplotypes that at least one sample called as one of the most likely
+//        final Set<Haplotype> selectedHaplotypes = new HashSet<>();
+//        selectedHaplotypes.add(findReferenceHaplotype(haplotypes)); // ref is always one of the selected
+//
+//        // our annoying map from allele -> haplotype
+//        final Map<Allele, Haplotype> allele2Haplotype = new HashMap<>();
+//        for ( final Haplotype h : haplotypes ) {
+//            h.setScore(h.isReference() ? Double.MAX_VALUE : 0.0); // set all of the scores to 0 (lowest value) for all non-ref haplotypes
+//            allele2Haplotype.put(Allele.create(h, h.isReference()), h);
+//        }
+//
+//        // for each sample, compute the most likely pair of haplotypes
+//        for ( final Map.Entry<String, PerReadAlleleLikelihoodMap> entry : stratifiedReadMap.entrySet() ) {
+//            // get the two most likely haplotypes under a diploid model for this sample
+//            final MostLikelyAllele mla = entry.getValue().getMostLikelyDiploidAlleles();
+//
+//            if ( mla != null ) { // there was something to evaluate in this sample
+//                // note that there must be at least 2 haplotypes
+//                final Haplotype best = updateSelectHaplotype(allele2Haplotype, mla.getMostLikelyAllele());
+//                final Haplotype second = updateSelectHaplotype(allele2Haplotype, mla.getSecondMostLikelyAllele());
+//
+////            if ( DEBUG ) {
+////                logger.info("Chose haplotypes " + best + " " + best.getCigar() + " and " + second + " " + second.getCigar() + " for sample " + entry.getKey());
+////            }
+//
+//                // add these two haplotypes to the set of haplotypes that have been selected
+//                selectedHaplotypes.add(best);
+//                selectedHaplotypes.add(second);
+//
+//                // we've already selected all of our haplotypes, and we don't need to prune them down
+//                if ( selectedHaplotypes.size() == haplotypes.size() && haplotypes.size() < maxNumHaplotypesInPopulation )
+//                    break;
 //            }
-
-                // add these two haplotypes to the set of haplotypes that have been selected
-                selectedHaplotypes.add(best);
-                selectedHaplotypes.add(second);
-
-                // we've already selected all of our haplotypes, and we don't need to prune them down
-                if ( selectedHaplotypes.size() == haplotypes.size() && haplotypes.size() < maxNumHaplotypesInPopulation )
-                    break;
-            }
-        }
-
-        // take the best N haplotypes forward, in order of the number of samples that choose them
-        final int nSamples = stratifiedReadMap.size();
-        final List<Haplotype> bestHaplotypes = selectBestHaplotypesAccordingToScore(selectedHaplotypes, nSamples, maxNumHaplotypesInPopulation);
-
-        if ( DEBUG ) {
-            logger.info("Chose " + (bestHaplotypes.size() - 1) + " alternate haplotypes to genotype in all samples.");
-            for ( final Haplotype h : bestHaplotypes ) {
-                logger.info("\tHaplotype " + h.getCigar() + " selected for further genotyping" + (h.isNonReference() ? " found " + (int)h.getScore() + " haplotypes" : " as ref haplotype"));
-            }
-        }
-        return bestHaplotypes;
-    }
-
-    /**
-     * Find the haplotype that isRef(), or @throw ReviewedStingException if one isn't found
-     * @param haplotypes non-null list of haplotypes
-     * @return the reference haplotype
-     */
-    private static Haplotype findReferenceHaplotype( final List<Haplotype> haplotypes ) {
-        for( final Haplotype h : haplotypes ) {
-            if( h.isReference() ) return h;
-        }
-        throw new ReviewedStingException( "No reference haplotype found in the list of haplotypes!" );
-    }
+//        }
+//
+//        // take the best N haplotypes forward, in order of the number of samples that choose them
+//        final int nSamples = stratifiedReadMap.size();
+//        final List<Haplotype> bestHaplotypes = selectBestHaplotypesAccordingToScore(selectedHaplotypes, nSamples, maxNumHaplotypesInPopulation);
+//
+//        if ( DEBUG ) {
+//            logger.info("Chose " + (bestHaplotypes.size() - 1) + " alternate haplotypes to genotype in all samples.");
+//            for ( final Haplotype h : bestHaplotypes ) {
+//                logger.info("\tHaplotype " + h.getCigar() + " selected for further genotyping" + (h.isNonReference() ? " found " + (int)h.getScore() + " haplotypes" : " as ref haplotype"));
+//            }
+//        }
+//        return bestHaplotypes;
+//    }
+//
+//    /**
+//     * Find the haplotype that isRef(), or @throw ReviewedStingException if one isn't found
+//     * @param haplotypes non-null list of haplotypes
+//     * @return the reference haplotype
+//     */
+//    private static Haplotype findReferenceHaplotype( final List<Haplotype> haplotypes ) {
+//        for( final Haplotype h : haplotypes ) {
+//            if( h.isReference() ) return h;
+//        }
+//        throw new ReviewedStingException( "No reference haplotype found in the list of haplotypes!" );
+//    }
 
     // --------------------------------------------------------------------------------
     //
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
index 3c6e409b9..97431368e 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
@@ -48,11 +48,11 @@ package org.broadinstitute.sting.gatk.walkers.indels;
 
 import com.google.java.contract.Ensures;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.haplotype.Haplotype;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.clipping.ReadClipper;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.haplotype.Haplotype;
 import org.broadinstitute.sting.utils.pairhmm.ArrayLoglessPairHMM;
 import org.broadinstitute.sting.utils.pairhmm.Log10PairHMM;
 import org.broadinstitute.sting.utils.pairhmm.LoglessPairHMM;
@@ -65,6 +65,7 @@ import org.broadinstitute.variant.variantcontext.Allele;
 
 import java.util.Arrays;
 import java.util.LinkedHashMap;
+import java.util.LinkedList;
 import java.util.Map;
 
 //import org.broadinstitute.sting.utils.pairhmm.LoglessCachingPairHMM;
@@ -206,6 +207,39 @@ public class PairHMMIndelErrorModel {
         }
     }
 
+    private LinkedHashMap<Allele, Haplotype> trimHaplotypes(final LinkedHashMap<Allele, Haplotype> haplotypeMap,
+                                                            long startLocationInRefForHaplotypes,
+                                                            long stopLocationInRefForHaplotypes,
+                                                            final ReferenceContext ref){
+
+        final LinkedHashMap<Allele, Haplotype> trimmedHaplotypeMap = new LinkedHashMap<>();
+        for (final Allele a: haplotypeMap.keySet()) {
+
+            final Haplotype haplotype = haplotypeMap.get(a);
+
+            if (stopLocationInRefForHaplotypes > haplotype.getStopPosition())
+                stopLocationInRefForHaplotypes = haplotype.getStopPosition();
+
+            if (startLocationInRefForHaplotypes < haplotype.getStartPosition())
+                startLocationInRefForHaplotypes = haplotype.getStartPosition();
+            else if (startLocationInRefForHaplotypes > haplotype.getStopPosition())
+                startLocationInRefForHaplotypes = haplotype.getStopPosition();
+
+            final long indStart = startLocationInRefForHaplotypes - haplotype.getStartPosition();
+            final long indStop =  stopLocationInRefForHaplotypes - haplotype.getStartPosition();
+
+            if (DEBUG)
+                System.out.format("indStart: %d indStop: %d WinStart:%d WinStop:%d start: %d stop: %d\n",
+                        indStart, indStop, ref.getWindow().getStart(), ref.getWindow().getStop(), startLocationInRefForHaplotypes, stopLocationInRefForHaplotypes);
+
+            // get the trimmed haplotype-bases array and create a new haplotype based on it. Pack this into the new map
+            final byte[] trimmedHaplotypeBases = Arrays.copyOfRange(haplotype.getBases(), (int)indStart, (int)indStop);
+            final Haplotype trimmedHaplotype = new Haplotype(trimmedHaplotypeBases, haplotype.isReference());
+            trimmedHaplotypeMap.put(a, trimmedHaplotype);
+        }
+        return trimmedHaplotypeMap;
+    }
+
 
     public synchronized double[] computeDiploidReadHaplotypeLikelihoods(final ReadBackedPileup pileup,
                                                                         final LinkedHashMap<Allele, Haplotype> haplotypeMap,
@@ -231,6 +265,8 @@ public class PairHMMIndelErrorModel {
                                                                           final int[] readCounts) {
         final double readLikelihoods[][] = new double[pileup.getNumberOfElements()][haplotypeMap.size()];
 
+        final LinkedList<GATKSAMRecord> readList = new LinkedList<>();
+        final Map<GATKSAMRecord, byte[]> readGCPArrayMap = new LinkedHashMap<>();
         int readIdx=0;
         for (PileupElement p: pileup) {
             // > 1 when the read is a consensus read representing multiple independent observations
@@ -369,86 +405,30 @@ public class PairHMMIndelErrorModel {
                         baseDeletionQualities = contextLogGapOpenProbabilities;
                     }
 
-                    byte[] currentHaplotypeBases = null;
-                    boolean firstHap = true;
-                    double readLikelihood;
-                    Allele currentAllele = null;
-                    for (Allele a: haplotypeMap.keySet()) {
+                    // Create a new read based on the current one, but with trimmed bases/quals, for use in the HMM
+                    final GATKSAMRecord processedRead = GATKSAMRecord.createQualityModifiedRead(read, readBases, readQuals, baseInsertionQualities, baseDeletionQualities);
+                    readList.add(processedRead);
 
-                        Haplotype haplotype = haplotypeMap.get(a);
+                    // Pack the shortened read and its associated gap-continuation-penalty array into a map, as required by PairHMM
+                    readGCPArrayMap.put(processedRead,contextLogGapContinuationProbabilities);
 
-                        if (stopLocationInRefForHaplotypes > haplotype.getStopPosition())
-                            stopLocationInRefForHaplotypes = haplotype.getStopPosition();
+                    // Create a map of alleles to a new set of haplotypes, whose bases have been trimmed to the approprate genomic locations
+                    final Map<Allele, Haplotype> trimmedHaplotypeMap = trimHaplotypes(haplotypeMap, startLocationInRefForHaplotypes, stopLocationInRefForHaplotypes, ref);
 
-                        if (startLocationInRefForHaplotypes < haplotype.getStartPosition())
-                            startLocationInRefForHaplotypes = haplotype.getStartPosition();
-                        else if (startLocationInRefForHaplotypes > haplotype.getStopPosition())
-                            startLocationInRefForHaplotypes = haplotype.getStopPosition();
+                    // Get the likelihoods for our clipped read against each of our trimmed haplotypes.
+                    final PerReadAlleleLikelihoodMap singleReadRawLikelihoods = pairHMM.computeLikelihoods(readList, trimmedHaplotypeMap, readGCPArrayMap);
 
-                        final long indStart = startLocationInRefForHaplotypes - haplotype.getStartPosition();
-                        final long indStop =  stopLocationInRefForHaplotypes - haplotype.getStartPosition();
-
-
-                        if (DEBUG)
-                            System.out.format("indStart: %d indStop: %d WinStart:%d WinStop:%d start: %d stop: %d readLength: %d C:%s\n",
-                                    indStart, indStop, ref.getWindow().getStart(), ref.getWindow().getStop(), startLocationInRefForHaplotypes, stopLocationInRefForHaplotypes, read.getReadLength(), read.getCigar().toString());
-
-                        // peak at the next haplotype in the list
-                        final byte[] nextHaplotypeBases = Arrays.copyOfRange(haplotype.getBases(), (int)indStart, (int)indStop);
-                        // process the current haplotype in the list
-                        if (currentHaplotypeBases != null) {
-                            // it's possible that the indel starts at the last base of the haplotypes
-                            if ( currentHaplotypeBases.length == 0 ) {
-                                readLikelihood = -Double.MAX_VALUE;
-                            } else {
-                                if (firstHap) {
-                                    //no need to reallocate arrays for each new haplotype, as length won't change
-                                    pairHMM.initialize(readBases.length, currentHaplotypeBases.length);
-                                    firstHap = false;
-                                }
-
-                                readLikelihood = pairHMM.computeReadLikelihoodGivenHaplotypeLog10(currentHaplotypeBases, readBases, readQuals,
-                                        baseInsertionQualities, baseDeletionQualities, contextLogGapContinuationProbabilities, firstHap, nextHaplotypeBases);
-                            }
-
-                            if (DEBUG) {
-                                System.out.println("H:"+new String(currentHaplotypeBases));
-                                System.out.println("R:"+new String(readBases));
-                                System.out.format("L:%4.2f\n",readLikelihood);
-                            }
-
-                            perReadAlleleLikelihoodMap.add(p, currentAllele, readLikelihood);
-                            readLikelihoods[readIdx][j++] = readLikelihood;
-                        }
-                        // update the current haplotype
-                        currentHaplotypeBases = nextHaplotypeBases;
-                        currentAllele = a;
-                    }
-                    // process the final haplotype
-                    if (currentHaplotypeBases != null) {
-                        // it's possible that the indel starts at the last base of the haplotypes
-                        if ( currentHaplotypeBases.length == 0 ) {
-                            readLikelihood = -Double.MAX_VALUE;
-                        } else {
-                            if (firstHap) {
-                                //no need to reallocate arrays for each new haplotype, as length won't change
-                                pairHMM.initialize(readBases.length, currentHaplotypeBases.length);
-                                firstHap = false;
-                            }
-                            // there is no next haplotype, so pass null for nextHaplotypeBases.
-                            readLikelihood = pairHMM.computeReadLikelihoodGivenHaplotypeLog10(currentHaplotypeBases, readBases, readQuals,
-                                    baseInsertionQualities, baseDeletionQualities, contextLogGapContinuationProbabilities, firstHap, null);
-                        }
-
-                        if (DEBUG) {
-                            System.out.println("H:"+new String(currentHaplotypeBases));
-                            System.out.println("R:"+new String(readBases));
-                            System.out.format("L:%4.2f\n",readLikelihood);
-                        }
-
-                        perReadAlleleLikelihoodMap.add(p, currentAllele, readLikelihood);
+                    // Pack the original pilup element, each allele, and each associated log10 likelihood into a final map, and add each likelihood to the array
+                    for (Allele a: trimmedHaplotypeMap.keySet()){
+                        double readLikelihood = singleReadRawLikelihoods.getLikelihoodAssociatedWithReadAndAllele(processedRead, a);
+                        perReadAlleleLikelihoodMap.add(p, a, readLikelihood);
                         readLikelihoods[readIdx][j++] = readLikelihood;
                     }
+                    // The readList for sending to the HMM should only ever contain 1 read, as each must be clipped individually
+                    readList.remove(processedRead);
+
+                    // The same is true for the read/GCP-array map
+                    readGCPArrayMap.remove(processedRead);
                 }
             }
             readIdx++;
@@ -472,16 +452,16 @@ public class PairHMMIndelErrorModel {
         return !((read.getAlignmentStart() >= eventStartPos-eventLength && read.getAlignmentStart() <= eventStartPos+1) || (read.getAlignmentEnd() >= eventStartPos && read.getAlignmentEnd() <= eventStartPos + eventLength));
     }
 
-    private int computeFirstDifferingPosition(byte[] b1, byte[] b2) {
-        if (b1.length != b2.length)
-            return 0; // sanity check
-
-        for (int i=0; i < b1.length; i++ ){
-            if ( b1[i]!= b2[i] )
-                return i;
-        }
-        return b1.length;
-    }
+//    private int computeFirstDifferingPosition(byte[] b1, byte[] b2) {
+//        if (b1.length != b2.length)
+//            return 0; // sanity check
+//
+//        for (int i=0; i < b1.length; i++ ){
+//            if ( b1[i]!= b2[i] )
+//                return i;
+//        }
+//        return b1.length;
+//    }
 
     private static double[] getDiploidHaplotypeLikelihoods(final int numHaplotypes, final int readCounts[], final double readLikelihoods[][]) {
         final double[][] haplotypeLikehoodMatrix = new double[numHaplotypes][numHaplotypes];
diff --git a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/ArrayLoglessPairHMM.java b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/ArrayLoglessPairHMM.java
index 4b996e770..a693ec22d 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/ArrayLoglessPairHMM.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/ArrayLoglessPairHMM.java
@@ -49,6 +49,7 @@ package org.broadinstitute.sting.utils.pairhmm;
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import org.broadinstitute.sting.utils.QualityUtils;
+
 import java.util.Arrays;
 
 /**
diff --git a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/CnyPairHMM.java b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/CnyPairHMM.java
index d92b918ba..b80036bb2 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/CnyPairHMM.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/CnyPairHMM.java
@@ -47,12 +47,16 @@
 package org.broadinstitute.sting.utils.pairhmm;
 
 import org.broadinstitute.sting.utils.haplotype.Haplotype;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.variant.variantcontext.Allele;
 
 import java.io.File;
 import java.lang.reflect.Field;
 import java.util.Arrays;
 import java.util.LinkedList;
 import java.util.List;
+import java.util.Map;
 
 public final class CnyPairHMM extends PairHMM implements BatchPairHMM {
     private static class HmmInput {
@@ -62,14 +66,14 @@ public final class CnyPairHMM extends PairHMM implements BatchPairHMM {
         public byte[] deletionGOP;
         public byte[] overallGCP;
         public List<Haplotype> haplotypes;
-    };
+    }
 
     public static class ResultQueue {
         private int offset;
         private List<double[]> batchResults;
 
         public ResultQueue() {
-            batchResults = new LinkedList<double[]>();
+            batchResults = new LinkedList<>();
             offset = 0;
         }
 
@@ -92,7 +96,7 @@ public final class CnyPairHMM extends PairHMM implements BatchPairHMM {
     final static String libName = "gmvhdl_gatk_hmm";
 
     private static boolean loaded = false;
-    private List<HmmInput> batchRequests = new LinkedList<HmmInput>();
+    private List<HmmInput> batchRequests = new LinkedList<>();
     private ResultQueue resultQueue = new ResultQueue();
 
     static public boolean isAvailable() {
@@ -184,6 +188,55 @@ public final class CnyPairHMM extends PairHMM implements BatchPairHMM {
         return results;
     }
 
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public PerReadAlleleLikelihoodMap computeLikelihoods(final List<GATKSAMRecord> reads, final Map<Allele, Haplotype> alleleHaplotypeMap, final Map<GATKSAMRecord, byte[]> GCPArrayMap){
+
+        // initialize the pairHMM if necessary
+        if (! initialized) {
+            int readMaxLength = findMaxReadLength(reads);
+            int haplotypeMaxLength = findMaxHaplotypeLength(alleleHaplotypeMap);
+            initialize(readMaxLength, haplotypeMaxLength);
+        }
+
+        // Pass the read bases/quals, and the haplotypes as a list into the HMM
+        performBatchAdditions(reads, alleleHaplotypeMap, GCPArrayMap);
+
+        // Get the log10-likelihoods for each read/haplotype ant pack into the results map
+        final PerReadAlleleLikelihoodMap likelihoodMap = new PerReadAlleleLikelihoodMap();
+        collectLikelihoodResults(reads, alleleHaplotypeMap, likelihoodMap);
+
+        return likelihoodMap;
+    }
+
+    private void collectLikelihoodResults(List<GATKSAMRecord> reads, Map<Allele, Haplotype> alleleHaplotypeMap, PerReadAlleleLikelihoodMap likelihoodMap) {
+        for(final GATKSAMRecord read : reads){
+            final double[] likelihoods = batchGetResult();
+            int jjj = 0;
+            for (Allele allele : alleleHaplotypeMap.keySet()){
+                final double log10l = likelihoods[jjj];
+                likelihoodMap.add(read, allele, log10l);
+                jjj++;
+            }
+        }
+    }
+
+    private void performBatchAdditions(List<GATKSAMRecord> reads, Map<Allele, Haplotype> alleleHaplotypeMap, Map<GATKSAMRecord, byte[]> GCPArrayMap) {
+        final List<Haplotype> haplotypeList = getHaplotypeList(alleleHaplotypeMap);
+        for(final GATKSAMRecord read : reads){
+            final byte[] readBases = read.getReadBases();
+            final byte[] readQuals = read.getBaseQualities();
+            final byte[] readInsQuals = read.getBaseInsertionQualities();
+            final byte[] readDelQuals = read.getBaseDeletionQualities();
+            final byte[] overallGCP = GCPArrayMap.get(read);
+
+            batchAdd(haplotypeList, readBases, readQuals, readInsQuals, readDelQuals, overallGCP);
+        }
+    }
+
+
     protected double subComputeReadLikelihoodGivenHaplotypeLog10( final byte[] haplotypeBases,
                                                                   final byte[] readBases,
                                                                   final byte[] readQuals,
@@ -196,6 +249,14 @@ public final class CnyPairHMM extends PairHMM implements BatchPairHMM {
         return 0.0;
     }
 
+    private List<Haplotype> getHaplotypeList(Map<Allele, Haplotype> alleleHaplotypeMap){
+        final List<Haplotype> haplotypeList = new LinkedList<>();
+        for (Allele a : alleleHaplotypeMap.keySet()){
+             haplotypeList.add(alleleHaplotypeMap.get(a));
+        }
+        return haplotypeList;
+    }
+
     private void enqueuePrepare(byte[] haplotypeBases, byte[] readBases) {
         double[] results = null;
         int n = dequeueRequirement(haplotypeBases.length, readBases.length);
diff --git a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/LoglessPairHMM.java b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/LoglessPairHMM.java
index e745ca1f5..de2994927 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/LoglessPairHMM.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/LoglessPairHMM.java
@@ -70,17 +70,6 @@ public final class LoglessPairHMM extends N2MemoryPairHMM {
     private static final int deletionToDeletion = 5;
 
 
-    /**
-     * {@inheritDoc}
-     */
-    @Override
-    public void initialize(final int readMaxLength, final int haplotypeMaxLength ) {
-        super.initialize(readMaxLength, haplotypeMaxLength);
-
-        transition = new double[paddedMaxReadLength][6];
-        prior = new double[paddedMaxReadLength][paddedMaxHaplotypeLength];
-    }
-
     /**
      * {@inheritDoc}
      */
diff --git a/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java b/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java
index 70be85f54..af22eb7f9 100644
--- a/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java
+++ b/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java
@@ -110,7 +110,7 @@ public class PerReadAlleleLikelihoodMap {
      * @return a map from each allele to a list of reads that 'support' the allele
      */
     protected Map<Allele,List<GATKSAMRecord>> getAlleleStratifiedReadMap() {
-        final Map<Allele, List<GATKSAMRecord>> alleleReadMap = new HashMap<Allele, List<GATKSAMRecord>>(alleles.size());
+        final Map<Allele, List<GATKSAMRecord>> alleleReadMap = new HashMap<>(alleles.size());
         for ( final Allele allele : alleles )
             alleleReadMap.put(allele, new ArrayList<GATKSAMRecord>());
 
@@ -152,7 +152,7 @@ public class PerReadAlleleLikelihoodMap {
      /**
      * Does the current map contain the key associated with a particular SAM record in pileup?
      * @param p                 Pileup element
-     * @return
+     * @return true if the map contains pileup element, else false
      */
     public boolean containsPileupElement(final PileupElement p) {
         return likelihoodReadMap.containsKey(p.getRead());
@@ -176,9 +176,9 @@ public class PerReadAlleleLikelihoodMap {
         return likelihoodReadMap.keySet();
     }
 
-    public Collection<Map<Allele,Double>> getLikelihoodMapValues() {
-        return likelihoodReadMap.values();
-    }
+//    public Collection<Map<Allele,Double>> getLikelihoodMapValues() {
+//        return likelihoodReadMap.values();
+//    }
 
     public int getNumberOfStoredElements() {
         return likelihoodReadMap.size();
@@ -191,6 +191,21 @@ public class PerReadAlleleLikelihoodMap {
         return likelihoodReadMap.get(p.getRead());
     }
 
+
+    /**
+     * Get the log10 likelihood associated with an individual read/allele
+     *
+     * @param read the read whose likelihood we want
+     * @param allele the allele whose likelihood we want
+     * @return the log10 likelihood that this read matches this allele
+     */
+    public double getLikelihoodAssociatedWithReadAndAllele(final GATKSAMRecord read, final Allele allele){
+        if (!allelesSet.contains(allele) || !likelihoodReadMap.containsKey(read))
+            return 0.0;
+
+        return likelihoodReadMap.get(read).get(allele);
+    }
+
     /**
      * Get the most likely alleles estimated across all reads in this object
      *
diff --git a/public/java/src/org/broadinstitute/sting/utils/pairhmm/Log10PairHMM.java b/public/java/src/org/broadinstitute/sting/utils/pairhmm/Log10PairHMM.java
index e7bc5cb56..83b87da95 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pairhmm/Log10PairHMM.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pairhmm/Log10PairHMM.java
@@ -85,9 +85,6 @@ public final class Log10PairHMM extends N2MemoryPairHMM {
             Arrays.fill(insertionMatrix[iii], Double.NEGATIVE_INFINITY);
             Arrays.fill(deletionMatrix[iii], Double.NEGATIVE_INFINITY);
         }
-
-        transition = new double[paddedMaxReadLength][6];
-        prior = new double[paddedMaxReadLength][paddedMaxHaplotypeLength];
     }
 
     /**
diff --git a/public/java/src/org/broadinstitute/sting/utils/pairhmm/N2MemoryPairHMM.java b/public/java/src/org/broadinstitute/sting/utils/pairhmm/N2MemoryPairHMM.java
index a091a0716..c02461c03 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pairhmm/N2MemoryPairHMM.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pairhmm/N2MemoryPairHMM.java
@@ -26,10 +26,6 @@
 package org.broadinstitute.sting.utils.pairhmm;
 
 import com.google.java.contract.Requires;
-import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.MathUtils;
-
-import java.util.Arrays;
 
 /**
  * Superclass for PairHMM that want to use a full read x haplotype matrix for their match, insertion, and deletion matrix
@@ -58,6 +54,9 @@ abstract class N2MemoryPairHMM extends PairHMM {
         matchMatrix = new double[paddedMaxReadLength][paddedMaxHaplotypeLength];
         insertionMatrix = new double[paddedMaxReadLength][paddedMaxHaplotypeLength];
         deletionMatrix = new double[paddedMaxReadLength][paddedMaxHaplotypeLength];
+
+        transition = new double[paddedMaxReadLength][6];
+        prior = new double[paddedMaxReadLength][paddedMaxHaplotypeLength];
     }
 
     /**
diff --git a/public/java/src/org/broadinstitute/sting/utils/pairhmm/PairHMM.java b/public/java/src/org/broadinstitute/sting/utils/pairhmm/PairHMM.java
index eb52f4a85..ce3d43a06 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pairhmm/PairHMM.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pairhmm/PairHMM.java
@@ -28,9 +28,14 @@ package org.broadinstitute.sting.utils.pairhmm;
 import com.google.java.contract.Requires;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.haplotype.Haplotype;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.variant.variantcontext.Allele;
 
 import java.util.Arrays;
-
+import java.util.List;
+import java.util.Map;
 /**
  * Util class for performing the pair HMM for local alignment. Figure 4.3 in Durbin 1998 book.
  *
@@ -59,7 +64,7 @@ public abstract class PairHMM {
     protected int maxHaplotypeLength, maxReadLength;
     protected int paddedMaxReadLength, paddedMaxHaplotypeLength;
     protected int paddedReadLength, paddedHaplotypeLength;
-    private boolean initialized = false;
+    protected boolean initialized = false;
 
     // only used for debugging purposes
     protected boolean doNotUseTristateCorrection = false;
@@ -73,7 +78,7 @@ public abstract class PairHMM {
      * @param haplotypeMaxLength the max length of haplotypes we want to use with this PairHMM
      * @param readMaxLength the max length of reads we want to use with this PairHMM
      */
-    public void initialize( final int readMaxLength, final int haplotypeMaxLength ) {
+    protected void initialize( final int readMaxLength, final int haplotypeMaxLength ) {
         if ( readMaxLength <= 0 ) throw new IllegalArgumentException("READ_MAX_LENGTH must be > 0 but got " + readMaxLength);
         if ( haplotypeMaxLength <= 0 ) throw new IllegalArgumentException("HAPLOTYPE_MAX_LENGTH must be > 0 but got " + haplotypeMaxLength);
 
@@ -90,6 +95,79 @@ public abstract class PairHMM {
         initialized = true;
     }
 
+    protected int findMaxReadLength(final List<GATKSAMRecord> reads) {
+        int listMaxReadLength = 0;
+        for(GATKSAMRecord read : reads){
+            final int readLength = read.getReadLength();
+            if( readLength > listMaxReadLength ) { listMaxReadLength = readLength; }
+        }
+        return listMaxReadLength;
+    }
+
+    protected int findMaxHaplotypeLength(final Map<Allele, Haplotype> haplotypeMap) {
+        int listMaxHaplotypeLength = 0;
+        for( final Allele a: haplotypeMap.keySet() ) {
+            final Haplotype h = haplotypeMap.get(a);
+            final int haplotypeLength = h.getBases().length;
+            if( haplotypeLength > listMaxHaplotypeLength ) { listMaxHaplotypeLength = haplotypeLength; }
+        }
+        return listMaxHaplotypeLength;
+    }
+
+    /**
+     *  Given a list of reads and haplotypes, for every read compute the total probability of said read arising from
+     *  each haplotype given base substitution, insertion, and deletion probabilities.
+     *
+     * @param reads the list of reads
+     * @param alleleHaplotypeMap the list of haplotypes
+     * @param GCPArrayMap Each read is associated with an array containing the gap continuation penalties for use in the model. Length of each GCP-array must match that of its read.
+     * @return a PerReadAlleleLikelihoodMap containing each read, haplotype-allele, and the log10 probability of
+     *          said read coming from the said haplotype under the provided error model
+     */
+    public PerReadAlleleLikelihoodMap computeLikelihoods(final List<GATKSAMRecord> reads, final Map<Allele, Haplotype> alleleHaplotypeMap, final Map<GATKSAMRecord, byte[]> GCPArrayMap) {
+
+        // (re)initialize the pairHMM only if necessary
+        final int readMaxLength = findMaxReadLength(reads);
+        final int haplotypeMaxLength = findMaxHaplotypeLength(alleleHaplotypeMap);
+        if (!initialized || readMaxLength > maxReadLength || haplotypeMaxLength > maxHaplotypeLength) { initialize(readMaxLength, haplotypeMaxLength); }
+
+        final PerReadAlleleLikelihoodMap likelihoodMap = new PerReadAlleleLikelihoodMap();
+        for(GATKSAMRecord read : reads){
+            final byte[] readBases = read.getReadBases();
+            final byte[] readQuals = read.getBaseQualities();
+            final byte[] readInsQuals = read.getBaseInsertionQualities();
+            final byte[] readDelQuals = read.getBaseDeletionQualities();
+            final byte[] overallGCP = GCPArrayMap.get(read);
+
+            // peak at the next haplotype in the list (necessary to get nextHaplotypeBases, which is required for caching in the array implementation)
+            byte[] currentHaplotypeBases = null;
+            boolean isFirstHaplotype = true;
+            Allele currentAllele = null;
+            double log10l;
+            for (final Allele allele : alleleHaplotypeMap.keySet()){
+                final Haplotype haplotype = alleleHaplotypeMap.get(allele);
+                final byte[] nextHaplotypeBases = haplotype.getBases();
+                if (currentHaplotypeBases != null) {
+                     log10l = computeReadLikelihoodGivenHaplotypeLog10(currentHaplotypeBases,
+                            readBases, readQuals, readInsQuals, readDelQuals, overallGCP, isFirstHaplotype, nextHaplotypeBases);
+                    likelihoodMap.add(read, currentAllele, log10l);
+                }
+                // update the current haplotype
+                currentHaplotypeBases = nextHaplotypeBases;
+                currentAllele = allele;
+            }
+            // process the final haplotype
+            if (currentHaplotypeBases != null) {
+
+                // there is no next haplotype, so pass null for nextHaplotypeBases.
+                log10l = computeReadLikelihoodGivenHaplotypeLog10(currentHaplotypeBases,
+                        readBases, readQuals, readInsQuals, readDelQuals, overallGCP, isFirstHaplotype, null);
+                likelihoodMap.add(read, currentAllele, log10l);
+            }
+        }
+        return likelihoodMap;
+    }
+
     /**
      * Compute the total probability of read arising from haplotypeBases given base substitution, insertion, and deletion
      * probabilities.
@@ -110,7 +188,7 @@ public abstract class PairHMM {
      *                          parameters are the same, and only the haplotype bases are changing underneath us
      * @return the log10 probability of read coming from the haplotype under the provided error model
      */
-    public final double computeReadLikelihoodGivenHaplotypeLog10( final byte[] haplotypeBases,
+    protected final double computeReadLikelihoodGivenHaplotypeLog10( final byte[] haplotypeBases,
                                                                   final byte[] readBases,
                                                                   final byte[] readQuals,
                                                                   final byte[] insertionGOP,
@@ -118,6 +196,7 @@ public abstract class PairHMM {
                                                                   final byte[] overallGCP,
                                                                   final boolean recacheReadValues,
                                                                   final byte[] nextHaploytpeBases) {
+
         if ( ! initialized ) throw new IllegalStateException("Must call initialize before calling computeReadLikelihoodGivenHaplotypeLog10");
         if ( haplotypeBases == null ) throw new IllegalArgumentException("haplotypeBases cannot be null");
         if ( haplotypeBases.length > maxHaplotypeLength ) throw new IllegalArgumentException("Haplotype bases is too long, got " + haplotypeBases.length + " but max is " + maxHaplotypeLength);
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 c39245730..93718b04d 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
@@ -139,7 +139,7 @@ public class GATKSAMRecord extends BAMRecord {
     }
 
     public static GATKSAMRecord createRandomRead(int length) {
-        List<CigarElement> cigarElements = new LinkedList<CigarElement>();
+        List<CigarElement> cigarElements = new LinkedList<>();
         cigarElements.add(new CigarElement(length, CigarOperator.M));
         Cigar cigar = new Cigar(cigarElements);
         return ArtificialSAMUtils.createArtificialRead(cigar);
@@ -536,10 +536,7 @@ public class GATKSAMRecord extends BAMRecord {
      * @return True if an attribute has been set for this key.
      */
     public boolean containsTemporaryAttribute(Object key) {
-        if(temporaryAttributes != null) {
-            return temporaryAttributes.containsKey(key);
-        }
-        return false;
+        return temporaryAttributes != null && temporaryAttributes.containsKey(key);
     }
 
     /**
@@ -556,7 +553,7 @@ public class GATKSAMRecord extends BAMRecord {
      */
     public Object setTemporaryAttribute(Object key, Object value) {
         if(temporaryAttributes == null) {
-            temporaryAttributes = new HashMap<Object, Object>();
+            temporaryAttributes = new HashMap<>();
         }
         return temporaryAttributes.put(key, value);
     }
@@ -750,6 +747,46 @@ public class GATKSAMRecord extends BAMRecord {
         return emptyRead;
     }
 
+    /**
+     * Creates a new GATKSAMRecord with the source read's header, read group and mate
+     * information, but with the following fields set to user-supplied values:
+     *  - Read Bases
+     *  - Base Qualities
+     *  - Base Insertion Qualities
+     *  - Base Deletion Qualities
+     *
+     *  Cigar string is empty (not-null)
+     *
+     * Use this method if you want to create a new GATKSAMRecord based on
+     * another GATKSAMRecord, but with modified bases and qualities
+     *
+     * @param read a read to copy the header from
+     * @param readBases an array containing the new bases you wish use in place of the originals
+     * @param baseQualities an array containing the new base qualities you wish use in place of the originals
+     * @param baseInsertionQualities an array containing the new base insertion qaulities
+     * @param baseDeletionQualities an array containing the new base deletion qualities
+     * @return a read with modified bases and qualities, safe for the GATK
+     */
+    public static GATKSAMRecord createQualityModifiedRead(final GATKSAMRecord read,
+                                                          final byte[] readBases,
+                                                          final byte[] baseQualities,
+                                                          final byte[] baseInsertionQualities,
+                                                          final byte[] baseDeletionQualities) {
+        if ( baseQualities.length != readBases.length || baseInsertionQualities.length != readBases.length || baseDeletionQualities.length != readBases.length )
+            throw new IllegalArgumentException("Read bases and read quality arrays aren't the same size: Bases:" + readBases.length
+                                                + " vs Base Q's:" + baseQualities.length
+                                                + " vs Insert Q's:" + baseInsertionQualities.length
+                                                + " vs Delete Q's:" + baseDeletionQualities.length);
+
+        final GATKSAMRecord processedRead = GATKSAMRecord.emptyRead(read);
+        processedRead.setReadBases(readBases);
+        processedRead.setBaseQualities(baseQualities, EventType.BASE_SUBSTITUTION);
+        processedRead.setBaseQualities(baseInsertionQualities, EventType.BASE_INSERTION);
+        processedRead.setBaseQualities(baseDeletionQualities, EventType.BASE_DELETION);
+
+        return processedRead;
+    }
+
     /**
      * Shallow copy of everything, except for the attribute list and the temporary attributes. 
      * A new list of the attributes is created for both, but the attributes themselves are copied by reference.  
@@ -762,7 +799,7 @@ public class GATKSAMRecord extends BAMRecord {
     public Object clone() throws CloneNotSupportedException {
         final GATKSAMRecord clone = (GATKSAMRecord) super.clone();
         if (temporaryAttributes != null) {
-            clone.temporaryAttributes = new HashMap<Object, Object>();
+            clone.temporaryAttributes = new HashMap<>();
             for (Object attribute : temporaryAttributes.keySet())
                 clone.setTemporaryAttribute(attribute, temporaryAttributes.get(attribute));
         }

From 9c1023c933cb34a5368c58643659bfcbcdcc86f5 Mon Sep 17 00:00:00 2001
From: Ami Levy-Moonshine <ami@broadinstitute.org>
Date: Mon, 18 Nov 2013 11:44:24 -0500
Subject: [PATCH 50/77] fix a (ugly) weird error from last commit that changed
 all the scala files to end with MoleculoPipeline.scala

---
 .../sting/queue/extensions/gatk/GATKExtensionsGenerator.java    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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 bf675503b..ced0809f7 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
@@ -325,7 +325,7 @@ public class GATKExtensionsGenerator extends CommandLineProgram {
      * @throws IOException If the file cannot be written.
      */
     private void writeFile(String fullClassName, String content) throws IOException {
-        File outputFile = new File(outputDirectory, fullClassName.replace(".", "/") + "MoleculoPipeline.scala");
+        File outputFile = new File(outputDirectory, fullClassName.replace(".", "/") + ".scala");
         if (outputFile.exists()) {
             String existingContent = FileUtils.readFileToString(outputFile);
             if (StringUtils.equals(content, existingContent))

From 6ad841cec575024fd186b9d0aeb7f8f69f49ee9d Mon Sep 17 00:00:00 2001
From: Ami Levy-Moonshine <ami@broadinstitute.org>
Date: Thu, 7 Nov 2013 14:54:35 -0500
Subject: [PATCH 51/77] Rewrite ReadLengthDistribution to count the read
 lengths into a hash table first and only at the end to produce a GATK report
 table. Before that fix, the tool was couldn't work with more then one RG
 before. - Address all review comments

---
 .../diagnostics/ReadLengthDistribution.java   | 101 +++++++++++++-----
 1 file changed, 77 insertions(+), 24 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java
index a269a94bc..796c817ff 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java
@@ -38,7 +38,10 @@ import org.broadinstitute.sting.utils.help.HelpConstants;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.io.PrintStream;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
 
 /**
  * Outputs the read lengths of all the reads in a file.
@@ -77,51 +80,101 @@ public class ReadLengthDistribution extends ReadWalker<Integer, Integer> {
     @Output
     public PrintStream out;
 
-    private GATKReport report;
+    //A map from RG to its column number (its index in an int[] array)
+    private Map<SAMReadGroupRecord,Integer> readGroupsLocation;
+    //Each line in the table is a read length and each column it the number of reads of a specific RG with that length. Thus a table is a map between read lengths to array of values (one for each RG).
+    private Map<Integer,int[]> table;
+    private List<SAMReadGroupRecord> readGroups;
 
     public void initialize() {
-        final List<SAMReadGroupRecord> readGroups = getToolkit().getSAMFileHeader().getReadGroups();
+        readGroups = getToolkit().getSAMFileHeader().getReadGroups();
+        readGroupsLocation = new HashMap<>();
+        table = new TreeMap<>();
+        int readGroupsNum = 0;
 
-        report = new GATKReport();
-        report.addTable("ReadLengthDistribution", "Table of read length distributions", 1 + (readGroups.isEmpty() ? 1 : readGroups.size()));
-        GATKReportTable table = report.getTable("ReadLengthDistribution");
-
-        table.addColumn("readLength");
-
-        if (readGroups.isEmpty())
-            table.addColumn("SINGLE_SAMPLE");
-        else
-            for (SAMReadGroupRecord rg : readGroups)
-                table.addColumn(rg.getSample());
-    }
-
-    public boolean filter(ReferenceContext ref, GATKSAMRecord read) {
-        return ( !read.getReadPairedFlag() || read.getReadPairedFlag() && read.getFirstOfPairFlag());
+        if (!readGroups.isEmpty()){
+            for (SAMReadGroupRecord rg : readGroups){
+                readGroupsLocation.put(rg,readGroupsNum);
+                readGroupsNum++;
+            }
+        }
     }
 
     @Override
-    public Integer map(ReferenceContext referenceContext, GATKSAMRecord samRecord, RefMetaDataTracker RefMetaDataTracker) {
-        GATKReportTable table = report.getTable("ReadLengthDistribution");
+    public Integer map(final ReferenceContext referenceContext,final GATKSAMRecord samRecord,final RefMetaDataTracker RefMetaDataTracker) {
 
-        int length = Math.abs(samRecord.getReadLength());
-        String sample = samRecord.getReadGroup().getSample();
+        final int length = Math.abs(samRecord.getReadLength());
+        final SAMReadGroupRecord rg = samRecord.getReadGroup();
 
-        table.increment(length, sample);
+        increment(table,length, rg);
 
         return null;
     }
 
+    final private void increment(final Map<Integer,int[]> table,final int length,final SAMReadGroupRecord rg){
+        if(readGroupsLocation.isEmpty()){
+            if(table.containsKey(length))
+                table.get(length)[0]++;
+            else{
+                final int[] newLength = {1};
+                table.put(length,newLength);
+            }
+        }
+        else{
+            final int rgLocation = readGroupsLocation.get(rg);
+            if(table.containsKey(length))
+                table.get(length)[rgLocation]++;
+            else{
+                table.put(length,new int[readGroupsLocation.size()]);
+                table.get(length)[rgLocation]++;
+            }
+        }
+    }
+
     @Override
     public Integer reduceInit() {
         return null;
     }
 
     @Override
-    public Integer reduce(Integer integer, Integer integer1) {
+    public Integer reduce(final Integer integer,final Integer integer1) {
         return null;
     }
 
-    public void onTraversalDone(Integer sum) {
+    public void onTraversalDone(final Integer sum) {
+        final GATKReport report = createGATKReport();
         report.print(out);
     }
+
+    final private GATKReport createGATKReport(){
+        final GATKReport report = new GATKReport();
+        report.addTable("ReadLengthDistribution", "Table of read length distributions", 1 + (readGroupsLocation.isEmpty() ? 1 : readGroupsLocation.size()));
+        final GATKReportTable tableReport = report.getTable("ReadLengthDistribution");
+
+        tableReport.addColumn("readLength");
+
+        if (readGroupsLocation.isEmpty()){
+            tableReport.addColumn("SINGLE_SAMPLE");
+            int rowIndex = 0;
+            for (Integer length : table.keySet()){
+                tableReport.set(rowIndex,0,length);
+                tableReport.set(rowIndex,1,table.get(length)[0]);
+                rowIndex++;
+            }
+        }
+        else{
+            for (SAMReadGroupRecord rg : readGroups)
+                tableReport.addColumn(rg.getSample());
+            int rowIndex = 0;
+            for (Integer length : table.keySet()){
+                tableReport.set(rowIndex,0,length);
+                for (int i=0; i < readGroupsLocation.size(); i++)
+                    tableReport.set(rowIndex,i+1,table.get(length)[i]);
+                rowIndex++;
+            }
+
+        }
+
+        return report;
+    }
 }

From e6ef37de1de3a1659f3c9a267f462d1fc70f46dc Mon Sep 17 00:00:00 2001
From: Ami Levy-Moonshine <ami@broadinstitute.org>
Date: Thu, 7 Nov 2013 17:16:14 -0500
Subject: [PATCH 52/77] Add an option to filter the read bases that are taking
 into account for the coveraged intervals. For that, new two arguments were
 added: minBaseQuality and minMappingQuality

---
 .../walkers/diagnostics/FindCoveredIntervals.java | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/FindCoveredIntervals.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/FindCoveredIntervals.java
index ad6023579..bd69cbdbd 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/FindCoveredIntervals.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/FindCoveredIntervals.java
@@ -101,11 +101,24 @@ public class FindCoveredIntervals extends ActiveRegionWalker<GenomeLoc, Long> {
     @Argument(fullName = "coverage_threshold", shortName = "cov", doc = "The minimum allowable coverage to be considered covered", required = false)
     private int coverageThreshold = 20;
 
+    @Argument(fullName = "minBaseQuality", shortName = "minBQ", doc = "The minimum allowable base quality score to be counted for coverage",required = false)
+    private int minBaseQuality = 0;
+
+    @Argument(fullName = "minMappingQuality", shortName = "minMQ", doc = "The minimum allowable mapping quality score to be counted for coverage",required = false)
+    private int minMappingQuality = 0;
+
+
+
+
     @Override
     // Look to see if the region has sufficient coverage
     public ActivityProfileState isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) {
 
-        int depth = context.getBasePileup().getBaseFilteredPileup(coverageThreshold).depthOfCoverage();
+        int depth;
+        if(minBaseQuality == 0 && minMappingQuality == 0)
+            depth = context.getBasePileup().getBaseFilteredPileup(coverageThreshold).depthOfCoverage();
+        else
+            depth = context.getBasePileup().getBaseAndMappingFilteredPileup(minBaseQuality,minMappingQuality).depthOfCoverage();
 
         // note the linear probability scale
         return new ActivityProfileState(ref.getLocus(), Math.min(depth / coverageThreshold, 1));

From b42ccdce112bdc158adf8194950deb7fbc781254 Mon Sep 17 00:00:00 2001
From: Geraldine Van der Auwera <vdauwera@broadinstitute.org>
Date: Tue, 19 Nov 2013 15:05:41 -0500
Subject: [PATCH 53/77] Tweaked gatkdocs index template

---
 settings/helpTemplates/common.html                 | 4 ++--
 settings/helpTemplates/generic.index.template.html | 4 ++--
 settings/helpTemplates/generic.template.html       | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/settings/helpTemplates/common.html b/settings/helpTemplates/common.html
index 677fdf861..f4fb74af1 100644
--- a/settings/helpTemplates/common.html
+++ b/settings/helpTemplates/common.html
@@ -58,7 +58,7 @@
         <div class="navbar navbar-fixed-top">
             <div class="navbar-inner">
                 <div class="container-fluid">
-                    <a class="brand" href="index.html">GATK | Technical Documentation</a>
+                    <a class="brand" href="index.html">GATK | Tool Documentation</a>
                 </div>
             </div>
         </div>
@@ -82,7 +82,7 @@
         <hr>
         <p class="see-also">See also 
         	<a href="${guideIndex}">Guide Index</a> | 
-        	<a href="index.html">Technical Documentation Index</a> | 
+        	<a href="index.html">Tool Documentation Index</a> | 
         	<a href="${forum}">Support Forum</a>
         </p>
 
diff --git a/settings/helpTemplates/generic.index.template.html b/settings/helpTemplates/generic.index.template.html
index b3e3d0212..a5650d55e 100644
--- a/settings/helpTemplates/generic.index.template.html
+++ b/settings/helpTemplates/generic.index.template.html
@@ -53,8 +53,8 @@
     </div>
 </#macro>
 
-<@makeHeader title="Technical Documentation Index" isIndex=true />
-<h1>Technical Documentation Index
+<@makeHeader title="GATK | Tool Documentation Index" isIndex=true />
+<h1>Tool Documentation Index
     <small>${version}</small>
 </h1>
 <div class="accordion" id="index">
diff --git a/settings/helpTemplates/generic.template.html b/settings/helpTemplates/generic.template.html
index b78bba48c..eea741669 100644
--- a/settings/helpTemplates/generic.template.html
+++ b/settings/helpTemplates/generic.template.html
@@ -88,7 +88,7 @@
 </#macro>
 
 <?php $group = '${group}'; ?>
-<@makeHeader title="${name} documentation" isIndex=false />
+<@makeHeader title="GATK | ${name} documentation" isIndex=false />
 <section class="span4">
     <aside class="well">
         <h2>Categories</h2>

From adb77b406fb5385c80165b0c94bc2fe07c0b530a Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 20 Nov 2013 15:49:54 -0500
Subject: [PATCH 54/77] Fixed poor implementation of isRefSource() and
 isRefSink() among others.

There was already a note in the code about how wrong the implementation was.
The bad code was causing a single-node graph to get cleaned up into nothing when pruning tails.
Delivers PT #61069820.
---
 .../haplotypecaller/graphs/BaseGraph.java     | 79 ++++++++-----------
 .../readthreading/ReadThreadingGraph.java     |  2 +-
 ...lexAndSymbolicVariantsIntegrationTest.java |  2 +-
 .../graphs/BaseGraphUnitTest.java             | 48 ++++++++++-
 4 files changed, 82 insertions(+), 49 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java
index bd179ef41..a1ec13882 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java
@@ -95,10 +95,13 @@ public class BaseGraph<V extends BaseVertex, E extends BaseEdge> extends Default
      */
     public boolean isReferenceNode( final V v ) {
         if( v == null ) { throw new IllegalArgumentException("Attempting to test a null vertex."); }
-        for( final BaseEdge e : edgesOf(v) ) {
-            if( e.isRef() ) { return true; }
+
+        for ( final BaseEdge e : edgesOf(v) ) {
+            if ( e.isRef() ) { return true; }
         }
-        return false;
+
+        // edge case: if the graph only has one node then it's a ref node, otherwise it's not
+        return (vertexSet().size() == 1);
     }
 
     /**
@@ -154,62 +157,46 @@ public class BaseGraph<V extends BaseVertex, E extends BaseEdge> extends Default
         return v.getAdditionalSequence(isSource(v));
     }
 
-    /**
-     * @param e the edge to test
-     * @return  true if this edge is a reference source edge
-     */
-    public boolean isRefSource( final E e ) {
-        if( e == null ) { throw new IllegalArgumentException("Attempting to test a null edge."); }
-        for( final E edgeToTest : incomingEdgesOf(getEdgeSource(e)) ) {
-            if( edgeToTest.isRef() ) { return false; }
-        }
-        return true;
-    }
-
     /**
      * @param v the vertex to test
      * @return  true if this vertex is a reference source
      */
     public boolean isRefSource( final V v ) {
         if( v == null ) { throw new IllegalArgumentException("Attempting to test a null vertex."); }
-        for( final E edgeToTest : incomingEdgesOf(v) ) {
-            if( edgeToTest.isRef() ) { return false; }
+
+        // confirm that no incoming edges are reference edges
+        for ( final E edgeToTest : incomingEdgesOf(v) ) {
+            if ( edgeToTest.isRef() ) { return false; }
         }
-        return true;
+
+        // confirm that there is an outgoing reference edge
+        for ( final E edgeToTest : outgoingEdgesOf(v) ) {
+            if ( edgeToTest.isRef() ) { return true; }
+        }
+
+        // edge case: if the graph only has one node then it's a ref sink, otherwise it's not
+        return (vertexSet().size() == 1);
     }
 
     /**
-     * @param e the edge to test
-     * @return  true if this edge is a reference sink edge
-     */
-    public boolean isRefSink( final E e ) {
-        if( e == null ) { throw new IllegalArgumentException("Attempting to test a null edge."); }
-        for( final E edgeToTest : outgoingEdgesOf(getEdgeTarget(e)) ) {
-            if( edgeToTest.isRef() ) { return false; }
-        }
-        return true;
-    }
-
-    /**
-     * // TODO -- the logic of this test is just wrong
      * @param v the vertex to test
      * @return  true if this vertex is a reference sink
      */
     public boolean isRefSink( final V v ) {
         if( v == null ) { throw new IllegalArgumentException("Attempting to test a null vertex."); }
-        for( final E edgeToTest : outgoingEdgesOf(v) ) {
-            if( edgeToTest.isRef() ) { return false; }
-        }
-        return true;
-    }
 
-    /**
-     * Is this both a refsink node and a reference node
-     * @param v a non-null vertex
-     * @return true if v is both a sink and a reference node
-     */
-    public boolean isRefNodeAndRefSink(final V v) {
-        return isRefSink(v) && isReferenceNode(v);
+        // confirm that no outgoing edges are reference edges
+        for ( final E edgeToTest : outgoingEdgesOf(v) ) {
+            if ( edgeToTest.isRef() ) { return false; }
+        }
+
+        // confirm that there is an incoming reference edge
+        for ( final E edgeToTest : incomingEdgesOf(v) ) {
+            if ( edgeToTest.isRef() ) { return true; }
+        }
+
+        // edge case: if the graph only has one node then it's a ref source, otherwise it's not
+        return (vertexSet().size() == 1);
     }
 
     /**
@@ -217,7 +204,7 @@ public class BaseGraph<V extends BaseVertex, E extends BaseEdge> extends Default
      */
     public V getReferenceSourceVertex( ) {
         for( final V v : vertexSet() ) {
-            if( isReferenceNode(v) && isRefSource(v) ) {
+            if( isRefSource(v) ) {
                 return v;
             }
         }
@@ -229,7 +216,7 @@ public class BaseGraph<V extends BaseVertex, E extends BaseEdge> extends Default
      */
     public V getReferenceSinkVertex( ) {
         for( final V v : vertexSet() ) {
-            if( isReferenceNode(v) && isRefSink(v) ) {
+            if( isRefSink(v) ) {
                 return v;
             }
         }
@@ -490,7 +477,7 @@ public class BaseGraph<V extends BaseVertex, E extends BaseEdge> extends Default
         // Run through the graph and clean up singular orphaned nodes
         final List<V> verticesToRemove = new LinkedList<>();
         for( final V v : vertexSet() ) {
-            if( inDegreeOf(v) == 0 && outDegreeOf(v) == 0 ) {
+            if( inDegreeOf(v) == 0 && outDegreeOf(v) == 0 && !isRefSource(v) ) {
                 verticesToRemove.add(v);
             }
         }
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java
index 2a94ece96..04671a178 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java
@@ -487,7 +487,7 @@ public class ReadThreadingGraph extends BaseGraph<MultiDeBruijnVertex, MultiSamp
         int attempted = 0;
         int nRecovered = 0;
         for ( final MultiDeBruijnVertex v : vertexSet() ) {
-            if ( outDegreeOf(v) == 0 && ! isRefNodeAndRefSink(v) ) {
+            if ( outDegreeOf(v) == 0 && ! isRefSink(v) ) {
                 attempted++;
                 nRecovered += recoverDanglingChain(v, pruneFactor);
             }
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
index cdfacaaf3..3907ffbd6 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
@@ -94,6 +94,6 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
     @Test
     public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
         HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
-                "8e6a2002c59eafb78bdbf1db9660164b");
+                "f74d68cbc1ecb66a7128258e111cd030");
     }
 }
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java
index 1c539e404..e07adc0f6 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java
@@ -95,7 +95,7 @@ public class BaseGraphUnitTest extends BaseTest {
     }
 
     @Test
-         public void testRemoveSingletonOrphanVertices() throws Exception {
+    public void testRemoveSingletonOrphanVertices() throws Exception {
         // all vertices in graph are connected
         final List<SeqVertex> kept = new LinkedList<SeqVertex>(graph.vertexSet());
         final SeqVertex rm1 = new SeqVertex("CAGT");
@@ -116,6 +116,52 @@ public class BaseGraphUnitTest extends BaseTest {
         Assert.assertFalse(graph.containsVertex(rm2));
     }
 
+    @Test
+    public void testRemoveSingletonOrphanVerticesOnSingleRefNode() throws Exception {
+        final SeqGraph original = new SeqGraph();
+        original.addVertex(v1);
+        original.removeSingletonOrphanVertices();
+        Assert.assertTrue(original.containsVertex(v1));
+        Assert.assertEquals(original.vertexSet().size(), 1);
+    }
+
+    @Test
+    public void testIsRefSourceAndSink() throws Exception {
+
+        final SeqGraph g = new SeqGraph();
+        g.addVertex(v1);
+        Assert.assertTrue(g.isRefSource(v1));
+        Assert.assertTrue(g.isRefSink(v1));
+        Assert.assertTrue(g.isReferenceNode(v1));
+
+        g.addVertices(v2, v3, v4, v5);
+        g.addEdge(v1, v2);
+        g.addEdge(v2, v3);
+        final BaseEdge refEdge = new BaseEdge(true, 1);
+        g.addEdge(v3, v4, refEdge);
+        g.addEdge(v4, v5);
+
+        Assert.assertFalse(g.isRefSource(v1));
+        Assert.assertFalse(g.isRefSink(v1));
+        Assert.assertFalse(g.isReferenceNode(v1));
+
+        Assert.assertFalse(g.isRefSource(v2));
+        Assert.assertFalse(g.isRefSink(v2));
+        Assert.assertFalse(g.isReferenceNode(v2));
+
+        Assert.assertTrue(g.isRefSource(v3));
+        Assert.assertFalse(g.isRefSink(v3));
+        Assert.assertTrue(g.isReferenceNode(v3));
+
+        Assert.assertFalse(g.isRefSource(v4));
+        Assert.assertTrue(g.isRefSink(v4));
+        Assert.assertTrue(g.isReferenceNode(v4));
+
+        Assert.assertFalse(g.isRefSource(v5));
+        Assert.assertFalse(g.isRefSink(v5));
+        Assert.assertFalse(g.isReferenceNode(v5));
+    }
+
     @Test
     public void testRemovePathsNotConnectedToRef() throws Exception {
         final SeqGraph graph = new SeqGraph();

From 0fac4fb3b66039b429d7a286dfcd719307398a08 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 21 Nov 2013 10:21:25 -0500
Subject: [PATCH 55/77] Make the reference model calculation work with reduced
 reads.

It's just a matter of using PileupElement.getRepresentativeCount() instead of '++'.
---
 .../ReferenceConfidenceModel.java             |  6 +++---
 .../ReferenceConfidenceModelUnitTest.java     | 21 ++++++++++++++++++-
 2 files changed, 23 insertions(+), 4 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModel.java
index 2c123880d..4ec56f706 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModel.java
@@ -296,9 +296,9 @@ public class ReferenceConfidenceModel {
                     if( hqSoftClips != null && p.isNextToSoftClip() ) {
                         hqSoftClips.add(AlignmentUtils.calcNumHighQualitySoftClips(p.getRead(), (byte) 28));
                     }
-                    result.AD_Ref_Any[1]++;
+                    result.AD_Ref_Any[1] += p.getRepresentativeCount();
                 } else {
-                    result.AD_Ref_Any[0]++;
+                    result.AD_Ref_Any[0] += p.getRepresentativeCount();
                 }
                 result.genotypeLikelihoods[AA] += p.getRepresentativeCount() * QualityUtils.qualToProbLog10(qual);
                 result.genotypeLikelihoods[AB] += p.getRepresentativeCount() * MathUtils.approximateLog10SumLog10( QualityUtils.qualToProbLog10(qual) + MathUtils.LOG_ONE_HALF, QualityUtils.qualToErrorProbLog10(qual) + MathUtils.LOG_ONE_THIRD + MathUtils.LOG_ONE_HALF );
@@ -483,7 +483,7 @@ public class ReferenceConfidenceModel {
 
             // todo -- this code really should handle CIGARs directly instead of relying on the above tests
             if ( isReadInformativeAboutIndelsOfSize(read.getReadBases(), read.getBaseQualities(), offset, ref, pileupOffsetIntoRef, maxIndelSize) ) {
-                nInformative++;
+                nInformative += p.getRepresentativeCount();
                 if( nInformative > MAX_N_INDEL_INFORMATIVE_READS ) {
                     return MAX_N_INDEL_INFORMATIVE_READS;
                 }
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java
index 5c6ae93e5..d163c0497 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java
@@ -47,7 +47,6 @@
 package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
 
 import net.sf.samtools.SAMFileHeader;
-import org.apache.commons.lang.ArrayUtils;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
@@ -164,6 +163,26 @@ public class ReferenceConfidenceModelUnitTest extends BaseTest {
         }
     }
 
+    @Test
+    public void testCalcNIndelInformativeReducedReads() {
+        final String bases = "ACGGGTTTGGAC";
+        final byte[] quals = Utils.dupBytes((byte)30, bases.length());
+        final int count = 10;
+        final int[] counts = new int[bases.length()];
+        for ( int i = 0; i < counts.length; i++ )
+            counts[i] = count;
+        final int position = 100;
+
+        final GATKSAMRecord read = ArtificialSAMUtils.createArtificialReducedRead(header, "foo", 0, position, counts.length, counts);
+        read.setReadString(bases);
+        read.setBaseQualities(quals);
+        read.setCigarString(bases.length() + "M");
+        final GenomeLoc loc = new UnvalidatingGenomeLoc("20", 0, position, position);
+        final ReadBackedPileup pileup = new ReadBackedPileupImpl(loc, Collections.singletonList(read), 0);
+        final int actual = model.calcNIndelInformativeReads(pileup, 0, bases.getBytes(), 3);
+        Assert.assertEquals(actual, count);
+    }
+
     @Test
     public void testClose() {
         model.close();

From 25bc6e64aed8f71e45ef079d056a62506697c615 Mon Sep 17 00:00:00 2001
From: Geraldine Van der Auwera <vdauwera@broadinstitute.org>
Date: Fri, 22 Nov 2013 14:47:53 -0500
Subject: [PATCH 56/77] Patched Queue extensions lacking a main class
 definition

---
 .../sting/queue/extensions/picard/CalculateHsMetrics.scala       | 1 +
 .../sting/queue/extensions/picard/CollectGcBiasMetrics.scala     | 1 +
 .../sting/queue/extensions/picard/CollectMultipleMetrics.scala   | 1 +
 3 files changed, 3 insertions(+)

diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CalculateHsMetrics.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CalculateHsMetrics.scala
index 92d71536e..3fd9a3c6d 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CalculateHsMetrics.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CalculateHsMetrics.scala
@@ -38,6 +38,7 @@ import net.sf.picard.analysis.MetricAccumulationLevel
  */
 class CalculateHsMetrics extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardMetricsFunction {
   analysisName = "CalculateHsMetrics"
+  javaMainClass = "net.sf.picard.analysis.directed.CalculateHsMetrics"
 
   @Input(doc="The input SAM or BAM files to analyze.  Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true)
   var input: Seq[File] = Nil
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectGcBiasMetrics.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectGcBiasMetrics.scala
index 7c4c3f26a..14c10c581 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectGcBiasMetrics.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectGcBiasMetrics.scala
@@ -37,6 +37,7 @@ import java.io.File
  */
 class CollectGcBiasMetrics extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardMetricsFunction {
   analysisName = "CollectGcBiasMetrics"
+  javaMainClass = "net.sf.picard.analysis.CollectGcBiasMetrics"
 
   @Input(doc="The input SAM or BAM files to analyze.  Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true)
   var input: Seq[File] = Nil
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectMultipleMetrics.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectMultipleMetrics.scala
index cac436906..3c122ee60 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectMultipleMetrics.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectMultipleMetrics.scala
@@ -37,6 +37,7 @@ import java.io.File
  */
 class CollectMultipleMetrics extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardMetricsFunction{
   analysisName = "CollectMultipleMetrics"
+  javaMainClass = "net.sf.picard.analysis.CollectMultipleMetrics"
 
   @Input(doc="The input SAM or BAM files to analyze.  Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true)
   var input: Seq[File] = Nil

From 429582589f7e8b73527c76be3f6227711249c1f3 Mon Sep 17 00:00:00 2001
From: Geraldine Van der Auwera <vdauwera@broadinstitute.org>
Date: Tue, 26 Nov 2013 15:53:29 -0500
Subject: [PATCH 57/77] Set SAMFileWriter to create index in ReadUtils to fix
 SplitSamFile issue

---
 .../src/org/broadinstitute/sting/utils/sam/ReadUtils.java     | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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 ab866013f..39f227840 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
@@ -152,8 +152,8 @@ public class ReadUtils {
     public static SAMFileWriter createSAMFileWriterWithCompression(SAMFileHeader header, boolean presorted, String file, int compression) {
         validateCompressionLevel(compression);
         if (file.endsWith(".bam"))
-            return new SAMFileWriterFactory().makeBAMWriter(header, presorted, new File(file), compression);
-        return new SAMFileWriterFactory().makeSAMOrBAMWriter(header, presorted, new File(file));
+            return new SAMFileWriterFactory().setCreateIndex(true).makeBAMWriter(header, presorted, new File(file), compression);
+        return new SAMFileWriterFactory().setCreateIndex(true).makeSAMOrBAMWriter(header, presorted, new File(file));
     }
 
     public static int validateCompressionLevel(final int requestedCompressionLevel) {

From 1f777c4898894786466a8910bf29d0d78188fa95 Mon Sep 17 00:00:00 2001
From: Chris Hartl <chartl@broadinstitute.org>
Date: Thu, 21 Nov 2013 02:49:38 -0500
Subject: [PATCH 58/77] Introducing the latest-and-greatest in genotyping:
 CalculatePosteriors.

CalculatePosteriors enables the user to calculate genotype likelihood posteriors (and set genotypes accordingly) given one or more panels containing allele counts (for instance, calculating NA12878 genotypes based on 1000G EUR frequencies). The uncertainty in allele frequency is modeled by a Dirichlet distribution (parameters being the observed allele counts across each allele), and the genotype state is modeled by assuming independent draws (Hardy-Weinberg Equilibrium). This leads to the Dirichlet-Multinomial distribution.

Currently this is implemented only for ploidy=2. It should be straightforward to generalize. In addition there's a parameter for "EM" that currently does nothing but throw an exception -- another extension of this method is to run an EM over the Maximum A-Posteriori (MAP) allele count in the input sample as follows:
 while not converged:
  * AC = [external AC] + [sample AC]
  * Prior = DirichletMultinomial[AC]
  * Posteriors = [sample GL + Prior]
  * sample AC = MLEAC(Posteriors)

This is more useful for large callsets with small panels than for small callsets with large panels -- the latter of these being the more common usecase.

Fully unit tested.

Reviewer (Eric) jumped in to address many of his own comments plus removed public->protected dependencies.
---
 .../LikelihoodCalculationEngine.java          | 213 ++++++++++-
 .../LikelihoodCalculationEngineUnitTest.java  | 330 ++++++++++++++++-
 .../broadinstitute/sting/utils/MathUtils.java |  30 ++
 .../org/broadinstitute/sting/utils/Utils.java |  14 +
 .../variant/GATKVariantContextUtils.java      |  10 +-
 .../sting/utils/MathUtilsUnitTest.java        | 334 ++++++++++++++++++
 .../GATKVariantContextUtilsUnitTest.java      |   7 +-
 7 files changed, 924 insertions(+), 14 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
index 4eb728390..9cd0f5f49 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
@@ -52,6 +52,7 @@ import net.sf.samtools.SAMUtils;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.QualityUtils;
+import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.haplotype.Haplotype;
@@ -60,7 +61,9 @@ import org.broadinstitute.sting.utils.recalibration.covariates.RepeatCovariate;
 import org.broadinstitute.sting.utils.recalibration.covariates.RepeatLengthCovariate;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
-import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.variant.variantcontext.*;
+import org.broadinstitute.variant.vcf.VCFConstants;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -572,4 +575,212 @@ public class LikelihoodCalculationEngine {
         }
     }
 
+    // --------------------------------------------------------------------------------
+    //
+    // Posterior GL calculations
+    //
+    // --------------------------------------------------------------------------------
+
+    public static VariantContext calculatePosteriorGLs(final VariantContext vc1,
+                                                       final Collection<VariantContext> resources,
+                                                       final int numRefSamplesFromMissingResources,
+                                                       final double globalFrequencyPriorDirichlet,
+                                                       final boolean useInputSamples,
+                                                       final boolean useEM,
+                                                       final boolean useAC) {
+        if ( useEM )
+            throw new IllegalArgumentException("EM loop for posterior GLs not yet implemented");
+
+        final Map<Allele,Integer> totalAlleleCounts = new HashMap<>();
+        for ( final VariantContext resource : resources ) {
+            addAlleleCounts(totalAlleleCounts,resource,useAC);
+        }
+
+        if ( useInputSamples ) {
+            addAlleleCounts(totalAlleleCounts,vc1,useAC);
+        }
+
+        totalAlleleCounts.put(vc1.getReference(),totalAlleleCounts.get(vc1.getReference())+numRefSamplesFromMissingResources);
+
+        // now extract the counts of the alleles present within vc1, and in order
+        final double[] alleleCounts = new double[vc1.getNAlleles()];
+        int alleleIndex = 0;
+        for ( final Allele allele : vc1.getAlleles() ) {
+
+            alleleCounts[alleleIndex++] = globalFrequencyPriorDirichlet + ( totalAlleleCounts.containsKey(allele) ?
+                    totalAlleleCounts.get(allele) : 0 );
+        }
+
+        final List<double[]> likelihoods = new ArrayList<>(vc1.getNSamples());
+        for ( final Genotype genotype : vc1.getGenotypes() ) {
+            likelihoods.add(genotype.hasLikelihoods() ? genotype.getLikelihoods().getAsVector() : null );
+        }
+
+        final List<double[]> posteriors = calculatePosteriorGLs(likelihoods,alleleCounts,vc1.getMaxPloidy(2));
+
+        final GenotypesContext newContext = GenotypesContext.create();
+        for ( int genoIdx = 0; genoIdx < vc1.getNSamples(); genoIdx ++ ) {
+            final GenotypeBuilder builder = new GenotypeBuilder(vc1.getGenotype(genoIdx));
+            if ( posteriors.get(genoIdx) != null ) {
+                GATKVariantContextUtils.updateGenotypeAfterSubsetting(vc1.getAlleles(), builder,
+                        GATKVariantContextUtils.GenotypeAssignmentMethod.USE_PLS_TO_ASSIGN, posteriors.get(genoIdx), vc1.getAlleles());
+                builder.attribute(VCFConstants.GENOTYPE_POSTERIORS_KEY,
+                        Utils.listFromPrimitives(GenotypeLikelihoods.fromLog10Likelihoods(posteriors.get(genoIdx)).getAsPLs()));
+
+            }
+            newContext.add(builder.make());
+        }
+
+        final List<Integer> priors = Utils.listFromPrimitives(
+                GenotypeLikelihoods.fromLog10Likelihoods(getDirichletPrior(alleleCounts, vc1.getMaxPloidy(2))).getAsPLs());
+
+        return new VariantContextBuilder(vc1).genotypes(newContext).attribute("PG",priors).make();
+    }
+
+    /**
+     * Given genotype likelihoods and known allele counts, calculate the posterior likelihoods
+     * over the genotype states
+     * @param genotypeLikelihoods - the genotype likelihoods for the individual
+     * @param knownAlleleCountsByAllele - the known allele counts in the population. For AC=2 AN=12 site, this is {10,2}
+     * @param ploidy - the ploidy to assume
+     * @return - the posterior genotype likelihoods
+     */
+    protected static List<double[]> calculatePosteriorGLs(final List<double[]> genotypeLikelihoods,
+                                                       final double[] knownAlleleCountsByAllele,
+                                                       final int ploidy) {
+        if ( ploidy != 2 ) {
+            throw new IllegalStateException("Genotype posteriors not yet implemented for ploidy != 2");
+        }
+
+        final double[] genotypePriorByAllele = getDirichletPrior(knownAlleleCountsByAllele,ploidy);
+        final List<double[]> posteriors = new ArrayList<>(genotypeLikelihoods.size());
+        for ( final double[] likelihoods : genotypeLikelihoods ) {
+            double[] posteriorLikelihoods = null;
+
+            if ( likelihoods != null ) {
+                if ( likelihoods.length != genotypePriorByAllele.length ) {
+                    throw new IllegalStateException(String.format("Likelihoods not of correct size: expected %d, observed %d",
+                            knownAlleleCountsByAllele.length*(knownAlleleCountsByAllele.length+1)/2,likelihoods.length));
+                }
+
+                posteriorLikelihoods = new double[genotypePriorByAllele.length];
+                for ( int genoIdx = 0; genoIdx < likelihoods.length; genoIdx ++ ) {
+                    posteriorLikelihoods[genoIdx] = likelihoods[genoIdx] + genotypePriorByAllele[genoIdx];
+                }
+
+                posteriorLikelihoods = MathUtils.toLog10(MathUtils.normalizeFromLog10(posteriorLikelihoods));
+
+            }
+
+            posteriors.add(posteriorLikelihoods);
+        }
+
+        return posteriors;
+    }
+
+    // convenience function for a single genotypelikelihoods array. Just wraps.
+    protected static double[] calculatePosteriorGLs(final double[] genotypeLikelihoods,
+                                                 final double[] knownAlleleCountsByAllele,
+                                                 final int ploidy) {
+        return calculatePosteriorGLs(Arrays.asList(genotypeLikelihoods),knownAlleleCountsByAllele,ploidy).get(0);
+    }
+
+
+    /**
+     * Given known allele counts (whether external, from the sample, or both), calculate the prior distribution
+     * over genotype states. This assumes
+     *   1) Random sampling of alleles (known counts are unbiased, and frequency estimate is Dirichlet)
+     *   2) Genotype states are independent (Hardy-Weinberg)
+     * These assumptions give rise to a Dirichlet-Multinomial distribution of genotype states as a prior
+     * (the "number of trials" for the multinomial is simply the ploidy)
+     * @param knownCountsByAllele - the known counts per allele. For an AC=2, AN=12 site this is {10,2}
+     * @param ploidy - the number of chromosomes in the sample. For now restricted to 2.
+     * @return - the Dirichlet-Multinomial distribution over genotype states
+     */
+    protected static double[] getDirichletPrior(final double[] knownCountsByAllele, final int ploidy) {
+        if ( ploidy != 2 ) {
+            throw new IllegalStateException("Genotype priors not yet implemented for ploidy != 2");
+        }
+
+        // multi-allelic format is
+        // AA AB BB AC BC CC AD BD CD DD ...
+        final double sumOfKnownCounts = MathUtils.sum(knownCountsByAllele);
+        final double[] priors = new double[knownCountsByAllele.length*(knownCountsByAllele.length+1)/2];
+        int priorIndex = 0;
+        for ( int allele2 = 0; allele2 < knownCountsByAllele.length; allele2++ ) {
+            for ( int allele1 = 0; allele1 <= allele2; allele1++) {
+                final int[] counts = new int[knownCountsByAllele.length];
+                counts[allele1] += 1;
+                counts[allele2] += 1;
+                priors[priorIndex++] = MathUtils.dirichletMultinomial(knownCountsByAllele,sumOfKnownCounts,counts,ploidy);
+            }
+        }
+
+        return priors;
+    }
+
+    private static void addAlleleCounts(final Map<Allele,Integer> counts, final VariantContext context, final boolean useAC) {
+        final int[] ac;
+        if ( context.hasAttribute(VCFConstants.MLE_ALLELE_COUNT_KEY) && ! useAC ) {
+            ac = extractInts(context.getAttribute(VCFConstants.MLE_ALLELE_COUNT_KEY));
+        } else if ( context.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) ) {
+            ac = extractInts(context.getAttribute(VCFConstants.ALLELE_COUNT_KEY));
+        } else {
+            ac = new int[context.getAlternateAlleles().size()];
+            int idx = 0;
+            for ( final Allele allele : context.getAlternateAlleles() ) {
+                ac[idx++] = context.getCalledChrCount(allele);
+            }
+        }
+
+        for ( final Allele allele : context.getAlleles() ) {
+            final int count;
+            if ( allele.isReference() ) {
+                if ( context.hasAttribute(VCFConstants.ALLELE_NUMBER_KEY) ) {
+                    count = context.getAttributeAsInt(VCFConstants.ALLELE_NUMBER_KEY,-1) - (int) MathUtils.sum(ac);
+                } else {
+                    count = context.getCalledChrCount() - (int) MathUtils.sum(ac);
+                }
+            } else {
+                count = ac[context.getAlternateAlleles().indexOf(allele)];
+            }
+            if ( ! counts.containsKey(allele) ) {
+                counts.put(allele,0);
+            }
+            counts.put(allele,count + counts.get(allele));
+        }
+    }
+
+    public static int[] extractInts(final Object integerListContainingVCField) {
+        List<Integer> mleList = null;
+        if ( integerListContainingVCField instanceof List ) {
+            if ( ((List) integerListContainingVCField).get(0) instanceof String ) {
+                mleList = new ArrayList<>(((List) integerListContainingVCField).size());
+                for ( Object s : ((List)integerListContainingVCField)) {
+                    mleList.add(Integer.parseInt((String) s));
+                }
+            } else {
+                mleList = (List<Integer>) integerListContainingVCField;
+            }
+        } else if ( integerListContainingVCField instanceof Integer ) {
+            mleList = Arrays.asList((Integer) integerListContainingVCField);
+        } else if ( integerListContainingVCField instanceof String ) {
+            mleList = Arrays.asList(Integer.parseInt((String)integerListContainingVCField));
+        }
+        if ( mleList == null )
+            throw new IllegalArgumentException(String.format("VCF does not have properly formatted "+
+                    VCFConstants.MLE_ALLELE_COUNT_KEY+" or "+VCFConstants.ALLELE_COUNT_KEY));
+
+        final int[] mle = new int[mleList.size()];
+
+        if ( ! ( mleList.get(0) instanceof Integer ) ) {
+            throw new IllegalStateException("BUG: The AC values should be an Integer, but was "+mleList.get(0).getClass().getCanonicalName());
+        }
+
+        for ( int idx = 0; idx < mle.length; idx++) {
+            mle[idx] = mleList.get(idx);
+        }
+
+        return mle;
+    }
 }
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngineUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngineUnitTest.java
index 38b00ab07..2bbb7c725 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngineUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngineUnitTest.java
@@ -58,19 +58,34 @@ import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.pairhmm.PairHMM;
 import org.broadinstitute.sting.utils.recalibration.covariates.RepeatCovariate;
 import org.broadinstitute.sting.utils.recalibration.covariates.RepeatLengthCovariate;
+import org.broadinstitute.variant.variantcontext.*;
+import org.broadinstitute.variant.vcf.VCFConstants;
 import org.testng.Assert;
+import org.testng.annotations.BeforeSuite;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
+import java.util.*;
 
 /**
  * Unit tests for LikelihoodCalculationEngine
  */
 public class LikelihoodCalculationEngineUnitTest extends BaseTest {
 
+    Allele Aref, T, C, G, Cref, ATC, ATCATC;
+
+    @BeforeSuite
+    public void setup() {
+        // alleles
+        Aref = Allele.create("A", true);
+        Cref = Allele.create("C", true);
+        T = Allele.create("T");
+        C = Allele.create("C");
+        G = Allele.create("G");
+        ATC = Allele.create("ATC");
+        ATCATC = Allele.create("ATCATC");
+    }
+
     @Test
     public void testNormalizeDiploidLikelihoodMatrixFromLog10() {
         double[][] likelihoodMatrix = {
@@ -263,4 +278,313 @@ public class LikelihoodCalculationEngineUnitTest extends BaseTest {
         }
         return true;
     }
+
+
+    private String arraysEq(int[] a, int[] b) {
+        if ( a.length != b.length ) {
+            return String.format("NEQ: %s | %s",Arrays.toString(a),Arrays.toString(b));
+        }
+        for ( int idx = 0; idx < a.length; idx++) {
+            if ( a[idx] - b[idx] > 1 || b[idx] - a[idx] > 1) {
+                return String.format("NEQ: %s | %s",Arrays.toString(a),Arrays.toString(b));
+            }
+        }
+
+        return "";
+    }
+
+    private int[] _mleparse(List<Integer> s) {
+        int[] mle = new int[s.size()];
+        for ( int idx = 0; idx < mle.length; idx ++) {
+            mle[idx] = s.get(idx);
+        }
+
+        return mle;
+    }
+
+    private Genotype makeGwithPLs(String sample, Allele a1, Allele a2, double[] pls) {
+        Genotype gt = new GenotypeBuilder(sample, Arrays.asList(a1, a2)).PL(pls).make();
+        if ( pls != null && pls.length > 0 ) {
+            Assert.assertNotNull(gt.getPL());
+            Assert.assertTrue(gt.getPL().length > 0);
+            for ( int i : gt.getPL() ) {
+                Assert.assertTrue(i >= 0);
+            }
+            Assert.assertNotEquals(Arrays.toString(gt.getPL()),"[0]");
+        }
+        return gt;
+    }
+
+    private Genotype makeG(String sample, Allele a1, Allele a2) {
+        return GenotypeBuilder.create(sample, Arrays.asList(a1, a2));
+    }
+
+    private Genotype makeG(String sample, Allele a1, Allele a2, int... pls) {
+        return new GenotypeBuilder(sample, Arrays.asList(a1, a2)).PL(pls).make();
+    }
+
+    private VariantContext makeVC(String source, List<Allele> alleles, Genotype... genotypes) {
+        int start = 10;
+        int stop = start; // alleles.contains(ATC) ? start + 3 : start;
+        return new VariantContextBuilder(source, "1", start, stop, alleles).genotypes(Arrays.asList(genotypes)).filters(null).make();
+    }
+
+    @Test
+    private void testCalculatePosteriorNoExternalData() {
+        VariantContext test1 = makeVC("1",Arrays.asList(Aref,T), makeG("s1",Aref,T,20,0,10),
+                makeG("s2",T,T,60,40,0),
+                makeG("s3",Aref,Aref,0,30,90));
+        test1 = new VariantContextBuilder(test1).attribute(VCFConstants.MLE_ALLELE_COUNT_KEY,3).make();
+        VariantContext test1result = LikelihoodCalculationEngine.calculatePosteriorGLs(test1, new ArrayList<VariantContext>(), 0, 0.001, true, false, false);
+        Genotype test1exp1 = makeGwithPLs("s1",Aref,T,new double[]{-2.20686, -0.03073215, -1.20686});
+        Assert.assertTrue(test1exp1.hasPL());
+        Genotype test1exp2 = makeGwithPLs("s2",T,T,new double[]{-6.000066, -3.823938, -6.557894e-05});
+        Genotype test1exp3 = makeGwithPLs("s3",Aref,Aref,new double[]{-0.0006510083, -2.824524, -9.000651});
+        Assert.assertEquals("java.util.ArrayList",test1result.getGenotype(0).getAnyAttribute(VCFConstants.GENOTYPE_POSTERIORS_KEY).getClass().getCanonicalName());
+        Assert.assertEquals(arraysEq(test1exp1.getPL(), _mleparse((List<Integer>)test1result.getGenotype(0).getAnyAttribute(VCFConstants.GENOTYPE_POSTERIORS_KEY))), "");
+        Assert.assertEquals(arraysEq(test1exp2.getPL(),_mleparse((List<Integer>)test1result.getGenotype(1).getAnyAttribute(VCFConstants.GENOTYPE_POSTERIORS_KEY))), "");
+        Assert.assertEquals(arraysEq(test1exp3.getPL(),_mleparse((List<Integer>)test1result.getGenotype(2).getAnyAttribute(VCFConstants.GENOTYPE_POSTERIORS_KEY))), "");
+
+        // AA AB BB AC BC CC
+        // AA AC CC AT CT TT
+        VariantContext test2 = makeVC("2",Arrays.asList(Aref,C,T),
+                makeG("s1",Aref,T,30,10,60,0,15,90),
+                makeG("s2",Aref,C,40,0,10,30,40,80),
+                makeG("s3",Aref,Aref,0,5,8,15,20,40),
+                makeG("s4",C,T,80,40,12,20,0,10));
+        test2 = new VariantContextBuilder(test2).attribute(VCFConstants.MLE_ALLELE_COUNT_KEY,new ArrayList<Integer>(Arrays.asList(2,2))).make();
+        VariantContext test2result = LikelihoodCalculationEngine.calculatePosteriorGLs(test2,new ArrayList<VariantContext>(),5,0.001,true,false,false);
+        Genotype test2exp1 = makeGwithPLs("s1",Aref,T,new double[]{-2.647372, -1.045139, -6.823193, -0.04513873, -2.198182, -9.823193});
+        Genotype test2exp2 = makeGwithPLs("s2",Aref,C,new double[]{-3.609957, -0.007723248, -1.785778, -3.007723, -4.660767, -8.785778});
+        Genotype test2exp3 = makeGwithPLs("s3",Aref,Aref,new double[] {-0.06094877, -0.9587151, -2.03677,-1.958715,  -3.111759, -5.23677});
+        Genotype test2exp4 = makeGwithPLs("s4",C,T,new double[]{-7.016534, -3.4143, -1.392355, -1.4143, -0.06734388, -1.192355});
+        Assert.assertEquals(arraysEq(test2exp1.getPL(),(int[]) _mleparse((List<Integer>)test2result.getGenotype(0).getAnyAttribute(VCFConstants.GENOTYPE_POSTERIORS_KEY))), "");
+        Assert.assertEquals(arraysEq(test2exp2.getPL(),(int[]) _mleparse((List<Integer>)test2result.getGenotype(1).getAnyAttribute(VCFConstants.GENOTYPE_POSTERIORS_KEY))), "");
+        Assert.assertEquals(arraysEq(test2exp3.getPL(),(int[]) _mleparse((List<Integer>)test2result.getGenotype(2).getAnyAttribute(VCFConstants.GENOTYPE_POSTERIORS_KEY))), "");
+        Assert.assertEquals(arraysEq(test2exp4.getPL(),(int[]) _mleparse((List<Integer>)test2result.getGenotype(3).getAnyAttribute(VCFConstants.GENOTYPE_POSTERIORS_KEY))), "");
+    }
+
+    @Test
+    private void testCalculatePosteriorSamplePlusExternal() {
+        VariantContext testOverlappingBase = makeVC("1", Arrays.asList(Aref,T), makeG("s1",T,T,40,20,0),
+                makeG("s2",Aref,T,18,0,24),
+                makeG("s3",Aref,T,22,0,12));
+        List<VariantContext> supplTest1 = new ArrayList<>(3);
+        supplTest1.add(new VariantContextBuilder(makeVC("2",Arrays.asList(Aref,T))).attribute(VCFConstants.MLE_ALLELE_COUNT_KEY,2).attribute(VCFConstants.ALLELE_NUMBER_KEY,10).make());
+        supplTest1.add(new VariantContextBuilder(makeVC("3",Arrays.asList(Aref,T))).attribute(VCFConstants.ALLELE_COUNT_KEY,4).attribute(VCFConstants.ALLELE_NUMBER_KEY,22).make());
+        supplTest1.add(makeVC("4",Arrays.asList(Aref,T),
+                makeG("s_1",T,T),
+                makeG("s_2",Aref,T)));
+        VariantContext test1result = LikelihoodCalculationEngine.calculatePosteriorGLs(testOverlappingBase,supplTest1,0,0.001,true,false,false);
+        // the counts here are ref=30, alt=14
+        Genotype test1exp1 = makeGwithPLs("t1",T,T,new double[]{-3.370985, -1.415172, -0.01721766});
+        Genotype test1exp2 = makeGwithPLs("t2",Aref,T,new double[]{-1.763792, -0.007978791, -3.010024});
+        Genotype test1exp3 = makeGwithPLs("t3",Aref,T,new double[]{-2.165587, -0.009773643, -1.811819});
+        Assert.assertEquals(arraysEq(test1exp1.getPL(),_mleparse((List<Integer>) test1result.getGenotype(0).getAnyAttribute(VCFConstants.GENOTYPE_POSTERIORS_KEY))), "");
+        Assert.assertEquals(arraysEq(test1exp2.getPL(),_mleparse((List<Integer>) test1result.getGenotype(1).getAnyAttribute(VCFConstants.GENOTYPE_POSTERIORS_KEY))), "");
+        Assert.assertEquals(arraysEq(test1exp3.getPL(),_mleparse((List<Integer>) test1result.getGenotype(2).getAnyAttribute(VCFConstants.GENOTYPE_POSTERIORS_KEY))), "");
+
+        VariantContext testNonOverlapping = makeVC("1", Arrays.asList(Aref,T), makeG("s1",T,T,3,1,0));
+        List<VariantContext> other = Arrays.asList(makeVC("2",Arrays.asList(Aref,C),makeG("s2",C,C,10,2,0)));
+        VariantContext test2result = LikelihoodCalculationEngine.calculatePosteriorGLs(testNonOverlapping,other,0,0.001,true,false,false);
+        Genotype test2exp1 = makeGwithPLs("SGV",T,T,new double[]{-4.078345, -3.276502, -0.0002661066});
+        Assert.assertEquals(arraysEq(test2exp1.getPL(),_mleparse((List<Integer>) test2result.getGenotype(0).getAnyAttribute(VCFConstants.GENOTYPE_POSTERIORS_KEY))), "");
+    }
+
+    private double[] pl2gl(int[] pl) {
+        double[] gl = new double[pl.length];
+        for ( int idx = 0; idx < gl.length; idx++ ) {
+            gl[idx] = pl[idx]/(-10.0);
+        }
+
+        return MathUtils.normalizeFromLog10(gl,true);
+    }
+
+    @Test
+    private void testCalculatePosterior() {
+        int[][] likelihood_PLs  = new int[][]{
+                new int[]{3,0,3},
+                new int[]{99,0,99},
+                new int[]{50,20,0},
+                new int[]{10,0,50},
+                new int[]{80,60,0},
+                new int[]{0,42,44}};
+
+        int[] altCounts = new int[]{10,40,90};
+        int[] altAlleleNum = new int[]{100,500,1000};
+
+        double[] expected_post_10_100 = new double[] {
+                9.250326e-03, 3.020208e-01, 6.887289e-01,
+                7.693433e-12, 1.000000e+00, 5.728111e-10,
+                1.340156e-07, 2.192982e-03, 9.978069e-01,
+                6.073718e-03, 9.938811e-01, 4.522159e-05,
+                1.343101e-10, 2.197802e-07, 9.999998e-01,
+                9.960193e-01, 1.028366e-03, 2.952290e-03
+        };
+
+        double[] expected_post_10_500 = new double[] {
+                4.226647e-04, 7.513277e-02, 9.244446e-01,
+                1.413080e-12, 1.000000e+00, 3.090662e-09,
+                4.570232e-09, 4.071661e-04, 9.995928e-01,
+                1.120916e-03, 9.986339e-01, 2.451646e-04,
+                4.572093e-12, 4.073320e-08, 1.000000e+00,
+                9.151689e-01, 5.144399e-03, 7.968675e-02
+        };
+
+        double[] expected_post_10_1000 = new double[] {
+                1.077685e-04, 3.870477e-02, 9.611875e-01,
+                6.994030e-13, 1.000000e+00, 6.237975e-09,
+                1.120976e-09, 2.017756e-04, 9.997982e-01,
+                5.549722e-04, 9.989500e-01, 4.949797e-04,
+                1.121202e-12, 2.018163e-08, 1.000000e+00,
+                7.318346e-01, 8.311615e-03, 2.598538e-01
+        };
+
+        double[] expected_post_40_100 = new double[] {
+                1.102354e-01, 6.437516e-01, 2.460131e-01,
+                4.301328e-11, 1.000000e+00, 9.599306e-11,
+                4.422850e-06, 1.294493e-02, 9.870507e-01,
+                3.303763e-02, 9.669550e-01, 7.373032e-06,
+                4.480868e-09, 1.311474e-06, 9.999987e-01,
+                9.997266e-01, 1.846199e-04, 8.882157e-05
+        };
+
+        double[] expected_post_40_500 = new double[] {
+                5.711785e-03, 2.557266e-01, 7.385617e-01,
+                5.610428e-12, 1.000000e+00, 7.254558e-10,
+                7.720262e-08, 1.732352e-03, 9.982676e-01,
+                4.436495e-03, 9.955061e-01, 5.736604e-05,
+                7.733659e-11, 1.735358e-07, 9.999998e-01,
+                9.934793e-01, 1.406575e-03, 5.114153e-03
+        };
+
+        double[] expected_post_40_1000 = new double[] {
+                1.522132e-03, 1.422229e-01, 8.562549e-01,
+                2.688330e-12, 1.000000e+00, 1.512284e-09,
+                1.776184e-08, 8.317737e-04, 9.991682e-01,
+                2.130611e-03, 9.977495e-01, 1.198547e-04,
+                1.777662e-11, 8.324661e-08, 9.999999e-01,
+                9.752770e-01, 2.881677e-03, 2.184131e-02
+        };
+
+        double[] expected_post_90_100 = new double[] {
+                6.887289e-01, 3.020208e-01, 9.250326e-03,
+                5.728111e-10, 1.000000e+00, 7.693433e-12,
+                6.394346e-04, 1.405351e-01, 8.588255e-01,
+                3.127146e-01, 6.872849e-01, 4.200075e-07,
+                7.445327e-07, 1.636336e-05, 9.999829e-01,
+                9.999856e-01, 1.386699e-05, 5.346906e-07
+        };
+
+        double[] expected_post_90_500 = new double[] {
+                2.528165e-02, 4.545461e-01, 5.201723e-01,
+                1.397100e-11, 1.000000e+00, 2.874546e-10,
+                4.839050e-07, 4.360463e-03, 9.956391e-01,
+                1.097551e-02, 9.890019e-01, 2.258221e-05,
+                4.860244e-10, 4.379560e-07, 9.999996e-01,
+                9.986143e-01, 5.677671e-04, 8.179741e-04
+        };
+
+        double[] expected_post_90_1000 = new double[] {
+                7.035938e-03, 2.807708e-01, 7.121932e-01,
+                6.294627e-12, 1.000000e+00, 6.371561e-10,
+                9.859771e-08, 1.971954e-03, 9.980279e-01,
+                4.974874e-03, 9.949748e-01, 5.035678e-05,
+                9.879252e-11, 1.975850e-07, 9.999998e-01,
+                9.947362e-01, 1.255272e-03, 4.008518e-03
+        };
+
+        double[][] expectations = new double[][] {
+                expected_post_10_100,
+                expected_post_10_500,
+                expected_post_10_1000,
+                expected_post_40_100,
+                expected_post_40_500,
+                expected_post_40_1000,
+                expected_post_90_100,
+                expected_post_90_500,
+                expected_post_90_1000
+        };
+
+        int testIndex = 0;
+        for ( int altCount : altCounts ) {
+            for ( int numAlt : altAlleleNum ) {
+                double[] knownCounts = new double[2];
+                knownCounts[0] = altCount;
+                knownCounts[1] = numAlt-altCount;
+                int expected_index = 0;
+                for ( int gl_index = 0; gl_index < likelihood_PLs.length; gl_index++ ) {
+                    double[] post = LikelihoodCalculationEngine.calculatePosteriorGLs(pl2gl(likelihood_PLs[gl_index]), knownCounts, 2);
+                    for ( int i = 0; i < post.length; i++ ) {
+                        double expected = expectations[testIndex][expected_index++];
+                        double observed = Math.pow(10.0,post[i]);
+                        double err = Math.abs( (expected-observed)/expected );
+                        Assert.assertTrue(err < 1e-4, String.format("Counts: %s | Expected: %e | Observed: %e | pre %s | prior %s | post %s",
+                                Arrays.toString(knownCounts), expected,observed, Arrays.toString(pl2gl(likelihood_PLs[gl_index])),
+                                Arrays.toString(LikelihoodCalculationEngine.getDirichletPrior(knownCounts,2)),Arrays.toString(post)));
+                    }
+                }
+                testIndex++;
+            }
+        }
+    }
+
+    private boolean arraysApproxEqual(double[] a, double[] b, double tol) {
+        if ( a.length != b.length ) {
+            return false;
+        }
+
+        for ( int idx = 0; idx < a.length; idx++ ) {
+            if ( Math.abs(a[idx]-b[idx]) > tol ) {
+                return false;
+            }
+        }
+
+        return true;
+    }
+
+    private String errMsgArray(double[] a, double[] b) {
+        return String.format("Expected %s, Observed %s", Arrays.toString(a), Arrays.toString(b));
+    }
+
+    @Test
+    private void testPosteriorMultiAllelic() {
+        // AA AB BB AC BC CC AD BD CD DD
+        int[] PL_one = new int[] {40,20,30,0,15,25};
+        int[] PL_two = new int[] {0,20,10,99,99,99};
+        int[] PL_three = new int[] {50,40,0,30,30,10,20,40,80,50};
+        int[] PL_four  = new int[] {99,90,85,10,5,30,40,20,40,30,0,12,20,14,5};
+        int[] PL_five = new int[] {60,20,30,0,40,10,8,12,18,22,40,12,80,60,20};
+        double[] counts_one = new double[]{100.001,40.001,2.001};
+        double[] counts_two = new double[]{2504.001,16.001,218.001};
+        double[] counts_three = new double[]{10000.001,500.001,25.001,0.001};
+        double[] counts_four = new double[]{4140.001,812.001,32.001,104.001,12.001};
+        double[] counts_five = new double[]{80.001,40.001,8970.001,200.001,1922.001};
+
+        double expected_one[] = new double[] { -2.684035, -0.7852596, -2.4735, -0.08608339, -1.984017, -4.409852 };
+        double expected_two[] = new double[] { -5.736189e-05, -3.893688, -5.362878, -10.65938, -12.85386, -12.0186};
+        double expected_three[] = new double[] {-2.403234, -2.403276, -0.004467802, -2.70429, -4.005319, -3.59033, -6.102247, -9.403276, -14.70429, -13.40284};
+        double expected_four[] = new double[] {-7.828677, -7.335196, -7.843136, -0.7395892, -0.947033, -5.139092, -3.227715,
+                -1.935159, -5.339552, -4.124552, -0.1655353, -2.072979, -4.277372, -3.165498, -3.469589 };
+        double expected_five[] = new double[] { -9.170334, -5.175724, -6.767055, -0.8250021, -5.126027, -0.07628661, -3.276762,
+                -3.977787, -2.227065, -4.57769, -5.494041, -2.995066, -7.444344, -7.096104, -2.414187};
+
+        double[] post1 = LikelihoodCalculationEngine.calculatePosteriorGLs(pl2gl(PL_one),counts_one,2);
+        double[] post2 = LikelihoodCalculationEngine.calculatePosteriorGLs(pl2gl(PL_two),counts_two,2);
+        double[] post3 = LikelihoodCalculationEngine.calculatePosteriorGLs(pl2gl(PL_three),counts_three,2);
+        double[] post4 = LikelihoodCalculationEngine.calculatePosteriorGLs(pl2gl(PL_four),counts_four,2);
+        double[] post5 = LikelihoodCalculationEngine.calculatePosteriorGLs(pl2gl(PL_five),counts_five,2);
+
+        double[] expecPrior5 = new double[] {-4.2878195, -4.2932090, -4.8845400, -1.9424874, -2.2435120, -0.1937719, -3.5942477,
+                -3.8952723, -1.5445506, -3.4951749, -2.6115263, -2.9125508, -0.5618292, -2.2135895,
+                -1.5316722};
+
+        Assert.assertTrue(arraysApproxEqual(expecPrior5, LikelihoodCalculationEngine.getDirichletPrior(counts_five,2),1e-5),errMsgArray(expecPrior5,LikelihoodCalculationEngine.getDirichletPrior(counts_five,2)));
+
+        Assert.assertTrue(arraysApproxEqual(expected_one,post1,1e-6),errMsgArray(expected_one,post1));
+        Assert.assertTrue(arraysApproxEqual(expected_two,post2,1e-5),errMsgArray(expected_two,post2));
+        Assert.assertTrue(arraysApproxEqual(expected_three,post3,1e-5),errMsgArray(expected_three,post3));
+        Assert.assertTrue(arraysApproxEqual(expected_four,post4,1e-5),errMsgArray(expected_four,post4));
+        Assert.assertTrue(arraysApproxEqual(expected_five,post5,1e-5),errMsgArray(expected_five,post5));
+    }
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
index bfae7e94c..8697fcab6 100644
--- a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
@@ -1472,4 +1472,34 @@ public class MathUtils {
         return sliceListByIndices(sampleIndicesWithoutReplacement(list.size(),N),list);
     }
 
+    /**
+     * Return the likelihood of observing the counts of categories having sampled a population
+     * whose categorial frequencies are distributed according to a Dirichlet distribution
+     * @param dirichletParams - params of the prior dirichlet distribution
+     * @param dirichletSum - the sum of those parameters
+     * @param counts - the counts of observation in each category
+     * @param countSum - the sum of counts (number of trials)
+     * @return - associated likelihood
+     */
+    public static double dirichletMultinomial(final double[] dirichletParams, final double dirichletSum,
+                                              final int[] counts, final int countSum) {
+        if ( dirichletParams.length != counts.length ) {
+            throw new IllegalStateException("The number of dirichlet parameters must match the number of categories");
+        }
+        // todo -- lots of lnGammas here. At some point we can safely switch to x * ( ln(x) - 1)
+        double likelihood = log10MultinomialCoefficient(countSum,counts);
+        likelihood += log10Gamma(dirichletSum);
+        likelihood -= log10Gamma(dirichletSum+countSum);
+        for ( int idx = 0; idx < counts.length; idx++ ) {
+            likelihood += log10Gamma(counts[idx] + dirichletParams[idx]);
+            likelihood -= log10Gamma(dirichletParams[idx]);
+        }
+
+        return likelihood;
+    }
+
+    public static double dirichletMultinomial(double[] params, int[] counts) {
+        return dirichletMultinomial(params,sum(params),counts,(int) sum(counts));
+    }
+
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/Utils.java b/public/java/src/org/broadinstitute/sting/utils/Utils.java
index 75bd6a3d1..5cb141074 100644
--- a/public/java/src/org/broadinstitute/sting/utils/Utils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/Utils.java
@@ -835,4 +835,18 @@ public class Utils {
         // don't perform array copies if we need to copy everything anyways
         return  ( trimFromFront == 0 && trimFromBack == 0 ) ? seq : Arrays.copyOfRange(seq, trimFromFront, seq.length - trimFromBack);
     }
+
+    /**
+     * Simple wrapper for sticking elements of a int[] array into a List<Integer>
+     * @param ar - the array whose elements should be listified
+     * @return - a List<Integer> where each element has the same value as the corresponding index in @ar
+     */
+    public static List<Integer> listFromPrimitives(final int[] ar) {
+        final ArrayList<Integer> lst = new ArrayList<>(ar.length);
+        for ( final int d : ar ) {
+            lst.add(d);
+        }
+
+        return lst;
+    }
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
index 11cd27a9f..03bb9763c 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
@@ -565,11 +565,11 @@ public class GATKVariantContextUtils {
      * @param newLikelihoods a vector of likelihoods to use if the method requires PLs, should be log10 likelihoods, cannot be null
      * @param allelesToUse the alleles we are using for our subsetting
      */
-    protected static void updateGenotypeAfterSubsetting(final List<Allele> originalGT,
-                                                        final GenotypeBuilder gb,
-                                                        final GenotypeAssignmentMethod assignmentMethod,
-                                                        final double[] newLikelihoods,
-                                                        final List<Allele> allelesToUse) {
+    public static void updateGenotypeAfterSubsetting(final List<Allele> originalGT,
+                                                     final GenotypeBuilder gb,
+                                                     final GenotypeAssignmentMethod assignmentMethod,
+                                                     final double[] newLikelihoods,
+                                                     final List<Allele> allelesToUse) {
         gb.noAD();
         switch ( assignmentMethod ) {
             case SET_TO_NO_CALL:
diff --git a/public/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java
index a13797523..de049fe89 100644
--- a/public/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java
@@ -522,4 +522,338 @@ public class MathUtilsUnitTest extends BaseTest {
         final Comparable actual = MathUtils.median(values);
         Assert.assertEquals(actual, expected, "Failed with " + values);
     }
+
+
+
+    // man. All this to test dirichlet.
+
+    private double[] unwrap(List<Double> stuff) {
+        double[] unwrapped = new double[stuff.size()];
+        int idx = 0;
+        for ( Double d : stuff ) {
+            unwrapped[idx++] = d == null ? 0.0 : d;
+        }
+
+        return unwrapped;
+    }
+
+    /**
+     * The PartitionGenerator generates all of the partitions of a number n, e.g.
+     * 5 + 0
+     * 4 + 1
+     * 3 + 2
+     * 3 + 1 + 1
+     * 2 + 2 + 1
+     * 2 + 1 + 1 + 1
+     * 1 + 1 + 1 + 1 + 1
+     *
+     * This is used to help enumerate the state space over which the Dirichlet-Multinomial is defined,
+     * to ensure that the distribution function is properly implemented
+     */
+    class PartitionGenerator implements Iterator<List<Integer>> {
+        // generate the partitions of an integer, each partition sorted numerically
+        int n;
+        List<Integer> a;
+        int y;
+        int k;
+        int state;
+        int x;
+        int l;
+
+        public PartitionGenerator(int n) {
+            this.n = n;
+            this.y = n - 1;
+            this.k = 1;
+            this.a = new ArrayList<Integer>();
+            for ( int i = 0; i < n; i++ ) {
+                this.a.add(i);
+            }
+            this.state = 0;
+        }
+
+        public void remove()  { /* do nothing */ }
+
+        public boolean hasNext() { return ! ( this.k == 0 && state == 0 ); }
+
+        private String dataStr()  {
+            return String.format("a = [%s]  k = %d  y = %d  state = %d  x = %d  l = %d",
+                    Utils.join(",",a), k, y, state, x, l);
+        }
+
+        public List<Integer> next() {
+            if ( this.state == 0 ) {
+                this.x = a.get(k-1)+1;
+                k -= 1;
+                this.state = 1;
+            }
+
+            if ( this.state == 1 ) {
+                while ( 2*x <= y ) {
+                    this.a.set(k,x);
+                    this.y -= x;
+                    this.k++;
+                }
+                this.l = 1+this.k;
+                this.state = 2;
+            }
+
+            if ( this.state == 2 ) {
+                if ( x <= y ) {
+                    this.a.set(k,x);
+                    this.a.set(l,y);
+                    x += 1;
+                    y -= 1;
+                    return this.a.subList(0, this.k + 2);
+                } else {
+                    this.state =3;
+                }
+            }
+
+            if ( this.state == 3 ) {
+                this.a.set(k,x+y);
+                this.y = x + y - 1;
+                this.state = 0;
+                return a.subList(0, k + 1);
+            }
+
+            throw new IllegalStateException("Cannot get here");
+        }
+
+        public String toString() {
+            StringBuffer buf = new StringBuffer();
+            buf.append("{ ");
+            while ( hasNext() ) {
+                buf.append("[");
+                buf.append(Utils.join(",",next()));
+                buf.append("],");
+            }
+            buf.deleteCharAt(buf.lastIndexOf(","));
+            buf.append(" }");
+            return buf.toString();
+        }
+
+    }
+
+    /**
+     * NextCounts is the enumerator over the state space of the multinomial dirichlet.
+     *
+     * It filters the partition of the total sum to only those with a number of terms
+     * equal to the number of categories.
+     *
+     * It then generates all permutations of that partition.
+     *
+     * In so doing it enumerates over the full state space.
+     */
+    class NextCounts implements Iterator<int[]> {
+
+        private PartitionGenerator partitioner;
+        private int numCategories;
+        private int[] next;
+
+        public NextCounts(int numCategories, int totalCounts) {
+            partitioner = new PartitionGenerator(totalCounts);
+            this.numCategories = numCategories;
+            next = nextFromPartitioner();
+        }
+
+        public void remove() { /* do nothing */ }
+
+        public boolean hasNext() { return next != null; }
+
+        public int[] next() {
+            int[] toReturn = clone(next);
+            next = nextPermutation();
+            if ( next == null ) {
+                next = nextFromPartitioner();
+            }
+
+            return toReturn;
+        }
+
+        private int[] clone(int[] arr) {
+            int[] a = new int[arr.length];
+            for ( int idx = 0; idx < a.length ; idx ++) {
+                a[idx] = arr[idx];
+            }
+
+            return a;
+        }
+
+        private int[] nextFromPartitioner() {
+            if ( partitioner.hasNext() ) {
+                List<Integer> nxt = partitioner.next();
+                while ( partitioner.hasNext() && nxt.size() > numCategories ) {
+                    nxt = partitioner.next();
+                }
+
+                if ( nxt.size() > numCategories ) {
+                    return null;
+                } else {
+                    int[] buf = new int[numCategories];
+                    for ( int idx = 0; idx < nxt.size(); idx++ ) {
+                        buf[idx] = nxt.get(idx);
+                    }
+                    Arrays.sort(buf);
+                    return buf;
+                }
+            }
+
+            return null;
+        }
+
+        public int[] nextPermutation() {
+            return MathUtilsUnitTest.nextPermutation(next);
+        }
+
+    }
+
+    public static int[] nextPermutation(int[] next) {
+        // the counts can swap among each other. The int[] is originally in ascending order
+        // this generates the next array in lexicographic order descending
+
+        // locate the last occurrence where next[k] < next[k+1]
+        int gt = -1;
+        for ( int idx = 0; idx < next.length-1; idx++) {
+            if ( next[idx] < next[idx+1] ) {
+                gt = idx;
+            }
+        }
+
+        if ( gt == -1 ) {
+            return null;
+        }
+
+        int largestLessThan = gt+1;
+        for ( int idx = 1 + largestLessThan; idx < next.length; idx++) {
+            if ( next[gt] < next[idx] ) {
+                largestLessThan = idx;
+            }
+        }
+
+        int val = next[gt];
+        next[gt] = next[largestLessThan];
+        next[largestLessThan] = val;
+
+        // reverse the tail of the array
+        int[] newTail = new int[next.length-gt-1];
+        int ctr = 0;
+        for ( int idx = next.length-1; idx > gt; idx-- ) {
+            newTail[ctr++] = next[idx];
+        }
+
+        for ( int idx = 0; idx < newTail.length; idx++) {
+            next[gt+idx+1] = newTail[idx];
+        }
+
+        return next;
+    }
+
+
+    // before testing the dirichlet multinomial, we need to test the
+    // classes used to test the dirichlet multinomial
+
+    @Test
+    public void testPartitioner() {
+        int[] numsToTest = new int[]{1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20};
+        int[] expectedSizes = new int[]{1, 2, 3, 5, 7, 11, 15, 22, 30, 42, 56, 77, 101, 135, 176, 231, 297, 385, 490, 627};
+        for ( int testNum = 0; testNum < numsToTest.length; testNum++ ) {
+            PartitionGenerator gen = new PartitionGenerator(numsToTest[testNum]);
+            int size = 0;
+            while ( gen.hasNext() ) {
+                logger.debug(gen.dataStr());
+                size += 1;
+                gen.next();
+            }
+            Assert.assertEquals(size,expectedSizes[testNum],
+                    String.format("Expected %d partitions, observed %s",expectedSizes[testNum],new PartitionGenerator(numsToTest[testNum]).toString()));
+        }
+    }
+
+    @Test
+    public void testNextPermutation() {
+        int[] arr = new int[]{1,2,3,4};
+        int[][] gens = new int[][] {
+                new int[]{1,2,3,4},
+                new int[]{1,2,4,3},
+                new int[]{1,3,2,4},
+                new int[]{1,3,4,2},
+                new int[]{1,4,2,3},
+                new int[]{1,4,3,2},
+                new int[]{2,1,3,4},
+                new int[]{2,1,4,3},
+                new int[]{2,3,1,4},
+                new int[]{2,3,4,1},
+                new int[]{2,4,1,3},
+                new int[]{2,4,3,1},
+                new int[]{3,1,2,4},
+                new int[]{3,1,4,2},
+                new int[]{3,2,1,4},
+                new int[]{3,2,4,1},
+                new int[]{3,4,1,2},
+                new int[]{3,4,2,1},
+                new int[]{4,1,2,3},
+                new int[]{4,1,3,2},
+                new int[]{4,2,1,3},
+                new int[]{4,2,3,1},
+                new int[]{4,3,1,2},
+                new int[]{4,3,2,1} };
+        for ( int gen = 0; gen < gens.length; gen ++ ) {
+            for ( int idx = 0; idx < 3; idx++ ) {
+                Assert.assertEquals(arr[idx],gens[gen][idx],
+                 String.format("Error at generation %d, expected %s, observed %s",gen,Arrays.toString(gens[gen]),Arrays.toString(arr)));
+            }
+            arr = nextPermutation(arr);
+        }
+    }
+
+    private double[] addEpsilon(double[] counts) {
+        double[] d = new double[counts.length];
+        for ( int i = 0; i < counts.length; i ++ ) {
+            d[i] = counts[i] + 1e-3;
+        }
+        return d;
+    }
+
+    @Test
+    public void testDirichletMultinomial() {
+        List<double[]> testAlleles = Arrays.asList(
+                new double[]{80,240},
+                new double[]{1,10000},
+                new double[]{0,500},
+                new double[]{5140,20480},
+                new double[]{5000,800,200},
+                new double[]{6,3,1000},
+                new double[]{100,400,300,800},
+                new double[]{8000,100,20,80,2},
+                new double[]{90,20000,400,20,4,1280,720,1}
+        );
+
+        Assert.assertTrue(! Double.isInfinite(MathUtils.log10Gamma(1e-3)) && ! Double.isNaN(MathUtils.log10Gamma(1e-3)));
+
+        int[] numAlleleSampled = new int[]{2,5,10,20,25};
+        for ( double[] alleles : testAlleles ) {
+            for ( int count : numAlleleSampled ) {
+                // test that everything sums to one. Generate all multinomial draws
+                List<Double> likelihoods = new ArrayList<Double>(100000);
+                NextCounts generator = new NextCounts(alleles.length,count);
+                double maxLog = Double.MIN_VALUE;
+                //List<String> countLog = new ArrayList<String>(200);
+                while ( generator.hasNext() ) {
+                    int[] thisCount = generator.next();
+                    //countLog.add(Arrays.toString(thisCount));
+                    Double likelihood = MathUtils.dirichletMultinomial(addEpsilon(alleles),thisCount);
+                    Assert.assertTrue(! Double.isNaN(likelihood) && ! Double.isInfinite(likelihood),
+                            String.format("Likelihood for counts %s and nAlleles %d was %s",
+                                    Arrays.toString(thisCount),alleles.length,Double.toString(likelihood)));
+                    if ( likelihood > maxLog )
+                        maxLog = likelihood;
+                    likelihoods.add(likelihood);
+                }
+                //System.out.printf("%d likelihoods and max is (probability) %e\n",likelihoods.size(),Math.pow(10,maxLog));
+                Assert.assertEquals(MathUtils.sumLog10(unwrap(likelihoods)),1.0,1e-7,
+                        String.format("Counts %d and alleles %d have nLikelihoods %d. \n Counts: %s",
+                                count,alleles.length,likelihoods.size(), "NODEBUG"/*,countLog*/));
+            }
+        }
+    }
 }
diff --git a/public/java/test/org/broadinstitute/sting/utils/variant/GATKVariantContextUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variant/GATKVariantContextUtilsUnitTest.java
index 220e64f7d..575fe4936 100644
--- a/public/java/test/org/broadinstitute/sting/utils/variant/GATKVariantContextUtilsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variant/GATKVariantContextUtilsUnitTest.java
@@ -32,6 +32,7 @@ import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.variant.variantcontext.*;
+import org.broadinstitute.variant.vcf.VCFConstants;
 import org.testng.Assert;
 import org.testng.annotations.BeforeSuite;
 import org.testng.annotations.DataProvider;
@@ -56,11 +57,7 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
         ATCATC = Allele.create("ATCATC");
     }
 
-    private Genotype makeG(String sample, Allele a1, Allele a2) {
-        return GenotypeBuilder.create(sample, Arrays.asList(a1, a2));
-    }
-
-    private Genotype makeG(String sample, Allele a1, Allele a2, double log10pError, double... pls) {
+    private Genotype makeG(String sample, Allele a1, Allele a2, double log10pError, int... pls) {
         return new GenotypeBuilder(sample, Arrays.asList(a1, a2)).log10PError(log10pError).PL(pls).make();
     }
 

From 51d1a267259adf3279892327d7fab95282c2b1a4 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 26 Nov 2013 22:36:35 -0500
Subject: [PATCH 59/77] Bug fix for something Guillermo added to UG before he
 left to support calling indels from reduced reads.

His code was excessively clipping reads because it was looking at their cigar string instead of just
the read length.  This meant that it was basically impossible to call large deletions in UG even with
perfect evidence in the reads (as reported by Craig D).

Integration tests change because (IMO after looking at sites in IGV) reads with indels similar to the one
being genotyped used to be given too much likelihood and now give less.

Added unit tests for new methods.
---
 .../indels/PairHMMIndelErrorModel.java        |  46 ++++--
 ...dGenotyperIndelCallingIntegrationTest.java |   4 +-
 .../UnifiedGenotyperIntegrationTest.java      |   4 +-
 ...GenotyperNormalCallingIntegrationTest.java |   2 +-
 .../PairHMMIndelErrorModelUnitTest.java       | 133 ++++++++++++++++++
 5 files changed, 172 insertions(+), 17 deletions(-)
 create mode 100644 protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModelUnitTest.java

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
index 97431368e..a273cf01d 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
@@ -68,8 +68,6 @@ import java.util.LinkedHashMap;
 import java.util.LinkedList;
 import java.util.Map;
 
-//import org.broadinstitute.sting.utils.pairhmm.LoglessCachingPairHMM;
-
 
 public class PairHMMIndelErrorModel {
     public static final int BASE_QUAL_THRESHOLD = 20;
@@ -256,6 +254,28 @@ public class PairHMMIndelErrorModel {
         
     }
 
+    /**
+     * Should we clip a downstream portion of a read because it spans off the end of a haplotype?
+     *
+     * @param read               the read in question
+     * @param refWindowStop      the end of the reference window
+     * @return true if the read needs to be clipped, false otherwise
+     */
+    protected static boolean mustClipDownstream(final GATKSAMRecord read, final int refWindowStop) {
+        return ( !read.isEmpty() && read.getSoftStart() < refWindowStop && read.getSoftStart() + read.getReadLength() > refWindowStop );
+    }
+
+    /**
+     * Should we clip a upstream portion of a read because it spans off the end of a haplotype?
+     *
+     * @param read               the read in question
+     * @param refWindowStart     the start of the reference window
+     * @return true if the read needs to be clipped, false otherwise
+     */
+    protected static boolean mustClipUpstream(final GATKSAMRecord read, final int refWindowStart) {
+        return ( !read.isEmpty() && read.getSoftStart() < refWindowStart && read.getSoftEnd() > refWindowStart );
+    }
+
     @Ensures("result != null && result.length == pileup.getNumberOfElements()")
     public synchronized double[][] computeGeneralReadHaplotypeLikelihoods(final ReadBackedPileup pileup,
                                                                           final LinkedHashMap<Allele, Haplotype> haplotypeMap, 
@@ -285,9 +305,8 @@ public class PairHMMIndelErrorModel {
                 // in them - a value of 1 will in theory do but we use a slightly higher one just for safety sake, mostly
                 // in case bases at edge of reads have lower quality.
                 final int trailingBases = 3;
-                final int extraOffset = Math.abs(eventLength);
-                final int refWindowStart = ref.getWindow().getStart()+(trailingBases+extraOffset);
-                final int refWindowStop  = ref.getWindow().getStop()-(trailingBases+extraOffset);
+                final int refWindowStart = ref.getWindow().getStart() + trailingBases;
+                final int refWindowStop  = ref.getWindow().getStop() - trailingBases;
 
                 if (DEBUG) {
                     System.out.format("Read Name:%s, aln start:%d aln stop:%d orig cigar:%s\n",p.getRead().getReadName(), p.getRead().getAlignmentStart(), p.getRead().getAlignmentEnd(), p.getRead().getCigarString());
@@ -295,11 +314,13 @@ public class PairHMMIndelErrorModel {
 
                 GATKSAMRecord read = ReadClipper.hardClipAdaptorSequence(p.getRead());
 
-                if (!read.isEmpty() && (read.getSoftEnd() > refWindowStop && read.getSoftStart() < refWindowStop))
-                    read = ReadClipper.hardClipByReferenceCoordinatesRightTail(read, refWindowStop);
+                // if the read extends beyond the downstream (right) end of the reference window, clip it
+                if ( mustClipDownstream(read, refWindowStop) )
+                    read = ReadClipper.hardClipByReadCoordinates(read, read.getSoftStart() + read.getReadLength() - refWindowStop + 1, read.getReadLength() - 1);
 
-                if (!read.isEmpty() && (read.getSoftStart() < refWindowStart && read.getSoftEnd() > refWindowStart))
-                    read = ReadClipper.hardClipByReferenceCoordinatesLeftTail (read, refWindowStart);
+                // if the read extends beyond the upstream (left) end of the reference window, clip it
+                if ( mustClipUpstream(read, refWindowStart) )
+                    read = ReadClipper.hardClipByReferenceCoordinatesLeftTail(read, refWindowStart);
 
                 if (read.isEmpty())
                     continue;
@@ -337,8 +358,9 @@ public class PairHMMIndelErrorModel {
                  * trailingBases is a padding constant(=3) and we additionally add abs(eventLength) to both sides of read to be able to
                  * differentiate context between two haplotypes
                  */
-                long startLocationInRefForHaplotypes = Math.max(readStart + numStartSoftClippedBases - trailingBases - ReadUtils.getFirstInsertionOffset(read)-extraOffset, 0);
-                long stopLocationInRefForHaplotypes =  readEnd -numEndSoftClippedBases  + trailingBases + ReadUtils.getLastInsertionOffset(read)+extraOffset;
+                final int absEventLength = Math.abs(eventLength);
+                long startLocationInRefForHaplotypes = Math.max(readStart + numStartSoftClippedBases - trailingBases - ReadUtils.getFirstInsertionOffset(read) - absEventLength, 0);
+                long stopLocationInRefForHaplotypes = readEnd - numEndSoftClippedBases + trailingBases + ReadUtils.getLastInsertionOffset(read) + absEventLength;
 
                 if (DEBUG)
                     System.out.format("orig Start:%d orig stop: %d\n", startLocationInRefForHaplotypes, stopLocationInRefForHaplotypes);
@@ -412,7 +434,7 @@ public class PairHMMIndelErrorModel {
                     // Pack the shortened read and its associated gap-continuation-penalty array into a map, as required by PairHMM
                     readGCPArrayMap.put(processedRead,contextLogGapContinuationProbabilities);
 
-                    // Create a map of alleles to a new set of haplotypes, whose bases have been trimmed to the approprate genomic locations
+                    // Create a map of alleles to a new set of haplotypes, whose bases have been trimmed to the appropriate genomic locations
                     final Map<Allele, Haplotype> trimmedHaplotypeMap = trimHaplotypes(haplotypeMap, startLocationInRefForHaplotypes, stopLocationInRefForHaplotypes, ref);
 
                     // Get the likelihoods for our clipped read against each of our trimmed haplotypes.
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
index 7fa716168..9556f9bf1 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
@@ -101,7 +101,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 1:10,000,000-10,500,000",
                 1,
-                Arrays.asList("c6f0fa039ca5672469838bc9f52c72d3"));
+                Arrays.asList("3d12bdb816d27bf7c9efb4c13dc2aec7"));
 
         executeTest(String.format("test indel calling, multiple technologies"), spec);
     }
@@ -136,7 +136,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation +
                         "low_coverage_CEU.chr1.10k-11k.bam -o %s -L " + result.get(0).getAbsolutePath(), 1,
-                Arrays.asList("8682738c2c66b502cdbf7db466a5c3e2"));
+                Arrays.asList("a2c8e83f37cd1e114b42af4b873f57bc"));
         executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
     }
 
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index 74cd3f16e..2cdddd49f 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -260,7 +260,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 1:10,000,000-10,100,000",
                 1,
-                Arrays.asList("9f4e663e3b156b14fd55df3f5f0336a5"));
+                Arrays.asList("150b31ba05113ca1996b548be5170d6d"));
 
         executeTest(String.format("test multiple technologies"), spec);
     }
@@ -279,7 +279,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -L 1:10,000,000-10,100,000" +
                         " -baq CALCULATE_AS_NECESSARY",
                 1,
-                Arrays.asList("260bb73e2900334d5c3ff8123be0d2d8"));
+                Arrays.asList("7d0ee85cd89f4addd84c5511daaaa5c5"));
 
         executeTest(String.format("test calling with BAQ"), spec);
     }
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java
index afec97b84..18554e157 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java
@@ -64,7 +64,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest 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("7f26ca78e550afa28df11d593c90ec9a"));
+                Arrays.asList("ec0977e3fd3e2ac29c9821f0ca830455"));
         executeTest("test MultiSample Pilot1", spec);
     }
 
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModelUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModelUnitTest.java
new file mode 100644
index 000000000..38c06c25f
--- /dev/null
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModelUnitTest.java
@@ -0,0 +1,133 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*  
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*  
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*  
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*  
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*  
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. 
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.  
+*  
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY 
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*  
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*  
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*  
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*  
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt. 
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. 
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.sting.gatk.walkers.indels;
+
+
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import net.sf.samtools.SAMFileHeader;
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.util.*;
+
+public class PairHMMIndelErrorModelUnitTest extends BaseTest {
+
+    private SAMFileHeader header;
+
+    @BeforeClass
+    public void setup() throws FileNotFoundException {
+        final IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
+        header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
+    }
+
+    private static final int refWindowStart = 1000;
+    private static final int refWindowEnd = 1100;
+
+    @DataProvider(name = "ClipUpstreamProvider")
+    public Object[][] ClipUpstreamTestData() {
+        List<Object[]> tests = new ArrayList<Object[]>();
+
+        for ( final int readStart : Arrays.asList(900, 950, 990, 1000) ) {
+            for ( final int readLength : Arrays.asList(10, 50, 100) ) {
+                for ( final int delLength : Arrays.asList(0, 5, 10) ) {
+                    tests.add(new Object[]{readStart, readLength, delLength});
+                }
+            }
+        }
+
+        return tests.toArray(new Object[][]{});
+    }
+
+    @Test(dataProvider = "ClipUpstreamProvider", enabled = true)
+    public void clipUpstreamTest(final int readStart, final int readLength, final int delLength) {
+
+        final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "basicRead", 0, readStart, readLength);
+        if ( delLength == 0 )
+            read.setCigarString(readLength + "M");
+        else
+            read.setCigarString((readLength / 2) + "M" + delLength + "D" + (readLength / 2) + "M");
+
+        final boolean result = PairHMMIndelErrorModel.mustClipUpstream(read, refWindowStart);
+        Assert.assertEquals(result, read.getSoftStart() < refWindowStart && read.getSoftEnd() > refWindowStart);
+    }
+
+    @DataProvider(name = "ClipDownstreamProvider")
+    public Object[][] ClipDownstreamTestData() {
+        List<Object[]> tests = new ArrayList<Object[]>();
+
+        for ( final int readStart : Arrays.asList(1000, 1050, 1090, 1100) ) {
+            for ( final int readLength : Arrays.asList(10, 50, 100) ) {
+                for ( final int delLength : Arrays.asList(0, 5, 10) ) {
+                    tests.add(new Object[]{readStart, readLength, delLength});
+                }
+            }
+        }
+
+        return tests.toArray(new Object[][]{});
+    }
+
+    @Test(dataProvider = "ClipDownstreamProvider", enabled = true)
+    public void clipDownstreamTest(final int readStart, final int readLength, final int delLength) {
+
+        final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "basicRead", 0, readStart, readLength);
+        if ( delLength == 0 )
+            read.setCigarString(readLength + "M");
+        else
+            read.setCigarString((readLength / 2) + "M" + delLength + "D" + (readLength / 2) + "M");
+
+        final boolean result = PairHMMIndelErrorModel.mustClipDownstream(read, refWindowEnd);
+        Assert.assertEquals(result, read.getSoftStart() < refWindowEnd && read.getSoftStart() + readLength > refWindowEnd);
+    }
+}
\ No newline at end of file

From df6499e58c0e1a8d48a8d53c6522452b57c65cc9 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 27 Nov 2013 15:53:11 -0500
Subject: [PATCH 60/77] Bug fix for RR: stop (incorrectly) pulling the MQ out
 of the SAMRecord as a byte instead of an int.

For reads with high MQs (greater than max byte) the MQ was being treated as negative and failing
the min MQ filter.

Added unit test.

Delivers PT#61567540.
---
 .../reducereads/SlidingWindow.java            |  9 ++++----
 .../reducereads/SlidingWindowUnitTest.java    | 23 +++++++++++++++++++
 2 files changed, 28 insertions(+), 4 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
index 964c6b401..d5aa8f944 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
@@ -1033,7 +1033,7 @@ public class SlidingWindow {
     protected void actuallyUpdateHeaderForRead(final LinkedList<HeaderElement> header, final GATKSAMRecord read, final boolean removeRead, final int startIndex) {
 
         final Iterator<HeaderElement> headerElementIterator = header.listIterator(startIndex);
-        final byte mappingQuality = (byte) read.getMappingQuality();
+        final int mappingQuality = read.getMappingQuality();
         final boolean isNegativeStrand = read.getReadNegativeStrandFlag();
 
         // iterator variables
@@ -1062,14 +1062,15 @@ public class SlidingWindow {
 
                     break;
                 case D:
-                    // deletions are added to the baseCounts with the read mapping quality as it's quality score
+                    // deletions are added to the baseCounts with the read mapping quality as its quality score
                     final int nDeletionBases = cigarElement.getLength();
+                    final byte MQbyte = mappingQuality > Byte.MAX_VALUE ? Byte.MAX_VALUE : (byte)mappingQuality;
                     for ( int i = 0; i < nDeletionBases; i++ ) {
                         headerElement = headerElementIterator.next();
                         if (removeRead)
-                            headerElement.removeBase(BaseUtils.Base.D.base, mappingQuality, mappingQuality, mappingQuality, mappingQuality, MIN_BASE_QUAL_TO_COUNT, MIN_MAPPING_QUALITY, false, isNegativeStrand);
+                            headerElement.removeBase(BaseUtils.Base.D.base, MQbyte, MQbyte, MQbyte, mappingQuality, MIN_BASE_QUAL_TO_COUNT, MIN_MAPPING_QUALITY, false, isNegativeStrand);
                         else
-                            headerElement.addBase(BaseUtils.Base.D.base, mappingQuality, mappingQuality, mappingQuality, mappingQuality, MIN_BASE_QUAL_TO_COUNT, MIN_MAPPING_QUALITY, false, isNegativeStrand);
+                            headerElement.addBase(BaseUtils.Base.D.base, MQbyte, MQbyte, MQbyte, mappingQuality, MIN_BASE_QUAL_TO_COUNT, MIN_MAPPING_QUALITY, false, isNegativeStrand);
                     }
                     locationIndex += nDeletionBases;
                     break;
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java
index 720f00f98..c49a671e2 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java
@@ -860,6 +860,29 @@ public class SlidingWindowUnitTest extends BaseTest {
             Assert.assertEquals(windowHeader.get(i).getBaseCounts(SlidingWindow.ConsensusType.POSITIVE_CONSENSUS).countOfBase(BaseUtils.Base.A.base), 0);
     }
 
+    @Test
+    public void testUpdateHeaderForReadWithHighMQ() {
+
+        // set up the window header
+        final int currentHeaderStart = 100;
+        final LinkedList<HeaderElement> windowHeader = new LinkedList<>();
+        for ( int i = 0; i < readLength; i++ )
+            windowHeader.add(new HeaderElement(currentHeaderStart + i));
+
+        // set up the read
+        final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "basicRead", 0, currentHeaderStart, readLength);
+        read.setReadBases(Utils.dupBytes((byte) 'A', readLength));
+        read.setBaseQualities(Utils.dupBytes((byte)30, readLength));
+        read.setMappingQuality(180);
+        read.setReadNegativeStrandFlag(false);
+
+        // add the read and make sure it's not filtered because of low MQ (byte vs. int)
+        final SlidingWindow slidingWindow = new SlidingWindow("1", 0, 10, header, new GATKSAMReadGroupRecord("test"), 0, 0.05, 0.05, 0.05, 20, 20, 10, ReduceReads.DownsampleStrategy.Normal, false);
+        slidingWindow.actuallyUpdateHeaderForRead(windowHeader, read, false, 0);
+        for ( int i = 0; i < readLength; i++ )
+            Assert.assertEquals(windowHeader.get(i).getBaseCounts(SlidingWindow.ConsensusType.POSITIVE_CONSENSUS).countOfBase(BaseUtils.Base.A.base), 1);
+    }
+
     //////////////////////////////////////////////////////////////////////////////////
     //// This section tests functionality related to polyploid consensus creation ////
     //////////////////////////////////////////////////////////////////////////////////

From b57054c63cf95bf639486374e8e99c44a90ada58 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Mon, 30 Sep 2013 11:14:35 -0400
Subject: [PATCH 61/77] Various VQSR optimizations in both runtime and
 accuracy.

-- For very large whole genome datasets with over 2M variants overlapping the training data randomly downsample the training set that gets used to build the Gaussian mixture model.
-- Annotations are ordered by the difference in means between known and novel instead of by their standard deviation.
-- Removed the training set quality score threshold.
-- Now uses 2 gaussians by default for the negative model.
-- Num bad argument has been removed and the cutoffs are now chosen by the model itself by looking at the LOD scores.
-- Model plots are now generated much faster.
-- Stricter threshold for determining model convergence.
-- All VQSR integration tests change because of these changes to the model.
-- Add test for downsampling of training data.
---
 .../ApplyRecalibration.java                   | 112 +++++++++-----
 .../GaussianMixtureModel.java                 |   2 +-
 .../variantrecalibration/TrancheManager.java  |   6 +-
 .../VariantDataManager.java                   | 139 ++++++++----------
 .../VariantRecalibrator.java                  |  62 ++++----
 ...VariantRecalibratorArgumentCollection.java |  39 +++--
 .../VariantRecalibratorEngine.java            |   2 +-
 .../ApplyRecalibrationUnitTest.java           |  68 +++++++++
 .../VariantDataManagerUnitTest.java           |  82 ++++++++++-
 ...ntRecalibrationWalkersIntegrationTest.java |  26 ++--
 10 files changed, 364 insertions(+), 174 deletions(-)
 create mode 100644 protected/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
index 314efe2a2..4b5237087 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
@@ -46,10 +46,8 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Input;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.commandline.RodBinding;
+import org.apache.commons.math.util.MathUtils;
+import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -112,6 +110,9 @@ import java.util.*;
 @PartitionBy(PartitionType.LOCUS)
 public class ApplyRecalibration extends RodWalker<Integer, Integer> implements TreeReducible<Integer> {
 
+    public static final String LOW_VQSLOD_FILTER_NAME = "LOW_VQSLOD";
+    private final double DEFAULT_VQSLOD_CUTOFF = 0.0;
+
     /////////////////////////////
     // Inputs
     /////////////////////////////
@@ -122,7 +123,7 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> implements T
     public List<RodBinding<VariantContext>> input;
     @Input(fullName="recal_file", shortName="recalFile", doc="The input recal file used by ApplyRecalibration", required=true)
     protected RodBinding<VariantContext> recal;
-    @Input(fullName="tranches_file", shortName="tranchesFile", doc="The input tranches file describing where to cut the data", required=true)
+    @Input(fullName="tranches_file", shortName="tranchesFile", doc="The input tranches file describing where to cut the data", required=false)
     protected File TRANCHES_FILE;
 
     /////////////////////////////
@@ -134,8 +135,13 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> implements T
     /////////////////////////////
     // Command Line Arguments
     /////////////////////////////
+    @Advanced
     @Argument(fullName="ts_filter_level", shortName="ts_filter_level", doc="The truth sensitivity level at which to start filtering", required=false)
-    protected double TS_FILTER_LEVEL = 99.0;
+    protected Double TS_FILTER_LEVEL = null;
+    @Advanced
+    @Argument(fullName="lodCutoff", shortName="lodCutoff", doc="The VQSLOD score below which to start filtering", required=false)
+    protected Double VQSLOD_CUTOFF = null;
+
     /**
      * For this to work properly, the -ignoreFilter argument should also be applied to the VariantRecalibration command.
      */
@@ -160,13 +166,15 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> implements T
     //---------------------------------------------------------------------------------------------------------------
 
     public void initialize() {
-        for ( final Tranche t : Tranche.readTranches(TRANCHES_FILE) ) {
-            if ( t.ts >= TS_FILTER_LEVEL ) {
-                tranches.add(t);
+        if( TS_FILTER_LEVEL != null ) {
+            for ( final Tranche t : Tranche.readTranches(TRANCHES_FILE) ) {
+                if ( t.ts >= TS_FILTER_LEVEL ) {
+                    tranches.add(t);
+                }
+                logger.info(String.format("Read tranche " + t));
             }
-            logger.info(String.format("Read tranche " + t));
+            Collections.reverse(tranches); // this algorithm wants the tranches ordered from best (lowest truth sensitivity) to worst (highest truth sensitivity)
         }
-        Collections.reverse(tranches); // this algorithm wants the tranches ordered from best (lowest truth sensitivity) to worst (highest truth sensitivity)
 
         for( final RodBinding rod : input ) {
             inputNames.add( rod.getName() );
@@ -183,19 +191,32 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> implements T
         final TreeSet<String> samples = new TreeSet<>();
         samples.addAll(SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames));
 
-        if( tranches.size() >= 2 ) {
-            for( int iii = 0; iii < tranches.size() - 1; iii++ ) {
-                final Tranche t = tranches.get(iii);
-                hInfo.add(new VCFFilterHeaderLine(t.name, String.format("Truth sensitivity tranche level for " + t.model.toString() + " model at VQS Lod: " + t.minVQSLod + " <= x < " + tranches.get(iii+1).minVQSLod)));
+        if( TS_FILTER_LEVEL != null ) {
+            // if the user specifies both ts_filter_level and lodCutoff then throw a user error
+            if( VQSLOD_CUTOFF != null ) {
+                throw new UserException("Arguments --ts_filter_level and --lodCutoff are mutually exclusive. Please only specify one option.");
             }
-        }
-        if( tranches.size() >= 1 ) {
-            hInfo.add(new VCFFilterHeaderLine(tranches.get(0).name + "+", String.format("Truth sensitivity tranche level for " + tranches.get(0).model.toString() + " model at VQS Lod < " + tranches.get(0).minVQSLod)));
-        } else {
-            throw new UserException("No tranches were found in the file or were above the truth sensitivity filter level " + TS_FILTER_LEVEL);
-        }
 
-        logger.info("Keeping all variants in tranche " + tranches.get(tranches.size()-1));
+            if( tranches.size() >= 2 ) {
+                for( int iii = 0; iii < tranches.size() - 1; iii++ ) {
+                    final Tranche t = tranches.get(iii);
+                    hInfo.add(new VCFFilterHeaderLine(t.name, String.format("Truth sensitivity tranche level for " + t.model.toString() + " model at VQS Lod: " + t.minVQSLod + " <= x < " + tranches.get(iii+1).minVQSLod)));
+                }
+            }
+            if( tranches.size() >= 1 ) {
+                hInfo.add(new VCFFilterHeaderLine(tranches.get(0).name + "+", String.format("Truth sensitivity tranche level for " + tranches.get(0).model.toString() + " model at VQS Lod < " + tranches.get(0).minVQSLod)));
+            } else {
+                throw new UserException("No tranches were found in the file or were above the truth sensitivity filter level " + TS_FILTER_LEVEL);
+            }
+
+            logger.info("Keeping all variants in tranche " + tranches.get(tranches.size()-1));
+        } else {
+            if( VQSLOD_CUTOFF == null ) {
+                VQSLOD_CUTOFF = DEFAULT_VQSLOD_CUTOFF;
+            }
+            hInfo.add(new VCFFilterHeaderLine(LOW_VQSLOD_FILTER_NAME, "VQSLOD < " + VQSLOD_CUTOFF));
+            logger.info("Keeping all variants with VQSLOD >= " + VQSLOD_CUTOFF);
+        }
 
         final VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
         vcfWriter.writeHeader(vcfHeader);
@@ -245,7 +266,6 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> implements T
                 }
 
                 VariantContextBuilder builder = new VariantContextBuilder(vc);
-                String filterString = null;
 
                 // Annotate the new record with its VQSLOD and the worst performing annotation
                 builder.attribute(VariantRecalibrator.VQS_LOD_KEY, lod);
@@ -255,21 +275,7 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> implements T
                 if ( recalDatum.hasAttribute(VariantRecalibrator.NEGATIVE_LABEL_KEY))
                     builder.attribute(VariantRecalibrator.NEGATIVE_LABEL_KEY, true);
 
-                for( int i = tranches.size() - 1; i >= 0; i-- ) {
-                    final Tranche tranche = tranches.get(i);
-                    if( lod >= tranche.minVQSLod ) {
-                        if( i == tranches.size() - 1 ) {
-                            filterString = VCFConstants.PASSES_FILTERS_v4;
-                        } else {
-                            filterString = tranche.name;
-                        }
-                        break;
-                    }
-                }
-
-                if( filterString == null ) {
-                    filterString = tranches.get(0).name+"+";
-                }
+                final String filterString = generateFilterString(lod);
 
                 if( filterString.equals(VCFConstants.PASSES_FILTERS_v4) ) {
                     builder.passFilters();
@@ -289,6 +295,36 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> implements T
         return 1; // This value isn't used for anything
     }
 
+    /**
+     * Generate the VCF filter string for this record based on the provided lod score
+     * @param lod non-null double
+     * @return the String to use as the VCF filter field
+     */
+    protected String generateFilterString( final double lod ) {
+        String filterString = null;
+        if( TS_FILTER_LEVEL != null ) {
+            for( int i = tranches.size() - 1; i >= 0; i-- ) {
+                final Tranche tranche = tranches.get(i);
+                if( lod >= tranche.minVQSLod ) {
+                    if( i == tranches.size() - 1 ) {
+                        filterString = VCFConstants.PASSES_FILTERS_v4;
+                    } else {
+                        filterString = tranche.name;
+                    }
+                    break;
+                }
+            }
+
+            if( filterString == null ) {
+                filterString = tranches.get(0).name+"+";
+            }
+        } else {
+            filterString = ( lod < VQSLOD_CUTOFF ? LOW_VQSLOD_FILTER_NAME : VCFConstants.PASSES_FILTERS_v4 );
+        }
+
+        return filterString;
+    }
+
     private static VariantContext getMatchingRecalVC(final VariantContext target, final List<VariantContext> recalVCs) {
         for( final VariantContext recalVC : recalVCs ) {
             if ( target.getEnd() == recalVC.getEnd() ) {
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
index ed26bc17a..9e36e5dbe 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
@@ -267,7 +267,7 @@ public class GaussianMixtureModel {
     public double evaluateDatumMarginalized( final VariantDatum datum ) {
         int numRandomDraws = 0;
         double sumPVarInGaussian = 0.0;
-        final int numIterPerMissingAnnotation = 10; // Trade off here between speed of computation and accuracy of the marginalization
+        final int numIterPerMissingAnnotation = 20; // 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++ ) {
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java
index 30377b63e..ab6b4adda 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java
@@ -160,11 +160,11 @@ public class TrancheManager {
         }
     }
 
-    public static List<Tranche> findTranches( final ArrayList<VariantDatum> data, final double[] tranches, final SelectionMetric metric, final VariantRecalibratorArgumentCollection.Mode model ) {
+    public static List<Tranche> findTranches( final List<VariantDatum> data, final double[] tranches, final SelectionMetric metric, final VariantRecalibratorArgumentCollection.Mode model ) {
         return findTranches( data, tranches, metric, model, null );
     }
 
-    public static List<Tranche> findTranches( final ArrayList<VariantDatum> data, final double[] trancheThresholds, final SelectionMetric metric, final VariantRecalibratorArgumentCollection.Mode model, final File debugFile ) {
+    public static List<Tranche> findTranches( final List<VariantDatum> data, final double[] trancheThresholds, final SelectionMetric metric, final VariantRecalibratorArgumentCollection.Mode model, final File debugFile ) {
         logger.info(String.format("Finding %d tranches for %d variants", trancheThresholds.length, data.size()));
 
         Collections.sort( data, new VariantDatum.VariantDatumLODComparator() );
@@ -172,7 +172,7 @@ public class TrancheManager {
 
         if ( debugFile != null) { writeTranchesDebuggingInfo(debugFile, data, metric); }
 
-        List<Tranche> tranches = new ArrayList<Tranche>();
+        List<Tranche> tranches = new ArrayList<>();
         for ( double trancheThreshold : trancheThresholds ) {
             Tranche t = findTranche(data, metric, trancheThreshold, model);
 
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
index 65b1c2322..ac4654f73 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -71,7 +71,7 @@ import java.util.*;
  */
 
 public class VariantDataManager {
-    private ExpandingArrayList<VariantDatum> data;
+    private List<VariantDatum> data;
     private double[] meanVector;
     private double[] varianceVector; // this is really the standard deviation
     public List<String> annotationKeys;
@@ -88,30 +88,30 @@ public class VariantDataManager {
         trainingSets = new ArrayList<>();
     }
 
-    public void setData( final ExpandingArrayList<VariantDatum> data ) {
+    public void setData( final List<VariantDatum> data ) {
         this.data = data;
     }
 
-    public ExpandingArrayList<VariantDatum> getData() {
+    public List<VariantDatum> getData() {
         return data;
     }
 
     public void normalizeData() {
         boolean foundZeroVarianceAnnotation = false;
         for( int iii = 0; iii < meanVector.length; iii++ ) {
-            final double theMean = mean(iii);
-            final double theSTD = standardDeviation(theMean, iii);
+            final double theMean = mean(iii, true);
+            final double theSTD = standardDeviation(theMean, iii, true);
             logger.info( annotationKeys.get(iii) + String.format(": \t mean = %.2f\t standard deviation = %.2f", theMean, theSTD) );
             if( Double.isNaN(theMean) ) {
                 throw new UserException.BadInput("Values for " + annotationKeys.get(iii) + " annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. See " + HelpConstants.forumPost("discussion/49/using-variant-annotator"));
             }
 
-            foundZeroVarianceAnnotation = foundZeroVarianceAnnotation || (theSTD < 1E-6);
+            foundZeroVarianceAnnotation = foundZeroVarianceAnnotation || (theSTD < 1E-5);
             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 );
+                datum.annotations[iii] = ( datum.isNull[iii] ? 0.1 * GenomeAnalysisEngine.getRandomGenerator().nextGaussian() : ( datum.annotations[iii] - theMean ) / theSTD );
             }
         }
         if( foundZeroVarianceAnnotation ) {
@@ -129,7 +129,7 @@ public class VariantDataManager {
 
         // re-order the data by increasing standard deviation so that the results don't depend on the order things were specified on the command line
         // standard deviation over the training points is used as a simple proxy for information content, perhaps there is a better thing to use here
-        final List<Integer> theOrder = calculateSortOrder(varianceVector);
+        final List<Integer> theOrder = calculateSortOrder(meanVector);
         annotationKeys = reorderList(annotationKeys, theOrder);
         varianceVector = ArrayUtils.toPrimitive(reorderArray(ArrayUtils.toObject(varianceVector), theOrder));
         meanVector = ArrayUtils.toPrimitive(reorderArray(ArrayUtils.toObject(meanVector), theOrder));
@@ -137,40 +137,41 @@ public class VariantDataManager {
             datum.annotations = ArrayUtils.toPrimitive(reorderArray(ArrayUtils.toObject(datum.annotations), theOrder));
             datum.isNull = ArrayUtils.toPrimitive(reorderArray(ArrayUtils.toObject(datum.isNull), theOrder));
         }
+        logger.info("Annotations are now ordered by their information content: " + annotationKeys.toString());
     }
 
     /**
      * Get a list of indices which give the ascending sort order of the data array
-     * @param data the data to consider
+     * @param inputVector the data to consider
      * @return a non-null list of integers with length matching the length of the input array
      */
-    protected List<Integer> calculateSortOrder(final double[] data) {
-        final List<Integer> theOrder = new ArrayList<>(data.length);
-        final List<MyStandardDeviation> sortedData = new ArrayList<>(data.length);
+    protected List<Integer> calculateSortOrder(final double[] inputVector) {
+        final List<Integer> theOrder = new ArrayList<>(inputVector.length);
+        final List<MyDoubleForSorting> toBeSorted = new ArrayList<>(inputVector.length);
         int count = 0;
-        for( final double d : data ) {
-            sortedData.add(new MyStandardDeviation(d, count++));
+        for( int iii = 0; iii < inputVector.length; iii++ ) {
+            toBeSorted.add(new MyDoubleForSorting(-1.0 * Math.abs(inputVector[iii] - mean(iii, false)), count++));
         }
-        Collections.sort(sortedData); // sort the data in ascending order
-        for( final MyStandardDeviation d : sortedData ) {
+        Collections.sort(toBeSorted);
+        for( final MyDoubleForSorting d : toBeSorted ) {
             theOrder.add(d.originalIndex); // read off the sort order by looking at the index field
         }
         return theOrder;
     }
 
-    // small private class to assist in reading off the new ordering of the standard deviation array
-    private class MyStandardDeviation implements Comparable<MyStandardDeviation> {
-        final Double standardDeviation;
+    // small private class to assist in reading off the new ordering of the annotation array
+    private class MyDoubleForSorting implements Comparable<MyDoubleForSorting> {
+        final Double myData;
         final int originalIndex;
 
-        public MyStandardDeviation( final double standardDeviation, final int originalIndex ) {
-            this.standardDeviation = standardDeviation;
+        public MyDoubleForSorting(final double myData, final int originalIndex) {
+            this.myData = myData;
             this.originalIndex = originalIndex;
         }
 
         @Override
-        public int compareTo(final MyStandardDeviation other) {
-            return standardDeviation.compareTo(other.standardDeviation);
+        public int compareTo(final MyDoubleForSorting other) {
+            return myData.compareTo(other.myData);
         }
     }
 
@@ -233,92 +234,77 @@ public class VariantDataManager {
         return false;
     }
 
-    public ExpandingArrayList<VariantDatum> getTrainingData() {
-        final ExpandingArrayList<VariantDatum> trainingData = new ExpandingArrayList<>();
+    public List<VariantDatum> getTrainingData() {
+        final List<VariantDatum> trainingData = new ExpandingArrayList<>();
         for( final VariantDatum datum : data ) {
-            if( datum.atTrainingSite && !datum.failingSTDThreshold && datum.originalQual > VRAC.QUAL_THRESHOLD ) {
+            if( datum.atTrainingSite && !datum.failingSTDThreshold ) {
                 trainingData.add( datum );
             }
         }
         logger.info( "Training with " + trainingData.size() + " variants after standard deviation thresholding." );
-        if( trainingData.size() < VRAC.NUM_BAD_VARIANTS) {
+        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." );
+        } else if( trainingData.size() > VRAC.MAX_NUM_TRAINING_DATA ) {
+            logger.warn( "WARNING: Very large training set detected. Downsampling to " + VRAC.MAX_NUM_TRAINING_DATA + " training variants." );
+            Collections.shuffle(trainingData);
+            return trainingData.subList(0, VRAC.MAX_NUM_TRAINING_DATA);
         }
         return trainingData;
     }
 
-    public ExpandingArrayList<VariantDatum> selectWorstVariants( final int minimumNumber ) {
-        // The return value is the list of training variants
-        final ExpandingArrayList<VariantDatum> trainingData = new ExpandingArrayList<>();
+    public List<VariantDatum> selectWorstVariants() {
+        final List<VariantDatum> trainingData = new ExpandingArrayList<>();
 
-        // 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 );
-            }
-        }
-        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, new VariantDatum.VariantDatumLODComparator() );
-        final int numToAdd = minimumNumber - trainingData.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. You can try lowering the --numBadVariants argument but this is unsafe." );
-        }
-        int index = 0, numAdded = 0;
-        while( numAdded < numToAdd && index < data.size() ) {
-            final VariantDatum datum = data.get(index++);
-            if( datum != null && !datum.atAntiTrainingSite && !datum.failingSTDThreshold && !Double.isInfinite(datum.lod) ) {
+            if( datum != null && !datum.failingSTDThreshold && !Double.isInfinite(datum.lod) && datum.lod < VRAC.BAD_LOD_CUTOFF ) {
                 datum.atAntiTrainingSite = true;
                 trainingData.add( datum );
-                numAdded++;
             }
         }
-        logger.info( "Additionally training with worst " + numToAdd + " scoring variants --> " + (trainingData.size() - numBadSitesAdded) + " variants with LOD <= " + String.format("%.4f", data.get(index).lod) + "." );
+
+        logger.info( "Training with worst " + trainingData.size() + " scoring variants --> variants with LOD <= " + String.format("%.4f", VRAC.BAD_LOD_CUTOFF) + "." );
+
         return trainingData;
     }
 
-    public ExpandingArrayList<VariantDatum> getRandomDataForPlotting( int numToAdd ) {
-        numToAdd = Math.min(numToAdd, data.size());
-        final ExpandingArrayList<VariantDatum> returnData = new ExpandingArrayList<>();
-        // add numToAdd non-anti training sites to plot
-        for( int iii = 0; iii < numToAdd; iii++) {
-            final VariantDatum datum = data.get(GenomeAnalysisEngine.getRandomGenerator().nextInt(data.size()));
-            if( ! datum.atAntiTrainingSite && !datum.failingSTDThreshold ) {
-                returnData.add(datum);
-            }
-        }
+    public List<VariantDatum> getEvaluationData() {
+        final List<VariantDatum> evaluationData = new ExpandingArrayList<>();
 
-        final int MAX_ANTI_TRAINING_SITES = 10000;
-        int nAntiTrainingAdded = 0;
-        // Add all anti-training sites to visual
         for( final VariantDatum datum : data ) {
-            if ( nAntiTrainingAdded > MAX_ANTI_TRAINING_SITES )
-                break;
-            else if ( datum.atAntiTrainingSite ) {
-                returnData.add(datum);
-                nAntiTrainingAdded++;
+            if( datum != null && !datum.failingSTDThreshold && !datum.atTrainingSite && !datum.atAntiTrainingSite ) {
+                evaluationData.add( datum );
             }
         }
 
+        return evaluationData;
+    }
+
+    public List<VariantDatum> getRandomDataForPlotting( final int numToAdd, final List<VariantDatum> trainingData, final List<VariantDatum> antiTrainingData, final List<VariantDatum> evaluationData ) {
+        final List<VariantDatum> returnData = new ExpandingArrayList<>();
+        Collections.shuffle(trainingData);
+        Collections.shuffle(antiTrainingData);
+        Collections.shuffle(evaluationData);
+        returnData.addAll(trainingData.subList(0, Math.min(numToAdd, trainingData.size())));
+        returnData.addAll(antiTrainingData.subList(0, Math.min(numToAdd, antiTrainingData.size())));
+        returnData.addAll(evaluationData.subList(0, Math.min(numToAdd, evaluationData.size())));
+        Collections.shuffle(returnData);
         return returnData;
     }
 
-    private double mean( final int index ) {
+    protected double mean( final int index, final boolean trainingData ) {
         double sum = 0.0;
         int numNonNull = 0;
         for( final VariantDatum datum : data ) {
-            if( datum.atTrainingSite && !datum.isNull[index] ) { sum += datum.annotations[index]; numNonNull++; }
+            if( (trainingData == datum.atTrainingSite) && !datum.isNull[index] ) { sum += datum.annotations[index]; numNonNull++; }
         }
         return sum / ((double) numNonNull);
     }
 
-    private double standardDeviation( final double mean, final int index ) {
+    protected double standardDeviation( final double mean, final int index, final boolean trainingData ) {
         double sum = 0.0;
         int numNonNull = 0;
         for( final VariantDatum datum : data ) {
-            if( datum.atTrainingSite && !datum.isNull[index] ) { sum += ((datum.annotations[index] - mean)*(datum.annotations[index] - mean)); numNonNull++; }
+            if( (trainingData == datum.atTrainingSite) && !datum.isNull[index] ) { sum += ((datum.annotations[index] - mean)*(datum.annotations[index] - mean)); numNonNull++; }
         }
         return Math.sqrt( sum / ((double) numNonNull) );
     }
@@ -343,12 +329,9 @@ public class VariantDataManager {
         try {
             value = vc.getAttributeAsDouble( annotationKey, Double.NaN );
             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(); }
+            if( jitter && annotationKey.equalsIgnoreCase("HaplotypeScore") && MathUtils.compareDoubles(value, 0.0, 0.01) == 0 ) { value += 0.01 * GenomeAnalysisEngine.getRandomGenerator().nextGaussian(); }
+            if( jitter && annotationKey.equalsIgnoreCase("FS") && MathUtils.compareDoubles(value, 0.0, 0.01) == 0 ) { value += 0.01 * GenomeAnalysisEngine.getRandomGenerator().nextGaussian(); }
+            if( jitter && annotationKey.equalsIgnoreCase("InbreedingCoeff") && MathUtils.compareDoubles(value, 0.0, 0.01) == 0 ) { value += 0.01 * GenomeAnalysisEngine.getRandomGenerator().nextGaussian(); }
         } catch( Exception e ) {
             value = Double.NaN; // The VQSR works with missing data by marginalizing over the missing dimension when evaluating the Gaussian mixture model
         }
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index c3f575022..1c32b852b 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -48,6 +48,7 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
+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.refdata.RefMetaDataTracker;
@@ -142,7 +143,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     public static final String VQS_LOD_KEY = "VQSLOD"; // Log odds ratio of being a true variant versus being false under the trained gaussian mixture model
     public static final String CULPRIT_KEY = "culprit"; // The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out
     public static final String NEGATIVE_LABEL_KEY = "NEGATIVE_TRAIN_SITE"; // this variant was used in the negative training set
-    public static final String POSITIVE_LABEL_KEY = "POSITIVE_TRAIN_SITE"; // this variant was used in the positive traning set
+    public static final String POSITIVE_LABEL_KEY = "POSITIVE_TRAIN_SITE"; // this variant was used in the positive training set
     private static final String PLOT_TRANCHES_RSCRIPT = "plot_Tranches.R";
 
     @ArgumentCollection private VariantRecalibratorArgumentCollection VRAC = new VariantRecalibratorArgumentCollection();
@@ -208,8 +209,11 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     private String[] IGNORE_INPUT_FILTERS = null;
     @Output(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, defaultToStdout=false)
     private File RSCRIPT_FILE = null;
-    @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 the model reporting plots", required=false)
-    protected double TS_FILTER_LEVEL = 99.0;
+
+    @Hidden
+    @Argument(fullName="replicate", shortName="replicate", doc="Used to debug the random number generation inside the VQSR. Do not use.", required=false)
+    protected int REPLICATE = 200;
+    private ArrayList<Double> replicate = new ArrayList<>();
 
     /////////////////////////////
     // Debug Arguments
@@ -223,7 +227,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     /////////////////////////////
     private VariantDataManager dataManager;
     private PrintStream tranchesStream;
-    private final Set<String> ignoreInputFilterSet = new TreeSet<String>();
+    private final Set<String> ignoreInputFilterSet = new TreeSet<>();
     private final VariantRecalibratorEngine engine = new VariantRecalibratorEngine( VRAC );
 
     //---------------------------------------------------------------------------------------------------------------
@@ -232,8 +236,9 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     //
     //---------------------------------------------------------------------------------------------------------------
 
+    @Override
     public void initialize() {
-        dataManager = new VariantDataManager( new ArrayList<String>(Arrays.asList(USE_ANNOTATIONS)), VRAC );
+        dataManager = new VariantDataManager( new ArrayList<>(Arrays.asList(USE_ANNOTATIONS)), VRAC );
 
         if (RSCRIPT_FILE != null && !RScriptExecutor.RSCRIPT_EXISTS)
             Utils.warnUser(logger, String.format(
@@ -262,9 +267,13 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         }
 
 
-        final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
+        final Set<VCFHeaderLine> hInfo = new HashSet<>();
         ApplyRecalibration.addVQSRStandardHeaderLines(hInfo);
         recalWriter.writeHeader( new VCFHeader(hInfo) );
+
+        for( int iii = 0; iii < REPLICATE * 2; iii++ ) {
+            replicate.add(GenomeAnalysisEngine.getRandomGenerator().nextDouble());
+        }
     }
 
     //---------------------------------------------------------------------------------------------------------------
@@ -273,8 +282,9 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     //
     //---------------------------------------------------------------------------------------------------------------
 
+    @Override
     public ExpandingArrayList<VariantDatum> map( final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context ) {
-        final ExpandingArrayList<VariantDatum> mapList = new ExpandingArrayList<VariantDatum>();
+        final ExpandingArrayList<VariantDatum> mapList = new ExpandingArrayList<>();
 
         if( tracker == null ) { // For some reason RodWalkers get map calls with null trackers
             return mapList;
@@ -294,7 +304,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
 
                     // Loop through the training data sets and if they overlap this loci then update the prior and training status appropriately
                     dataManager.parseTrainingSets( tracker, context.getLocation(), vc, datum, TRUST_ALL_POLYMORPHIC );
-                    double priorFactor = QualityUtils.qualToProb( datum.prior );
+                    final double priorFactor = QualityUtils.qualToProb( datum.prior );
                     datum.prior = Math.log10( priorFactor ) - Math.log10( 1.0 - priorFactor );
 
                     mapList.add( datum );
@@ -311,15 +321,18 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     //
     //---------------------------------------------------------------------------------------------------------------
 
+    @Override
     public ExpandingArrayList<VariantDatum> reduceInit() {
-        return new ExpandingArrayList<VariantDatum>();
+        return new ExpandingArrayList<>();
     }
 
+    @Override
     public ExpandingArrayList<VariantDatum> reduce( final ExpandingArrayList<VariantDatum> mapValue, final ExpandingArrayList<VariantDatum> reduceSum ) {
         reduceSum.addAll( mapValue );
         return reduceSum;
     }
 
+    @Override
     public ExpandingArrayList<VariantDatum> treeReduce( final ExpandingArrayList<VariantDatum> lhs, final ExpandingArrayList<VariantDatum> rhs ) {
         rhs.addAll( lhs );
         return rhs;
@@ -331,21 +344,23 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     //
     //---------------------------------------------------------------------------------------------------------------
 
+    @Override
     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(), VRAC.MAX_GAUSSIANS );
+        final List<VariantDatum> positiveTrainingData = dataManager.getTrainingData();
+        final GaussianMixtureModel goodModel = engine.generateModel( positiveTrainingData, VRAC.MAX_GAUSSIANS );
         engine.evaluateData( dataManager.getData(), goodModel, false );
 
         // Generate the negative model using the worst performing data and evaluate each variant contrastively
-        final ExpandingArrayList<VariantDatum> negativeTrainingData = dataManager.selectWorstVariants( VRAC.NUM_BAD_VARIANTS );
+        final List<VariantDatum> negativeTrainingData = dataManager.selectWorstVariants();
         final GaussianMixtureModel badModel = engine.generateModel( negativeTrainingData, Math.min(VRAC.MAX_GAUSSIANS_FOR_NEGATIVE_MODEL, VRAC.MAX_GAUSSIANS));
         engine.evaluateData( dataManager.getData(), badModel, true );
 
         if( badModel.failedToConverge || goodModel.failedToConverge ) {
-            throw new UserException("NaN LOD value assigned. Clustering with this few variants and these annotations is unsafe. Please consider " + (badModel.failedToConverge ? "raising the number of variants used to train the negative model (via --numBadVariants 3000, for example)." : "lowering the maximum number of Gaussians allowed for use in the model (via --maxGaussians 4, for example).") );
+            throw new UserException("NaN LOD value assigned. Clustering with this few variants and these annotations is unsafe. Please consider " + (badModel.failedToConverge ? "raising the number of variants used to train the negative model (via --minNumBadVariants 5000, for example)." : "lowering the maximum number of Gaussians allowed for use in the model (via --maxGaussians 4, for example).") );
         }
 
         engine.calculateWorstPerformingAnnotation( dataManager.getData(), goodModel, badModel );
@@ -356,19 +371,11 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         final List<Tranche> tranches = TrancheManager.findTranches( dataManager.getData(), TS_TRANCHES, metric, VRAC.MODE );
         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 ) {
-                lodCutoff = tranche.minVQSLod;
-            }
-        }
-
         logger.info( "Writing out recalibration table..." );
         dataManager.writeOutRecalibrationTable( recalWriter );
         if( RSCRIPT_FILE != null ) {
             logger.info( "Writing out visualization Rscript file...");
-            createVisualizationScript( dataManager.getRandomDataForPlotting( 6000 ), goodModel, badModel, lodCutoff, dataManager.getAnnotationKeys().toArray(new String[USE_ANNOTATIONS.length]) );
+            createVisualizationScript( dataManager.getRandomDataForPlotting( 1000, positiveTrainingData, negativeTrainingData, dataManager.getEvaluationData() ), goodModel, badModel, 0.0, dataManager.getAnnotationKeys().toArray(new String[USE_ANNOTATIONS.length]) );
         }
 
         if(VRAC.MODE == VariantRecalibratorArgumentCollection.Mode.INDEL) {
@@ -385,7 +392,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         }
     }
 
-    private void createVisualizationScript( final ExpandingArrayList<VariantDatum> randomData, final GaussianMixtureModel goodModel, final GaussianMixtureModel badModel, final double lodCutoff, final String[] annotationKeys ) {
+    private void createVisualizationScript( final List<VariantDatum> randomData, final GaussianMixtureModel goodModel, final GaussianMixtureModel badModel, final double lodCutoff, final String[] annotationKeys ) {
         PrintStream stream;
         try {
             stream = new PrintStream(RSCRIPT_FILE);
@@ -409,7 +416,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
             for( int jjj = iii + 1; jjj < annotationKeys.length; jjj++) {
                 logger.info( "Building " + annotationKeys[iii] + " x " + annotationKeys[jjj] + " plot...");
 
-                final ExpandingArrayList<VariantDatum> fakeData = new ExpandingArrayList<VariantDatum>();
+                final List<VariantDatum> fakeData = new ExpandingArrayList<>();
                 double minAnn1 = 100.0, maxAnn1 = -100.0, minAnn2 = 100.0, maxAnn2 = -100.0;
                 for( final VariantDatum datum : randomData ) {
                     minAnn1 = Math.min(minAnn1, datum.annotations[iii]);
@@ -418,8 +425,9 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
                     maxAnn2 = Math.max(maxAnn2, datum.annotations[jjj]);
                 }
                 // Create a fake set of data which spans the full extent of these two annotation dimensions in order to calculate the model PDF projected to 2D
-                for(double ann1 = minAnn1; ann1 <= maxAnn1; ann1+=0.1) {
-                    for(double ann2 = minAnn2; ann2 <= maxAnn2; ann2+=0.1) {
+                final double NUM_STEPS = 60.0;
+                for(double ann1 = minAnn1; ann1 <= maxAnn1; ann1+= (maxAnn1 - minAnn1) / NUM_STEPS) {
+                    for(double ann2 = minAnn2; ann2 <= maxAnn2; ann2+= (maxAnn2 - minAnn2) / NUM_STEPS) {
                         final VariantDatum datum = new VariantDatum();
                         datum.prior = 0.0;
                         datum.annotations = new double[randomData.get(0).annotations.length];
@@ -441,7 +449,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
 
                 stream.print("surface <- c(");
                 for( final VariantDatum datum : fakeData ) {
-                    stream.print(String.format("%.3f, %.3f, %.3f, ",
+                    stream.print(String.format("%.4f, %.4f, %.4f, ",
                             dataManager.denormalizeDatum(datum.annotations[iii], iii),
                             dataManager.denormalizeDatum(datum.annotations[jjj], jjj),
                             Math.min(4.0, Math.max(-4.0, datum.lod))));
@@ -451,7 +459,7 @@ 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,",
+                    stream.print(String.format("%.4f, %.4f, %.4f, %d, %d,",
                             dataManager.denormalizeDatum(datum.annotations[iii], iii),
                             dataManager.denormalizeDatum(datum.annotations[jjj], jjj),
                             (datum.lod < lodCutoff ? -1.0 : 1.0),
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
index 5a319d8f5..b501655f8 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
@@ -73,27 +73,48 @@ public class VariantRecalibratorArgumentCollection {
 
     @Argument(fullName = "mode", shortName = "mode", doc = "Recalibration mode to employ: 1.) SNP for recalibrating only SNPs (emitting indels untouched in the output VCF); 2.) INDEL for indels (emitting SNPs untouched in the output VCF); and 3.) BOTH for recalibrating both SNPs and indels simultaneously (for testing purposes only, not recommended for general use).", required = false)
     public VariantRecalibratorArgumentCollection.Mode MODE = VariantRecalibratorArgumentCollection.Mode.SNP;
+
+    @Advanced
     @Argument(fullName="maxGaussians", shortName="mG", doc="The maximum number of Gaussians for the positive model to try during variational Bayes algorithm.", required=false)
-    public int MAX_GAUSSIANS = 10;
+    public int MAX_GAUSSIANS = 8;
 
     @Advanced
     @Argument(fullName="maxNegativeGaussians", shortName="mNG", doc="The maximum number of Gaussians for the negative model to try during variational Bayes algorithm.  The actual maximum used is the min of the mG and mNG arguments.  Note that this number should be small (like 4) to achieve the best results", required=false)
-    public int MAX_GAUSSIANS_FOR_NEGATIVE_MODEL = 4;
+    public int MAX_GAUSSIANS_FOR_NEGATIVE_MODEL = 2;
 
+    @Advanced
     @Argument(fullName="maxIterations", shortName="mI", doc="The maximum number of VBEM iterations to be performed in variational Bayes algorithm. Procedure will normally end when convergence is detected.", required=false)
-    public int MAX_ITERATIONS = 100;
+    public int MAX_ITERATIONS = 150;
+
+    @Advanced
     @Argument(fullName="numKMeans", shortName="nKM", doc="The number of k-means iterations to perform in order to initialize the means of the Gaussians in the Gaussian mixture model.", required=false)
-    public int NUM_KMEANS_ITERATIONS = 30;
+    public int NUM_KMEANS_ITERATIONS = 100;
+
+    @Advanced
     @Argument(fullName="stdThreshold", shortName="std", doc="If a variant has annotations more than -std standard deviations away from mean then don't use it for building the Gaussian mixture model.", required=false)
-    public double STD_THRESHOLD = 14.0;
-    @Argument(fullName="qualThreshold", shortName="qual", doc="If a known variant has raw QUAL value less than -qual then don't use it for building the Gaussian mixture model.", required=false)
-    public double QUAL_THRESHOLD = 80.0;
+    public double STD_THRESHOLD = 10.0;
+
+    @Advanced
     @Argument(fullName="shrinkage", shortName="shrinkage", doc="The shrinkage parameter in the variational Bayes algorithm.", required=false)
     public double SHRINKAGE = 1.0;
+
+    @Advanced
     @Argument(fullName="dirichlet", shortName="dirichlet", doc="The dirichlet parameter in the variational Bayes algorithm.", required=false)
     public double DIRICHLET_PARAMETER = 0.001;
+
+    @Advanced
     @Argument(fullName="priorCounts", shortName="priorCounts", doc="The number of prior counts to use in the variational Bayes algorithm.", required=false)
     public double PRIOR_COUNTS = 20.0;
-    @Argument(fullName="numBadVariants", shortName="numBad", doc="The number of worst scoring variants to use when building the Gaussian mixture model of bad variants.", required=false)
-    public int NUM_BAD_VARIANTS = 1000;
+
+    @Advanced
+    @Argument(fullName="maxNumTrainingData", shortName="maxNumTrainingData", doc="Maximum number of training data to be used in building the Gaussian mixture model. Training sets large than this will be randomly downsampled.", required=false)
+    protected int MAX_NUM_TRAINING_DATA = 2500000;
+
+    @Advanced
+    @Argument(fullName="minNumBadVariants", shortName="minNumBad", doc="The minimum number of worst scoring variants to use when building the Gaussian mixture model of bad variants.", required=false)
+    public int MIN_NUM_BAD_VARIANTS = 1000;
+
+    @Advanced
+    @Argument(fullName="badLodCutoff", shortName="badLodCutoff", doc="The LOD score below which to be used when building the Gaussian mixture model of bad variants.", required=false)
+    public double BAD_LOD_CUTOFF = -5.0;
 }
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
index ffde46394..3828e6e20 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
@@ -69,7 +69,7 @@ public class VariantRecalibratorEngine {
     // the unified argument collection
     final private VariantRecalibratorArgumentCollection VRAC;
 
-    private final static double MIN_PROB_CONVERGENCE = 2E-2;
+    private final static double MIN_PROB_CONVERGENCE = 2E-3;
 
     /////////////////////////////
     // Public Methods to interface with the Engine
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java
new file mode 100644
index 000000000..120e4bea2
--- /dev/null
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java
@@ -0,0 +1,68 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+*
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
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+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
+
+import junit.framework.Assert;
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.variant.vcf.VCFConstants;
+import org.testng.annotations.Test;
+
+/**
+ * Created with IntelliJ IDEA.
+ * User: rpoplin
+ * Date: 11/29/13
+ */
+
+public class ApplyRecalibrationUnitTest extends BaseTest {
+    @Test
+    public final void testGenerateFilterString() {
+        final ApplyRecalibration ar = new ApplyRecalibration();
+        ar.VQSLOD_CUTOFF = 0.0;
+        Assert.assertTrue(ar.generateFilterString(5.0).equals(VCFConstants.PASSES_FILTERS_v4));
+        Assert.assertTrue(ar.generateFilterString(-5.0).equals(ApplyRecalibration.LOW_VQSLOD_FILTER_NAME));
+    }
+}
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManagerUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManagerUnitTest.java
index cbb115cf7..754fe30a2 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManagerUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManagerUnitTest.java
@@ -61,11 +61,85 @@ import java.util.List;
  */
 
 public class VariantDataManagerUnitTest extends BaseTest {
+
     @Test
     public final void testCalculateSortOrder() {
-        final double[] data = {2.0, 3.0, 0.0, 1.0, 4.0, 68.0, 5.0};
-        VariantDataManager vdm = new VariantDataManager(new ArrayList<String>(), new VariantRecalibratorArgumentCollection());
-        final List<Integer> order = vdm.calculateSortOrder(data);
-        Assert.assertArrayEquals(new int[]{2,3,0,1,4,6,5}, ArrayUtils.toPrimitive(order.toArray(new Integer[order.size()])));
+        final double passingQual = 400.0;
+        final VariantRecalibratorArgumentCollection VRAC = new VariantRecalibratorArgumentCollection();
+
+        VariantDataManager vdm = new VariantDataManager(new ArrayList<String>(), VRAC);
+
+        final List<VariantDatum> theData = new ArrayList<>();
+        final VariantDatum datum1 = new VariantDatum();
+        datum1.atTrainingSite = true;
+        datum1.failingSTDThreshold = false;
+        datum1.originalQual = passingQual;
+        datum1.annotations = new double[]{0.0,-10.0,10.0};
+        datum1.isNull = new boolean[]{false, false, false};
+        theData.add(datum1);
+
+        final VariantDatum datum2 = new VariantDatum();
+        datum2.atTrainingSite = true;
+        datum2.failingSTDThreshold = false;
+        datum2.originalQual = passingQual;
+        datum2.annotations = new double[]{0.0,-9.0,15.0};
+        datum2.isNull = new boolean[]{false, false, false};
+        theData.add(datum2);
+
+        final VariantDatum datum3 = new VariantDatum();
+        datum3.atTrainingSite = false;
+        datum3.failingSTDThreshold = false;
+        datum3.originalQual = passingQual;
+        datum3.annotations = new double[]{0.0,1.0,999.0};
+        datum3.isNull = new boolean[]{false, false, false};
+        theData.add(datum3);
+
+        final VariantDatum datum4 = new VariantDatum();
+        datum4.atTrainingSite = false;
+        datum4.failingSTDThreshold = false;
+        datum4.originalQual = passingQual;
+        datum4.annotations = new double[]{0.015,2.0,1001.11};
+        datum4.isNull = new boolean[]{false, false, false};
+        theData.add(datum4);
+
+        vdm.setData(theData);
+
+        final double[] meanVector = new double[3];
+        for( int iii = 0; iii < meanVector.length; iii++ ) {
+            meanVector[iii] = vdm.mean(iii, true);
+        }
+        final List<Integer> order = vdm.calculateSortOrder(meanVector);
+        Assert.assertArrayEquals(new int[]{2,1,0}, ArrayUtils.toPrimitive(order.toArray(new Integer[order.size()])));
+    }
+
+    @Test
+    public final void testDownSamplingTrainingData() {
+        final int MAX_NUM_TRAINING_DATA = 5000;
+        final double passingQual = 400.0;
+        final VariantRecalibratorArgumentCollection VRAC = new VariantRecalibratorArgumentCollection();
+        VRAC.MAX_NUM_TRAINING_DATA = MAX_NUM_TRAINING_DATA;
+
+        VariantDataManager vdm = new VariantDataManager(new ArrayList<String>(), VRAC);
+        final List<VariantDatum> theData = new ArrayList<>();
+        for( int iii = 0; iii < MAX_NUM_TRAINING_DATA * 10; iii++) {
+            final VariantDatum datum = new VariantDatum();
+            datum.atTrainingSite = true;
+            datum.failingSTDThreshold = false;
+            datum.originalQual = passingQual;
+            theData.add(datum);
+        }
+
+        for( int iii = 0; iii < MAX_NUM_TRAINING_DATA * 2; iii++) {
+            final VariantDatum datum = new VariantDatum();
+            datum.atTrainingSite = false;
+            datum.failingSTDThreshold = false;
+            datum.originalQual = passingQual;
+            theData.add(datum);
+        }
+
+        vdm.setData(theData);
+        final List<VariantDatum> trainingData = vdm.getTrainingData();
+
+        Assert.assertTrue( trainingData.size() == MAX_NUM_TRAINING_DATA );
     }
 }
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
index aab4c8d3d..f3e57b48a 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
@@ -79,9 +79,9 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
     }
 
     VRTest lowPass = new VRTest(validationDataLocation + "phase1.projectConsensus.chr20.raw.snps.vcf",
-            "0f4ceeeb8e4a3c89f8591d5e531d8410",  // tranches
-            "c979a102669498ef40dde47ca4133c42",  // recal file
-            "8f60fd849537610b653b321869e94641"); // cut VCF
+            "6f029dc7d16e63e19c006613cd0a5cff",  // tranches
+            "73c7897441622c9b37376eb4f071c560",  // recal file
+            "11a28df79b92229bd317ac49a3ed0fa1"); // cut VCF
 
     @DataProvider(name = "VRTest")
     public Object[][] createData1() {
@@ -126,9 +126,9 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
     }
 
     VRTest bcfTest = new VRTest(privateTestDir + "vqsr.bcf_test.snps.unfiltered.bcf",
-            "6539e025997579cd0c7da12219cbc572",  // tranches
-            "778e61f81ab3d468b75f684bef0478e5",  // recal file
-            "21e96b0bb47e2976f53f11181f920e51"); // cut VCF
+            "3ad7f55fb3b072f373cbce0b32b66df4",  // tranches
+            "e747c08131d58d9a4800720f6ca80e0c",  // recal file
+            "e5808af3af0f2611ba5a3d172ab2557b"); // cut VCF
 
     @DataProvider(name = "VRBCFTest")
     public Object[][] createVRBCFTest() {
@@ -178,15 +178,15 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
 
     VRTest indelUnfiltered = new VRTest(
             validationDataLocation + "combined.phase1.chr20.raw.indels.unfiltered.sites.vcf", // all FILTERs as .
-            "8906fdae8beca712f5ff2808d35ef02d",  // tranches
-            "07ffea25e04f6ef53079bccb30bd6a7b",  // recal file
-            "8b3ef71cad71e8eb48a856a27ae4f8d5"); // cut VCF
+            "9a331328370889168a7aa3a625f73620",  // tranches
+            "2cbbd146d68c40200b782e0226f71976",  // recal file
+            "64dd98a5ab80cf5fd9a36eb66b38268e"); // cut VCF
 
     VRTest indelFiltered = new VRTest(
             validationDataLocation + "combined.phase1.chr20.raw.indels.filtered.sites.vcf", // all FILTERs as PASS
-            "8906fdae8beca712f5ff2808d35ef02d",  // tranches
-            "07ffea25e04f6ef53079bccb30bd6a7b",  // recal file
-            "3d69b280370cdd9611695e4893591306"); // cut VCF
+            "9a331328370889168a7aa3a625f73620",  // tranches
+            "2cbbd146d68c40200b782e0226f71976",  // recal file
+            "c0ec662001e829f5779a9d13b1d77d80"); // cut VCF
 
     @DataProvider(name = "VRIndelTest")
     public Object[][] createTestVariantRecalibratorIndel() {
@@ -242,7 +242,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -tranchesFile " + privateTestDir + "VQSR.mixedTest.tranches" +
                         " -recalFile " + privateTestDir + "VQSR.mixedTest.recal",
-                Arrays.asList("20c23643a78c5b95abd1526fdab8960d"));
+                Arrays.asList("03a0ed00af6aac76d39e569f90594a02"));
         executeTest("testApplyRecalibrationSnpAndIndelTogether", spec);
     }
 

From 0f99778a594de2ab0d219e11a020e050cd4809c3 Mon Sep 17 00:00:00 2001
From: Valentin Ruano-Rubio <valentin@broadinstitute.org>
Date: Mon, 18 Nov 2013 12:07:59 -0500
Subject: [PATCH 63/77] Adding Graph-based likelihood ratio calculation to HC

  To active this feature add '--likelihoodCalculationEngine GraphBased' to the HC command line.

New HC Options (both Advanced and Hidden):
==========================================

  --likelihoodCalculationEngine PairHMM/GraphBased/Random (default PairHMM)

Specifies what engine should be used to generate read vs haplotype likelihoods.

  PairHMM : standard full-PairHMM approach.
  GraphBased : using the assembly graph to accelarate the process.
  Random : generate random likelihoods - used for benchmarking purposes only.

  --heterogeneousKmerSizeResolution COMBO_MIN/COMBO_MAX/MAX_ONLY/MIN_ONLY (default COMBO_MIN)

It idicates how to merge haplotypes produced using different kmerSizes.
Only has effect when used in combination with (--likelihooCalculationEngine GraphBased)

  COMBO_MIN : use the smallest kmerSize with all haplotypes.
  COMBO_MAX : use the larger kmerSize with all haplotypes.
  MIN_ONLY : use the smallest kmerSize with haplotypes assembled using it.
  MAX_ONLY : use the larger kmerSize with haplotypes asembled using it.

Major code changes:
===================

 * Introduce multiple likelihood calculation engines (before there was just one).

 * Assembly results from different kmerSies are now packed together using the AssemblyResultSet class.

 * Added yet another PairHMM implementation with a different API in order to spport
   local PairHMM calculations, (e.g. a segment of the read vs a segment of the haplotype).

Major components:
================

 * FastLoglessPairHMM: New pair-hmm implemtation using some heuristic to speed up partial PairHMM calculations

 * GraphBasedLikelihoodCalculationEngine: delegates onto GraphBasedLikelihoodCalculationEngineInstance the exectution
     of the graph-based likelihood approach.

 * GraphBasedLikelihoodCalculationEngineInstance: one instance per active-region, implements the graph traversals
     to calcualte the likelihoods using the graph as an scafold.

 * HaplotypeGraph: haplotype threading graph where build from the assembly haplotypes. This structure is the one
     used by GraphBasedLikelihoodCalculationEngineInstance to do its work.

 * ReadAnchoring and KmerSequenceGraphMap: contain information as how a read map on the HaplotypeGraph that is
     used by GraphBasedLikelihoodCalcuationEngineInstance to do its work.

Remove mergeCommonChains from HaplotypeGraph creation

Fixed bamboo issues with HaplotypeGraphUnitTest

Fixed probrems with HaplotypeCallerIntegrationTest

Fixed issue with GraphLikelihoodVsLoglessAccuracyIntegrationTest

Fixed ReadThreadingLikelihoodCalculationEngine issues

Moved event-block iteration outside GraphBased*EngineInstance

Removed unecessary parameter from ReadAnchoring constructor.
Fixed test problem

Added a bit more documentation to EventBlockSearchEngine

Fixing some private - protected dependency issues

Further refactoring making GraphBased*Instance and HaplotypeGraph slimmer. Addressed last pull request commit comments

Fixed FastLoglessPairHMM public -> protected dependency

Fixed probrem with HaplotypeGraph unit test

Adding Graph-based likelihood ratio calculation to HC

  To active this feature add '--likelihoodCalculationEngine GraphBased' to the HC command line.

New HC Options (both Advanced and Hidden):
==========================================

  --likelihoodCalculationEngine PairHMM/GraphBased/Random (default PairHMM)

Specifies what engine should be used to generate read vs haplotype likelihoods.

  PairHMM : standard full-PairHMM approach.
  GraphBased : using the assembly graph to accelarate the process.
  Random : generate random likelihoods - used for benchmarking purposes only.

  --heterogeneousKmerSizeResolution COMBO_MIN/COMBO_MAX/MAX_ONLY/MIN_ONLY (default COMBO_MIN)

It idicates how to merge haplotypes produced using different kmerSizes.
Only has effect when used in combination with (--likelihooCalculationEngine GraphBased)

  COMBO_MIN : use the smallest kmerSize with all haplotypes.
  COMBO_MAX : use the larger kmerSize with all haplotypes.
  MIN_ONLY : use the smallest kmerSize with haplotypes assembled using it.
  MAX_ONLY : use the larger kmerSize with haplotypes asembled using it.

Major code changes:
===================

 * Introduce multiple likelihood calculation engines (before there was just one).

 * Assembly results from different kmerSies are now packed together using the AssemblyResultSet class.

 * Added yet another PairHMM implementation with a different API in order to spport
   local PairHMM calculations, (e.g. a segment of the read vs a segment of the haplotype).

Major components:
================

 * FastLoglessPairHMM: New pair-hmm implemtation using some heuristic to speed up partial PairHMM calculations

 * GraphBasedLikelihoodCalculationEngine: delegates onto GraphBasedLikelihoodCalculationEngineInstance the exectution
     of the graph-based likelihood approach.

 * GraphBasedLikelihoodCalculationEngineInstance: one instance per active-region, implements the graph traversals
     to calcualte the likelihoods using the graph as an scafold.

 * HaplotypeGraph: haplotype threading graph where build from the assembly haplotypes. This structure is the one
     used by GraphBasedLikelihoodCalculationEngineInstance to do its work.

 * ReadAnchoring and KmerSequenceGraphMap: contain information as how a read map on the HaplotypeGraph that is
     used by GraphBasedLikelihoodCalcuationEngineInstance to do its work.

Remove mergeCommonChains from HaplotypeGraph creation

Fixed bamboo issues with HaplotypeGraphUnitTest

Fixed probrems with HaplotypeCallerIntegrationTest

Fixed issue with GraphLikelihoodVsLoglessAccuracyIntegrationTest

Fixed ReadThreadingLikelihoodCalculationEngine issues

Moved event-block iteration outside GraphBased*EngineInstance

Removed unecessary parameter from ReadAnchoring constructor.
Fixed test problem

Added a bit more documentation to EventBlockSearchEngine

Fixing some private - protected dependency issues

Further refactoring making GraphBased*Instance and HaplotypeGraph slimmer. Addressed last pull request commit comments

Fixed FastLoglessPairHMM public -> protected dependency

Fixed probrem with HaplotypeGraph unit test
---
 .../haplotypecaller/ActiveRegionTrimmer.java  |    7 +
 .../haplotypecaller/AssemblyResult.java       |   18 +
 .../haplotypecaller/AssemblyResultSet.java    |  466 +++++++
 .../walkers/haplotypecaller/EventBlock.java   |  169 +++
 .../haplotypecaller/EventBlockFinder.java     |  287 +++++
 .../haplotypecaller/GenotypingEngine.java     |    2 +-
 ...GraphBasedLikelihoodCalculationEngine.java |  158 +++
 ...edLikelihoodCalculationEngineInstance.java |  911 +++++++++++++
 .../haplotypecaller/HaplotypeCaller.java      |  268 ++--
 .../haplotypecaller/HaplotypeRoute.java       |  129 ++
 .../HeterogeneousKmerSizeResolution.java      |  110 ++
 .../gatk/walkers/haplotypecaller/Kmer.java    |   76 +-
 .../walkers/haplotypecaller/KmerSequence.java |  461 +++++++
 .../haplotypecaller/KmerSequenceGraphMap.java |  209 +++
 .../LikelihoodCalculationEngine.java          |  764 +----------
 .../haplotypecaller/LocalAssemblyEngine.java  |   36 +-
 .../PairHMMLikelihoodCalculationEngine.java   |  834 ++++++++++++
 .../RandomLikelihoodCalculationEngine.java    |   82 ++
 .../haplotypecaller/ReadAnchoring.java        |  366 ++++++
 .../walkers/haplotypecaller/ReadCost.java     |   80 ++
 .../ReadSegmentComparator.java                |   86 ++
 .../haplotypecaller/ReadSegmentCost.java      |  112 ++
 .../haplotypecaller/graphs/BaseGraph.java     |    2 +-
 .../haplotypecaller/graphs/BaseVertex.java    |   32 +-
 .../graphs/DeBruijnVertex.java                |    4 +-
 .../graphs/KmerSearchableGraph.java           |   74 ++
 .../walkers/haplotypecaller/graphs/Path.java  |  101 +-
 .../walkers/haplotypecaller/graphs/Route.java |  285 +++++
 .../haplotypecaller/graphs/RouteFinder.java   |  196 +++
 .../haplotypecaller/graphs/SeqGraph.java      |   22 +-
 .../haplotypecaller/graphs/SeqVertex.java     |    2 +-
 .../graphs/SharedVertexSequenceSplitter.java  |    2 +-
 .../haplotypecaller/graphs/VertexOrder.java   |   62 +
 .../readthreading/HaplotypeGraph.java         | 1016 +++++++++++++++
 .../readthreading/MultiDeBruijnVertex.java    |    8 +-
 .../readthreading/ReadThreadingAssembler.java |   13 +-
 .../readthreading/ReadThreadingGraph.java     |  257 +++-
 .../sting/utils/SequenceComplexity.java       |  100 ++
 .../sting/utils/collections/CountSet.java     |  521 ++++++++
 .../haplotype/HaplotypeLDCalculator.java      |    4 +-
 .../CalledHaplotypeBAMWriter.java             |   11 +-
 .../HaplotypeBAMWriter.java                   |    5 +
 .../utils/pairhmm/FastLoglessPairHMM.java     |  813 ++++++++++++
 .../sting/utils/pairhmm/FlexibleHMM.java      |  100 ++
 .../sting/utils/pairhmm/LoglessPairHMM.java   |   18 +-
 .../sting/utils/sam/ClippedGATKSAMRecord.java |  107 ++
 .../ActiveRegionTestDataSetUnitTest.java      |  424 ++++++
 .../AssemblyResultSetUnitTest.java            |  249 ++++
 .../gatk/walkers/haplotypecaller/Civar.java   | 1135 +++++++++++++++++
 .../haplotypecaller/CivarUnitTest.java        |  401 ++++++
 ...LikelihoodCalculationEnginesBenchmark.java |  131 ++
 .../HaplotypeCallerIntegrationTest.java       |   10 +
 .../LocalAssemblyEngineUnitTest.java          |    5 +-
 ...MLikelihoodCalculationEngineUnitTest.java} |   47 +-
 ...ngLikelihoodCalculationEngineUnitTest.java |  375 ++++++
 .../graphs/BaseGraphUnitTest.java             |   12 +-
 .../graphs/CommonSuffixMergerUnitTest.java    |    4 +-
 .../graphs/CommonSuffixSplitterUnitTest.java  |    8 +-
 .../graphs/HaplotypeGraphUnitTest.java        |  238 ++++
 .../graphs/KBestPathsUnitTest.java            |   14 +-
 .../graphs/LowWeightChainPrunerUnitTest.java  |   19 +-
 .../haplotypecaller/graphs/PathUnitTest.java  |    4 +-
 .../haplotypecaller/graphs/RouteUnitTest.java |  261 ++++
 .../graphs/SeqGraphUnitTest.java              |   59 +-
 .../SharedVertexSequenceSplitterUnitTest.java |    6 +-
 .../ReadThreadingGraphUnitTest.java           |   14 +
 .../broadinstitute/sting/utils/RandomDNA.java |  127 ++
 .../utils/collections/CountSetUnitTest.java   |  249 ++++
 .../pairhmm/ActiveRegionTestDataSet.java      |  589 +++++++++
 .../pairhmm/FastLoglessPairHMMUnitTest.java   |  177 +++
 .../sting/utils/pairhmm/PairHMMUnitTest.java  |    6 +-
 .../gatk/walkers/ActiveRegionWalker.java      |    2 +
 .../broadinstitute/sting/utils/BaseUtils.java |   42 +
 .../broadinstitute/sting/utils/MathUtils.java |    2 -
 .../sting/utils/QualityUtils.java             |    1 +
 .../org/broadinstitute/sting/utils/Utils.java |    1 -
 .../utils/activeregion/ActiveRegion.java      |   18 +-
 .../utils/genotyper/MostLikelyAllele.java     |    2 +-
 .../genotyper/PerReadAlleleLikelihoodMap.java |   10 +-
 .../sting/utils/haplotype/Haplotype.java      |   31 +-
 .../sting/utils/pairhmm/Log10PairHMM.java     |   92 +-
 .../sting/utils/pairhmm/N2MemoryPairHMM.java  |    7 +
 .../sting/utils/pairhmm/PairHMM.java          |    2 +-
 .../utils/pairhmm/PairHMMReadyHaplotypes.java |  182 +++
 .../org/broadinstitute/sting/BaseTest.java    |    1 +
 .../sting/TestNGTestTransformer.java          |    2 +-
 .../org/broadinstitute/sting/WalkerTest.java  |    1 -
 .../sting/utils/GenomeLocParserUnitTest.java  |    2 +-
 88 files changed, 13268 insertions(+), 1080 deletions(-)
 create mode 100644 protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSet.java
 create mode 100644 protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlock.java
 create mode 100644 protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlockFinder.java
 create mode 100644 protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java
 create mode 100644 protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java
 create mode 100644 protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeRoute.java
 create mode 100644 protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HeterogeneousKmerSizeResolution.java
 create mode 100644 protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequence.java
 create mode 100644 protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequenceGraphMap.java
 create mode 100644 protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
 create mode 100644 protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java
 create mode 100644 protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadAnchoring.java
 create mode 100644 protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadCost.java
 create mode 100644 protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentComparator.java
 create mode 100644 protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentCost.java
 create mode 100644 protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KmerSearchableGraph.java
 create mode 100644 protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Route.java
 create mode 100644 protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/RouteFinder.java
 create mode 100644 protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/VertexOrder.java
 create mode 100644 protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/HaplotypeGraph.java
 create mode 100644 protected/java/src/org/broadinstitute/sting/utils/SequenceComplexity.java
 create mode 100644 protected/java/src/org/broadinstitute/sting/utils/collections/CountSet.java
 create mode 100644 protected/java/src/org/broadinstitute/sting/utils/pairhmm/FastLoglessPairHMM.java
 create mode 100644 protected/java/src/org/broadinstitute/sting/utils/pairhmm/FlexibleHMM.java
 create mode 100644 protected/java/src/org/broadinstitute/sting/utils/sam/ClippedGATKSAMRecord.java
 create mode 100644 protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java
 create mode 100644 protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSetUnitTest.java
 create mode 100644 protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Civar.java
 create mode 100644 protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/CivarUnitTest.java
 create mode 100644 protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java
 rename protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/{LikelihoodCalculationEngineUnitTest.java => PairHMMLikelihoodCalculationEngineUnitTest.java} (92%)
 create mode 100644 protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java
 create mode 100644 protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/HaplotypeGraphUnitTest.java
 create mode 100644 protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/RouteUnitTest.java
 create mode 100644 protected/java/test/org/broadinstitute/sting/utils/RandomDNA.java
 create mode 100644 protected/java/test/org/broadinstitute/sting/utils/collections/CountSetUnitTest.java
 create mode 100644 protected/java/test/org/broadinstitute/sting/utils/pairhmm/ActiveRegionTestDataSet.java
 create mode 100644 protected/java/test/org/broadinstitute/sting/utils/pairhmm/FastLoglessPairHMMUnitTest.java
 create mode 100644 public/java/src/org/broadinstitute/sting/utils/pairhmm/PairHMMReadyHaplotypes.java

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTrimmer.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTrimmer.java
index 4de90b337..f1db5bcd7 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTrimmer.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTrimmer.java
@@ -86,6 +86,7 @@ class ActiveRegionTrimmer {
         if ( maxDistanceInExtensionForGenotyping < 0 ) throw new IllegalArgumentException("maxDistanceInExtensionForGenotyping must be >= 0 but got " + maxDistanceInExtensionForGenotyping);
         if ( parser == null ) throw new IllegalArgumentException("parser cannot be null");
 
+        logger.debug("Trimmer created with parameters " + logTrimming + " " + snpPadding + " " + nonSnpPadding + " " + maxDistanceInExtensionForGenotyping);
         this.logTrimming = logTrimming;
         this.snpPadding = snpPadding;
         this.nonSnpPadding = nonSnpPadding;
@@ -105,6 +106,7 @@ class ActiveRegionTrimmer {
      * @return a new ActiveRegion trimmed down to just what's needed for genotyping, or null if we couldn't do this successfully
      */
     public ActiveRegion trimRegion(final ActiveRegion region, final TreeSet<VariantContext> allVariantsWithinExtendedRegion, final boolean emitReferenceConfidence) {
+
         if ( allVariantsWithinExtendedRegion.isEmpty() ) // no variants, so just return the current region
             return null;
 
@@ -125,6 +127,10 @@ class ActiveRegionTrimmer {
         // we don't actually have anything in the region after removing variants that don't overlap the region's full location
         if ( trimLoc == null ) return null;
 
+//        final GenomeLoc maxSpan = parser.createPaddedGenomeLoc(region.getLocation(), maxDistanceInExtensionForGenotyping);
+        // Try to have one kmer before and after any event.
+
+        final GenomeLoc regionLoc = region.getLocation();
         final GenomeLoc maxSpan = parser.createPaddedGenomeLoc(region.getLocation(), maxDistanceInExtensionForGenotyping);
         final GenomeLoc idealSpan = parser.createPaddedGenomeLoc(trimLoc, pad);
         final GenomeLoc finalSpan = maxSpan.intersect(idealSpan);
@@ -132,6 +138,7 @@ class ActiveRegionTrimmer {
         final ActiveRegion trimmedRegion = region.trim(finalSpan);
         if ( logTrimming ) {
             logger.info("events     : " + withinActiveRegion);
+            logger.info("region     : " + regionLoc);
             logger.info("trimLoc    : " + trimLoc);
             logger.info("pad        : " + pad);
             logger.info("idealSpan  : " + idealSpan);
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResult.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResult.java
index f07dbb392..658ffc10e 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResult.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResult.java
@@ -47,6 +47,7 @@
 package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
 
 import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.SeqGraph;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.ReadThreadingGraph;
 
 /**
  * Result of assembling, with the resulting graph and status
@@ -57,6 +58,7 @@ import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.SeqGraph;
  */
 public class AssemblyResult {
     private final Status status;
+    private ReadThreadingGraph threadingGraph;
     private final SeqGraph graph;
 
     /**
@@ -72,9 +74,25 @@ public class AssemblyResult {
         this.graph = graph;
     }
 
+    /**
+     * Returns the threading-graph associated with this assembly-result.
+     */
+    public void setThreadingGraph(final ReadThreadingGraph threadingGraph) {
+        this.threadingGraph = threadingGraph;
+    }
+
+    public ReadThreadingGraph getThreadingGraph() {
+        return threadingGraph;
+    }
+
     public Status getStatus() { return status; }
     public SeqGraph getGraph() { return graph; }
 
+    public int getKmerSize() {
+        return graph.getKmerSize();
+    }
+
+
     /**
      * Status of the assembly result
      */
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSet.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSet.java
new file mode 100644
index 000000000..091c09e8d
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSet.java
@@ -0,0 +1,466 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*  
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*  
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*  
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*  
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*  
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. 
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.  
+*  
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY 
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*  
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*  
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*  
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*  
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt. 
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. 
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
+
+import org.apache.log4j.Logger;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.ReadThreadingGraph;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
+import org.broadinstitute.sting.utils.collections.CountSet;
+import org.broadinstitute.sting.utils.collections.CountSet;
+import org.broadinstitute.sting.utils.haplotype.Haplotype;
+
+import java.io.PrintWriter;
+import java.io.StringWriter;
+import java.util.*;
+
+/**
+ * Collection of read assembly using several kmerSizes.
+ *
+ * <p>
+ *     There could be a different assembly per each kmerSize. In turn, haplotypes are result of one of those
+ *     assemblies.
+ * </p>
+ *
+ * <p>
+ *     Where there is more than one possible kmerSize that generates a haplotype we consider the smaller one.
+ * </p>
+ *
+ * @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.com&gt;
+ */
+public  class AssemblyResultSet {
+
+    private final Map<Integer,AssemblyResult> assemblyResultByKmerSize;
+    private final Set<Haplotype> haplotypes;
+    private final Map<Haplotype,AssemblyResult> assemblyResultByHaplotype;
+    private ActiveRegion regionForGenotyping;
+    private byte[] fullReferenceWithPadding;
+    private GenomeLoc paddedReferenceLoc;
+    private boolean variationPresent;
+    private Haplotype refHaplotype;
+    private boolean wasTrimmed = false;
+    private final CountSet kmerSizes;
+
+    /**
+     * Constructs a new empty assembly result set.
+     */
+    public AssemblyResultSet() {
+        assemblyResultByKmerSize = new LinkedHashMap<>(4);
+        haplotypes = new LinkedHashSet<>(10);
+        assemblyResultByHaplotype = new LinkedHashMap<>(10);
+        kmerSizes = new CountSet(4);
+    }
+
+    /**
+     * Trims an assembly result set down based on a new set of trimmed haplotypes.
+     *
+     * @param originalByTrimmedHaplotypes map from trimmed to original haplotypes.
+     * @param trimmedActiveRegion the trimmed down active region.
+     *
+     * @throws NullPointerException if any argument in {@code null} or
+     *      if there are {@code null} entries in {@code originalByTrimmedHaplotypes} for trimmed haplotype keys.
+     * @throws IllegalArgumentException if there is no reference haplotype amongst the trimmed ones.
+     *
+     *
+     * @return never {@code null}, a new trimmed assembly result set.
+     */
+    public AssemblyResultSet trimTo(final ActiveRegion trimmedActiveRegion,
+                                    final Map<Haplotype,Haplotype> originalByTrimmedHaplotypes) {
+        if (refHaplotype == null) throw new IllegalStateException();
+        if (trimmedActiveRegion == null) throw new NullPointerException();
+        final AssemblyResultSet result = new AssemblyResultSet();
+
+        for (final Haplotype trimmed : originalByTrimmedHaplotypes.keySet()) {
+            final Haplotype original = originalByTrimmedHaplotypes.get(trimmed);
+            if (original == null)
+                throw new NullPointerException("all trimmed haplotypes must have an original one");
+            final AssemblyResult as = assemblyResultByHaplotype.get(original);
+            if (as == null) result.add(trimmed); else result.add(trimmed, as);
+        }
+
+        result.setRegionForGenotyping(trimmedActiveRegion);
+        result.setFullReferenceWithPadding(this.fullReferenceWithPadding);
+        result.setPaddedReferenceLoc(this.paddedReferenceLoc);
+        if (result.refHaplotype == null)
+            throw new IllegalStateException("missing reference haplotype in the trimmed set");
+        result.wasTrimmed = true;
+        return result;
+    }
+
+    /**
+     * Query the reference haplotype in the result set.
+     * @return {@code null} if none wasn't yet added, otherwise a reference haplotype.
+     */
+    public Haplotype getReferenceHaplotype() {
+        return refHaplotype;
+    }
+
+    /**
+     * Checks whether there is any variation present in the assembly result set.
+     *
+     * <p>
+     *     This is equivalent to whether there is more than one haplotype.
+     * </p>
+     *
+     * @return {@code true} if there is variation present, {@code false} otherwise.
+     */
+    public boolean isVariationPresent() {
+        return variationPresent && haplotypes.size() > 1;
+    }
+
+    /**
+     * Dumps debugging information into a print-writer.
+     *
+     * @param pw where to dump the information.
+     *
+     * @throws NullPointerException if {@code pw} is {@code null}.
+     */
+    public void debugDump(final PrintWriter pw) {
+        if (getHaplotypeList().size() == 0) {
+            return;
+        }
+        pw.println("Active Region " + this.regionForGenotyping.getLocation());
+        pw.println("Extended Act Region " + this.getRegionForGenotyping().getExtendedLoc());
+        pw.println("Ref haplotype coords " + getHaplotypeList().get(0).getGenomeLocation());
+        pw.println("Haplotype count " + haplotypes.size());
+        final Map<Integer,Integer> kmerSizeToCount = new HashMap<>();
+
+        for (final Map.Entry<Haplotype,AssemblyResult> e : assemblyResultByHaplotype.entrySet()) {
+            final AssemblyResult as = e.getValue();
+            final int kmerSize = as.getGraph().getKmerSize();
+            if (kmerSizeToCount.containsKey(kmerSize)) {
+                kmerSizeToCount.put(kmerSize,kmerSizeToCount.get(kmerSize) + 1);
+            } else {
+                kmerSizeToCount.put(kmerSize,1);
+            }
+        }
+        pw.println("Kmer sizes count " + kmerSizeToCount.entrySet().size() );
+        Integer[] kmerSizes = new Integer[kmerSizeToCount.size()];
+        kmerSizes = kmerSizeToCount.keySet().toArray(kmerSizes);
+        Arrays.sort(kmerSizes);
+        pw.println("Kmer sizes values " + Arrays.toString(kmerSizes));
+        for (int size : kmerSizes) {
+            pw.println("Kmer size " + size + " count " + kmerSizeToCount.get(size));
+        }
+    }
+
+    /**
+     * Adds a haplotype to the result set without indicating a generating assembly result.
+     *
+     * <p>
+     *     It is possible to call this method with the same haplotype several times. In that the second and further
+     *     calls won't have any effect (thus returning {@code false}).
+     * </p>
+     *
+     * @param h the haplotype to add to the assembly result set.
+     *
+     * @throws NullPointerException if {@code h} is {@code null}
+     * @throws IllegalArgumentException if {@code h} does not have a genome location.
+     *
+     * @return {@code true} if the assembly result set has been modified as a result of this call.
+     */
+    public boolean add(final Haplotype h) {
+        if (h == null) throw new NullPointerException("input haplotype cannot be null");
+        if (h.getGenomeLocation() == null)
+            throw new IllegalArgumentException("the haplotype provided must have a genomic location");
+        if (haplotypes.contains(h))
+            return false;
+        haplotypes.add(h);
+        updateReferenceHaplotype(h);
+        return true;
+    }
+
+    /**
+     * Adds simultaneously a haplotype and the generating assembly-result.
+     *
+     * <p>
+     *     Haplotypes and their assembly-result can be added multiple times although just the first call will have
+     *     any effect (return value is {@code true}).
+     * </p>
+     *
+     *
+     * @param h haplotype to add.
+     * @param ar assembly-result that is assumed to have given rise to that haplotype.
+     *
+     * @throws NullPointerException if {@code h} or {@code ar} is {@code null}.
+     * @throws IllegalArgumentException if {@code h} has not defined genome location.
+     *
+     * @return {@code true} iff this called changes the assembly result set.
+     */
+    public boolean add(final Haplotype h, final AssemblyResult ar) {
+        if (h == null) throw new NullPointerException("input haplotype cannot be null");
+        if (ar == null) throw new NullPointerException("input assembly-result cannot be null");
+        if (h.getGenomeLocation() == null)
+            throw new IllegalArgumentException("the haplotype provided must have a genomic location");
+
+        final boolean assemblyResultAdditionReturn =  add(ar);
+
+        if (haplotypes.contains(h)) {
+            final AssemblyResult previousAr = assemblyResultByHaplotype.get(h);
+            if (previousAr == null) {
+                assemblyResultByHaplotype.put(h, ar);
+                return true;
+            } else if (!previousAr.equals(ar))
+                throw new IllegalStateException("there is already a different assembly result for the input haplotype");
+            else
+                return assemblyResultAdditionReturn;
+        } else {
+            haplotypes.add(h);
+            assemblyResultByHaplotype.put(h,ar);
+            updateReferenceHaplotype(h);
+            if (h.isNonReference()) variationPresent = true;
+            return true;
+        }
+    }
+
+    /**
+     * Add a assembly-result object.
+     *
+     * @param ar the assembly result to add.
+     *
+     * @throws NullPointerException if {@code ar} is {@code null}.
+     * @throws IllegalStateException if there is an assembly result with the same kmerSize.
+     * @return {@code true} iff this addition changed the assembly result set.
+     */
+    public boolean add(final AssemblyResult ar) {
+        if (ar == null)
+            throw new NullPointerException();
+        final int kmerSize = ar.getKmerSize();
+        if (assemblyResultByKmerSize.containsKey(kmerSize)) {
+            if (!assemblyResultByKmerSize.get(kmerSize).equals(ar))
+                throw new IllegalStateException("a different assembly result with the same kmerSize was already added");
+            return false;
+        } else {
+            assemblyResultByKmerSize.put(kmerSize, ar);
+            kmerSizes.add(kmerSize);
+            return true;
+        }
+    }
+
+    /**
+     * Returns the current region for genotyping.
+     *
+     * @return might be {@code null}.
+     */
+    public ActiveRegion getRegionForGenotyping() {
+        return regionForGenotyping;
+    }
+
+    /**
+     * Sets the region for genotyping.
+     *
+     * @param regionForGenotyping the new value.
+     */
+    public void setRegionForGenotyping(final ActiveRegion regionForGenotyping) {
+        this.regionForGenotyping = regionForGenotyping;
+    }
+
+    /**
+     * Returns the current full reference with padding.
+     *
+     * @return might be {@code null}.
+     */
+    public byte[] getFullReferenceWithPadding() {
+        return fullReferenceWithPadding;
+    }
+
+    /**
+     * Sets the full reference with padding base sequence.
+     *
+     * @param fullReferenceWithPadding the new value.
+     */
+    public void setFullReferenceWithPadding(final byte[] fullReferenceWithPadding) {
+        this.fullReferenceWithPadding = fullReferenceWithPadding;
+    }
+
+    /**
+     * Returns the padded reference location.
+     *
+     * @return might be {@code null}
+     */
+    public GenomeLoc getPaddedReferenceLoc() {
+        return paddedReferenceLoc;
+    }
+
+    /**
+     * Changes the padded reference location.
+     * @param paddedReferenceLoc the new value.
+     */
+    public void setPaddedReferenceLoc(final GenomeLoc paddedReferenceLoc) {
+        this.paddedReferenceLoc = paddedReferenceLoc;
+    }
+
+    /**
+     * Returns the number of haplotypes in the assembly result set.
+     * @return {@code 0} or greater.
+     */
+    public int getHaplotypeCount() {
+        return haplotypes.size();
+    }
+
+    /**
+     * Returns the haplotypes as a list.
+     *
+     * <p>
+     *     The result is unmodifiable.
+     * </p>
+     *
+     * @return never {@code null}, but perhaps a empty list if no haplotype was generated during assembly.
+     */
+    public List<Haplotype> getHaplotypeList() {
+        return Arrays.asList(haplotypes.toArray(new Haplotype[haplotypes.size()]));
+    }
+
+    /**
+     * Returns the maximum kmerSize available.
+     *
+     * @throws IllegalStateException if no assembly-result was added to the set, thus there is no kmerSize.
+     *
+     * @return greater than 0.
+     */
+    public int getMaximumKmerSize() {
+        if (kmerSizes.size() == 0)
+            throw new IllegalStateException("there is yet no kmerSize in this assembly result set");
+        return kmerSizes.max();
+    }
+
+    /**
+     * Indicates whether there are more than one kmerSize in the set.
+     *
+     * @return {@code true} iff there is more than one kmerSize assembly in the set.
+     */
+    public boolean hasMultipleKmerSizes() {
+        return kmerSizes.size() > 1;
+    }
+
+    /**
+     * Returns the minimum kmerSize available.
+     *
+     * @throws IllegalStateException if no assembly-result was added to the set, thus there is no kmerSize.
+     *
+     * @return greater than 0.
+     */
+    public int getMinimumKmerSize() {
+        if (kmerSizes.size() == 0)
+            throw new IllegalStateException("there is yet no kmerSize in this assembly result set");
+        return kmerSizes.min();
+    }
+
+    /**
+     * Returns a read-threading graph in the assembly set that has a particular kmerSize.
+     *
+     * @param kmerSize the requested kmerSize.
+     *
+     * @return {@code null} if there is no read-threading-graph amongst assembly results with that kmerSize.
+     */
+    public ReadThreadingGraph getUniqueReadThreadingGraph(final int kmerSize) {
+        final AssemblyResult assemblyResult = assemblyResultByKmerSize.get(kmerSize);
+        if (assemblyResult == null) return null;
+        return assemblyResult.getThreadingGraph();
+    }
+
+    /**
+     * Checks whether this assembly result set was trimmed.
+     *
+     * @return {@code true} iff this assembly result set was trimmed.
+     */
+    public boolean wasTrimmed() {
+        return wasTrimmed;
+    }
+
+    /**
+     * Marks the assembly as not having variation even if it has more than one haplotype.
+     */
+    public void resetVariationPresent() {
+        variationPresent = false;
+    }
+
+    /**
+     * Dumps debugging information into a logger.
+     *
+     * @param logger where to dump the information.
+     *
+     * @throws NullPointerException if {@code logger} is {@code null}.
+     */
+    public void debugDump(final Logger logger) {
+        final StringWriter sw = new StringWriter();
+        final PrintWriter pw = new PrintWriter(sw);
+        debugDump(pw);
+        final String str = sw.toString();
+        final String[] lines = str.split("\n");
+        for (final String line : lines) {
+            if (line.isEmpty()) {
+                continue;
+            }
+            logger.debug(line);
+        }
+    }
+
+    /**
+     * Given whether a new haplotype that has been already added to {@link #haplotypes} collection is the
+     * reference haplotype and updates {@link #refHaplotype} accordingly.
+     *
+     * <p>
+     *     This method assumes that the colling code has verified that the haplotype was not already in {@link #haplotypes}
+     *     I.e. that it is really a new one. Otherwise it will result in an exception if it happen to be a reference
+     *     haplotype and this has already be set. This is the case even if the new haplotypes and the current reference
+     *     are equal.
+     * </p>
+     *
+     * @param newHaplotype the new haplotype.
+     * @throws NullPointerException if {@code newHaplotype} is {@code null}.
+     * @throws IllegalStateException if there is already a reference haplotype.
+     */
+    private void updateReferenceHaplotype(final Haplotype newHaplotype) {
+        if (!newHaplotype.isReference()) return;
+        if (refHaplotype == null)
+            refHaplotype = newHaplotype;
+        else // assumes that we have checked wether the haplotype is already in the collection and so is no need to check equality.
+            throw new IllegalStateException("the assembly-result-set already have a reference haplotype that is different");
+    }
+
+}
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlock.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlock.java
new file mode 100644
index 000000000..be7305085
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlock.java
@@ -0,0 +1,169 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+*
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
+
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.MultiSampleEdge;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.Route;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.HaplotypeGraph;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex;
+
+import java.util.*;
+
+/**
+ * Represents an event block in the graph.
+ *
+ * <p>
+ *     Event block is defined as the non-trivial section of the haplotype-graph between two vertices along the
+ *     reference route, that has at least one alternative route between those two vertices.
+ * </p>
+ *
+ * @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.org&gt;
+ */
+public class EventBlock {
+
+    private final HaplotypeGraph graph;
+
+    private final MultiDeBruijnVertex source;
+
+    private final int sourcePosition;
+
+    private final MultiDeBruijnVertex sink;
+
+    private final int sinkPosition;
+
+    private Set<Route<MultiDeBruijnVertex,MultiSampleEdge>> routesAcross;
+
+
+    /**
+     * Constructs a event block given the base haplotype graph and the source and sink vertice (both included in the block)
+     * @param graph the base haplotype graph.
+     * @param source the starting vertex.
+     * @param sink the ending vertex.
+     *
+     * @throws NullPointerException if any of the input is {@code null}.
+     * @throws IllegalArgumentException if {@code source} or {@code sink} are not part of the graphs reference route,
+     *      such a route does not exists, any of the vertices is not part of such a route or they are out of order.
+     */
+    public EventBlock(final HaplotypeGraph graph, final MultiDeBruijnVertex source, final MultiDeBruijnVertex sink) {
+        if (graph == null) throw new NullPointerException("the graph cannot be null");
+        if (source == null) throw new NullPointerException("the source vertex is null");
+        if (sink == null) throw new NullPointerException("the sink node is null");
+        this.graph = graph;
+        this.source = source;
+        this.sink = sink;
+        final HaplotypeRoute route = graph.getReferenceRoute();
+        if (route == null)
+            throw new IllegalArgumentException("there is reference route in the graph");
+        this.sourcePosition = route.getVertexPosition(source);
+        this.sinkPosition = route.getVertexPosition(sink);
+        if (sourcePosition == -1)
+            throw new IllegalArgumentException("the source vertex does not belong to the reference route");
+        if (sinkPosition == -1)
+            throw new IllegalArgumentException("the sink vertex does not belong to the reference route");
+        if (sourcePosition > sinkPosition)
+            throw new IllegalArgumentException("source and sink vertices are out of order in reference route");
+    }
+
+    /**
+     * Returns a reference to the event block graph.
+     *
+     * @return never {@code null}.
+     */
+    public HaplotypeGraph getGraph() {
+        return graph;
+    }
+
+    /**
+     * Returns a reference to the block starting vertex.
+     *
+     * @return never {@code null}.
+     */
+    public MultiDeBruijnVertex getSource() {
+        return source;
+    }
+
+    /**
+     * Returns the reference ot the end block vertex.
+     *
+     * @return never {@code null}.
+     */
+    public MultiDeBruijnVertex getSink() {
+        return sink;
+    }
+
+    /**
+     * Returns all possible routes between the event block start and end vertices.
+     * @return never {@code null}, and unmodifiable route set.
+     */
+    public Set<Route<MultiDeBruijnVertex,MultiSampleEdge>> getRoutesAcross() {
+        // catching:
+        if (routesAcross != null) return routesAcross;
+
+        final Set<Route<MultiDeBruijnVertex, MultiSampleEdge>> result = new HashSet<>(10); // 10 is rather generous.
+
+        // bread-first iterative search for all paths.
+        final Queue<Route<MultiDeBruijnVertex, MultiSampleEdge>> queue = new LinkedList<>();
+
+        queue.add(new Route<>(source, graph)); // the seed is the empty route at the start vertex.
+
+        final HaplotypeRoute referenceRoute = graph.getReferenceRoute();
+
+        while (!queue.isEmpty()) {
+            final Route<MultiDeBruijnVertex, MultiSampleEdge> route = queue.remove();
+            final MultiDeBruijnVertex routeEndVertex = route.getLastVertex();
+
+            if (routeEndVertex == sink) // bingo!!!
+                result.add(route);
+            else { // only queue promising extension of this route.
+                final int routeEndPosition = referenceRoute.getVertexPosition(routeEndVertex);
+                if (routeEndPosition == -1 || (routeEndPosition >= sourcePosition && routeEndPosition < sinkPosition))
+                    for (final MultiSampleEdge e : graph.outgoingEdgesOf(routeEndVertex))
+                        queue.add(new Route<>(route, e));
+            }
+        }
+        return routesAcross = Collections.unmodifiableSet(result);
+    }
+}
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlockFinder.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlockFinder.java
new file mode 100644
index 000000000..ca4985cef
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlockFinder.java
@@ -0,0 +1,287 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+*
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
+
+import com.google.java.contract.Requires;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.MultiSampleEdge;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.HaplotypeGraph;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex;
+import org.broadinstitute.sting.utils.collections.CountSet;
+import org.broadinstitute.sting.utils.collections.CountSet;
+import org.broadinstitute.sting.utils.collections.Pair;
+
+import java.util.*;
+
+/**
+ * Encapsulates the graph traversals needed to find event-blocks.
+ *
+ * @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.org&gt;
+ */
+public class EventBlockFinder {
+
+    private final HaplotypeGraph graph;
+
+    private final Map<Pair<MultiDeBruijnVertex,MultiDeBruijnVertex>,EventBlock> eventBlockCache;
+
+    /**
+     * Constructs a new engine.
+     *
+     * @param graph the base haplotype graph to iterate over.
+     */
+    public EventBlockFinder(final HaplotypeGraph graph) {
+        if (graph == null) throw new NullPointerException();
+        this.graph = graph;
+        eventBlockCache = new HashMap<>(20);
+    }
+
+    /**
+     * Create a new traversal object based on a read anchoring.
+     * @param anchoring
+     * @return never {@code null}.
+     */
+    public Traversal traversal(final ReadAnchoring anchoring) {
+        if (anchoring == null) throw new NullPointerException();
+        return new Traversal(anchoring);
+    }
+
+
+    public class Traversal implements Iterable<EventBlock> {
+
+        private final ReadAnchoring anchoring;
+
+        private EventBlock lastEventBlock;
+
+
+        private Traversal(final ReadAnchoring anchoring) {
+            this.anchoring = anchoring;
+            lastEventBlock = findLastEventBlock(anchoring);
+        }
+
+        @Override
+        public java.util.Iterator<EventBlock> iterator() {
+            return lastEventBlock == null ? Collections.EMPTY_SET.iterator() : new Iterator();
+        }
+
+        private class Iterator implements java.util.Iterator<EventBlock> {
+
+            private MultiDeBruijnVertex currentVertex;
+
+            private Iterator() {
+                currentVertex = anchoring.leftAnchorVertex;
+            }
+
+            @Override
+            public boolean hasNext() {
+                return currentVertex != null;
+            }
+
+            @Override
+            public EventBlock next() {
+                final EventBlock result;
+                if (currentVertex == null)
+                    throw new NoSuchElementException("going beyond last event block");
+                else if (currentVertex == lastEventBlock.getSource()) {
+                    result = lastEventBlock;
+                    currentVertex = null;
+                } else {
+                    final EventBlock candidate = findEventBlock(anchoring,false,currentVertex,lastEventBlock.getSource());
+                    if (candidate == null) {
+                        result = findEventBlock(anchoring,false,currentVertex,anchoring.rightAnchorVertex);
+                        currentVertex = null;
+                    } else {
+                        result = candidate;
+                        currentVertex = candidate.getSink();
+                    }
+                }
+                return result;
+            }
+
+            @Override
+            public void remove() {
+                throw new UnsupportedOperationException();
+            }
+        }
+    }
+
+    /**
+     * Finds the last event block.
+     * <p>
+     * It can do it forward or backwards.
+     * </p>
+     *
+     * @param anchoring target read anchoring information.
+     * @return {@code null} if there is no event block, depending on {@code backwards} before or after current
+     */
+    private EventBlock findLastEventBlock(
+            final ReadAnchoring anchoring) {
+        return findEventBlock(anchoring,true,anchoring.leftAnchorVertex,anchoring.rightAnchorVertex);
+    }
+
+    /**
+     * Finds an event block forward or backwards along the reference route.
+     * @param anchoring the read anchoring information.
+     * @param backwards true if the block should be constructed from right to left.
+     * @param leftVertex the left vertex
+     * @param rightVertex the right vertex
+     * @return {@code null} if there is no such a event block between these coordinates.
+     */
+    private EventBlock findEventBlock(
+            final ReadAnchoring anchoring, final boolean backwards,
+            final MultiDeBruijnVertex leftVertex, final MultiDeBruijnVertex rightVertex) {
+
+        MultiDeBruijnVertex currentVertex = backwards ? rightVertex : leftVertex;
+        boolean foundEvent = false;
+        final CountSet pathSizes = new CountSet(10); // typically more than enough.
+        pathSizes.setTo(0);
+
+        // Map between reference vertices where there is some expected open alternative path rejoining and the
+        // predicted length of paths rejoining at that point counting from the beginning of the block.
+        final Map<MultiDeBruijnVertex, CountSet> expectedAlternativePathRejoins = new HashMap<>(4);
+
+        // Keeps record of possible left-clipping veritces; those that are located before any event path furcation
+        // has been found. The value indicates the blockLength at the time we traverse that node.
+        final Deque<Pair<MultiDeBruijnVertex, Integer>> possibleClippingPoints = new LinkedList<>();
+
+        // We keep the distance from the beggining of the block (leftVertex).
+        int blockLength = 0;
+        while (currentVertex != null) {
+            int openingDegree = backwards ? graph.outDegreeOf(currentVertex) : graph.inDegreeOf(currentVertex);
+            if (openingDegree > 1) {
+                final CountSet joiningPathLengths = expectedAlternativePathRejoins.remove(currentVertex);
+                if (joiningPathLengths != null)
+                    pathSizes.addAll(joiningPathLengths);
+            }
+            final boolean isValidBlockEnd = isValidBlockEnd(anchoring, currentVertex, expectedAlternativePathRejoins);
+            if (foundEvent && isValidBlockEnd) // !gotcha we found a valid block end.
+                break;
+            else if (!foundEvent && isValidBlockEnd) // if no event has been found yet, still is a good clipping point.
+                possibleClippingPoints.addLast(new Pair<>(currentVertex, blockLength));
+
+            // We reached the end:
+            if (currentVertex == (backwards ? leftVertex : rightVertex))
+                break;
+
+            // process next vertices, the next one on the reference and also possible start of alternative paths,
+            // updates traversal structures accordingly.
+            currentVertex = advanceOnReferencePath(anchoring, backwards, currentVertex, pathSizes, expectedAlternativePathRejoins);
+            foundEvent |= expectedAlternativePathRejoins.size() > 0;
+            pathSizes.incAll(1);
+            blockLength++;
+        }
+
+        // we have not found an event, thus there is no block to report:
+        if (!foundEvent)
+            return null;
+
+        // We try to clip off as much as we can from the beginning of the block before any event, but at least
+        // leaving enough block length to meet the shortest path unless all paths have the same size (SNPs only)
+        final int maxClipping = pathSizes.size() <= 1 ? blockLength : pathSizes.min();
+        MultiDeBruijnVertex clippingEnd = backwards ? anchoring.rightAnchorVertex : anchoring.leftAnchorVertex;
+        while (!possibleClippingPoints.isEmpty()) {
+            final Pair<MultiDeBruijnVertex, Integer> candidate = possibleClippingPoints.removeLast();
+            if (candidate.getSecond() <= maxClipping) {
+                clippingEnd = candidate.getFirst();
+                break;
+            }
+        }
+
+        return resolveEventBlock(backwards ? new Pair<>(currentVertex, clippingEnd) : new Pair<>(clippingEnd, currentVertex));
+    }
+
+    /**
+     * Gets or constructs a event-block through the cache.
+     * @param borders the source and sink vertex pair for the requested event block.
+     * @return never {@code null}
+     */
+    @Requires("borders != null && border.getFirst() != null && border.getSecond() != null")
+    private EventBlock resolveEventBlock(final Pair<MultiDeBruijnVertex,MultiDeBruijnVertex> borders) {
+        EventBlock result = eventBlockCache.get(borders);
+        if (result == null)
+            eventBlockCache.put(borders,result = new EventBlock(graph, borders.getFirst(),borders.getSecond()));
+        return result;
+    }
+
+    /**
+     * Move on vertex along the reference path checking for the presence of new opening alternative paths.
+     *
+     * @param anchoring anchoring information on the targeted read.
+     * @param backwards whether we are extending the block backwards or forwards.
+     * @param currentVertex the current vertex.
+     * @param pathSizes current block path sizes.
+     * @param expectedAlternativePathRejoins information about location of vertices along the reference path where open alternative paths will rejoin.
+     * @return the next current-vertex, never {@code null} unless there is a bug.
+     */
+    private MultiDeBruijnVertex advanceOnReferencePath(final ReadAnchoring anchoring, final boolean backwards, final MultiDeBruijnVertex currentVertex, final CountSet pathSizes, final Map<MultiDeBruijnVertex, CountSet> expectedAlternativePathRejoins) {
+        final Set<MultiSampleEdge> nextEdges = backwards ? graph.incomingEdgesOf(currentVertex) : graph.outgoingEdgesOf(currentVertex);
+        MultiDeBruijnVertex nextReferenceVertex = null;
+        for (final MultiSampleEdge e : nextEdges) {
+            final MultiDeBruijnVertex nextVertex = backwards ? graph.getEdgeSource(e) : graph.getEdgeTarget(e);
+            if (e.isRef())
+                nextReferenceVertex = nextVertex;
+            else {
+                final CountSet pathSizesPlusOne = pathSizes.clone();
+                pathSizesPlusOne.incAll(1);
+                graph.calculateRejoins(nextVertex, expectedAlternativePathRejoins, anchoring.referenceWithinAnchorsMap.keySet(), pathSizesPlusOne, true, backwards);
+            }
+        }
+        return nextReferenceVertex;
+    }
+
+    /**
+     * Check whether the current vertex is a valid block end.
+     *
+     * @param anchoring reads anchoring information necessary to make the evaluation.
+     * @param currentVertex target potential block end
+     * @param expectedAlternativePathRejoins traversal states regarding open alternative paths.
+     *
+     * @return {@code true} iff so.
+     */
+    private boolean isValidBlockEnd(final ReadAnchoring anchoring, final MultiDeBruijnVertex currentVertex, final Map<MultiDeBruijnVertex, CountSet> expectedAlternativePathRejoins) {
+        final boolean isUniqueKmer = anchoring.uniqueKmerOffsets.containsKey(currentVertex);
+        final boolean isAnchorable = graph.getAnchorableVertices().contains(currentVertex) && isUniqueKmer && expectedAlternativePathRejoins.size() == 0;
+        return isUniqueKmer && isAnchorable;
+    }
+}
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
index cc89792d5..697d162fd 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
@@ -337,7 +337,7 @@ public class GenotypingEngine {
         for( final String sample : alleleReadMap.keySet() ) {
             final int numHaplotypes = mergedVC.getAlleles().size();
             final double[] genotypeLikelihoods = new double[numHaplotypes * (numHaplotypes+1) / 2];
-            final double[][] haplotypeLikelihoodMatrix = LikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods(sample, alleleReadMap, mergedVC.getAlleles(), true);
+            final double[][] haplotypeLikelihoodMatrix = PairHMMLikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods(sample, alleleReadMap, mergedVC.getAlleles(), true);
             int glIndex = 0;
             for( int iii = 0; iii < numHaplotypes; iii++ ) {
                 for( int jjj = 0; jjj <= iii; jjj++ ) {
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java
new file mode 100644
index 000000000..8a35ccb05
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java
@@ -0,0 +1,158 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+*
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
+
+import org.apache.log4j.Logger;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.SeqGraph;
+import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
+import org.broadinstitute.sting.utils.exceptions.StingException;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.haplotype.Haplotype;
+import org.broadinstitute.sting.utils.pairhmm.FlexibleHMM;
+import org.broadinstitute.sting.utils.pairhmm.FastLoglessPairHMM;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+
+import java.io.File;
+import java.io.FileWriter;
+import java.io.PrintWriter;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * Read likelihood calculation engine base on applying heuristic on the assembly graph.
+ */
+public class GraphBasedLikelihoodCalculationEngine implements LikelihoodCalculationEngine {
+
+    private static Logger logger = Logger.getLogger(GraphBasedLikelihoodCalculationEngine.class);
+
+    /**
+     * Gap extension penalty in Phred scale.
+     */
+    private byte gcpHMM;
+
+    /**
+     * Fast-hmm implementation reused across active regions.
+     */
+    private FlexibleHMM hmm;
+
+    /**
+     * The worst reference vs best-alternative haplotype ratio for any read. The reference haplotype likelihood
+     * is changes to meet this maximum is needed.
+     */
+    private double log10GlobalReadMismappingRate;
+
+    /**
+     * How we resolve cases in where we have haplotypes coming from different kmer sizes.
+     */
+    private HeterogeneousKmerSizeResolution heterogeneousKmerSizeResolution;
+
+    private enum DebugMode { NONE, DEBUG, EXTRA_DEBUG };
+
+    private DebugMode debugMode;
+
+    /**
+     * Creates a new likelihood engine.
+     *
+     * @param gapExtensionPenalty the gap extension penalty Phred scale.
+     * @param log10GlobalReadMismappingRate the global read mismapping rate.
+     * @param heterogeneousKmerSizeResolution who to resolve assembly with haplotypes generated from different kmerSizes.
+     * @param debug whether to output some debug messages.
+     * @param debugHaplotypeGraphAndLikelihoods whether to generate haplotype graph and likelihood files, please only use with small intervals.
+     */
+    public GraphBasedLikelihoodCalculationEngine(final int gapExtensionPenalty, final double log10GlobalReadMismappingRate,
+                                                 final HeterogeneousKmerSizeResolution heterogeneousKmerSizeResolution,
+                                                 final boolean debug, final boolean debugHaplotypeGraphAndLikelihoods) {
+        gcpHMM = (byte) gapExtensionPenalty;
+        hmm = new FastLoglessPairHMM(gcpHMM);
+        this.log10GlobalReadMismappingRate = log10GlobalReadMismappingRate;
+        this.heterogeneousKmerSizeResolution = heterogeneousKmerSizeResolution;
+        debugMode = debugHaplotypeGraphAndLikelihoods ? DebugMode.EXTRA_DEBUG : debug ? DebugMode.DEBUG : DebugMode.NONE;
+    }
+
+
+    @Override
+    public Map<String, PerReadAlleleLikelihoodMap> computeReadLikelihoods(final AssemblyResultSet assemblyResultSet, final Map<String, List<GATKSAMRecord>> perSampleReadList) {
+        final GraphBasedLikelihoodCalculationEngineInstance graphLikelihoodEngine =
+                new GraphBasedLikelihoodCalculationEngineInstance(assemblyResultSet,
+                        hmm,log10GlobalReadMismappingRate,heterogeneousKmerSizeResolution);
+        final List<Haplotype> haplotypes = assemblyResultSet.getHaplotypeList();
+        final List<Haplotype> supportedHaplotypes = graphLikelihoodEngine.getHaplotypeList();
+        if (supportedHaplotypes.size() != haplotypes.size()) logger.warn("Some haplotypes were drop due to missing route on the graph (supported / all): " + supportedHaplotypes.size() + "/" + haplotypes.size());
+        final Map<String,PerReadAlleleLikelihoodMap> result = graphLikelihoodEngine.computeReadLikelihoods(supportedHaplotypes,
+                perSampleReadList );
+        if (debugMode != DebugMode.NONE) graphLikelihoodDebugDumps(assemblyResultSet.getRegionForGenotyping(), graphLikelihoodEngine,result);
+        return result;
+    }
+
+    /**
+     * A few debug messages associated with the GraphBased likelihoods engine.
+     */
+    private void graphLikelihoodDebugDumps(final ActiveRegion originalActiveRegion, final GraphBasedLikelihoodCalculationEngineInstance graphLikelihoodEngine,
+                                           final Map<String, PerReadAlleleLikelihoodMap> result) {
+        if (graphLikelihoodEngine.hasCycles())
+            logger.debug("Resulting haplotype graph combining several kmer sizes has cycles");
+        else if (graphLikelihoodEngine.haplotypeGraph.hasNonReferenceEnds())
+            logger.debug("Resulting haplotype graph has ends that do not belong to the reference: " + originalActiveRegion.getLocation());
+        else if (!graphLikelihoodEngine.hasVariation())
+            logger.debug("Resulting haplotype graph does not contain any alternative haplotype path");
+        if (debugMode == DebugMode.EXTRA_DEBUG) {
+            graphLikelihoodEngine.printGraph(originalActiveRegion.getLocation() + "-" + graphLikelihoodEngine.getKmerSize() + "-haplotypeGraph.dot");
+            final SeqGraph sq = graphLikelihoodEngine.haplotypeGraph.convertToSequenceGraph();
+            sq.simplifyGraph();
+            sq.printGraph(new File(originalActiveRegion.getLocation() + "-" + graphLikelihoodEngine.getKmerSize() + "-haplotypeSeqGraph.dot"), 10000);
+            try {
+                FileWriter fw = new FileWriter(new File(originalActiveRegion.getLocation() + "-likelihoods.txt"));
+                PrintWriter pw = new PrintWriter(fw);
+                //Note: we only output the first sample likelihoods, perhaps should output all of them but for debugging this is normally what is needed.
+                pw.println(result.entrySet().iterator().next().getValue().toString());
+                pw.close();
+                fw.close();
+            } catch (Exception ex) {
+                throw new StingException("", ex);
+            }
+        }
+    }
+}
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java
new file mode 100644
index 000000000..9d861a445
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java
@@ -0,0 +1,911 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*  
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*  
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*  
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*  
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*  
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. 
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.  
+*  
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY 
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*  
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*  
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*  
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*  
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt. 
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. 
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
+
+import org.apache.log4j.Logger;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.MultiSampleEdge;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.Path;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.Route;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.HaplotypeGraph;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.collections.CountSet;
+import org.broadinstitute.sting.utils.collections.CountSet;
+import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.haplotype.Haplotype;
+import org.broadinstitute.sting.utils.pairhmm.FlexibleHMM;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.variant.variantcontext.Allele;
+
+import java.util.*;
+
+/**
+ * Fast pseudo-likelihood calculation engine based on the assembly haplotype graph.
+ *
+ * <p>
+ *     An instance is good for active region. {@link GraphBasedLikelihoodCalculationEngine} instance them on demand
+ *     as requested by the {@code HaplotypeCaller} code.
+ * </p>
+ */
+public class GraphBasedLikelihoodCalculationEngineInstance {
+
+    private final static Logger logger = Logger.getLogger(GraphBasedLikelihoodCalculationEngineInstance.class);
+
+
+    /**
+     * Unified kmer size used for the Haplotype graph.
+     */
+    protected final int kmerSize;
+
+    /**
+     * Reference to the haplotype graph.
+     */
+    protected final HaplotypeGraph haplotypeGraph;
+
+    /**
+     * Haplotypes included in the haplotype graph.
+     */
+    private final List<Haplotype> haplotypes;
+
+    /**
+     * Whether there is some variation present in the haplotype assembly.
+     */
+    private final boolean hasVariation;
+
+
+    /**
+     * Counts of reads that anchoread somewhere.
+     *
+     * <p>Used for debugging purposes</p>
+     */
+    private int anchoredReads = 0;
+
+    /**
+     * Count of reads that didn't anchor anywere.
+     *
+     * <p>Used for debugging purposes</p>
+     */
+    private int nonAnchoredReads = 0;
+
+    /**
+     * Pair-hmm implementation to use to calculate read likelihoods.
+     */
+    private final FlexibleHMM hmm;
+
+    /**
+     * Maximum likelihood difference between the reference haplotype and the best alternative haplotype.
+     *
+     * <p>If the difference is greater for a read, the reference haplotype likelihood is increase in order to not go
+     *  beyond this limit</p>
+     */
+    protected final double log10globalReadMismappingRate;
+
+    protected final EventBlockFinder eventBlockSearchEngine;
+
+
+    /**
+     * Constructs a new engine based on the results of the assembly.
+     *
+     * @param assemblyResultSet                           assembly-result set
+     * @param hmm                           fast-hmm implementation to use.
+     * @param log10globalReadMismappingRate maximum cost for the reference haplotype vs the best alternative available.
+     * @param heterogeneousKmerSizeResolution multi-kmersize dataset resolution.
+     * @throws NullPointerException     if any argument is null.
+     * @throws IllegalArgumentException if log10globalReadMismappingRate >= 0.
+     */
+    public GraphBasedLikelihoodCalculationEngineInstance(final AssemblyResultSet assemblyResultSet, final FlexibleHMM hmm, final double log10globalReadMismappingRate, final HeterogeneousKmerSizeResolution heterogeneousKmerSizeResolution) {
+        if (heterogeneousKmerSizeResolution  == null) throw new NullPointerException("the kmerSize resolution cannot be null");
+        if (assemblyResultSet == null) throw new NullPointerException("the assembly result set cannot be null");
+        if (hmm == null) throw new NullPointerException("the fast-hmm component cannot be null");
+        if (log10globalReadMismappingRate >= 0)
+            throw new IllegalArgumentException("the global reading mismapping rate cannot be positive or zero");
+
+        this.hmm = hmm;
+        this.log10globalReadMismappingRate = log10globalReadMismappingRate;
+
+        haplotypes = new ArrayList<>(assemblyResultSet.getHaplotypeList());
+        Collections.sort(haplotypes, Haplotype.ALPHANUMERICAL_COMPARATOR);
+
+        // make sure that kmerSize is not bigger than the smallest haplotype. It can well happen when there are cycles and kmerSize inflates.
+        final Haplotype referenceHaplotype = assemblyResultSet.getReferenceHaplotype();
+        int minHaplotypeLength = referenceHaplotype.length();
+        for (final Haplotype h : haplotypes)
+            if (minHaplotypeLength > h.length())
+                minHaplotypeLength = h.length();
+
+        // Determine the kmerSize to use for the unified haplotype assembly graph
+
+        kmerSize = Math.min(minHaplotypeLength,
+                heterogeneousKmerSizeResolution.useMaximum() ? assemblyResultSet.getMaximumKmerSize() : assemblyResultSet.getMinimumKmerSize());
+
+        haplotypeGraph = new HaplotypeGraph(kmerSize,haplotypes);
+
+
+        if (haplotypeGraph.hasCycles())
+            Utils.warnUser(logger, "cycle caused at merging haplotypes with different kmerSizes: active region " + assemblyResultSet.getRegionForGenotyping() + " will be skipped");
+
+        //TODO haplpotypeGraph.getReferenceSourceVertex() == null
+        //TODO Is a quick patch to ignore cases where the trimming has rendered kmerSize so big that is bigger than the haplotype
+        //TODO and reduction to the minimum haplotype size result in no unique kmers.
+        //TODO the actual solution: we need to impose a maximum trimming at least for Graph-based HC runs as we are loosing
+        //TODO a bit of sensitivity as trimming results in lack of unique kmers.
+        if (haplotypeGraph.hasCycles() || haplotypeGraph.getReferenceHaplotype() == null) {
+            hasVariation = false;
+            eventBlockSearchEngine = null;
+            return;
+        }
+
+        haplotypeGraph.mergeCommonChains();
+        //TODO recover dangling ends. Did not work the last time I tried but may be worth to retry.
+        //haplotypeGraph.recoverDanglingTails(-1);
+        logger.debug("using haplotype graph with kmerSize " + haplotypeGraph.getKmerSize());
+
+        hasVariation = !haplotypeGraph.hasCycles() && haplotypeGraph.getHaplotypes().size() > 1;
+
+        eventBlockSearchEngine = new EventBlockFinder(haplotypeGraph);
+    }
+
+    /**
+     * Determines whether based on result from assembly and the relevant user options we can reuse th existing
+     *
+     * @param assemblyResultSet assembly result set.
+     * @param kmerSize intended kmerSize for the haplotype graph.
+     * @param heterogeneousKmerSizeResolution user instruction as to how to resolve situation where we have haplotypes comming from different kmer sizes.
+     * @return {@code true} iff we can reuse an existing read-threading graph with that kmerSize in the assembly result set.
+     */
+    @SuppressWarnings("unused")
+    private static boolean canReuseReadThreadingGraphAsHaplotypeGraph(final AssemblyResultSet assemblyResultSet, final int kmerSize, final HeterogeneousKmerSizeResolution heterogeneousKmerSizeResolution) {
+        return !assemblyResultSet.wasTrimmed() && (!assemblyResultSet.hasMultipleKmerSizes() || heterogeneousKmerSizeResolution.combinesKmerSizes()) &&
+                assemblyResultSet.getUniqueReadThreadingGraph(kmerSize) != null;
+    }
+
+    /**
+     * Checks whether the underlying haplotype graph assembly contains any variation worth analyzing.
+     *
+     * @return {@code true} iff so.
+     */
+    public boolean hasVariation() {
+        return hasVariation;
+    }
+
+    /**
+     * Calculates the likelihood of reads across many samples evaluated against haplotypes resulting from the
+     * active region assembly process.
+     *
+     * @param haplotypes to evaluate.
+     * @param perSampleReadList the input read sets stratified per sample.
+     *
+     * @throws NullPointerException if either parameter is {@code null}.
+     *
+     * @return never {@code null}, and with at least one entry for input sample (keys in {@code perSampleReadList}.
+     *    The value maps can be potentially empty though.
+     */
+    public Map<String, PerReadAlleleLikelihoodMap> computeReadLikelihoods(
+            final List<Haplotype> haplotypes,
+            final Map<String, List<GATKSAMRecord>> perSampleReadList) {
+        // General preparation on the input haplotypes:
+        Collections.sort(haplotypes, Haplotype.ALPHANUMERICAL_COMPARATOR);
+        final Map<Haplotype, Allele> alleleVersions = new LinkedHashMap<>(haplotypes.size());
+        for (final Haplotype haplotype : haplotypes)
+            alleleVersions.put(haplotype, Allele.create(haplotype,haplotype.isReference()));
+
+        // The actual work:
+        final HashMap<String, PerReadAlleleLikelihoodMap> result = new HashMap<>(perSampleReadList.size());
+        for (final Map.Entry<String, List<GATKSAMRecord>> e : perSampleReadList.entrySet()) {
+            final String sample = e.getKey();
+            final List<GATKSAMRecord> reads = e.getValue();
+            final Set<GATKSAMRecord> mayNeedAdjustment = new HashSet<>(reads.size());
+            // Get the cost/likelihood of each read at relevant subpaths on the tree:
+            final Map<MultiDeBruijnVertex, Set<ReadSegmentCost>> costsByEndingVertex = calculatePathCostsByRead(reads, mayNeedAdjustment);
+            // Create the resulting per-read maps:
+            final PerReadAlleleLikelihoodMap prallm = calculatePerReadAlleleLikelihoodMap(haplotypes, costsByEndingVertex, alleleVersions);
+            result.put(sample, prallm);
+        }
+        logger.debug("Likelihood analysis summary: reads anchored " + anchoredReads + "/" + (anchoredReads + nonAnchoredReads) + "");
+        return result;
+    }
+
+
+    /**
+     * Prints a graph into a dot file.
+     *
+     * @param fileName name of the output file.
+     */
+    public void printGraph(final String fileName) {
+        if (haplotypeGraph != null)
+            haplotypeGraph.printGraph(fileName);
+    }
+
+    /**
+     * Returns the kmerSize the engine is using to match read vs graph kmers thus reducing computation.
+     *
+     * @return greater than 0.
+     */
+    public int getKmerSize() {
+        return kmerSize;
+    }
+
+    /**
+     * Tells whether the underlying haplotype graph contained cycles.
+     *
+     * @return {@code true} iff so.
+     */
+    public boolean hasCycles() {
+        // It is set to null if it contained cycles.
+        return haplotypeGraph == null;
+    }
+
+
+    /**
+     * Builds the result per-read allele likelihood map.
+     *
+     * @param haplotypes          haplotypes to process.
+     * @param costsEndingByVertex Read vs haplotype graph subpaths cost indexed by ending vertex.
+     * @param alleleVersions      map between haplotypes and the corresponding allele.
+     * @return never {@code null} although perhaps empty.
+     */
+    protected PerReadAlleleLikelihoodMap calculatePerReadAlleleLikelihoodMap(
+            final Collection<Haplotype> haplotypes,
+            final Map<MultiDeBruijnVertex, Set<ReadSegmentCost>> costsEndingByVertex, final Map<Haplotype, Allele> alleleVersions) {
+
+        final PerReadAlleleLikelihoodMap result = new PerReadAlleleLikelihoodMap();
+        if (haplotypeGraph == null)
+            return result;
+        final Map<GATKSAMRecord, Double> maxAlleleLogLk = new HashMap<>(anchoredReads + nonAnchoredReads + 10);
+        final Set<Haplotype> supportedHaplotypes = new LinkedHashSet<>(haplotypeGraph.getHaplotypes());
+        supportedHaplotypes.retainAll(haplotypes);
+        for (final Haplotype haplotype : supportedHaplotypes)
+            calculatePerReadAlleleLikelihoodMapHaplotypeProcessing(haplotype, alleleVersions, result, maxAlleleLogLk, costsEndingByVertex);
+
+        //TODO Does not seem to be needed in practice:
+        //TODO furhter testing/evaluation required before removing it completely.
+        //makeLikelihoodAdjustment(alleleVersions, result, maxAlternativeAlleleLogLk.keySet(), maxAlternativeAlleleLogLk);
+        applyGlobalReadMismappingRate(alleleVersions, result, maxAlleleLogLk);
+        return result;
+    }
+
+    /**
+     * Work done per haplotype to build the result per-read allele likelihood map.
+     * <p/>
+     * <p>
+     * Basically for each haplotype we go through its path in the graph collecting all the read cost that we find
+     * on the way. For each read present we add up all its cost resulting in a single value per read, i.e. its
+     * "likelihood".
+     * </p>
+     *
+     * @param haplotype                 the target haplotype
+     * @param alleleVersions            allele version of the haplotypes. These are the ones to be used in the final output.
+     * @param result                    target where to add the read-vs-haplotype likelihoods.
+     * @param maxAlleleLogLk   where to place the maximum likelihood achieve on any haplotype for each read.
+     * @param costsEndingByVertex       read costs assorted by their end vertex.
+     */
+    private void calculatePerReadAlleleLikelihoodMapHaplotypeProcessing(final Haplotype haplotype,
+                                                                        final Map<Haplotype, Allele> alleleVersions,
+                                                                        final PerReadAlleleLikelihoodMap result,
+                                                                        final Map<GATKSAMRecord, Double> maxAlleleLogLk,
+                                                                        final Map<MultiDeBruijnVertex, Set<ReadSegmentCost>> costsEndingByVertex) {
+        final HaplotypeRoute haplotypeRoute = haplotypeGraph.getHaplotypeRoute(haplotype);
+        final Set<MultiDeBruijnVertex> haplotypeVertices = haplotypeRoute.vertexSet();
+        final Map<GATKSAMRecord, ReadCost> readCostByRead = new HashMap<>();
+        final Set<MultiDeBruijnVertex> visitedVertices = new HashSet<>(haplotypeVertices.size());
+        final List<MultiSampleEdge> edgeList = haplotypeRoute.getEdges();
+        MultiDeBruijnVertex currentVertex = haplotypeRoute.getFirstVertex();
+        Route<MultiDeBruijnVertex, MultiSampleEdge> pathSoFar = new Route<>(currentVertex, haplotypeGraph);
+        final Iterator<MultiSampleEdge> edgeIterator = edgeList.iterator();
+        while (true) {
+            visitedVertices.add(currentVertex);
+            final Set<ReadSegmentCost> finishingAtElementCostSet = costsEndingByVertex.get(currentVertex);
+            updateReadCosts(readCostByRead, visitedVertices, pathSoFar, finishingAtElementCostSet);
+            if (!edgeIterator.hasNext()) break;
+            final MultiSampleEdge nextEdge = edgeIterator.next();
+            pathSoFar = new Route<>(pathSoFar, nextEdge);
+            currentVertex = pathSoFar.getLastVertex();
+        }
+
+        final List<ReadCost> readCosts = new ArrayList<>(readCostByRead.values());
+        Collections.sort(readCosts, ReadCost.COMPARATOR);
+        for (final ReadCost rc : readCosts)
+            result.add(rc.read, alleleVersions.get(haplotype), rc.cost);
+
+        for (final ReadCost rc : readCosts) {
+            final Double currentMax = maxAlleleLogLk.get(rc.read);
+            if (currentMax == null || currentMax < rc.cost)
+                maxAlleleLogLk.put(rc.read, rc.cost);
+        }
+    }
+
+    /**
+     * Update the read cost based on the path cost found at a vertex.
+     *
+     * @param readCosts                 collection of read costs so far
+     * @param visitedVertices           visited vertices collection.
+     * @param pathSoFar                 the haplotype path visited so far.
+     * @param finishingAtElementCostSet collection of path cost to process
+     */
+    private void updateReadCosts(final Map<GATKSAMRecord, ReadCost> readCosts,
+                                 final Set<MultiDeBruijnVertex> visitedVertices,
+                                 final Route<MultiDeBruijnVertex, MultiSampleEdge> pathSoFar,
+                                 final Set<ReadSegmentCost> finishingAtElementCostSet) {
+        if (finishingAtElementCostSet != null) {
+            for (final ReadSegmentCost pc : finishingAtElementCostSet) {
+                if (!visitedVertices.contains(pc.path.getFirstVertex()))
+                    continue;
+                if (!pathSoFar.isSuffix(pc.path))
+                    continue;
+                ReadCost rc = readCosts.get(pc.read);
+                if (rc == null)
+                    readCosts.put(pc.read, rc = new ReadCost(pc.read));
+                rc.cost += pc.cost;
+            }
+        }
+    }
+
+    /**
+     * Likelihood penalty for unreported haplotype vs read likelihood with respect to the worst reported one.
+     */
+    private static final int UNREPORTED_HAPLOTYPE_LIKELIHOOD_PENALTY = -3;
+
+    /**
+     * Re-scales all haplotype vs read likelihoods so that for read, the best haplotype, hash likelihood 0.
+     *
+     * @param alleleVersions map between input haplotypes and output alleles.
+     * @param result where to change the likelihoods.
+     * @param mayNeedAdjustment set of read that might need adjustment. Others might be ignored.
+     * @param maxAlternative map from each read and the maximum alternative haplotype likelihood.
+     */
+    @SuppressWarnings("unused")
+    private void makeLikelihoodAdjustment(final Map<Haplotype, Allele> alleleVersions,
+                                          final PerReadAlleleLikelihoodMap result,
+                                          final Set<GATKSAMRecord> mayNeedAdjustment,
+                                          final Map<GATKSAMRecord, Double> maxAlternative) {
+        final Map<GATKSAMRecord, Map<Allele, Double>> map = result.getLikelihoodReadMap();
+
+        for (final GATKSAMRecord read : mayNeedAdjustment) {
+            final Map<Allele, Double> existingLikelihoods = map.get(read);
+            if (existingLikelihoods != null) {
+                Allele bestAllele = null;
+                double worstRelativeLikelihood = 0;
+                double bestRelativeLikelihood = Double.NEGATIVE_INFINITY;
+                for (final Map.Entry<Allele, Double> entry : map.get(read).entrySet()) {
+                    final double candidateRelativeLikelihood = entry.getValue();
+                    if (candidateRelativeLikelihood > bestRelativeLikelihood) {
+                        bestAllele = entry.getKey();
+                        bestRelativeLikelihood = candidateRelativeLikelihood;
+                    }
+                    if (!Double.isInfinite(candidateRelativeLikelihood) && worstRelativeLikelihood > candidateRelativeLikelihood)
+                        worstRelativeLikelihood = candidateRelativeLikelihood;
+                }
+
+                worstRelativeLikelihood += UNREPORTED_HAPLOTYPE_LIKELIHOOD_PENALTY;
+                if (bestAllele == null)
+                    throw new IllegalStateException("No best allele for read " + read.getReadName());
+                final double bestLikelihood = 0.0; // the best becomes zero.
+                maxAlternative.put(read, bestLikelihood);
+                for (final Map.Entry<Haplotype, Allele> entry : alleleVersions.entrySet()) {
+                    final Allele a = entry.getValue();
+                    final Double relativeLikelihoodO = existingLikelihoods.get(a);
+                    final double relativeLikelihood = relativeLikelihoodO == null ? worstRelativeLikelihood : relativeLikelihoodO;
+                    final double likelihood = relativeLikelihood - bestRelativeLikelihood + bestLikelihood;
+                    if (likelihood > 0)
+                        throw new IllegalStateException("Likelihood larger than 1 with read " + read.getReadName());
+                    existingLikelihoods.put(a, likelihood);
+                }
+            }
+        }
+    }
+
+    /**
+     * Makes sure that the reference allele likelihood is not too much smaller that the best alternative allele.
+     * The justification of this constraint is explained in
+     * {@link PairHMMLikelihoodCalculationEngine#computeDiploidHaplotypeLikelihoods}.
+     *
+     * @param alleleVersions            correspondence between input haplotypes and output alleles.
+     * @param result                    the target result map.
+     * @param maxAlleleLogLk for each read indicates the likelihood of the best alternative allele.
+     */
+    private void applyGlobalReadMismappingRate(final Map<Haplotype, Allele> alleleVersions,
+                                               final PerReadAlleleLikelihoodMap result,
+                                               final Map<GATKSAMRecord, Double> maxAlleleLogLk) {
+        if (!Double.isNaN(log10globalReadMismappingRate) && !Double.isInfinite(log10globalReadMismappingRate)) {
+            final Allele referenceAllele = alleleVersions.get(haplotypeGraph.getReferenceHaplotype());
+            for (final Map.Entry<GATKSAMRecord, Map<Allele, Double>> entry : result.getLikelihoodReadMap().entrySet()) {
+                final GATKSAMRecord read = entry.getKey();
+                final Map<Allele, Double> likelihoods = entry.getValue();
+                final Double maxLogLk = maxAlleleLogLk.get(read);
+                if (maxAlleleLogLk == null) continue;
+                final Double referenceLogLk = likelihoods.get(referenceAllele);
+                final Double minReferenceLogLk = maxLogLk + log10globalReadMismappingRate;
+                if (referenceLogLk == null || referenceLogLk < minReferenceLogLk)
+                    likelihoods.put(referenceAllele, minReferenceLogLk);
+            }
+        }
+    }
+
+    /**
+     * Calculates path costs for a set of reads.
+     * <p/>
+     * <p>
+     * The resulting map has one entry per read, where the read is the key and the value list of path-cost sets.
+     * Each element in that list corresponds to an event block. Each path cost in one of those sets indicate the
+     * likelihood (cost) of traversing a possible path across the event block using that read.
+     * </p>
+     *
+     * @param reads             reads to analyze.
+     * @param mayNeedAdjustment set where to add reads whose likelihood might need adjustment.
+     * @return never {@code null}.
+     */
+    protected Map<MultiDeBruijnVertex, Set<ReadSegmentCost>> calculatePathCostsByRead(
+            final List<GATKSAMRecord> reads, final Set<GATKSAMRecord> mayNeedAdjustment) {
+        final Map<MultiDeBruijnVertex, Set<ReadSegmentCost>> result = new HashMap<>(reads.size());
+        if (!hasVariation)
+            return Collections.emptyMap();
+        for (final GATKSAMRecord r : reads) {
+            calculatePathCostsByRead(r, mayNeedAdjustment, result);
+        }
+        return result;
+    }
+
+    /**
+     * Calculates path cost for a single read.
+     *
+     * @param read              target read.
+     * @param mayNeedAdjustment set where to add read whose likelihood might need adjustment.
+     * @param result       map where to add the result.
+     */
+    private void calculatePathCostsByRead(final GATKSAMRecord read, final Set<GATKSAMRecord> mayNeedAdjustment,
+                                          final Map<MultiDeBruijnVertex, Set<ReadSegmentCost>> result) {
+
+        final ReadAnchoring anchoring = new ReadAnchoring(read,haplotypeGraph);
+        // cannot anchor so go the tradition pair-hmm way.
+        hmm.loadRead(read);
+        if (!anchoring.isAnchoredSomewhere()) {
+            defaultToRegularPairHMM(anchoring, result);
+            nonAnchoredReads++;
+            return;
+        }
+
+        calculateReadSegmentCosts(anchoring, hmm, result);
+
+        if (!anchoring.isPerfectAnchoring()) danglingEndPathCosts(anchoring, hmm, result);
+        mayNeedAdjustment.add(read);
+        anchoredReads++;
+    }
+
+    /**
+     * Calculates read vs haplotype likelihoods using the classic PairHMM approach.
+     * <p/>
+     * <p>
+     * It basically compares the read with each haplotype full path without short cuts.
+     * </p>
+     *
+     * @param anchoring      anchoring information of the read.
+     * @param destination where to leave the results indexed by ending veretex.
+     */
+    private void defaultToRegularPairHMM(final ReadAnchoring anchoring, final Map<MultiDeBruijnVertex,Set<ReadSegmentCost>> destination) {
+
+        for (final Map.Entry<Haplotype, HaplotypeRoute> entry : haplotypeGraph.getHaplotypeRouteMap().entrySet()) {
+            if (entry.getValue() == null) continue;
+            final byte[] haplotypeBases = entry.getKey().getBases();
+            hmm.loadHaplotypeBases(haplotypeBases);
+            final double cost = hmm.calculateLocalLikelihood(0, anchoring.read.getReadLength(), 0, haplotypeBases.length, false);
+            final ReadSegmentCost readSegmentCost = new ReadSegmentCost(anchoring.read, entry.getValue(), cost);
+            addReadSegmentCost(destination, readSegmentCost);
+        }
+    }
+
+    /**
+     * Add a new read-segment-cost to an ending vertex indexed map.
+     * @param destination where to add the read-segment-cost.
+     * @param cost the read-segment-cost to add.
+     */
+    private void addReadSegmentCost(final Map<MultiDeBruijnVertex,Set<ReadSegmentCost>> destination, final ReadSegmentCost cost) {
+        final MultiDeBruijnVertex endVertex = cost.path.getLastVertex();
+        Set<ReadSegmentCost> vpcSet = destination.get(endVertex);
+        if (vpcSet == null)
+            destination.put(endVertex, vpcSet = new HashSet<>(10));
+        vpcSet.add(cost);
+    }
+
+    /**
+     * Calculate the likelihood cost of path section of a read across the graph.
+     * <p/>
+     * <p>
+     * Given a read, its anchors and other unique kmer mapable to the reference path we can divide the graph
+     * into event blocks: a set of one or more variations and the possible path across that block.
+     * </p>
+     * <p/>
+     * <p>
+     * The result value will have  one element fo reach block. Each element is the set of all path costs (likelihoods)
+     * to traverse the block using all possible paths (different haplotypes).
+     * </p>
+     * <p/>
+     * <p>
+     * The current implementation has some added complexity in order to avoid a situation in where the last part
+     * of the anchored section of the read is thrown out. We first determine the last event block boundaries and we
+     * make sure that we won't run over its left limit when covering for earlier event blocks.
+     * </p>
+     *
+     * @param anchoring        target read graph anchoring information.
+     * @param hmm                       the pair-hmm calculation engine. It must have been loaded with the same {@code read} already.
+     * @param destination where to add the costs.
+     */
+    private void calculateReadSegmentCosts(final ReadAnchoring anchoring, final FlexibleHMM hmm, final Map<MultiDeBruijnVertex, Set<ReadSegmentCost>> destination) {
+
+        final EventBlockFinder.Traversal traversal = eventBlockSearchEngine.traversal(anchoring);
+
+        for (final EventBlock eventBlock : traversal) {
+
+          //  final Set<Route<MultiDeBruijnVertex, MultiSampleEdge>> acrossBlockPaths =
+          //          calculateAllPathsBetweenVertices(anchoring,
+          //                  eventBlock.getSource(), eventBlock.getSink());//eventBlock.getRoutesAcross();
+
+            final Set<Route<MultiDeBruijnVertex, MultiSampleEdge>> acrossBlockPaths = eventBlock.getRoutesAcross();
+
+            int leftBlockBoundaryIndex = anchoring.uniqueKmerOffsets.get(eventBlock.getSource());
+            int rightBlockBoundaryIndex = anchoring.uniqueKmerOffsets.get(eventBlock.getSink());
+            calculateCostForPathSet(anchoring.read, acrossBlockPaths, hmm, leftBlockBoundaryIndex, rightBlockBoundaryIndex, true, false, null, null, destination);
+        }
+    }
+
+    /**
+     * Calculate path cost for a set of paths across a event block.
+     *
+     * @param read the target read.
+     * @param acrossBlockPaths event block paths to evaluate.
+     * @param hmm pair-hmm engine to use to calculate likelihoods.
+     * @param beforeBlockReadOffset kmer offset on the read for the vertex kmer before the block.
+     * @param afterBlockReadOffset  kmer offset on the read for the vertex kmer after the block.
+     * @param doClipping whether to perform any clipping in order to save cpu time.
+     * @param prependVertex if not null, the end cost path with be prepended with this vertex.
+     * @param appendVertex if not null, the end cost path will be appended with this vertex.
+     * @param includePathEnds whether to include or exclude the vertices at the very end or beginning of the paths.
+     */
+    private void calculateCostForPathSet(
+            final GATKSAMRecord read, final Set<Route<MultiDeBruijnVertex, MultiSampleEdge>> acrossBlockPaths,
+            final FlexibleHMM hmm, final int beforeBlockReadOffset, final int afterBlockReadOffset,
+            final boolean doClipping, final boolean includePathEnds,
+            final MultiDeBruijnVertex prependVertex,
+            final MultiDeBruijnVertex appendVertex,
+            final Map<MultiDeBruijnVertex,Set<ReadSegmentCost>> destination) {
+
+
+        final Set<ReadSegmentCost> readSegmentCosts = new TreeSet<>(ReadSegmentComparator.INSTANCE);
+
+        final int readStart = beforeBlockReadOffset + kmerSize;
+        final int readEnd = Math.max(readStart, afterBlockReadOffset + kmerSize - 1);
+        final byte[][] pathBases = new byte[acrossBlockPaths.size()][];
+        final CountSet pathSizes = new CountSet(acrossBlockPaths.size());
+        int nextPath = 0;
+
+        // Complete the read segment cost with the corresponding path bases
+        for (final Route<MultiDeBruijnVertex, MultiSampleEdge> p : acrossBlockPaths) {
+            final ReadSegmentCost readSegmentCost = new ReadSegmentCost(read, p, Double.NaN);
+            pathBases[nextPath++] = readSegmentCost.bases = eventBlockPathBases(p, includePathEnds);
+            pathSizes.add(readSegmentCost.bases.length);
+            readSegmentCosts.add(readSegmentCost);
+        }
+
+        // Add the read 'path size'.
+        pathSizes.add(readEnd - readStart);
+
+        final byte[] readBases = hmm.getReadBases();
+
+        // Perform right clipping of bases that are common to all paths and read.
+        int rightClipping = !doClipping ? 0 : calculateRightClipping(readEnd, pathBases, readBases,pathSizes);
+
+        // Calculate the costs.
+        for (final ReadSegmentCost readSegmentCost : readSegmentCosts) {
+            hmm.loadHaplotypeBases(readSegmentCost.bases);
+            readSegmentCost.cost = hmm.calculateLocalLikelihood(Math.max(0, readStart), readEnd - rightClipping, 0, readSegmentCost.bases.length - rightClipping, false);
+            if (prependVertex != null)
+                readSegmentCost.path = new Route<>(prependVertex,readSegmentCost.path);
+            if (appendVertex != null)
+                readSegmentCost.path = new Route<>(readSegmentCost.path,appendVertex);
+            addReadSegmentCost(destination,readSegmentCost);
+        }
+
+
+    }
+
+    /**
+     * Determines how much we can clip away from the right side of a set of path without loosing accuracy when comparing
+     * likelihood vs the read.
+     *
+     * @param readEnd     exclusive position right after the last one of the region considered.
+     * @param pathBases   bases of possible path in the same event block.
+     * @param readBases   full length read bases.
+     * @param pathSizes   path size set.
+     *
+     * @return 0 or greater.
+     */
+    private int calculateRightClipping(final int readEnd, final byte[][] pathBases,
+                                       final byte[] readBases, final CountSet pathSizes) {
+        final int maxClipping = pathSizes.size() > 1 ? 0 : Math.min(pathSizes.min(), kmerSize - 1);
+        int rightClipping = 0;
+        while (rightClipping < maxClipping) {
+            final byte readBase = readBases[readEnd - rightClipping - 1];
+            boolean dontGoFurther = false;
+            for (int i = 0; !dontGoFurther && i < pathBases.length; i++)
+                if (pathBases[i][pathBases[i].length - rightClipping - 1] != readBase)
+                    dontGoFurther = true;
+            if (dontGoFurther)
+                break;
+            rightClipping++;
+        }
+        return rightClipping;
+    }
+
+    /**
+     * Calculates a graph path bases.
+     * <p/>
+     * <p>
+     * When the path starts on a source vertex, all its sequence is considered as part of the path bases. For regular
+     * vertices start only the suffix (last) base is considered.
+     * </p>
+     *
+     * @param path            the targeted path.
+     * @param includePathEnds whether the bases included in the first and last vertex of the path should be included or excluded.
+     * @return never {@code null} but perhaps a zero-length base array if the final requested path length is zero.
+     */
+    //TODO this method could be moved to the Path class, but require consider how to make the API more concise.
+    private byte[] eventBlockPathBases(final Path<MultiDeBruijnVertex, MultiSampleEdge> path,
+                                       final boolean includePathEnds) {
+        // We first calculate the size of the return.
+        final List<MultiDeBruijnVertex> vertices = path.getVertices();
+        final boolean pathStartsAtSource = haplotypeGraph.isSource(path.getFirstVertex());
+        final int resultLength = includePathEnds
+                ? vertices.size() + (pathStartsAtSource ? path.getFirstVertex().getSequence().length - 1 : 0)
+                : vertices.size() - 2;
+        // Trivial empty return cases:
+        if (resultLength <= 0)
+            return new byte[0];
+        final byte[] result = new byte[resultLength];
+        if (result.length == 0) {
+            return result;
+        }
+        // General return cases:
+        final ListIterator<MultiDeBruijnVertex> it = vertices.listIterator(includePathEnds ? 0 : 1); // skip the vertex (exclusive)
+        for (int i = 0; i < resultLength; i++) { // i < resultLength implicitly skips the last vertex (exclusive).
+            final MultiDeBruijnVertex vertex = it.next();
+            if (i == 0 && includePathEnds && pathStartsAtSource) {
+                System.arraycopy(vertex.getSequence(), 0, result, 0, kmerSize);
+                i = kmerSize - 1;
+            } else
+                result[i] = vertex.getSuffix();
+        }
+        return result;
+    }
+
+    /**
+     * Calculate the path cost of dangling ends.
+     * <p/>
+     * <p>
+     * A dangling end is the section of the read that falls before the left anchor or after the right anchor.
+     * </p>
+     *
+     * @param anchoring anchoring information of the read vs the haplotype assembly graph.
+     * @param hmm       the PairHMM engine to use to calculate likelihoods.
+     * @param destination cost destination.
+     */
+    private void danglingEndPathCosts(final ReadAnchoring anchoring, final FlexibleHMM hmm, final Map<MultiDeBruijnVertex,Set<ReadSegmentCost>> destination) {
+        if (anchoring.leftAnchorIndex > 0 || anchoring.leftAnchorIndex == 0
+                && anchoring.leftAnchorVertex.hasAmbiguousSequence())
+            leftDanglingEndPathCosts(anchoring, hmm,destination);
+
+        if (anchoring.rightAnchorIndex < anchoring.read.getReadLength() - kmerSize)
+            rightDanglingEndPathCosts(anchoring, hmm, destination);
+    }
+
+    /**
+     * Generates all relevant right dangling end path costs.
+     *
+     * @param anchoring the anchoring information for the read under analysis.
+     * @param hmm       pair-hmm implementation to use to calculate likelihoods. It is assumed to be loaded with
+     *                  the same read as {@code anchoring} refers to.
+     * @param destination where the place the resulting read-segment-costs.
+     */
+    private void rightDanglingEndPathCosts(final ReadAnchoring anchoring, final FlexibleHMM hmm,
+                                           final Map<MultiDeBruijnVertex,Set<ReadSegmentCost>> destination) {
+        final int readStart = anchoring.rightAnchorIndex;
+        final int readEnd = anchoring.read.getReadLength() - kmerSize + 1;
+        final Set<Route<MultiDeBruijnVertex, MultiSampleEdge>> haplotypeRoutes =
+                extendsHaplotypeRoutesForwards(anchoring.rightAnchorVertex);
+        if (haplotypeRoutes.size() >= 2)
+            calculateCostForPathSet(anchoring.read,
+                    haplotypeRoutes, hmm, readStart, readEnd, false, true,anchoring.rightAnchorVertex,null,destination);
+
+    }
+
+    /**
+     * Generates all relevant left dangling end path costs.
+     *
+     * @param anchoring the anchoring information for the read under analysis.
+     * @param hmm       pair-hmm implementation to use to calculate likelihoods. It is assumed to be loaded with
+     *                  the same read as {@code anchoring} refers to.
+     * @param destination where the place the resulting read-segment-costs.
+     */
+    private void leftDanglingEndPathCosts(final ReadAnchoring anchoring, final FlexibleHMM hmm,
+                                          final Map<MultiDeBruijnVertex,Set<ReadSegmentCost>> destination) {
+        final int readStart = -kmerSize;
+        final int readEnd = anchoring.leftAnchorIndex;
+        final Set<Route<MultiDeBruijnVertex, MultiSampleEdge>> haplotypeRoutes =
+                extendsHaplotypeRoutesBackwards(anchoring.leftAnchorVertex);
+        if (haplotypeRoutes.size() >= 2) // if there is just one haplotype route there is no relevant variation in the dangling end.
+            calculateCostForPathSet(anchoring.read, haplotypeRoutes, hmm,
+                    readStart, readEnd, false, true, null, anchoring.leftAnchorVertex, destination);
+    }
+
+    /**
+     * Construct haplotype routes prefixes to an anchor vertex.
+     * <p/>
+     * <p>
+     * The output should contain a route for each haplotype that includes the input anchor vertex.
+     * This route would be the prefix of the haplotype that finishes at that vertex.
+     * </p>
+     *
+     * @param anchorVertex the target anchor vertex.
+     * @return never {@code null}.
+     */
+    private Set<Route<MultiDeBruijnVertex, MultiSampleEdge>> extendsHaplotypeRoutesBackwards(
+            final MultiDeBruijnVertex anchorVertex) {
+        final Set<Route<MultiDeBruijnVertex, MultiSampleEdge>> result = new HashSet<>(haplotypes.size());
+        for (final MultiDeBruijnVertex parent : haplotypeGraph.incomingVerticesOf(anchorVertex))
+            extendsHaplotypeRoutesFrom(parent, result, false);
+        return result;
+    }
+
+    /**
+     * Construct haplotype routes suffix from an anchor vertex.
+     * <p/>
+     * <p>
+     * The output should contain a route for each haplotype that includes the input anchor vertex.
+     * This route would be the suffix of the haplotype that starts at that vertex.
+     * </p>
+     *
+     * @param anchorVertex the target anchor vertex.
+     * @return never {@code null}.
+     */
+    private Set<Route<MultiDeBruijnVertex, MultiSampleEdge>> extendsHaplotypeRoutesForwards(
+            final MultiDeBruijnVertex anchorVertex) {
+        final Set<Route<MultiDeBruijnVertex, MultiSampleEdge>> result = new HashSet<>(haplotypes.size());
+        for (final MultiDeBruijnVertex parent : haplotypeGraph.outgoingVerticesOf(anchorVertex))
+            extendsHaplotypeRoutesFrom(parent, result, true);
+        return result;
+    }
+
+    /**
+     * Extends from a vertex considering path furcations that are part of some valid haplotype
+     * <p/>
+     * <p>
+     * In other words, it will ignore subpaths that are not valid part of an assembled haplotype.
+     * </p>
+     *
+     * @param start   start seed vertex.
+     * @param result  destination for found extensions.
+     * @param forward whether to traverse edges forward or backwards.
+     */
+    private void extendsHaplotypeRoutesFrom(final MultiDeBruijnVertex start, final Set<Route<MultiDeBruijnVertex, MultiSampleEdge>> result, final boolean forward) {
+        final Set<HaplotypeRoute> validHaplotypeRoutes = haplotypeGraph.getEnclosingHaplotypeRoutes(start);
+        if (validHaplotypeRoutes.size() == 0) return;
+        final Deque<Pair<Route<MultiDeBruijnVertex, MultiSampleEdge>, Set<HaplotypeRoute>>> queue = new LinkedList<>();
+        queue.add(new Pair<>(new Route<>(start, haplotypeGraph), validHaplotypeRoutes));
+        while (!queue.isEmpty()) {
+            final Pair<Route<MultiDeBruijnVertex, MultiSampleEdge>, Set<HaplotypeRoute>> current = queue.remove();
+            final Route<MultiDeBruijnVertex, MultiSampleEdge> path = current.getFirst();
+            final MultiDeBruijnVertex vertex = forward ? path.getLastVertex() : path.getFirstVertex();
+            final Set<HaplotypeRoute> validRoutes = current.getSecond();
+            for (final HaplotypeRoute hr : validRoutes) {
+                final MultiDeBruijnVertex routeEndVertex = forward ? hr.getLastVertex() : hr.getFirstVertex();
+                if (vertex.equals(routeEndVertex)) {
+                    result.add(path);
+                    break;
+                }
+            }
+            final Set<MultiDeBruijnVertex> nextVertices = forward ? haplotypeGraph.outgoingVerticesOf(vertex) :
+                    haplotypeGraph.incomingVerticesOf(vertex);
+            for (final MultiDeBruijnVertex candidate : nextVertices) {
+                extendsHaplotypeRoutesFrom$ProcessCandidateExtendingVertex(forward, queue, path, validRoutes, candidate);
+            }
+        }
+    }
+
+    /**
+     * Check on an candidate vertice to exted a path.
+     *
+     * <p>
+     *     This method updates the traversal queue accordingly.
+     * </p>
+     *
+     * @param forward whether the extension is forward, or backwards.
+     * @param queue queue with open paths yet to be explored.
+     * @param path path extension to evaluate.
+     * @param validRoutes collection of valid haplotype routes used to discard non-informative extensions.
+     * @param candidate the candidate extending vertex.
+     */
+    private void extendsHaplotypeRoutesFrom$ProcessCandidateExtendingVertex(
+            final boolean forward,
+            final Deque<Pair<Route<MultiDeBruijnVertex, MultiSampleEdge>, Set<HaplotypeRoute>>> queue,
+            final Route<MultiDeBruijnVertex, MultiSampleEdge> path,
+            final Set<HaplotypeRoute> validRoutes, final MultiDeBruijnVertex candidate) {
+        final Set<HaplotypeRoute> parentValidHaplotypes = haplotypeGraph.getEnclosingHaplotypeRoutes(candidate);
+        switch (parentValidHaplotypes.size()) {
+            case 0:
+                return;
+            case 1:
+                if (validRoutes.containsAll(parentValidHaplotypes))
+                    queue.add(new Pair<>(forward ? new Route<>(path, candidate) : new Route<>(candidate, path), parentValidHaplotypes));
+                else
+                    return;
+                break;
+            default:
+                if (parentValidHaplotypes.size() == validRoutes.size() && parentValidHaplotypes.containsAll(validRoutes)) {
+                    queue.add(new Pair<>(forward ? new Route<>(path, candidate) : new Route<>(candidate, path), parentValidHaplotypes));
+                } else {
+                    final Set<HaplotypeRoute> newValidHaplotypeRoutes = new HashSet<>(validRoutes.size());
+                    for (final HaplotypeRoute hr : validRoutes)
+                        if (parentValidHaplotypes.contains(hr))
+                            newValidHaplotypeRoutes.add(hr);
+                    if (newValidHaplotypeRoutes.size() == 0)
+                        return;
+                    queue.add(new Pair<>(forward ? new Route<>(path, candidate) : new Route<>(candidate, path), newValidHaplotypeRoutes));
+                }
+        }
+    }
+
+    public List<Haplotype> getHaplotypeList() {
+        return new ArrayList<>(haplotypeGraph.getHaplotypes());
+    }
+
+    /**
+     * Returns the haplotype graph associated with this instance.
+     * @return never {@code null}
+     */
+    public HaplotypeGraph getHaplotypeGraph() {
+        return haplotypeGraph;
+    }
+}
\ No newline at end of file
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
index 360d0979f..d795f5b90 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
@@ -154,6 +154,17 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
     @Output(doc="File to which variants should be written")
     protected VariantContextWriter vcfWriter = null;
 
+    @Hidden
+    @Advanced
+    @Argument(fullName="likelihoodCalculationEngine",shortName="likelihoodEngine",
+            doc="what likelihood calculation engine to use to calculate the relative likelihood of reads vs haplotypes",required=false)
+    protected LikelihoodCalculationEngine.Implementation likelihoodEngineImplementation = LikelihoodCalculationEngine.Implementation.PairHMM;
+
+    @Hidden
+    @Advanced
+    @Argument(fullName="heterogeneousKmerSizeResolution",shortName="hksr",doc="how to solve heterogeneous kmer situations using the fast method",required=false)
+    protected HeterogeneousKmerSizeResolution heterogeneousKmerSizeResultion = HeterogeneousKmerSizeResolution.COMBO_MIN;
+
     @Output(fullName="graphOutput", shortName="graph", doc="File to which debug assembly graph information should be written", required = false, defaultToStdout = false)
     protected PrintStream graphWriter = null;
 
@@ -200,6 +211,8 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
      */
     @ArgumentCollection
     protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
+    private double log10GlobalReadMismappingRate;
+
     public RodBinding<VariantContext> getDbsnpRodBinding() { return dbsnp.dbsnp; }
 
     /**
@@ -479,7 +492,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
      */
     @Advanced
     @Argument(fullName = "pcr_indel_model", shortName = "pcrModel", doc = "The PCR indel model to use", required = false)
-    public LikelihoodCalculationEngine.PCR_ERROR_MODEL pcrErrorModel = LikelihoodCalculationEngine.PCR_ERROR_MODEL.CONSERVATIVE;
+    public PairHMMLikelihoodCalculationEngine.PCR_ERROR_MODEL pcrErrorModel = PairHMMLikelihoodCalculationEngine.PCR_ERROR_MODEL.CONSERVATIVE;
 
     // -----------------------------------------------------------------------------------------------
     // done with Haplotype caller parameters
@@ -498,10 +511,8 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
     // the genotyping engine
     private GenotypingEngine genotypingEngine = null;
 
-    private VariantAnnotatorEngine annotationEngine = null;
-
     // fasta reference reader to supplement the edges of the reference sequence
-    private CachingIndexedFastaSequenceFile referenceReader;
+    protected CachingIndexedFastaSequenceFile referenceReader;
 
     // reference base padding size
     private static final int REFERENCE_PADDING = 500;
@@ -563,7 +574,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
         }
 
         // initialize the output VCF header
-        annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit());
+        final VariantAnnotatorEngine annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit());
 
         Set<VCFHeaderLine> headerInfo = new HashSet<>();
 
@@ -624,7 +635,6 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
         if ( phredScaledGlobalReadMismappingRate < 0 ) phredScaledGlobalReadMismappingRate = -1;
 
         // configure the global mismapping rate
-        final double log10GlobalReadMismappingRate;
         if ( phredScaledGlobalReadMismappingRate < 0 ) {
             log10GlobalReadMismappingRate = - Double.MAX_VALUE;
         } else {
@@ -633,7 +643,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
         }
 
         // create our likelihood calculation engine
-        likelihoodCalculationEngine = new LikelihoodCalculationEngine( (byte)gcpHMM, DEBUG, pairHMM, log10GlobalReadMismappingRate, noFpga, pcrErrorModel );
+        likelihoodCalculationEngine = createLikelihoodCalculationEngine();
 
         final MergeVariantsAcrossHaplotypes variantMerger = mergeVariantsViaLD ? new LDMerger(DEBUG, 10, 1) : new MergeVariantsAcrossHaplotypes();
 
@@ -651,6 +661,26 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
                 getToolkit().getGenomeLocParser());
     }
 
+    /**
+     * Instantiates the appropriate likelihood calculation engine.
+     *
+     * @return never {@code null}.
+     */
+    private LikelihoodCalculationEngine createLikelihoodCalculationEngine() {
+        switch (likelihoodEngineImplementation) {
+            case PairHMM:
+                return new PairHMMLikelihoodCalculationEngine( (byte)gcpHMM, DEBUG, pairHMM, log10GlobalReadMismappingRate, noFpga, pcrErrorModel );
+            case GraphBased:
+                return new GraphBasedLikelihoodCalculationEngine( (byte)gcpHMM,log10GlobalReadMismappingRate,heterogeneousKmerSizeResultion,DEBUG,debugGraphTransformations);
+            case Random:
+                return new RandomLikelihoodCalculationEngine();
+            default:
+                //Note: we do not include in the error message list as it is of no grand public interest.
+                throw new UserException("Unsupported likelihood calculation engine '" + likelihoodCalculationEngine +
+                        "'. Please use one of the following instead: 'PairHMM' and 'GraphBased'.");
+        }
+    }
+
     //---------------------------------------------------------------------------------------------------------------
     //
     // isActive
@@ -748,7 +778,8 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
         }
 
         // run the local assembler, getting back a collection of information on how we should proceed
-        final AssemblyResult assemblyResult = assembleReads(originalActiveRegion, activeAllelesToGenotype);
+        final AssemblyResultSet assemblyResult = assembleReads(originalActiveRegion, activeAllelesToGenotype);
+        final ActiveRegion regionForGenotyping = assemblyResult.getRegionForGenotyping();
 
         // abort early if something is out of the acceptable range
         if( ! assemblyResult.isVariationPresent() ) {
@@ -758,17 +789,26 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
         if (dontGenotype) return NO_CALLS; // user requested we not proceed
 
         // filter out reads from genotyping which fail mapping quality based criteria
-        final Collection<GATKSAMRecord> filteredReads = filterNonPassingReads( assemblyResult.regionForGenotyping );
+        final Collection<GATKSAMRecord> filteredReads = filterNonPassingReads( regionForGenotyping );
         final Map<String, List<GATKSAMRecord>> perSampleFilteredReadList = splitReadsBySample( filteredReads );
 
-        if( assemblyResult.regionForGenotyping.size() == 0 ) {
+        if( regionForGenotyping.size() == 0 ) {
             // no reads remain after filtering so nothing else to do!
             return referenceModelForNoVariation(originalActiveRegion, false);
         }
 
         // evaluate each sample's reads against all haplotypes
         //logger.info("Computing read likelihoods with " + assemblyResult.regionForGenotyping.size() + " reads");
-        final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap = likelihoodCalculationEngine.computeReadLikelihoods( assemblyResult.haplotypes, splitReadsBySample( assemblyResult.regionForGenotyping.getReads() ) );
+        final List<Haplotype> haplotypes = assemblyResult.getHaplotypeList();
+        final Map<String,List<GATKSAMRecord>> reads = splitReadsBySample( regionForGenotyping.getReads() );
+
+        // Calculate the likelihoods: CPU intesive part.
+        final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap =
+                likelihoodCalculationEngine.computeReadLikelihoods(assemblyResult,reads);
+
+
+
+
 
         // Note: we used to subset down at this point to only the "best" haplotypes in all samples for genotyping, but there
         //  was a bad interaction between that selection and the marginalization that happens over each event when computing
@@ -777,12 +817,12 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
         //  in the genotyping, but we lose information if we select down to a few haplotypes.  [EB]
 
         final GenotypingEngine.CalledHaplotypes calledHaplotypes = genotypingEngine.assignGenotypeLikelihoods( UG_engine,
-                assemblyResult.haplotypes,
+                haplotypes,
                 stratifiedReadMap,
                 perSampleFilteredReadList,
-                assemblyResult.fullReferenceWithPadding,
-                assemblyResult.paddedReferenceLoc,
-                assemblyResult.regionForGenotyping.getLocation(),
+                assemblyResult.getFullReferenceWithPadding(),
+                assemblyResult.getPaddedReferenceLoc(),
+                regionForGenotyping.getLocation(),
                 getToolkit().getGenomeLocParser(),
                 metaDataTracker,
                 activeAllelesToGenotype );
@@ -790,9 +830,9 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
         // TODO -- must disable if we are doing NCT, or set the output type of ! presorted
         if ( bamWriter != null ) {
             haplotypeBAMWriter.writeReadsAlignedToHaplotypes(
-                    assemblyResult.haplotypes,
-                    assemblyResult.paddedReferenceLoc,
-                    assemblyResult.haplotypes,
+                    haplotypes,
+                    assemblyResult.getPaddedReferenceLoc(),
+                    haplotypes,
                     calledHaplotypes.getCalledHaplotypes(),
                     stratifiedReadMap);
         }
@@ -804,50 +844,14 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
                 // no called all of the potential haplotypes
                 return referenceModelForNoVariation(originalActiveRegion, false);
             } else
-                return referenceConfidenceModel.calculateRefConfidence(assemblyResult.getRefHaplotype(),
-                        calledHaplotypes.getCalledHaplotypes(), assemblyResult.paddedReferenceLoc, assemblyResult.regionForGenotyping,
+                return referenceConfidenceModel.calculateRefConfidence(assemblyResult.getReferenceHaplotype(),
+                        calledHaplotypes.getCalledHaplotypes(), assemblyResult.getPaddedReferenceLoc(), regionForGenotyping,
                         stratifiedReadMap, calledHaplotypes.getCalls());
         } else {
             return calledHaplotypes.getCalls();
         }
     }
 
-    private final static class AssemblyResult {
-        final List<Haplotype> haplotypes;
-        final ActiveRegion regionForGenotyping;
-        final byte[] fullReferenceWithPadding;
-        final GenomeLoc paddedReferenceLoc;
-        final boolean variationPresent;
-        final Haplotype refHaplotype;
-
-        private AssemblyResult(List<Haplotype> haplotypes, ActiveRegion regionForGenotyping, byte[] fullReferenceWithPadding, GenomeLoc paddedReferenceLoc, boolean variationPresent) {
-            this.haplotypes = haplotypes;
-            this.regionForGenotyping = regionForGenotyping;
-            this.fullReferenceWithPadding = fullReferenceWithPadding;
-            this.paddedReferenceLoc = paddedReferenceLoc;
-            this.variationPresent = variationPresent;
-
-            Haplotype firstRefHaplotype = null;
-            for ( final Haplotype h : haplotypes ) {
-                if ( h.isReference() ) {
-                    if ( firstRefHaplotype != null ) throw new IllegalArgumentException("Found two haplotypes marked as reference " + firstRefHaplotype + " and " + h);
-                    firstRefHaplotype = h;
-                }
-            }
-
-            if ( firstRefHaplotype == null ) throw new IllegalArgumentException("Couldn't find a reference haplotype in " + haplotypes);
-            this.refHaplotype = firstRefHaplotype;
-        }
-
-        public Haplotype getRefHaplotype() {
-            return refHaplotype;
-        }
-
-        public boolean isVariationPresent() {
-            return variationPresent && haplotypes.size() > 1;
-        }
-    }
-
     /**
      * High-level function that runs the assembler on the active region reads,
      * returning a data structure with the resulting information needed
@@ -857,7 +861,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
      * @param activeAllelesToGenotype additional alleles we might need to genotype (can be empty)
      * @return the AssemblyResult describing how to proceed with genotyping
      */
-    protected AssemblyResult assembleReads(final ActiveRegion activeRegion, final List<VariantContext> activeAllelesToGenotype) {
+    protected AssemblyResultSet assembleReads(final ActiveRegion activeRegion, final List<VariantContext> activeAllelesToGenotype) {
         // Create the reference haplotype which is the bases from the reference that make up the active region
         finalizeActiveRegion(activeRegion); // handle overlapping fragments, clip adapter and low qual tails
 
@@ -871,13 +875,19 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
             readErrorCorrector = new ReadErrorCorrector(kmerLengthForReadErrorCorrection, MIN_TAIL_QUALITY_WITH_ERROR_CORRECTION, minObservationsForKmerToBeSolid, DEBUG, fullReferenceWithPadding);
 
         try {
-            final List<Haplotype> haplotypes = assemblyEngine.runLocalAssembly( activeRegion, referenceHaplotype, fullReferenceWithPadding, paddedReferenceLoc, activeAllelesToGenotype, readErrorCorrector );
-            if ( ! dontTrimActiveRegions ) {
-                return trimActiveRegion(activeRegion, haplotypes, activeAllelesToGenotype, fullReferenceWithPadding, paddedReferenceLoc);
-            } else {
-                // we don't want to trim active regions, so go ahead and use the old one
-                return new AssemblyResult(haplotypes, activeRegion, fullReferenceWithPadding, paddedReferenceLoc, true);
-            }
+            final AssemblyResultSet assemblyResultSet = assemblyEngine.runLocalAssembly( activeRegion, referenceHaplotype, fullReferenceWithPadding, paddedReferenceLoc, activeAllelesToGenotype,readErrorCorrector );
+            assemblyResultSet.debugDump(logger);
+
+            if (  ! dontTrimActiveRegions ) {
+                final ActiveRegion trimmedActiveRegion = trimActiveRegion(assemblyResultSet,activeAllelesToGenotype);
+                if (trimmedActiveRegion != null)
+                    return trimAssemblyResultSet(assemblyResultSet, trimmedActiveRegion);
+                else {
+                    assemblyResultSet.resetVariationPresent();
+                    return assemblyResultSet;
+                }
+            } else
+                return assemblyResultSet;
         } catch ( final Exception e ) {
             // Capture any exception that might be thrown, and write out the assembly failure BAM if requested
             if ( captureAssemblyFailureBAM ) {
@@ -948,72 +958,89 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
         return map;
     }
 
-    /**
-     * Trim down the active region to just enough to properly genotype the events among the haplotypes
-     *
-     * @param originalActiveRegion our full active region
-     * @param haplotypes the list of haplotypes we've created from assembly
-     * @param activeAllelesToGenotype additional alleles we might need to genotype (can be empty)
-     * @param fullReferenceWithPadding the reference bases over the full padded location
-     * @param paddedReferenceLoc the span of the reference bases
-     * @return an AssemblyResult containing the trimmed active region with all of the reads we should use
-     *         trimmed down as well, and a revised set of haplotypes.  If trimming down the active region results
-     *         in only the reference haplotype over the non-extended active region, returns null.
-     */
-    private AssemblyResult trimActiveRegion(final ActiveRegion originalActiveRegion,
-                                            final List<Haplotype> haplotypes,
-                                            final List<VariantContext> activeAllelesToGenotype,
-                                            final byte[] fullReferenceWithPadding,
-                                            final GenomeLoc paddedReferenceLoc) {
-        if ( DEBUG ) logger.info("Trimming active region " + originalActiveRegion + " with " + haplotypes.size() + " haplotypes");
-
-        EventMap.buildEventMapsForHaplotypes(haplotypes, fullReferenceWithPadding, paddedReferenceLoc, DEBUG);
-        final TreeSet<VariantContext> allVariantsWithinFullActiveRegion = EventMap.getAllVariantContexts(haplotypes);
+    private ActiveRegion trimActiveRegion(final AssemblyResultSet resultSet, final Collection<VariantContext> activeAllelesToGenotype) {
+        if ( DEBUG ) logger.info("Trimming active region " + resultSet.getRegionForGenotyping() + " with " + resultSet.getHaplotypeCount() + " haplotypes");
+        final List<Haplotype> haplotypeList = resultSet.getHaplotypeList();
+        final ActiveRegion originalGenotypingRegion = resultSet.getRegionForGenotyping();
+        EventMap.buildEventMapsForHaplotypes(haplotypeList, resultSet.getFullReferenceWithPadding(), resultSet.getPaddedReferenceLoc(), DEBUG);
+        final TreeSet<VariantContext> allVariantsWithinFullActiveRegion = EventMap.getAllVariantContexts(haplotypeList);
         allVariantsWithinFullActiveRegion.addAll(activeAllelesToGenotype);
-        final ActiveRegion trimmedActiveRegion = trimmer.trimRegion(originalActiveRegion, allVariantsWithinFullActiveRegion, false); // TODO -- should pass emitReferenceConfidence()
 
+        final ActiveRegion trimmedActiveRegion = trimmer.trimRegion(originalGenotypingRegion, allVariantsWithinFullActiveRegion,false);
         if ( trimmedActiveRegion == null ) {
             // there were no variants found within the active region itself, so just return null
             if ( DEBUG ) logger.info("No variation found within the active region, skipping the region :-)");
-            return new AssemblyResult(haplotypes, originalActiveRegion, fullReferenceWithPadding, paddedReferenceLoc, false);
-        }
-
-        // trim down the haplotypes
-        final Set<Haplotype> haplotypeSet = new HashSet<>(haplotypes.size());
-        for ( final Haplotype h : haplotypes ) {
-            final Haplotype trimmed = h.trim(trimmedActiveRegion.getExtendedLoc());
-            if ( trimmed != null ) {
-                haplotypeSet.add(trimmed);
-            } else if ( DEBUG ) {
-                logger.info("Throwing out haplotype " + h + " with cigar " + h.getCigar() + " because it starts with or ends with an insertion or deletion when trimmed to " + trimmedActiveRegion.getExtendedLoc());
-            }
-        }
-
-        // create the final list of trimmed haplotypes
-        final List<Haplotype> trimmedHaplotypes = new ArrayList<>(haplotypeSet);
-
-        // sort haplotypes to take full advantage of haplotype start offset optimizations in PairHMM
-        Collections.sort( trimmedHaplotypes, new HaplotypeSizeAndBaseComparator() );
-
-        if ( DEBUG ) logger.info("Trimmed region to " + trimmedActiveRegion.getLocation() + " size " + trimmedActiveRegion.getLocation().size() + " reduced number of haplotypes from " + haplotypes.size() + " to only " + trimmedHaplotypes.size());
-        if ( DEBUG ) {
-            for ( final Haplotype remaining: trimmedHaplotypes ) {
-                logger.info("  Remains: " + remaining + " cigar " + remaining.getCigar());
-            }
+            return null;
         }
 
         // trim down the reads and add them to the trimmed active region
-        final List<GATKSAMRecord> trimmedReads = new ArrayList<>(originalActiveRegion.getReads().size());
-        for( final GATKSAMRecord read : originalActiveRegion.getReads() ) {
-            final GATKSAMRecord clippedRead = ReadClipper.hardClipToRegion( read, trimmedActiveRegion.getExtendedLoc().getStart(), trimmedActiveRegion.getExtendedLoc().getStop() );
-            if( trimmedActiveRegion.readOverlapsRegion(clippedRead) && clippedRead.getReadLength() > 0 ) {
+        final List<GATKSAMRecord> trimmedReads = new ArrayList<>(originalGenotypingRegion.getReads().size());
+        for( final GATKSAMRecord read : originalGenotypingRegion.getReads() ) {
+            final GATKSAMRecord clippedRead = ReadClipper.hardClipToRegion( read,
+                    trimmedActiveRegion.getExtendedLoc().getStart(), trimmedActiveRegion.getExtendedLoc().getStop() );
+            if( trimmedActiveRegion.readOverlapsRegion(clippedRead) && clippedRead.getReadLength() > 0 )
                 trimmedReads.add(clippedRead);
-            }
         }
         trimmedActiveRegion.clearReads();
         trimmedActiveRegion.addAll(ReadUtils.sortReadsByCoordinate(trimmedReads));
 
-        return new AssemblyResult(trimmedHaplotypes, trimmedActiveRegion, fullReferenceWithPadding, paddedReferenceLoc, true);
+        return trimmedActiveRegion;
+    }
+
+
+    /**
+     * Trims a assembly result set according to the active-region trimming.
+     *
+     * @param resultSet the original assembly result set.
+     * @param trimmedActiveRegion the trimmed active region to trim to.
+     * @return the assembly result set trimmed.
+     */
+    private AssemblyResultSet trimAssemblyResultSet(final AssemblyResultSet resultSet, final ActiveRegion trimmedActiveRegion) {
+        if ( DEBUG ) logger.info("Trimming active region " + resultSet.getRegionForGenotyping() + " with " + resultSet.getHaplotypeCount() + " haplotypes");
+
+        final List<Haplotype> haplotypeList = resultSet.getHaplotypeList();
+
+        // trim down the haplotypes
+        final Map<Haplotype,Haplotype> originalByTrimmedHaplotypes = new HashMap<>();
+
+        for ( final Haplotype h : haplotypeList ) {
+            final Haplotype trimmed = h.trim(trimmedActiveRegion.getExtendedLoc());
+
+            if ( trimmed != null ) {
+                if (originalByTrimmedHaplotypes.containsKey(trimmed)) {
+                    if (trimmed.isReference()) {
+                        originalByTrimmedHaplotypes.remove(trimmed);
+                        originalByTrimmedHaplotypes.put(trimmed, h);
+                    }
+                } else
+                    originalByTrimmedHaplotypes.put(trimmed,h);
+            } else if (h.isReference())
+                throw new IllegalStateException("trimming eliminates the reference haplotype");
+            else if ( DEBUG ) {
+                logger.info("Throwing out haplotype " + h + " with cigar " + h.getCigar() +
+                        " because it starts with or ends with an insertion or deletion when trimmed to " +
+                        trimmedActiveRegion.getExtendedLoc());
+            }
+        }
+
+        // create the final list of trimmed haplotypes
+        final List<Haplotype> trimmedHaplotypes = new ArrayList<>(originalByTrimmedHaplotypes.keySet());
+
+        // resort the trimmed haplotypes.
+        Collections.sort(trimmedHaplotypes,new HaplotypeSizeAndBaseComparator());
+        final Map<Haplotype,Haplotype> sortedOriginalByTrimmedHaplotypes = new LinkedHashMap<>(trimmedHaplotypes.size());
+        for (final Haplotype trimmed : trimmedHaplotypes)
+            sortedOriginalByTrimmedHaplotypes.put(trimmed,originalByTrimmedHaplotypes.get(trimmed));
+
+
+        if ( DEBUG ) logger.info("Trimmed region to " + trimmedActiveRegion.getLocation() + " size " +
+                trimmedActiveRegion.getLocation().size() + " reduced number of haplotypes from " +
+                haplotypeList.size() + " to only " + trimmedHaplotypes.size());
+        if ( DEBUG )
+            for ( final Haplotype remaining: trimmedHaplotypes )
+                logger.info("Remains: " + remaining + " cigar " + remaining.getCigar());
+
+        return resultSet.trimTo(trimmedActiveRegion,sortedOriginalByTrimmedHaplotypes);
     }
 
     //---------------------------------------------------------------------------------------------------------------
@@ -1039,7 +1066,9 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
     public void onTraversalDone(Integer result) {
         if ( emitReferenceConfidence == ReferenceConfidenceMode.GVCF ) ((GVCFWriter)vcfWriter).close(false); // GROSS -- engine forces us to close our own VCF writer since we wrapped it
         referenceConfidenceModel.close();
-        likelihoodCalculationEngine.close();
+        //TODO remove the need to call close here for debugging, the likelihood output stream should be managed
+        //TODO (open & close) at the walker, not the engine.
+        //likelihoodCalculationEngine.close();
         logger.info("Ran local assembly on " + result + " active regions");
     }
 
@@ -1050,6 +1079,8 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
     //---------------------------------------------------------------------------------------------------------------
 
     private void finalizeActiveRegion( final ActiveRegion activeRegion ) {
+        if (activeRegion.isFinalized()) return;
+
         if( DEBUG ) { logger.info("Assembling " + activeRegion.getLocation() + " with " + activeRegion.size() + " reads:    (with overlap region = " + activeRegion.getExtendedLoc() + ")"); }
 
         // Loop through the reads hard clipping the adaptor and low quality tails
@@ -1094,6 +1125,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
 
         activeRegion.clearReads();
         activeRegion.addAll(downsampledReads);
+        activeRegion.setFinalized(true);
     }
 
     private Set<GATKSAMRecord> filterNonPassingReads( final ActiveRegion activeRegion ) {
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeRoute.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeRoute.java
new file mode 100644
index 000000000..5887864e3
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeRoute.java
@@ -0,0 +1,129 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+*
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
+
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.MultiSampleEdge;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.Route;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex;
+
+import java.util.*;
+
+/**
+ * Graph route that represent an haplotype on the haplotype assembly graph.
+ *
+ * @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.com&gt;
+ */
+public class HaplotypeRoute extends Route<MultiDeBruijnVertex,MultiSampleEdge> {
+
+    protected final Set<MultiDeBruijnVertex> vertexSet;
+
+    protected final Map<MultiDeBruijnVertex,Integer> vertexOrder;
+
+    protected final Set<MultiDeBruijnVertex> forkAndJoins;
+
+    /**
+     * Constructs a HaplotypeRoute given its route.
+     *
+     * @param route the haplotype route.
+     */
+    public HaplotypeRoute(final Route<MultiDeBruijnVertex, MultiSampleEdge> route) {
+        super(route);
+        vertexOrder = new LinkedHashMap<>(route.length() + 1);
+        int nextOrder = 0;
+        vertexOrder.put(getFirstVertex(),nextOrder++);
+        for (final MultiSampleEdge edge : edgesInOrder)
+            vertexOrder.put(graph.getEdgeTarget(edge), nextOrder++);
+        Route<MultiDeBruijnVertex,MultiSampleEdge> currentRoute = this;
+        forkAndJoins = new HashSet<>(route.length());
+        while (currentRoute != null) {
+          if (currentRoute.lastVertexIsForkOrJoin())
+              forkAndJoins.add(currentRoute.getLastVertex());
+          currentRoute = currentRoute.getPrefixRouteWithLastVertexThatIsForkOrJoin();
+        }
+        vertexSet = Collections.unmodifiableSet(new HashSet<>(vertexOrder.keySet()));
+    }
+
+
+
+    @SuppressWarnings("unused")
+    public Route<MultiDeBruijnVertex,MultiSampleEdge> subRoute(final MultiDeBruijnVertex start, final MultiDeBruijnVertex end) {
+       final Integer startOrder = vertexOrder.get(start);
+       final Integer endOrder = vertexOrder.get(end);
+       if (startOrder == null || endOrder == null)
+           return null;
+       else if (startOrder > endOrder)
+           return null;
+       else {
+           Route<MultiDeBruijnVertex,MultiSampleEdge> result = new Route<>(start,graph);
+           for (final MultiSampleEdge edge : edgesInOrder.subList(startOrder,endOrder))
+                result = new Route(result,edge);
+           return result;
+       }
+    }
+
+    /**
+     * Returns the set of vertex on the route.
+     * @return read only, never {@code null} vertex set.
+     */
+    public Set<MultiDeBruijnVertex> vertexSet() {
+        return vertexSet;
+    }
+
+
+    /**
+     * Returns the position of the vertex in the route.
+     *
+     * @param vertex the query vertex.
+     *
+     * @throws NullPointerException if {@code vertex} is {@code null}.
+     *
+     * @return -1 if there is no such a vertex in the route, otherwise a number between 0 and {@link #length()} - 1.
+     */
+    public int getVertexPosition(final MultiDeBruijnVertex vertex) {
+        final Integer result = vertexOrder.get(vertex);
+        return result == null ? -1 : result;
+    }
+}
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HeterogeneousKmerSizeResolution.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HeterogeneousKmerSizeResolution.java
new file mode 100644
index 000000000..b56d942ae
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HeterogeneousKmerSizeResolution.java
@@ -0,0 +1,110 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*  
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*  
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*  
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*  
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*  
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. 
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.  
+*  
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY 
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*  
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*  
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*  
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*  
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt. 
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. 
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
+
+/**
+ * How to resolve the haplotype graph when haplotypes where generated from a mixture of different kmerSizes.
+ */
+public enum HeterogeneousKmerSizeResolution {
+
+    /**
+     * Combine haplotypes using a haplotype graph with the largest kmerSize amongst the ones that generated some haplotype.
+     */
+    COMBO_MAX,
+
+    /**
+     * Combine haplotypes using a haplotype graph with the largest kmerSize amongst the ones that generated some haplotype.
+     */
+    COMBO_MIN,
+
+    /**
+     * Take just the haplotypes from largest kmersize that generated any.
+     */
+    MAX_ONLY,
+
+    /**
+     * Take just the haplotypes from the smallest kmerSize that generated any.
+     */
+    @SuppressWarnings("unused")
+    MIN_ONLY;
+
+    /**
+     * Indicates whether we should use the maximum kmerSize for the haplotypeGraph or not.
+     *
+     * @return true if we need to use the maximum, false otherwise.
+     */
+    public boolean useMaximum() {
+        switch (this) {
+            case COMBO_MAX: return true;
+            case MAX_ONLY: return true;
+            default: return false;
+        }
+    }
+
+    /**
+     * Indicates whether we should use the minimum kmerSize for the haplotypeGraph or not.
+     *
+     * @return true if we need to use the minimum, false otherwise.
+     */
+    @SuppressWarnings("unused")
+    public boolean useMinimum() {
+        return ! useMaximum();
+    }
+
+    /**
+     * Tell whether this policy combines kmer-sizes or not.
+     * @return true iff it does.
+     */
+    public boolean combinesKmerSizes() {
+        switch (this) {
+            case COMBO_MAX: return true;
+            case COMBO_MIN: return true;
+            default: return false;
+        }
+
+    }
+}
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Kmer.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Kmer.java
index 2e757722b..056f7991f 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Kmer.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Kmer.java
@@ -49,8 +49,6 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
 import com.google.java.contract.Requires;
 
 import java.util.Arrays;
-import java.util.HashMap;
-import java.util.Map;
 
 /**
  * Fast wrapper for byte[] kmers
@@ -68,7 +66,7 @@ import java.util.Map;
  */
 public class Kmer {
     // this values may be updated in the course of interacting with this kmer
-    private byte[] bases;
+    protected byte[] bases;
     protected int start;
 
     // two constants
@@ -126,6 +124,16 @@ public class Kmer {
         this.hash = kmer.hash;
     }
 
+    public Kmer(final Kmer kmer, final byte nextChar) {
+        final byte[] sequence = new byte[kmer.length];
+        System.arraycopy(kmer.bases,kmer.start + 1,sequence,0,kmer.length - 1);
+        sequence[kmer.length - 1] = nextChar;
+        bases = sequence;
+        start = 0;
+        length = kmer.length;
+        hash = myHashCode(bases,start,length);
+    }
+
     /**
      * Create a derived shallow kmer that starts at newStart and has newLength bases
      * @param newStart the new start of kmer, where 0 means that start of the kmer, 1 means skip the first base
@@ -144,6 +152,7 @@ public class Kmer {
      * @return a non-null byte[] containing length() bases of this kmer, regardless of how this kmer was created
      */
     public byte[] bases() {
+
         if ( start != 0 || bases.length != length ) {
             // update operation.  Rip out the exact byte[] and update start so we don't ever do this again
             bases = Arrays.copyOfRange(bases, start, start + length);
@@ -153,6 +162,44 @@ public class Kmer {
         return bases;
     }
 
+
+    /**
+     * Copies kmer bytes into a byte array.
+     *
+     * @param start first position of the kmer to copy
+     * @param dest  what array to copy into
+     * @param offset what position the first byte to copy should go into the destination array.
+     * @param length how many bytes to copy
+     *
+     * @throws IllegalArgumentException if <code>start</code> is negative or combined with <code>length</code> it goes
+     *        beyond the end of the kmer. Also if <code>length</code> is negative.
+     * @throws NullPointerException if dest is <code>null</code>
+     * @throws ArrayIndexOutOfBoundsException if dest does not have capacity to received the data.
+     */
+    public void copyTo(final int start, final byte[] dest, final int offset, final int length) {
+        if (start + length > this.length) {
+            throw new IllegalArgumentException("request goes beyond end of kmer");
+        }
+        if (length < 0) {
+            throw new IllegalArgumentException("requested length cannot be negative");
+        }
+        System.arraycopy(bases,this.start + start,dest,offset,length);
+    }
+
+    /**
+     * Copies kmer bytes into a byte array.
+     *
+     * @param dest  what array to copy into
+     * @param offset what position the first byte to copy should go into the destination array.
+     *
+     * @throws IllegalArgumentException if <code>start</code> is negative or combined with <code>length</code> it goes
+     *        beyond the end of the kmer. Also if <code>length</code> is negative.
+     * @throws NullPointerException if dest is <code>null</code>
+     */
+    public void copyTo(final byte[] dest, final int offset) {
+        System.arraycopy(bases,start,dest,offset,length);
+    }
+
     /**
      * Backdoor method for fast base peeking: avoids copying like bases() and doesn't modify internal state.
      * Intended to be used for fast computation of neighboring kmers
@@ -219,13 +266,13 @@ public class Kmer {
 
     @Override
     public String toString() {
-        return "Kmer{" + new String(bases()) + "}";
+        return "Kmer{" + new String(bases,start,length) + "}";
     }
 
     @Override
     public boolean equals(Object o) {
         if (this == o) return true;
-        if (o == null || getClass() != o.getClass()) return false;
+        if (o == null || !Kmer.class.isAssignableFrom(o.getClass())) return false;
 
         final Kmer kmer = (Kmer) o;
 
@@ -264,4 +311,23 @@ public class Kmer {
 
         return result;
     }
+
+    public byte base(final int i) {
+        return bases[start + i];
+    }
+
+    public Kmer shift(final byte nextChar) {
+        if (bases.length > start + length && bases[start + length] == nextChar) {
+           return new Kmer(bases,start + 1,length);
+        } else {
+           final byte[] newBases = new byte[length];
+           System.arraycopy(bases,start + 1,newBases,0,length - 1);
+           newBases[length - 1] = nextChar;
+           return new Kmer(newBases,0,length);
+        }
+    }
+
+    public byte lastBase() {
+        return bases[start + length - 1];
+    }
 }
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequence.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequence.java
new file mode 100644
index 000000000..a6c35bce0
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequence.java
@@ -0,0 +1,461 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*  
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*  
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*  
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*  
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*  
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. 
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.  
+*  
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY 
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*  
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*  
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*  
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*  
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt. 
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. 
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
+
+
+import com.sun.istack.internal.NotNull;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.haplotype.Haplotype;
+
+import java.lang.reflect.Array;
+import java.util.*;
+
+/**
+ * Represent a sequence of kmers where any two consecutive kmers overlap in kmer length - 1 elements.
+ *
+ * @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.com&gt;
+ */
+public class KmerSequence implements List<Kmer> {
+    private final byte[] sequence;
+    private final int start;
+    private final int size;
+    private final int kmerSize;
+    private final int rawLength;
+
+    /**
+     * Creates a kmer sequence from a read's sequence.
+     *
+     * @param read the read to represent as a sequence of kmers.
+     * @param kmerSize the kmer size.
+     */
+    public KmerSequence(final SAMRecord read, final int kmerSize) {
+        this(read.getReadBases(), kmerSize);
+    }
+
+    /**
+     * Creates a kmer sequence from a haplotype's sequence.
+     *
+     * @param hap the haplotype to represent as a sequence of kmers.
+     * @param kmerSize the kmer size.
+     */
+    public KmerSequence(final Haplotype hap, final int kmerSize) {
+        this(hap.getBases(), kmerSize);
+    }
+
+    /**
+     * Creates a kmer sequence out of a byte sequence.
+     *
+     * @param sequence the byte array to represent as a kmer sequence.
+     * @param kmerSize the kmer size.
+     */
+    public KmerSequence(final byte[] sequence, final int kmerSize) {
+        this(sequence,0,Math.max(0,sequence.length - kmerSize + 1),kmerSize, sequence.length);
+    }
+
+
+    /**
+     * Creates a kmer sequence out of a range of a byte array
+     *
+     * @param sequence the input array.
+     * @param start inclusive first position of the array that maps to the first position in the first kmer.
+     * @param size number kmers in the output.
+     * @param kmerSize kmer length in bases.
+     * @param rawLength the of the range in bases.
+     */
+    protected KmerSequence(final byte[] sequence, final int start, final int size, final int kmerSize, final int rawLength) {
+        if (sequence == null) {
+            throw new IllegalArgumentException("start must be 0 or greater");
+        }
+        if (rawLength > sequence.length - start) {
+            throw new IllegalArgumentException("the raw sequence length goes beyond the array capacity");
+        }
+        if (size < 0) {
+            throw new IllegalArgumentException("the length cannot be negative");
+        }
+        if (start < 0) {
+            throw new IllegalArgumentException("start must be 0 or greater");
+        }
+        if (size > 0 && size + kmerSize - 1 > rawLength) {
+            throw new IllegalArgumentException(
+                    String.format("the kmerSize (%d) + size (%d) - 1 cannot be larger than rawLength (%d)",kmerSize,size,rawLength) );
+        }
+        this.sequence = sequence;
+        this.start = start;
+        this.size = size;
+        this.kmerSize = kmerSize;
+        this.rawLength = rawLength;
+    }
+
+    public int kmerSize() {
+        return kmerSize;
+    }
+
+    public KmerSequence subsequence(final int from, final int to) {
+        if (from < 0 || from > to) {
+            throw new IllegalArgumentException();
+        }
+        if (to > size) {
+            throw new IllegalArgumentException();
+        }
+        return new KmerSequence(sequence,this.start + from,to - from,kmerSize,rawLength - from - (size - to));
+    }
+
+
+    @Override
+    public int size() {
+        return size;
+    }
+
+    @Override
+    public boolean isEmpty() {
+        return size == 0;
+    }
+
+    @Override
+    public boolean contains(final Object o) {
+        if (o instanceof Kmer) {
+            if (o instanceof MyKmer) {
+                final MyKmer k = (MyKmer) o;
+                if (k.bases == sequence && k.start >= start && k.length == kmerSize && k.start < start + size) {
+                    return true;
+                }
+            }
+            final Kmer k = (Kmer) o;
+            if (k.length != kmerSize) {
+                return false;
+            }
+            for (int i = 0; i < size; i++) {
+                int j;
+                for (j = 0; j < kmerSize; j++) {
+                    if (sequence[start + i + j] != k.bases[k.start + j]) {
+                         break;
+                    }
+                }
+                if (j == kmerSize) {
+                    return true;
+                }
+            }
+            return false;
+        } else {
+            return false;
+        }
+    }
+
+    @Override
+    @NotNull
+    public Iterator<Kmer> iterator() {
+        return new Iterator<Kmer>() {
+
+            private int offset = 0;
+
+            @Override
+            public boolean hasNext() {
+                return offset < size;
+            }
+
+            @Override
+            public Kmer next() {
+                return new Kmer(sequence,start + offset,kmerSize);
+            }
+
+            @Override
+            public void remove() {
+                throw new UnsupportedOperationException();
+            }
+        };
+    }
+
+    @NotNull
+    @Override
+    public Object[] toArray() {
+        return toArray(new Kmer[size()]);
+    }
+
+    @Override
+    @NotNull
+    @SuppressWarnings("unchecked")
+    public <T> T[] toArray(@NotNull final T[] a) {
+        if (a == null) {
+            throw new IllegalArgumentException();
+        } else if (!a.getClass().getComponentType().isAssignableFrom(Kmer.class)) {
+            throw new IllegalArgumentException();
+        } else {
+            T[] result;
+            if (a.length < size) {
+                result = (T[]) Array.newInstance(a.getClass().getComponentType(), size);
+            } else {
+                result = a;
+            }
+            for (int i = 0; i < size; i++) {
+                result[i] = (T) new Kmer(sequence,start + i,kmerSize);
+            }
+            return result;
+        }
+    }
+
+    @Override
+    public boolean add(final Kmer kmer) {
+        throw new UnsupportedOperationException();
+    }
+
+    @Override
+    public boolean remove(final Object o) {
+        throw new UnsupportedOperationException();
+    }
+
+    @Override
+    public boolean containsAll(final Collection<?> c) {
+        for (final Object o : c)
+            if (!contains(o))
+                return false;
+        return true;
+    }
+
+    @Override
+    public boolean addAll(final Collection<? extends Kmer> c) {
+        throw new UnsupportedOperationException();
+    }
+
+    @Override
+    public boolean addAll(final int index, @NotNull final Collection<? extends Kmer> c) {
+        throw new UnsupportedOperationException();
+    }
+
+    @Override
+    public boolean removeAll(@NotNull final Collection<?> c) {
+        throw new UnsupportedOperationException();
+    }
+
+    @Override
+    public boolean retainAll(@NotNull final Collection<?> c) {
+        throw new UnsupportedOperationException();
+    }
+
+    @Override
+    public void clear() {
+        throw new UnsupportedOperationException();
+    }
+
+    @Override
+    public Kmer get(final int index) {
+        if (index < 0 || index >= size) {
+            throw new IllegalArgumentException();
+        }
+        return new Kmer(sequence,start + index,kmerSize);
+    }
+
+    @Override
+    public Kmer set(final int index, final Kmer element) {
+        throw new UnsupportedOperationException();
+    }
+
+    @Override
+    public void add(final int index, final Kmer element) {
+        throw new UnsupportedOperationException();
+    }
+
+    @Override
+    public Kmer remove(final int index) {
+        throw new UnsupportedOperationException();
+    }
+
+    @Override
+    public int indexOf(final Object o) {
+        if (o instanceof Kmer) {
+            final Kmer k = (Kmer) o;
+            if (k.length != kmerSize) {
+                return -1;
+            }
+            for (int i = 0; i < size; i++) {
+                int j;
+                for (j = 0; j < kmerSize; j++) {
+                    if (sequence[start + i + j] != k.bases[k.start + j]) {
+                        break;
+                    }
+                }
+                if (j == kmerSize) {
+                    return i;
+                }
+            }
+            return -1;
+        } else {
+            return -1;
+        }
+    }
+
+    @Override
+    public int lastIndexOf(final Object o) {
+        if (o instanceof Kmer) {
+            final Kmer k = (Kmer) o;
+            if (k.length != kmerSize) {
+                return -1;
+            }
+            for (int i = size - 1; i >= 0; i--) {
+                int j;
+                for (j = kmerSize - 1; j >= 0; j--) {
+                    if (sequence[start + i + j] != k.bases[k.start + j]) {
+                        break;
+                    }
+                }
+                if (j == 0) {
+                    return i;
+                }
+            }
+            return -1;
+        } else {
+            return -1;
+        }
+    }
+
+    @Override
+    @NotNull
+    public ListIterator<Kmer> listIterator() {
+        return new MyListIterator(0);
+    }
+
+    @Override
+    @NotNull
+    public ListIterator<Kmer> listIterator(final int index) {
+        return new MyListIterator(index);
+    }
+
+    @Override
+    @NotNull
+    public List<Kmer> subList(final int fromIndex, final int toIndex) {
+        return subsequence(fromIndex,toIndex);
+    }
+
+    /**
+     * Returns the byte array representation of the kmer sequence.
+     * @return never {@code null}.
+     */
+    @NotNull
+    public byte[] getBytes() {
+        if (start == 0 && rawLength == sequence.length)
+            return sequence;
+        else
+            return Arrays.copyOfRange(sequence, start, rawLength + start);
+    }
+
+    /**
+     * Internal class that implements the {@link Kmer} more efficiently
+     * making reference to the sequence's own byte array.
+     */
+    protected class MyKmer extends Kmer {
+
+        /**
+         * Create a new instance give the offset in the byte array.
+         * @param start the start base offset for the kmer.
+         */
+        public MyKmer(final int start) {
+            super(sequence,start,kmerSize);
+        }
+    }
+
+    /**
+     * Iterator implementation of Kmer elements.
+     */
+    private class MyListIterator implements ListIterator<Kmer> {
+
+        private int i = 0;
+
+        /**
+         * Creates a iterator at certain offset in the sequence.
+         * @param idx the start position or kmer offset.
+         */
+        private MyListIterator(final int idx) {
+            i = idx;
+        }
+
+        @Override
+        public boolean hasNext() {
+            return i < size;
+        }
+
+        @Override
+        public Kmer next() {
+            return new Kmer(sequence,start + i++,kmerSize);
+        }
+
+        @Override
+        public boolean hasPrevious() {
+            return i > 0;
+        }
+
+        @Override
+        public Kmer previous() {
+            return new Kmer(sequence,start + --i,kmerSize);
+        }
+
+        @Override
+        public int nextIndex() {
+            return i;
+        }
+
+        @Override
+        public int previousIndex() {
+            return i - 1;
+        }
+
+        @Override
+        public void remove() {
+            throw new UnsupportedOperationException();
+        }
+
+        @Override
+        public void set(final Kmer kmer) {
+            throw new UnsupportedOperationException();
+        }
+
+        @Override
+        public void add(final Kmer kmer) {
+            throw new UnsupportedOperationException();
+        }
+
+    }
+
+}
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequenceGraphMap.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequenceGraphMap.java
new file mode 100644
index 000000000..d71f99116
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequenceGraphMap.java
@@ -0,0 +1,209 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*  
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*  
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*  
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*  
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*  
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. 
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.  
+*  
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY 
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*  
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*  
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*  
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*  
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt. 
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. 
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
+
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.BaseEdge;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.BaseVertex;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.KmerSearchableGraph;
+
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Collections;
+import java.util.Arrays;
+import java.util.ArrayList;
+
+/**
+ * Contains information as to how a kmer sequence maps to an (assembly) graph.
+ *
+ * @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.com&gt;
+ */
+public class KmerSequenceGraphMap<V extends BaseVertex,E extends BaseEdge> {
+
+    protected final KmerSequence sequence;
+    protected final KmerSearchableGraph<V,E> graph;
+    protected final int kmerSize;
+
+    private List<V> vertexList;
+
+    private List<V> vertexMatchOnlyList;
+
+    private Set<V> vertexSet;
+
+    private Map<V,Integer> vertexOffset;
+
+    //private List<VertexSegment<V>> vertexSegmentList;
+
+    /**
+     * Constructs a new Kmer sequence graph map give the graph and sequence.
+     *
+     * @param g the graph to map to.
+     * @param s the sequence to map.
+     * @throws NullPointerException if either the graph or the sequence is <code>null</code>.
+     * @throws IllegalArgumentException if the kmer sizes of the input graph and sequence are not the same.
+     */
+    public KmerSequenceGraphMap(final KmerSearchableGraph<V, E> g, final KmerSequence s) {
+        if (s.kmerSize() != g.getKmerSize()) {
+            throw new IllegalArgumentException("kmer size for the graph (" + g.getKmerSize() + ") and the sequence (" + s.kmerSize() + ") are different");
+        }
+        sequence = s;
+        graph = g;
+        kmerSize = s.kmerSize();
+    }
+
+    /**
+     * Vertices that form part of the kmer sequence path along the graph.
+     *
+     * <p>The ith position in the resulting list corresponds to the ith kmer in the sequence</p>.
+     *
+     * <p>
+     *     The resulting list will contain null values for those kmers where there is no unique kmer match in the
+     *     graph.
+     * </p>
+     *
+     * @return never {@code null}
+     */
+    public List<V> vertexList() {
+        if (vertexList == null)
+            buildVertexCollections();
+        return vertexList;
+    }
+
+    /**
+     * Vertices that form part of the kmer sequence path along the graph.
+     *
+     * <p> Only contains unique kmer vertices where the non-unique ones have been sliced out from the list</p>
+     *
+     * @return never {@code null}
+     */
+    public List<V> vertexMatchOnlyList() {
+        if (vertexMatchOnlyList == null) {
+            buildVertexCollections();
+        }
+        return vertexMatchOnlyList;
+    }
+
+
+    /**
+     * Return a map from vertices to their kmer offset in the kmer sequence.
+     * @return never {@code null}
+     */
+    public Map<V,Integer> vertexOffset() {
+        if (vertexOffset == null) {
+            buildVertexCollections();
+        }
+        return vertexOffset;
+    }
+
+    /**
+     * Set of all vertices with unique kmers in the kmer sequence.
+     * <p>
+     *     This structure is more appropriate to query whether a vertex belong or not to such a set.
+     * </p>
+     * @return never {@code null}.
+     */
+    public Set<V> vertexSet() {
+        if (vertexSet == null) {
+            buildVertexCollections();
+        }
+        return vertexSet;
+    }
+
+    /**
+     * Updates vertex structures.
+     */
+    protected void buildVertexCollections() {
+        @SuppressWarnings("unchecked")
+        final V[] result = (V[]) new BaseVertex[sequence.size()];
+        final Set<V> set = new HashSet<>(sequence.size());
+        final Map<V,Integer> posMap = new HashMap<>(sequence.size());
+        @SuppressWarnings("unchecked")
+        final V[] matchOnly = (V[]) new BaseVertex[sequence.size()];
+        int next = 0;
+        int matchOnlyNext = 0;
+        for (int i = 0; i < sequence.size(); i++) {
+            final Kmer k = sequence.get(i);
+            final V v = graph.findKmer(k);
+            if (v != null) {
+                set.add(v);
+                posMap.put(v,i);
+                matchOnly[matchOnlyNext++] = v;
+            }
+            result[next++] = v;
+        }
+        vertexList = Arrays.asList(result);
+        vertexMatchOnlyList = Arrays.asList(Arrays.copyOf(matchOnly,matchOnlyNext));
+        vertexSet = Collections.unmodifiableSet(set);
+        vertexOffset = Collections.unmodifiableMap(posMap);
+    }
+
+    /**
+     * Returns the list of kmers in the sequence that do not have a unique mapping on the graph.
+     * @return never {@code null}
+     */
+    @SuppressWarnings("unused")
+    public List<Kmer> missingKmers() {
+        if (vertexList == null) {
+            buildVertexCollections();
+        }
+        if (vertexList.size() == vertexMatchOnlyList.size()) {
+            return Collections.emptyList();
+        } else {
+            final List<Kmer> result = new ArrayList<>(vertexList.size() - vertexMatchOnlyList.size());
+            final int size = sequence.size();
+            for (int i = 0; i < vertexList.size(); i++) {
+                if (vertexList.get(i) == null) {
+                    result.add(sequence.get(i));
+                }
+            }
+            return result;
+        }
+    }
+
+}
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
index 9cd0f5f49..0626f2268 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
@@ -46,741 +46,47 @@
 
 package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
 
-import com.google.java.contract.Ensures;
-import com.google.java.contract.Requires;
-import net.sf.samtools.SAMUtils;
-import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.QualityUtils;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.haplotype.Haplotype;
-import org.broadinstitute.sting.utils.pairhmm.*;
-import org.broadinstitute.sting.utils.recalibration.covariates.RepeatCovariate;
-import org.broadinstitute.sting.utils.recalibration.covariates.RepeatLengthCovariate;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.sam.ReadUtils;
-import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
-import org.broadinstitute.variant.variantcontext.*;
-import org.broadinstitute.variant.vcf.VCFConstants;
 
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.PrintStream;
-import java.util.*;
-
-public class LikelihoodCalculationEngine {
-    private final static Logger logger = Logger.getLogger(LikelihoodCalculationEngine.class);
-
-    private static final byte BASE_QUALITY_SCORE_THRESHOLD = (byte) 18; // Base quals less than this value are squashed down to min possible qual
-
-    private final byte constantGCP;
-    private final double log10globalReadMismappingRate;
-    private final boolean DEBUG;
-
-    private final PairHMM.HMM_IMPLEMENTATION hmmType;
-    private final boolean noFpga;
-
-    private final ThreadLocal<PairHMM> pairHMMThreadLocal = new ThreadLocal<PairHMM>() {
-        @Override
-        protected PairHMM initialValue() {
-            switch (hmmType) {
-                case EXACT: return new Log10PairHMM(true);
-                case ORIGINAL: return new Log10PairHMM(false);
-                case LOGLESS_CACHING:
-                    if (noFpga || !CnyPairHMM.isAvailable())
-                        return new LoglessPairHMM();
-                    else
-                        return new CnyPairHMM();
-                case ARRAY_LOGLESS:
-                    if (noFpga || !CnyPairHMM.isAvailable())
-                        return new ArrayLoglessPairHMM();
-                    else
-                        return new CnyPairHMM();
-                default:
-                    throw new UserException.BadArgumentValue("pairHMM", "Specified pairHMM implementation is unrecognized or incompatible with the HaplotypeCaller. Acceptable options are ORIGINAL, EXACT, CACHING, LOGLESS_CACHING, and ARRAY_LOGLESS.");
-            }
-        }
-    };
-//    Attempted to do as below, to avoid calling pairHMMThreadLocal.get() later on, but it resulted in a NullPointerException
-//    private final PairHMM pairHMM = pairHMMThreadLocal.get();
-
-    private final static boolean WRITE_LIKELIHOODS_TO_FILE = false;
-    private final static String LIKELIHOODS_FILENAME = "likelihoods.txt";
-    private final PrintStream likelihoodsStream;
-
-    public enum PCR_ERROR_MODEL {
-        /** no specialized PCR error model will be applied; if base insertion/deletion qualities are present they will be used */
-        NONE,
-        /** a more aggressive model will be applied that sacrifices true positives in order to remove more false positives */
-        AGGRESSIVE,
-        /** a less aggressive model will be applied that tries to maintain a high true positive rate at the expense of allowing more false positives */
-        CONSERVATIVE
-    }
-
-    private final PCR_ERROR_MODEL pcrErrorModel;
-
-    /**
-     * The expected rate of random sequencing errors for a read originating from its true haplotype.
-     *
-     * For example, if this is 0.01, then we'd expect 1 error per 100 bp.
-     */
-    private final static double EXPECTED_ERROR_RATE_PER_BASE = 0.02;
-
-    /**
-     * Create a new LikelihoodCalculationEngine using provided parameters and hmm to do its calculations
-     *
-     * @param constantGCP the gap continuation penalty to use with the PairHMM
-     * @param debug should we emit debugging information during the calculation?
-     * @param hmmType the type of the HMM to use
-     * @param log10globalReadMismappingRate the global mismapping probability, in log10(prob) units.  A value of
-     *                                      -3 means that the chance that a read doesn't actually belong at this
-     *                                      location in the genome is 1 in 1000.  The effect of this parameter is
-     *                                      to cap the maximum likelihood difference between the reference haplotype
-     *                                      and the best alternative haplotype by -3 log units.  So if the best
-     *                                      haplotype is at -10 and this parameter has a value of -3 then even if the
-     *                                      reference haplotype gets a score of -100 from the pairhmm it will be
-     *                                      assigned a likelihood of -13.
-     * @param noFpga disable FPGA acceleration
-     */
-    public LikelihoodCalculationEngine( final byte constantGCP, final boolean debug, final PairHMM.HMM_IMPLEMENTATION hmmType, final double log10globalReadMismappingRate, final boolean noFpga, final PCR_ERROR_MODEL pcrErrorModel ) {
-        this.hmmType = hmmType;
-        this.constantGCP = constantGCP;
-        this.DEBUG = debug;
-        this.log10globalReadMismappingRate = log10globalReadMismappingRate;
-        this.noFpga = noFpga;
-        this.pcrErrorModel = pcrErrorModel;
-
-        initializePCRErrorModel();
-
-        if ( WRITE_LIKELIHOODS_TO_FILE ) {
-            try {
-                likelihoodsStream = new PrintStream(new FileOutputStream(new File(LIKELIHOODS_FILENAME)));
-            } catch ( FileNotFoundException e ) {
-                throw new RuntimeException(e);
-            }
-        } else {
-            likelihoodsStream = null;
-        }
-    }
-
-    public void close() {
-        if ( likelihoodsStream != null ) likelihoodsStream.close();
-    }
-
-    private void writeDebugLikelihoods(final GATKSAMRecord processedRead, final Haplotype haplotype, final double log10l){
-        if ( WRITE_LIKELIHOODS_TO_FILE ) {
-            likelihoodsStream.printf("%s %s %s %s %s %s %f%n",
-                    haplotype.getBaseString(),
-                    new String(processedRead.getReadBases() ),
-                    SAMUtils.phredToFastq(processedRead.getBaseQualities() ),
-                    SAMUtils.phredToFastq(processedRead.getBaseInsertionQualities() ),
-                    SAMUtils.phredToFastq(processedRead.getBaseDeletionQualities() ),
-                    SAMUtils.phredToFastq(constantGCP),
-                    log10l);
-        }
-    }
-
-    private Map<Allele, Haplotype> createAlleleMap(List<Haplotype> haplotypes){
-        final int numHaplotypes = haplotypes.size();
-        final Map<Allele, Haplotype> alleleMap = new LinkedHashMap<>(numHaplotypes);
-        for ( final Haplotype haplotype : haplotypes ) {
-            final Allele allele = Allele.create(haplotype, true);
-            alleleMap.put(allele, haplotype);
-        }
-        return alleleMap;
-    }
-
-    private Map<GATKSAMRecord, byte[]> fillGCPArrays(List<GATKSAMRecord> reads){
-        final Map<GATKSAMRecord, byte []> GCPArrayMap = new LinkedHashMap<>();
-        for (GATKSAMRecord read: reads){
-            byte [] GCPArray = new byte[read.getReadBases().length];
-            Arrays.fill( GCPArray, constantGCP ); // Is there a way to derive empirical estimates for this from the data?
-            GCPArrayMap.put(read, GCPArray);
-        }
-        return GCPArrayMap;
-    }
-
-    private void capMinimumReadQualities(GATKSAMRecord read, byte[] readQuals, byte[] readInsQuals, byte[] readDelQuals) {
-        for( int kkk = 0; kkk < readQuals.length; kkk++ ) {
-            readQuals[kkk] = (byte) Math.min( 0xff & readQuals[kkk], read.getMappingQuality()); // cap base quality by mapping quality, as in UG
-            readQuals[kkk] = ( readQuals[kkk] < BASE_QUALITY_SCORE_THRESHOLD ? QualityUtils.MIN_USABLE_Q_SCORE : readQuals[kkk] );
-            readInsQuals[kkk] = ( readInsQuals[kkk] < QualityUtils.MIN_USABLE_Q_SCORE ? QualityUtils.MIN_USABLE_Q_SCORE : readInsQuals[kkk] );
-            readDelQuals[kkk] = ( readDelQuals[kkk] < QualityUtils.MIN_USABLE_Q_SCORE ? QualityUtils.MIN_USABLE_Q_SCORE : readDelQuals[kkk] );
-        }
-    }
-
-    /**
-     * Pre-processing of the reads to be evaluated at the current location from the current sample.
-     * We apply the PCR Error Model, and cap the minimum base, insertion, and deletion qualities of each read.
-     * Modified copies of reads are packed into a new list, while original reads are retained for downstream use
-     *
-     * @param reads The original list of unmodified reads
-     * @return processedReads. A new list of reads, in the same order, whose qualities have been altered by PCR error model and minimal quality thresholding
-     */
-    private List<GATKSAMRecord> modifyReadQualities(final List<GATKSAMRecord> reads) {
-        List<GATKSAMRecord> processedReads = new LinkedList<>();
-        for ( GATKSAMRecord read : reads ) {
-
-            final byte[] readBases = read.getReadBases();
-
-            // NOTE -- must clone anything that gets modified here so we don't screw up future uses of the read
-            final byte[] readQuals = read.getBaseQualities().clone();
-            final byte[] readInsQuals = read.getBaseInsertionQualities().clone();
-            final byte[] readDelQuals = read.getBaseDeletionQualities().clone();
-
-            applyPCRErrorModel(readBases, readInsQuals, readDelQuals);
-            capMinimumReadQualities(read, readQuals, readInsQuals, readDelQuals);
-
-            // Create a new copy of the read and sets its base qualities to the modified versions.
-            // Pack this into a new list for return
-            final GATKSAMRecord processedRead = GATKSAMRecord.createQualityModifiedRead(read, readBases, readQuals, readInsQuals, readDelQuals);
-            processedReads.add(processedRead);
-        }
-        return processedReads;
-    }
-
-    /**
-     * Post-processing of the read/allele likelihoods.
-     *
-     * We send quality-capped reads to the pairHMM for evaluation, and it returns a map containing these capped reads.
-     * We wish to return a map containing the original, unmodified reads.
-     *
-     * At the same time, we want to effectively set a lower cap on the reference score, based on the global mis-mapping rate.
-     * This protects us from the case where the assembly has produced haplotypes
-     * that are very divergent from reference, but are supported by only one read.  In effect
-     * we capping how badly scoring the reference can be for any read by the chance that the read
-     * itself just doesn't belong here
-     *
-     * @param perReadAlleleLikelihoodMap the original map returned by the PairHMM. Contains the processed reads, the haplotype Alleles, and their log10ls
-     * @param reads Our original, unmodified reads
-     * @param processedReads Reads whose minimum base,insertion,deletion qualities have been capped; these were actually used to derive log10ls
-     * @param alleleHaplotypeMap The map associating the Allele and Haplotype versions of each haplotype
-     *
-     * @return processedReadAlleleLikelihoodMap; a new PRALM containing the original reads, and their haplotype log10ls including capped reference log10ls
-     */
-    private PerReadAlleleLikelihoodMap capReferenceHaplotypeLikelihoods(PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap, List<GATKSAMRecord> reads, List<GATKSAMRecord> processedReads, Map<Allele, Haplotype> alleleHaplotypeMap){
-
-        // a new read/allele map, to contain the uncapped reads, haplotypes, and potentially the capped reference log10ls
-        final PerReadAlleleLikelihoodMap processedReadAlleleLikelihoodMap = new PerReadAlleleLikelihoodMap();
-
-        Allele refAllele = null;
-        final int numReads = reads.size();
-        for (int readIndex = 0; readIndex < numReads; readIndex++) {
-
-            // Get the original and quality-modified read from their respective lists
-            // Note that this requires both lists to have reads in the same order
-            final GATKSAMRecord originalRead = reads.get(readIndex);
-            final GATKSAMRecord processedRead = processedReads.get(readIndex);
-
-            // keep track of the reference likelihood and the best non-ref likelihood
-            double refLog10l = Double.NEGATIVE_INFINITY;
-            double bestNonReflog10L = Double.NEGATIVE_INFINITY;
-
-            for ( Allele allele : alleleHaplotypeMap.keySet() ) {
-                final double log10l = perReadAlleleLikelihoodMap.getLikelihoodAssociatedWithReadAndAllele(processedRead, allele);
-                final Haplotype haplotype = alleleHaplotypeMap.get(allele);
-                if ( haplotype.isNonReference() )
-                    bestNonReflog10L = Math.max(bestNonReflog10L, log10l);
-                else {
-                    refAllele = allele;
-                    refLog10l = log10l;
-                }
-                writeDebugLikelihoods(processedRead, haplotype, log10l);
-
-                // add the ORIGINAL (non-capped) read to the final map, along with the current haplotype and associated log10l
-                processedReadAlleleLikelihoodMap.add(originalRead, allele, log10l);
-            }
-
-            // ensure that the reference haplotype is no worse than the best non-ref haplotype minus the global
-            // mismapping rate.  This protects us from the case where the assembly has produced haplotypes
-            // that are very divergent from reference, but are supported by only one read.  In effect
-            // we capping how badly scoring the reference can be for any read by the chance that the read
-            // itself just doesn't belong here
-            final double worstRefLog10Allowed = bestNonReflog10L + log10globalReadMismappingRate;
-            if ( refLog10l < (worstRefLog10Allowed) ) {
-                processedReadAlleleLikelihoodMap.add(originalRead, refAllele, worstRefLog10Allowed);
-            }
-        }
-        return processedReadAlleleLikelihoodMap;
-    }
-
-
-    public Map<String, PerReadAlleleLikelihoodMap> computeReadLikelihoods( final List<Haplotype> haplotypes, final Map<String, List<GATKSAMRecord>> perSampleReadList ) {
-
-        // Add likelihoods for each sample's reads to our stratifiedReadMap
-        final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap = new LinkedHashMap<>();
-        for( final Map.Entry<String, List<GATKSAMRecord>> sampleEntry : perSampleReadList.entrySet() ) {
-            // evaluate the likelihood of the reads given those haplotypes
-            final PerReadAlleleLikelihoodMap map = computeReadLikelihoods(haplotypes, sampleEntry.getValue());
-
-            map.filterPoorlyModelledReads(EXPECTED_ERROR_RATE_PER_BASE);
-            stratifiedReadMap.put(sampleEntry.getKey(), map);
-        }
-
-        return stratifiedReadMap;
-    }
-
-    private PerReadAlleleLikelihoodMap computeReadLikelihoods( final List<Haplotype> haplotypes, final List<GATKSAMRecord> reads) {
-
-        // Modify the read qualities by applying the PCR error model and capping the minimum base,insertion,deletion qualities
-        List<GATKSAMRecord> processedReads = modifyReadQualities(reads);
-
-        // Get alleles corresponding to our haplotypees
-        Map<Allele, Haplotype> alleleHaplotypeMap = createAlleleMap(haplotypes);
-
-        // Get an array containing the constantGCP for each read in our modified read list
-        Map<GATKSAMRecord,byte[]> GCPArrayMap = fillGCPArrays(processedReads);
-
-        // Run the PairHMM to calculate the log10 likelihood of each (processed) reads' arising from each haplotype
-        PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = pairHMMThreadLocal.get().computeLikelihoods(processedReads, alleleHaplotypeMap, GCPArrayMap);
-
-        // Generate a new map containing the original, unmodified reads, and with minimal reference haplotype log10ls determined from the global mis-mapping rate
-
-        return capReferenceHaplotypeLikelihoods(perReadAlleleLikelihoodMap, reads, processedReads, alleleHaplotypeMap);
-    }
-
-    @Requires({"alleleOrdering.size() > 0"})
-    @Ensures({"result.length == result[0].length", "result.length == alleleOrdering.size()"})
-    public static double[][] computeDiploidHaplotypeLikelihoods( final String sample,
-                                                                 final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap,
-                                                                 final List<Allele> alleleOrdering,
-                                                                 final boolean normalize ) {
-        return computeDiploidHaplotypeLikelihoods(Collections.singleton(sample), stratifiedReadMap, alleleOrdering, normalize);
-    }
-
-    @Requires({"alleleOrdering.size() > 0"})
-    @Ensures({"result.length == result[0].length", "result.length == alleleOrdering.size()"})
-    public static double[][] computeDiploidHaplotypeLikelihoods( final Set<String> samples,
-                                                                 final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap,
-                                                                 final List<Allele> alleleOrdering,
-                                                                 final boolean normalize) {
-
-        final int numHaplotypes = alleleOrdering.size();
-        final double[][] haplotypeLikelihoodMatrix = new double[numHaplotypes][numHaplotypes];
-        for( int iii = 0; iii < numHaplotypes; iii++ ) {
-            Arrays.fill(haplotypeLikelihoodMatrix[iii], Double.NEGATIVE_INFINITY);
-        }
-
-        // compute the diploid haplotype likelihoods
-        for( int iii = 0; iii < numHaplotypes; iii++ ) {
-            final Allele iii_allele = alleleOrdering.get(iii);
-            for( int jjj = 0; jjj <= iii; jjj++ ) {
-                final Allele jjj_allele = alleleOrdering.get(jjj);
-                double haplotypeLikelihood = 0.0;
-                for( final String sample : samples ) {
-                    for( final Map.Entry<GATKSAMRecord, Map<Allele,Double>> entry : stratifiedReadMap.get(sample).getLikelihoodReadMap().entrySet() ) {
-                        // Compute log10(10^x1/2 + 10^x2/2) = log10(10^x1+10^x2)-log10(2)
-                        // First term is approximated by Jacobian log with table lookup.
-                        haplotypeLikelihood += ReadUtils.getMeanRepresentativeReadCount( entry.getKey() ) *
-                                ( MathUtils.approximateLog10SumLog10(entry.getValue().get(iii_allele), entry.getValue().get(jjj_allele)) + MathUtils.LOG_ONE_HALF );
-                    }
-                }
-                haplotypeLikelihoodMatrix[iii][jjj] = haplotypeLikelihood;
-            }
-        }
-
-        // normalize the diploid likelihoods matrix
-        return normalize ? normalizeDiploidLikelihoodMatrixFromLog10( haplotypeLikelihoodMatrix ) : haplotypeLikelihoodMatrix;
-    }
-
-    @Requires({"likelihoodMatrix.length == likelihoodMatrix[0].length"})
-    @Ensures({"result.length == result[0].length", "result.length == likelihoodMatrix.length"})
-    protected static double[][] normalizeDiploidLikelihoodMatrixFromLog10( final double[][] likelihoodMatrix ) {
-        final int numHaplotypes = likelihoodMatrix.length;
-        double[] genotypeLikelihoods = new double[numHaplotypes*(numHaplotypes+1)/2];
-        int index = 0;
-        for( int iii = 0; iii < numHaplotypes; iii++ ) {
-            for( int jjj = 0; jjj <= iii; jjj++ ){
-                genotypeLikelihoods[index++] = likelihoodMatrix[iii][jjj];
-            }
-        }
-        genotypeLikelihoods = MathUtils.normalizeFromLog10(genotypeLikelihoods, false, true);
-        index = 0;
-        for( int iii = 0; iii < numHaplotypes; iii++ ) {
-            for( int jjj = 0; jjj <= iii; jjj++ ){
-                likelihoodMatrix[iii][jjj] = genotypeLikelihoods[index++];
-            }
-        }
-        return likelihoodMatrix;
-    }
-
-    // --------------------------------------------------------------------------------
-    //
-    // System to compute the best N haplotypes for genotyping
-    //
-    // --------------------------------------------------------------------------------
-//
-//    /**
-//     * Helper function for selectBestHaplotypesFromEachSample that updates the score of haplotype haplotypeAsAllele
-//     * @param map an annoying map object that moves us between the allele and haplotype representation
-//     * @param haplotypeAsAllele the allele version of the haplotype
-//     * @return the haplotype version, with its score incremented by 1 if its non-reference
-//     */
-//    private Haplotype updateSelectHaplotype(final Map<Allele, Haplotype> map, final Allele haplotypeAsAllele) {
-//        final Haplotype h = map.get(haplotypeAsAllele); // TODO -- fixme when haplotypes are properly generic
-//        if ( h.isNonReference() ) h.setScore(h.getScore() + 1); // ref is already at max value
-//        return h;
-//    }
-//
-//    /**
-//     * Take the best N haplotypes and return them as a list
-//     *
-//     * Only considers the haplotypes selectedHaplotypes that were actually selected by at least one sample
-//     * as it's preferred haplotype.  Takes the best N haplotypes from selectedHaplotypes in decreasing
-//     * order of score (so higher score haplotypes are preferred).  The N we take is determined by
-//     *
-//     * N = min(2 * nSamples + 1, maxNumHaplotypesInPopulation)
-//     *
-//     * where 2 * nSamples is the number of chromosomes in 2 samples including the reference, and our workload is
-//     * bounded by maxNumHaplotypesInPopulation as that number can grow without bound
-//     *
-//     * @param selectedHaplotypes a non-null set of haplotypes with scores >= 1
-//     * @param nSamples the number of samples used to select the haplotypes
-//     * @param maxNumHaplotypesInPopulation the maximum number of haplotypes we're allowed to take, regardless of nSamples
-//     * @return a list of N or fewer haplotypes, with the reference haplotype first
-//     */
-//    private List<Haplotype> selectBestHaplotypesAccordingToScore(final Set<Haplotype> selectedHaplotypes, final int nSamples, final int maxNumHaplotypesInPopulation) {
-//        final List<Haplotype> selectedHaplotypesList = new ArrayList<>(selectedHaplotypes);
-//        Collections.sort(selectedHaplotypesList, new HaplotypeScoreComparator());
-//        final int numChromosomesInSamplesPlusRef = 2 * nSamples + 1;
-//        final int haplotypesToKeep = Math.min(numChromosomesInSamplesPlusRef, maxNumHaplotypesInPopulation);
-//        final List<Haplotype> bestHaplotypes = selectedHaplotypesList.size() <= haplotypesToKeep ? selectedHaplotypesList : selectedHaplotypesList.subList(0, haplotypesToKeep);
-//        if ( bestHaplotypes.get(0).isNonReference()) throw new IllegalStateException("BUG: reference haplotype should be first in list");
-//        return bestHaplotypes;
-//    }
-//
-//    /**
-//     * Select the best haplotypes for genotyping the samples in stratifiedReadMap
-//     *
-//     * Selects these haplotypes by counting up how often each haplotype is selected as one of the most likely
-//     * haplotypes per sample.  What this means is that each sample computes the diploid genotype likelihoods for
-//     * all possible pairs of haplotypes, and the pair with the highest likelihood has each haplotype each get
-//     * one extra count for each haplotype (so hom-var haplotypes get two counts).  After performing this calculation
-//     * the best N haplotypes are selected (@see #selectBestHaplotypesAccordingToScore) and a list of the
-//     * haplotypes in order of score are returned, ensuring that at least one of the haplotypes is reference.
-//     *
-//     * @param haplotypes a list of all haplotypes we're considering
-//     * @param stratifiedReadMap a map from sample -> read likelihoods per haplotype
-//     * @param maxNumHaplotypesInPopulation the max. number of haplotypes we can select from haplotypes
-//     * @return a list of selected haplotypes with size <= maxNumHaplotypesInPopulation
-//     */
-//    public List<Haplotype> selectBestHaplotypesFromEachSample(final List<Haplotype> haplotypes, final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap, final int maxNumHaplotypesInPopulation) {
-//        if ( haplotypes.size() < 2 ) throw new IllegalArgumentException("Must have at least 2 haplotypes to consider but only have " + haplotypes);
-//
-//        if ( haplotypes.size() == 2 ) return haplotypes; // fast path -- we'll always want to use 2 haplotypes
-//
-//        // all of the haplotypes that at least one sample called as one of the most likely
-//        final Set<Haplotype> selectedHaplotypes = new HashSet<>();
-//        selectedHaplotypes.add(findReferenceHaplotype(haplotypes)); // ref is always one of the selected
-//
-//        // our annoying map from allele -> haplotype
-//        final Map<Allele, Haplotype> allele2Haplotype = new HashMap<>();
-//        for ( final Haplotype h : haplotypes ) {
-//            h.setScore(h.isReference() ? Double.MAX_VALUE : 0.0); // set all of the scores to 0 (lowest value) for all non-ref haplotypes
-//            allele2Haplotype.put(Allele.create(h, h.isReference()), h);
-//        }
-//
-//        // for each sample, compute the most likely pair of haplotypes
-//        for ( final Map.Entry<String, PerReadAlleleLikelihoodMap> entry : stratifiedReadMap.entrySet() ) {
-//            // get the two most likely haplotypes under a diploid model for this sample
-//            final MostLikelyAllele mla = entry.getValue().getMostLikelyDiploidAlleles();
-//
-//            if ( mla != null ) { // there was something to evaluate in this sample
-//                // note that there must be at least 2 haplotypes
-//                final Haplotype best = updateSelectHaplotype(allele2Haplotype, mla.getMostLikelyAllele());
-//                final Haplotype second = updateSelectHaplotype(allele2Haplotype, mla.getSecondMostLikelyAllele());
-//
-////            if ( DEBUG ) {
-////                logger.info("Chose haplotypes " + best + " " + best.getCigar() + " and " + second + " " + second.getCigar() + " for sample " + entry.getKey());
-////            }
-//
-//                // add these two haplotypes to the set of haplotypes that have been selected
-//                selectedHaplotypes.add(best);
-//                selectedHaplotypes.add(second);
-//
-//                // we've already selected all of our haplotypes, and we don't need to prune them down
-//                if ( selectedHaplotypes.size() == haplotypes.size() && haplotypes.size() < maxNumHaplotypesInPopulation )
-//                    break;
-//            }
-//        }
-//
-//        // take the best N haplotypes forward, in order of the number of samples that choose them
-//        final int nSamples = stratifiedReadMap.size();
-//        final List<Haplotype> bestHaplotypes = selectBestHaplotypesAccordingToScore(selectedHaplotypes, nSamples, maxNumHaplotypesInPopulation);
-//
-//        if ( DEBUG ) {
-//            logger.info("Chose " + (bestHaplotypes.size() - 1) + " alternate haplotypes to genotype in all samples.");
-//            for ( final Haplotype h : bestHaplotypes ) {
-//                logger.info("\tHaplotype " + h.getCigar() + " selected for further genotyping" + (h.isNonReference() ? " found " + (int)h.getScore() + " haplotypes" : " as ref haplotype"));
-//            }
-//        }
-//        return bestHaplotypes;
-//    }
-//
-//    /**
-//     * Find the haplotype that isRef(), or @throw ReviewedStingException if one isn't found
-//     * @param haplotypes non-null list of haplotypes
-//     * @return the reference haplotype
-//     */
-//    private static Haplotype findReferenceHaplotype( final List<Haplotype> haplotypes ) {
-//        for( final Haplotype h : haplotypes ) {
-//            if( h.isReference() ) return h;
-//        }
-//        throw new ReviewedStingException( "No reference haplotype found in the list of haplotypes!" );
-//    }
-
-    // --------------------------------------------------------------------------------
-    //
-    // Experimental attempts at PCR error rate modeling
-    //
-    // --------------------------------------------------------------------------------
-
-    protected static final int MAX_STR_UNIT_LENGTH = 8;
-    protected static final int MAX_REPEAT_LENGTH = 20;
-    protected static final int MIN_ADJUSTED_QSCORE = 10;
-    protected static final double INITIAL_QSCORE = 40.0;
-
-    private byte[] pcrIndelErrorModelCache = new byte[MAX_REPEAT_LENGTH * MAX_STR_UNIT_LENGTH + 1];
-    private final RepeatCovariate repeatCovariate = new RepeatLengthCovariate();
-
-    private void initializePCRErrorModel() {
-        if ( pcrErrorModel == PCR_ERROR_MODEL.NONE )
-            return;
-
-        repeatCovariate.initialize(MAX_STR_UNIT_LENGTH, MAX_REPEAT_LENGTH);
-
-        pcrIndelErrorModelCache = new byte[MAX_REPEAT_LENGTH + 1];
-
-        final double rateFactor = pcrErrorModel == PCR_ERROR_MODEL.AGGRESSIVE ? 2.0 : 3.0;
-
-        for( int iii = 0; iii <= MAX_REPEAT_LENGTH; iii++ )
-            pcrIndelErrorModelCache[iii] = getErrorModelAdjustedQual(iii, rateFactor);
-    }
-
-    protected static byte getErrorModelAdjustedQual(final int repeatLength, final double rateFactor) {
-        return (byte) Math.max(MIN_ADJUSTED_QSCORE, MathUtils.fastRound( INITIAL_QSCORE - Math.exp(((double) repeatLength) / (rateFactor * Math.PI)) + 1.0 ));
-    }
-
-    protected void applyPCRErrorModel( final byte[] readBases, final byte[] readInsQuals, final byte[] readDelQuals ) {
-        if ( pcrErrorModel == PCR_ERROR_MODEL.NONE )
-            return;
-
-        for ( int iii = 1; iii < readBases.length; iii++ ) {
-            final int repeatLength = repeatCovariate.findTandemRepeatUnits(readBases, iii-1).getSecond();
-            readInsQuals[iii-1] = (byte) Math.min(0xff & readInsQuals[iii-1], 0xff & pcrIndelErrorModelCache[repeatLength]);
-            readDelQuals[iii-1] = (byte) Math.min(0xff & readDelQuals[iii-1], 0xff & pcrIndelErrorModelCache[repeatLength]);
-        }
-    }
-
-    // --------------------------------------------------------------------------------
-    //
-    // Posterior GL calculations
-    //
-    // --------------------------------------------------------------------------------
-
-    public static VariantContext calculatePosteriorGLs(final VariantContext vc1,
-                                                       final Collection<VariantContext> resources,
-                                                       final int numRefSamplesFromMissingResources,
-                                                       final double globalFrequencyPriorDirichlet,
-                                                       final boolean useInputSamples,
-                                                       final boolean useEM,
-                                                       final boolean useAC) {
-        if ( useEM )
-            throw new IllegalArgumentException("EM loop for posterior GLs not yet implemented");
-
-        final Map<Allele,Integer> totalAlleleCounts = new HashMap<>();
-        for ( final VariantContext resource : resources ) {
-            addAlleleCounts(totalAlleleCounts,resource,useAC);
-        }
-
-        if ( useInputSamples ) {
-            addAlleleCounts(totalAlleleCounts,vc1,useAC);
-        }
-
-        totalAlleleCounts.put(vc1.getReference(),totalAlleleCounts.get(vc1.getReference())+numRefSamplesFromMissingResources);
-
-        // now extract the counts of the alleles present within vc1, and in order
-        final double[] alleleCounts = new double[vc1.getNAlleles()];
-        int alleleIndex = 0;
-        for ( final Allele allele : vc1.getAlleles() ) {
-
-            alleleCounts[alleleIndex++] = globalFrequencyPriorDirichlet + ( totalAlleleCounts.containsKey(allele) ?
-                    totalAlleleCounts.get(allele) : 0 );
-        }
-
-        final List<double[]> likelihoods = new ArrayList<>(vc1.getNSamples());
-        for ( final Genotype genotype : vc1.getGenotypes() ) {
-            likelihoods.add(genotype.hasLikelihoods() ? genotype.getLikelihoods().getAsVector() : null );
-        }
-
-        final List<double[]> posteriors = calculatePosteriorGLs(likelihoods,alleleCounts,vc1.getMaxPloidy(2));
-
-        final GenotypesContext newContext = GenotypesContext.create();
-        for ( int genoIdx = 0; genoIdx < vc1.getNSamples(); genoIdx ++ ) {
-            final GenotypeBuilder builder = new GenotypeBuilder(vc1.getGenotype(genoIdx));
-            if ( posteriors.get(genoIdx) != null ) {
-                GATKVariantContextUtils.updateGenotypeAfterSubsetting(vc1.getAlleles(), builder,
-                        GATKVariantContextUtils.GenotypeAssignmentMethod.USE_PLS_TO_ASSIGN, posteriors.get(genoIdx), vc1.getAlleles());
-                builder.attribute(VCFConstants.GENOTYPE_POSTERIORS_KEY,
-                        Utils.listFromPrimitives(GenotypeLikelihoods.fromLog10Likelihoods(posteriors.get(genoIdx)).getAsPLs()));
-
-            }
-            newContext.add(builder.make());
-        }
-
-        final List<Integer> priors = Utils.listFromPrimitives(
-                GenotypeLikelihoods.fromLog10Likelihoods(getDirichletPrior(alleleCounts, vc1.getMaxPloidy(2))).getAsPLs());
-
-        return new VariantContextBuilder(vc1).genotypes(newContext).attribute("PG",priors).make();
-    }
-
-    /**
-     * Given genotype likelihoods and known allele counts, calculate the posterior likelihoods
-     * over the genotype states
-     * @param genotypeLikelihoods - the genotype likelihoods for the individual
-     * @param knownAlleleCountsByAllele - the known allele counts in the population. For AC=2 AN=12 site, this is {10,2}
-     * @param ploidy - the ploidy to assume
-     * @return - the posterior genotype likelihoods
-     */
-    protected static List<double[]> calculatePosteriorGLs(final List<double[]> genotypeLikelihoods,
-                                                       final double[] knownAlleleCountsByAllele,
-                                                       final int ploidy) {
-        if ( ploidy != 2 ) {
-            throw new IllegalStateException("Genotype posteriors not yet implemented for ploidy != 2");
-        }
-
-        final double[] genotypePriorByAllele = getDirichletPrior(knownAlleleCountsByAllele,ploidy);
-        final List<double[]> posteriors = new ArrayList<>(genotypeLikelihoods.size());
-        for ( final double[] likelihoods : genotypeLikelihoods ) {
-            double[] posteriorLikelihoods = null;
-
-            if ( likelihoods != null ) {
-                if ( likelihoods.length != genotypePriorByAllele.length ) {
-                    throw new IllegalStateException(String.format("Likelihoods not of correct size: expected %d, observed %d",
-                            knownAlleleCountsByAllele.length*(knownAlleleCountsByAllele.length+1)/2,likelihoods.length));
-                }
-
-                posteriorLikelihoods = new double[genotypePriorByAllele.length];
-                for ( int genoIdx = 0; genoIdx < likelihoods.length; genoIdx ++ ) {
-                    posteriorLikelihoods[genoIdx] = likelihoods[genoIdx] + genotypePriorByAllele[genoIdx];
-                }
-
-                posteriorLikelihoods = MathUtils.toLog10(MathUtils.normalizeFromLog10(posteriorLikelihoods));
-
-            }
-
-            posteriors.add(posteriorLikelihoods);
-        }
-
-        return posteriors;
-    }
-
-    // convenience function for a single genotypelikelihoods array. Just wraps.
-    protected static double[] calculatePosteriorGLs(final double[] genotypeLikelihoods,
-                                                 final double[] knownAlleleCountsByAllele,
-                                                 final int ploidy) {
-        return calculatePosteriorGLs(Arrays.asList(genotypeLikelihoods),knownAlleleCountsByAllele,ploidy).get(0);
+import java.util.List;
+import java.util.Map;
+
+/**
+ * Common interface for assembly-haplotype vs reads likelihood engines.
+ */
+public interface LikelihoodCalculationEngine {
+
+    enum Implementation {
+        /**
+         * Classic full pair-hmm all haplotypes vs all reads.
+         */
+        PairHMM,
+
+        /**
+         * Graph-base likelihoods.
+         */
+        GraphBased,
+
+        /**
+         * Random likelihoods, used to establish a baseline benchmark for other meaningful implementations.
+         */
+        Random
     }
 
 
     /**
-     * Given known allele counts (whether external, from the sample, or both), calculate the prior distribution
-     * over genotype states. This assumes
-     *   1) Random sampling of alleles (known counts are unbiased, and frequency estimate is Dirichlet)
-     *   2) Genotype states are independent (Hardy-Weinberg)
-     * These assumptions give rise to a Dirichlet-Multinomial distribution of genotype states as a prior
-     * (the "number of trials" for the multinomial is simply the ploidy)
-     * @param knownCountsByAllele - the known counts per allele. For an AC=2, AN=12 site this is {10,2}
-     * @param ploidy - the number of chromosomes in the sample. For now restricted to 2.
-     * @return - the Dirichlet-Multinomial distribution over genotype states
+     * Calculates the likelihood of reads across many samples evaluated against haplotypes resulting from the
+     * active region assembly process.
+     *
+     * @param assemblyResultSet the input assembly results.
+     * @param perSampleReadList the input read sets stratified per sample.
+     *
+     * @throws NullPointerException if either parameter is {@code null}.
+     *
+     * @return never {@code null}, and with at least one entry for input sample (keys in {@code perSampleReadList}.
+     *    The value maps can be potentially empty though.
      */
-    protected static double[] getDirichletPrior(final double[] knownCountsByAllele, final int ploidy) {
-        if ( ploidy != 2 ) {
-            throw new IllegalStateException("Genotype priors not yet implemented for ploidy != 2");
-        }
-
-        // multi-allelic format is
-        // AA AB BB AC BC CC AD BD CD DD ...
-        final double sumOfKnownCounts = MathUtils.sum(knownCountsByAllele);
-        final double[] priors = new double[knownCountsByAllele.length*(knownCountsByAllele.length+1)/2];
-        int priorIndex = 0;
-        for ( int allele2 = 0; allele2 < knownCountsByAllele.length; allele2++ ) {
-            for ( int allele1 = 0; allele1 <= allele2; allele1++) {
-                final int[] counts = new int[knownCountsByAllele.length];
-                counts[allele1] += 1;
-                counts[allele2] += 1;
-                priors[priorIndex++] = MathUtils.dirichletMultinomial(knownCountsByAllele,sumOfKnownCounts,counts,ploidy);
-            }
-        }
-
-        return priors;
-    }
-
-    private static void addAlleleCounts(final Map<Allele,Integer> counts, final VariantContext context, final boolean useAC) {
-        final int[] ac;
-        if ( context.hasAttribute(VCFConstants.MLE_ALLELE_COUNT_KEY) && ! useAC ) {
-            ac = extractInts(context.getAttribute(VCFConstants.MLE_ALLELE_COUNT_KEY));
-        } else if ( context.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) ) {
-            ac = extractInts(context.getAttribute(VCFConstants.ALLELE_COUNT_KEY));
-        } else {
-            ac = new int[context.getAlternateAlleles().size()];
-            int idx = 0;
-            for ( final Allele allele : context.getAlternateAlleles() ) {
-                ac[idx++] = context.getCalledChrCount(allele);
-            }
-        }
-
-        for ( final Allele allele : context.getAlleles() ) {
-            final int count;
-            if ( allele.isReference() ) {
-                if ( context.hasAttribute(VCFConstants.ALLELE_NUMBER_KEY) ) {
-                    count = context.getAttributeAsInt(VCFConstants.ALLELE_NUMBER_KEY,-1) - (int) MathUtils.sum(ac);
-                } else {
-                    count = context.getCalledChrCount() - (int) MathUtils.sum(ac);
-                }
-            } else {
-                count = ac[context.getAlternateAlleles().indexOf(allele)];
-            }
-            if ( ! counts.containsKey(allele) ) {
-                counts.put(allele,0);
-            }
-            counts.put(allele,count + counts.get(allele));
-        }
-    }
-
-    public static int[] extractInts(final Object integerListContainingVCField) {
-        List<Integer> mleList = null;
-        if ( integerListContainingVCField instanceof List ) {
-            if ( ((List) integerListContainingVCField).get(0) instanceof String ) {
-                mleList = new ArrayList<>(((List) integerListContainingVCField).size());
-                for ( Object s : ((List)integerListContainingVCField)) {
-                    mleList.add(Integer.parseInt((String) s));
-                }
-            } else {
-                mleList = (List<Integer>) integerListContainingVCField;
-            }
-        } else if ( integerListContainingVCField instanceof Integer ) {
-            mleList = Arrays.asList((Integer) integerListContainingVCField);
-        } else if ( integerListContainingVCField instanceof String ) {
-            mleList = Arrays.asList(Integer.parseInt((String)integerListContainingVCField));
-        }
-        if ( mleList == null )
-            throw new IllegalArgumentException(String.format("VCF does not have properly formatted "+
-                    VCFConstants.MLE_ALLELE_COUNT_KEY+" or "+VCFConstants.ALLELE_COUNT_KEY));
-
-        final int[] mle = new int[mleList.size()];
-
-        if ( ! ( mleList.get(0) instanceof Integer ) ) {
-            throw new IllegalStateException("BUG: The AC values should be an Integer, but was "+mleList.get(0).getClass().getCanonicalName());
-        }
-
-        for ( int idx = 0; idx < mle.length; idx++) {
-            mle[idx] = mleList.get(idx);
-        }
-
-        return mle;
-    }
+    public Map<String, PerReadAlleleLikelihoodMap> computeReadLikelihoods(AssemblyResultSet assemblyResultSet,
+                               Map<String, List<GATKSAMRecord>> perSampleReadList);
 }
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java
index 165fb71db..d0e28d878 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java
@@ -124,15 +124,16 @@ public abstract class LocalAssemblyEngine {
      * @param refLoc                    GenomeLoc object corresponding to the reference sequence with padding
      * @param activeAllelesToGenotype   the alleles to inject into the haplotypes during GGA mode
      * @param readErrorCorrector        a ReadErrorCorrector object, if read are to be corrected before assembly. Can be null if no error corrector is to be used.
-     * @return                          a non-empty list of all the haplotypes that are produced during assembly
+     * @return                          the resulting assembly-result-set
      */
-    public List<Haplotype> runLocalAssembly(final ActiveRegion activeRegion,
+    public AssemblyResultSet runLocalAssembly(final ActiveRegion activeRegion,
                                             final Haplotype refHaplotype,
                                             final byte[] fullReferenceWithPadding,
                                             final GenomeLoc refLoc,
                                             final List<VariantContext> activeAllelesToGenotype,
                                             final ReadErrorCorrector readErrorCorrector) {
         if( activeRegion == null ) { throw new IllegalArgumentException("Assembly engine cannot be used with a null ActiveRegion."); }
+        if( activeRegion.getExtendedLoc() == null ) { throw new IllegalArgumentException("Active region must have an extended location."); }
         if( refHaplotype == null ) { throw new IllegalArgumentException("Reference haplotype cannot be null."); }
         if( fullReferenceWithPadding.length != refLoc.size() ) { throw new IllegalArgumentException("Reference bases and reference loc must be the same size."); }
         if( pruneFactor < 0 ) { throw new IllegalArgumentException("Pruning factor cannot be negative"); }
@@ -153,26 +154,32 @@ public abstract class LocalAssemblyEngine {
         }
 
         final List<SeqGraph> nonRefGraphs = new LinkedList<>();
+        final AssemblyResultSet resultSet = new AssemblyResultSet();
+        resultSet.setRegionForGenotyping(activeRegion);
+        resultSet.setFullReferenceWithPadding(fullReferenceWithPadding);
+        resultSet.setPaddedReferenceLoc(refLoc);
+        final GenomeLoc activeRegionExtendedLocation = activeRegion.getExtendedLoc();
+        refHaplotype.setGenomeLocation(activeRegionExtendedLocation);
+        resultSet.add(refHaplotype);
+        final Map<SeqGraph,AssemblyResult> assemblyResultByGraph = new HashMap<>();
         // create the graphs by calling our subclass assemble method
         for ( final AssemblyResult result : assemble(correctedReads, refHaplotype, activeAlleleHaplotypes) ) {
             if ( result.getStatus() == AssemblyResult.Status.ASSEMBLED_SOME_VARIATION ) {
                 // do some QC on the graph
                 sanityCheckGraph(result.getGraph(), refHaplotype);
                 // add it to graphs with meaningful non-reference features
+                assemblyResultByGraph.put(result.getGraph(),result);
                 nonRefGraphs.add(result.getGraph());
             }
+
         }
 
+        findBestPaths (nonRefGraphs, refHaplotype, refLoc, activeRegionExtendedLocation, assemblyResultByGraph, resultSet);
+
         // print the graphs if the appropriate debug option has been turned on
         if ( graphWriter != null ) { printGraphs(nonRefGraphs); }
 
-        if ( nonRefGraphs.isEmpty() ) {
-            // we couldn't assemble any meaningful graphs, so return just the reference haplotype
-            return Collections.singletonList(refHaplotype);
-        } else {
-            // find the best paths in the graphs and return them as haplotypes
-            return findBestPaths( nonRefGraphs, refHaplotype, refLoc, activeRegion.getExtendedLoc() );
-        }
+        return resultSet;
     }
 
     /**
@@ -198,8 +205,10 @@ public abstract class LocalAssemblyEngine {
         return new ArrayList<>(returnHaplotypes);
     }
 
+
     @Ensures({"result.contains(refHaplotype)"})
-    protected List<Haplotype> findBestPaths(final List<SeqGraph> graphs, final Haplotype refHaplotype, final GenomeLoc refLoc, final GenomeLoc activeRegionWindow) {
+    protected List<Haplotype> findBestPaths(final List<SeqGraph> graphs, final Haplotype refHaplotype, final GenomeLoc refLoc, final GenomeLoc activeRegionWindow,
+                                            final Map<SeqGraph,AssemblyResult> assemblyResultByGraph, final AssemblyResultSet assemblyResultSet) {
         // add the reference haplotype separately from all the others to ensure that it is present in the list of haplotypes
         final Set<Haplotype> returnHaplotypes = new LinkedHashSet<>();
         returnHaplotypes.add( refHaplotype );
@@ -235,7 +244,9 @@ public abstract class LocalAssemblyEngine {
                     h.setCigar(cigar);
                     h.setAlignmentStartHapwrtRef(activeRegionStart);
                     h.setScore(path.getScore());
+                    h.setGenomeLocation(activeRegionWindow);
                     returnHaplotypes.add(h);
+                    assemblyResultSet.add(h, assemblyResultByGraph.get(graph));
 
                     if ( debug )
                         logger.info("Adding haplotype " + h.getCigar() + " from graph with kmer " + graph.getKmerSize());
@@ -243,8 +254,6 @@ public abstract class LocalAssemblyEngine {
             }
         }
 
-        // add genome locs to the haplotypes
-        for ( final Haplotype h : returnHaplotypes ) h.setGenomeLocation(activeRegionWindow);
 
         if ( returnHaplotypes.size() < returnHaplotypes.size() )
             logger.info("Found " + returnHaplotypes.size() + " candidate haplotypes of " + returnHaplotypes.size() + " possible combinations to evaluate every read against at " + refLoc);
@@ -262,8 +271,8 @@ public abstract class LocalAssemblyEngine {
         }
 
         return new ArrayList<>(returnHaplotypes);
-    }
 
+    }
     /**
      * We use CigarOperator.N as the signal that an incomplete or too divergent bubble was found during bubble traversal
      * @param c the cigar to test
@@ -326,7 +335,6 @@ public abstract class LocalAssemblyEngine {
             seqGraph.addEdge(complete, dummy, new BaseEdge(true, 0));
         }
         printDebugGraphTransform(seqGraph, new File("sequenceGraph.5.final.dot"));
-
         return new AssemblyResult(AssemblyResult.Status.ASSEMBLED_SOME_VARIATION, seqGraph);
     }
 
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
new file mode 100644
index 000000000..9e54f7947
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
@@ -0,0 +1,834 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*  
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*  
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*  
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*  
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*  
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. 
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.  
+*  
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY 
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*  
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*  
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*  
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*  
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt. 
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. 
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
+
+import com.google.java.contract.Ensures;
+import com.google.java.contract.Requires;
+import net.sf.samtools.SAMUtils;
+import org.apache.log4j.Logger;
+import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.QualityUtils;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.haplotype.Haplotype;
+import org.broadinstitute.sting.utils.pairhmm.*;
+import org.broadinstitute.sting.utils.recalibration.covariates.RepeatCovariate;
+import org.broadinstitute.sting.utils.recalibration.covariates.RepeatLengthCovariate;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.sting.utils.sam.ReadUtils;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.variant.variantcontext.*;
+import org.broadinstitute.variant.vcf.VCFConstants;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.PrintStream;
+import java.util.*;
+
+public class PairHMMLikelihoodCalculationEngine implements LikelihoodCalculationEngine {
+    private final static Logger logger = Logger.getLogger(PairHMMLikelihoodCalculationEngine.class);
+
+    private static final byte BASE_QUALITY_SCORE_THRESHOLD = (byte) 18; // Base quals less than this value are squashed down to min possible qual
+
+    private final byte constantGCP;
+    private final double log10globalReadMismappingRate;
+    private final boolean DEBUG;
+
+    private final PairHMM.HMM_IMPLEMENTATION hmmType;
+    private final boolean noFpga;
+
+    private final ThreadLocal<PairHMM> pairHMMThreadLocal = new ThreadLocal<PairHMM>() {
+        @Override
+        protected PairHMM initialValue() {
+            switch (hmmType) {
+                case EXACT: return new Log10PairHMM(true);
+                case ORIGINAL: return new Log10PairHMM(false);
+                case LOGLESS_CACHING:
+                    if (noFpga || !CnyPairHMM.isAvailable())
+                        return new LoglessPairHMM();
+                    else
+                        return new CnyPairHMM();
+                case ARRAY_LOGLESS:
+                    if (noFpga || !CnyPairHMM.isAvailable())
+                        return new ArrayLoglessPairHMM();
+                    else
+                        return new CnyPairHMM();
+                default:
+                    throw new UserException.BadArgumentValue("pairHMM", "Specified pairHMM implementation is unrecognized or incompatible with the HaplotypeCaller. Acceptable options are ORIGINAL, EXACT, CACHING, LOGLESS_CACHING, and ARRAY_LOGLESS.");
+            }
+        }
+    };
+//    Attempted to do as below, to avoid calling pairHMMThreadLocal.get() later on, but it resulted in a NullPointerException
+//    private final PairHMM pairHMM = pairHMMThreadLocal.get();
+
+    private final static boolean WRITE_LIKELIHOODS_TO_FILE = false;
+    private final static String LIKELIHOODS_FILENAME = "likelihoods.txt";
+    private final PrintStream likelihoodsStream;
+
+    public enum PCR_ERROR_MODEL {
+        /** no specialized PCR error model will be applied; if base insertion/deletion qualities are present they will be used */
+        NONE,
+        /** a more aggressive model will be applied that sacrifices true positives in order to remove more false positives */
+        AGGRESSIVE,
+        /** a less aggressive model will be applied that tries to maintain a high true positive rate at the expense of allowing more false positives */
+        CONSERVATIVE
+    }
+
+    private final PCR_ERROR_MODEL pcrErrorModel;
+
+    /**
+     * The expected rate of random sequencing errors for a read originating from its true haplotype.
+     *
+     * For example, if this is 0.01, then we'd expect 1 error per 100 bp.
+     */
+    private final static double EXPECTED_ERROR_RATE_PER_BASE = 0.02;
+
+    /**
+     * Create a new PairHMMLikelihoodCalculationEngine using provided parameters and hmm to do its calculations
+     *
+     * @param constantGCP the gap continuation penalty to use with the PairHMM
+     * @param debug should we emit debugging information during the calculation?
+     * @param hmmType the type of the HMM to use
+     * @param log10globalReadMismappingRate the global mismapping probability, in log10(prob) units.  A value of
+     *                                      -3 means that the chance that a read doesn't actually belong at this
+     *                                      location in the genome is 1 in 1000.  The effect of this parameter is
+     *                                      to cap the maximum likelihood difference between the reference haplotype
+     *                                      and the best alternative haplotype by -3 log units.  So if the best
+     *                                      haplotype is at -10 and this parameter has a value of -3 then even if the
+     *                                      reference haplotype gets a score of -100 from the pairhmm it will be
+     *                                      assigned a likelihood of -13.
+     * @param noFpga disable FPGA acceleration
+     */
+    public PairHMMLikelihoodCalculationEngine( final byte constantGCP, final boolean debug, final PairHMM.HMM_IMPLEMENTATION hmmType, final double log10globalReadMismappingRate, final boolean noFpga, final PCR_ERROR_MODEL pcrErrorModel ) {
+        this.hmmType = hmmType;
+        this.constantGCP = constantGCP;
+        this.DEBUG = debug;
+        this.log10globalReadMismappingRate = log10globalReadMismappingRate;
+        this.noFpga = noFpga;
+        this.pcrErrorModel = pcrErrorModel;
+
+        initializePCRErrorModel();
+
+        if ( WRITE_LIKELIHOODS_TO_FILE ) {
+            try {
+                likelihoodsStream = new PrintStream(new FileOutputStream(new File(LIKELIHOODS_FILENAME)));
+            } catch ( FileNotFoundException e ) {
+                throw new RuntimeException(e);
+            }
+        } else {
+            likelihoodsStream = null;
+        }
+    }
+
+    public void close() {
+        if ( likelihoodsStream != null ) likelihoodsStream.close();
+    }
+
+    private void writeDebugLikelihoods(final GATKSAMRecord processedRead, final Haplotype haplotype, final double log10l){
+        if ( WRITE_LIKELIHOODS_TO_FILE ) {
+            likelihoodsStream.printf("%s %s %s %s %s %s %f%n",
+                    haplotype.getBaseString(),
+                    new String(processedRead.getReadBases() ),
+                    SAMUtils.phredToFastq(processedRead.getBaseQualities() ),
+                    SAMUtils.phredToFastq(processedRead.getBaseInsertionQualities() ),
+                    SAMUtils.phredToFastq(processedRead.getBaseDeletionQualities() ),
+                    SAMUtils.phredToFastq(constantGCP),
+                    log10l);
+        }
+    }
+
+    private Map<Allele, Haplotype> createAlleleMap(List<Haplotype> haplotypes){
+        final int numHaplotypes = haplotypes.size();
+        final Map<Allele, Haplotype> alleleMap = new LinkedHashMap<>(numHaplotypes);
+        for ( final Haplotype haplotype : haplotypes ) {
+            final Allele allele = Allele.create(haplotype, true);
+            alleleMap.put(allele, haplotype);
+        }
+        return alleleMap;
+    }
+
+    private Map<GATKSAMRecord, byte[]> fillGCPArrays(List<GATKSAMRecord> reads){
+        final Map<GATKSAMRecord, byte []> GCPArrayMap = new LinkedHashMap<>();
+        for (GATKSAMRecord read: reads){
+            byte [] GCPArray = new byte[read.getReadBases().length];
+            Arrays.fill( GCPArray, constantGCP ); // Is there a way to derive empirical estimates for this from the data?
+            GCPArrayMap.put(read, GCPArray);
+        }
+        return GCPArrayMap;
+    }
+
+    private void capMinimumReadQualities(GATKSAMRecord read, byte[] readQuals, byte[] readInsQuals, byte[] readDelQuals) {
+        for( int kkk = 0; kkk < readQuals.length; kkk++ ) {
+            readQuals[kkk] = (byte) Math.min( 0xff & readQuals[kkk], read.getMappingQuality()); // cap base quality by mapping quality, as in UG
+            readQuals[kkk] = ( readQuals[kkk] < BASE_QUALITY_SCORE_THRESHOLD ? QualityUtils.MIN_USABLE_Q_SCORE : readQuals[kkk] );
+            readInsQuals[kkk] = ( readInsQuals[kkk] < QualityUtils.MIN_USABLE_Q_SCORE ? QualityUtils.MIN_USABLE_Q_SCORE : readInsQuals[kkk] );
+            readDelQuals[kkk] = ( readDelQuals[kkk] < QualityUtils.MIN_USABLE_Q_SCORE ? QualityUtils.MIN_USABLE_Q_SCORE : readDelQuals[kkk] );
+        }
+    }
+
+    /**
+     * Pre-processing of the reads to be evaluated at the current location from the current sample.
+     * We apply the PCR Error Model, and cap the minimum base, insertion, and deletion qualities of each read.
+     * Modified copies of reads are packed into a new list, while original reads are retained for downstream use
+     *
+     * @param reads The original list of unmodified reads
+     * @return processedReads. A new list of reads, in the same order, whose qualities have been altered by PCR error model and minimal quality thresholding
+     */
+    private List<GATKSAMRecord> modifyReadQualities(final List<GATKSAMRecord> reads) {
+        List<GATKSAMRecord> processedReads = new LinkedList<>();
+        for ( GATKSAMRecord read : reads ) {
+
+            final byte[] readBases = read.getReadBases();
+
+            // NOTE -- must clone anything that gets modified here so we don't screw up future uses of the read
+            final byte[] readQuals = read.getBaseQualities().clone();
+            final byte[] readInsQuals = read.getBaseInsertionQualities().clone();
+            final byte[] readDelQuals = read.getBaseDeletionQualities().clone();
+
+            applyPCRErrorModel(readBases, readInsQuals, readDelQuals);
+            capMinimumReadQualities(read, readQuals, readInsQuals, readDelQuals);
+
+            // Create a new copy of the read and sets its base qualities to the modified versions.
+            // Pack this into a new list for return
+            final GATKSAMRecord processedRead = GATKSAMRecord.createQualityModifiedRead(read, readBases, readQuals, readInsQuals, readDelQuals);
+            processedReads.add(processedRead);
+        }
+        return processedReads;
+    }
+
+    /**
+     * Post-processing of the read/allele likelihoods.
+     *
+     * We send quality-capped reads to the pairHMM for evaluation, and it returns a map containing these capped reads.
+     * We wish to return a map containing the original, unmodified reads.
+     *
+     * At the same time, we want to effectively set a lower cap on the reference score, based on the global mis-mapping rate.
+     * This protects us from the case where the assembly has produced haplotypes
+     * that are very divergent from reference, but are supported by only one read.  In effect
+     * we capping how badly scoring the reference can be for any read by the chance that the read
+     * itself just doesn't belong here
+     *
+     * @param perReadAlleleLikelihoodMap the original map returned by the PairHMM. Contains the processed reads, the haplotype Alleles, and their log10ls
+     * @param reads Our original, unmodified reads
+     * @param processedReads Reads whose minimum base,insertion,deletion qualities have been capped; these were actually used to derive log10ls
+     * @param alleleHaplotypeMap The map associating the Allele and Haplotype versions of each haplotype
+     *
+     * @return processedReadAlleleLikelihoodMap; a new PRALM containing the original reads, and their haplotype log10ls including capped reference log10ls
+     */
+    private PerReadAlleleLikelihoodMap capReferenceHaplotypeLikelihoods(PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap, List<GATKSAMRecord> reads, List<GATKSAMRecord> processedReads, Map<Allele, Haplotype> alleleHaplotypeMap){
+
+        // a new read/allele map, to contain the uncapped reads, haplotypes, and potentially the capped reference log10ls
+        final PerReadAlleleLikelihoodMap processedReadAlleleLikelihoodMap = new PerReadAlleleLikelihoodMap();
+
+        Allele refAllele = null;
+        final int numReads = reads.size();
+        for (int readIndex = 0; readIndex < numReads; readIndex++) {
+
+            // Get the original and quality-modified read from their respective lists
+            // Note that this requires both lists to have reads in the same order
+            final GATKSAMRecord originalRead = reads.get(readIndex);
+            final GATKSAMRecord processedRead = processedReads.get(readIndex);
+
+            // keep track of the reference likelihood and the best non-ref likelihood
+            double refLog10l = Double.NEGATIVE_INFINITY;
+            double bestNonReflog10L = Double.NEGATIVE_INFINITY;
+
+            for ( Allele allele : alleleHaplotypeMap.keySet() ) {
+                final double log10l = perReadAlleleLikelihoodMap.getLikelihoodAssociatedWithReadAndAllele(processedRead, allele);
+                final Haplotype haplotype = alleleHaplotypeMap.get(allele);
+                if ( haplotype.isNonReference() )
+                    bestNonReflog10L = Math.max(bestNonReflog10L, log10l);
+                else {
+                    refAllele = allele;
+                    refLog10l = log10l;
+                }
+                writeDebugLikelihoods(processedRead, haplotype, log10l);
+
+                // add the ORIGINAL (non-capped) read to the final map, along with the current haplotype and associated log10l
+                processedReadAlleleLikelihoodMap.add(originalRead, allele, log10l);
+            }
+
+            // ensure that the reference haplotype is no worse than the best non-ref haplotype minus the global
+            // mismapping rate.  This protects us from the case where the assembly has produced haplotypes
+            // that are very divergent from reference, but are supported by only one read.  In effect
+            // we capping how badly scoring the reference can be for any read by the chance that the read
+            // itself just doesn't belong here
+            final double worstRefLog10Allowed = bestNonReflog10L + log10globalReadMismappingRate;
+            if ( refLog10l < (worstRefLog10Allowed) ) {
+                processedReadAlleleLikelihoodMap.add(originalRead, refAllele, worstRefLog10Allowed);
+            }
+        }
+        return processedReadAlleleLikelihoodMap;
+    }
+
+    /**
+     * Initialize our pairHMM with parameters appropriate to the haplotypes and reads we're going to evaluate
+     *
+     * After calling this routine the PairHMM will be configured to best evaluate all reads in the samples
+     * against the set of haplotypes
+     *
+     * @param haplotypes a non-null list of haplotypes
+     * @param perSampleReadList a mapping from sample -> reads
+     */
+    private void initializePairHMM(final List<Haplotype> haplotypes, final Map<String, List<GATKSAMRecord>> perSampleReadList) {
+        int X_METRIC_LENGTH = 0;
+        for( final Map.Entry<String, List<GATKSAMRecord>> sample : perSampleReadList.entrySet() ) {
+            for( final GATKSAMRecord read : sample.getValue() ) {
+               final int readLength = read.getReadLength();
+               if( readLength > X_METRIC_LENGTH ) { X_METRIC_LENGTH = readLength; }
+            }
+        }
+        int Y_METRIC_LENGTH = 0;
+        for( final Haplotype h : haplotypes ) {
+            final int haplotypeLength = h.getBases().length;
+            if( haplotypeLength > Y_METRIC_LENGTH ) { Y_METRIC_LENGTH = haplotypeLength; }
+        }
+
+        // initialize arrays to hold the probabilities of being in the match, insertion and deletion cases
+        pairHMMThreadLocal.get().initialize(X_METRIC_LENGTH, Y_METRIC_LENGTH);
+    }
+
+
+    @Override
+    public Map<String, PerReadAlleleLikelihoodMap> computeReadLikelihoods( final AssemblyResultSet assemblyResultSet, final Map<String, List<GATKSAMRecord>> perSampleReadList ) {
+
+        final List<Haplotype> haplotypes = assemblyResultSet.getHaplotypeList();
+        // configure the HMM
+        initializePairHMM(haplotypes, perSampleReadList);
+
+        // Add likelihoods for each sample's reads to our stratifiedReadMap
+        final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap = new LinkedHashMap<>();
+        for( final Map.Entry<String, List<GATKSAMRecord>> sampleEntry : perSampleReadList.entrySet() ) {
+             // evaluate the likelihood of the reads given those haplotypes
+            final PerReadAlleleLikelihoodMap map = computeReadLikelihoods(haplotypes, sampleEntry.getValue());
+
+            map.filterPoorlyModelledReads(EXPECTED_ERROR_RATE_PER_BASE);
+            stratifiedReadMap.put(sampleEntry.getKey(), map);
+        }
+
+        return stratifiedReadMap;
+    }
+
+
+    public Map<String, PerReadAlleleLikelihoodMap> computeReadLikelihoods( final List<Haplotype> haplotypes, final Map<String, List<GATKSAMRecord>> perSampleReadList ) {
+
+        // Add likelihoods for each sample's reads to our stratifiedReadMap
+        final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap = new LinkedHashMap<>();
+        for( final Map.Entry<String, List<GATKSAMRecord>> sampleEntry : perSampleReadList.entrySet() ) {
+            // evaluate the likelihood of the reads given those haplotypes
+            final PerReadAlleleLikelihoodMap map = computeReadLikelihoods(haplotypes, sampleEntry.getValue());
+
+            map.filterPoorlyModelledReads(EXPECTED_ERROR_RATE_PER_BASE);
+            stratifiedReadMap.put(sampleEntry.getKey(), map);
+        }
+
+        return stratifiedReadMap;
+    }
+
+    private PerReadAlleleLikelihoodMap computeReadLikelihoods( final List<Haplotype> haplotypes, final List<GATKSAMRecord> reads) {
+
+        // Modify the read qualities by applying the PCR error model and capping the minimum base,insertion,deletion qualities
+        List<GATKSAMRecord> processedReads = modifyReadQualities(reads);
+
+        // Get alleles corresponding to our haplotypees
+        Map<Allele, Haplotype> alleleHaplotypeMap = createAlleleMap(haplotypes);
+
+        // Get an array containing the constantGCP for each read in our modified read list
+        Map<GATKSAMRecord,byte[]> GCPArrayMap = fillGCPArrays(processedReads);
+
+        // Run the PairHMM to calculate the log10 likelihood of each (processed) reads' arising from each haplotype
+        PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = pairHMMThreadLocal.get().computeLikelihoods(processedReads, alleleHaplotypeMap, GCPArrayMap);
+
+        // Generate a new map containing the original, unmodified reads, and with minimal reference haplotype log10ls determined from the global mis-mapping rate
+
+        return capReferenceHaplotypeLikelihoods(perReadAlleleLikelihoodMap, reads, processedReads, alleleHaplotypeMap);
+    }
+
+    @Requires({"alleleOrdering.size() > 0"})
+    @Ensures({"result.length == result[0].length", "result.length == alleleOrdering.size()"})
+    public static double[][] computeDiploidHaplotypeLikelihoods( final String sample,
+                                                                 final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap,
+                                                                 final List<Allele> alleleOrdering,
+                                                                 final boolean normalize ) {
+        return computeDiploidHaplotypeLikelihoods(Collections.singleton(sample), stratifiedReadMap, alleleOrdering, normalize);
+    }
+
+    @Requires({"alleleOrdering.size() > 0"})
+    @Ensures({"result.length == result[0].length", "result.length == alleleOrdering.size()"})
+    public static double[][] computeDiploidHaplotypeLikelihoods( final Set<String> samples,
+                                                                 final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap,
+                                                                 final List<Allele> alleleOrdering,
+                                                                 final boolean normalize) {
+
+        final int numHaplotypes = alleleOrdering.size();
+        final double[][] haplotypeLikelihoodMatrix = new double[numHaplotypes][numHaplotypes];
+        for( int iii = 0; iii < numHaplotypes; iii++ ) {
+            Arrays.fill(haplotypeLikelihoodMatrix[iii], Double.NEGATIVE_INFINITY);
+        }
+
+        // compute the diploid haplotype likelihoods
+        for( int iii = 0; iii < numHaplotypes; iii++ ) {
+            final Allele iii_allele = alleleOrdering.get(iii);
+            for( int jjj = 0; jjj <= iii; jjj++ ) {
+                final Allele jjj_allele = alleleOrdering.get(jjj);
+                double haplotypeLikelihood = 0.0;
+                for( final String sample : samples ) {
+                    for( final Map.Entry<GATKSAMRecord, Map<Allele,Double>> entry : stratifiedReadMap.get(sample).getLikelihoodReadMap().entrySet() ) {
+                        // Compute log10(10^x1/2 + 10^x2/2) = log10(10^x1+10^x2)-log10(2)
+                        // First term is approximated by Jacobian log with table lookup.
+                        haplotypeLikelihood += ReadUtils.getMeanRepresentativeReadCount( entry.getKey() ) *
+                                ( MathUtils.approximateLog10SumLog10(entry.getValue().get(iii_allele), entry.getValue().get(jjj_allele)) + MathUtils.LOG_ONE_HALF );
+                    }
+                }
+                haplotypeLikelihoodMatrix[iii][jjj] = haplotypeLikelihood;
+            }
+        }
+
+        // normalize the diploid likelihoods matrix
+        return normalize ? normalizeDiploidLikelihoodMatrixFromLog10( haplotypeLikelihoodMatrix ) : haplotypeLikelihoodMatrix;
+    }
+
+    @Requires({"likelihoodMatrix.length == likelihoodMatrix[0].length"})
+    @Ensures({"result.length == result[0].length", "result.length == likelihoodMatrix.length"})
+    protected static double[][] normalizeDiploidLikelihoodMatrixFromLog10( final double[][] likelihoodMatrix ) {
+        final int numHaplotypes = likelihoodMatrix.length;
+        double[] genotypeLikelihoods = new double[numHaplotypes*(numHaplotypes+1)/2];
+        int index = 0;
+        for( int iii = 0; iii < numHaplotypes; iii++ ) {
+            for( int jjj = 0; jjj <= iii; jjj++ ){
+                genotypeLikelihoods[index++] = likelihoodMatrix[iii][jjj];
+            }
+        }
+        genotypeLikelihoods = MathUtils.normalizeFromLog10(genotypeLikelihoods, false, true);
+        index = 0;
+        for( int iii = 0; iii < numHaplotypes; iii++ ) {
+            for( int jjj = 0; jjj <= iii; jjj++ ){
+                likelihoodMatrix[iii][jjj] = genotypeLikelihoods[index++];
+            }
+        }
+        return likelihoodMatrix;
+    }
+
+    // --------------------------------------------------------------------------------
+    //
+    // System to compute the best N haplotypes for genotyping
+    //
+    // --------------------------------------------------------------------------------
+//
+//    /**
+//     * Helper function for selectBestHaplotypesFromEachSample that updates the score of haplotype haplotypeAsAllele
+//     * @param map an annoying map object that moves us between the allele and haplotype representation
+//     * @param haplotypeAsAllele the allele version of the haplotype
+//     * @return the haplotype version, with its score incremented by 1 if its non-reference
+//     */
+//    private Haplotype updateSelectHaplotype(final Map<Allele, Haplotype> map, final Allele haplotypeAsAllele) {
+//        final Haplotype h = map.get(haplotypeAsAllele); // TODO -- fixme when haplotypes are properly generic
+//        if ( h.isNonReference() ) h.setScore(h.getScore() + 1); // ref is already at max value
+//        return h;
+//    }
+//
+//    /**
+//     * Take the best N haplotypes and return them as a list
+//     *
+//     * Only considers the haplotypes selectedHaplotypes that were actually selected by at least one sample
+//     * as it's preferred haplotype.  Takes the best N haplotypes from selectedHaplotypes in decreasing
+//     * order of score (so higher score haplotypes are preferred).  The N we take is determined by
+//     *
+//     * N = min(2 * nSamples + 1, maxNumHaplotypesInPopulation)
+//     *
+//     * where 2 * nSamples is the number of chromosomes in 2 samples including the reference, and our workload is
+//     * bounded by maxNumHaplotypesInPopulation as that number can grow without bound
+//     *
+//     * @param selectedHaplotypes a non-null set of haplotypes with scores >= 1
+//     * @param nSamples the number of samples used to select the haplotypes
+//     * @param maxNumHaplotypesInPopulation the maximum number of haplotypes we're allowed to take, regardless of nSamples
+//     * @return a list of N or fewer haplotypes, with the reference haplotype first
+//     */
+//    private List<Haplotype> selectBestHaplotypesAccordingToScore(final Set<Haplotype> selectedHaplotypes, final int nSamples, final int maxNumHaplotypesInPopulation) {
+//        final List<Haplotype> selectedHaplotypesList = new ArrayList<>(selectedHaplotypes);
+//        Collections.sort(selectedHaplotypesList, new HaplotypeScoreComparator());
+//        final int numChromosomesInSamplesPlusRef = 2 * nSamples + 1;
+//        final int haplotypesToKeep = Math.min(numChromosomesInSamplesPlusRef, maxNumHaplotypesInPopulation);
+//        final List<Haplotype> bestHaplotypes = selectedHaplotypesList.size() <= haplotypesToKeep ? selectedHaplotypesList : selectedHaplotypesList.subList(0, haplotypesToKeep);
+//        if ( bestHaplotypes.get(0).isNonReference()) throw new IllegalStateException("BUG: reference haplotype should be first in list");
+//        return bestHaplotypes;
+//    }
+//
+//    /**
+//     * Select the best haplotypes for genotyping the samples in stratifiedReadMap
+//     *
+//     * Selects these haplotypes by counting up how often each haplotype is selected as one of the most likely
+//     * haplotypes per sample.  What this means is that each sample computes the diploid genotype likelihoods for
+//     * all possible pairs of haplotypes, and the pair with the highest likelihood has each haplotype each get
+//     * one extra count for each haplotype (so hom-var haplotypes get two counts).  After performing this calculation
+//     * the best N haplotypes are selected (@see #selectBestHaplotypesAccordingToScore) and a list of the
+//     * haplotypes in order of score are returned, ensuring that at least one of the haplotypes is reference.
+//     *
+//     * @param haplotypes a list of all haplotypes we're considering
+//     * @param stratifiedReadMap a map from sample -> read likelihoods per haplotype
+//     * @param maxNumHaplotypesInPopulation the max. number of haplotypes we can select from haplotypes
+//     * @return a list of selected haplotypes with size <= maxNumHaplotypesInPopulation
+//     */
+//    public List<Haplotype> selectBestHaplotypesFromEachSample(final List<Haplotype> haplotypes, final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap, final int maxNumHaplotypesInPopulation) {
+//        if ( haplotypes.size() < 2 ) throw new IllegalArgumentException("Must have at least 2 haplotypes to consider but only have " + haplotypes);
+//
+//        if ( haplotypes.size() == 2 ) return haplotypes; // fast path -- we'll always want to use 2 haplotypes
+//
+//        // all of the haplotypes that at least one sample called as one of the most likely
+//        final Set<Haplotype> selectedHaplotypes = new HashSet<>();
+//        selectedHaplotypes.add(findReferenceHaplotype(haplotypes)); // ref is always one of the selected
+//
+//        // our annoying map from allele -> haplotype
+//        final Map<Allele, Haplotype> allele2Haplotype = new HashMap<>();
+//        for ( final Haplotype h : haplotypes ) {
+//            h.setScore(h.isReference() ? Double.MAX_VALUE : 0.0); // set all of the scores to 0 (lowest value) for all non-ref haplotypes
+//            allele2Haplotype.put(Allele.create(h, h.isReference()), h);
+//        }
+//
+//        // for each sample, compute the most likely pair of haplotypes
+//        for ( final Map.Entry<String, PerReadAlleleLikelihoodMap> entry : stratifiedReadMap.entrySet() ) {
+//            // get the two most likely haplotypes under a diploid model for this sample
+//            final MostLikelyAllele mla = entry.getValue().getMostLikelyDiploidAlleles();
+//
+//            if ( mla != null ) { // there was something to evaluate in this sample
+//                // note that there must be at least 2 haplotypes
+//                final Haplotype best = updateSelectHaplotype(allele2Haplotype, mla.getMostLikelyAllele());
+//                final Haplotype second = updateSelectHaplotype(allele2Haplotype, mla.getSecondMostLikelyAllele());
+//
+////            if ( DEBUG ) {
+////                logger.info("Chose haplotypes " + best + " " + best.getCigar() + " and " + second + " " + second.getCigar() + " for sample " + entry.getKey());
+////            }
+//
+//                // add these two haplotypes to the set of haplotypes that have been selected
+//                selectedHaplotypes.add(best);
+//                selectedHaplotypes.add(second);
+//
+//                // we've already selected all of our haplotypes, and we don't need to prune them down
+//                if ( selectedHaplotypes.size() == haplotypes.size() && haplotypes.size() < maxNumHaplotypesInPopulation )
+//                    break;
+//            }
+//        }
+//
+//        // take the best N haplotypes forward, in order of the number of samples that choose them
+//        final int nSamples = stratifiedReadMap.size();
+//        final List<Haplotype> bestHaplotypes = selectBestHaplotypesAccordingToScore(selectedHaplotypes, nSamples, maxNumHaplotypesInPopulation);
+//
+//        if ( DEBUG ) {
+//            logger.info("Chose " + (bestHaplotypes.size() - 1) + " alternate haplotypes to genotype in all samples.");
+//            for ( final Haplotype h : bestHaplotypes ) {
+//                logger.info("\tHaplotype " + h.getCigar() + " selected for further genotyping" + (h.isNonReference() ? " found " + (int)h.getScore() + " haplotypes" : " as ref haplotype"));
+//            }
+//        }
+//        return bestHaplotypes;
+//    }
+//
+//    /**
+//     * Find the haplotype that isRef(), or @throw ReviewedStingException if one isn't found
+//     * @param haplotypes non-null list of haplotypes
+//     * @return the reference haplotype
+//     */
+//    private static Haplotype findReferenceHaplotype( final List<Haplotype> haplotypes ) {
+//        for( final Haplotype h : haplotypes ) {
+//            if( h.isReference() ) return h;
+//        }
+//        throw new ReviewedStingException( "No reference haplotype found in the list of haplotypes!" );
+//    }
+
+    // --------------------------------------------------------------------------------
+    //
+    // Experimental attempts at PCR error rate modeling
+    //
+    // --------------------------------------------------------------------------------
+
+    protected static final int MAX_STR_UNIT_LENGTH = 8;
+    protected static final int MAX_REPEAT_LENGTH = 20;
+    protected static final int MIN_ADJUSTED_QSCORE = 10;
+    protected static final double INITIAL_QSCORE = 40.0;
+
+    private byte[] pcrIndelErrorModelCache = new byte[MAX_REPEAT_LENGTH * MAX_STR_UNIT_LENGTH + 1];
+    private final RepeatCovariate repeatCovariate = new RepeatLengthCovariate();
+
+    private void initializePCRErrorModel() {
+        if ( pcrErrorModel == PCR_ERROR_MODEL.NONE )
+            return;
+
+        repeatCovariate.initialize(MAX_STR_UNIT_LENGTH, MAX_REPEAT_LENGTH);
+
+        pcrIndelErrorModelCache = new byte[MAX_REPEAT_LENGTH + 1];
+
+        final double rateFactor = pcrErrorModel == PCR_ERROR_MODEL.AGGRESSIVE ? 2.0 : 3.0;
+
+        for( int iii = 0; iii <= MAX_REPEAT_LENGTH; iii++ )
+            pcrIndelErrorModelCache[iii] = getErrorModelAdjustedQual(iii, rateFactor);
+    }
+
+    protected static byte getErrorModelAdjustedQual(final int repeatLength, final double rateFactor) {
+        return (byte) Math.max(MIN_ADJUSTED_QSCORE, MathUtils.fastRound( INITIAL_QSCORE - Math.exp(((double) repeatLength) / (rateFactor * Math.PI)) + 1.0 ));
+    }
+
+    protected void applyPCRErrorModel( final byte[] readBases, final byte[] readInsQuals, final byte[] readDelQuals ) {
+        if ( pcrErrorModel == PCR_ERROR_MODEL.NONE )
+            return;
+
+        for ( int iii = 1; iii < readBases.length; iii++ ) {
+            final int repeatLength = repeatCovariate.findTandemRepeatUnits(readBases, iii-1).getSecond();
+            readInsQuals[iii-1] = (byte) Math.min(0xff & readInsQuals[iii-1], 0xff & pcrIndelErrorModelCache[repeatLength]);
+            readDelQuals[iii-1] = (byte) Math.min(0xff & readDelQuals[iii-1], 0xff & pcrIndelErrorModelCache[repeatLength]);
+        }
+    }
+
+    // --------------------------------------------------------------------------------
+    //
+    // Posterior GL calculations
+    //
+    // --------------------------------------------------------------------------------
+
+    public static VariantContext calculatePosteriorGLs(final VariantContext vc1,
+                                                       final Collection<VariantContext> resources,
+                                                       final int numRefSamplesFromMissingResources,
+                                                       final double globalFrequencyPriorDirichlet,
+                                                       final boolean useInputSamples,
+                                                       final boolean useEM,
+                                                       final boolean useAC) {
+        if ( useEM )
+            throw new IllegalArgumentException("EM loop for posterior GLs not yet implemented");
+
+        final Map<Allele,Integer> totalAlleleCounts = new HashMap<>();
+        for ( final VariantContext resource : resources ) {
+            addAlleleCounts(totalAlleleCounts,resource,useAC);
+        }
+
+        if ( useInputSamples ) {
+            addAlleleCounts(totalAlleleCounts,vc1,useAC);
+        }
+
+        totalAlleleCounts.put(vc1.getReference(),totalAlleleCounts.get(vc1.getReference())+numRefSamplesFromMissingResources);
+
+        // now extract the counts of the alleles present within vc1, and in order
+        final double[] alleleCounts = new double[vc1.getNAlleles()];
+        int alleleIndex = 0;
+        for ( final Allele allele : vc1.getAlleles() ) {
+
+            alleleCounts[alleleIndex++] = globalFrequencyPriorDirichlet + ( totalAlleleCounts.containsKey(allele) ?
+                    totalAlleleCounts.get(allele) : 0 );
+        }
+
+        final List<double[]> likelihoods = new ArrayList<>(vc1.getNSamples());
+        for ( final Genotype genotype : vc1.getGenotypes() ) {
+            likelihoods.add(genotype.hasLikelihoods() ? genotype.getLikelihoods().getAsVector() : null );
+        }
+
+        final List<double[]> posteriors = calculatePosteriorGLs(likelihoods,alleleCounts,vc1.getMaxPloidy(2));
+
+        final GenotypesContext newContext = GenotypesContext.create();
+        for ( int genoIdx = 0; genoIdx < vc1.getNSamples(); genoIdx ++ ) {
+            final GenotypeBuilder builder = new GenotypeBuilder(vc1.getGenotype(genoIdx));
+            if ( posteriors.get(genoIdx) != null ) {
+                GATKVariantContextUtils.updateGenotypeAfterSubsetting(vc1.getAlleles(), builder,
+                        GATKVariantContextUtils.GenotypeAssignmentMethod.USE_PLS_TO_ASSIGN, posteriors.get(genoIdx), vc1.getAlleles());
+                builder.attribute(VCFConstants.GENOTYPE_POSTERIORS_KEY,
+                        Utils.listFromPrimitives(GenotypeLikelihoods.fromLog10Likelihoods(posteriors.get(genoIdx)).getAsPLs()));
+
+            }
+            newContext.add(builder.make());
+        }
+
+        final List<Integer> priors = Utils.listFromPrimitives(
+                GenotypeLikelihoods.fromLog10Likelihoods(getDirichletPrior(alleleCounts, vc1.getMaxPloidy(2))).getAsPLs());
+
+        return new VariantContextBuilder(vc1).genotypes(newContext).attribute("PG",priors).make();
+    }
+
+    /**
+     * Given genotype likelihoods and known allele counts, calculate the posterior likelihoods
+     * over the genotype states
+     * @param genotypeLikelihoods - the genotype likelihoods for the individual
+     * @param knownAlleleCountsByAllele - the known allele counts in the population. For AC=2 AN=12 site, this is {10,2}
+     * @param ploidy - the ploidy to assume
+     * @return - the posterior genotype likelihoods
+     */
+    protected static List<double[]> calculatePosteriorGLs(final List<double[]> genotypeLikelihoods,
+                                                       final double[] knownAlleleCountsByAllele,
+                                                       final int ploidy) {
+        if ( ploidy != 2 ) {
+            throw new IllegalStateException("Genotype posteriors not yet implemented for ploidy != 2");
+        }
+
+        final double[] genotypePriorByAllele = getDirichletPrior(knownAlleleCountsByAllele,ploidy);
+        final List<double[]> posteriors = new ArrayList<>(genotypeLikelihoods.size());
+        for ( final double[] likelihoods : genotypeLikelihoods ) {
+            double[] posteriorLikelihoods = null;
+
+            if ( likelihoods != null ) {
+                if ( likelihoods.length != genotypePriorByAllele.length ) {
+                    throw new IllegalStateException(String.format("Likelihoods not of correct size: expected %d, observed %d",
+                            knownAlleleCountsByAllele.length*(knownAlleleCountsByAllele.length+1)/2,likelihoods.length));
+                }
+
+                posteriorLikelihoods = new double[genotypePriorByAllele.length];
+                for ( int genoIdx = 0; genoIdx < likelihoods.length; genoIdx ++ ) {
+                    posteriorLikelihoods[genoIdx] = likelihoods[genoIdx] + genotypePriorByAllele[genoIdx];
+                }
+
+                posteriorLikelihoods = MathUtils.toLog10(MathUtils.normalizeFromLog10(posteriorLikelihoods));
+
+            }
+
+            posteriors.add(posteriorLikelihoods);
+        }
+
+        return posteriors;
+    }
+
+    // convenience function for a single genotypelikelihoods array. Just wraps.
+    protected static double[] calculatePosteriorGLs(final double[] genotypeLikelihoods,
+                                                 final double[] knownAlleleCountsByAllele,
+                                                 final int ploidy) {
+        return calculatePosteriorGLs(Arrays.asList(genotypeLikelihoods),knownAlleleCountsByAllele,ploidy).get(0);
+    }
+
+
+    /**
+     * Given known allele counts (whether external, from the sample, or both), calculate the prior distribution
+     * over genotype states. This assumes
+     *   1) Random sampling of alleles (known counts are unbiased, and frequency estimate is Dirichlet)
+     *   2) Genotype states are independent (Hardy-Weinberg)
+     * These assumptions give rise to a Dirichlet-Multinomial distribution of genotype states as a prior
+     * (the "number of trials" for the multinomial is simply the ploidy)
+     * @param knownCountsByAllele - the known counts per allele. For an AC=2, AN=12 site this is {10,2}
+     * @param ploidy - the number of chromosomes in the sample. For now restricted to 2.
+     * @return - the Dirichlet-Multinomial distribution over genotype states
+     */
+    protected static double[] getDirichletPrior(final double[] knownCountsByAllele, final int ploidy) {
+        if ( ploidy != 2 ) {
+            throw new IllegalStateException("Genotype priors not yet implemented for ploidy != 2");
+        }
+
+        // multi-allelic format is
+        // AA AB BB AC BC CC AD BD CD DD ...
+        final double sumOfKnownCounts = MathUtils.sum(knownCountsByAllele);
+        final double[] priors = new double[knownCountsByAllele.length*(knownCountsByAllele.length+1)/2];
+        int priorIndex = 0;
+        for ( int allele2 = 0; allele2 < knownCountsByAllele.length; allele2++ ) {
+            for ( int allele1 = 0; allele1 <= allele2; allele1++) {
+                final int[] counts = new int[knownCountsByAllele.length];
+                counts[allele1] += 1;
+                counts[allele2] += 1;
+                priors[priorIndex++] = MathUtils.dirichletMultinomial(knownCountsByAllele,sumOfKnownCounts,counts,ploidy);
+            }
+        }
+
+        return priors;
+    }
+
+    private static void addAlleleCounts(final Map<Allele,Integer> counts, final VariantContext context, final boolean useAC) {
+        final int[] ac;
+        if ( context.hasAttribute(VCFConstants.MLE_ALLELE_COUNT_KEY) && ! useAC ) {
+            ac = extractInts(context.getAttribute(VCFConstants.MLE_ALLELE_COUNT_KEY));
+        } else if ( context.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) ) {
+            ac = extractInts(context.getAttribute(VCFConstants.ALLELE_COUNT_KEY));
+        } else {
+            ac = new int[context.getAlternateAlleles().size()];
+            int idx = 0;
+            for ( final Allele allele : context.getAlternateAlleles() ) {
+                ac[idx++] = context.getCalledChrCount(allele);
+            }
+        }
+
+        for ( final Allele allele : context.getAlleles() ) {
+            final int count;
+            if ( allele.isReference() ) {
+                if ( context.hasAttribute(VCFConstants.ALLELE_NUMBER_KEY) ) {
+                    count = context.getAttributeAsInt(VCFConstants.ALLELE_NUMBER_KEY,-1) - (int) MathUtils.sum(ac);
+                } else {
+                    count = context.getCalledChrCount() - (int) MathUtils.sum(ac);
+                }
+            } else {
+                count = ac[context.getAlternateAlleles().indexOf(allele)];
+            }
+            if ( ! counts.containsKey(allele) ) {
+                counts.put(allele,0);
+            }
+            counts.put(allele,count + counts.get(allele));
+        }
+    }
+
+    public static int[] extractInts(final Object integerListContainingVCField) {
+        List<Integer> mleList = null;
+        if ( integerListContainingVCField instanceof List ) {
+            if ( ((List) integerListContainingVCField).get(0) instanceof String ) {
+                mleList = new ArrayList<>(((List) integerListContainingVCField).size());
+                for ( Object s : ((List)integerListContainingVCField)) {
+                    mleList.add(Integer.parseInt((String) s));
+                }
+            } else {
+                mleList = (List<Integer>) integerListContainingVCField;
+            }
+        } else if ( integerListContainingVCField instanceof Integer ) {
+            mleList = Arrays.asList((Integer) integerListContainingVCField);
+        } else if ( integerListContainingVCField instanceof String ) {
+            mleList = Arrays.asList(Integer.parseInt((String)integerListContainingVCField));
+        }
+        if ( mleList == null )
+            throw new IllegalArgumentException(String.format("VCF does not have properly formatted "+
+                    VCFConstants.MLE_ALLELE_COUNT_KEY+" or "+VCFConstants.ALLELE_COUNT_KEY));
+
+        final int[] mle = new int[mleList.size()];
+
+        if ( ! ( mleList.get(0) instanceof Integer ) ) {
+            throw new IllegalStateException("BUG: The AC values should be an Integer, but was "+mleList.get(0).getClass().getCanonicalName());
+        }
+
+        for ( int idx = 0; idx < mle.length; idx++) {
+            mle[idx] = mleList.get(idx);
+        }
+
+        return mle;
+    }
+}
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java
new file mode 100644
index 000000000..b8dba7b86
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java
@@ -0,0 +1,82 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+*
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
+
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.haplotype.Haplotype;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.variant.variantcontext.Allele;
+
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Random;
+
+/**
+ * Random likelihoods generator, used for testing/benchmarking purposes.
+ */
+public class RandomLikelihoodCalculationEngine implements LikelihoodCalculationEngine {
+
+    @Override
+    public Map<String, PerReadAlleleLikelihoodMap> computeReadLikelihoods(final AssemblyResultSet assemblyResultSet, final Map<String, List<GATKSAMRecord>> reads) {
+        final List<Haplotype> haplotypes = assemblyResultSet.getHaplotypeList();
+        final Map<String,PerReadAlleleLikelihoodMap> result = new HashMap<>(reads.size());
+        final Map<Haplotype,Allele> alleles = new HashMap<>(haplotypes.size());
+        for (final Haplotype haplotype : haplotypes)
+            alleles.put(haplotype,Allele.create(haplotype,false));
+        final Random rnd = GenomeAnalysisEngine.getRandomGenerator();
+        for (final String sample : reads.keySet()) {
+            final PerReadAlleleLikelihoodMap pralm = new PerReadAlleleLikelihoodMap();
+            for (final GATKSAMRecord read : reads.get(sample))
+                for (final Haplotype haplotype : haplotypes )
+                    pralm.add(read,alleles.get(haplotype),-Math.abs(rnd.nextDouble()));
+            result.put(sample,pralm);
+        }
+
+        return result;
+    }
+}
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadAnchoring.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadAnchoring.java
new file mode 100644
index 000000000..b4d2e1a2f
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadAnchoring.java
@@ -0,0 +1,366 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+*
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
+
+import com.google.java.contract.Requires;
+import org.apache.log4j.Logger;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.MultiSampleEdge;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.Path;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.HaplotypeGraph;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+
+import java.util.*;
+
+/**
+ * Collects information as to how a read maps into the haplotype graph that is needed to calculate its likelihood
+ * using the graph-based approach.
+ */
+public class ReadAnchoring {
+
+    private static final Logger logger = Logger.getLogger(ReadAnchoring.class);
+
+    /** Holds a reference to the read itself */
+    protected final GATKSAMRecord read;
+    protected final Map<MultiDeBruijnVertex,Integer> uniqueKmerOffsets;
+
+    /**
+     * Kmer offset on the read of the left anchor
+     * <p>
+     * {@code -1} if there is no left anchor.
+     * </p>
+     */
+    protected int leftAnchorIndex;
+
+    /**
+     * Vertex in the graph where the left anchor falls.
+     * <p>
+     *     {@code null} if there is no left anchor.
+     * </p>
+     */
+    protected MultiDeBruijnVertex leftAnchorVertex;
+
+    /**
+     * Kmer offset on the read of the right anchor.
+     *
+     * <p>
+     *     {@code -1} if there is no right anchor.
+     * </p>
+     */
+    protected int rightAnchorIndex;
+
+    /**
+     * Vertex in the graph where the right anchor falls.
+     *
+     * <p>
+     *     {@code null} if there is no right anchor.
+     * </p>
+     */
+    protected MultiDeBruijnVertex rightAnchorVertex;
+
+    /**
+     * Kmer sequence mapping information for the read sequence.
+     *
+     * never {@code null}.
+     */
+    protected final KmerSequenceGraphMap<MultiDeBruijnVertex, MultiSampleEdge> graphMap;
+
+    /**
+     * Alignment of read kmers on the reference haplotype kmers.
+     *
+     * <p>
+     *     There is one entry for each base in the read.
+     *
+     * </p>
+     * <p>
+     *     The i-th entry indicates what kmer in the reference haplotype correspond to the kmer on the read starting
+     *     at is i-th base.
+     * </p>
+     *
+     * <p>
+     *     {@code -1} means that there is no match.
+     * </p>
+     *
+     * <p>
+     *     The last kmerSize - 1 entry of the array are {@code -1}
+     * </p>
+     */
+    protected final int[] referenceAlignment;
+
+    /**
+     * Maps between reference path vertex that are found between anchors and the kmer offset they map uniquely to
+     * on the read.
+     */
+    protected final Map<MultiDeBruijnVertex, Integer> referenceWithinAnchorsMap;
+
+    /**
+     * Creates the read's anchoring information for the haplotype-graph.
+     *
+     * @param read the targeted read.
+     * @param haplotypeGraph the targeted graph.
+     *
+     * @throws NullPointerException if any argument is {@code null}.
+     * @throws IllegalArgumentException if elements in {@code anchorableVertices} are not vertex in {@code haplotypeGraph}
+     */
+    public ReadAnchoring(final GATKSAMRecord read, final HaplotypeGraph haplotypeGraph) {
+        this.read = read;
+        final byte[] readBases = read.getReadBases();
+        final KmerSequence readKmers = new KmerSequence(read, haplotypeGraph.getKmerSize());
+        graphMap = new KmerSequenceGraphMap<>(haplotypeGraph, readKmers);
+        final Map<MultiDeBruijnVertex, Integer> vertexOffset = graphMap.vertexOffset();
+        referenceAlignment = calculateUniqueKmerAlignment(0, readBases.length, haplotypeGraph.getReferenceRoute(), vertexOffset, haplotypeGraph.getKmerSize());
+        leftAnchorIndex = -1;
+        leftAnchorVertex = null;
+        for (int i = 0; i < readBases.length - haplotypeGraph.getKmerSize() + 1; i++) {
+            if (referenceAlignment[i] == -1) continue;
+            final MultiDeBruijnVertex candidate = haplotypeGraph.findKmer(readKmers.get(i));
+            if (candidate != null && haplotypeGraph.getAnchorableVertices().contains(candidate)) {
+                leftAnchorIndex = i;
+                leftAnchorVertex = candidate;
+                break;
+            }
+        }
+        rightAnchorIndex = leftAnchorIndex;
+        rightAnchorVertex = leftAnchorVertex;
+        if (leftAnchorIndex != -1) {
+            for (int i = readBases.length - haplotypeGraph.getKmerSize(); i > leftAnchorIndex; i--) {
+                if (referenceAlignment[i] == -1) continue;
+                final MultiDeBruijnVertex candidate = haplotypeGraph.findKmer(readKmers.get(i));
+                if (candidate != null && haplotypeGraph.getAnchorableVertices().contains(candidate)) {
+                    rightAnchorIndex = i;
+                    rightAnchorVertex = candidate;
+                    break;
+                }
+            }
+        }
+        referenceWithinAnchorsMap = buildReferenceWithinBoundariesMap(read, haplotypeGraph,
+                vertexOffset, leftAnchorVertex, rightAnchorVertex);
+        uniqueKmerOffsets = buildReadUniqueKmerOffsets(haplotypeGraph);
+    }
+
+    /**
+     * For a given read, returns the set of reference path vertices that falls between the two anchor vertices.
+     * <p/>
+     * <p>
+     * The resulting map has as key the reference vertices between those two boundaries (inclusive) and
+     * the value is the corresponding offset in the kmer.
+     * </p>
+     *
+     * @param read                 the target read.
+     * @param readVertexKmerOffset map between vertices and their kmer offset on the read.
+     * @param leftAnchorVertex     left anchor vertex.
+     * @param rightAnchorVertex    right anchor vertex.
+     * @return never {@code null}, but empty if the anchors are out of order in the reference.
+     */
+    private Map<MultiDeBruijnVertex, Integer> buildReferenceWithinBoundariesMap(
+            final GATKSAMRecord read, final HaplotypeGraph haplotypeGraph,
+            final Map<MultiDeBruijnVertex, Integer> readVertexKmerOffset,
+            final MultiDeBruijnVertex leftAnchorVertex, final MultiDeBruijnVertex rightAnchorVertex) {
+        if (leftAnchorVertex == null)
+            return Collections.emptyMap();
+
+        final Map<MultiDeBruijnVertex, Integer> result = new HashMap<>();
+        MultiDeBruijnVertex nextVertex = leftAnchorVertex;
+
+        int leftAnchorOffset = 0;
+        while (nextVertex != null) {
+            result.put(nextVertex, leftAnchorOffset++);
+            if (nextVertex == rightAnchorVertex)
+                break;
+            nextVertex = haplotypeGraph.getNextReferenceVertex(nextVertex);
+        }
+        if (nextVertex == null) {
+            logger.warn("unexpected event kmers out of order between read anchor kmers: " + read.getReadString()
+                    + " Offending kmer offsets: " + readVertexKmerOffset.get(leftAnchorVertex) + " " + readVertexKmerOffset.get(rightAnchorVertex)
+                    + " sequences: " +
+                    read.getReadString().substring(readVertexKmerOffset.get(leftAnchorVertex), haplotypeGraph.getKmerSize() + readVertexKmerOffset.get(leftAnchorVertex)) +
+                    " " + read.getReadString().substring(readVertexKmerOffset.get(rightAnchorVertex), haplotypeGraph.getKmerSize() + readVertexKmerOffset.get(rightAnchorVertex)) +
+                    " Reference haplotype: " + haplotypeGraph.getReferenceHaplotype().getBaseString());
+            return Collections.emptyMap();
+        }
+        return result;
+    }
+
+    /**
+     * Builds a map between unique kmers in the reference path and their kmer offset in the read.
+     *
+     * @param haplotypeGraph the anchoring graph.
+     *
+     * @return never {@code null}.
+     */
+    private Map<MultiDeBruijnVertex,Integer> buildReadUniqueKmerOffsets(final HaplotypeGraph haplotypeGraph) {
+        if (!hasValidAnchors())
+            return Collections.emptyMap();
+        final Map<MultiDeBruijnVertex, Integer> vertexOffset = graphMap.vertexOffset();
+        final Set<MultiDeBruijnVertex> readUniqueKmerVertices = new HashSet<>(vertexOffset.size());
+        readUniqueKmerVertices.add(leftAnchorVertex);
+        readUniqueKmerVertices.add(rightAnchorVertex);
+        for (int i = leftAnchorIndex + 1; i < rightAnchorIndex; i++) {
+            if (referenceAlignment[i] != -1) {
+                readUniqueKmerVertices.add(haplotypeGraph.findKmer(graphMap.sequence.get(i)));
+            }
+        }
+        final Map<MultiDeBruijnVertex, Integer> validVertexOffset = new HashMap<>(graphMap.vertexOffset());
+        validVertexOffset.keySet().retainAll(readUniqueKmerVertices);
+        return validVertexOffset;
+    }
+
+    /**
+     * Checks whether it has some anchoring kmer and these are valid, i.e. the left anchor is the same or preceedes the right anchor in the reference path.
+     * @return {@code true} iff so.
+     */
+    public boolean hasValidAnchors() {
+        return referenceWithinAnchorsMap.size() >= 1;
+    }
+
+    /**
+     * Calculates an array indicating for each kmer in the read what is the offset of that kmer in a path.
+     * <p/>
+     * <p>
+     * The result is of the same length as the read. Position ith indicates the offset of the read kmer that
+     * start at that position in the input path. Non matching kmers have -1 instead.
+     * </p>
+     *
+     * @param readStart            inclusive first position of the read to consider.
+     * @param readEnd              exclusive position after last to be considered.
+     * @param path                 the path to which to align against.
+     * @param readUniqueKmerOffset map of vertices to the kmer offset with the read.
+     * @return never {@code null}.
+     */
+    private int[] calculateUniqueKmerAlignment(final int readStart, final int readEnd, final Path<MultiDeBruijnVertex, MultiSampleEdge> path,
+                                               final Map<MultiDeBruijnVertex, Integer> readUniqueKmerOffset, final int kmerSize) {
+
+        final int[] result = new int[readEnd - readStart];
+        Arrays.fill(result, -1);
+        int i = 0;
+        for (final MultiDeBruijnVertex v : path.getVertices()) {
+            final Integer kmerReadOffset = readUniqueKmerOffset.get(v);
+            if (kmerReadOffset != null) {
+                final int kro = kmerReadOffset;
+                if (kro >= readStart && kro < readEnd - kmerSize + 1) {
+                    result[kro - readStart] = i;
+                }
+            }
+            i++;
+        }
+        // Now we remove conflicting mappings:
+        // A conflicting mapping is when to kmer mapping suggest that
+        // the same read position maps to two different bases in the path.
+        maskOutConflictingKmerAlignments(result,kmerSize);
+        return result;
+    }
+
+    /**
+     * Mark with -1 those kmer matches that result in read base mapping conflicts.
+     *
+     * @param result in/out changed in-situ.
+     */
+    @Requires("result != null")
+    private void maskOutConflictingKmerAlignments(final int[] result, final int kmerSize) {
+        int i;
+        int lastKmer = -1;
+        int lastKmerPos = -1;
+        for (i = 0; i < result.length; i++) {
+            final int kmer = result[i];
+            if (kmer == -1)
+                continue;
+            if (lastKmer == -1) {
+                lastKmer = kmer;
+                lastKmerPos = i;
+            } else if (lastKmer + kmerSize - 1 >= kmer && (i - lastKmerPos) != (kmer - lastKmer)) { // kmer overlap. fixing by eliminating offending kmers alignments.
+                int iSkip = result.length;  // iSkip will contain the next position minus 1 to visit in the next iteration of the enclosing loop.
+                for (int j = i; j < result.length; j++)
+                    if (result[j] != -1) {
+                        if (lastKmer + kmerSize - 1 >= result[j])
+                            result[j] = -1;
+                        else {
+                            iSkip = j;
+                            break;
+                        }
+                    }
+                // then backwards and do the same.
+                int j = lastKmerPos;
+                lastKmer = -1;
+                lastKmerPos = -1;
+                for (; j >= 0; j--)
+                    if (result[j] != -1) {
+                        if (result[j] + kmerSize - 1 >= kmer)
+                            result[j] = -1;
+                        else {
+                            lastKmer = result[j];
+                            lastKmerPos = j;
+                            break;
+                        }
+                    }
+                i = iSkip;
+            } else {
+                lastKmer = kmer;
+                lastKmerPos = i;
+            }
+        }
+    }
+
+    /**
+     * Checks whether it is anchored at all.
+     *
+     * @return {@code true} iff so.
+     */
+    public boolean isAnchoredSomewhere() {
+        return hasValidAnchors();
+        //return hasValidAnchors();
+    }
+
+    /**
+     * Whether the read is anchored perfectly, there are no non-aligned bases.
+     *
+     * @return {@code true} iff so.
+     */
+    public boolean isPerfectAnchoring() {
+        return hasValidAnchors() && leftAnchorIndex == 0 && rightAnchorIndex == read.getReadLength() - graphMap.kmerSize &&
+               !leftAnchorVertex.hasAmbiguousSequence();
+    }
+
+}
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadCost.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadCost.java
new file mode 100644
index 000000000..a344eea61
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadCost.java
@@ -0,0 +1,80 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+*
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
+
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+
+import java.util.Comparator;
+
+/**
+ * A pair read-likelihood (cost).
+ */
+public class ReadCost {
+    public final GATKSAMRecord read;
+
+    /**
+     * Holds the cost value. Public for convenience, please use with care.
+     */
+    public double cost;
+
+    public ReadCost(final GATKSAMRecord r) {
+        read = r;
+    }
+
+
+    /**
+     * Comparator used to sort ReadCosts
+     */
+    public static final Comparator<ReadCost> COMPARATOR = new Comparator<ReadCost>() {
+        @Override
+        public int compare(final ReadCost o1, final ReadCost o2) {
+            final String s1 = o1.read.getReadName() + (o1.read.getReadPairedFlag() ? (o1.read.getFirstOfPairFlag() ? "/1" : "/2") : "");
+            final String s2 = o2.read.getReadName() + (o2.read.getReadPairedFlag() ? (o2.read.getFirstOfPairFlag() ? "/1" : "/2") : "");
+            return s1.compareTo(s2);
+        }
+    };
+
+}
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentComparator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentComparator.java
new file mode 100644
index 000000000..2efe42337
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentComparator.java
@@ -0,0 +1,86 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+*
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
+
+import java.util.Comparator;
+
+/**
+ * Sorts path costs.
+ * <p>
+ *     Path costs are first sorted by their path base sequence in alphanumerical order.
+ * </p>
+ *
+ * <p>
+ *     When these are the same, we consider their unique ids {@link ReadSegmentCost#uniqueId()} to break the tie.
+ * </p>
+ *
+ */
+class ReadSegmentComparator implements Comparator<ReadSegmentCost> {
+
+    public static final Comparator<? super ReadSegmentCost> INSTANCE = new ReadSegmentComparator();
+
+    @Override
+    public int compare(final ReadSegmentCost o1, final ReadSegmentCost o2) {
+        int minLength = Math.min(o1.bases.length, o2.bases.length);
+        for (int i = 0; i < minLength; i++) {
+            if (o1.bases[i] == o2.bases[i])
+                continue;
+            else if (o1.bases[i] < o2.bases[i]) {
+                return -1;
+            } else {
+                return 1;
+            }
+        }
+        if (o1.bases.length < o2.bases.length) {
+            return -1;
+        } else if (o1.bases.length > o2.bases.length) {
+            return 1;
+        } else {
+            return Long.compare(o1.uniqueId(),o2.uniqueId());
+        }
+
+    }
+}
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentCost.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentCost.java
new file mode 100644
index 000000000..9020e3426
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentCost.java
@@ -0,0 +1,112 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+*
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
+
+import com.google.java.contract.Requires;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.MultiSampleEdge;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.Route;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+
+import java.util.concurrent.atomic.AtomicLong;
+
+/**
+ * Path cost indicate the cost (alignment likelihood) of traversing a section of the graph using a segement of a read.
+ *
+ * <p>A path can be a whole haplotype path as well as just a smaller haplotype segment</p>.
+ *
+ * <p>We would generate many of this objects for each read. The final likelihood of a read vs each haplotype
+ * would be the summation of the path-cost of that read along the corresponding haplotype path.</p>
+ */
+class ReadSegmentCost {
+
+    public Route<MultiDeBruijnVertex, MultiSampleEdge> path;
+    public GATKSAMRecord read;
+
+    /**
+     * Holds the cost value. It public and non-final for convenience.
+     */
+    protected double cost;
+
+    /**
+     * Caches the path bases (the haplotype segment bases).
+     */
+    protected byte[] bases;
+
+    /**
+     * Construct a new path cost.
+     * @param read the corresponding read.
+     * @param path the corresponding path.
+     * @param cost initial cost estimate. Might be updated later.
+     */
+    @Requires("route != null")
+    public ReadSegmentCost(final GATKSAMRecord read,
+                    final Route<MultiDeBruijnVertex, MultiSampleEdge> path, double cost) {
+        this.read = read;
+        this.path = path;
+        this.cost = cost;
+    }
+
+    /**
+     * Used to generate unique identifiers for path cost object.
+     */
+    private static final AtomicLong pathCostUniqueIdGenerator = new AtomicLong();
+
+    /**
+     * Holds the path cost unique identifier.
+     */
+    private Long uniqueId;
+
+    /**
+     * Returns the this path-cost unique identifier.
+     * @return
+     */
+    public long uniqueId() {
+        if (uniqueId == null)
+            uniqueId = pathCostUniqueIdGenerator.incrementAndGet();
+        return uniqueId;
+    }
+}
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java
index a1ec13882..edd8dbb16 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java
@@ -68,7 +68,7 @@ import java.util.*;
 @Invariant("!this.isAllowingMultipleEdges()")
 public class BaseGraph<V extends BaseVertex, E extends BaseEdge> extends DefaultDirectedGraph<V, E> {
     protected final static Logger logger = Logger.getLogger(BaseGraph.class);
-    private final int kmerSize;
+    protected final int kmerSize;
 
     /**
      * Construct a TestGraph with kmerSize
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseVertex.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseVertex.java
index 18a3ce1eb..63f087979 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseVertex.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseVertex.java
@@ -48,6 +48,8 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs;
 
 import com.google.java.contract.Ensures;
 
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.HaplotypeGraph;
+
 import java.util.Arrays;
 
 /**
@@ -181,7 +183,7 @@ public class BaseVertex {
 
     /**
      * Set additional debugging information for this vertex
-     * @param info
+     * @param info the new info value.
      */
     public void setAdditionalInfo(final String info) {
         if ( info == null ) throw new IllegalArgumentException("info cannot be null");
@@ -192,4 +194,32 @@ public class BaseVertex {
      * @return the additional information for display about this vertex
      */
     public String additionalInfo() { return additionalInfo; }
+
+    /**
+     * Checks whether the vertex sequence is ambiguous or not.
+     *
+     * <p>
+     *     Ambiguity may come about as a result of either:
+     *     <ul>
+     *        <li>by construction as the generating sequence (read or haplotype) had ambiguous bases</li>
+     *        <li>or because this vertex is the result of merging two or more vertices with some variation upstream
+     *        no more than kmerSize bases away (e.g. by executing  {@link HaplotypeGraph#mergeCommonChains}</li>
+     *     </ul>
+     * </p>
+     *
+     * @return {@code true} iff so.
+     */
+    public boolean hasAmbiguousSequence() {
+        for (final byte base : sequence)
+            switch (Character.toUpperCase(base)) {
+                case 'A' :
+                case 'T' :
+                case 'G' :
+                case 'C' :
+                    continue;
+                default :
+                    return true;
+            }
+        return false;
+    }
 }
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/DeBruijnVertex.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/DeBruijnVertex.java
index 4d9441efe..ec2ccff20 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/DeBruijnVertex.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/DeBruijnVertex.java
@@ -78,7 +78,7 @@ public class DeBruijnVertex extends BaseVertex {
      * @return integer >= 1
      */
     @Ensures("result >= 1")
-    public int getKmer() {
+    public int getKmerSize() {
         return sequence.length;
     }
 
@@ -100,7 +100,7 @@ public class DeBruijnVertex extends BaseVertex {
      * @return a byte
      */
     public byte getSuffix() {
-        return sequence[getKmer() - 1];
+        return sequence[getKmerSize() - 1];
     }
 
     /**
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KmerSearchableGraph.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KmerSearchableGraph.java
new file mode 100644
index 000000000..94dc98b6c
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KmerSearchableGraph.java
@@ -0,0 +1,74 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*  
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*  
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*  
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*  
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*  
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. 
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.  
+*  
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY 
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*  
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*  
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*  
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*  
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt. 
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. 
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs;
+
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.Kmer;
+
+/**
+ * Common interface for those graphs that implement vertex by kmer look-up.
+ *
+ * @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.org&gt;
+ */
+public interface KmerSearchableGraph<V extends BaseVertex, E extends BaseEdge> {
+
+    /**
+     * Returns the vertex that represents or contains the last base of a given kmer.
+     * @param k the query kmer.
+     *
+     * @throws NullPointerException if {@code k} is {@code null}.
+     * @return {@code null} if there is no such a kmer in the graph or it is not unique.
+     */
+    V findKmer(Kmer k);
+
+    /**
+     * The kmer-size of indexed kmers.
+     *
+     * @return greater than 0.
+     */
+    int getKmerSize();
+
+}
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java
index 2e84e1d22..6901d16ef 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java
@@ -72,17 +72,17 @@ public class Path<T extends BaseVertex, E extends BaseEdge> {
     private final static Logger logger = Logger.getLogger(Path.class);
 
     // the last vertex seen in the path
-    private final T lastVertex;
+    protected final T lastVertex;
 
     // the list of edges comprising the path
     private Set<E> edgesAsSet = null;
-    private final LinkedList<E> edgesInOrder;
+    protected final ArrayList<E> edgesInOrder;
 
     // the scores for the path
-    private final int totalScore;
+    protected final int totalScore;
 
     // the graph from which this path originated
-    private final BaseGraph<T, E> graph;
+    protected final BaseGraph<T, E> graph;
 
     // used in the bubble state machine to apply Smith-Waterman to the bubble sequence
     // these values were chosen via optimization against the NA12878 knowledge base
@@ -99,7 +99,7 @@ public class Path<T extends BaseVertex, E extends BaseEdge> {
         if ( ! graph.containsVertex(initialVertex) ) throw new IllegalArgumentException("Vertex " + initialVertex + " must be part of graph " + graph);
 
         lastVertex = initialVertex;
-        edgesInOrder = new LinkedList<E>();
+        edgesInOrder = new ArrayList<>(0);
         totalScore = 0;
         this.graph = graph;
     }
@@ -114,11 +114,29 @@ public class Path<T extends BaseVertex, E extends BaseEdge> {
         return path;
     }
 
+    /**
+     * Create a new path with the same field values.
+     *
+     * @param p the template path.
+     *
+     * @throws NullPointerException if {@code p} is {@code null}.
+     */
+    protected Path(final Path<T,E> p) {
+        this.edgesInOrder = p.edgesInOrder;
+        this.lastVertex = p.lastVertex;
+        this.edgesAsSet = p.edgesAsSet;
+        this.totalScore = p.totalScore;
+        this.graph = p.graph;
+    }
+
     /**
      * Create a new Path extending p with edge
      *
-     * @param p the path to extend
-     * @param edge the edge to extend path by
+     * @param p the path to extend.
+     * @param edge the edge to extend path with.
+     *
+     * @throws IllegalArgumentException if {@code p} or {@code edge} are {@code null}, or {@code edge} is
+     * not part of {@code p}'s graph, or {@code edge} does not have as a source the last vertex in {@code p}.
      */
     public Path(final Path<T,E> p, final E edge) {
         if ( p == null ) throw new IllegalArgumentException("Path cannot be null");
@@ -128,11 +146,43 @@ public class Path<T extends BaseVertex, E extends BaseEdge> {
 
         graph = p.graph;
         lastVertex = p.graph.getEdgeTarget(edge);
-        edgesInOrder = new LinkedList<E>(p.getEdges());
+        edgesInOrder = new ArrayList<>(p.length() + 1);
+        edgesInOrder.addAll(p.edgesInOrder);
         edgesInOrder.add(edge);
         totalScore = p.totalScore + edge.getMultiplicity();
     }
 
+    /**
+     * Length of the path in edges.
+     *
+     * @return {@code 0} or greater.
+     */
+    public int length() {
+        return edgesInOrder.size();
+    }
+
+    /**
+     * Prepend a path with an edge.
+     *
+     * @param edge the extending edge.
+     * @param p the original path.
+     *
+     * @throws IllegalArgumentException if {@code p} or {@code edge} are {@code null}, or {@code edge} is
+     * not part of {@code p}'s graph, or {@code edge} does not have as a target the first vertex in {@code p}.
+     */
+    public Path(final E edge, final Path<T,E> p) {
+        if ( p == null ) throw new IllegalArgumentException("Path cannot be null");
+        if ( edge == null ) throw new IllegalArgumentException("Edge cannot be null");
+        if ( ! p.graph.containsEdge(edge) ) throw new IllegalArgumentException("Graph must contain edge " + edge + " but it doesn't");
+        if ( ! p.graph.getEdgeTarget(edge).equals(p.getFirstVertex())) { throw new IllegalStateException("Edges added to path must be contiguous."); }
+        graph = p.graph;
+        lastVertex = p.lastVertex;
+        edgesInOrder = new ArrayList<>(p.length() + 1);
+        edgesInOrder.add(edge);
+        edgesInOrder.addAll(p.getEdges());
+        totalScore = p.totalScore + edge.getMultiplicity();
+    }
+
     /**
      * Get the collection of edges leaving the last vertex of this path
      * @return a non-null collection
@@ -168,6 +218,27 @@ public class Path<T extends BaseVertex, E extends BaseEdge> {
         return getVertices().contains(v);
     }
 
+    /**
+     * Checks whether a given path is a suffix of this path.
+     *
+     * @param other the path to compare against.
+     * @throws IllegalArgumentException if <code>other</code> is <code>null</code>, or the come from
+     *   different graphs.
+     * @return true if <code>other</code> is a suffix of this path.
+     */
+    public boolean isSuffix(final Path<T, E> other) {
+        if ( other == null ) throw new IllegalArgumentException("path cannot be null");
+        if (other.getGraph() != this.getGraph()) throw new IllegalArgumentException("the other path most belong to the same path");
+        if (!lastVertex.equals(other.lastVertex))
+          return false;
+        final ListIterator<E> myIt = edgesInOrder.listIterator(edgesInOrder.size());
+        final ListIterator<E> otherIt = other.edgesInOrder.listIterator(other.edgesInOrder.size());
+        while (myIt.hasPrevious() && otherIt.hasPrevious())
+            if (otherIt.previous() != myIt.previous())
+                return false;
+        return !otherIt.hasPrevious();
+    }
+
     /**
      * Check that two paths have the same edges and total score
      * @param path the other path we might be the same as
@@ -182,13 +253,13 @@ public class Path<T extends BaseVertex, E extends BaseEdge> {
         final StringBuilder b = new StringBuilder("Path{score=" + totalScore + ", path=");
         boolean first = true;
         for ( final T v : getVertices() ) {
-            if ( first ) {
+            if ( first )
                 first = false;
-            } else {
+            else
                 b.append(" -> ");
-            }
             b.append(v.getSequenceString());
         }
+        b.append('}');
         return b.toString();
     }
 
@@ -249,7 +320,11 @@ public class Path<T extends BaseVertex, E extends BaseEdge> {
      * @return a non-null vertex
      */
     public T getFirstVertex() {
-        return getGraph().getEdgeSource(edgesInOrder.pollFirst());
+        if (edgesInOrder.size() == 0) {
+            return lastVertex;
+        } else {
+            return getGraph().getEdgeSource(edgesInOrder.get(0));
+        }
     }
 
     /**
@@ -260,7 +335,7 @@ public class Path<T extends BaseVertex, E extends BaseEdge> {
     public byte[] getBases() {
         if( getEdges().isEmpty() ) { return graph.getAdditionalSequence(lastVertex); }
 
-        byte[] bases = graph.getAdditionalSequence(graph.getEdgeSource(edgesInOrder.getFirst()));
+        byte[] bases = graph.getAdditionalSequence(graph.getEdgeSource(edgesInOrder.get(0)));
         for( final E e : edgesInOrder ) {
             bases = ArrayUtils.addAll(bases, graph.getAdditionalSequence(graph.getEdgeTarget(e)));
         }
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Route.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Route.java
new file mode 100644
index 000000000..1cf986c00
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Route.java
@@ -0,0 +1,285 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+*
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs;
+
+
+import java.util.List;
+import java.util.ListIterator;
+
+/**
+ * Represents a route or path through a graph.
+ * <p>
+ *     In contrast with a {@link Path}, a route keeps track of the
+ * path taken at furcations in order to speed up some path comparisions like the
+ * one implemented by {@link #isSuffix}.
+ * </p>
+ *
+ * @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.org&gt;
+ */
+public class Route<V extends BaseVertex, E extends BaseEdge> extends Path<V,E> {
+
+    protected final Route<V,E> previousRouteWithLastVertexThatIsForkOrJoin;
+    protected final boolean lastVertexIsForkOrJoin;
+
+    /**
+     * Create a zero length route with a start in a particular vertex:
+     *
+     * @param initialVertex the first vertex of the route.
+     * @param graph the new route's graph.
+     *
+     * @throws IllegalArgumentException if {@code initialVertex} or {@code graph} are {@code null}.
+     *      or if {@code initialVertex} does not belong to {@code graph}.
+     */
+    public Route(final V initialVertex, final BaseGraph<V, E> graph) {
+        super(initialVertex, graph);
+        previousRouteWithLastVertexThatIsForkOrJoin = null;
+        lastVertexIsForkOrJoin = graph.inDegreeOf(initialVertex) > 1;
+    }
+
+    @Override
+    public boolean equals(final Object other) {
+        if (other == null) return false;
+        if (other == this) return true;
+        if (! (other instanceof Route)) return false;
+        @SuppressWarnings("unchecked")
+        final Route<V,E> otherRoute = (Route<V,E>) other;
+        return otherRoute.length() == this.length() && isSuffix(otherRoute);
+    }
+
+    /**
+     * Extends a route into a new instance.
+     *
+     * @param prefix the route to extend.
+     * @param nextVertex the vertex to extend the route to.
+     *
+     * @throws IllegalArgumentException if {@code prefix} is {@code null} or {@code nextVertex} is {@code null}
+     *   or {@code nextVertex} does not belong to {@code prefix}'s graph or there is no edge that in the graph
+     *   that would connect {@code prefix}'s last vertex with {@code nextVertex} directly.
+     */
+    public Route(final Route<V,E> prefix, final V nextVertex) {
+        this(prefix,resolveSuffixEdge(prefix,nextVertex));
+    }
+
+
+    /**
+     * Extends a route into a new instance.
+     *
+     * @param prevVertex the vertex to extend the route to.
+     * @param suffix the route to extend.
+     *
+     * @throws IllegalArgumentException if {@code suffix} is {@code null} or {@code prevVertex} is {@code null}
+     *   or {@code prevVertex} does not belong to {@code suffix}'s graph or there is no edge that in the graph
+     *   that would connect {@code suffix}'s first vertex with {@code prevVertex} directly.
+     */
+    public Route(final V prevVertex, final Route<V,E> suffix) {
+        this(resolvePrefixEdge(prevVertex, suffix),suffix);
+    }
+
+    /**
+     * Resolves the prefix edge as required by {@link Route(V,Route)}.
+     */
+    private static <V extends BaseVertex,E extends BaseEdge>  E resolvePrefixEdge(final V prevVertex, final Route<V, E> suffix) {
+        if (prevVertex == null) throw new NullPointerException();
+        if (!suffix.getGraph().containsVertex(prevVertex)) throw new IllegalArgumentException();
+        final E result = suffix.getGraph().getEdge(prevVertex,suffix.getFirstVertex());
+        if (result == null)
+            throw new IllegalArgumentException("there is no such edge in the graph");
+        return result;
+    }
+
+    /**
+     * Resolves the suffix edge as required by {@link Route(Route,V)}
+     */
+    private static <V extends BaseVertex,E extends BaseEdge>  E resolveSuffixEdge(final Route<V,E> prefix, final V nextVertex) {
+        if (nextVertex == null) throw new IllegalArgumentException();
+        if (!prefix.getGraph().containsVertex(nextVertex)) throw new IllegalArgumentException();
+        final E result = prefix.getGraph().getEdge(prefix.getLastVertex(),nextVertex);
+        if (result == null)
+            throw new IllegalArgumentException("there is no such edge in the graph");
+        return result;
+    }
+
+    /**
+     * Extends a route by prefixing an edge.
+     *
+     * @param initialEdge the extending edge.
+     * @param suffix the original path.
+     *
+     * @throws IllegalArgumentException if {@code suffix} or {@code initialEdge} are {@code null}, or {@code initialEdge} is
+     * not part of {@code suffix}'s graph, or {@code initialEdge} does not have as a target the first vertex in {@code suffix}.
+     */
+    public Route(final E initialEdge, final Route<V,E> suffix) {
+        super(initialEdge,suffix);
+        final V firstVertex = getFirstVertex();
+        if(suffix.length() == 0) {
+            lastVertexIsForkOrJoin = suffix.lastVertexIsForkOrJoin || graph.outDegreeOf(firstVertex) > 1;
+            previousRouteWithLastVertexThatIsForkOrJoin = graph.inDegreeOf(firstVertex) > 1 ? new Route<>(firstVertex,graph) : null;
+        } else {
+            lastVertexIsForkOrJoin = suffix.lastVertexIsForkOrJoin;
+            if (suffix.previousRouteWithLastVertexThatIsForkOrJoin != null)
+                previousRouteWithLastVertexThatIsForkOrJoin = new Route<>(initialEdge,suffix.previousRouteWithLastVertexThatIsForkOrJoin);
+            else
+                previousRouteWithLastVertexThatIsForkOrJoin = graph.outDegreeOf(firstVertex) > 1 ?
+                        new Route<>(new Route<>(firstVertex,graph),edgesInOrder.get(0)) :
+                            graph.inDegreeOf(firstVertex) > 1 ? new Route<>(firstVertex,graph) : null;
+        }
+    }
+
+    /**
+     * Create copy of an existing route.
+     * @param route the route to copy
+     *
+     * @throws NullPointerException if {@code route} is {@code null}.
+     */
+    protected Route(final Route<V, E> route) {
+        super(route);
+        lastVertexIsForkOrJoin = route.lastVertexIsForkOrJoin;
+        previousRouteWithLastVertexThatIsForkOrJoin = route.previousRouteWithLastVertexThatIsForkOrJoin;
+    }
+
+    /**
+     * Create a new Route extending another one with an edge
+     *
+     * @param route the route to extend.
+     * @param edge the edge to extend the route with.
+     *
+     * @throws IllegalArgumentException if {@code route} or {@code edge} are {@code null}, or {@code edge} is
+     * not part of {@code route}'s graph, or {@code edge} does not have as a source the last vertex in {@code route}.
+     */
+    public Route(final Route<V, E> route, final E edge) {
+        super(route, edge);
+        lastVertexIsForkOrJoin = graph.outDegreeOf(route.lastVertex) > 1 || graph.inDegreeOf(lastVertex) > 1;
+        previousRouteWithLastVertexThatIsForkOrJoin = route.lastVertexIsForkOrJoin ? route : route.previousRouteWithLastVertexThatIsForkOrJoin;
+    }
+
+    @Override
+    public boolean isSuffix(final Path<V,E> other) {
+        if (other == this)
+            return true;
+        else if (other == null)
+            throw new IllegalArgumentException("other path must not be null");
+        else if (getGraph() != other.getGraph())
+            throw new IllegalArgumentException("other path must be part of the same graph");
+        else if (other instanceof Route)
+            return isRouteSuffix((Route<V,E>)other);
+        else
+            return super.isSuffix(other);
+    }
+
+    @Override
+    public String toString() {
+        return super.toString().replace("Path{", "Route{");
+    }
+
+    /**
+     * Faster version when comparing with a route.
+     */
+    protected boolean isRouteSuffix(final Route<V,E> other) {
+        if (other.getGraph() != this.getGraph())
+            throw new IllegalArgumentException("you cannot compare routes on different graphs");
+        else if (lastVertex != other.lastVertex)  // obvious case.
+            return false;
+        else if (this.previousRouteWithLastVertexThatIsForkOrJoin == null
+                && other.previousRouteWithLastVertexThatIsForkOrJoin != null) // I am shorter or different path for sure.
+            return false;
+        else if (this.edgesInOrder.size() < other.edgesInOrder.size())  // I am shorter regardless of path, no way Jose!
+            return false;
+        else if (this.previousRouteWithLastVertexThatIsForkOrJoin == null || other.previousRouteWithLastVertexThatIsForkOrJoin == null) {
+            final ListIterator<E> myEdges = edgesInOrder.listIterator(edgesInOrder.size());
+            final ListIterator<E> otherEdges = other.edgesInOrder.listIterator(other.edgesInOrder.size());
+            while (otherEdges.hasPrevious())
+                if (myEdges.previous() != otherEdges.previous())
+                    return false;
+            return true;
+        } else
+            return (other.previousRouteWithLastVertexThatIsForkOrJoin == this.previousRouteWithLastVertexThatIsForkOrJoin)
+                || (previousRouteWithLastVertexThatIsForkOrJoin.lastVertex == other.previousRouteWithLastVertexThatIsForkOrJoin.lastVertex
+              && previousRouteWithLastVertexThatIsForkOrJoin.isRouteSuffix(other.previousRouteWithLastVertexThatIsForkOrJoin));
+    }
+
+    /**
+     * Checks whether the last vertex in the route is a fork or a joining vertex.
+     * @return {@code true} iff so.
+     */
+    public boolean lastVertexIsForkOrJoin() {
+        return lastVertexIsForkOrJoin;
+    }
+
+    /**
+     * Returns the longest prefix route that has as a last vertex a join or furcation vertex.
+     *
+     * @return never {@code null}.
+     */
+    public Route<V,E> getPrefixRouteWithLastVertexThatIsForkOrJoin() {
+        return previousRouteWithLastVertexThatIsForkOrJoin;
+    }
+
+
+
+    /**
+     * Splice out the first few vertices of the route.
+     *
+     * @param length how many vertices to splice out
+     * @return a new route without those spliced vertices.
+     *
+     * @throws IllegalArgumentException if {@code length} is equal to the route's length or greater or if it is negative.
+     * Notice that non-vertex route are no legal routes.
+     */
+    public Route<V,E> splicePrefix(final int length) {
+        if (length == 0)
+            return this;
+        if (length >= length())
+            throw new IllegalArgumentException("prefix slicing to long");
+        if (length < 0)
+            throw new IllegalArgumentException("prefix cannot be negative");
+
+        final List<E> resultEdges = getEdges().subList(length,length());
+        Route<V,E> result = new Route<>(graph.getEdgeSource(resultEdges.get(0)),this);
+        for (final E edge : resultEdges)
+            result = new Route<>(result,edge);
+        return result;
+    }
+}
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/RouteFinder.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/RouteFinder.java
new file mode 100644
index 000000000..ac6837d33
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/RouteFinder.java
@@ -0,0 +1,196 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+*
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs;
+
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.KmerSequence;
+import org.broadinstitute.sting.utils.collections.Pair;
+
+import java.util.Stack;
+
+/**
+ * A collection of route building methods.
+ *
+ * @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.org&gt;
+ */
+public class RouteFinder {
+
+
+    /**
+     * Completes a path backwards in the graph that would explain the sequence if bytes ending in the vertex provided.
+     *
+     * @param graph the graph to build the path upon.
+     * @param sequence contains the sequence to backtrack.
+     * @param start inclusive start position of the sequence to backtrack.
+     * @param end exclusive end position of the sequence to backtrack.
+     * @param vertex final vertex of the resulting path.
+     * @return {@code null} if there is not such path, otherwise a path such that vertex is the last vertex of it
+     * and its sequence is squence[start to end] + v.getSuffix();
+     */
+    private static <V extends BaseVertex, E extends BaseEdge> Route<V,E> extendRouteBackwards(final BaseGraph<V, E> graph,
+                                                                                             final byte[] sequence,
+                                                                                             final int start,
+                                                                                             final int end,
+                                                                                             final V vertex) {
+        final Route<V,E> emptyPath = new Route<>(vertex,graph);
+        if (end <= start) // trivial case.
+            return emptyPath;
+        final int kmerSize = graph.getKmerSize();
+        final Stack<Pair<Route<V,E>,Integer>> stack = new Stack<>();
+        stack.ensureCapacity(end - start + 1);
+        stack.push(new Pair<>(emptyPath,end));
+        while (!stack.isEmpty()) {
+            final Pair<Route<V,E>,Integer> next = stack.pop();
+            final Route<V,E> nextRoute = next.getFirst();
+            final int nextEnd = next.getSecond();
+            if (nextEnd <= start) {
+                return nextRoute.splicePrefix(kmerSize - 1); // gotcha!!!
+            }
+            final V nextFirstVertex = nextRoute.getFirstVertex();
+            if (graph.isSource(nextFirstVertex)) {
+                final byte[] fullFirstVertexSequence = nextFirstVertex.getSequence();
+                if (nextEnd - start != fullFirstVertexSequence.length - 1) {
+                    continue; // you need to have the right length to accept a source vertex.
+                }
+                boolean mismatchFound = false;
+                for (int i = 0; i < fullFirstVertexSequence.length - 1; i++) {
+                    if (fullFirstVertexSequence[i] != sequence[i + start]) {
+                        mismatchFound = true;
+                        break;
+                    }
+                }
+                if (!mismatchFound)
+                    return nextRoute;
+            } else {
+                final Integer newNextEnd = nextEnd - 1;
+                for (final E edge : graph.incomingEdgesOf(nextFirstVertex)) {
+                    final V prevVertex = graph.getEdgeSource(edge);
+                    final byte[] prevSequence = prevVertex.getSequence();
+                    final byte prevByte = prevSequence[prevSequence.length - 1];
+                    if (prevByte == sequence[newNextEnd]) {
+                        stack.push(new Pair<>(new Route<>(edge,nextRoute),newNextEnd));
+                    }
+                }
+            }
+        }
+        return null;
+    }
+
+    /**
+     * Completes a path forward in the graph that would explain the sequence if bytes starting by the prefix provided.
+     *
+     * @param sequence missing sequence we want to
+     * @param start inclusive first position in {@code sequence} that starts the extension
+     * @param end exclusive position after the last of bases to be added to the extension.
+     * @param prefix the seed prefix of the path.
+     * @return {@code null} if there is not such path, otherwise a path such that vertex is the last vertex of it
+     * and its sequence is prefix.getBases() + sequence[start to end];
+     */
+    private static  <V extends BaseVertex, E extends BaseEdge> Route<V,E> extendRouteForwards(
+            final BaseGraph<V, E> graph, final byte[] sequence, final int start, final int end,
+            final Route<V, E> prefix) {
+        if (end <= start) // trivial case.
+            return prefix;
+
+        final Stack<Pair<Route<V,E>,Integer>> stack = new Stack<>();
+        stack.ensureCapacity(end - start + 1);
+        stack.push(new Pair<>(prefix,start));
+        while (!stack.isEmpty()) {
+            final Pair<Route<V,E>,Integer> next = stack.pop();
+            final Route<V,E> nextRoute = next.getFirst();
+            final int nextStart = next.getSecond();
+            if (end <= nextStart)
+                return nextRoute; // gotcha!!!
+            final V lastVertex = nextRoute.getLastVertex();
+            final Integer newNextStart = nextStart + 1;
+                for (final E edge : graph.outgoingEdgesOf(lastVertex)) {
+                    final V nextVertex = graph.getEdgeTarget(edge);
+                    final byte[] nextSequence = nextVertex.getSequence();
+                    final byte nextByte = nextSequence[nextSequence.length - 1];
+                    if (nextByte == sequence[nextStart]) {
+                        stack.push(new Pair<>(new Route<>(nextRoute,edge),newNextStart));
+                    }
+                }
+        }
+        return null;
+    }
+
+    /**
+     * Construct a new route object give a sequence using unique kmer mappings.
+     *
+     * @param sequence base sequence.
+     * @return {@code null} if there is no way such route on the graph or the start kmer is not unique.
+     */
+    @SuppressWarnings("unchecked")
+    public static <V extends BaseVertex, E extends BaseEdge> Route<V,E> findRoute(final BaseGraph<V,E> graph,
+                                                                                  final byte[] sequence) {
+        if (graph == null)
+            throw new NullPointerException();
+        if (!(graph instanceof KmerSearchableGraph))
+            throw new IllegalArgumentException("the input graph must implement " + KmerSearchableGraph.class.getName());
+
+        final int kmerSize = graph.getKmerSize();
+        final KmerSequence haplotypeKmers = new KmerSequence(sequence,kmerSize);
+
+        if (haplotypeKmers.kmerSize() != graph.getKmerSize())
+            throw new IllegalArgumentException("incompatible kmer sizes " + graph.getKmerSize() + " != " + haplotypeKmers.kmerSize());
+
+        V vertex = null;
+        int i;
+        for (i = 0; i < haplotypeKmers.size(); i++)
+            if ((vertex = ((KmerSearchableGraph<V,E>)graph).findKmer(haplotypeKmers.get(i))) != null)
+                break;
+        if (vertex == null)
+            return null;
+        if (!graph.containsVertex(vertex))
+            throw new IllegalStateException("vertex does not belong to graph.");
+        Route<V,E> result = i == 0 ? new Route<>(vertex,graph) :
+                extendRouteBackwards(graph, sequence, 0, i + kmerSize - 1, vertex);
+        if (result == null)
+            return null;
+        result = extendRouteForwards(graph, sequence, i + kmerSize, sequence.length, result);
+        return result;
+    }
+}
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraph.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraph.java
index 36c515073..c8c6abb86 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraph.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraph.java
@@ -62,7 +62,7 @@ import java.util.Set;
  * @author: depristo
  * @since 03/2013
  */
-public final class SeqGraph extends BaseGraph<SeqVertex, BaseEdge> {
+public class SeqGraph extends BaseGraph<SeqVertex, BaseEdge> {
     /**
      * Edge factory that creates non-reference multiplicity 1 edges
      */
@@ -89,13 +89,6 @@ public final class SeqGraph extends BaseGraph<SeqVertex, BaseEdge> {
      */
     private final static int MAX_REASONABLE_SIMPLIFICATION_CYCLES = 100;
 
-    /**
-     * Construct an empty SeqGraph
-     */
-    public SeqGraph() {
-        this(11);
-    }
-
     /**
      * Construct an empty SeqGraph where we'll add nodes based on a kmer size of kmer
      *
@@ -294,10 +287,8 @@ public final class SeqGraph extends BaseGraph<SeqVertex, BaseEdge> {
 
         // create the combined vertex, and add it to the graph
         // TODO -- performance problem -- can be optimized if we want
-        final List<byte[]> seqs = new LinkedList<byte[]>();
-        for ( SeqVertex v : linearChain ) seqs.add(v.getSequence());
-        final byte[] seqsCat = org.broadinstitute.sting.utils.Utils.concat(seqs.toArray(new byte[][]{}));
-        final SeqVertex addedVertex = new SeqVertex( seqsCat );
+
+        final SeqVertex addedVertex = mergeLinearChainVertices(linearChain);
         addVertex(addedVertex);
 
         final Set<BaseEdge> inEdges = incomingEdgesOf(first);
@@ -315,6 +306,13 @@ public final class SeqGraph extends BaseGraph<SeqVertex, BaseEdge> {
         return true;
     }
 
+    protected SeqVertex mergeLinearChainVertices(final List<SeqVertex> vertices) {
+        final List<byte[]> seqs = new LinkedList<byte[]>();
+        for ( SeqVertex v : vertices ) seqs.add(v.getSequence());
+        final byte[] seqsCat = org.broadinstitute.sting.utils.Utils.concat(seqs.toArray(new byte[][]{}));
+        return new SeqVertex( seqsCat );
+    }
+
     /**
      * Get the sum of the edge weights on a linear chain of at least 2 elements
      *
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqVertex.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqVertex.java
index 083747db4..ee1ece3f3 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqVertex.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqVertex.java
@@ -47,7 +47,7 @@
 package org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs;
 
 import com.google.java.contract.Requires;
-import org.broadinstitute.sting.utils.Utils;
+
 import java.util.Arrays;
 import java.util.concurrent.atomic.AtomicInteger;
 
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java
index 205d0027a..284062749 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java
@@ -189,7 +189,7 @@ public class SharedVertexSequenceSplitter {
      * Must be called before calling updateGraph
      */
     public void split() {
-        splitGraph = new SeqGraph();
+        splitGraph = new SeqGraph(outer.getKmerSize());
         newMiddles = new LinkedList<SeqVertex>();
         edgesToRemove = new LinkedList<BaseEdge>();
 
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/VertexOrder.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/VertexOrder.java
new file mode 100644
index 000000000..2b58fcbf0
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/VertexOrder.java
@@ -0,0 +1,62 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+*
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs;
+
+/**
+* Indicate a SeqGraph vertex topological order between to vertices.
+*/
+public enum VertexOrder {
+    BEFORE, AFTER, SAME, PARALLEL;
+
+    public VertexOrder inverse() {
+        switch (this) {
+            case BEFORE: return AFTER;
+            case AFTER: return BEFORE;
+            default: return this;
+        }
+    }
+
+}
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/HaplotypeGraph.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/HaplotypeGraph.java
new file mode 100644
index 000000000..55ff2f978
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/HaplotypeGraph.java
@@ -0,0 +1,1016 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+*
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading;
+
+import org.apache.log4j.Logger;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeRoute;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.Kmer;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.*;
+import org.broadinstitute.sting.utils.SequenceComplexity;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.collections.CountSet;
+import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.haplotype.Haplotype;
+
+import java.io.File;
+import java.io.PrintStream;
+import java.util.*;
+
+/**
+ *
+ * Threading graph subclass used to "re-thread" haplotypes instead of reads.
+ *
+ * Created with IntelliJ IDEA.
+ * User: valentin
+ * Date: 8/23/13
+ * Time: 2:42 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class HaplotypeGraph extends ReadThreadingGraph {
+
+    /**
+     * Maximum repeat unit length considered when looking for repeats that should not be considered as
+     * possible read anchor places along the reference path.
+     */
+    protected static final int DEFAULT_MAX_REPEAT_UNIT_LENGTH = 4;
+
+    /**
+     * Minimum repeat length to consider a region a repeat that should not be considered as possibl read anchor
+     * places along the reference path.
+     */
+    protected static final int DEFAULT_MIN_REPEAT_LENGTH_IN_UNITS = 6;
+
+    /**
+     * Reference haplotype
+     */
+    private Haplotype referenceHaplotype;
+
+    /**
+     * Reference haplotype bases
+     */
+    private byte[] referenceBases;
+
+    /**
+     * Sets of haplotypes in the graph.
+     */
+    private Set<Haplotype> haplotypes;
+
+    /**
+     * Route of haplotypes in the graph.
+     */
+    private HaplotypeRoute referenceRoute;
+
+    /**
+     * Set of vertices along the reference route.
+     */
+    private Set<MultiDeBruijnVertex> referenceVertices;
+
+    /**
+     * Holds haplotype routes by haplotype.
+     */
+    private Map<Haplotype,HaplotypeRoute> haplotypeRouteByHaplotype;
+
+    /**
+     * Holds haplotypes by contained vertices.
+     */
+    private Map<MultiDeBruijnVertex,Set<HaplotypeRoute>> haplotypesByVertex;
+
+    /**
+     * Reference to the logger for this class.
+     */
+    private static final Logger logger = Logger.getLogger(HaplotypeGraph.class);
+
+    /**
+     * What is the maximum STR unit length.
+     */
+    private int maxRepeatUnitLength = DEFAULT_MAX_REPEAT_UNIT_LENGTH;
+
+    /**
+     * What is the minimum length in units for a STR.
+     */
+    private int minRepeatLengthInUnits = DEFAULT_MIN_REPEAT_LENGTH_IN_UNITS;
+
+
+    /**
+     * Indicates that the haplotype data structures need update previous to querying.
+     */
+    private boolean needToUpdateHaplotypeStructures = true;
+    private Set<MultiDeBruijnVertex> anchorableVertices;
+
+    /**
+     * Constructs a haplotype graph from a describing string.
+     *
+     * <p>Used for testing</p>
+     * @param string the string representation of the haplotype graph.
+     */
+    public HaplotypeGraph(final String string) {
+        super(string);
+        haplotypes = new LinkedHashSet<>(10);
+        referenceVertices = Collections.emptySet();
+    }
+
+    /**
+     * Constructs a new haplotype graph given its kmerSize.
+     *
+     * @param kmerSize 1 or greater, the targeted kmerSize
+     *
+     * @throws IllegalArgumentException if {@code kmerSize} is 0 or negative.
+     */
+    public HaplotypeGraph(final int kmerSize) {
+        super(kmerSize);
+        haplotypes = new LinkedHashSet<>(10);
+        referenceVertices = Collections.emptySet();
+    }
+
+
+    /**
+     * Set of vertices along the reference haplotype path.
+     *
+     * @return never {@code} null but perhaps empty.
+     */
+    public Set<MultiDeBruijnVertex> getReferenceVertices() {
+        updateHaplotypeStructures();
+        return referenceVertices;
+    }
+
+    /**
+     * Returns the haplotype route given an haplotype.
+     * @param haplotype query haplotype
+     * @throws NullPointerException if {@code haplotype} is {@code null}.
+     * @throws IllegalArgumentException if {@code haplotype} is not a supported haplotype in the graph.
+     * @return never {@code null}.
+     */
+    public HaplotypeRoute getHaplotypeRoute(final Haplotype haplotype) {
+        updateHaplotypeStructures();
+        if (!haplotypes.contains(haplotype))
+            throw new IllegalArgumentException("input haplotype must be part of the haplotype graph haplotype set");
+        HaplotypeRoute result = haplotypeRouteByHaplotype.get(haplotype);
+        if (result == null)
+            haplotypeRouteByHaplotype.put(haplotype,result = buildHaplotypeRoute(haplotype));
+        return result;
+    }
+
+    /**
+     * Creates an haplotype route.
+     * @param haplotype the target haplotype
+     * @return {@code null} if there is no such a route in the graph.
+     */
+    private HaplotypeRoute buildHaplotypeRoute(final Haplotype haplotype) {
+        final Route<MultiDeBruijnVertex,MultiSampleEdge> route = RouteFinder.findRoute(this,haplotype.getBases());
+        if (route == null)
+            return null;
+        else
+            return new HaplotypeRoute(route);
+    }
+
+    /**
+     * Bases along the reference path.
+     *
+     * @return {@code null} if there is no reference.
+     */
+    @SuppressWarnings("unused")
+    public byte[] getReferenceBases() {
+        updateHaplotypeStructures();
+        return referenceBases;
+    }
+
+    /**
+     * Returns the reference haplotype
+     * @return {@code null} if there is no such a reference.
+     */
+    public Haplotype getReferenceHaplotype() {
+        updateHaplotypeStructures();
+        return referenceHaplotype;
+    }
+
+
+
+    /**
+     * Construct a haplotype graph given the haplotype list and the elected kmerSize.
+     *
+     * @param haplotypes whose path to add to the graph.
+     * @param kmerSize   the kmerSize use to compose the graph.
+     */
+    public HaplotypeGraph(final int kmerSize, final List<Haplotype> haplotypes) {
+        super(kmerSize);
+        referenceHaplotype = findReferenceHaplotypeOrFail(haplotypes);
+        this.haplotypes = new LinkedHashSet<>(haplotypes);
+        addSequence("anonymous", referenceHaplotype.getBases(), null, true);
+        for (final Haplotype h : haplotypes) {
+            if (h.isReference())
+                continue;
+            if (h.length() < kmerSize) {
+                Utils.warnUser(logger, "haplotype shorter than kmerSize " + h.length() + " < " + kmerSize + " will be dropped");
+            } else
+                addSequence("anonymous", h.getBases(), null, false);
+
+        }
+        buildGraphIfNecessary();
+    }
+
+    /**
+     * Returns the reference haplotype within the input collection.
+     *
+     * @param haplotypes the query haplotype set.
+     * @throws IllegalArgumentException if there is no reference haplotype.
+     * @throws NullPointerException if {@code haplotypes} is {@code null} or contains some {@code null} value.
+     * @return never {@code} null, a haplotype that is reference.
+     */
+    private Haplotype findReferenceHaplotypeOrFail(final List<Haplotype> haplotypes) {
+        for (final Haplotype h : haplotypes)
+            if (h.isReference())
+                return h;
+        throw new IllegalArgumentException("no reference haplotype present");
+    }
+
+    /**
+     * Constructs a new haplotype graph given a template read-threading graph and set of haplotypes
+     *
+     * @param template the template read-threading graph.
+     * @param haplotypes the haplotype set to consider
+     */
+    public HaplotypeGraph(final ReadThreadingGraph template, final List<Haplotype> haplotypes) {
+        this(template.getKmerSize());
+        referenceHaplotype = findReferenceHaplotypeOrFail(haplotypes);
+        this.haplotypes = new HashSet<>(haplotypes);
+        template.buildGraphIfNecessary();
+        uniqueKmers = new HashMap<>();
+        nonUniqueKmers = new HashSet<>();
+        // Copy vertices over.
+        addVertices(template.vertexSet());
+        // Copy edges over.
+        for (final MultiSampleEdge edge : template.edgeSet()) {
+              final MultiSampleEdge newEdge = addEdge(template.getEdgeSource(edge), template.getEdgeTarget(edge));
+              newEdge.setIsRef(newEdge.isRef());
+              newEdge.setMultiplicity(edge.getMultiplicity());
+        }
+        // Copy kmer lookup tables:
+        uniqueKmers.putAll(template.uniqueKmers);
+        nonUniqueKmers.addAll(template.nonUniqueKmers);
+        alreadyBuilt = true;
+    }
+
+    /**
+     * Update the haplotype data structures based in current edges and vertices.
+     */
+    private void updateHaplotypeStructures() {
+        if (!needToUpdateHaplotypeStructures)
+            return;
+        needToUpdateHaplotypeStructures = false;
+        haplotypeRouteByHaplotype = new LinkedHashMap<>(haplotypes.size());
+        final Iterator<Haplotype> haplotypeIterator = haplotypes.iterator();
+        final Set<Haplotype> nonFoundHaplotypes = new HashSet<>(haplotypes.size());
+        while (haplotypeIterator.hasNext()) {
+            final Haplotype haplotype = haplotypeIterator.next();
+            final HaplotypeRoute haplotypeRoute = buildHaplotypeRoute(haplotype);
+            if (haplotypeRoute == null) {
+                haplotypeIterator.remove();
+                nonFoundHaplotypes.add(haplotype);
+                if (haplotype.isReference()) {
+                    referenceHaplotype = null;
+                    referenceRoute = null;
+                    referenceVertices = Collections.emptySet();
+                    referenceBases = null;
+                }
+            } else {
+                if (haplotype.isReference()) {
+                    referenceHaplotype = haplotype;
+                    referenceRoute = haplotypeRoute;
+                    referenceVertices = haplotypeRoute.vertexSet();
+                    referenceBases = haplotypeRoute.getBases();
+                }
+                haplotypeRouteByHaplotype.put(haplotype, haplotypeRoute);
+            }
+        }
+        haplotypesByVertex = buildHaplotypesByVertex();
+        anchorableVertices = calculateAnchorableVertexSet();
+        logger.debug("some haplotypes do not have a path across the haplotype graph " + nonFoundHaplotypes.size());
+    }
+
+    /**
+     * Builds a map for each vertex to all the haplotype routes that pass thru it.
+     */
+    private Map<MultiDeBruijnVertex, Set<HaplotypeRoute>> buildHaplotypesByVertex() {
+        final Map<MultiDeBruijnVertex, Set<HaplotypeRoute>> result = new HashMap<>(referenceVertices.size());
+        final Set<HaplotypeRoute> allHaplotypeRoutes = new LinkedHashSet<>(haplotypeRouteByHaplotype.values());
+        for (final HaplotypeRoute haplotypeRoute : allHaplotypeRoutes) {
+            final Set<HaplotypeRoute> singleton = Collections.singleton(haplotypeRoute);
+            for (final MultiDeBruijnVertex vertex : haplotypeRoute.vertexSet())
+                if (!result.containsKey(vertex))
+                    result.put(vertex, singleton);
+                else {
+                    final Set<HaplotypeRoute> currentHrs = result.get(vertex);
+                    if (currentHrs.size() == haplotypes.size() - 1)
+                        result.put(vertex, allHaplotypeRoutes);
+                    else if (currentHrs.size() == 1) {
+                        final Set<HaplotypeRoute> newHrs = new LinkedHashSet<>(allHaplotypeRoutes.size());
+                        newHrs.addAll(currentHrs);
+                        newHrs.add(haplotypeRoute);
+                        result.put(vertex, newHrs);
+                    } else
+                        currentHrs.add(haplotypeRoute);
+                }
+        }
+        return result;
+    }
+
+
+    /**
+     * Debug convenient method to print a graph into a file in the .dot format.
+     * @param fileName name of the output file.
+     * @throws NullPointerException if {@code fileName} is {@code null}.
+     */
+    public void printGraph(final String fileName) {
+        super.printGraph(new File(fileName), 10000);
+    }
+
+
+
+
+    @Override
+    public void printGraph(final PrintStream graphWriter, final boolean writeHeader, final int pruneFactor) {
+        if ( writeHeader )
+            graphWriter.println("digraph assemblyGraphs {");
+
+
+        for( final MultiSampleEdge edge : edgeSet() ) {
+            graphWriter.println("\t" + getEdgeSource(edge).toString() + " -> " + getEdgeTarget(edge).toString() + " [" + (edge.getMultiplicity() > 0 && edge.getMultiplicity() <= pruneFactor ? "style=dotted,color=grey," : "") + "label=\"" + edge.getDotLabel() + "\"];");
+            if( edge.isRef() ) {
+                graphWriter.println("\t" + getEdgeSource(edge).toString() + " -> " + getEdgeTarget(edge).toString() + " [color=red];");
+            }
+        }
+
+        for( final MultiDeBruijnVertex v : vertexSet() )
+            graphWriter.println("\t" + v.toString() + " [label=\"" + v.getId() + ":" +  new String(getAdditionalSequence(v)) + v.additionalInfo() + "\",shape=box]");
+
+        if ( writeHeader )
+            graphWriter.println("}");
+    }
+
+
+    @Override
+    public Pair<MultiDeBruijnVertex,Integer> findStart(final SequenceForKmers seqForKmers) {
+        return getOrCreateKmerVertex(seqForKmers.sequence, 0, true);
+    }
+
+    /**
+     * Checks whether the graph has some sources or sink vertices that are not reference vertices.
+     *
+     * @return {@code true} iff so.
+     */
+    public boolean hasNonReferenceEnds() {
+        for (final MultiDeBruijnVertex end : getSources())
+            if (!isReferenceNode(end)) return true;
+        for (final MultiDeBruijnVertex end : getSinks())
+            if (!isReferenceNode(end)) return true;
+        return false;
+    }
+
+    /**
+     * Merges vertices that share exactly the same set of outgoing vertices.
+     * <p/>
+     * This is done in reversed topological order and since the graph is a DAG it ensure to return a graph
+     * that such merge is any longer possible. I.e. there is no need to run this method more than once.
+     * <p/>
+     * Notice that we will a record of distinct unique kmers that map to the same vertex that map now to the same
+     * merged vertex. Thus if vertices {@code X and Y} are merged then {@code findKmer(X.sequence) == findKmer(Y.sequence)}.
+     * <p/>
+     * Examples:
+     * <ul>
+     * <li>
+     *    {@code AAA -> AAC, CAA -> AAC} would become {@code NAA -> AAC}.
+     * </li><li>
+     *    {@code AAA -> AAC, AAA -> AAG, CAA -> AAC, CAA -> AAG} would become {@code NAA -> AAG, NAA -> AAG}
+     * </li><li>
+     *    {@code AAA -> AAC, AAA -> AAG, CAA -> AAC} would not change as {@code AAA} and {@code CAA}
+     *    do not share {@code AAG} as outgoing vertex.
+     * </li>
+     * <li>
+     *    {@code AAA -> AAC, AAC -> ACA, CAA -> AAC, GAC -> ACA } would become {@code NAA -> NAC, NAC -> ACA}.
+     * </li>
+     * </ul>
+     */
+    public void mergeCommonChains() {
+        final int vertexCount = vertexSet().size();
+        final Set<MultiDeBruijnVertex> refVertices = new HashSet<>(vertexCount);
+        final Map<MultiDeBruijnVertex,Integer> indexByVertex = new HashMap<>(vertexCount);
+        final int[] pendingChildren = new int[vertexCount];
+        final Deque<MultiDeBruijnVertex> readyVertices = new LinkedList<>();
+        final Set<MultiDeBruijnVertex> merged = new HashSet<>(1 + vertexCount / 10 );
+
+        // Initialize traversal data structures.
+        mergeCommonChainsInitialize(refVertices, indexByVertex, pendingChildren, readyVertices);
+
+        // Traversal in inverted topological order where children nodes are processed before their parents.
+        while (!readyVertices.isEmpty()) {
+            final MultiDeBruijnVertex currentVertex = readyVertices.remove();
+            if (merged.contains(currentVertex)) continue;
+
+            final Set<MultiDeBruijnVertex> mergeSet = new HashSet<>(2);
+            MultiDeBruijnVertex refVertex = mergeCommonChainsComposeMergeSet(refVertices, currentVertex, mergeSet);
+            mergeVertices(refVertex,mergeSet,indexByVertex,pendingChildren,readyVertices);
+            merged.addAll(mergeSet);
+        }
+        needToUpdateHaplotypeStructures = true;
+    }
+
+    /**
+     * Given a seed vertex, determines the mergin set of nodes that will be collapsed into one.
+     *
+     * @param refVertices reference path vertices
+     * @param currentVertex current vertex.
+     * @param mergeSet where to store the final merging set.
+     * @return the reference node if present that needs to be preserved as such. It might be {@code null}
+     */
+    private MultiDeBruijnVertex mergeCommonChainsComposeMergeSet(final Set<MultiDeBruijnVertex> refVertices,
+                                                                 final MultiDeBruijnVertex currentVertex,
+                                                                 final Set<MultiDeBruijnVertex> mergeSet) {
+        final boolean currentIsSource = isSource(currentVertex);
+        final Set<MultiDeBruijnVertex> children = outgoingVerticesOf(currentVertex);
+        if (children.size() == 0)
+            mergeSet.add(currentVertex);
+        else
+            for (final MultiDeBruijnVertex child : children)
+                mergeSet.addAll(incomingVerticesOf(child));
+
+        MultiDeBruijnVertex refVertex = refVertices.contains(currentVertex) ? currentVertex : null;
+        final Iterator<MultiDeBruijnVertex> candidatesIt = mergeSet.iterator();
+        while (candidatesIt.hasNext()) {
+            final MultiDeBruijnVertex candidate = candidatesIt.next();
+            if (candidate == currentVertex) continue;
+            if (isSource(candidate) != currentIsSource) {
+                candidatesIt.remove();
+                continue;
+            }
+            if (currentIsSource && !candidate.getSequenceString().equals(currentVertex.getSequenceString())) {
+                candidatesIt.remove();
+                continue;
+            }
+            if (!currentIsSource && candidate.getSuffix() != currentVertex.getSuffix()) {
+                candidatesIt.remove();
+                continue;
+            }
+            final Set<MultiDeBruijnVertex> candidateChildren = outgoingVerticesOf(candidate);
+            if (candidateChildren.size() != children.size())
+                candidatesIt.remove();
+            else {
+                boolean removed = false;
+                for (final MultiDeBruijnVertex candidateChild : candidateChildren)
+                    if (!children.contains(candidateChild)) {
+                        candidatesIt.remove();
+                        removed = true;
+                        break;
+                    }
+                if (refVertex == null && !removed && refVertices.contains(candidate)) refVertex = candidate;
+            }
+        }
+        return refVertex;
+    }
+
+    /**
+     * Initialize data-structures for {@link #mergeCommonChains}
+     *
+     * @param refVertices will contain reference path vertices.
+     * @param indexByVertex map vertex -> index in {@code pendingChildren}.
+     * @param pendingChildren number of children of a node that have not yet been processed.
+     * @param readyVertices vertices that are ready to be processed (all children have been processed).
+     */
+    private void mergeCommonChainsInitialize(final Set<MultiDeBruijnVertex> refVertices,
+                                             final Map<MultiDeBruijnVertex, Integer> indexByVertex,
+                                             final int[] pendingChildren,
+                                             final Deque<MultiDeBruijnVertex> readyVertices) {
+        int nextIndex = 0;
+        for (final MultiDeBruijnVertex v : vertexSet()) {
+            indexByVertex.put(v,nextIndex++);
+            if (isReferenceNode(v)) refVertices.add(v);
+        }
+
+        for (final Map.Entry<MultiDeBruijnVertex,Integer> entry : indexByVertex.entrySet())
+            if ((pendingChildren[entry.getValue()] = outDegreeOf(entry.getKey())) == 0)
+                readyVertices.add(entry.getKey());
+    }
+
+    // Perform the actual merge.
+    private void mergeVertices(final MultiDeBruijnVertex refVertex, final Collection<MultiDeBruijnVertex> vertices, final Map<MultiDeBruijnVertex,Integer> indexByVertex, final int[] pendingChildrenCounts, final Deque<MultiDeBruijnVertex> ready) {
+        if (vertices.size() == 0)
+            throw new IllegalArgumentException();
+        final MultiDeBruijnVertex vertexToKeep =  refVertex == null ? vertices.iterator().next() : refVertex;
+        final byte[] sequence = vertexToKeep.getSequence();
+        final Set<Kmer> uniqueKmersToUpdate = new HashSet<>(vertices.size());
+        final Set<MultiDeBruijnVertex> parentVertices = new HashSet<>(inDegreeOf(vertexToKeep) * 2);
+        parentVertices.addAll(incomingVerticesOf(vertexToKeep));
+        for (final MultiDeBruijnVertex p : parentVertices)
+            if (--pendingChildrenCounts[indexByVertex.get(p)] == 0)
+                ready.add(p);
+
+        final Kmer mergedKmer = new Kmer(sequence);
+        if (uniqueKmers.containsKey(mergedKmer)) {
+            uniqueKmersToUpdate.add(new Kmer(mergedKmer.bases().clone()));
+            uniqueKmers.remove(mergedKmer);
+        }
+        boolean foundMergedVertex = false;
+        for (final MultiDeBruijnVertex v : vertices)
+            if (v == vertexToKeep)
+                foundMergedVertex = true;
+            else {
+                final byte[] seq = v.getSequence();
+                final Kmer kmer = new Kmer(seq);
+                if (uniqueKmers.containsKey(kmer)) {
+                    uniqueKmersToUpdate.add(kmer);
+                    uniqueKmers.remove(kmer);
+                }
+                if (sequence.length != seq.length) throw new IllegalArgumentException("mismatched sizes " + sequence.length + " != "
+                        + seq.length + " " + new String(sequence) + " " + new String(seq));
+                for (int i = sequence.length - 1; i >= 0; i--) {
+
+                    if (sequence[i] != seq[i]) sequence[i] = 'N';
+                }
+                for (final MultiDeBruijnVertex p : incomingVerticesOf(v)) {
+                    if (--pendingChildrenCounts[indexByVertex.get(p)] == 0)
+                        ready.add(p);
+                    if (!parentVertices.contains(p)) {
+                        parentVertices.add(p);
+                        final MultiSampleEdge e = getEdge(p,v);
+                        addEdge(p,vertexToKeep,new MultiSampleEdge(e.isRef(),e.getMultiplicity(),1));
+                    } else {
+                        getEdge(p,vertexToKeep).incMultiplicity(getEdge(p,v).getMultiplicity());
+                    }
+                }
+                removeVertex(v);
+            }
+        if (!foundMergedVertex)
+            throw new IllegalArgumentException("merged vertex must be contained in the input set");
+        for (final Kmer kmer : uniqueKmersToUpdate)
+            uniqueKmers.put(kmer,vertexToKeep);
+    }
+
+    public Map<Kmer,MultiDeBruijnVertex> uniqueKmerMap() {
+        return Collections.unmodifiableMap(uniqueKmers);
+    }
+
+    @Override
+    public boolean equals(Object other) {
+        return (other instanceof HaplotypeGraph) && equals((HaplotypeGraph)other);
+    }
+
+
+    /**
+     * Simple debug representation of the haplotype graph.
+     * @return never {@code null}
+     */
+    @Override
+    public String toString() {
+        return getClass().getSimpleName() + "[ks=" + kmerSize + "](vs=" + vertexSet().size() + "," + edgeSet().size() + "){...}";
+    }
+
+    /**
+     * Returns set of valid haplotypes.
+     * @return never {@code null} but perhaps empty.
+     */
+    public Set<Haplotype> getHaplotypes() {
+        updateHaplotypeStructures();
+        return haplotypes;
+    }
+
+    /**
+     * Returns a map between valid haplotypes and corresponding routes in the graph.
+     * @return never {@code null} but perhaps empty.
+     */
+    public Map<Haplotype,HaplotypeRoute> getHaplotypeRouteMap() {
+        updateHaplotypeStructures();
+        return haplotypeRouteByHaplotype;
+    }
+
+    /**
+     * Returns set of haplotype routes that enclose a vertex.
+     * @param vertex the query vertex.
+     * @return never {@code null} but perhaps empty set.
+     */
+    public Set<HaplotypeRoute> getEnclosingHaplotypeRoutes(final MultiDeBruijnVertex vertex) {
+        updateHaplotypeStructures();
+        if (haplotypesByVertex == null)
+            return Collections.emptySet();
+        final Set<HaplotypeRoute> result = haplotypesByVertex.get(vertex);
+        if (result == null)
+            return Collections.emptySet();
+        else
+            return result;
+    }
+
+    /**
+     * Returns the reference route
+     *
+     * @return {@code null} if there is no valid reference haplotype.
+     */
+    public HaplotypeRoute getReferenceRoute() {
+        updateHaplotypeStructures();
+        return referenceRoute;
+    }
+
+    /***********************************************
+     * deep equals implementation, used in testing. *
+     ***********************************************/
+
+    /**
+     * Compare two haplotype threading graphs and it determines whether they have the same structure.
+     * <p/>
+     * This method goes a long way to figure out the equality and no equality of both graphs. However there
+     * are "pathological" case in where it might fail to see a difference. This is due to the fact that there
+     * is no guarantee of the uniqueness of sequences at source vertex.
+     * <p/>
+     * If there are more than one source vertex with the same sequence it try to match source vertices between both
+     * graphs matching all possible paths emanating from every pair of sources.
+     *
+     * <p>Note: in practice this is only used in for testing purposes</p.>
+     *
+     * @param other  the other graph to compare against.
+     * @return never {@code null}.
+     */
+    public boolean equals(HaplotypeGraph other) {
+        updateHaplotypeStructures();
+        if (other == null) return false;
+        if (other == this) return true;
+
+        if (!equals$ReferencePaths(this, other)) return false;
+        final Map<String,MultiDeBruijnVertex> thisSourcesBySequence = equalsBuildSourceBySequenceMap(this);
+        final Map<String,MultiDeBruijnVertex> otherSourcesBySequence = equalsBuildSourceBySequenceMap(other);
+        if (thisSourcesBySequence.size() != otherSourcesBySequence.size()) return false;
+        final List<MultiDeBruijnVertex> unmatchedLeft = new LinkedList<>();
+        final List<MultiDeBruijnVertex> unmatchedRight = new LinkedList<>();
+        final List<Pair<MultiDeBruijnVertex,MultiDeBruijnVertex>> sourcePairs = equals$matchVertexBySequenceMaps(thisSourcesBySequence,otherSourcesBySequence,unmatchedLeft,unmatchedRight);
+        if (unmatchedLeft.size() > 0 || unmatchedRight.size() > 0) return false;
+
+
+        final Deque<Pair<MultiDeBruijnVertex,MultiDeBruijnVertex>> pending = new LinkedList<>(sourcePairs);
+        final Set<MultiDeBruijnVertex> visited = new HashSet<>(vertexSet().size());
+        while (!pending.isEmpty()) {
+            final Pair<MultiDeBruijnVertex,MultiDeBruijnVertex> pair = pending.removeFirst();
+            final MultiDeBruijnVertex leftVertex = pair.getFirst();
+            final MultiDeBruijnVertex rightVertex = pair.getSecond();
+            final List<Pair<MultiDeBruijnVertex,MultiDeBruijnVertex>> childrenPairs = equals$matchVertexBySequenceMaps(equalsBuildChildrenBySuffixMap(this, leftVertex),
+                    equalsBuildChildrenBySuffixMap(other, rightVertex), unmatchedLeft, unmatchedRight);
+            if (unmatchedLeft.size() > 0 || unmatchedRight.size() > 0) return false;
+            for (final Pair<MultiDeBruijnVertex,MultiDeBruijnVertex> childPair : childrenPairs) {
+                final MultiDeBruijnVertex leftChild = childPair.getFirst();
+                final MultiDeBruijnVertex rightChild = childPair.getSecond();
+                final boolean leftVisited = visited.add(leftChild);
+                final boolean rightVisited = visited.add(rightChild);
+                if (leftVisited != rightVisited) return false; // visited before in different matchings.
+                if (leftVisited) continue;
+                pending.add(childPair);
+                visited.add(childPair.getFirst());
+                visited.add(childPair.getSecond());
+            }
+        }
+        return true;
+    }
+
+    // Note: in practice only use by equals(HaplotypeGraph) for testing purposes.
+    private boolean equals$ReferencePaths(final HaplotypeGraph g1, final HaplotypeGraph g2) {
+        MultiDeBruijnVertex refVertex1 = g1.getReferenceSourceVertex();
+        MultiDeBruijnVertex refVertex2 = g2.getReferenceSourceVertex();
+        if (refVertex1 == null && refVertex2 == null)
+            return true;
+        if (refVertex1 == null || refVertex2 == null)
+            return false;
+
+        if (!refVertex1.getSequenceString().equals(refVertex2.getSequenceString()))
+            return false;
+
+        while (refVertex1 != null && refVertex2 != null) {
+            if (refVertex1.getSuffix() != refVertex2.getSuffix()) return false;
+            refVertex1 = g1.getNextReferenceVertex(refVertex1);
+            refVertex2 = g2.getNextReferenceVertex(refVertex2);
+
+        }
+        return refVertex1 == refVertex2;
+    }
+
+    // Note: in practice only use by equals(HaplotypeGraph) for testing purposes.
+    private static Map<String, MultiDeBruijnVertex> equalsBuildChildrenBySuffixMap(final HaplotypeGraph graph,
+                                                                                   final MultiDeBruijnVertex vertex) {
+        final Map<String,MultiDeBruijnVertex> result = new HashMap<>();
+        for (final MultiDeBruijnVertex child : graph.outgoingVerticesOf(vertex))
+            result.put(new String(new byte[]{child.getSuffix()}), child);
+        return result;
+    }
+
+    // Note: in practice only use by equals(HaplotypeGraph) for testing purposes.
+    private static List<Pair<MultiDeBruijnVertex, MultiDeBruijnVertex>> equals$matchVertexBySequenceMaps(
+            final Map<String,MultiDeBruijnVertex> left, final Map<String, MultiDeBruijnVertex> right,
+            final Collection<MultiDeBruijnVertex> unmatchedLeft, final Collection<MultiDeBruijnVertex> unmatchedRight) {
+        final List<Pair<MultiDeBruijnVertex,MultiDeBruijnVertex>> result = new LinkedList<>();
+        for (final Map.Entry<String,MultiDeBruijnVertex> leftEntry : left.entrySet())
+            if (right.containsKey(leftEntry.getKey()))
+                result.add(new Pair<>(leftEntry.getValue(),right.get(leftEntry.getKey())));
+            else
+                unmatchedLeft.add(leftEntry.getValue());
+        for (final Map.Entry<String,MultiDeBruijnVertex> rightEntry : right.entrySet())
+            if (!left.containsKey(rightEntry.getKey()))
+                unmatchedRight.add(rightEntry.getValue());
+        return result;
+    }
+
+    // Note: in practice only use by equals(HaplotypeGraph) for testing purposes.
+    private static Map<String, MultiDeBruijnVertex> equalsBuildSourceBySequenceMap(final HaplotypeGraph other) {
+
+        final Set<MultiDeBruijnVertex> sources = other.getSources();
+        final Map<String,MultiDeBruijnVertex> result = new HashMap<>(sources.size());
+        final Map<String,List<MultiDeBruijnVertex>> collisions = new HashMap<>(sources.size());
+        for (final MultiDeBruijnVertex v : sources) {
+            final String sequence = v.getSequenceString();
+            if (result.containsKey(sequence)) { // we need to handle collision due to lack of uniqueness.
+                final List<MultiDeBruijnVertex> collisionList;
+                if (collisions.containsKey(sequence))
+                    collisionList = collisions.get(sequence);
+                else
+                    collisions.put(sequence,collisionList = new LinkedList<>());
+                collisionList.add(v);
+            } else {
+                result.put(sequence,v);
+            }
+        }
+        if (collisions.size() == 0)
+            return result;
+        for (final String s : collisions.keySet()) {
+            result.remove(s);
+            final List<MultiDeBruijnVertex> vertices = collisions.remove(s);
+            int number = 0;
+            final List<Pair<MultiDeBruijnVertex,String>> extendedSequences = new LinkedList<>();
+            for (final MultiDeBruijnVertex vertice : vertices)
+                extendedSequences.add(new Pair<>(vertice, equalsCollisionResolverExtendedSequence(other, vertice)));
+            Collections.sort(extendedSequences,new Comparator<Pair<MultiDeBruijnVertex,String>>(){
+                public int compare(final Pair<MultiDeBruijnVertex,String> p1, final Pair<MultiDeBruijnVertex,String> p2) {
+                    return p1.getSecond().compareTo(p2.getSecond());
+                }
+            });
+            for (final Pair<MultiDeBruijnVertex,String> p : extendedSequences)
+                result.put(p.getSecond() + '-' + (number++),p.getFirst());
+        }
+        return result;
+
+    }
+
+    // Note: in practice only use by equals(HaplotypeGraph) for testing purposes.
+    private static String equalsCollisionResolverExtendedSequence(final HaplotypeGraph graph, final MultiDeBruijnVertex source) {
+        final StringBuilder buffer = new StringBuilder(1000);
+        final Set<MultiDeBruijnVertex> visited = new HashSet<>(graph.vertexSet().size());
+        final Stack<MultiDeBruijnVertex> pending = new Stack<>();
+        final Stack<Integer> position = new Stack<>();
+        position.ensureCapacity(graph.vertexSet().size());
+        pending.ensureCapacity(graph.vertexSet().size());
+        pending.add(source);
+        position.add(0);
+        int lastPos = -1;
+        while (!pending.isEmpty()) {
+            final MultiDeBruijnVertex next = pending.pop();
+            if (visited.contains(next)) continue;
+            visited.add(next);
+            final int pos = position.pop();
+            final CharSequence sequence;
+            if (graph.isSource(next)) {
+                if (next == source) {
+                    sequence = new String(next.getSequence());
+                } else {
+                    sequence = new StringBuffer(next.getSequence().length).append(new String(next.getSequence())).reverse().append('$');
+                }
+            } else {
+                sequence = new String(new byte[] { next.getSuffix()});
+            }
+
+            if (pos != lastPos + 1) {
+                buffer.append('[').append(Math.abs(pos)).append(']');
+            }
+            buffer.append(sequence);
+            lastPos = pos + sequence.length() - 1;
+
+            final List<MultiDeBruijnVertex> parents = new LinkedList<>(graph.incomingVerticesOf(next));
+            Collections.sort(parents,new Comparator<MultiDeBruijnVertex>() {
+                @Override
+                public int compare(final MultiDeBruijnVertex o1, final MultiDeBruijnVertex o2) {
+                    return Byte.compare(o1.getSuffix(),o2.getSuffix());
+                }
+            });
+            for (final MultiDeBruijnVertex parent : parents) {
+                pending.push(parent);
+                position.push(lastPos + 1);
+            }
+
+            final List<MultiDeBruijnVertex> children = new LinkedList<>(graph.incomingVerticesOf(next));
+            Collections.sort(children,new Comparator<MultiDeBruijnVertex>() {
+                @Override
+                public int compare(final MultiDeBruijnVertex o1, final MultiDeBruijnVertex o2) {
+                    return Byte.compare(o1.getSuffix(),o2.getSuffix());
+                }
+            });
+            for (final MultiDeBruijnVertex child : graph.outgoingVerticesOf(next)) {
+                pending.push(child);
+                position.push(lastPos + 1);
+            }
+        }
+
+        return buffer.toString();
+    }
+
+
+    /**
+     * Calculates the subset of reference path vertices that are amenable to be anchoring vertices.
+     * <p/>
+     * <p>
+     * For a vertex to be anchorable:
+     * <ul>
+     * <li>Should not include bases from a repeat</li>,
+     * <li>There should not be in a middle of a event block</li>
+     * </ul>
+     * </p>
+     *
+     * @return never {@code null}.
+     */
+    private Set<MultiDeBruijnVertex> calculateAnchorableVertexSet() {
+        updateHaplotypeStructures();
+        if (referenceBases == null)
+            return Collections.emptySet();
+
+        // We first check what bases in the reference path bases are part of a repeat.
+        final boolean[] nonAnchorableDueToRepeats = SequenceComplexity.findBasesInShortUnitRepeats(
+                referenceBases, maxRepeatUnitLength, minRepeatLengthInUnits);
+
+        final Set<MultiDeBruijnVertex> result = new HashSet<>(100);
+        final Map<MultiDeBruijnVertex, CountSet> expectedRejoins = new HashMap<>();
+
+
+        MultiDeBruijnVertex currentVertex = getReferenceRoute().getFirstVertex();
+        final int sourceSequenceLength = currentVertex.getSequence().length;
+
+        // Determine whether the reference source vertex in anchorable discarding repeats:
+        boolean sourceIsAnchorable = true;
+        for (int i = 0; i < sourceSequenceLength; i++)
+            if (nonAnchorableDueToRepeats[i]) {
+                sourceIsAnchorable = false;
+                break;
+            }
+
+        // Update the nonAnchorableDueToRepeats array accordingly.
+        int index = currentVertex.getSequence().length - 1;
+        nonAnchorableDueToRepeats[index] = !sourceIsAnchorable;
+
+
+        // We keep record on all alternative path lengths:
+        final CountSet pathLengths = new CountSet(haplotypes.size());
+        pathLengths.setTo(0);
+
+        // Now we go through the reference path and determine which vertices are not part of event block.
+        // We keep track of open divergent paths in expectedRejoins. Thus only those vertices traversed
+        // when exptectedRejoins size 0 can be anchorable:
+        while (currentVertex != null) {
+            int inDegree = inDegreeOf(currentVertex);
+            if (inDegree > 1)
+                expectedRejoins.remove(currentVertex);
+            if (expectedRejoins.size() == 0 && !nonAnchorableDueToRepeats[index]) {
+                currentVertex.setAdditionalInfo(currentVertex.additionalInfo() + "*");
+                result.add(currentVertex);
+            }
+            final Set<MultiSampleEdge> nextEdges = outgoingEdgesOf(currentVertex);
+            MultiDeBruijnVertex nextReferenceVertex = null;
+            for (final MultiSampleEdge e : nextEdges) {
+                final MultiDeBruijnVertex nextVertex = getEdgeTarget(e);
+                if (e.isRef() && referenceVertices.contains(nextVertex))
+                    nextReferenceVertex = nextVertex;
+                else
+                    calculateRejoins(nextVertex, expectedRejoins, referenceVertices, pathLengths, false, false);
+            }
+            currentVertex = nextReferenceVertex;
+            index++;
+        }
+        return result;
+    }
+
+
+
+    /**
+     * Returns those vertices that can be used as anchors along the refererence route.
+     * @return never {@code null} but perhaps empty if there is no such a vertex.
+     */
+    public Set<MultiDeBruijnVertex> getAnchorableVertices() {
+        updateHaplotypeStructures();
+        return anchorableVertices;
+    }
+
+    /**
+     * Finds non-reference wondering paths that will rejoin the reference path from a particular node.
+     * <p/>
+     * <p>
+     * It only considers those paths that rejoin within the anchor points of a read.
+     * </p>
+     * <p/>
+     * <p>
+     * Rather than reporting explicitly the path vertice sequence, this method report the length of the paths
+     * found. These are dumped into {@code expectedRejoins} where the keys are refernce path vertex where paths rejoin
+     * and the value is the set of path lengths.
+     * </p>
+     * <p/>
+     * <p> The path lengths are calculated as the length from the startVertex plus the prefix sizes {@code prefixSizes} </p>
+     * <p/>
+     * <p> You can also ask the method to exhaustively find all paths ({@code exhaustive == true}) or just consider
+     * intermediate nodes once ({@code exhustive == false}). If the latter only the shortest paths are considered.</p>
+     * <p/>
+     * <p> Finally you also can check on paths backwards ({@code backwards == true}) or forwards ({@code backwards == false})</p>
+     *
+     * @param startVertex               the origin node for those paths.
+     * @param expectedRejoins           map where to place the found paths in a form of the rejoining non-reference vertex (key) and
+     *                                  set of path lengths (value).
+     * @param referenceWithinBoundaries reference vertices found between read anchors. The key are the vertices, the values are
+     *                                  the kmer's offset in the read.
+     * @param prefixSizes               prefix path sizes to be added to the rejoin path sizes.
+     * @param exhaustive                whether all paths should be considered or we only care about find out the rejoining vertices.
+     * @param backwards                 whether we want to find backward paths (inverse edge traversal).
+     *
+     * Note: it is marked as deprecated as this method signature may change in the future. It is public just because
+     *                                  is currently shared by several other classes, however it would not be surprising if
+     *                                  it gets refactored out at some point. So use with care.
+     */
+    @Deprecated
+    public void calculateRejoins(final MultiDeBruijnVertex startVertex, final Map<MultiDeBruijnVertex, CountSet> expectedRejoins,
+                                  final Set<MultiDeBruijnVertex> referenceWithinBoundaries, final CountSet prefixSizes,
+                                  final boolean exhaustive, final boolean backwards) {
+        Queue<MultiDeBruijnVertex> queue = new LinkedList<>();
+        Queue<CountSet> depths = new LinkedList<>();
+        queue.add(startVertex);
+        depths.add(prefixSizes);
+
+        final Set<MultiDeBruijnVertex> visited = new HashSet<>();
+        if (!exhaustive) visited.add(startVertex);
+        while (!queue.isEmpty()) {
+            final CountSet depth = depths.remove();
+            final MultiDeBruijnVertex v = queue.remove();
+            if (referenceVertices.contains(v)) {
+                if (referenceWithinBoundaries.contains(v)) {
+                    final CountSet previous = expectedRejoins.get(v);
+                    if (previous == null)
+                        expectedRejoins.put(v, depth.clone());
+                    else
+                        previous.addAll(depth);
+                }
+            } else {
+                final CountSet depthPlusOne = depth.clone();
+                depthPlusOne.incAll(1);
+                final Set<MultiSampleEdge> nextEdges = backwards ? incomingEdgesOf(v) : outgoingEdgesOf(v);
+                for (final MultiSampleEdge e : nextEdges) {
+                    final MultiDeBruijnVertex w = backwards ? getEdgeSource(e) : getEdgeTarget(e);
+                    if (visited.contains(w)) // avoid repetitive work.
+                        continue;
+                    if (!exhaustive) visited.add(w);
+                    queue.add(w);
+                    depths.add(depthPlusOne);
+                }
+            }
+        }
+    }
+
+}
+
+
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java
index 5752583c7..ef8c74d0b 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java
@@ -64,7 +64,7 @@ import java.util.concurrent.atomic.AtomicInteger;
  * Date: 4/17/13
  * Time: 3:20 PM
  */
-final class MultiDeBruijnVertex extends DeBruijnVertex {
+public final class MultiDeBruijnVertex extends DeBruijnVertex {
     private final static boolean KEEP_TRACK_OF_READS = false;
 
     // Note that using an AtomicInteger is critical to allow multi-threaded HaplotypeCaller
@@ -116,6 +116,10 @@ final class MultiDeBruijnVertex extends DeBruijnVertex {
 
     @Override
     public String additionalInfo() {
-        return KEEP_TRACK_OF_READS ? (! reads.contains("ref") ? "__" + Utils.join(",", reads) : "") : "";
+        return super.additionalInfo() + (KEEP_TRACK_OF_READS ? (! reads.contains("ref") ? "__" + Utils.join(",", reads) : "") : "");
+    }
+
+     int getId() {
+        return id;
     }
 }
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java
index 6500196d3..f33a4883f 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java
@@ -181,7 +181,7 @@ public class ReadThreadingAssembler extends LocalAssemblyEngine {
             return null;
         }
 
-        printDebugGraphTransform(rtgraph, new File("sequenceGraph.0.0.raw_readthreading_graph.dot"));
+        printDebugGraphTransform(rtgraph, new File("" + refHaplotype.getGenomeLocation() + "-sequenceGraph." + kmerSize + ".0.0.raw_readthreading_graph.dot"));
 
         // go through and prune all of the chains where all edges have <= pruneFactor.  This must occur
         // before recoverDanglingTails in the graph, so that we don't spend a ton of time recovering
@@ -195,20 +195,23 @@ public class ReadThreadingAssembler extends LocalAssemblyEngine {
         // remove all heading and trailing paths
         if ( removePathsNotConnectedToRef ) rtgraph.removePathsNotConnectedToRef();
 
-        printDebugGraphTransform(rtgraph, new File("sequenceGraph.0.1.cleaned_readthreading_graph.dot"));
+        printDebugGraphTransform(rtgraph, new File("" + refHaplotype.getGenomeLocation() + "-sequenceGraph." + kmerSize + ".0.1.cleaned_readthreading_graph.dot"));
 
         final SeqGraph initialSeqGraph = rtgraph.convertToSequenceGraph();
+        if (debugGraphTransformations) initialSeqGraph.printGraph(new File("" + refHaplotype.getGenomeLocation() + "-sequenceGraph." + kmerSize + ".0.1.initial_seqgraph.dot"),10000);
 
         // if the unit tests don't want us to cleanup the graph, just return the raw sequence graph
         if ( justReturnRawGraph ) return new AssemblyResult(AssemblyResult.Status.ASSEMBLED_SOME_VARIATION, initialSeqGraph);
 
-        if ( debug ) logger.info("Using kmer size of " + rtgraph.getKmerSize() + " in read threading assembler");
-        printDebugGraphTransform(initialSeqGraph, new File("sequenceGraph.0.2.initial_seqgraph.dot"));
+        if (debug) logger.info("Using kmer size of " + rtgraph.getKmerSize() + " in read threading assembler");
+        printDebugGraphTransform(initialSeqGraph, new File( "" + refHaplotype.getGenomeLocation() + "-sequenceGraph." + kmerSize + ".0.2.initial_seqgraph.dot"));
         initialSeqGraph.cleanNonRefPaths(); // TODO -- I don't this is possible by construction
 
         final AssemblyResult cleaned = cleanupSeqGraph(initialSeqGraph);
         final AssemblyResult.Status status = cleaned.getStatus() == AssemblyResult.Status.ASSEMBLED_SOME_VARIATION && requireReasonableNumberOfPaths && !reasonableNumberOfPaths(cleaned.getGraph()) ? AssemblyResult.Status.FAILED : cleaned.getStatus();
-        return new AssemblyResult(status, cleaned.getGraph());
+        final AssemblyResult result = new AssemblyResult(status, cleaned.getGraph());
+        result.setThreadingGraph(rtgraph);
+        return result;
     }
 
     /**
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java
index 04671a178..dc057294e 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java
@@ -65,8 +65,11 @@ import org.jgrapht.alg.CycleDetector;
 
 import java.io.File;
 import java.util.*;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+public class ReadThreadingGraph extends BaseGraph<MultiDeBruijnVertex, MultiSampleEdge> implements KmerSearchableGraph<MultiDeBruijnVertex,MultiSampleEdge> {
 
-public class ReadThreadingGraph extends BaseGraph<MultiDeBruijnVertex, MultiSampleEdge> {
     /**
      * Edge factory that encapsulates the numPruningSamples assembly parameter
      */
@@ -108,17 +111,17 @@ public class ReadThreadingGraph extends BaseGraph<MultiDeBruijnVertex, MultiSamp
     /**
      * A set of non-unique kmers that cannot be used as merge points in the graph
      */
-    private Set<Kmer> nonUniqueKmers;
+    protected Set<Kmer> nonUniqueKmers;
 
     /**
      * A map from kmers -> their corresponding vertex in the graph
      */
-    private Map<Kmer, MultiDeBruijnVertex> uniqueKmers = new LinkedHashMap<>();
+    protected Map<Kmer, MultiDeBruijnVertex> uniqueKmers = new LinkedHashMap<>();
 
     /**
      *
      */
-    final int kmerSize;
+
     final boolean debugGraphTransformations;
     final byte minBaseQualityToUseInAssembly;
 
@@ -129,16 +132,42 @@ public class ReadThreadingGraph extends BaseGraph<MultiDeBruijnVertex, MultiSamp
     // state variables, initialized in resetToInitialState()
     // --------------------------------------------------------------------------------
     private Kmer refSource;
-    private boolean alreadyBuilt;
-
-    public ReadThreadingGraph() {
-        this(25, false, (byte)6, 1);
-    }
+    protected boolean alreadyBuilt;
 
+    /**
+     * Constructs an empty read-threading-grpah provided the kmerSize.
+     * @param kmerSize 1 or greater.
+     *
+     * @throw IllegalArgumentException if (@code kmerSize) < 1.
+     */
     public ReadThreadingGraph(final int kmerSize) {
         this(kmerSize, false, (byte)6, 1);
     }
 
+
+    /**
+     * Return the collection of outgoing vertices that expand this vertex with a particular base.
+     *
+     * @param v original vertex.
+     * @param b expanding base.
+     * @return never null, but perhaps an empty set. You cannot assume that you can modify the result.
+     */
+    protected Set<MultiDeBruijnVertex> getNextVertices(final MultiDeBruijnVertex v, final byte b) {
+        if (v == null) throw new IllegalArgumentException("the input vertex cannot be null");
+        if (!vertexSet().contains(v)) throw new IllegalArgumentException("the vertex must be present in the graph");
+        final List<MultiDeBruijnVertex> result = new LinkedList<>();
+        for (final MultiDeBruijnVertex w : outgoingVerticesOf(v)) {
+            if (w.getSuffix() == b)
+                result.add(w);
+        }
+        switch (result.size()) {
+            case 0: return Collections.emptySet();
+            case 1: return Collections.singleton(result.get(0));
+            default:
+                    return new HashSet<>(result);
+        }
+    }
+
     /**
      * Create a new ReadThreadingAssembler using kmerSize for matching
      * @param kmerSize must be >= 1
@@ -147,7 +176,6 @@ public class ReadThreadingGraph extends BaseGraph<MultiDeBruijnVertex, MultiSamp
         super(kmerSize, new MyEdgeFactory(numPruningSamples));
 
         if ( kmerSize < 1 ) throw new IllegalArgumentException("bad minkKmerSize " + kmerSize);
-        this.kmerSize = kmerSize;
         this.debugGraphTransformations = debugGraphTransformations;
         this.minBaseQualityToUseInAssembly = minBaseQualityToUseInAssembly;
 
@@ -350,6 +378,7 @@ public class ReadThreadingGraph extends BaseGraph<MultiDeBruijnVertex, MultiSamp
         final int refIndexToMerge = lastRefIndex - matchingSuffix + 1 + (mustHandleLeadingDeletionCase ? 1 : 0);
 
         addEdge(danglingTailMergeResult.danglingPath.get(altIndexToMerge), danglingTailMergeResult.referencePath.get(refIndexToMerge), ((MyEdgeFactory)getEdgeFactory()).createEdge(false, 1));
+
         return 1;
     }
 
@@ -457,6 +486,33 @@ public class ReadThreadingGraph extends BaseGraph<MultiDeBruijnVertex, MultiSamp
         // clear
         pending.clear();
         alreadyBuilt = true;
+        for (final MultiDeBruijnVertex v : uniqueKmers.values())
+            v.setAdditionalInfo(v.additionalInfo() + "+");
+    }
+
+
+    @Override
+    public boolean removeVertex(MultiDeBruijnVertex V) {
+        final boolean result = super.removeVertex(V);
+        if (result) {
+            final byte[] sequence = V.getSequence();
+            final Kmer kmer = new Kmer(sequence);
+            uniqueKmers.remove(kmer);
+        }
+        return result;
+    }
+
+
+    public void removeSingletonOrphanVertices() {
+        // Run through the graph and clean up singular orphaned nodes
+        final List<MultiDeBruijnVertex> verticesToRemove = new LinkedList<>();
+        for( final MultiDeBruijnVertex v : vertexSet() ) {
+            if( inDegreeOf(v) == 0 && outDegreeOf(v) == 0 ) {
+                verticesToRemove.add(v);
+            }
+        }
+        this.removeVertex(null);
+        removeAllVertices(verticesToRemove);
     }
 
     /**
@@ -594,6 +650,7 @@ public class ReadThreadingGraph extends BaseGraph<MultiDeBruijnVertex, MultiSamp
         final SeqGraph seqGraph = new SeqGraph(kmerSize);
         final Map<MultiDeBruijnVertex, SeqVertex> vertexMap = new HashMap<MultiDeBruijnVertex, SeqVertex>();
 
+
         // create all of the equivalent seq graph vertices
         for ( final MultiDeBruijnVertex dv : vertexSet() ) {
             final SeqVertex sv = new SeqVertex(dv.getAdditionalSequence(isSource(dv)));
@@ -638,7 +695,7 @@ public class ReadThreadingGraph extends BaseGraph<MultiDeBruijnVertex, MultiSamp
      * @param seqForKmers the sequence we want to thread into the graph
      * @return a pair of the starting vertex and its position in seqForKmer
      */
-    private Pair<MultiDeBruijnVertex, Integer> findStart(final SequenceForKmers seqForKmers) {
+    protected Pair<MultiDeBruijnVertex, Integer> findStart(final SequenceForKmers seqForKmers) {
         final int uniqueStartPos = seqForKmers.isRef ? 0 : findUniqueStartPosition(seqForKmers.sequence, seqForKmers.start, seqForKmers.stop);
 
         if ( uniqueStartPos == -1 )
@@ -670,7 +727,7 @@ public class ReadThreadingGraph extends BaseGraph<MultiDeBruijnVertex, MultiSamp
      * @param allowRefSource if true, we will allow matches to the kmer that represents the reference starting kmer
      * @return a non-null vertex
      */
-    private Pair<MultiDeBruijnVertex, Integer> getOrCreateKmerVertex(final byte[] sequence, final int start, final boolean allowRefSource) {
+    protected Pair<MultiDeBruijnVertex, Integer> getOrCreateKmerVertex(final byte[] sequence, final int start, final boolean allowRefSource) {
         final Kmer kmer = new Kmer(sequence, start, kmerSize);
         final MultiDeBruijnVertex vertex = getUniqueKmerVertex(kmer, allowRefSource);
         if ( vertex != null ) {
@@ -688,9 +745,11 @@ public class ReadThreadingGraph extends BaseGraph<MultiDeBruijnVertex, MultiSamp
      */
     private MultiDeBruijnVertex getUniqueKmerVertex(final Kmer kmer, final boolean allowRefSource) {
         if ( ! allowRefSource && kmer.equals(refSource) ) return null;
+
         return uniqueKmers.get(kmer);
     }
 
+
     /**
      * Create a new vertex for kmer.  Add it to the uniqueKmers map if appropriate.
      *
@@ -809,4 +868,178 @@ public class ReadThreadingGraph extends BaseGraph<MultiDeBruijnVertex, MultiSamp
                 "kmerSize=" + kmerSize +
                 '}';
     }
+
+
+    @Override
+    public MultiDeBruijnVertex findKmer(final Kmer k) {
+        return uniqueKmers.get(k);
+    }
+
+    /*************************************************************
+     * Simple string representation support for testing purposes *
+     *************************************************************/
+
+    private static final Pattern PROPERTIES_PATTERN = Pattern.compile("^\\s*\\[[^\\]]*\\]");
+    private static final Pattern PATH_PATTERN = Pattern.compile("\\{((\\S+):)?([^\\}]*)\\}");
+    private static final Pattern KMERSIZE_EXTRACTOR_PATTERN = Pattern.compile("^\\s*\\[[^\\]]*(ks|kmerSize)\\s*=\\s*(\\d+)\\s*[,\\]]");
+
+
+    /**
+     * Constructs a read-threadingg-graph for a string representation.
+     *
+     * <p>
+     *     Note: only used for testing.
+     *     Checkout {@link HaplotypeGraphUnitTest} for examples.
+     * </p>
+     * @param s the string representation of the graph {@code null}.
+     */
+    public ReadThreadingGraph(final String s) {
+        super(kmerSizeFromString(s),new MyEdgeFactory(1));
+        debugGraphTransformations = false;
+        minBaseQualityToUseInAssembly = 0;
+        applyString(s);
+        alreadyBuilt = true;
+    }
+
+    /**
+     * Obtain the kmer size for the string representation.
+     * @param str the source string representation.
+     * @return 1 or greater.
+     * @throws IllegalArgumentException if {@code} str does not contain a valid representation.
+     */
+    private static int kmerSizeFromString(final String str) {
+        final Matcher matcher = KMERSIZE_EXTRACTOR_PATTERN.matcher(str);
+        if (matcher.find()) {
+            return Integer.parseInt(matcher.group(2));
+        } else
+            throw new IllegalArgumentException("the input graph spec does not indicate the kmerSize");
+    }
+
+    /**
+     * Apply description string into the graph.
+     *
+     * <p>
+     *     Note: this is done just for testing purposes.
+     *     Checkout {@link HaplotypeGraphUnitTest} for examples.
+     * </p>
+     * @param str the string representation.
+     */
+    private void applyString(final String str) {
+        final Matcher propertiesSectionMatcher = PROPERTIES_PATTERN.matcher(str);
+        final int pathStart = propertiesSectionMatcher.find() ? propertiesSectionMatcher.end() : 0;
+
+        final String pathString = str.substring(pathStart);
+        final Matcher pathMatcher = PATH_PATTERN.matcher(pathString);
+
+        boolean referenceFound = false;
+        final Map<String,MultiDeBruijnVertex> vertexById = new HashMap<>();
+
+        // Loop between path strings and add them one by one.
+        while (pathMatcher.find()) {
+            final String label = pathMatcher.group(2);
+            final boolean isReference = (label != null && label.equals("REF"));
+            if (referenceFound) {
+                if (isReference)
+                    throw new IllegalArgumentException("there are two reference paths");
+
+            } else
+                referenceFound |= isReference;
+
+            // Divide each path into its elements getting a list of sequences and labels if applies:
+            final String elementsString = pathMatcher.group(3);
+            final String[] elements = elementsString.split("\\s*->\\s*");
+            if (elements.length == 0)
+                throw new IllegalArgumentException("empty path not allowed");
+            final String[] seqs = new String[elements.length];
+            final String[] ids = new String[elements.length];
+            for (int i = 0; i < elements.length; i++) {
+                ids[i] = pathElementId(elements[i]);
+                seqs[i] = pathElementSeq(elements[i]);
+                if (seqs[i].isEmpty() && ids[i] == null)
+                    throw new IllegalArgumentException("path with empty element without an id");
+            }
+            final boolean isSource =  ids[0] == null || !vertexById.containsKey(ids[0]);
+            if (isSource && seqs[0].length() != kmerSize)
+                throw new IllegalArgumentException("source sequence length must be the same as the kmerSize "
+                        + ids[0] + " " + seqs[0] + " " + pathMatcher.group());
+            final MultiDeBruijnVertex firstVertex;
+            if (ids[0] != null && vertexById.containsKey(ids[0]))
+                firstVertex = vertexById.get(ids[0]);
+            else {
+                firstVertex = new MultiDeBruijnVertex(seqs[0].getBytes());
+                addVertex(firstVertex);
+                if (ids[0] != null)
+                    vertexById.put(ids[0],firstVertex);
+            }
+            if (!seqs[0].isEmpty() &&
+                    ((isSource && !firstVertex.getSequenceString().equals(seqs[0]))
+                            || (!isSource && firstVertex.getSuffix() != seqs[0].getBytes()[0])))
+                throw new IllegalArgumentException("mismatched first element sequence");
+
+            MultiDeBruijnVertex lastVertex = firstVertex;
+            for (int i = 1; i < elements.length; i++) {
+                if (seqs[i].length() > 1)
+                    throw new IllegalArgumentException("non-source vertex sequence must have length 1");
+                final MultiDeBruijnVertex nextVertex;
+                if (ids[i] == null || !vertexById.containsKey(ids[i])) {
+                    final Set<MultiDeBruijnVertex> nextVertices = getNextVertices(lastVertex,seqs[i].getBytes()[0]);
+                    if (nextVertices.size() == 0) {
+                        nextVertex = new MultiDeBruijnVertex(extendSequence(lastVertex.getSequence(),seqs[i].getBytes()[0]));
+                        addVertex(nextVertex);
+                    } else {
+                        nextVertex = nextVertices.iterator().next();
+                    }
+                    if (ids[i] != null)
+                        vertexById.put(ids[i],nextVertex);
+                } else {
+                    nextVertex = vertexById.get(ids[i]);
+                }
+                final MultiSampleEdge edge = addEdge(lastVertex,nextVertex);
+                if (isReference) edge.setIsRef(true);
+                lastVertex = nextVertex;
+            }
+        }
+    }
+
+    private static String pathElementId(final String element) {
+        final int parentesysPos = element.indexOf('(');
+
+        if (parentesysPos == -1)
+            return null;
+
+        final int closeParentesysPos = element.lastIndexOf(')');
+        if (closeParentesysPos == -1)
+            throw new IllegalArgumentException("non-closed id parantesys found in element: " + element);
+        final String result = element.substring(parentesysPos + 1,closeParentesysPos).trim();
+        if (result.isEmpty())
+            throw new IllegalArgumentException("empty id found in element: " + element);
+        return result;
+    }
+
+    /**
+     * Returns the lenght of a path element in the string representation.
+     * @param element the query element.
+     * @return 0 or greater.
+     */
+    private static String pathElementSeq(final String element) {
+        final int parentesysPos = element.indexOf('(');
+
+        if (parentesysPos == -1)
+            return element.trim();
+
+        return element.substring(0,parentesysPos).trim();
+    }
+
+    /**
+     * Add a base to the end of a byte sequence.
+     * @param sequence sequence where to add the base to.
+     * @param b base to add.
+     * @return never {@code null}, a new array each time.
+     */
+    private static byte[] extendSequence(final byte[] sequence, final byte b) {
+        final byte[] result = new byte[sequence.length];
+        System.arraycopy(sequence,1,result,0,sequence.length - 1);
+        result[result.length - 1] = b;
+        return result;
+    }
 }
\ No newline at end of file
diff --git a/protected/java/src/org/broadinstitute/sting/utils/SequenceComplexity.java b/protected/java/src/org/broadinstitute/sting/utils/SequenceComplexity.java
new file mode 100644
index 000000000..8040ca62a
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/utils/SequenceComplexity.java
@@ -0,0 +1,100 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+*
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+package org.broadinstitute.sting.utils;
+
+/**
+ * Helper class to handle sequence complexity analyses.
+ *
+ * @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.org&gt;
+ */
+public class SequenceComplexity {
+
+    /**
+     * Indicates what positions in a base sequence is found in homopolymers or STR repeat.
+     *
+     * <p>
+     * The result is an boolean array with as many positions as the input base array.
+     * </p>
+     * <p>
+     * Each entry the result makes reference to the base at the same position in the input, where {@code true}
+     * means that it forms part of a repeat.
+     * </p>
+     *
+     * @param bases the input bases.
+     * @param maxRepeatUnitLength what is the largest repeat unit to consider.
+     * @param minRepeatLengthInUnits what is minimum length of a repeat in units to consider it significantly long. Shorter
+     *                               repeats won't be considered as such.
+     * @return never {@code null} but an array with the same length as the reference haplotype.
+     */
+    public static boolean[] findBasesInShortUnitRepeats(final byte[] bases, final int maxRepeatUnitLength,
+                                                        final int minRepeatLengthInUnits) {
+        final boolean[] result = new boolean[bases.length];
+        final int[] repeatAbsoluteLengthCount = new int[maxRepeatUnitLength];
+        for (int i = 0; i < maxRepeatUnitLength; i++)
+            repeatAbsoluteLengthCount[i] = i + 1;
+        for (int i = 0; i < bases.length; i++)
+            for (int j = 1; j <= maxRepeatUnitLength; j++) {
+                final int prevI = i - j;
+                if (prevI < 0) continue;
+                if (bases[prevI] == bases[i]) // repeat continuation.
+                    repeatAbsoluteLengthCount[j - 1]++;
+                else if (minRepeatLengthInUnits <= (repeatAbsoluteLengthCount[j - 1] / j)) {  // end of a long enough repeat.
+                    for (int k = i - repeatAbsoluteLengthCount[j - 1]; k < i; k++)
+                        result[k] = true;
+                    repeatAbsoluteLengthCount[j - 1] = j;
+                } else { // end of not long enough repeat.
+                    repeatAbsoluteLengthCount[j - 1] = j;
+                }
+            }
+        // Do the marking for the last position in bases.
+        for (int j = 1; j <= maxRepeatUnitLength; j++)
+            if (minRepeatLengthInUnits <= (repeatAbsoluteLengthCount[j - 1] / j))
+                for (int k = bases.length - repeatAbsoluteLengthCount[j - 1]; k < bases.length; k++)
+                    result[k] = true;
+        return result;
+    }
+
+}
diff --git a/protected/java/src/org/broadinstitute/sting/utils/collections/CountSet.java b/protected/java/src/org/broadinstitute/sting/utils/collections/CountSet.java
new file mode 100644
index 000000000..e1de32bf6
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/utils/collections/CountSet.java
@@ -0,0 +1,521 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+*
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+package org.broadinstitute.sting.utils.collections;
+
+import com.google.java.contract.Requires;
+import com.sun.istack.internal.NotNull;
+
+import java.lang.reflect.Array;
+import java.util.*;
+
+/**
+ * Efficient implementation for a small set of integer primitive values.
+ * <p>
+ * It includes a increment operation incAll which is convenient when analyzing the read-threading graphs. Nevertheless
+ * it can be also be used in general purpose.
+ * </p>
+ * <p>
+ * It does not provide a O(1) look-up of its elements though. These are kept in a sorted array so look up is implemented
+ * using a binary search O(log n). Therefore it might not be optimal for problems that require large integer sets.
+ * </p>
+ * <p>
+ * Also note that addition can be costly for large sets unless done in order: O(n).
+ * </p>
+ * @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.org&gt;
+ */
+public class CountSet implements Cloneable, Set<Integer> {
+
+    /**
+     * The size of the set.
+     */
+    private int size;
+
+    /**
+     * Holds the element of the set within the subrange <code>[0 .. size - 1]</code> in ascending order.
+     */
+    private int[] elements;
+
+    /**
+     * Creates a copy of an existing int-set.
+     * @param template the intset to copy values from.
+     */
+    public CountSet(final CountSet template) {
+        elements = template.elements.clone();
+        size = template.size;
+    }
+
+    /**
+     * Creates a new set indicating the expected maximum number of elements it will contain.
+     * @param initialCapacity the desired initial capacity of the set.
+     * @throws IllegalArgumentException if <code>initialCapacity</code> is negative.
+     */
+    public CountSet(int initialCapacity) {
+        if (initialCapacity < 0)
+            throw new IllegalArgumentException();
+        elements = new int[initialCapacity];
+        size = 0;
+    }
+
+    /**
+     * Set the set contents to a single integer value.
+     * @param value the integer value to set the set to.
+     */
+    public void setTo(int value) {
+        ensureCapacity(1);
+        size = 1;
+        elements[0] = value;
+    }
+
+    /**
+     * Set the content of this set to a collection of integers.
+     * @param values the new values to be included in the set.
+     * @throws NullPointerException if <code>value</code> is <code>null</code>.
+     */
+    public void setTo(int ... values) {
+        ensureCapacity(values.length);
+        size = values.length;
+        System.arraycopy(values, 0, elements, 0, size);
+        Arrays.sort(elements,0,size);
+    }
+
+    /**
+     * Increase (or decrease) all elements in the set by a number.
+     * @param delta the number of add (or substract if negative) to all elements.
+     *
+     * @return <code>true</code> if the set changed as a result of this invocation, <code>false</code> otherwise.
+     */
+    public boolean incAll(final int delta) {
+        if (size == 0 || delta == 0)
+            return false;
+        for (int i = 0; i < size; i++)
+            elements[i] += delta;
+        return true;
+    }
+
+    /**
+     * Returns the smallest integer value in the set.
+     *
+     * @throws NoSuchElementException if the set is empty (thus there is no minimum).
+     * @return the smallest integer value in the set.
+     */
+    public int min() {
+        if (size == 0)
+            throw new NoSuchElementException("cannot have a min from an empty set");
+        return elements[0];
+    }
+
+    /**
+     * Returns the largest integer value in the set.
+     *
+     * @throws NoSuchElementException if the set is empty (thus there is no maximum).
+     * @return the largest integer value in the set.
+     */
+    public int max() {
+        if (size == 0)
+            throw new NoSuchElementException("cannot have a max from an empty set");
+        return elements[size - 1];
+    }
+
+    /**
+     * Adds a range of integer values to the collection.
+     *
+     * This method avoid the need to explicity indicate all values in that range. Notice that the range is fully inclusive.
+     * You can indicate a decrease range (fromValue > toValue).
+     *
+     * @param fromValue the first value to add in the set (inclusive).
+     * @param toValue the last value to add to the set (inclusive).
+     * @return <code>true</code> if the set changed as a result of this invocation, <code>false</code> otherwise.
+     */
+    public boolean addRange(final int fromValue, final int toValue) {
+        final int lowEnd;
+        final int highEnd;
+
+        if (fromValue <= toValue) {
+            lowEnd = fromValue; highEnd = toValue;
+        } else {
+            highEnd = fromValue; lowEnd = toValue;
+        }
+
+        //TODO to be optimized to add missing sub-ranges in one go:
+        boolean result = false;
+        for (int i = lowEnd; i <= highEnd; i++)
+            result = add(i) | result;
+        return result;
+    }
+
+    /**
+     * Add an integer value to the set.
+     * @param value to add to the set.
+     * @return <code>true</code> if the set changed as a result of this invocation, <code>false</code> otherwise.
+     */
+    public boolean add(final int value) {
+        int pos = Arrays.binarySearch(elements,0,size,value);
+        if (pos >= 0) return false;
+        int insertPos = - pos - 1;
+        ensureCapacity(size + 1);
+        System.arraycopy(elements, insertPos, elements, insertPos + 1, size - insertPos);
+        elements[insertPos] = value;
+        size++;
+        return true;
+    }
+
+    /**
+     * Add a arbitrary number of integers to the set.
+     *
+     * @param values integer to add to the set.
+     * @return <code>true</code> if the set changed as a result of this invocation, <code>false</code> otherwise.
+     */
+    public boolean addAll(final int ... values) {
+        ensureCapacity(size + values.length);
+        boolean result = false;
+        for (final int v : values)
+            result = add(v) | result;
+        return result;
+    }
+
+    @Override
+    public boolean addAll(final Collection<? extends Integer> numbers) {
+        ensureCapacity(size + numbers.size());
+        boolean result = false;
+        for (final Number n : numbers)
+            result = add(n.intValue()) | result;
+        return result;
+    }
+
+    /**
+     * Add all values within a range in an integer array.
+     *
+     * @param source array where the values to add are found.
+     * @param fromIndex first position from <code>source</code> to add (inclusive).
+     * @param toIndex index after the last position in <code>source</code> to add (thus exclusive).
+     * @throws NullPointerException if <code>source</code> is <code>null</code>.
+     * @throws NegativeArraySizeException if <code>fromIndex</code> or <code>toIndex</code> are negative.
+     * @throws ArrayIndexOutOfBoundsException if <code>fromIndex</code> or <code>toIndex</code> are beyond bounds
+     *    allowed <code>[0 .. source.length]</code>.
+     * @return <code>true</code> if the set changed as a result of this invocation, <code>false</code> otherwise.
+     */
+    public boolean addAll(final int[] source, final int fromIndex, final int toIndex) {
+        ensureCapacity(size + source.length);
+        boolean result = false;
+        for (int i = fromIndex; i < toIndex; i++)
+            result = add(source[i]) | result;
+        return result;
+    }
+
+
+    /**
+     * Add all elements present in a int-set.
+     *
+     * @param other the other inset.
+     *
+     * @throws NullPointerException if <code>other</code> is <code>null</code>.
+     * @return <code>true</code> if this set changed due to this operation, <code>false</code> otherwise.
+     */
+    public boolean addAll(final CountSet other) {
+        return addAll(other.elements,0,other.size);
+    }
+
+    /**
+     * Checks whether a integer value is included in the set.
+     * @param value the value to check.
+     * @return <code>true</code> if <code>value</code> is inside the set, <code>false</code> otherwise.
+     */
+    public boolean contains(final int value) {
+        return Arrays.binarySearch(elements,0,size,value) >= 0;
+    }
+
+    /**
+     * Make sure that this int-set has capacity to handle a number of elements.
+     * <p/>
+     * If the set has already that or greater capacity nothing would be changed.
+     *
+     * @param capacity the requested capacity.
+     */
+    private void ensureCapacity(final int capacity) {
+        if (elements.length >= capacity) return;
+        int newLength = Math.max(elements.length << 1, capacity);
+        elements = Arrays.copyOf(elements,newLength);
+    }
+
+
+    @Override
+    public int size() {
+        return size;
+    }
+
+    @Override
+    public boolean isEmpty() {
+        return size() == 0;
+    }
+
+    @Override
+    public boolean contains(final Object o) {
+        if (o instanceof Integer) {
+            final int i = (Integer)o;
+            return contains(i);
+        } else
+            return false;  //To change body of implemented methods use File | Settings | File Templates.
+    }
+
+    @Override
+    @NotNull
+    public Iterator<Integer> iterator() {
+        return new MyIterator();
+    }
+
+    @Override
+    @NotNull
+    public Object[] toArray() {
+        final Integer[] result = new Integer[size];
+        for (int i = 0; i < size; i++)
+            result[i] = elements[i];
+        return result;
+    }
+
+    @Override
+    @NotNull
+    @SuppressWarnings("unchecked")
+    public <T> T[] toArray(final T[] a) {
+        if (a == null)
+            throw new NullPointerException();
+
+        @SuppressWarnings("unchecked")
+        final Class<T> componentClass = (Class) a.getClass().getComponentType();
+        if (!componentClass.isAssignableFrom(Integer.class))
+            throw new ArrayStoreException();
+
+        @SuppressWarnings("unchecked")
+        final T[] dest = (a.length < size) ? (T[]) (Object[]) Array.newInstance(componentClass, size) : a;
+
+        for (int i = 0; i < size; i++)
+            dest[i] = (T) (Integer) elements[i];
+        return dest;
+    }
+
+    /**
+     * Copies the content of the set into an integer array. The result can be freely modified by the invoker.
+     * @return never <code>null</code> but a zero-length array if the set is empty.
+     */
+    @NotNull
+    public int[] toIntArray() {
+        return Arrays.copyOfRange(elements,0,size);
+    }
+
+    /**
+     * Copy the content of the set into an array.
+     * @param dest the destination array.
+     * @param offset where to store the first element of the set.
+     * @throws NullPointerException if <code>dest</code> is <code>null</code>.
+     * @throws ArrayIndexOutOfBoundsException if <code>offset</code> is out of range of there is not enough
+     * space after <code>offset</code> in the destination array to hold all values in the set.
+     */
+    public void copyTo(final int[] dest, int offset) {
+        if (dest == null)
+            throw new NullPointerException();
+        if (dest.length < (size + offset))
+            throw new ArrayIndexOutOfBoundsException("destination is to short");
+        System.arraycopy(elements,0,dest,offset,size);
+    }
+
+    /**
+     * Copy the content of the set into an array.
+     * @param dest the destination array.
+     * @throws NullPointerException if <code>dest</code> is <code>null</code>.
+     * @throws ArrayIndexOutOfBoundsException if there is not enough
+     * space after <code>offset</code> in the destination array to hold all values in the set.
+     */
+    public void copyTo(final int[] dest) {
+        copyTo(dest,0);
+    }
+
+
+    @Override
+    public boolean add(final Integer integer) {
+        return add((int) integer);
+    }
+
+    @Override
+    public boolean remove(final Object o) {
+        return o instanceof Integer && remove((int)o);
+    }
+
+    /**
+     * Removes a single integer value for the set.
+     * @param i the value to remove.
+     * @return <code>true</code> if the set has changed as a result of this invocation, <code>false</code> otherwise.
+     */
+    public boolean remove(final int i) {
+        final int pos = Arrays.binarySearch(elements,0,size,i);
+        if (pos < 0)
+            return false;
+        else {
+            removeIndex(pos);
+            return true;
+        }
+    }
+
+    @Override
+    public boolean containsAll(final Collection<?> c) {
+        for (final Object o : c)
+            if (!contains(o))
+                return false;
+        return true;
+    }
+
+
+    @Override
+    public boolean retainAll(final Collection<?> c) {
+        if (size == 0)
+            return false;
+        @SuppressWarnings("all")
+        final CountSet retainIndices = new CountSet(c.size() + 2);
+        retainIndices.add(-1);
+        retainIndices.add(size);
+        for (final Object o : c) {
+            if (!(o instanceof Integer))
+                continue;
+            final int pos = Arrays.binarySearch(elements,0,size,(int) o);
+            if (pos < 0)
+                continue;
+            retainIndices.add(pos);
+        }
+        if (retainIndices.size == 2) {
+            size = 0;
+            return true;
+        } else if (retainIndices.size == size + 2) {
+            return false;
+        } else {
+            for (int idx = retainIndices.size - 1; idx > 0; idx--) {
+                final int toIdx = retainIndices.elements[idx];
+                final int fromIdx = retainIndices.elements[idx - 1] + 1;
+                removeIndices(toIdx,fromIdx);
+            }
+            return true;
+        }
+    }
+
+    /**
+     * Removes the values found in a range of indexes in {@link #elements}.
+     * @param fromIdx first index to remove (inclusive).
+     * @param toIdx right after last index to remove (exclusive).
+     */
+    @Requires("fromIdx >= toIdx & fromIdx >= 0 & toIdx <= size")
+    private void removeIndices(final int fromIdx, final int toIdx) {
+       System.arraycopy(elements,toIdx,elements,fromIdx,size - toIdx);
+       size -= toIdx - fromIdx;
+    }
+
+    @Override
+    public boolean removeAll(final Collection<?> c) {
+        boolean result = false;
+        for (final Object o : c)
+            result = remove(o) | result;
+        return result;
+    }
+
+    @Requires("idx >= 0 && idx < size")
+    private void removeIndex(int idx) {
+        System.arraycopy(elements,idx+1,elements,idx,size - idx - 1);
+    }
+
+    @Override
+    public void clear() {
+        size = 0;
+    }
+
+    /**
+     * Returns a copy of this set which can be changed without modifying the original one.
+     * @return never {@code null}.
+     */
+    @NotNull
+    @SuppressWarnings("all")
+    public CountSet clone() {
+        return new CountSet(this);
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder(2 + size() * 10);
+        sb.append('{');
+        for (int i = 0; i < size; i++)
+            sb.append(elements[i]).append(',');
+        sb.replace(sb.length()-1,sb.length(),"}");
+        return sb.toString();
+
+    }
+
+
+    /**
+     * Custom iterator class for {@link CountSet IntSets}
+     */
+    private class MyIterator implements Iterator<Integer> {
+        /** What position I am in. */
+        private int next = 0;
+
+        @Override
+        public boolean hasNext() {
+            return next < size;
+        }
+
+        @Override
+        public Integer next() {
+            if (next >= size)
+                throw new NoSuchElementException();
+            return elements[next];
+        }
+
+        @Override
+        public void remove() {
+            if (next == 0)
+                throw new IllegalStateException();
+            if (next >= size)
+                throw new NoSuchElementException();
+            removeIndex(next - 1);
+        }
+    }
+
+
+}
diff --git a/protected/java/src/org/broadinstitute/sting/utils/haplotype/HaplotypeLDCalculator.java b/protected/java/src/org/broadinstitute/sting/utils/haplotype/HaplotypeLDCalculator.java
index 4609c3209..ba58c3ae8 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/haplotype/HaplotypeLDCalculator.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/haplotype/HaplotypeLDCalculator.java
@@ -47,7 +47,7 @@
 package org.broadinstitute.sting.utils.haplotype;
 
 import com.google.java.contract.Requires;
-import org.broadinstitute.sting.gatk.walkers.haplotypecaller.LikelihoodCalculationEngine;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.variant.variantcontext.Allele;
@@ -100,7 +100,7 @@ public class HaplotypeLDCalculator {
                 final Map<Haplotype, Double> map = new HashMap<Haplotype, Double>(haplotypes.size());
                 for( final Haplotype h : haplotypes ) {
                     // count up the co-occurrences of the events for the R^2 calculation
-                    final double haplotypeLikelihood = LikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods(sample, haplotypeReadMap, Collections.singletonList(Allele.create(h, true)), false)[0][0];
+                    final double haplotypeLikelihood = PairHMMLikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods(sample, haplotypeReadMap, Collections.singletonList(Allele.create(h, true)), false)[0][0];
                     map.put(h, haplotypeLikelihood);
                 }
                 haplotypeLikelihoodsPerSample.add(map);
diff --git a/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java b/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java
index 1e6d7c13c..4d48ca82a 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java
@@ -47,13 +47,16 @@
 package org.broadinstitute.sting.utils.haplotypeBAMWriter;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.haplotype.Haplotype;
 import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.haplotype.Haplotype;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.variant.variantcontext.Allele;
 
-import java.util.*;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
 
 /**
  * Writes a BAM containing just the reads in stratifiedReadMap aligned to their
@@ -98,7 +101,9 @@ class CalledHaplotypeBAMWriter extends HaplotypeBAMWriter {
         for ( final PerReadAlleleLikelihoodMap readAlleleLikelihoodMap : stratifiedReadMap.values() ) {
             for ( final Map.Entry<GATKSAMRecord, Map<Allele, Double>> entry : readAlleleLikelihoodMap.getLikelihoodReadMap().entrySet() ) {
                 final MostLikelyAllele bestAllele = PerReadAlleleLikelihoodMap.getMostLikelyAllele(entry.getValue(), allelesOfCalledHaplotypes);
-                writeReadAgainstHaplotype(entry.getKey(), alleleToHaplotypeMap.get(bestAllele.getMostLikelyAllele()), paddedReferenceLoc.getStart(), bestAllele.isInformative());
+                final Haplotype haplotype = alleleToHaplotypeMap.get(bestAllele.getMostLikelyAllele());
+                if (haplotype == null) continue;
+                writeReadAgainstHaplotype(entry.getKey(), haplotype, paddedReferenceLoc.getStart(), bestAllele.isInformative());
             }
         }
     }
diff --git a/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java b/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java
index df523b74d..6d839a832 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java
@@ -186,10 +186,15 @@ public abstract class HaplotypeBAMWriter {
             if( originalRead != null ) {
                 output.add(originalRead);
             }
+        } else if (haplotype == null) {
+            output.add(originalRead);
+            return;
         } else {
             final GATKSAMRecord alignedToRef = createReadAlignedToRef(originalRead, haplotype, referenceStart, isInformative);
             if ( alignedToRef != null ) {
                 output.add(alignedToRef);
+            } else {
+                output.add(originalRead);
             }
         }
     }
diff --git a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/FastLoglessPairHMM.java b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/FastLoglessPairHMM.java
new file mode 100644
index 000000000..2872bea37
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/FastLoglessPairHMM.java
@@ -0,0 +1,813 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*  
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*  
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*  
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*  
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*  
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. 
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.  
+*  
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY 
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*  
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*  
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*  
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
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+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
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+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt. 
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. 
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.sting.utils.pairhmm;
+
+import org.broadinstitute.sting.utils.QualityUtils;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * Fast partial PairHMM backed on the standard Logless PairHMM
+ *
+ */
+public class FastLoglessPairHMM extends LoglessPairHMM  implements FlexibleHMM {
+
+
+    /**
+     * Initial read length capacity.
+     */
+    private static final int INITIAL_READ_LENGTH_CAPACITY = 200;
+
+    /**
+     * Initial haplotype length capacity.
+     */
+    private static final int INITIAL_HAPLOTYPE_LENGTH_CAPACITY = 400;
+
+
+    /**
+     * Holds the current read capacity.
+     * <p>It can only go up overtime.</p>
+     */
+    private int readCapacity = INITIAL_READ_LENGTH_CAPACITY;
+
+    /**
+     * Holds the current haplotype length capacity.
+     * <p>It can only go up overtime.</p>
+     */
+    private int haplotypeCapacity = INITIAL_HAPLOTYPE_LENGTH_CAPACITY;
+
+    private int maxToCol;
+    private int haplotypeLength;
+
+    /**
+     * Returns the currently loaded read base qualities.
+     *
+     * @throws IllegalStateException if no read was previously loaded using {@link #loadRead}.
+     * @return never {@code null}.
+     */
+    public byte[] getReadQuals() {
+        if (readQuals == null)
+            throw new IllegalStateException("no read was loaded onto the pairhmm calculator");
+        return readQuals;
+    }
+
+    /**
+     * Returns the currently loaded read insertion qualities.
+     *
+     * @throws IllegalStateException if no read was previously loaded using {@link #loadRead}.
+     * @return never {@code null}.
+     */
+    @SuppressWarnings("unused")
+    public byte[] getReadInsQuals() {
+        if (readQuals == null)
+            throw new IllegalStateException("no read was loaded onto the pairhmm calculator");
+        return readInsQuals;
+    }
+
+    /**
+     * Returns the currently loaded read deletion qualities.
+     *
+     * @throws IllegalStateException if no read was previously loaded using {@link #loadRead}.
+     * @return never {@code null}.
+     */
+    @SuppressWarnings("unused")
+    public byte[] getReadDelQuals() {
+        if (readQuals == null)
+            throw new IllegalStateException("no read was loaded onto the pairhmm calculator");
+        return readDelQuals;
+    }
+
+    /**
+     * Returns the currently loaded read gap extension penalty..
+     *
+     * @throws IllegalStateException if no read was previously loaded using {@link #loadRead}.
+     * @return never {@code null}.
+     */
+    @SuppressWarnings("unused")
+    public byte[] getReadGepQuals() {
+        if (readQuals == null)
+            throw new IllegalStateException("no read was loaded onto the pairhmm calculator");
+        return readGepQuals;
+    }
+
+
+    /**
+     * Creates a new pair-hmm calculator instance give the gap continuation penalty.
+     *
+     * @param gcp the gap-continuation penalty.
+     */
+    public FastLoglessPairHMM(final byte gcp) {
+        constantGCP = gcp;
+        initialize(readCapacity,haplotypeCapacity);
+    }
+
+
+    @Override
+    public double subComputeReadLikelihoodGivenHaplotypeLog10(final byte[] haplotypeBases,
+                   final byte[] readBases,
+                   final byte[] readQuals,
+                   final byte[] insertionGOP,
+                   final byte[] deletionGOP,
+                   final byte[] overallGCP,
+                   final int hapStartIndex,
+                   final boolean recacheReadValues, final int nextHapStartIndex) {
+        this.readBases = readBases;
+        this.haplotypeBases = haplotypeBases;
+        this.haplotypeLength = haplotypeBases.length;
+        return super.subComputeReadLikelihoodGivenHaplotypeLog10(haplotypeBases,readBases,readQuals,
+                insertionGOP,deletionGOP,overallGCP,hapStartIndex,recacheReadValues,nextHapStartIndex);
+    }
+
+    /**
+     * Implement the last step summation to calculate the total likelihood.
+     *
+     * @param row number of the last row of the pair-hmm where the likelihood values are present.
+     * @param fromCol inclusive first column to include in the summation.
+     * @param toCol exclusive last column to include in the summation.
+     * @return 0 or less.
+     */
+    protected double finalLikelihoodCalculation(final int row,
+                                                final int fromCol, final int toCol) {
+
+        final double divider = Math.max(1,2 *(toCol - fromCol));
+        final double dividerInverse = 1.0 / divider;
+        double finalLikelihood = 0;
+
+        for (int j = fromCol; j < toCol; j++) {
+            finalLikelihood += matchMatrix[row][j] * dividerInverse;
+            finalLikelihood += insertionMatrix[row][j] * dividerInverse;
+        }
+        return StrictMath.log10(finalLikelihood) - INITIAL_CONDITION_LOG10 + StrictMath.log10(divider);
+    }
+
+    /**
+     * Initialize the matrix values for a problem including the trailing end of the read.
+     *
+     * <p>
+     *     Notice that you can improve performance by omitting filling reusable values from
+     *     previous haplotype calculations. You can set {@code haplotypeStartOffset} to skill
+     *     those columns.
+     * </p>
+     *
+     * @param readStart inclusive first position of the read used in the calculations.
+     * @param readEnd exclusive last position of the read considered in the calculations.
+     * @param haplotypeStartOffset offset of the haplotype right after the reusable prefix
+     *                             from previous calls.
+     *
+     *
+     */
+    protected void initializeMatrixValuesForTrailingProblem(final int readStart, final int readEnd,
+                                                            final int haplotypeStartOffset) {
+
+        @SuppressWarnings("all")
+        final int zeroRow = readStart;
+        final int toRow = readEnd + 1;
+        final int toCol = haplotypeLength + 1;
+
+        // fill first row with -Inf fot M and I but not for Deletion if leading
+        // to allow for free deletions at the beginning.
+        if (readStart == 0) {
+            // First row initialization:
+            Arrays.fill(matchMatrix[zeroRow],haplotypeStartOffset,toCol,0);
+            Arrays.fill(deletionMatrix[zeroRow],haplotypeStartOffset,toCol,INITIAL_CONDITION);
+
+            if (haplotypeStartOffset == 0)
+                for (int i = zeroRow + 1; i < toRow; i++)
+                    insertionMatrix[i][0] = matchMatrix[i][0] = deletionMatrix[i][0] = 0;
+
+        } else {
+            Arrays.fill(matchMatrix[zeroRow], Math.max(1,haplotypeStartOffset), toCol,0);
+            Arrays.fill(insertionMatrix[zeroRow], haplotypeStartOffset, toCol,0);
+            if (haplotypeStartOffset == 0) {
+                matchMatrix[zeroRow][0] = INITIAL_CONDITION;
+                deletionMatrix[zeroRow][0] = 0;
+            }
+            if (haplotypeStartOffset <= 1) deletionMatrix[zeroRow][1] = matchMatrix[zeroRow][1] * transition[zeroRow][matchToDeletion];
+            for (int i = Math.max(haplotypeStartOffset,2); i < toCol; i++) {
+                deletionMatrix[zeroRow][i] = deletionMatrix[zeroRow][i - 1]
+                        * transition[zeroRow][deletionToDeletion];
+            }
+
+            if (haplotypeStartOffset == 0) {
+                matchMatrix[zeroRow + 1][0] = deletionMatrix[zeroRow + 1][0] = 0;
+                insertionMatrix[zeroRow + 1][0] = matchMatrix[zeroRow][0] * transition[zeroRow + 1][matchToInsertion];
+
+
+                for (int i = zeroRow + 2; i < toRow; i++) {
+                  matchMatrix[i][0] = deletionMatrix[i][0] = 0;
+                  insertionMatrix[i][0] = insertionMatrix[i - 1][0]
+                          * transition[i][insertionToInsertion];
+                }
+            }
+        }
+    }
+
+    /**
+     * Initializes calculation matrices give the characteristics of the next and previous problems.
+     * @param currentProblem reference to the Lk calculation problem we are dealing currently.
+     * @param previousProblem reference to the Lk calculation problem that has been solved just before.
+     *
+     */
+    protected void initializeMatrixValues(final Problem currentProblem, final Problem previousProblem) {
+        if (previousProblem != null &&
+                previousProblem.readStart == currentProblem.readStart &&
+                previousProblem.hapStart == currentProblem.hapStart &&
+                maxToCol >= currentProblem.hapEnd + 1)
+            return;
+
+        final int zeroRow = currentProblem.readStart;
+        final int zeroCol = currentProblem.hapStart;
+        final int toRow = currentProblem.readEnd + 1;
+        final int toCol = currentProblem.hapEnd + 1;
+        maxToCol = toCol;
+
+        // fill first row with -Inf fot M and I but not for Deletion if leading
+        // to allow for free deletions at the beginning.
+        if (currentProblem.leading) {
+            // First row initialization:
+            Arrays.fill(matchMatrix[zeroRow],zeroCol,toCol,0);
+            Arrays.fill(deletionMatrix[zeroRow],zeroCol,toCol,INITIAL_CONDITION);
+
+            for (int i = zeroRow + 1; i < toRow; i++)
+                insertionMatrix[i][zeroCol] = matchMatrix[i][zeroCol] = deletionMatrix[i][zeroCol] = 0;
+
+        } else { // If not leading set the appropriate matching 1.0 prob and
+            // deletion + extension.
+
+            Arrays.fill(matchMatrix[zeroRow], zeroCol + 1, toCol,0);
+            Arrays.fill(insertionMatrix[zeroRow], zeroCol, toCol,0);
+            matchMatrix[zeroRow][zeroCol] = INITIAL_CONDITION;
+            deletionMatrix[zeroRow][zeroCol] = 0;
+            deletionMatrix[zeroRow][zeroCol + 1] = matchMatrix[zeroRow][zeroCol] * transition[zeroRow][matchToDeletion];
+            for (int i = zeroCol + 2; i < toCol; i++) {
+                deletionMatrix[zeroRow][i] = deletionMatrix[zeroRow][i - 1]
+                        * transition[zeroRow][deletionToDeletion];
+            }
+
+            matchMatrix[zeroRow + 1][zeroCol] = deletionMatrix[zeroRow + 1][zeroCol] = 0;
+            insertionMatrix[zeroRow + 1][zeroCol] = matchMatrix[zeroRow][zeroCol] * transition[zeroRow + 1][matchToInsertion];
+
+            for (int i = zeroRow + 2; i < toRow; i++) {
+                matchMatrix[i][zeroCol] = deletionMatrix[i][zeroCol] = 0;
+                insertionMatrix[i][zeroCol] = insertionMatrix[i - 1][zeroCol]
+                        * transition[i][insertionToInsertion];
+            }
+        }
+    }
+
+    /**
+     * Constant gap-continuation-penalty.
+     */
+    private final byte constantGCP;
+
+    /**
+     * Currently loaded haplotype base sequence.
+     */
+    private byte[] haplotypeBases;
+
+    /**
+     * Currently loaded read base sequence.
+     */
+    private byte[] readBases;
+
+    /**
+     * Read qualities.
+     */
+    private byte[] readQuals;
+
+    /**
+     * Read insertion qualities.
+     */
+    private byte[] readInsQuals;
+
+    /**
+     * Read deletion qualities.
+     */
+    private byte[] readDelQuals;
+
+    /**
+     * Read gap-extension-penalties.
+     */
+    private byte[] readGepQuals;
+
+    /**
+     * Cached results.
+     */
+    private Map<Problem, Double> cachedResults = new HashMap<>();
+
+    /**
+     * Loads the read that is going to be evaluated in following calls to {@link #calculateLocalLikelihoods}.
+     *
+     * @param read the target read.
+     * @throws NullPointerException if {@code read} is null.
+     */
+    @Override
+    public void loadRead(final GATKSAMRecord read) {
+        loadRead(read.getReadBases(),read.getBaseQualities(),read.getBaseInsertionQualities(),read.getBaseDeletionQualities(),read.getMappingQuality());
+    }
+
+    /**
+     * Loads the read that is going to be evaluated in following calls to {@link #calculateLocalLikelihoods}.
+     *
+     * @param readBases the read bases.
+     * @param readQuals the read base call quality scores.
+     * @param readInsQuals the read insertion quality scores.
+     * @param readDelQuals  the read deletion quality scores.
+     * @param mq the read mapping quality score.
+     * @throws NullPointerException if any of the arrays passed is {@code null}.
+     * @throws IllegalArgumentException if the arrays passed have incompatible sizes.
+     */
+    public void loadRead(final byte[] readBases, final byte[] readQuals, final byte[] readInsQuals, final byte[] readDelQuals, int mq) {
+        // TODO This is a copy&paste from PairHMM*Engine read data preparation code.
+        // TODO It is simply to difficult to share the code without changing that class and I don't want
+        // TODO to do so for now.
+        if (readBases.length != readQuals.length) throw new IllegalArgumentException("the read quality array length does not match the read base array length");
+        if (readBases.length != readInsQuals.length) throw new IllegalArgumentException("the read insert quality array length does not match the read base array length");
+        if (readBases.length != readDelQuals.length) throw new IllegalArgumentException("the read deletion quality length does not match the read base array length");
+        maxToCol = 0;
+
+        if (readBases.length > readCapacity) {
+            readCapacity = readBases.length;
+            initialize(readCapacity,haplotypeCapacity);
+        }
+        paddedReadLength = readBases.length + 1;
+        final byte[] overallGCP = new byte[readBases.length];
+        Arrays.fill(overallGCP, constantGCP); // Is there a way to derive
+
+        for (int kkk = 0; kkk < readQuals.length; kkk++) {
+            readQuals[kkk] = (byte) Math.min(0xff & readQuals[kkk],
+                    mq); // cap base quality by mapping
+            // TODO -- why is Q18 hard-coded here???
+            readQuals[kkk] = (readQuals[kkk] < (byte) 18 ? QualityUtils.MIN_USABLE_Q_SCORE
+                    : readQuals[kkk]);
+        }
+        this.readBases = readBases;
+        this.readQuals = readQuals;
+        this.readInsQuals = readInsQuals;
+        this.readDelQuals = readDelQuals;
+        this.readGepQuals = overallGCP;
+        initializeProbabilities(transition,readInsQuals, readDelQuals, overallGCP);
+        if (haplotypeBases != null)
+            fillPriorsTable(0);
+        cachedResults.clear();
+    }
+
+    @Override
+    public void loadHaplotypeBases(final byte[] haplotypeBases) {
+        if (readBases == null)
+            throw new IllegalStateException(
+                    "no read was loaded before the haplotype");
+        this.haplotypeBases = haplotypeBases.clone();
+        haplotypeLength = haplotypeBases.length;
+        paddedHaplotypeLength = haplotypeLength;
+        if (haplotypeCapacity < haplotypeLength) {
+            haplotypeCapacity = haplotypeLength;
+            initialize(readCapacity,haplotypeCapacity);
+            initializeProbabilities(transition, readInsQuals, readDelQuals, readGepQuals);
+        }
+        initializePriors(this.haplotypeBases, readBases, readQuals, 0);
+    }
+
+
+    /**
+     * Changes only the suffix of the currently loaded haplotype.
+     *
+     * <p>
+     *     If from is 0, this is equivalent to call {@link #loadHaplotypeBases(byte[])} directly.
+     * </p>
+     * @param from first position on the current haplotype to substitute with the new suffix.
+     *             It can be up to the length of the haplotype in such case this operation is in
+     *             effect just extending that haplotype.
+     * @param suffix the new bases for the end part of the current haplotype.
+     * @param suffixFrom inclusive first position of the actual suffix within the {@code suffix} array.
+     * @param suffixTo exclusive last position of the actual suffix within the {@code suffix} array.
+     *
+     * @throws IllegalStateException if no read was loaded with {@link #loadRead}.
+     * @throws IllegalArgumentException if from is more than 0 but no haplotype was loaded previously or if indices passed are inconsistent.
+     * @throws ArrayIndexOutOfBoundsException if indices passed are outside valid ranges.
+     */
+    public void changeHaplotypeSuffix(final int from, final byte[] suffix, final int suffixFrom, final int suffixTo) {
+        if (readBases == null)
+            throw new IllegalStateException(
+                    "no read was loaded before the haplotype");
+        if (haplotypeBases == null && from > 0)
+            throw new IllegalArgumentException("from cannot be larger than 0 if no haplotype bases was previously loaded");
+        if (suffixFrom < 0)
+            throw new ArrayIndexOutOfBoundsException("the suffix from index cannot be negative");
+        if (suffixTo > suffix.length)
+            throw new ArrayIndexOutOfBoundsException("the suffix to index cannot be larger than the suffix array length");
+        if (suffixFrom > suffixTo)
+            throw new IllegalArgumentException("the suffix to index cannot be smaller than the suffix from index");
+        if (from > haplotypeLength)
+            throw new IllegalArgumentException("the from index cannot be greater than the current haplotype length");
+        if (from < 0)
+            throw new IllegalArgumentException("the from index cannot be negative");
+
+        int startIndex = from;
+        if (haplotypeBases == null) {
+            haplotypeBases = Arrays.copyOfRange(suffix,suffixFrom,suffixTo);
+            haplotypeLength = suffixTo - suffixFrom;
+        } else {
+            final int newLength = from + suffixTo - suffixFrom;
+            if (haplotypeBases.length < newLength)
+                haplotypeBases = Arrays.copyOf(haplotypeBases,newLength);
+            System.arraycopy(suffix,suffixFrom,haplotypeBases,from,newLength - from);
+            haplotypeLength = newLength;
+        }
+        paddedHaplotypeLength = haplotypeLength + 1;
+        if (haplotypeCapacity < haplotypeLength) {
+            haplotypeCapacity = haplotypeLength;
+            initialize(readCapacity,haplotypeCapacity);
+            initializeProbabilities(transition, readInsQuals, readDelQuals, readGepQuals);
+            startIndex = 0;
+        }
+        //startIndex = 0;
+        fillPriorsTable(startIndex);
+    }
+
+    /**
+     * Returns the bases of the current haplotype.
+     *
+     * @throws IllegalStateException if no haplotype was loaded previously
+     * @return never {@code null}
+     */
+    public byte[] getHaplotypeBases() {
+        if (haplotypeBases == null)
+            throw new IllegalStateException();
+        return Arrays.copyOfRange(haplotypeBases,0,haplotypeLength);
+    }
+
+    /**
+     * Returns a debug representation of the pair-hmm.
+     * @return never {@code null}.
+     */
+    public String toString() {
+        return "" + haplotypeLength + ":" + new String(Arrays.copyOfRange(haplotypeBases,0,haplotypeLength));
+    }
+
+    @Override
+    protected void initializePriors(final byte[] hapBases, final byte[] readBases, final byte[] baseQuals, final int idx) {
+        haplotypeBases = hapBases;
+        haplotypeLength = haplotypeBases.length;
+        this.readBases = readBases;
+        this.readQuals = baseQuals;
+        fillPriorsTable(idx);
+    }
+
+    /**
+     * Fills the prior table up.
+     *
+     * <p>
+     *     It accepts an argument to save unnecessary prefix filling up.
+     * </p>
+     *
+     * @param idx first position in the haplotype to start filling from.
+     */
+    protected void fillPriorsTable(final int idx) {
+        for (int i = 0; i < readBases.length; i++) {
+            final byte x = readBases[i];
+            final byte qual = readQuals[i];
+            for (int j = idx; j < haplotypeLength; j++) {
+                final byte y = haplotypeBases[j];
+                prior[i+1][j+1] = ( x == y || x == (byte) 'N' || y == (byte) 'N' ?
+                        QualityUtils.qualToProb(qual) : (QualityUtils.qualToErrorProb(qual) / (doNotUseTristateCorrection ? 1.0 : TRISTATE_CORRECTION)) );
+            }
+        }
+    }
+
+
+    /**
+     * Decorates haplotype set with their likelihoods as compared with the currently loaded read.
+     *
+     *
+     * @param readStart inclusive start position of the targeted section of the read.
+     * @param readEnd exclusive end position just beyond the targeted section of the read.
+     * @param haplotypes in/out set of haplotypes.
+     */
+    public void calculateLocalLikelihoods(final int readStart, final int readEnd, final PairHMMReadyHaplotypes haplotypes) {
+        final PairHMMReadyHaplotypes.Iterator entryIterator = haplotypes.iterator();
+        boolean isFirst = true;
+        while (entryIterator.hasNext()) {
+            entryIterator.next();
+            final int startIndex = entryIterator.startIndex();
+            final byte[] bases = entryIterator.bases();
+            changeHaplotypeSuffix(startIndex,bases,startIndex,bases.length);
+            final double likelihood = calculateLikelihood(readStart, readEnd, startIndex, isFirst);
+            isFirst = false;
+            entryIterator.setLikelihood(likelihood);
+        }
+    }
+
+
+
+    @Override
+    public double calculateLocalLikelihood(final int readStart, final int readEnd,
+                                           final int hapStart, final int hapEnd, final boolean kmerMatch) {
+        if (readBases == null || haplotypeBases == null)
+            throw new IllegalStateException("read or haplotype was not loaded");
+        final int hapSegmentLength = hapEnd - hapStart;
+        final int readSegmentLength = readEnd - readStart;
+        // trivial case when there is a single base match.
+        if (kmerMatch) {
+            return calculateLocalLikelihoodsExactMatch(readStart, hapStart, hapSegmentLength, readSegmentLength);
+        } else if (hapSegmentLength == readSegmentLength) {
+            if (hapSegmentLength == 0) {
+                return calculateLocalLikelihoodEmptySquare(readStart, readEnd);
+            } else if (hapSegmentLength == 1) {
+                return calculateLocalLikelihoodSingleBase(readStart, readEnd, hapStart);
+            } else { // general (slower) solution.
+                return calculateLocalLikelihoodsGeneral(readStart, readEnd, hapStart, hapEnd);
+            }
+        } else if (hapSegmentLength == 0) { // must be full insertion we
+            return calculateLocalLikelihoodInsertion(readStart, readEnd);
+        } else if (readSegmentLength == 0) { // full deletion.
+            return calculateLocalLikelihoodDeletion(readStart, hapStart, hapEnd);
+        } else { // general (slower) solution.
+            return calculateLocalLikelihoodsGeneral(readStart, readEnd, hapStart, hapEnd);
+        }
+    }
+
+    /**
+     * Fast likelihood when the pair-hmm represents a deletion in the read.
+     */
+    private double calculateLocalLikelihoodDeletion(final int readStart, final int hapStart, final int hapEnd) {
+        double result = INITIAL_CONDITION;
+        if (readStart > 0) { // no penalty if at the beginning.
+            result *= transition[readStart][matchToDeletion];
+            result *=
+                    StrictMath.pow(transition[readStart][deletionToDeletion],hapEnd - hapStart - 1);
+            result *= transition[readStart][indelToMatch];
+        }
+        return StrictMath.log10(result) - INITIAL_CONDITION_LOG10;
+    }
+
+
+    /**
+     * Fast likelihood when the pair-hmm represents a insertion in the read.
+     */
+    private double calculateLocalLikelihoodInsertion(final int readStart, final int readEnd) {
+        double result = INITIAL_CONDITION;
+        result *= transition[readStart + 1][matchToInsertion];
+        for (int i = readStart + 1; i < readEnd; i++) {
+            result *= transition[i + 1][insertionToInsertion];
+        }
+        if (readEnd < readBases.length) {
+            result *= transition[readEnd + 1][indelToMatch];
+        }
+        return StrictMath.log10(result) - INITIAL_CONDITION_LOG10;
+    }
+
+    /**
+     * Single base mismatch fast likelihood calculation.
+     */
+    private double calculateLocalLikelihoodSingleBase(final int readStart, final int readEnd, final int hapStart) {
+        double result = INITIAL_CONDITION;
+        result *= prior[readStart + 1][hapStart + 1];
+        if (readStart > 0) {
+            result *= transition[readStart + 1][matchToMatch];
+        }
+        if (readEnd < readBases.length) {
+            result *= transition[readEnd + 1][matchToMatch];
+        }
+        return StrictMath.log10(result) - INITIAL_CONDITION_LOG10;
+    }
+
+    /**
+     * Empty square Pair-hmm.
+     */
+    private double calculateLocalLikelihoodEmptySquare(final int readStart, final int readEnd) {
+        double result = INITIAL_CONDITION;
+        if (readStart > 0 && readEnd < readBases.length) {
+            result *= transition[readStart + 1][matchToMatch];
+        }
+        return StrictMath.log10(result) - INITIAL_CONDITION_LOG10;
+    }
+
+    /**
+     * Likelihood assuming that there is a exact match between both sequences: read and haplotype
+     */
+    private double calculateLocalLikelihoodsExactMatch(final int readStart, final int hapStart, final int hapSegmentLength, final int readSegmentLength) {
+        double result = INITIAL_CONDITION;
+        if (hapSegmentLength == 1) {
+            result *= prior[readStart + 1][hapStart + 1];
+        } else {
+            for (int i = 0; i < readSegmentLength; i++) {
+                result *= prior[readStart + i + 1][hapStart + i + 1];
+                if (i > 0) {
+                    result *= transition[readStart + i + 1][matchToMatch];
+                }
+            }
+        }
+        return StrictMath.log10(result) - INITIAL_CONDITION_LOG10;
+    }
+
+    /**
+     * Revert to a general pair-hmm solution.
+     */
+    private double calculateLocalLikelihoodsGeneral(final int readStart, final int readEnd, final int hapStart, final int hapEnd) {
+        final Problem p = new Problem(readStart, readEnd, hapStart, hapEnd);
+        final Double cachedCost = cachedResults.get(p);
+        if (cachedCost != null) {
+            return cachedCost;
+        }
+        double cost = calculateLocalLikelihoodGeneral(p);
+        cachedResults.put(p, cost);
+        return cost;
+    }
+
+    /**
+     * Resolve the regular full pair-hmm.
+     *
+     * <p>
+     * With the possibility of reuse the previous haplotype common prefix by using
+     * a startIndex which is greater than 0.
+     */
+    private double calculateLikelihood(final int readStart, final int readEnd, final int startIndex, final boolean initializeEdges) {
+        final int edgeStart = initializeEdges ? 0 : startIndex + 1;
+        initializeMatrixValuesForTrailingProblem(readStart, readEnd, edgeStart);
+        updateTable(readStart + 1, readEnd + 1, startIndex + 1, haplotypeLength + 1);
+        if (readEnd == readBases.length)
+            return finalLikelihoodCalculation(readEnd,0,haplotypeLength + 1) - (readStart == 0 ? StrictMath.log10(haplotypeLength) : 0);
+        else {
+            final double divider = 3.0;
+            final double dividerInverted = 1.0 / divider;
+            return StrictMath.log10(matchMatrix[readEnd][haplotypeLength]
+                * transition[readEnd][matchToMatch] * dividerInverted +
+                insertionMatrix[readEnd][haplotypeLength]
+                        * transition[readEnd][indelToMatch] * dividerInverted +
+                deletionMatrix[readEnd][haplotypeLength]
+                        * transition[readEnd][indelToMatch] * dividerInverted) - INITIAL_CONDITION_LOG10 + StrictMath.log10(divider);
+        }
+    }
+
+
+    private double calculateLocalLikelihoodGeneral(final Problem p) {
+
+        initializeMatrixValues(p,null);
+        int fromCol = p.hapStart + 1;
+     //   if (previousProblem == null) {
+     //       fromCol = p.hapStart + 1;
+     //   } else {
+     //       final int sharedPrefix = previousProblem.followerStartIndex(p);
+     //       if (sharedPrefix >= 0)
+     //           fromCol = sharedPrefix + 1;
+     //       else
+     //           fromCol = p.hapStart + 1;
+     //   }
+     //   previousProblem = p;
+
+        updateTable(p.readStart + 1, p.readEnd + 1,
+                fromCol, p.hapEnd + 1);
+
+        if (p.trailing) {
+            return finalLikelihoodCalculation(p.readEnd,p.hapStart,p.hapEnd + 1)
+                    - (p.leading ? StrictMath.log10(p.hapEnd - p.hapStart) : 0);
+        } else {
+            final double divider = 3.0;
+            final double dividerInverted = 1.0 / divider;
+            return StrictMath.log10(matchMatrix[p.readEnd][p.hapEnd]
+                    * transition[p.readEnd][matchToMatch] * dividerInverted +
+                    insertionMatrix[p.readEnd][p.hapEnd]
+                            * transition[p.readEnd][indelToMatch] * dividerInverted +
+                    deletionMatrix[p.readEnd][p.hapEnd]
+                            * transition[p.readEnd][indelToMatch] * dividerInverted) - INITIAL_CONDITION_LOG10 + StrictMath.log10(divider);
+        }
+    }
+
+    private void updateTable(final int rowFrom, final int rowTo,
+                             final int colFrom, final int colTo) {
+
+        for (int i = rowFrom; i < rowTo; i++) {
+            for (int j = colFrom; j < colTo; j++) {
+                updateCell(i, j, prior[i][j], transition[i]);
+            }
+        }
+
+    }
+
+    /**
+     * Holds the properties of a pair-hmm computational problem.
+     */
+    public class Problem {
+        private final byte[] haplotypeSegment;
+        private final int readStart;
+        private final int readEnd;
+        private final int hapStart;
+        private final int hapEnd;
+        private final int hashCode;
+        private final boolean trailing;
+        private final boolean leading;
+
+        /**
+         * Construct a new project object.
+         * @param start inclusive start position on the read to consider.
+         * @param end exclusive after last position on the read to consider.
+         * @param hapStart inclusive start position on the haplotype to consider.
+         * @param hapEnd exclusive after last position on the haplotype to consider.
+         */
+        public Problem(final int start, final int end, final int hapStart,
+                       final int hapEnd) {
+            if (start < 0 || start > readBases.length)
+                throw new IllegalArgumentException("bad start index " + start);
+            if (end < start || end > readBases.length)
+                throw new IllegalArgumentException("bad end index " + end + " < " + start + " or " + end + " > " + readBases.length);
+            if (hapStart < 0 || hapStart > haplotypeLength)
+                throw new IllegalArgumentException("bad hap start index "
+                        + hapStart + " is larger than the haplotypeLength " + haplotypeLength);
+            if (hapEnd < hapStart || hapEnd > haplotypeLength)
+                throw new IllegalArgumentException("bad hap end index "
+                        + hapEnd + " outside [" + hapStart + ","
+                        + haplotypeLength + "]");
+
+            haplotypeSegment = Arrays.copyOfRange(haplotypeBases, hapStart, hapEnd);
+            readStart = start;
+            readEnd = end;
+            this.hapStart = hapStart;
+            this.hapEnd = hapEnd;
+            trailing = readEnd == readBases.length;
+            leading = readStart == 0;
+
+            hashCode = ((start * 31 + end) * 31 + Arrays.hashCode(haplotypeSegment) * 31);
+        }
+
+        @Override
+        public int hashCode() {
+            return hashCode;
+        }
+
+        @Override
+        public boolean equals(Object o) {
+            if (o == this)
+                return true;
+            else if (o == null)
+                return false;
+            else if (o.getClass() != this.getClass())
+                return false;
+            else {
+                final Problem p = (Problem) o;
+                return (p.hashCode == this.hashCode) && (p.readStart == this.readStart) && (p.readEnd == this.readEnd) && Arrays.equals(haplotypeSegment, p.haplotypeSegment);
+            }
+        }
+
+
+    }
+
+    /**
+     * Returns the currently loaded read base calls.
+     * @return {@code never null}.
+     */
+    public byte[] getReadBases() {
+        if (readBases == null)
+            throw new IllegalStateException("no read was previously loaded.");
+        return readBases;
+    }
+
+
+}
diff --git a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/FlexibleHMM.java b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/FlexibleHMM.java
new file mode 100644
index 000000000..d3d003731
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/FlexibleHMM.java
@@ -0,0 +1,100 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*  
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*  
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*  
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*  
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*  
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. 
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.  
+*  
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY 
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*  
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*  
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
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+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
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+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt. 
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. 
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.sting.utils.pairhmm;
+
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+
+/**
+ * API for the fast (partial) HMM calculation engine.
+ */
+public interface FlexibleHMM {
+
+    /**
+     * Load a read into the HMM calculation matrices.
+     * @param read the read record to load into the HMM calculating engine.
+     */
+    public void loadRead(GATKSAMRecord read);
+
+    /**
+     * Returns the current read bases.
+     *
+     * @return never null.
+     */
+    public byte[] getReadBases();
+
+    /**
+     * Loads a haplotype bases in the HMM calculation matrices.
+     * @param haplotype the haplotype sequence.
+     *
+     * @throws IllegalStateException if no read has been previously loaded.
+     * @throws NullPointerException if {@code haplotype} is {@code null}.
+     */
+    public void loadHaplotypeBases(byte[] haplotype);
+
+    /**
+     * Resolve the partial Fast PairHMM for a section of the read and haplotype
+     * @param readFrom inclusive offset of the first position on the read.
+     * @param readTo   exclusive offset of the last position on the read.
+     * @param haplotypeFrom inclusive offset of the first position on the haplotype.
+     * @param haplotypeTo exclusive offset of the last position on the haplotype.
+     * @param treatAsMatch can assume that both pieces are the same sequence.
+     * @return the cost the sub-HMM.
+     */
+    public double calculateLocalLikelihood(int readFrom, int readTo, int haplotypeFrom, int haplotypeTo, boolean treatAsMatch);
+
+    /**
+     * Load a read given its relevant information pieces by separate.
+     * @param bases read bases.
+     * @param bq base qualities.
+     * @param iq insertion qualities.
+     * @param dq deletion qualities.
+     * @param mq read mapping quality.
+     */
+    public void loadRead(byte[] bases, byte[] bq, byte[] iq, byte[] dq, int mq);
+
+
+}
diff --git a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/LoglessPairHMM.java b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/LoglessPairHMM.java
index de2994927..1feae2bfe 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/LoglessPairHMM.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/LoglessPairHMM.java
@@ -55,19 +55,19 @@ import org.broadinstitute.sting.utils.QualityUtils;
  * User: rpoplin, carneiro
  * Date: 10/16/12
  */
-public final class LoglessPairHMM extends N2MemoryPairHMM {
+public class LoglessPairHMM extends N2MemoryPairHMM {
     protected static final double INITIAL_CONDITION = Math.pow(2, 1020);
     protected static final double INITIAL_CONDITION_LOG10 = Math.log10(INITIAL_CONDITION);
 
     // we divide e by 3 because the observed base could have come from any of the non-observed alleles
     protected static final double TRISTATE_CORRECTION = 3.0;
 
-    private static final int matchToMatch = 0;
-    private static final int indelToMatch = 1;
-    private static final int matchToInsertion = 2;
-    private static final int insertionToInsertion = 3;
-    private static final int matchToDeletion = 4;
-    private static final int deletionToDeletion = 5;
+    protected static final int matchToMatch = 0;
+    protected static final int indelToMatch = 1;
+    protected static final int matchToInsertion = 2;
+    protected static final int insertionToInsertion = 3;
+    protected static final int matchToDeletion = 4;
+    protected static final int deletionToDeletion = 5;
 
 
     /**
@@ -128,7 +128,7 @@ public final class LoglessPairHMM extends N2MemoryPairHMM {
      * @param readQuals      the base quality scores of the read
      * @param startIndex     where to start updating the distanceMatrix (in case this read is similar to the previous read)
      */
-    public void initializePriors(final byte[] haplotypeBases, final byte[] readBases, final byte[] readQuals, final int startIndex) {
+    protected void initializePriors(final byte[] haplotypeBases, final byte[] readBases, final byte[] readQuals, final int startIndex) {
 
         // initialize the pBaseReadLog10 matrix for all combinations of read x haplotype bases
         // Abusing the fact that java initializes arrays with 0.0, so no need to fill in rows and columns below 2.
@@ -180,7 +180,7 @@ public final class LoglessPairHMM extends N2MemoryPairHMM {
      * @param prior            the likelihood editing distance matrix for the read x haplotype
      * @param transition        an array with the six transition relevant to this location
      */
-    private void updateCell( final int indI, final int indJ, final double prior, final double[] transition) {
+    protected void updateCell( final int indI, final int indJ, final double prior, final double[] transition) {
 
         matchMatrix[indI][indJ] = prior * ( matchMatrix[indI - 1][indJ - 1] * transition[matchToMatch] +
                                                  insertionMatrix[indI - 1][indJ - 1] * transition[indelToMatch] +
diff --git a/protected/java/src/org/broadinstitute/sting/utils/sam/ClippedGATKSAMRecord.java b/protected/java/src/org/broadinstitute/sting/utils/sam/ClippedGATKSAMRecord.java
new file mode 100644
index 000000000..e42f109b2
--- /dev/null
+++ b/protected/java/src/org/broadinstitute/sting/utils/sam/ClippedGATKSAMRecord.java
@@ -0,0 +1,107 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+*
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+package org.broadinstitute.sting.utils.sam;
+
+import java.util.Arrays;
+
+/**
+ * Represents a hard-clipped view of a read.
+ */
+public class ClippedGATKSAMRecord extends GATKSAMRecord {
+
+    private byte[] insertionQuals;
+
+    private byte[] deletionQuals;
+
+    /**
+     * Creates a hard-clipped view on a existing read record.
+     * @param read the underlying unclipped read.
+     * @param start inclusive first position in {@code read} included in the clipped view.
+     * @param end inclusive last position in {@code read} included in the clipped view.
+     */
+    public ClippedGATKSAMRecord(final GATKSAMRecord read, int start, int end) {
+        super(read.getHeader(), read.getReferenceIndex(), read.getAlignmentStart() + start, (short) read.getReadNameLength(),
+                (short) 100, -1, read.getCigarLength(), read.getFlags(), end - start,
+                read.getMateReferenceIndex(), read.getMateAlignmentStart(), read.getInferredInsertSize(),
+                new byte[0]);
+        this.setReadBases(Arrays.copyOfRange(read.getReadBases(), start, end));
+        this.setBaseQualities(Arrays.copyOfRange(read.getBaseQualities(),start,end));
+        this.setReadName(read.getReadName());
+        insertionQuals = Arrays.copyOfRange(read.getBaseInsertionQualities(),start,end);
+        deletionQuals = Arrays.copyOfRange(read.getBaseDeletionQualities(),start,end);
+    }
+
+    @Override
+    public byte[] getBaseDeletionQualities() {
+        return deletionQuals;
+    }
+
+    @Override
+    public byte[] getBaseInsertionQualities() {
+        return insertionQuals;
+    }
+
+    @Override
+    public int getMappingQuality() {
+        return 100;
+    }
+
+    @Override
+    public int hashCode() {
+        return getReadName().hashCode();
+    }
+
+    @Override
+    public boolean equals(Object o) {
+        if (o instanceof GATKSAMRecord) {
+            return getReadName().equals(((GATKSAMRecord)o).getReadName());
+        } else {
+            return false;
+        }
+    }
+
+
+}
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java
new file mode 100644
index 000000000..697186463
--- /dev/null
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java
@@ -0,0 +1,424 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*  
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*  
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*  
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*  
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*  
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. 
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.  
+*  
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY 
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*  
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*  
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*  
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*  
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt. 
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. 
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
+
+import com.google.caliper.Param;
+import org.apache.commons.codec.digest.DigestUtils;
+import org.broadinstitute.sting.utils.haplotype.Haplotype;
+import org.broadinstitute.sting.utils.pairhmm.ActiveRegionTestDataSet;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.*;
+
+/**
+ * Created with IntelliJ IDEA.
+ * User: valentin
+ * Date: 8/13/13
+ * Time: 2:48 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class ActiveRegionTestDataSetUnitTest  {
+
+
+
+    @Test(dataProvider="activeRegionTestDataSets")
+    public void testActiveRegionsDataSet(final ActiveRegionTestDataSet as, final int kmerSize, final int readLength, final String variation, final int readCount, final int regionSize, final byte bq, final byte iq, final byte dq) {
+        Assert.assertNotNull(as);
+        Assert.assertEquals(as.assemblyResultSet().getMaximumKmerSize(),kmerSize);
+        final List<GATKSAMRecord> reads = as.readList();
+        Assert.assertEquals(reads.size(),readCount);
+        for (final GATKSAMRecord r : reads) {
+            Assert.assertEquals(r.getReadLength(),readLength);
+        }
+
+        final List<Haplotype> haplotypes = as.haplotypeList();
+        final List<Civar> haplotypeCivars = Civar.fromCharSequence(variation).optionalizeAll().unroll();
+
+        Assert.assertEquals(haplotypes.size(),haplotypeCivars.size());
+        Assert.assertTrue(haplotypeCivars.size() > 1);
+        int variants = 0;
+        for (int i = 0; i < variation.length(); i++) {
+           final char c = variation.charAt(i);
+           switch (c) {
+               case 'W':
+               case 'T':
+               case 'C':
+               case 'D':
+               case 'I':
+                    variants++;
+               default:
+
+           }
+        }
+
+        Assert.assertEquals(haplotypes.size(),(int) Math.pow(2,variants));
+
+        final Map<String,Integer> haplotypeNumberByString = new HashMap<>();
+        for (int i = 0; i < haplotypes.size(); i++) {
+            final Haplotype hap = haplotypes.get(i);
+            final Civar civar = haplotypeCivars.get(i);
+            Assert.assertEquals(hap.getBaseString(),civar.applyTo(as.getReference()));
+            if (i == 0) {
+                Assert.assertEquals(hap.getBaseString(), as.getReference());
+            } else {
+                Assert.assertNotEquals(hap.getBaseString(),as.getReference());
+            }
+            Assert.assertFalse(haplotypeNumberByString.containsKey(hap.getBaseString()));
+            haplotypeNumberByString.put(hap.getBaseString(), i);
+        }
+
+        final int[] hapReadsNotInReference = new int[haplotypes.size()];
+
+        for (int i = 0; i < readCount; i++) {
+            final GATKSAMRecord r = as.readList().get(i);
+
+            final int hapNumber = i % haplotypes.size();
+            final int offset = i % (haplotypes.get(hapNumber).length() - readLength);
+            Assert.assertEquals(r.getReadString(),haplotypes.get(hapNumber).getBaseString().substring(offset,offset+readLength));
+            if (as.getReference().indexOf(r.getReadString()) == -1) {
+                hapReadsNotInReference[hapNumber]++;
+            }
+        }
+
+        Assert.assertEquals(hapReadsNotInReference[0],0);
+
+        for (int i = 1; i < hapReadsNotInReference.length; i++) {
+            Assert.assertNotEquals(hapReadsNotInReference[i],0);
+        }
+
+    }
+
+    /**
+     * Constructs a test data-set based on the given parameters.
+     * @param kmerSize length of the kmer.
+     * @param readLength length of the read.
+     * @param variation variation in that active region.
+     * @param readCount number of reads in the active region
+     * @param regionSize Active region size (~ size of the haplotype(s))
+     * @param bq Base quality value common for all base-calls.
+     * @param iq Insertion quality based for all read positions.
+     * @param dq Deletion quality based for all read positions.
+     * @return never null.
+     */
+    public static ActiveRegionTestDataSet createActiveRegionTestDataSet(final int kmerSize, final int readLength, final String variation, final int readCount, final int regionSize, final byte bq, final byte iq, final byte dq) {
+
+        final String reference = REF.substring(0, regionSize);
+
+        final ActiveRegionTestDataSet result = new ActiveRegionTestDataSet(kmerSize, reference,
+                new String[]{"Civar:" + variation},
+                new String[]{"*:" + readCount + ":" + readLength}, byteRepeat(bq, readLength), byteRepeat(dq, readLength), byteRepeat(iq, readLength));
+
+
+        return result;
+    }
+
+    @DataProvider(name="activeRegionTestDataSets")
+    public Iterator<Object[]> activeRegionTestDataSets() {
+        return new java.util.Iterator<Object[]>() {
+
+            private int i = 0;
+
+            @Override
+            public boolean hasNext() {
+                return i < ACTIVE_REGION_TEST_DATA_SET_PARAMETERS.length;
+            }
+
+            @Override
+            public Object[] next() {
+
+                final Object[] params = ACTIVE_REGION_TEST_DATA_SET_PARAMETERS[i++];
+                final int kmerSize = (Integer) params[0];
+                final int readLength = (Integer) params[1];
+                final String variation = (String) params[2];
+                final int readCount = (Integer) params[3];
+                final int regionSize = (Integer) params[4];
+                final ActiveRegionTestDataSet dataSet = createActiveRegionTestDataSet(kmerSize, readLength, variation, readCount, regionSize, (byte) 20, (byte) 35, (byte) 35);
+                return new Object[] { dataSet , kmerSize, readLength, variation, readCount, regionSize, (byte)20, (byte) 35, (byte) 35};
+            }
+
+            @Override
+            public void remove() {
+                throw new UnsupportedOperationException();
+            }
+        };
+    }
+
+    private static int[] KMER_SIZES = new int[] { 10 };
+    private static int[] READ_COUNTS = new int[] { 1000 };
+    private static int[] READ_LENGTHS = new int[] { 100 };
+    private static String[] VARIATION_CIVARS = new String[] {
+            "*1T*",
+            "*3Iacg*",
+            "*30Igctcggatgccttgcggggctccagagtcc*",
+            "*3D*",
+            "*30D*",
+            "*1T3=3Iacg*",
+            "*1T*3Iacg*",
+            "*1T8=1T8=1T8=1T8=1T*",
+            "*1T*1T*1T*1T*1T*"
+     };
+
+    private static int[] REGION_SIZE = new int[] { 300 };
+
+    static {
+        try {
+            if (KMER_SIZES == null) KMER_SIZES = intValues(HCLikelihoodCalculationEnginesBenchmark.class.getDeclaredField("kmerSize").getAnnotation(Param.class).value());
+            if (READ_COUNTS == null) READ_COUNTS = intValues(HCLikelihoodCalculationEnginesBenchmark.class.getDeclaredField("readCount").getAnnotation(Param.class).value());
+            if (READ_LENGTHS == null) READ_LENGTHS = intValues(HCLikelihoodCalculationEnginesBenchmark.class.getDeclaredField("readLength").getAnnotation(Param.class).value());
+            if (VARIATION_CIVARS == null) VARIATION_CIVARS = HCLikelihoodCalculationEnginesBenchmark.class.getDeclaredField("variation").getAnnotation(Param.class).value();
+            if (REGION_SIZE == null) REGION_SIZE = intValues(HCLikelihoodCalculationEnginesBenchmark.class.getDeclaredField("regionSize").getAnnotation(Param.class).value());
+
+        } catch (NoSuchFieldException e) {
+            throw new ExceptionInInitializerError(e);  //To change body of catch statement use File | Settings | File Templates.
+        }
+    }
+
+    private static int[] intValues(final String[] kmerSizes) {
+        final int[] result = new int[kmerSizes.length];
+        for (int i = 0; i < result.length; i++)
+            result[i] = Integer.parseInt(kmerSizes[i]);
+        return result;
+    }
+
+    private static final Object[][] ACTIVE_REGION_TEST_DATA_SET_PARAMETERS;
+
+    static {
+        final int totalLength = KMER_SIZES.length * READ_COUNTS.length * READ_LENGTHS.length * VARIATION_CIVARS.length * REGION_SIZE.length;
+        ACTIVE_REGION_TEST_DATA_SET_PARAMETERS = new Object[totalLength][];
+        int next = 0;
+        for (final int ks : KMER_SIZES)
+            for (final int rc : READ_COUNTS)
+                for (final int rl : READ_LENGTHS)
+                    for (final String v : VARIATION_CIVARS)
+                        for (final int rs : REGION_SIZE)
+                            ACTIVE_REGION_TEST_DATA_SET_PARAMETERS[next++] = new Object[] { ks, rl, v, rc, rs };
+
+    }
+
+    private static byte[] byteRepeat(final byte bq, final int readLength) {
+        final byte[] result = new byte[readLength];
+        Arrays.fill(result, bq);
+        return result;
+    }
+
+
+
+    private static final String REF =
+            "TCGAGAAATTTGTATCCCGCCCCCGCAGCTTGCCAGCTCTTTCAGTATCATGGAGCCCAT" +
+                    "GGTTGAATGAGTCCAATAACGAACTTCGACATGATAAAATCCCCCCCTCGCGACTTCCAG" +
+                    "AGAAGAAGACTACTGACTTGAGCGTTCCCAGCACTTCAGCCAAGGAAGTTACCAATTTTT" +
+                    "TGTTTCCGAATGACACGCGTCTCCTTGCGGGTAGATCGCCGACCGCAGAACTTACGAGCC" +
+                    "AGGGGAAACAGTAAGGCCTAATTAGGTAAAGGGAGTAAGTGCTCGAACGCTTCAGATGTA" +
+                    "ACCATATACTTACGCTGGATCTTCTCCCGCGAATTTTAACCCTCACCAACTACGAGATTT" +
+                    "GAGGTAAACCAAATAAGCACGTAGTGGCGCTATCCGACTGTTCCCAAATTGTAACTTATC" +
+                    "GTTCCGTGAAGGCCAGAGTTACTTCCCGGCCCTTTCCATGCGCGCACCATACCCTCCTAG" +
+                    "TTCCCCGGTTATCTCTCCGAGGAGGGAGTGAGCGATCCTCCGTTTACGTTTTGTTACCAA" +
+                    "TGACGTAGCTATGTATTTTGTACAGGTTGCCAACGGGTTTCACAATTCACAGATAGTGGG" +
+                    "GATCCCGGCAAAGGGCCTATATTTGCGGTCCAACTTAGGCGTAAACTACGATGGTACCTA" +
+                    "CTCAGACCCAGCTCGCGCGGCGTAAATAACGCACTCATCCCAGCTGATTCTCGGCGATCT" +
+                    "ACGCAGCGACATGATTATCAACAGCTGTCTGGCAGCTCTAATCTTTTACCATGGTCGTAA" +
+                    "AAGCCTCCAAGAGTTAGATCATACCTAACGCCACAAAAGTGACACGACGCCGATGGGTAC" +
+                    "CGGACTTTAGGTCGACCACAGTTCGGTAAGGGAGAGGCCCTGCGGCGTACTTCATTTTGT" +
+                    "ATATGCAACGTGCCCAAGTGGCGCCAGGCAAGTCTCAGCTGGTTCCTGTGTTAGCTCGAG" +
+                    "GCTAGGCATGGGAGCTGATTGAACATGGGTTGGGGGCCTCGAACCGTCGAGGACCCCATA" +
+                    "GTACCTCGGACACCAAGTAGGGCAGCCTATAGTTTGAAGCAGTACTATTTCAGGGGGGGA" +
+                    "GCCCTCATGGTCTCTTCTACTGATGACTCAACACGCTAGGGACGTGAAGTCGATTCCTTC" +
+                    "GATGGTTATAAATCAAAGGCTCAGAGTGCAGTCTGGAGCGCCCATCTAACGGTACGCATC" +
+                    "TCGATTGCTCGGTCGCCTTTCACACTCCGCGAAAATTCATACCGCTCATTCACTAGGTTG" +
+                    "CGAAGCCTACACTGATATATGAATCCAAGCTAGAGCAGGGCTCTTAAAATTCGGAGTTGT" +
+                    "AGATGCTCAATACTCCAATCGGTTTTTTCGTGCACCACCGCGGGTGGCTGACAAGGGTTT" +
+                    "GACATCGAGAAACAAGGCAGTTCCGGGCTGAAAGTAGCGCCGGGTAAGGTACGCGCCTGG" +
+                    "TATGGCAGGACTATGAAGCCAATACAAAGGCTACATCCTCACTCGGGTGGACGGAAACGC" +
+                    "AGAATTATGGTTACTTTTTGGATACGTGAAACATGTCCCATGGTAGCCCAAAGACTTGGG" +
+                    "AGTCTATCACCCCTAGGGCCCATTTCTGGATATAGACGCCAGGTTGAATCCGTATTTGGA" +
+                    "GGTACGATGGATCAGTCTGGGTGGGACGTGCTCCATTTATACCCTGCGCAGGCTGGACCG" +
+                    "AGGACCGCAAGATGCGACGGTGCACAAGTAATTGACAACAAACCATCGTGTTTTCATTAT" +
+                    "GGTACCAGGATCTTCAAGCCGAGTCAATCAAGCTCGGATTACAGTGTTTACCGCGTCTTG" +
+                    "CGGTTACTCACAAACTGTAATCCACCACAAGTCAAGCCATTGCCTCTCTGAGACGCCGTA" +
+                    "TGAATTAATATGTAAACTTTGCGCGGGTTCACTGCGATCCGTTCAGTCTCGTCCAAGGGC" +
+                    "ACAATCGAATTCCCATTTGTATGTTCGGCTAACTTCTACCCATCCCCCGAAGTTTAGCAG" +
+                    "GTCGTGAGGTGTCATGGAGGCTCTCGTTCATCCCGTGGGACATCAAGCTTCGCCTTGATA" +
+                    "AAGCACCCCGCTCGGGTGTAGCAGAGAAGACGCCTACTGAATTGTGCGATCCCTCCACCT" +
+                    "CAGCTAAGGTAGCTACCAATATTTAGTTTTTTAGCCTTGCGACAGACCTCCTACTTAGAT" +
+                    "TGCCACGCATTGAGCTAGCGAGTCAGCGATAAGCATGACGCGCTTTCAAGCGTCGCGAGT" +
+                    "ATGTGAACCAAGGCTCCGGACAGGACTATATACTTGGGTTTGATCTCGCCCCGACAACTG" +
+                    "CAAACCTCAACATTTATAGATTATAAGGTTAGCCGAAATTGCACGTGGTGGCGCCCGCCG" +
+                    "ACTGCTCCCCGAGTGTGGCTCTTTGATCTGACAACGCGCGACCTCCATCGCGGCCGATTG" +
+                    "TTTCTGCGGACCATGTCGTCCTCATAGTTTGGGCATGTTTCCGTTGTAGGAGTGAAGCCA" +
+                    "CTTAGCTTTGCGCCGTAGTCCCAATGAAAAACCTATGGACTTTGTTTTGGGTAGCATCAG" +
+                    "GAATCTGAACCCTGTGAATGTGGGGGTCGCGCGCATAGACCTTTATCTCCGGTTCAAGTT" +
+                    "AGGCATGAGGCTGCATGCTACGTTGTCACACCTACACTGCTCGAAGTAAATATGGGAAGC" +
+                    "GCGCGGCCTGGCCCGAGGCGTTCCGCGCCGCCACGTGTTCGTTAACTGTTGATTGGTGGC" +
+                    "ACATAAGCAATACCGTAGTCCCTCAAATTCAGCTCTGTTATCTCGAGCGTTATGTGTCAA" +
+                    "ATGGCGTAGAACGGGATTGACTGTTTGACACTAGCTGGTGTTCGGTTCGGTAACGGAGAA" +
+                    "TCTGTGGGGCTATGTCACTAATACTTTCGAAACGCCCCGTACCGATGCTGAACAAGTCGA" +
+                    "TGCAGGCTCCCGTCTTTGAATAGGGGTAAACATACAAGTCGATAGAAGATGGGTAGGGGC" +
+                    "CTCCAATTCATCCAACACTCTACGCCTTCTCCAAGAGCTAGTAGGGCACCCTGCAGTTGG" +
+                    "AAAGGGAACTATTTCGTAGGGCGAGCCCATACCGTCTCTCTTGCGGAAGACTTAACACGA" +
+                    "TAGGAAGCTGGAATAGTTTCGAACGATGGTTATTAATCCTAATAACGGAACGCTGTCTGG" +
+                    "AGGATGAGTGTGACGGAGTGTAACTCGATGAGTTACCCGCTAATCGAACTGGGCGAGAGA" +
+                    "TCCCAGCGCTGATGCACTCGATCCCGAGGCCTGACCCGACATATCAGCTCAGACTAGAGC" +
+                    "GGGGCTGTTGACGTTTGGGGTTGAAAAAATCTATTGTACCAATCGGCTTCAACGTGCTCC" +
+                    "ACGGCTGGCGCCTGAGGAGGGGCCCACACCGAGGAAGTAGACTGTTGCACGTTGGCGATG" +
+                    "GCGGTAGCTAACTAAGTCGCCTGCCACAACAACAGTATCAAAGCCGTATAAAGGGAACAT" +
+                    "CCACACTTTAGTGAATCGAAGCGCGGCATCAGAATTTCCTTTTGGATACCTGATACAAAG" +
+                    "CCCATCGTGGTCCTTAGACTTCGTGCACATACAGCTGCACCGCACGCATGTGGAATTAGA" +
+                    "GGCGAAGTACGATTCCTAGACCGACGTACGATACAACTATGTGGATGTGACGAGCTTCTT" +
+                    "TTATATGCTTCGCCCGCCGGACCGGCCTCGCGATGGCGTAGCTGCGCATAAGCAAATGAC" +
+                    "AATTAACCACTGTGTACTCGTTATAACATCTGGCAGTTAAAGTCGGGAGAATAGGAGCCG" +
+                    "CAATACACAGTTTACCGCATCTAGACCTAACTGAGATACTGCCATAGACGACTAGCCATC" +
+                    "CCTCTGGCTCTTAGATAGCCCGATACAGTGATTTTGAAAGGTTTGCGGGGCACAGCTATG" +
+                    "ACTTGCTTAGCTACGTGTGAGGGAAGGAACTTTTGCGTATTTGTATGTTCACCCGTCTAC" +
+                    "TACGCATGCGGGCAGATTATGTAGGTTGAGAGATGCGGGAGAAGTTCTCGACCTTCCCGT" +
+                    "GGGACGTGAACCTATCCCCTAATAGAGCATTCCGTTCGAGCATGGCAGTAAGTACGCCTT" +
+                    "CTCAATTGTGCTAACCTTCATCCCTATCAAAGCTTGGAGCCAATGATCAGGGTTATTCCC" +
+                    "TTGGGACAGACTTCCTACTCACAGTCGGTCACATTGGGCTACTCCATGGGTCTTCAGCTT" +
+                    "GACCCGGTCTGTTGGGCCGCGATTACGTGAGTTAGGGCCCCGGACTGCGCTGTATAGTCG" +
+                    "ATTCTCATCCGGCCCCCACATCTGGAAACCCCAACTTATTTAGATAACATGATTAGCCGA" +
+                    "AGTTGCACGGCGTGTCCACCGTGGAGTCCTCCCCGGGTGTCCCTCCTTCATTTGACGATA" +
+                    "AGCAGCGGCTACCACCATTGATTAACACAAGGAACGGTGATGTTAACATAGATTCGGCAC" +
+                    "ATTACTCTTGTAGGTGTGGAATCACTTAGCTACGCGGCGAAGCCTTATGGCAAAACCGAT" +
+                    "GGGCAATGATTCGGGTAGCGCTAAAAGTCCATAGCACGTGCATCCCAACGTGGCGTGCGT" +
+                    "ACAGCTTGACCACCGCTTCACGCTAAGGTGCTGGCCACATGCTAAATTGATGCGCCTGCA" +
+                    "CTGCTCAAAGGATAATTACGAAGCGGGCGGCCTGGCGGGAGCACTACCCCATCGACGCGT" +
+                    "ACTCGAATACTGTTTATTGCTCACACATGAACAAATTAGTAGAGTGCCACTTTCAGCCCT" +
+                    "CTTGTCGTCGGCGATGTGTGTAAAATGGCGTTGATGTGGATCGACTCTATAAAGGTATCT" +
+                    "ACTGATGCGTAGGGAGATCCGGAATCTATTGGCCTATGTCACTGAAACTATCCAAACACC" +
+                    "CCATGTCGATACTGAACGTATCGACGCATACCTCCTTCCTTGAAAACGCACAATCATACA" +
+                    "ACTGGGCACATAATGCGTACGCCCATCTAGTACACCCATCTCTGTGGGTCCAGTTCAAGA" +
+                    "GCTGGAAGAGCACCCTCCACAAGGTCAAGTGGTATCCTGGTAAGGTAAGCTCGTACCGTG" +
+                    "ATTCATGCGACAGGGGTAAGACCATCAGTAGTAGGGATAGTGCCAAACCTCACTCACCAC" +
+                    "TGCCAATAAGGGGTCCTTACCTGAAGAATAAGTGTCAGCCAGTGTAACCCGATGAGGAAC" +
+                    "CCAAAAGGCGAACCGGGCCAGACAACCCGGCGGTATCGCACTCAAAGCCGGGACACGACG" +
+                    "CGTCACAGCCGGTAAGAGTAACCCCGGAGTGAAGACCTATGGGGCTGGATAAAACTGCCG" +
+                    "TGGTAACCGCCTTCAACAACCCGAATACGTGGCACTTCAGGAGGCGCCCGGAGGGGGGAT" +
+                    "GTTTTCTACTATTCGAGGCCGTTCGTTATAACTAGTTGCGTTCCTAGCCGCTATAATTGT" +
+                    "CTCTTTGCCGACTAATGAGAACAACCACACCATAGCGATTTGACGCGGCGCCTCGGAATA" +
+                    "CCGTTTCAGCAGGCGCTTGGTAAGGCCATCGCGAATACCAGGTATCGTGTAAGTAGCGTA" +
+                    "GGCCCGCACGCAAGATAAACTGCTAGGGAACCGCGTTTCCACGACCGGTGCACGATTTAA" +
+                    "TTTCGCCGACGTGATGACATTCCAGGCAGTGCCTCTGCCGCCGGACCCCTCTCGTGATTG" +
+                    "GGTAGCTGGACATGCCCTTGTAAGATATAACAAGAGCCTGCCTGTCTAATGATCTCACGG" +
+                    "CGAAAGTCGGGGAGACAGCAGCGGCTGCAGACATTATACCGCAACAACACTAAGGTGAGA" +
+                    "TAACTCCGTAATTGACTACGCGTTCCTCTAGACCTTACTTGACCGGATACAGTGTCTTTG" +
+                    "ACACGTTTATGGGTTACAGCAATCACATCCAAGACTGGCTATGCACGAAGCAACTCTTGA" +
+                    "GTGTTAAAATGTTGACCCCTGTATTTGGGATGCGGGTAGTAGATGAGTGCAGGGACTCCG" +
+                    "AGGTCAAGTACATTACCCTCTCATAGGGGGCGTTCTAGATCACGTTACCACCATATCATT" +
+                    "CGAGCATGACACCATCTCCGCTGTGCCCATCCTAGTAGTCATTATTCCTATCACGCTTTC" +
+                    "GAGTGTCTGGTGGCGGATATCCCCCACGAATGAAAATGTTTTTCGCTGACAGTCATATTG" +
+                    "GGGTGCTCCTAAGCTTTTCCACTTGGCTGGGTCAGCTAGGCCTCCGTGCCCGGAGTTTCG" +
+                    "GCGCAGTGCTGCCGACAGCCGGCCATTGTCTTTGGGGCCTCATTCGAGGGTACCCGGACC" +
+                    "TATCTTGTCGGGACCACCCGGGGTAGTCGTTGGGCTTATGCACCGAAAAGCCCTGCGCCG" +
+                    "GCCTCCCCGCTACGGAAGGTGATAAGCTCCGGCAAGCAATTATGAACAACGCAAGGATCG" +
+                    "CGGATATAAACAGAGAAACGGCTGATTACACCTGTTCGTGTGGTATCGGTAAATAGCCTC" +
+                    "GCGGAGCCTTATGCCATACTCGTCCGCGGAGCACTCTGGTAATGCATATGGTCCACAGGA" +
+                    "CATTCGTCGCTTCCGGGTATGCGCTCTATTTGACGGTCCTTTGGCGCACAGATGCTGGCC" +
+                    "ACCATTTAAATTAGAGCGACTCCACATCTGTAAGGTCCGCCACGCAGACGACAGCCCAGG" +
+                    "GAGACCACTGACCGATCTACCTGAACGGCAACCTTCTGTATCGTACTGGGGCGGAGAGAT" +
+                    "AACTACAGTGCCGCTTACAGCCCCTCTGTCGTCGCCGACGTCTGTAGTCTAGCCTCATTA" +
+                    "TGATTGCACGCTATTGAGGCATTGACTGATGCCGGAAGACATCTGAAATGAACTGGTCTA" +
+                    "TGCGACAGAAACCGTGCACCTACCAAATCTCCTTAGTGTAGGTTCTGACCGATTCGTGCT" +
+                    "TCGTTGAGAACTCACATTTTAACAACAGAGGACATATGCCCTACCTCCATGATCTACTGA" +
+                    "CGTCCCTGAGGCTGCAATTCATGTAATGGGGCAGTATCCGCGGCAAGTCCTAGTGCAATG" +
+                    "GCGGTTTTTTACCCTCGTTCTGAAGAAGAGGCGACGCGGGTGCGGTCATCACTAATGTGG" +
+                    "AAATTGGGAAGACTCTCGGGCCTCCGCCTTTAGGCGGTGCTTACTCTTTCATAAAGGGGC" +
+                    "TGTTAGTTATGCCCCGCGAGGATTCGAAAAGGTGAGCCAACTCGGCCGATCCGGAGAGAC" +
+                    "GGGCTTCAAAGCTGCCTGACGACGGTTGTGGGCCCGTAACAAAATCCTCCCAATAAGCCC" +
+                    "CCGTGAGCGTCGGTTGAACAGCCCTGGTCGGCCCGACCAGAAGCCCGAATATATCGCTTT" +
+                    "ACGGCTCTTGGGCCGGGGTGCGTTACCTTGCAGAAATCGAGGCCGTCCGTTAATTCCTGT" +
+                    "TGCATTCATACCGCGTATATTTGTCTCTTTACCCGCTTACTTGGATAAGCATGGCATAGC" +
+                    "TTTTTATCGGAGCGCCTCCGTACACGGTACGATCGCACGCCTCGTGAGATCAATACGTAT" +
+                    "ACCAGGTGTCCTGTGAGCAGCGAAAGCCTAAACGGGAGATACACCGCCAAAAGTCCGTGT" +
+                    "GAATACGAGTCGTGGCAAATTTGGTCTGGCTGTGATCTAGATATTCCAGGCGGTACGTCT" +
+                    "GCTCTCGCGTGCCTCTAGTGGCTCGCTAGATAGTCTAGCCGCTGGTAAACACTCCATGAC" +
+                    "CCCGGCTCTCCATTGATGCCACGGCGATTGTTGGAGAGCCAGCAGCGACTGCAAACGTCA" +
+                    "GATCAGAGTAATACTAGCAAGCGATAAGTCCCTAACTGGTTGTGGCCTTCTGTAGAGTGA" +
+                    "ACTTCACCACATATGCTGTCTCTGGCACGTGGATGGTTTGGAGAAATCAGATTCAAGTCT" +
+                    "GATCAACCTTCAAACAGATCTAGAGTCTAAAACAGTGATCTCCTGCGTGCGAGATAGAAA" +
+                    "TACTAGGTAACTACAGGGACTGCGACGTTTTAAACGTTGGTCCGTCAGAAGCGCCATTCA" +
+                    "GGATCACGTTACCCCGAAAAAAAGGTACCAGGAGCTCTTCTCCTCTGCAGTCAGGTCTAT" +
+                    "AGAAACTACACCATTAACCTTCCTGAGAACCGGGAGGTGGGAATCCGTCACATATGAGAA" +
+                    "GGTATTTGCCCGATAATCAATACTCCAGGCTTCTAACTTTTTCCACTCGCTTGAGCCGGC" +
+                    "TTGGCCTTTCTGCCTGAAGATTCGTTGGACTGGTGCCAACGCGCAGGCATAGTTCCAGGA" +
+                    "GAATTATCCGGGGGCAGTGACAACCAACATCTCGGGTCTTGCCCAACCGGTCTACACGCT" +
+                    "GATATAGCGAATCACCGAGAACCCGGCGCCACGCAATGGAACGTCCTTAACTCTGGCAGG" +
+                    "CAATTAAAGGGAACGTATATATAACGCAAAAAAACTGGAAAATTGGCGAGAGAATCTTCT" +
+                    "CTCTGTCTATCGAAGAATGGCCACGCGGAGGCATGCGTCATGCTAGCGTGCGGGGTACTC" +
+                    "TTGCTATCCATTTGGGTCACAGGACACTCGCTGTTTTCGAATTTACCCTTTATGCGCCGG" +
+                    "TATTGAACCACGCTTATGCCCAGCATCGTTACAACCAGACTGATACTAGATGTATAATGT" +
+                    "CCGCCATGCAGACGAAACCAGTCGGAGATTACCGAGCATTCTATCACGTCGGCGACCACT" +
+                    "AGTGAGCTACTGGAGCCGAGGGGTAACGATGATGCCCCTAAGAACCTCTCGGTCGACGCA" +
+                    "AGCGATTACACTCCTGTCACATCATAATCGTTTGCTATTCAGGGGTTGACCAACACCGGA" +
+                    "TAGCTTTTCACTTGAAGTATTATGCACGACAGGGTGCGTGTACCAACTAAACCTGTTTTA" +
+                    "ACTTACCTCAGACTAGTTGGAAGTGTGGCTAGATCTTAGCTTTCGTCACTAGAGGGCCCA" +
+                    "CGCTTAGTTTTTATGATCCATTGATCTCCTAGACGCTGCAAGATTTGCAACCAGGCAGAC" +
+                    "TTAGCGGTAGGTCCTAGTGCAGCGGGACTTTTTTTCTATAGTCGTTGAGAGGAGGAGTCG" +
+                    "TCAGACCAGATACCTTTGATGTCCTGATTGGAAGGACCGTTGGCCCCCGACCCTTAGACA" +
+                    "GTGTACTCAGTTCTATAAACGAGCTATTAGATATGAGATCCGTAGATTGAAAAGGGTGAC" +
+                    "GGAATTCGCCCGGACGCAAAAGACGGACAGCTAGGTATCCTGAGCACGGTTGCGCGTCCG" +
+                    "AATCAAGCTCCTCTTTACAGGCCCCGGTTTCTGTTGGTCGTAGAGCGCAGAACGGATTGG" +
+                    "GGGGATGTACGACAATATCTCTTAGTCACCTTTGGGTCACGGTCTGCTACCTTACAGGAA" +
+                    "TTCAGACCGTCCTTTAATTTCCCTTGCATATATGTTGCGTTTCTTCGACCTTCTAACCGC" +
+                    "ACCCTTAGGACGAAGACAGATACGTTCTTACCCATACTCCACCGTTGGCAGCGGGATCGC" +
+                    "ATGTCCCACGTGAAACATTGCTAAACCCTCAGGCCTCTGAGCGACAAAAGCTTTAAAGGG" +
+                    "AAATTCGCGCCCATAACTTGGTCCGAATACGGGTTCTAGCATCGTTCGTCTGAGTTTGTT" +
+                    "CTATATAAAACGGGCGCAATGTCTGCTTTGATCAACCTCCAATACCTCGTATGATTGTGC" +
+                    "ACCCGCCGGTGACCACTCAATGATGTGGGGTCCCCGTTGCAACTACGAGGATTTATTGAG" +
+                    "ACCGACCTACGTTCGGCATTGTGGGCAGAGTGAAGTATTGGCAAACGTTAAGTGCCGAAC" +
+                    "TAGATCTGACCTAACGGTAAGAGAGTTTCATAATACGTCCAGCCGCATGCGCAGGGTACA" +
+                    "TTTGGACAGTATTGAATGGACTCTGATCAACCTTCACACCGATCTAGAAACGAGTGCGTA" +
+                    "GATCAGCCAGGTGCAAACCAAAAATTCTAGGTTACTAGAAGTTTTGCGACGTTCTAAGAG" +
+                    "TTGGACGAAATGTTTCGCGACCTAGGATGAGGTCGCCCTAGAAAATAGATTTCTGCTACT" +
+                    "CTCCTCATAAGCAGTCCGGTGTATCGAAAGTACAAGACTAGCCTTGCTAGCAACCGCGGG" +
+                    "CTGGGAGCCTAAGGCATCACTCAAGATACAGGCTCGGTAACGTACGCTCTAGCCATCTAA" +
+                    "CTATCCCCTATGTCTTATAGGGACCTACGTTATCTGCCTG";
+
+    protected final static String REF_MD5 = new String(DigestUtils.md5(REF));
+
+}
\ No newline at end of file
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSetUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSetUnitTest.java
new file mode 100644
index 000000000..564a475b0
--- /dev/null
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSetUnitTest.java
@@ -0,0 +1,249 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+*
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
+
+import net.sf.samtools.SAMFileHeader;
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.SeqGraph;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.ReadThreadingGraph;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.RandomDNA;
+import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
+import org.broadinstitute.sting.utils.haplotype.Haplotype;
+import org.broadinstitute.sting.utils.pairhmm.ActiveRegionTestDataSet;
+import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.*;
+
+/**
+ * Tests for {@link AssemblyResultSet}.
+ *
+ * @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.org&gt;
+ */
+public class AssemblyResultSetUnitTest extends BaseTest
+{
+    private GenomeLocParser genomeLocParser;
+    private SAMFileHeader header;
+
+    @BeforeClass
+    public void init() {
+        header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000000);
+        genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
+    }
+
+
+    @Test
+    public void testEmptyResultSet() {
+        final AssemblyResultSet subject = new AssemblyResultSet();
+
+        Assert.assertEquals(subject.getHaplotypeList().size(), 0);
+        Assert.assertEquals(subject.getHaplotypeCount(),0);
+        Assert.assertEquals(subject.getReferenceHaplotype(),null);
+        Assert.assertEquals(subject.getFullReferenceWithPadding(),null);
+        Assert.assertEquals(subject.getPaddedReferenceLoc(),null);
+        Assert.assertEquals(subject.getRegionForGenotyping(),null);
+        Assert.assertEquals(subject.getUniqueReadThreadingGraph(10),null);
+        Assert.assertFalse(subject.hasMultipleKmerSizes());
+    }
+
+    @Test
+    public void testAddReferenceHaplotype() {
+
+        final Haplotype ref = new Haplotype("ACGT".getBytes(),true);
+        ref.setGenomeLocation(genomeLocParser.createGenomeLoc("chr1",1,ref.length() + 1 ));
+        final AssemblyResultSet subject = new AssemblyResultSet();
+
+        Assert.assertTrue(subject.add(ref));
+        Assert.assertFalse(subject.add(ref));
+
+        Assert.assertEquals(subject.getReferenceHaplotype(),ref);
+        Assert.assertEquals(subject.getHaplotypeCount(),1);
+        Assert.assertEquals(subject.getHaplotypeList().size(),1);
+    }
+
+    @Test(dataProvider="assemblyResults")
+    public void testAddManyHaplotypes(final java.util.List<AssemblyResult> assemblyResults,
+                                      final java.util.List<java.util.List<Haplotype>> haplotypes) {
+        final AssemblyResultSet subject = new AssemblyResultSet();
+        for (int i = 0; i < haplotypes.size(); i++) {
+            final int haplotypeCountBefore = subject.getHaplotypeCount();
+            final java.util.List<Haplotype> haplos = haplotypes.get(i);
+            final AssemblyResult ar = assemblyResults.get(i);
+            for (final Haplotype h : haplos) {
+                Assert.assertTrue(subject.add(h, ar));
+                Assert.assertFalse(subject.add(h,ar));
+                if (h.isReference())
+                    Assert.assertEquals(subject.getReferenceHaplotype(),h);
+            }
+            final int haplotypeCountAfter = subject.getHaplotypeCount();
+            Assert.assertEquals(haplos.size(),haplotypeCountAfter - haplotypeCountBefore);
+            Assert.assertTrue(subject.getMaximumKmerSize() >= ar.getKmerSize());
+            Assert.assertTrue(subject.getMinimumKmerSize() <= ar.getKmerSize());
+            Assert.assertEquals(subject.getUniqueReadThreadingGraph(ar.getKmerSize()), ar.getThreadingGraph());
+        }
+    }
+
+    @Test(dataProvider="trimmingData")
+    public void testTrimTo(final Map<Haplotype,AssemblyResult> haplotypesAndResultSets, final ActiveRegion original) {
+        final AssemblyResultSet subject = new AssemblyResultSet();
+        for (final Map.Entry<Haplotype,AssemblyResult> entry : haplotypesAndResultSets.entrySet())
+            subject.add(entry.getKey(),entry.getValue());
+        subject.setRegionForGenotyping(original);
+        final GenomeLoc originalLocation = original.getExtendedLoc();
+        final int length = originalLocation.size();
+        final GenomeLoc newLocation = originalLocation.setStop(originalLocation.setStart(originalLocation,originalLocation.getStart() + length / 2),originalLocation.getStop() - length / 2);
+        final ActiveRegion newRegion = original.trim(newLocation);
+
+        final Map<Haplotype,Haplotype> originalHaplotypesByTrimmed = new HashMap<>(haplotypesAndResultSets.size());
+        for (final Haplotype h : haplotypesAndResultSets.keySet())
+            originalHaplotypesByTrimmed.put(h.trim(newRegion.getExtendedLoc()), h);
+
+        final AssemblyResultSet trimmed = subject.trimTo(newRegion, originalHaplotypesByTrimmed);
+
+        Assert.assertFalse(subject.wasTrimmed());
+        Assert.assertTrue(trimmed.wasTrimmed());
+
+        for (final Haplotype h : trimmed.getHaplotypeList()) {
+            Assert.assertEquals(h.getGenomeLocation(),newLocation);
+            Assert.assertEquals(h.getBases().length,newLocation.size());
+        }
+    }
+
+    @DataProvider(name="trimmingData")
+    public Iterator<Object[]> trimmingData() {
+        final ActiveRegion activeRegion = new ActiveRegion(genomeLocParser.createGenomeLoc("chr1",1000,1100),genomeLocParser,25);
+        final int length = activeRegion.getExtendedLoc().size();
+        final RandomDNA rnd = new RandomDNA(13); // keep it prepoducible by fixing the seed to lucky 13.
+        final ActiveRegionTestDataSet actd = new ActiveRegionTestDataSet(10,new String(rnd.nextBases(length)),new String[] {
+                "Civar:*1T*" }, new String[0], new byte[0], new byte[0], new byte[0]);
+
+        final List<Haplotype> haplotypes = actd.haplotypeList();
+        for (final Haplotype h : haplotypes)
+            h.setGenomeLocation(activeRegion.getExtendedLoc());
+
+        final ReadThreadingGraph rtg = new ReadThreadingGraph(10);
+        for (final Haplotype h : haplotypes)
+            rtg.addSequence("seq-" + Math.abs(h.hashCode()), h.getBases(), null, h.isReference());
+        final SeqGraph seqGraph = rtg.convertToSequenceGraph();
+        final AssemblyResult ar = new AssemblyResult(AssemblyResult.Status.ASSEMBLED_SOME_VARIATION,seqGraph);
+        ar.setThreadingGraph(rtg);
+        final Map<Haplotype,AssemblyResult> result =
+                new HashMap<>();
+        for (final Haplotype h : haplotypes)
+            result.put(h,ar);
+        return Collections.singleton(new Object[] {result,activeRegion}).iterator();
+
+    }
+
+
+
+
+    @DataProvider(name="assemblyResults")
+    public java.util.Iterator<Object[]> assemblyResults() {
+        final int size = THREE_KS_GRAPH_AND_HAPLOTYPES.length * (1 + TEN_KS_GRAPH_AND_HAPLOTYPES.length);
+        final Object[][] result = new Object[size][];
+
+        for (int i = 0; i < THREE_KS_GRAPH_AND_HAPLOTYPES.length; i++) {
+            final ReadThreadingGraph rtg = new ReadThreadingGraph((String) THREE_KS_GRAPH_AND_HAPLOTYPES[i][0]);
+            final AssemblyResult ar = new AssemblyResult(AssemblyResult.Status.ASSEMBLED_SOME_VARIATION,rtg.convertToSequenceGraph());
+            ar.setThreadingGraph(rtg);
+            final Object[] haplotypeStrings = (Object[]) THREE_KS_GRAPH_AND_HAPLOTYPES[i][1];
+            final Haplotype[] haplotypes = new Haplotype[haplotypeStrings.length];
+            for (int j = 0; j < haplotypeStrings.length; j++) {
+                haplotypes[j] = new Haplotype(((String)haplotypeStrings[j]).getBytes(),j == 0);
+                haplotypes[j].setGenomeLocation(genomeLocParser.createGenomeLoc("chr1",1,haplotypes[j].length() + 1));
+            }
+            result[i] = new Object[] { Collections.singletonList(ar),Arrays.asList(Arrays.asList(haplotypes))};
+            for (int j = 0; j < TEN_KS_GRAPH_AND_HAPLOTYPES.length; j++) {
+                final ReadThreadingGraph rtg10 = new ReadThreadingGraph((String) TEN_KS_GRAPH_AND_HAPLOTYPES[j][0]);
+                final AssemblyResult ar10 = new AssemblyResult(AssemblyResult.Status.ASSEMBLED_SOME_VARIATION,rtg10.convertToSequenceGraph());
+                ar10.setThreadingGraph(rtg10);
+                final Object[] haplotypeStrings10 = (Object[]) TEN_KS_GRAPH_AND_HAPLOTYPES[j][1];
+                final Haplotype[] haplotype10 = new Haplotype[haplotypeStrings10.length];
+                for (int k = 0; k < haplotypeStrings10.length; k++) {
+                    haplotype10[k] = new Haplotype(((String)haplotypeStrings10[k]).getBytes(),false);
+                    haplotype10[k].setGenomeLocation(genomeLocParser.createGenomeLoc("chr1", 1, haplotype10[k].length() + 1));
+                }
+
+                result[THREE_KS_GRAPH_AND_HAPLOTYPES.length + i * TEN_KS_GRAPH_AND_HAPLOTYPES.length + j] = new Object[] { Arrays.asList(ar,ar10),
+                        Arrays.asList( Arrays.asList(haplotypes), Arrays.asList(haplotype10)) };
+            }
+        }
+        return Arrays.asList(result).iterator();
+    }
+
+
+    private static final Object[][] THREE_KS_GRAPH_AND_HAPLOTYPES = new Object[][] {
+            {"[ks=3]{REF: ACT}",new Object[] {"ACT"}},
+            {"[ks=3]{REF: ACT(3) -> T(1)      ->      G(2) -> A}" +
+                    "{ (3) -> A -> G ->          (2) }" +
+                    "{  (1) -> A -> G ->  (2) }",new Object[] {"ACTTGA","ACTAGGA","ACTTAGGA"}},
+            {"[ks=3]{REF: ACT -> C(1) -> G}{ACT -> C(1) -> G}{ACT -> C(1) -> G}", new Object[] {"ACTCG"}} ,
+            {"[ks=3]{REF: ACT -> A(1) -> G -> A(2) -> C -> G -> T }" +
+                    "{A(1) -> T -> A(2) }", new Object[] {"ACTAGACGT","ACTATACGT"}}  ,
+            {"[ks=3]{REF: ACT -> A -> T(2) -> C -> A -> G -> T -> A -> C -> G -> T -> A(1) -> T}" +
+                    "{ ACT -> A -> T(2) -> C -> T -> A -> C -> G -> T -> A(1) -> T}",
+                           new Object[] {"ACTATCAGTACGTAT","ACTATCTACGTAT"}} ,
+            {"[ks=3]{REF: ACT -> A -> T    -> C -> A -> G -> T -> A -> C -> G -> T -> A    -> T}",
+                           new Object[] {"ACTATCAGTACGTAT"}},
+            {"[ks=3]{REF: ACT -> A -> T(1) }" +
+                    "{ ACT -> A -> T(1) }", new Object[] {"ACTAT"}},
+            {"[ks=3]{REF: TTT -> A(1) -> C -> T(2)}{ A(1) -> T(2) } ", new Object[] {"TTTACT","TTTAT"}}
+    };
+
+    private static final Object[][] TEN_KS_GRAPH_AND_HAPLOTYPES = new Object[][] {
+            {"[ks=10]{ACTAGTAAAT -> A -> T -> A -> A -> T -> A", new Object[] {"ACTAGTAAATATAATA"}},
+            {"[ks=10]{ATAGTAATAA(1) -> A -> C -> T -> A(2) -> C}{ (1) -> C -> C -> C -> A(2) -> C}",
+                    new Object[] {"ATAGTAATAAACTAC","ATAGTAATAACCCAC"}},
+
+    };
+
+}
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Civar.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Civar.java
new file mode 100644
index 000000000..cfdda7c4d
--- /dev/null
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Civar.java
@@ -0,0 +1,1135 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+*
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
+
+import com.google.java.contract.Requires;
+import net.sf.samtools.Cigar;
+import net.sf.samtools.CigarElement;
+import net.sf.samtools.CigarOperator;
+
+import java.util.*;
+
+/**
+ * Compact Idosyncratic Variation Alignment Report.
+ * <p/>
+ * Allows to specify variation of a sequence.
+ * <p/>
+ */
+public class Civar {
+
+
+    protected List<Element> elements;
+    private String string;
+    private transient int minimumTemplateSize = -1;
+    private transient Boolean expands = null;
+    private transient int starCount = -1;
+    private Boolean hasEmbeddedCivars = null;
+    private Boolean hasOptionalVariation = null;
+    private Boolean hasVariation = null;
+    private Boolean allVariationIsOptional;
+
+
+    protected Civar(final List<Element> elements) {
+        this.elements = elements;
+    }
+
+    public static Civar fromCharSequence(final CharSequence cs, final int from, final int to) {
+        return Parser.parse(cs, from, to);
+    }
+
+    public static Civar fromCharSequence(final CharSequence cs) {
+        return fromCharSequence(cs, 0, cs.length());
+    }
+
+    @Override
+    public String toString() {
+        if (string == null)
+            analyzeCivar();
+        return string;
+    }
+
+    /**
+     * Correspond to the minimum template sequence size to which this civar can be applied to.
+     */
+    public int minimumTemplateSequenceSize() {
+        if (minimumTemplateSize < 0)
+            analyzeCivar();
+        return minimumTemplateSize;
+    }
+
+    public boolean expands() {
+        if (expands == null)
+            analyzeCivar();
+        return expands;
+    }
+
+    public boolean hasEmbeddedCivars() {
+        if (hasEmbeddedCivars == null)
+            analyzeCivar();
+        return hasEmbeddedCivars;
+    }
+
+    public List<Civar> unroll() {
+        if (!isUnrolled()) {
+            final List<Civar> result = new LinkedList<>();
+            unroll(0, new LinkedList<Element>(), "", result);
+            return result;
+        } else {
+            return Collections.singletonList(this);
+        }
+    }
+
+    public Civar optionalizeAll() {
+        if (allElementsAreOptional()) {
+            return this;
+        }
+        final Element[] newElements = new Element[this.elements.size()];
+        int next = 0;
+        for (final Element e : elements) {
+           final Element newElement = e.clone();
+           if (newElement.operator() == Operator.EMBEDDED) {
+               newElement.embedded = newElement.embedded.optionalizeAll();
+           }
+           newElement.makeOptional();
+           newElements[next++] = newElement;
+        }
+        return new Civar(Collections.unmodifiableList(Arrays.asList(newElements)));
+    }
+
+    private boolean allElementsAreOptional() {
+        if (allVariationIsOptional == null)
+            analyzeCivar();
+        return allVariationIsOptional;
+    }
+
+
+    private void unroll(final int elementIndex, final LinkedList<Element> leftElements, final String leftString, final List<Civar> dest) {
+        if (elementIndex == elements.size()) {
+            final Civar result = new Civar(Collections.unmodifiableList(new ArrayList<>(leftElements)));
+            dest.add(result);
+            return;
+        }
+        final Element currentElement = elements.get(elementIndex);
+        if (currentElement.operator() == Operator.EMBEDDED) {
+            List<Civar> embeddedUnroll = currentElement.embedded.unroll();
+            Civar novar = null;
+            for (final Civar c : embeddedUnroll) {
+                if (!c.hasVariation()) {
+                    novar = c;
+                    break;
+                }
+            }
+            if (novar == null && currentElement.isOptional()) {
+
+                embeddedUnroll = new LinkedList<>(embeddedUnroll);
+                embeddedUnroll.add(0, currentElement.embedded.novarEquivalent());
+            }
+
+            for (final Civar embedded: embeddedUnroll) {
+                final Element embeddedElement = new Element(embedded,false);
+                leftElements.add(embeddedElement);
+                unroll(elementIndex + 1, leftElements, leftString + embeddedElement.toString(), dest);
+                leftElements.removeLast();
+            }
+        } else if (currentElement.isOptional() && currentElement.isVariant()) {
+            leftElements.add(currentElement.matchEquivalent());
+            unroll(elementIndex + 1, leftElements, leftString + currentElement.matchEquivalent().toString(), dest);
+            leftElements.removeLast();
+            leftElements.add(currentElement.mandatoryEquivalent());
+            unroll(elementIndex + 1, leftElements, leftString + currentElement.mandatoryEquivalent().toString(), dest);
+            leftElements.removeLast();
+        } else {
+            leftElements.add(currentElement);
+            unroll(elementIndex + 1, leftElements, leftString + currentElement.toString(), dest);
+            leftElements.removeLast();
+        }
+    }
+
+    private Civar novarEquivalent() {
+        int mtss = minimumTemplateSequenceSize();
+        int sc = starCount();
+        if (mtss > 0) {
+            if (sc > 0) {
+                final Civar newEmbedded = new Civar(Collections.unmodifiableList(Arrays.asList(
+                        new Element(Operator.MATCH,mtss,false,false),new Element(Operator.MATCH,sc,true,false))));
+                //newEmbedded.string = newEmbedded.elements.get(0).toString() + newEmbedded.elements.get(1).toString();
+                return newEmbedded;
+            } else {
+                return new Civar(Collections.unmodifiableList(Collections.singletonList(new Element(Operator.MATCH, mtss, false, false))));
+            }
+        } else if (sc > 0) {
+            return new Civar(Collections.unmodifiableList(Collections.singletonList(new Element(Operator.MATCH, sc, true, false))));
+        } else {
+            return new Civar((List<Element>) (List) Collections.emptyList());
+        }
+    }
+
+    public String applyTo(final CharSequence seq) {
+        return applyTo(seq,0,seq.length());
+    }
+
+    public List<ElementOffset> eventOffsets(final CharSequence seq, final int from, final int to) {
+        if (!isUnrolled())
+            throw new UnsupportedOperationException("you cannot apply an unrolled Civar to a DNA sequence");
+        final List<ElementOffset> result = new ArrayList<>(elements().size());
+        final CharSequence sequence = seq;
+
+        int sequenceLength = sequence.length();
+        int minSeqLen = minimumTemplateSequenceSize();
+        if (!expands() && sequenceLength != minSeqLen)
+            throw new IllegalArgumentException("the sequence provided does not match this Civar size " + sequence.length() + " != " + minSeqLen);
+        if (sequenceLength < minSeqLen)
+            throw new IllegalArgumentException("the sequence provided is too small for this Civar " + sequence.length() + " < " + minSeqLen);
+        int starCount = starCount();
+        int paddingTotal = sequenceLength - minSeqLen;
+        int starPadding = starCount == 0 ? 0 : paddingTotal / starCount;
+        int excessPadding = starCount == 0 ? paddingTotal : paddingTotal % starCount;
+        int nextInSeq = 0;
+        int nextElement = 0;
+
+        int outputLength = 0;
+        while (nextInSeq < sequenceLength && nextElement < elements().size()) {
+            final Element e = elements().get(nextElement++);
+            final int outputStart = outputLength;
+            final int sequenceStart = nextInSeq;
+            int size = e.expands() ? starPadding * e.size() : e.size();
+            if (e.expands() && excessPadding != 0) {
+                size++;
+                excessPadding--;
+            }
+            switch (e.operator()) {
+                case EMBEDDED:
+                    throw new IllegalStateException("supposed to be unrolled Civar");
+                case DELETION:
+                    nextInSeq += size;
+                    break;
+                case INSERTION:
+                    outputLength += size;
+                    break;
+                default:
+                    outputLength += size;
+                    nextInSeq += size;
+                    break;
+            }
+            final int outputEnd = outputLength;
+            final int sequenceEnd = nextInSeq;
+            if (outputEnd > from && outputStart < to) {
+                result.add(new ElementOffset(e,Math.max(outputStart - from,0),
+                      Math.min(outputEnd - from, to -from),
+                      sequenceStart + Math.max(from - outputStart,0),
+                      sequenceEnd - Math.max(outputEnd - to,0)));
+            }
+        }
+        if (nextInSeq != sequenceLength) {
+            throw new IllegalStateException("probable bug: mismatched sequence and Civar application length " + nextInSeq + " != " + to);
+        }
+        return result;
+    }
+
+    public String applyTo(final CharSequence seq, final int from, final int to) {
+
+        final CharSequence sequence = seq.subSequence(from, to);
+        if (!isUnrolled())
+            throw new UnsupportedOperationException("you cannot apply an unrolled Civar to a DNA sequence");
+
+        int referenceLength = sequence.length();
+        int minSeqLen = minimumTemplateSequenceSize();
+        if (!expands() && referenceLength != minSeqLen)
+            throw new IllegalArgumentException("the sequence provided does not match this Civar size " + sequence.length() + " != " + minSeqLen);
+        if (referenceLength < minSeqLen)
+            throw new IllegalArgumentException("the sequence provided is too small for this Civar " + sequence.length() + " < " + minSeqLen);
+        int starCount = starCount();
+        int paddingTotal = referenceLength - minSeqLen;
+        int starPadding = starCount == 0 ? 0 : paddingTotal / starCount;
+        int excessPadding = starCount == 0 ? paddingTotal : paddingTotal % starCount;
+        int nextInSeq = 0;
+        int nextElement = 0;
+
+        final StringBuffer sb = new StringBuffer(sequence.length() * 2);
+        while (nextInSeq < to && nextElement < elements.size()) {
+            final Element e = elements.get(nextElement++);
+            int size = e.expands() ? starPadding * e.size() : e.size();
+            if (e.expands() && excessPadding != 0) {
+                size++;
+                excessPadding--;
+            }
+            switch (e.operator()) {
+                case EMBEDDED:
+                    throw new IllegalStateException("supposed to be unrolled Civar");
+                case MATCH:
+                    sb.append(sequence.subSequence(nextInSeq, nextInSeq += size));
+                    break;
+                case DELETION:
+                    nextInSeq += size;
+                    break;
+                case INSERTION:
+                    final CharSequence xmer = e.xmer().toString().toUpperCase();
+                    while (size >= xmer.length()) {
+                        sb.append(xmer);
+                        size -= xmer.length();
+                    }
+                    sb.append(xmer.subSequence(0, size));
+                    break;
+                case TRANSITION:
+                    transition(sequence, nextInSeq, sb, size);
+                    nextInSeq += size;
+                    break;
+                case TRANSVERSION:
+                    transversion(sequence, nextInSeq, sb, size);
+                    nextInSeq += size;
+                    break;
+                case COMPLEMENT:
+                    complement(sequence, nextInSeq, sb, size);
+                    nextInSeq += size;
+                    break;
+            }
+        }
+        if (nextInSeq != referenceLength) {
+            throw new IllegalStateException("probable bug: mismatched sequence and Civar application length " + nextInSeq + " != " + to);
+        }
+        return sb.toString();
+    }
+
+
+    private static char transversion(final char c) {
+        switch (Character.toUpperCase(c)) {
+            case 'A':
+                return 'C';
+            case 'G':
+                return 'T';
+            case 'C':
+                return 'A';
+            case 'T':
+                return 'G';
+            default:
+                return c;
+        }
+    }
+
+    private static char complement(final char c) {
+        switch (Character.toUpperCase(c)) {
+            case 'A':
+                return 'T';
+            case 'G':
+                return 'C';
+            case 'T':
+                return 'A';
+            case 'C':
+                return 'G';
+            default:
+                return c;
+        }
+
+    }
+
+    private static char transition(final char c) {
+        switch (Character.toUpperCase(c)) {
+            case 'A':
+                return 'G';
+            case 'G':
+                return 'A';
+            case 'T':
+                return 'C';
+            case 'C':
+                return 'T';
+            default:
+                return c;
+        }
+
+    }
+
+    private void transition(final CharSequence charSequence, final int from, final StringBuffer dest, final int length) {
+        for (int i = from; i < length + from; i++) {
+            dest.append(transition(charSequence.charAt(i)));
+        }
+    }
+
+    private void transversion(final CharSequence cs, final int from, final StringBuffer dest, final int length) {
+        for (int i = from; i < length + from; i++) {
+            dest.append(transversion(cs.charAt(i)));
+        }
+    }
+
+    private void complement(final CharSequence cs, final int from, final StringBuffer dest, final int length) {
+        for (int i = from; i < length + from; i++) {
+            dest.append(complement(cs.charAt(i)));
+        }
+    }
+
+    private static List<Element> cle(final List<Element> original) {
+        if (original.size() == 0)
+            return original;
+        if (original.size() == 1) {
+            final Element e = original.get(0);
+            if (e.operator() == Operator.EMBEDDED) {
+                return original;
+            } else if (e.size() == 0) {
+                return Collections.emptyList();
+            } else {
+                return original;
+            }
+        } else {
+            final ArrayList<Element> result = new ArrayList<>(original);
+            for (int i = 0; i < result.size(); ) {
+                final Element e = result.get(i);
+                if (e.operator() == Operator.EMBEDDED) {
+                    i++;
+                } else if (e.size() == 0) {
+                    result.remove(i);
+                } else if (i == result.size() - 1) {
+                    i++;
+                } else {
+                    final Element next = result.get(i + 1);
+                    if (next.operator() != e.operator()) {
+                        i++;
+                    } else if (e.operator() != Operator.INSERTION) {
+                        if (next.expands() == e.expands()) {
+                            result.remove(i + 1);
+                            result.set(i, new Element(e.operator(), e.size() + next.size(), e.expands(), false, null));
+                        } else if (e.expands()) {
+                            int j;
+                            for (j = i + 1; j < result.size(); j++) {
+                                if (result.get(j).operator() == Operator.MATCH && result.get(j).expands()) {
+                                    break;
+                                }
+                            }
+                            result.add(j, e);
+                            result.remove(i);
+                        }
+                    } else {         // INSERTION my be fussed if their sizes correspond to the xmers without expansions
+                        if (!e.expands() && !next.expands() && e.xmer().length() == e.size() && next.xmer().length() == next.size()) {
+                            result.remove(i + 1);
+                            result.set(i, new Element(Operator.INSERTION, e.size() + next.size(), false,  false, e.xmer().toString() + next.xmer().toString()));
+                        }
+                    }
+                }
+            }
+            return result;
+        }
+    }
+
+
+    protected void analyzeCivar() {
+        int minimumTemplateSize = 0;
+        boolean expands = false;
+        int starCount = 0;
+        boolean hasEmbeddedCivars = false;
+        boolean hasOptionalElements = false;
+        boolean allElementsAreOptional = true;
+        boolean hasVariation = false;
+        StringBuffer strBuffer = new StringBuffer(100);
+        for (final Element e : elements) {
+            strBuffer.append(e.toString());
+            if (e.operator() == Operator.EMBEDDED) {
+                hasEmbeddedCivars = true;
+                if (e.embedded.hasVariation()) {
+                    hasVariation = true;
+                    allElementsAreOptional &= (e.optional || e.embedded.allElementsAreOptional());
+                    hasOptionalElements |= e.optional || e.embedded.hasOptionalVariationElements();
+                }
+                minimumTemplateSize += e.embedded.minimumTemplateSequenceSize();
+                if (e.embedded.expands()) {
+                    expands = true;
+                    starCount += e.embedded.starCount();
+                }
+            } else {
+                if (e.isVariant()) {
+                    hasVariation = true;
+                    allElementsAreOptional &= e.optional;
+                    hasOptionalElements |= e.optional;
+                }
+                if (e.expands()) {
+                    starCount += e.size();
+                    expands = true;
+                    continue;
+                }
+                if (e.operator() == Operator.INSERTION)
+                    continue;
+                minimumTemplateSize += e.size();
+            }
+        }
+        this.string = strBuffer.toString();
+        this.hasVariation = hasVariation;
+        this.allVariationIsOptional = allElementsAreOptional;
+        this.hasOptionalVariation = hasOptionalElements;
+        this.hasEmbeddedCivars = hasEmbeddedCivars;
+        this.starCount = starCount;
+        this.expands = expands;
+        this.minimumTemplateSize = minimumTemplateSize;
+    }
+
+    public boolean isUnrolled() {
+        return !hasOptionalVariationElements();
+    }
+
+    public boolean hasVariation() {
+        if (hasVariation == null)
+            analyzeCivar();
+        return hasVariation;
+    }
+
+    private boolean hasOptionalVariationElements() {
+        if (hasOptionalVariation == null)
+            analyzeCivar();
+        return hasOptionalVariation;
+    }
+
+    private int starCount() {
+        if (starCount == -1)
+            analyzeCivar();
+        return starCount;
+    }
+
+    public List<Element> elements() {
+        return elements;
+    }
+
+
+    public enum Operator {
+
+        MATCH('='), INSERTION('I'), DELETION('D'), TRANSITION('T'), EMBEDDED('('),
+
+        /**
+         * Transversion that is not to the complement nucleotide
+         */
+        TRANSVERSION('V'),
+
+        /**
+         * Transverison to the complement nucleotide A <-> T or C <-> G
+         */
+        COMPLEMENT('C'),
+
+        /**
+         * Marks
+         */
+        START('^'), END('$');
+
+        public final char charValue;
+
+        Operator(final char c) {
+            charValue = c;
+        }
+
+        /**
+         * Does this operator represents a SNP.
+         *
+         * @return <code>true</code> is so, <code>false</code> otherwise.
+         */
+        public boolean isSnp() {
+            switch (this) {
+                case TRANSITION:
+                case TRANSVERSION:
+                case COMPLEMENT:
+                    return true;
+                default:
+                    return false;
+            }
+        }
+
+        /**
+         * Checks whether the operation requires an x-mer.
+         *
+         * @return <code>true</code> if so, <code>false</code> otherwise
+         */
+        public boolean requiresXmer() {
+            return this == INSERTION;
+        }
+
+        public boolean acceptsXmer() {
+            return this == INSERTION;
+        }
+
+        public static Operator fromChar(final char c) {
+            switch (c) {
+                case 'I':
+                    return INSERTION;
+                case 'V':
+                    return TRANSVERSION;
+                case 'T':
+                    return TRANSITION;
+                case 'C':
+                    return COMPLEMENT;
+                case 'M':
+                case '=':
+                    return MATCH;
+                case '?':
+                    return START;
+                case '$':
+                    return END;
+                case 'D':
+                    return DELETION;
+                default:
+                    throw new IllegalArgumentException("the chacter " + c + " does not denote a valid Civar operator");
+            }
+        }
+    }
+
+
+    public static class Element implements Cloneable {
+
+        protected int size;
+        protected boolean expands;
+        protected Operator o;
+
+        protected CharSequence xmer;
+        protected Civar embedded;
+        protected boolean optional;
+
+
+        public Element(final Civar c, boolean optional) {
+            this(Operator.EMBEDDED, 1, false, optional);
+            embedded = c;
+        }
+
+        @Override
+        protected Element clone() {
+            try {
+                return (Element) super.clone();
+            } catch (CloneNotSupportedException e) {
+                throw new RuntimeException("unexpected exception ", e);
+            }
+        }
+
+
+        /**
+         * Calculate the length provided the the length of the padding unit and how much
+         * exceed padding is still available.
+         *
+         * @param starPadding
+         * @param excessPaddingRemaining
+         *
+         * @return never {@code null}.
+         */
+        public int size(final int starPadding, final int excessPaddingRemaining) {
+            if (!expands)
+                return size;
+            else
+                return size * (starPadding) + Math.min(excessPaddingRemaining,size);
+        }
+
+        /**
+         * Returns the size of this element.
+         * <p/>
+         * If the element is non-explandable this value is the exact size of the indicated operation in term of bases
+         * (deleted, inserted, changed, etc...)
+         * <p/>
+         * If the element is expandable, this is relative size respect with other expandable elements.
+         *
+         * @return never negative, and typically greater than 0; 0 would be use for possible future symbolic operands.
+         */
+        public int size() {
+            return size;
+        }
+
+        /**
+         * Checks whether this is an expandable element.
+         *
+         * @return <code>true</code> if so, <code>false</code> otherwise.
+         */
+        public boolean expands() {
+            return expands;
+        }
+
+        public boolean isOptional() {
+            return optional;
+        }
+
+        /**
+         * Returns the appendix sequence for those elements for which it applies.
+         *
+         * @return never <code>null</code> but perhaps an empty sequence. You must not attempt to modify the returned element.
+         */
+        public CharSequence xmer() {
+            return xmer;
+        }
+
+
+        /**
+         * Returns the operator for this element.
+         *
+         * @return never <code>null</code>.
+         */
+        public Operator operator() {
+            return o;
+        }
+
+        protected Element(final Operator o, final int size, final boolean expands, final boolean optional) {
+            if (o == null)
+                throw new IllegalArgumentException("operator cannot be null");
+            if (size < 0)
+                throw new IllegalArgumentException("element size cannot be negative");
+            this.o = o;
+            this.optional = optional;
+            this.expands = expands;
+            this.size = size;
+        }
+
+        /**
+         * Constructs an element given its properties.
+         *
+         * @param o       the operator for this element.
+         * @param size    the size of the element
+         * @param expands if the element is expandable.
+         * @param xmer    the xmer for this element.
+         */
+        public Element(final Operator o, final int size, final boolean expands, final boolean optional, final String xmer) {
+            this(o,size,expands,optional);
+            if ((xmer == null || xmer.length() == 0) && o.requiresXmer())
+                throw new IllegalArgumentException("operator  " + o + " requires a x-mer");
+            if ((xmer != null && !o.acceptsXmer()))
+                throw new IllegalArgumentException("operator  " + o + " does not accept a x-mer");
+            this.xmer = xmer;
+        }
+
+        public String toString() {
+            if (operator() == Operator.EMBEDDED) {
+                return "(" + embedded.toString() + ")";
+            }
+            final String sizeString = expands ? (size == 1 ? "*":"" + size) : ("" + size);
+            final String sizeAndOperator = sizeString + operator().charValue;
+            final String sizeAndOperatorAndXmer = o == Operator.INSERTION ? sizeAndOperator + xmer : sizeAndOperator;
+            return optional ? sizeAndOperatorAndXmer + "?" : sizeAndOperatorAndXmer;
+        }
+
+        protected void makeOptional() {
+            if (o != Operator.MATCH)
+                optional = true;
+        }
+
+        public boolean isVariant() {
+            switch (o) {
+                case MATCH: return false;
+                default:
+                    return true;
+            }
+        }
+
+        private Element matchEquivalent() {
+            switch (o) {
+                case MATCH: return this;
+                case INSERTION: return new Element(Operator.MATCH,0,false,false);
+                case EMBEDDED:
+                    int mtss = embedded.minimumTemplateSequenceSize();
+                    int sc = embedded.starCount();
+                    if (mtss > 0) {
+                        if (sc > 0) {
+                            final Civar newEmbedded = new Civar(Collections.unmodifiableList(Arrays.asList(
+                                    new Element(Operator.MATCH,mtss,false,false),new Element(Operator.MATCH,sc,true,false))));
+                            //newEmbedded.string = newEmbedded.elements.get(0).toString() + newEmbedded.elements.get(1).toString();
+                            return new Element(newEmbedded,false);
+                        } else {
+                            return new Element(Operator.MATCH,mtss,false,false);
+                        }
+                    } else if (sc > 0) {
+                        return new Element(Operator.MATCH,sc,true,false);
+
+                    } else {
+                        return new Element(Operator.MATCH,0,false,false);
+                    }
+                default:
+                    return new Element(Operator.MATCH,size,expands,false);
+            }
+        }
+
+        public Element mandatoryEquivalent() {
+            final Element result = this.clone();
+            result.optional = false;
+            return result;
+        }
+
+        public int excessPaddingUsed(final int excessPadding) {
+            return expands ? Math.min(excessPadding,size) : 0;
+        }
+    }
+
+    protected static class Parser {
+
+        public static Civar parse(final CharSequence cs, final int from, final int to) {
+            if (cs == null)
+                throw new NullPointerException("the input char-sequence cannot be null");
+            if (from < 0)
+                throw new IndexOutOfBoundsException("the from index cannot be negative");
+            if (to < from)
+                throw new IllegalArgumentException("the to index cannot less than the from index");
+            if (to > cs.length())
+                throw new IllegalArgumentException("the to index cannot be greater than the end of the sequence");
+            if (cs == null)
+                throw new IllegalArgumentException("cs cannot be null");
+
+            final String s = cs.subSequence(from, to).toString();
+            final LinkedList<Token> tokens = tokenize(s, 0, s.length());
+            final LinkedList<Element> elements = elementize(tokens, s);
+            final Civar result;
+            if (elements.size() == 0) {
+                result = new Civar((List<Element>) (List) Collections.emptyList());
+            } else if (elements.size() == 1) {
+                result = new Civar(Collections.singletonList(elements.getFirst()));
+            } else {
+                result = new Civar(Collections.unmodifiableList(Arrays.asList(elements.toArray(new Element[elements.size()]))));
+            }
+            //result.string = s;
+            return result;
+        }
+
+        @Requires("tokens != null")
+        private static LinkedList<Element> elementize(final LinkedList<Token> tokens, final CharSequence cs) {
+            LinkedList<Element> elements = new LinkedList<>();
+            Stack<Token> stack = new Stack<>();
+            while (!tokens.isEmpty()) {
+                Token nextToken = tokens.pollFirst();
+                stack.push(nextToken);
+                switch (nextToken.type) {
+                    case OPERATOR:
+                        if (nextToken.asOperator() == Operator.INSERTION) break;
+                        stack.push(Token.element(popOperation(stack, null,cs)));
+                        break;
+                    case XMER:
+                        stack.push(Token.element(popOperation(stack, stack.pop().asXmer(),cs)));
+                        break;
+                    case CLOSE_BRACKET:
+                        stack.push(Token.element(popEmbedded(stack, cs)));
+                        break;
+                    case QMARK:
+                        stack.pop();
+                        final Token t;
+                        stack.push(t = Token.element(popOperation(stack,null,cs)));
+                        t.asElement().makeOptional();
+                        break;
+                    default:
+                }
+            }
+
+            for (int i = 0; i < stack.size(); i++) {
+                final Token t = stack.get(i);
+                if (t.type == TokenType.ELEMENT) {
+                    elements.add(t.asElement());
+                } else if (t.type == TokenType.STAR) {
+                    elements.add(new Element(Operator.MATCH,1,true, false, null));
+                } else if (t.type == TokenType.NUMBER) {
+                    if (i < stack.size() - 1) {
+                        if (stack.get(i+1).type == TokenType.STAR) {
+                            elements.add(new Element(Operator.MATCH,t.asNumber(),true, false, null));
+                            i++;
+                        } else {
+                            elements.add(new Element(Operator.MATCH,t.asNumber(),false, false, null));
+                        }
+                    } else {
+                        elements.add(new Element(Operator.MATCH,t.asNumber(),false, false, null));
+                    }
+                } else {
+                   throw new IllegalArgumentException("Invalid Civar string: " + cs);
+                }
+            }
+            return elements;
+        }
+
+        private static Element popEmbedded(final Stack<Token> stack, final CharSequence cs) {
+            Token closeBracket = stack.pop();// remove close parentesis.
+            LinkedList<Element> embeddedElements = new LinkedList<>();
+            while (!stack.isEmpty()) {
+                final Token nextToken = stack.pop();
+                if (nextToken.type == TokenType.OPEN_BRACKET) {
+                    final Civar embeddedCivar = new Civar(Collections.unmodifiableList(embeddedElements));
+                    //embeddedCivar.string = cs.subSequence(nextToken.asNumber() + 1, closeBracket.asNumber()).toString();
+                    return new Element(embeddedCivar,false);
+                } else if (nextToken.type != TokenType.ELEMENT) {
+                    throw new IllegalArgumentException("Civar format error");
+                } else {
+                    embeddedElements.add(0, nextToken.asElement());
+                }
+            }
+            throw new IllegalArgumentException("Civar format error");
+        }
+
+        private static Element popOperation(final Stack<Token> stack, final String xmer, final CharSequence cs) {
+            if (stack.isEmpty()) {
+                throw new IllegalArgumentException("Invalid Civar string: " + cs);
+            }
+            Token operator = stack.pop();
+            if (operator.type == TokenType.ELEMENT) {
+                return operator.asElement();
+            }
+            if (operator.type != TokenType.OPERATOR) {
+                throw new IllegalArgumentException("Invalid Civar string:" + operator.type +  " " + cs);
+            }
+            if (stack.isEmpty()) {
+                return new Element(operator.asOperator(), 1, false, false, xmer);
+            } else {
+                Token sizeOrStar = stack.pop();
+                if (sizeOrStar.type == TokenType.STAR) {
+                    if (stack.isEmpty()) {
+                        return new Element(operator.asOperator(), 1, true, false, xmer);
+                    } else if (stack.peek().type == TokenType.NUMBER) {
+                        return new Element(operator.asOperator(), stack.pop().asNumber(), true, false, xmer);
+                    } else {
+                        return new Element(operator.asOperator(), 1, true, false, xmer);
+                    }
+                } else if (sizeOrStar.type == TokenType.NUMBER) {
+                    return new Element(operator.asOperator(), sizeOrStar.asNumber(), false, false, xmer);
+                } else {
+                    stack.push(sizeOrStar);
+                    return new Element(operator.asOperator(), 1, false, false, xmer);
+                }
+            }
+        }
+
+
+        private static LinkedList<Token> tokenize(final CharSequence cs, final int from, final int to) {
+            final LinkedList<Token> tokens = new LinkedList<>();
+            int i = from;
+            while (i < to) {
+                char c = cs.charAt(i++);
+                // NUMBER tokens
+                if (Character.isDigit(c)) {
+                    int num = 0;
+                    do {
+                        num = num * 10 + (c - '0');
+                        if (i == to)
+                            break;
+                        c = cs.charAt(i++);
+                    }
+                    while (Character.isDigit(c) || (i-- == 0)); // || (i-- == 0) is a trick to "pushback" the first non digit character.
+                    tokens.add(Token.number(num));
+                } else if (c == '*') {
+                    tokens.add(Token.star());
+                } else if (c == '(') {
+                    tokens.add(Token.openBracket(i - 1));
+                } else if (c == ')') {
+                    tokens.add(Token.closeBracket(i - 1));
+                } else if (c == '?') {
+                    tokens.add(Token.qmark());
+                } else if (c == '=') {
+                    tokens.add(Token.operator(Operator.MATCH));
+                } else if (Character.isLetter(c)) {
+                    if (Character.isUpperCase(c)) {
+                        tokens.add(Token.operator(Operator.fromChar(c)));
+                    } else {
+                        int start = i - 1;
+                        do {
+                            if (i == to)
+                                break;
+                            c = cs.charAt(i++);
+                        } while (Character.isLowerCase(c) || (i-- == 0));
+                        tokens.add(Token.xmer(cs.subSequence(start, i)));
+                    }
+                } else {
+                    throw new IllegalArgumentException("the Civar string contains invalid characters starting with '" + c + '"');
+                }
+            }
+            return tokens;
+        }
+
+
+        public Civar parse(final CharSequence cs) {
+            if (cs == null)
+                throw new IllegalArgumentException("cs cannot be null");
+            return parse(cs, 0, cs.length());
+        }
+
+
+    }
+
+    /**
+     * Transforms a civar into the equivalent Cigar.
+     * @return never {@code null}.
+     */
+    public Cigar toCigar(final int templateLength) {
+
+        int minSeqLen = minimumTemplateSequenceSize();
+        if (!expands() && templateLength != minSeqLen)
+            throw new IllegalArgumentException("the sequence provided does not match this Civar size " + templateLength + " != " + minSeqLen);
+        if (templateLength < minSeqLen)
+            throw new IllegalArgumentException("the sequence provided is too small for this Civar " + templateLength + " < " + minSeqLen);
+        int starCount = starCount();
+        int paddingTotal = templateLength - minSeqLen;
+        int starPadding = starCount == 0 ? 0 : paddingTotal / starCount;
+        int excessPadding = starCount == 0 ? paddingTotal : paddingTotal % starCount;
+
+       // We first get the equivalent cigar elements for the elements in the Civar.
+       final List<CigarElement> cigarElements = new LinkedList<>();
+
+       for (final Element e : this.elements()) {
+            final int size = e.size(starPadding,excessPadding);
+            excessPadding -= e.excessPaddingUsed(excessPadding);
+
+            switch (e.operator()) {
+                case EMBEDDED:
+                    cigarElements.addAll(e.embedded.toCigar(size).getCigarElements());
+                    break;
+                case MATCH:
+                case TRANSITION:
+                case COMPLEMENT:
+                case TRANSVERSION:
+                    cigarElements.add(new CigarElement(size, CigarOperator.M));
+                    break;
+                case INSERTION:
+                    cigarElements.add(new CigarElement(size,CigarOperator.I));
+                    break;
+                case DELETION:
+                    cigarElements.add(new CigarElement(size,CigarOperator.D));
+                    break;
+                default:
+            }
+       }
+
+       // No we look for consequitive elements with the same operator and we merge them.
+       final ListIterator<CigarElement> it = cigarElements.listIterator();
+       while (it.hasNext()) {
+            final CigarElement thisElement = it.next();
+            if (!it.hasNext())
+                continue;
+            final CigarElement nextElement = it.next();
+            if (thisElement.getOperator() == nextElement.getOperator()) {
+                final int nextLength = nextElement.getLength();
+                it.remove();
+                it.previous();
+                it.set(new CigarElement(thisElement.getLength() + nextLength, thisElement.getOperator()));
+            } else
+                it.previous();
+       }
+       return new Cigar(cigarElements);
+    }
+
+
+
+    protected static enum TokenType {
+        OPERATOR, XMER, NUMBER, STAR, OPEN_BRACKET, CLOSE_BRACKET, ELEMENT, START, END, QMARK;
+    }
+
+    protected static class Token {
+        public final TokenType type;
+        public final Object content;
+
+        @Requires("type != null && content != null")
+        protected Token(final TokenType type, final Object content) {
+            this.type = type;
+            this.content = content;
+
+        }
+
+        public String toString() {
+            switch (this.type) {
+                case STAR: return "*";
+                case OPEN_BRACKET: return "(";
+                case CLOSE_BRACKET: return ")";
+                default:
+                    return String.valueOf(content);
+            }
+        }
+
+
+        public Operator asOperator() {
+            return (Operator) content;
+        }
+
+        public String asXmer() {
+            return ((CharSequence) content).toString();
+        }
+
+        public int asNumber() {
+            return ((Number) content).intValue();
+        }
+
+        public Element asElement() {
+            return ((Element) content);
+        }
+
+        protected static Token xmer(final CharSequence cs) {
+            return new Token(TokenType.XMER, cs);
+
+        }
+
+        protected static Token operator(final Operator o) {
+            return new Token(TokenType.OPERATOR, o);
+        }
+
+        protected static Token number(final int n) {
+            return new Token(TokenType.NUMBER, n);
+        }
+
+
+
+        protected static Token star() {
+            return new Token(TokenType.STAR, null);
+        }
+
+        protected static Token openBracket(int offset) {
+            return new Token(TokenType.OPEN_BRACKET, offset);
+        }
+
+        protected static Token closeBracket(int offset) {
+            return new Token(TokenType.CLOSE_BRACKET, offset);
+        }
+
+        protected static Token element(final Element e) {
+            return new Token(TokenType.ELEMENT, e);
+        }
+
+
+        public static Token qmark() {
+            return new Token(TokenType.QMARK, null);
+        }
+    }
+
+
+    public static class ElementOffset {
+        public final Element element;
+        public final int sequenceFrom;
+        public final int sequenceTo;
+        public final int templateFrom;
+        public final int templateTo;
+
+
+        @Requires("e != null && from >= 0 && to >= from && tFrom >= 0 && tTo >= tFrom")
+        protected ElementOffset(final Element e, final int from, final int to, final int tFrom, final int tTo) {
+            element = e;
+            sequenceFrom = from;
+            sequenceTo = to;
+            templateFrom = tFrom;
+            templateTo = tTo;
+        }
+    }
+}
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/CivarUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/CivarUnitTest.java
new file mode 100644
index 000000000..10f9a3803
--- /dev/null
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/CivarUnitTest.java
@@ -0,0 +1,401 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+*
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
+
+import org.broadinstitute.sting.BaseTest;
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.Set;
+
+/**
+ * Created with IntelliJ IDEA.
+ * User: valentin
+ * Date: 8/7/13
+ * Time: 5:58 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class CivarUnitTest extends BaseTest {
+
+
+    @Test(dataProvider="validCivarExamples")
+    public void testValidCivarInstanciation(final String civarString) {
+
+        final Civar civar = Civar.fromCharSequence(civarString);
+        Assert.assertNotNull(civar);
+    }
+
+
+    @Test(dataProvider="expectedElementLengths")
+    public void testValidCivarElementLength(final String civarString, final int expected) {
+
+        final Civar civar = Civar.fromCharSequence(civarString);
+        Assert.assertEquals(civar.elements().size(), expected);
+    }
+
+
+    @Test(dataProvider="expectedElementSizes")
+    public void testValidCivarElementSizes(final String civarString, final int[] expected) {
+
+        final Civar civar = Civar.fromCharSequence(civarString);
+        Assert.assertEquals(civar.elements().size(),expected.length);
+        for (int i  = 0; i < expected.length; i++) {
+            Assert.assertEquals(civar.elements().get(i).size(),expected[i]);
+        }
+    }
+
+    @Test(dataProvider="expectedElementOperators")
+    public void testValidCivarElementOperators(final String civarString, final String expected) {
+
+        final Civar civar = Civar.fromCharSequence(civarString);
+        Assert.assertEquals(civar.elements().size(),expected.length());
+        for (int i  = 0; i < expected.length(); i++) {
+            Assert.assertEquals(civar.elements().get(i).operator().charValue,expected.charAt(i));
+        }
+    }
+
+    @Test(dataProvider="expectedMinimumSequenceLength")
+    public void testValidCivarMinimumSequenceLength(final String civarString, final int expected) {
+        final Civar civar = Civar.fromCharSequence(civarString);
+        Assert.assertEquals(civar.minimumTemplateSequenceSize(),expected);
+    }
+
+    @Test(dataProvider="expectedHasVariation")
+    public void testValidCivarHasVariation(final String civarString, final boolean expected) {
+        final Civar civar = Civar.fromCharSequence(civarString);
+        Assert.assertEquals(civar.hasVariation(),expected);
+    }
+
+
+    @Test(dataProvider="invalidCivarExamples", expectedExceptions = {IllegalArgumentException.class})
+    public void testInvalidInstanciation(final String civarString) {
+
+        final Civar civar = Civar.fromCharSequence(civarString);
+    }
+
+    @Test(dataProvider="unrolledTestDataIsUnrolledExamples")
+    public void testInUnrolled(final String civarString, final boolean expected) {
+        final Civar civar = Civar.fromCharSequence(civarString);
+        Assert.assertEquals(civar.isUnrolled(),expected);
+    }
+
+    @Test(dataProvider="unrolledTestDataUnrolledCivarExamples")
+    public void testValidCivarUnrolling(final String civarString, final String[] expected) {
+        Set<String> expectedSet = new HashSet<>();
+        expectedSet.addAll(Arrays.asList(expected));
+
+        final Civar civar = Civar.fromCharSequence(civarString);
+        java.util.List<Civar> unrolledList = civar.unroll();
+        Assert.assertEquals(unrolledList.size(),expected.length);
+        for (int i  = 0; i < expected.length; i++) {
+            Assert.assertTrue(expectedSet.contains(unrolledList.get(i).toString()),
+                    "Unrolled civar " + unrolledList.get(i).toString() + " not present in expected Set: " +
+                            Arrays.toString(expected) + ". Unrolled set is: " + Arrays.toString(unrolledList.toArray()));
+        }
+    }
+
+    @Test(dataProvider="applyToDataExamples")
+    public void testValidCivarUnrolling(final String civarString, final String before, final String expectedAfter) {
+        final Civar civar = Civar.fromCharSequence(civarString);
+        Assert.assertEquals(civar.applyTo(before),expectedAfter);
+    }
+
+    @Test(dataProvider="optionizeDataExamples")
+    public void testValidOptionizeAll(final String civarString, final String expected) {
+        final Civar civar = Civar.fromCharSequence(civarString);
+        Assert.assertEquals(civar.optionalizeAll().toString(),expected);
+    }
+
+    @DataProvider(name="validCivarExamples")
+    public Iterator<Object[]> validCivarExamples() {
+        return new Iterator<Object[]>() {
+
+            int i = 0;
+
+            @Override
+            public boolean hasNext() {
+                return i < VALID_CIVAR_EXAMPLES.length;
+            }
+
+            @Override
+            public Object[] next() {
+                return new Object[] { VALID_CIVAR_EXAMPLES[i++][0] };
+            }
+
+            @Override
+            public void remove() {
+                throw new UnsupportedOperationException();
+            }
+        };
+    }
+
+    @DataProvider(name="expectedHasVariation")
+    public Iterator<Object[]> expectedHasVariation () {
+        return validCivarExamples(5);
+    }
+
+    @DataProvider(name="expectedMinimumSequenceLength")
+    public Iterator<Object[]> expectedMinimumSequenceLength () {
+        return validCivarExamples(4);
+    }
+
+    @DataProvider(name="expectedElementOperators")
+    public Iterator<Object[]> expectedElementOperators() {
+        return validCivarExamples(3);
+    }
+
+    @DataProvider(name="expectedElementSizes")
+    public Iterator<Object[]> expectedElementSizes() {
+        return validCivarExamples(2);
+    }
+
+    @DataProvider(name="expectedElementLengths")
+    public Iterator<Object[]> expectedElementLengths() {
+        return validCivarExamples(1);
+    }
+
+    public Iterator<Object[]> validCivarExamples(final int field) {
+        return new Iterator<Object[]>() {
+
+            int i = 0;
+
+            @Override
+            public boolean hasNext() {
+                return i < VALID_CIVAR_EXAMPLES.length;
+            }
+
+            @Override
+            public Object[] next() {
+                return new Object[] { VALID_CIVAR_EXAMPLES[i][0], VALID_CIVAR_EXAMPLES[i++][field] };
+            }
+
+            @Override
+            public void remove() {
+                throw new UnsupportedOperationException();
+            }
+        };
+    }
+
+    @DataProvider(name="unrolledTestDataIsUnrolledExamples")
+    public Iterator<Object[]> unrolledTestDataIsUnrolledExamples() {
+        return unrolledTestDataExamples(1);
+    }
+
+    @DataProvider(name="unrolledTestDataUnrolledCivarExamples")
+    public Iterator<Object[]> unrolledTestDataUnrolledCivarExamples() {
+        return unrolledTestDataExamples(2);
+    }
+
+    public Iterator<Object[]> unrolledTestDataExamples(final int field) {
+        return new Iterator<Object[]>() {
+
+            int i = 0;
+
+            @Override
+            public boolean hasNext() {
+                return i < UNROLLED_TEST_DATA.length;
+            }
+
+            @Override
+            public Object[] next() {
+                return new Object[] { UNROLLED_TEST_DATA[i][0], UNROLLED_TEST_DATA[i++][field] };
+            }
+
+            @Override
+            public void remove() {
+                throw new UnsupportedOperationException();
+            }
+        };
+    }
+
+    @DataProvider(name="optionizeDataExamples")
+    public Iterator<Object[]> optionizeDataExamples() {
+        return optionizeDataExamples(1);
+    }
+
+    public Iterator<Object[]> optionizeDataExamples(final int field) {
+        return new Iterator<Object[]>() {
+
+            int i = 0;
+
+            @Override
+            public boolean hasNext() {
+                return i < OPTIONIZED_TEST_DATA.length;
+            }
+
+            @Override
+            public Object[] next() {
+                return new Object[] { OPTIONIZED_TEST_DATA[i][0], OPTIONIZED_TEST_DATA[i++][field] };
+            }
+
+            @Override
+            public void remove() {
+                throw new UnsupportedOperationException();
+            }
+        };
+    }
+
+    @DataProvider(name="applyToDataExamples")
+    public Iterator<Object[]> applyToDataExamples() {
+        return new Iterator<Object[]>() {
+
+            int i = 0;
+
+            @Override
+            public boolean hasNext() {
+                return i < APPLY_TO_TEST_DATA.length;
+            }
+
+            @Override
+            public Object[] next() {
+                return APPLY_TO_TEST_DATA[i++];
+            }
+
+            @Override
+            public void remove() {
+                throw new UnsupportedOperationException();
+            }
+        };
+    }
+
+    @DataProvider(name="invalidCivarExamples")
+    public Object[][] invalidCivarExamples() {
+            return INVALID_CIVAR_EXAMPLES;
+    }
+
+    // columns : Civar string, number of elements.
+    private static final Object[][] INVALID_CIVAR_EXAMPLES = new Object[][] {
+            {"(100="},
+            {"*=)"},
+            {"10(=2T30="},
+            {"2*=2T/3*="},
+            {"3I(acc)"},
+            {"a"},
+            {")"},
+            {"100&=1"},
+            {"?100="},
+
+    };
+
+
+    private static final Object[][] VALID_CIVAR_EXAMPLES = new Object[][] {
+            {"100=", 1, ints(100), "=", 100, false },
+            {"*=", 1 , ints(1), "=", 0, false },
+            {"10=2T30=", 3, ints(10,2,30), "=T=",42 , true},
+            {"*=2T3*=", 3, ints(1,2,3), "=T=",2 , true},
+            {"3Iacc",1 , ints(3), "I", 0, true},
+            {"Ia",1, ints(1), "I", 0, true},
+            {"10D",1, ints(10), "D", 10, true},
+            {"*", 1, ints(1), "=", 0, false},
+            {"*D", 1, ints(1), "D", 0, true},
+            {"10(1D)10=",3, ints(10,1,10), "=(=", 21, true},
+            {"1*",1, ints(1), "=", 0, false},
+            {"1*2*",2, ints(1,2), "==", 0, false},
+            {"*11",2, ints(1,11), "==", 11, false},
+            {"100=1T100=", 3, ints(100,1,100), "=T=", 201, true},
+            {"100=3Iacg101=", 3, ints(100,3,101), "=I=", 201, true},
+            {"100=30Igctcggatgccttgcggggctccagagtcc101=", 3 , ints(100,30,101), "=I=", 201, true},
+            {"99=3D99=", 3, ints(99,3,99), "=D=", 201, true},
+            {"84=30D84=", 3, ints(84,30,84), "=D=", 198, true},
+            {"91=1T9=3Iacg100=", 5, ints(91,1,9,3,100), "=T=I=", 201, true},
+            {"71=1T29=3Iacg100=",5, ints(71,1,29,3,100), "=T=I=",201, true},
+            {"75=1T8=1T8=1T8=1T8=1T75=", 11, ints(75,1,8,1,8,1,8,1,8,1,75), "=T=T=T=T=T=",187, true},
+            {"75=1T?8=", 3, ints(75,1,8), "=T=", 84, true}
+    };
+
+    private static final Object[][] UNROLLED_TEST_DATA = new Object[][] {
+            { "10=1D10=", true, strs( "10=1D10=") },
+            { "10=(1D)10=", true, strs( "10=(1D)10=") },
+            { "10=1D?10=", false, strs("10=1=10=", "10=1D10=") },
+            { "10=1D?10=3Iacg?10=", false , strs("10=1=10=0=10=","10=1=10=3Iacg10=", "10=1D10=0=10=", "10=1D10=3Iacg10=") },
+            {  "10=1D?10=" , false, strs("10=1D10=","10=1=10=") },
+            {  "100=1T?100=" , false, strs("100=1T100=","100=1=100=") },
+            {  "100=3Iacg?101=" , false, strs("100=3Iacg101=","100=0=101=") },
+            {  "100=30Igctcggatgccttgcggggctccagagtcc?101=", false ,strs("100=30Igctcggatgccttgcggggctccagagtcc101=", "100=0=101=") },
+            {  "99=3D?99=", false , strs("99=3D99=","99=3=99=") },
+            {  "84=30D?84=", false, strs("84=30D84=", "84=30=84=")},
+            {  "91=1T?9=3Iacg?100=", false, strs("91=1T9=3Iacg100=", "91=1=9=3Iacg100=", "91=1=9=0=100=", "91=1T9=0=100=") },
+            {  "71=1T?29=3Iacg?100=", false , strs("71=1T29=3Iacg100=","71=1=29=3Iacg100=","71=1=29=0=100=", "71=1T29=0=100=") },
+           // {  "75=1T?8=1T?8=1T?8=1T?8=1T?75=", false, },
+            {  "75=1T?8=", false, strs("75=1T8=","75=1=8=") }
+    };
+
+    private static final Object[][] OPTIONIZED_TEST_DATA = new Object[][] {
+            { "10=1D10=", "10=1D?10=" },
+            {"100=1T100=","100=1T?100=" },
+            {"100=3Iacg101=", "100=3Iacg?101=" },
+            {"100=30Igctcggatgccttgcggggctccagagtcc101=","100=30Igctcggatgccttgcggggctccagagtcc?101="},
+            {"99=3D99=", "99=3D?99="},
+            {"84=30D84=", "84=30D?84="},
+            {"91=1T9=3Iacg100=", "91=1T?9=3Iacg?100="},
+            {"71=1T29=3Iacg100=","71=1T?29=3Iacg?100="},
+            {"75=1T8=1T8=1T8=1T8=1T75=", "75=1T?8=1T?8=1T?8=1T?8=1T?75="},
+            {"75=1T?8=", "75=1T?8="}
+    };
+
+    private static final Object[][] APPLY_TO_TEST_DATA = new Object[][] {
+            {"3=1D3=", "ACTAACT", "ACTACT" },
+            {"*=1C*=","ACTTACT", "ACTAACT" },
+            {"4=3Iacg3=","ACTGACT","ACTGACGACT" },
+            {"*=30Igctcggatgccttgcggggctccagagtcc*=","AA","AGCTCGGATGCCTTGCGGGGCTCCAGAGTCCA"},
+            {"*=3D*=", "ACTTTAC","ACAC"},
+            {"1=30D1=", "AGCTCGGATGCCTTGCGGGGCTCCAGAGTCCA","AA"},
+    };
+
+
+    private static int[] ints(final int ... iii) {
+        return iii;
+    }
+
+    private static String[] strs(final String ... sss) {
+        return sss;
+    }
+
+}
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java
new file mode 100644
index 000000000..a98c4e03a
--- /dev/null
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java
@@ -0,0 +1,131 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+*
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
+
+import com.google.caliper.Param;
+import com.google.caliper.SimpleBenchmark;
+import org.broadinstitute.sting.utils.pairhmm.ActiveRegionTestDataSet;
+import org.broadinstitute.sting.utils.pairhmm.FastLoglessPairHMM;
+import org.broadinstitute.sting.utils.pairhmm.PairHMM;
+
+import java.util.Collections;
+import java.util.Random;
+
+/**
+ * Created with IntelliJ IDEA.
+ * User: valentin
+ * Date: 8/6/13
+ * Time: 3:00 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class HCLikelihoodCalculationEnginesBenchmark extends SimpleBenchmark {
+// ./private/shell/googleCaliperCommand.csh org.broadinstitute.sting.gatk.walkers.haplotypecaller.HCLikelihoodCalculationEnginesBenchmark --saveResults build/benchmark/HCLikelihoodCalculationEnginesBenchmark
+
+//    @Param({"10", "25"})
+    @Param({"10"})
+    protected int kmerSize;
+
+
+//    @Param({"100","250"})
+    @Param({"100"})
+    protected int readLength;
+
+    @Param({"*1T*", "*3Iacg*","*30Igctcggatgccttgcggggctccagagtcc*",
+            "*3D*","*30D*","*1T3=3Iacg*","*1T*3Iacg*","*1T8=1T8=1T8=1T8=1T*","*1T*1T*1T*1T*1T*"})
+//    @Param({"*1T*"})
+    protected String variation;
+
+    @Param({"10000"})
+//    @Param({"100", "300", "1000"})// "3000", "10000"})
+    protected int readCount;
+
+//    @Param({"300","1000","3000"})
+    @Param({"300"})
+    protected int regionSize;
+
+    // Invariants:
+
+    protected final byte bq = 20;
+
+    protected final byte iq = 35;
+
+    protected final byte dq = 35;
+
+    protected ActiveRegionTestDataSet dataSet;
+
+    @Param({"true"})
+    public boolean withErrors;
+
+    @Param({"13"})
+    public int randomSeed;
+
+    public void setUp() {
+       dataSet = ActiveRegionTestDataSetUnitTest.createActiveRegionTestDataSet(kmerSize, readLength, variation, readCount, regionSize, bq, iq, dq);
+       final Random rnd = new Random(randomSeed);
+       if (withErrors) dataSet.introduceErrors(rnd);
+    }
+
+    @SuppressWarnings("unused")
+    public void timeGraphBasedLikelihoods(final int reps) {
+        for (int i = 0; i < reps; i++) {
+            GraphBasedLikelihoodCalculationEngineInstance rtlce = new GraphBasedLikelihoodCalculationEngineInstance(dataSet.assemblyResultSet(), new FastLoglessPairHMM((byte)10),Double.NEGATIVE_INFINITY,HeterogeneousKmerSizeResolution.COMBO_MAX);
+            rtlce.computeReadLikelihoods(dataSet.haplotypeList(), Collections.singletonMap("anonymous", dataSet.readList()));
+        }
+    }
+
+    @SuppressWarnings("unused")
+    public void timeLoglessPairHMM(final int reps) {
+        for (int i = 0; i < reps; i++) {
+            final PairHMMLikelihoodCalculationEngine engine = new PairHMMLikelihoodCalculationEngine((byte) 10, false,
+                    PairHMM.HMM_IMPLEMENTATION.LOGLESS_CACHING, -3, true, PairHMMLikelihoodCalculationEngine.PCR_ERROR_MODEL.NONE);
+            engine.computeReadLikelihoods(dataSet.assemblyResultSet(), Collections.singletonMap("anonymous", dataSet.readList()));
+        }
+    }
+
+
+
+
+}
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index f7056ef58..c27208194 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -91,6 +91,16 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
         HCTest(NA12878_BAM, "", "439ce9024f04aad08eab1526d887e295");
     }
 
+    @Test
+    public void testHaplotypeCallerGraphBasedSingleSample() {
+        HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "213df0bdaa78a695e9336128333e4407");
+    }
+
+    @Test
+    public void testHaplotypeCallerGraphBasedMultiSample() {
+        HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "ceee711cac50b4bb66a084acb9264941");
+    }
+
     @Test(enabled = false) // can't annotate the rsID's yet
     public void testHaplotypeCallerSingleSampleWithDbsnp() {
         HCTest(NA12878_BAM, "-D " + b37dbSNP132, "");
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java
index 9dcc18275..9f13efc9c 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java
@@ -55,10 +55,8 @@ import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.ReadThreadingAssembler;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.UnvalidatingGenomeLoc;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
-import org.broadinstitute.sting.utils.collections.PrimitivePair;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.haplotype.Haplotype;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
@@ -213,7 +211,8 @@ public class LocalAssemblyEngineUnitTest extends BaseTest {
         final ActiveRegion activeRegion = new ActiveRegion(loc, null, true, genomeLocParser, 0);
         activeRegion.addAll(reads);
 //        logger.warn("Assembling " + activeRegion + " with " + engine);
-        return assembler.runLocalAssembly(activeRegion, refHaplotype, refBases, loc, Collections.<VariantContext>emptyList(), null);
+        final AssemblyResultSet assemblyResultSet =  assembler.runLocalAssembly(activeRegion, refHaplotype, refBases, loc, Collections.<VariantContext>emptyList(), null);
+        return assemblyResultSet.getHaplotypeList();
     }
 
     @DataProvider(name = "SimpleAssemblyTestData")
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngineUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java
similarity index 92%
rename from protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngineUnitTest.java
rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java
index 2bbb7c725..1b63f2971 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngineUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java
@@ -68,9 +68,9 @@ import org.testng.annotations.Test;
 import java.util.*;
 
 /**
- * Unit tests for LikelihoodCalculationEngine
+ * Unit tests for PairHMMLikelihoodCalculationEngine
  */
-public class LikelihoodCalculationEngineUnitTest extends BaseTest {
+public class PairHMMLikelihoodCalculationEngineUnitTest extends BaseTest {
 
     Allele Aref, T, C, G, Cref, ATC, ATCATC;
 
@@ -100,7 +100,7 @@ public class LikelihoodCalculationEngineUnitTest extends BaseTest {
         };
 
 
-        Assert.assertTrue(compareDoubleArrays(LikelihoodCalculationEngine.normalizeDiploidLikelihoodMatrixFromLog10(likelihoodMatrix), normalizedMatrix));
+        Assert.assertTrue(compareDoubleArrays(PairHMMLikelihoodCalculationEngine.normalizeDiploidLikelihoodMatrixFromLog10(likelihoodMatrix), normalizedMatrix));
 
         double[][] likelihoodMatrix2 = {
                 {-90.2,     0,      0,        0},
@@ -114,7 +114,7 @@ public class LikelihoodCalculationEngineUnitTest extends BaseTest {
                 {-4.9,  -15.4,  -33.8,        0},
                 {-4.9,  -15.4,  -33.8,   -997.9},
         };
-        Assert.assertTrue(compareDoubleArrays(LikelihoodCalculationEngine.normalizeDiploidLikelihoodMatrixFromLog10(likelihoodMatrix2), normalizedMatrix2));
+        Assert.assertTrue(compareDoubleArrays(PairHMMLikelihoodCalculationEngine.normalizeDiploidLikelihoodMatrixFromLog10(likelihoodMatrix2), normalizedMatrix2));
     }
 
     @DataProvider(name = "PcrErrorModelTestProvider")
@@ -133,30 +133,31 @@ public class LikelihoodCalculationEngineUnitTest extends BaseTest {
     @Test(dataProvider = "PcrErrorModelTestProvider", enabled = true)
     public void createPcrErrorModelTest(final String repeat, final int repeatLength) {
 
-        final LikelihoodCalculationEngine engine = new LikelihoodCalculationEngine((byte)0, false, PairHMM.HMM_IMPLEMENTATION.ORIGINAL, 0.0, true, LikelihoodCalculationEngine.PCR_ERROR_MODEL.CONSERVATIVE);
+        final PairHMMLikelihoodCalculationEngine engine = new PairHMMLikelihoodCalculationEngine((byte)0, false,
+                PairHMM.HMM_IMPLEMENTATION.ORIGINAL, 0.0, true,
+                PairHMMLikelihoodCalculationEngine.PCR_ERROR_MODEL.CONSERVATIVE);
 
         final String readString = Utils.dupString(repeat, repeatLength);
         final byte[] insQuals = new byte[readString.length()];
         final byte[] delQuals = new byte[readString.length()];
-        Arrays.fill(insQuals, (byte)LikelihoodCalculationEngine.INITIAL_QSCORE);
-        Arrays.fill(delQuals, (byte)LikelihoodCalculationEngine.INITIAL_QSCORE);
+        Arrays.fill(insQuals, (byte)PairHMMLikelihoodCalculationEngine.INITIAL_QSCORE);
+        Arrays.fill(delQuals, (byte)PairHMMLikelihoodCalculationEngine.INITIAL_QSCORE);
 
         engine.applyPCRErrorModel(readString.getBytes(), insQuals, delQuals);
 
         final RepeatCovariate repeatCovariate = new RepeatLengthCovariate();
-        repeatCovariate.initialize(LikelihoodCalculationEngine.MAX_STR_UNIT_LENGTH, LikelihoodCalculationEngine.MAX_REPEAT_LENGTH);
+        repeatCovariate.initialize(PairHMMLikelihoodCalculationEngine.MAX_STR_UNIT_LENGTH, PairHMMLikelihoodCalculationEngine.MAX_REPEAT_LENGTH);
 
         for ( int i = 1; i < insQuals.length; i++ ) {
 
             final int repeatLengthFromCovariate = repeatCovariate.findTandemRepeatUnits(readString.getBytes(), i-1).getSecond();
-            final byte adjustedScore = LikelihoodCalculationEngine.getErrorModelAdjustedQual(repeatLengthFromCovariate, 3.0);
+            final byte adjustedScore = PairHMMLikelihoodCalculationEngine.getErrorModelAdjustedQual(repeatLengthFromCovariate, 3.0);
 
             Assert.assertEquals(insQuals[i-1], adjustedScore);
             Assert.assertEquals(delQuals[i-1], adjustedScore);
         }
     }
 
-    // BUGBUG: LikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods has changed! Need to make new unit tests!
     /*
     private class BasicLikelihoodTestProvider extends TestDataProvider {
         public Double readLikelihoodForHaplotype1;
@@ -210,7 +211,7 @@ public class LikelihoodCalculationEngineUnitTest extends BaseTest {
             }
             final HashSet<String> sampleSet = new HashSet<String>(1);
             sampleSet.add("myTestSample");
-            return LikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods(sampleSet, haplotypes);
+            return PairHMMLikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods(sampleSet, haplotypes);
         }
     }
 
@@ -335,7 +336,7 @@ public class LikelihoodCalculationEngineUnitTest extends BaseTest {
                 makeG("s2",T,T,60,40,0),
                 makeG("s3",Aref,Aref,0,30,90));
         test1 = new VariantContextBuilder(test1).attribute(VCFConstants.MLE_ALLELE_COUNT_KEY,3).make();
-        VariantContext test1result = LikelihoodCalculationEngine.calculatePosteriorGLs(test1, new ArrayList<VariantContext>(), 0, 0.001, true, false, false);
+        VariantContext test1result = PairHMMLikelihoodCalculationEngine.calculatePosteriorGLs(test1, new ArrayList<VariantContext>(), 0, 0.001, true, false, false);
         Genotype test1exp1 = makeGwithPLs("s1",Aref,T,new double[]{-2.20686, -0.03073215, -1.20686});
         Assert.assertTrue(test1exp1.hasPL());
         Genotype test1exp2 = makeGwithPLs("s2",T,T,new double[]{-6.000066, -3.823938, -6.557894e-05});
@@ -353,7 +354,7 @@ public class LikelihoodCalculationEngineUnitTest extends BaseTest {
                 makeG("s3",Aref,Aref,0,5,8,15,20,40),
                 makeG("s4",C,T,80,40,12,20,0,10));
         test2 = new VariantContextBuilder(test2).attribute(VCFConstants.MLE_ALLELE_COUNT_KEY,new ArrayList<Integer>(Arrays.asList(2,2))).make();
-        VariantContext test2result = LikelihoodCalculationEngine.calculatePosteriorGLs(test2,new ArrayList<VariantContext>(),5,0.001,true,false,false);
+        VariantContext test2result = PairHMMLikelihoodCalculationEngine.calculatePosteriorGLs(test2,new ArrayList<VariantContext>(),5,0.001,true,false,false);
         Genotype test2exp1 = makeGwithPLs("s1",Aref,T,new double[]{-2.647372, -1.045139, -6.823193, -0.04513873, -2.198182, -9.823193});
         Genotype test2exp2 = makeGwithPLs("s2",Aref,C,new double[]{-3.609957, -0.007723248, -1.785778, -3.007723, -4.660767, -8.785778});
         Genotype test2exp3 = makeGwithPLs("s3",Aref,Aref,new double[] {-0.06094877, -0.9587151, -2.03677,-1.958715,  -3.111759, -5.23677});
@@ -375,7 +376,7 @@ public class LikelihoodCalculationEngineUnitTest extends BaseTest {
         supplTest1.add(makeVC("4",Arrays.asList(Aref,T),
                 makeG("s_1",T,T),
                 makeG("s_2",Aref,T)));
-        VariantContext test1result = LikelihoodCalculationEngine.calculatePosteriorGLs(testOverlappingBase,supplTest1,0,0.001,true,false,false);
+        VariantContext test1result = PairHMMLikelihoodCalculationEngine.calculatePosteriorGLs(testOverlappingBase,supplTest1,0,0.001,true,false,false);
         // the counts here are ref=30, alt=14
         Genotype test1exp1 = makeGwithPLs("t1",T,T,new double[]{-3.370985, -1.415172, -0.01721766});
         Genotype test1exp2 = makeGwithPLs("t2",Aref,T,new double[]{-1.763792, -0.007978791, -3.010024});
@@ -386,7 +387,7 @@ public class LikelihoodCalculationEngineUnitTest extends BaseTest {
 
         VariantContext testNonOverlapping = makeVC("1", Arrays.asList(Aref,T), makeG("s1",T,T,3,1,0));
         List<VariantContext> other = Arrays.asList(makeVC("2",Arrays.asList(Aref,C),makeG("s2",C,C,10,2,0)));
-        VariantContext test2result = LikelihoodCalculationEngine.calculatePosteriorGLs(testNonOverlapping,other,0,0.001,true,false,false);
+        VariantContext test2result = PairHMMLikelihoodCalculationEngine.calculatePosteriorGLs(testNonOverlapping,other,0,0.001,true,false,false);
         Genotype test2exp1 = makeGwithPLs("SGV",T,T,new double[]{-4.078345, -3.276502, -0.0002661066});
         Assert.assertEquals(arraysEq(test2exp1.getPL(),_mleparse((List<Integer>) test2result.getGenotype(0).getAnyAttribute(VCFConstants.GENOTYPE_POSTERIORS_KEY))), "");
     }
@@ -514,14 +515,14 @@ public class LikelihoodCalculationEngineUnitTest extends BaseTest {
                 knownCounts[1] = numAlt-altCount;
                 int expected_index = 0;
                 for ( int gl_index = 0; gl_index < likelihood_PLs.length; gl_index++ ) {
-                    double[] post = LikelihoodCalculationEngine.calculatePosteriorGLs(pl2gl(likelihood_PLs[gl_index]), knownCounts, 2);
+                    double[] post = PairHMMLikelihoodCalculationEngine.calculatePosteriorGLs(pl2gl(likelihood_PLs[gl_index]), knownCounts, 2);
                     for ( int i = 0; i < post.length; i++ ) {
                         double expected = expectations[testIndex][expected_index++];
                         double observed = Math.pow(10.0,post[i]);
                         double err = Math.abs( (expected-observed)/expected );
                         Assert.assertTrue(err < 1e-4, String.format("Counts: %s | Expected: %e | Observed: %e | pre %s | prior %s | post %s",
                                 Arrays.toString(knownCounts), expected,observed, Arrays.toString(pl2gl(likelihood_PLs[gl_index])),
-                                Arrays.toString(LikelihoodCalculationEngine.getDirichletPrior(knownCounts,2)),Arrays.toString(post)));
+                                Arrays.toString(PairHMMLikelihoodCalculationEngine.getDirichletPrior(knownCounts,2)),Arrays.toString(post)));
                     }
                 }
                 testIndex++;
@@ -569,17 +570,17 @@ public class LikelihoodCalculationEngineUnitTest extends BaseTest {
         double expected_five[] = new double[] { -9.170334, -5.175724, -6.767055, -0.8250021, -5.126027, -0.07628661, -3.276762,
                 -3.977787, -2.227065, -4.57769, -5.494041, -2.995066, -7.444344, -7.096104, -2.414187};
 
-        double[] post1 = LikelihoodCalculationEngine.calculatePosteriorGLs(pl2gl(PL_one),counts_one,2);
-        double[] post2 = LikelihoodCalculationEngine.calculatePosteriorGLs(pl2gl(PL_two),counts_two,2);
-        double[] post3 = LikelihoodCalculationEngine.calculatePosteriorGLs(pl2gl(PL_three),counts_three,2);
-        double[] post4 = LikelihoodCalculationEngine.calculatePosteriorGLs(pl2gl(PL_four),counts_four,2);
-        double[] post5 = LikelihoodCalculationEngine.calculatePosteriorGLs(pl2gl(PL_five),counts_five,2);
+        double[] post1 = PairHMMLikelihoodCalculationEngine.calculatePosteriorGLs(pl2gl(PL_one),counts_one,2);
+        double[] post2 = PairHMMLikelihoodCalculationEngine.calculatePosteriorGLs(pl2gl(PL_two),counts_two,2);
+        double[] post3 = PairHMMLikelihoodCalculationEngine.calculatePosteriorGLs(pl2gl(PL_three),counts_three,2);
+        double[] post4 = PairHMMLikelihoodCalculationEngine.calculatePosteriorGLs(pl2gl(PL_four),counts_four,2);
+        double[] post5 = PairHMMLikelihoodCalculationEngine.calculatePosteriorGLs(pl2gl(PL_five),counts_five,2);
 
         double[] expecPrior5 = new double[] {-4.2878195, -4.2932090, -4.8845400, -1.9424874, -2.2435120, -0.1937719, -3.5942477,
                 -3.8952723, -1.5445506, -3.4951749, -2.6115263, -2.9125508, -0.5618292, -2.2135895,
                 -1.5316722};
 
-        Assert.assertTrue(arraysApproxEqual(expecPrior5, LikelihoodCalculationEngine.getDirichletPrior(counts_five,2),1e-5),errMsgArray(expecPrior5,LikelihoodCalculationEngine.getDirichletPrior(counts_five,2)));
+        Assert.assertTrue(arraysApproxEqual(expecPrior5, PairHMMLikelihoodCalculationEngine.getDirichletPrior(counts_five,2),1e-5),errMsgArray(expecPrior5,PairHMMLikelihoodCalculationEngine.getDirichletPrior(counts_five,2)));
 
         Assert.assertTrue(arraysApproxEqual(expected_one,post1,1e-6),errMsgArray(expected_one,post1));
         Assert.assertTrue(arraysApproxEqual(expected_two,post2,1e-5),errMsgArray(expected_two,post2));
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java
new file mode 100644
index 000000000..a6d2644cd
--- /dev/null
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java
@@ -0,0 +1,375 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*  
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*  
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*  
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*  
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*  
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. 
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.  
+*  
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY 
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*  
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*  
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*  
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*  
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
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+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt. 
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. 
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
+
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.HaplotypeGraph;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.haplotype.Haplotype;
+import org.broadinstitute.sting.utils.pairhmm.ActiveRegionTestDataSet;
+import org.broadinstitute.sting.utils.pairhmm.FastLoglessPairHMM;
+import org.broadinstitute.sting.utils.pairhmm.FlexibleHMM;
+import org.broadinstitute.sting.utils.pairhmm.PairHMM;
+import org.broadinstitute.sting.utils.sam.ClippedGATKSAMRecord;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.testng.Assert;
+import org.testng.Reporter;
+import org.testng.SkipException;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.*;
+
+/**
+ * Created with IntelliJ IDEA.
+ * User: valentin
+ * Date: 8/4/13
+ * Time: 10:20 PM
+ * To change this template use File | Settings | File Templates.
+ */
+@Test(enabled=false)
+public class ReadThreadingLikelihoodCalculationEngineUnitTest extends ActiveRegionTestDataSetUnitTest {
+
+
+//    private static FastHMM hmm = new MLLog10PairHMM((byte)10); // new FastLoglessPairHMM((byte)10);
+
+    private static FlexibleHMM hmm = new FastLoglessPairHMM((byte)10);
+
+    // for debugging purposes:
+    private static final boolean DUMP_LIKELIHOODS = false;
+    private PrintWriter likelihoodDumpWriter = null;
+    private File likelihoodDumpFile = null;
+
+
+    @BeforeClass
+    private void setUp() throws IOException {
+       if (DUMP_LIKELIHOODS) {
+           likelihoodDumpFile = File.createTempFile("rtlce-test", ".txt");
+           Reporter.log("Dumping Likelihoods in file '" + likelihoodDumpFile + "'",true);
+           likelihoodDumpWriter = new PrintWriter(likelihoodDumpFile);//new FileWriter(f));
+       }
+    }
+
+    @AfterClass
+    private void tearDown() throws IOException {
+        if (DUMP_LIKELIHOODS) {
+            likelihoodDumpWriter.close();
+            Reporter.log("Dumped Likelihoods in file '" + likelihoodDumpFile + "'", true);
+        }
+    }
+
+    @Test(dataProvider="activeRegionTestDataSets",enabled=false)
+    public void testActiveRegionsDataSet(final ActiveRegionTestDataSet as, final int kmerSize, final int readLength, final String variation, final int readCount, final int regionSize, final byte bq, final byte iq, final byte dq) {
+        super.testActiveRegionsDataSet(as,kmerSize,readLength,variation,readCount,regionSize,bq,iq,dq);
+    }
+        /** How many missing read record are tolerated in the graph based approach. For example a read is missed
+         * if it does not map to the reference path with at least two kmers in non overlapping positions. This constant
+         * indictes the proportion of reads reacords that we can miss with respect to all possible
+         */
+    private static final double READ_SKIP_TOLERANCE = 0.01;
+
+    //final PairHMMLikelihoodCalculationEngine fullPairHMM = new PairHMMLikelihoodCalculationEngine((byte)10, false,
+    //        PairHMM.HMM_IMPLEMENTATION.LOGLESS_CACHING, -3);
+    final PairHMMLikelihoodCalculationEngine fullPairHMM = new PairHMMLikelihoodCalculationEngine((byte)10, false,
+            PairHMM.HMM_IMPLEMENTATION.LOGLESS_CACHING, Double.NEGATIVE_INFINITY,true, PairHMMLikelihoodCalculationEngine.PCR_ERROR_MODEL.NONE);
+
+    // When using likelihoods it should be around 0.05 since
+    // When using maximum-likelihoods it can be as low as 0.00001
+    private static final double SIGNIFICANT_LnLK_RATIO_DIFF_FRACTION = hmm instanceof FastLoglessPairHMM ? 0.1 : 0.00001;
+
+
+    // Some case is kind of expected to have differences between PairHMM and GraphBased Flexible PairHMM.
+    // Is therefore difficult to test for the to give similar results in a unit test....
+    // This is left for for example Integration tests like GraphBasedVsLoglessAccuracyIntegrationTest.
+    // There code herein is maintain around for historical purposes, but disabled.
+    @Test(dataProvider="readLikekihoodRatioTestData",enabled=false)
+    public void testReadLikelihoodRatios(final ActiveRegionTestDataSet ds, final GATKSAMRecord read, final Allele a1,
+                                         final Allele a2, final PerReadAlleleLikelihoodMap loglessLks,
+                                         final PerReadAlleleLikelihoodMap graphLks, final List<Civar.ElementOffset> readEventOffsets, final List<Civar.ElementOffset> firstAlleleCivar, final List<Civar.ElementOffset> secondAlleleCivar ) {
+
+        checkForLongEventsThatMightCauseFailures(readEventOffsets, firstAlleleCivar, secondAlleleCivar);
+        final Map<Allele,Double> logless = loglessLks.getLikelihoodReadMap().get(read);
+        final Map<Allele,Double> graph = graphLks.getLikelihoodReadMap().get(read);
+        final double loglessA1Lk = logless.get(a1);
+        final double loglessA2Lk = logless.get(a2);
+        if (graph == null)
+            throw new SkipException("no likelihoods produced for this read using the graph method: Lla1= " + loglessA1Lk + " Lla2= " + loglessA2Lk + "LlDiff=" + (loglessA2Lk - loglessA1Lk)  );
+
+        final Double graphA1Lk = graph.get(a1);
+        final Double graphA2Lk = graph.get(a2);
+        if (graphA1Lk == null)
+            throw new SkipException("no likelihoods produced for this read in the first haplotype: Lla1= " + loglessA1Lk + " Lla2= " + loglessA2Lk + "LlDiff=" + (loglessA2Lk - loglessA1Lk)  );
+        if (graphA2Lk == null)
+            throw new SkipException("no likelihoods produced for this read in the second haplotype:  Lla1= " + loglessA1Lk + " Lla2= " + loglessA2Lk + "LlDiff=" + (loglessA2Lk - loglessA1Lk)  );
+
+        final double loglessDiff = loglessA1Lk - loglessA2Lk;
+        final double graphDiff = graphA1Lk - graphA2Lk;
+        final double epsilon = calculateEpsilon(graphDiff,loglessDiff);
+        dumpLikelihoods(read,loglessA1Lk,loglessA2Lk,graphA1Lk,graphA2Lk,read.getReadString() + " " + a1.getBaseString() + " " + a2.getBaseString());
+        Assert.assertEquals(graphDiff,loglessDiff,epsilon,String.format("Delta(%f,%f) = %f > %f",graphDiff,loglessDiff,Math.abs(graphDiff - loglessDiff),epsilon));
+
+    }
+
+    private double calculateEpsilon(final double graphDiff, final double loglessDiff) {
+        if (hmm instanceof FastLoglessPairHMM)
+            return Math.max(0.01,Math.max(Math.abs(loglessDiff),Math.abs(graphDiff)) * SIGNIFICANT_LnLK_RATIO_DIFF_FRACTION);
+        else
+            return SIGNIFICANT_LnLK_RATIO_DIFF_FRACTION;
+    }
+
+    private static final double MIN_READ_ACROSS_SIZE_FOR_INDEL_EVENTS = 0.8; // 50% percent.
+    private static final double MIN_LARGE_INDEL = 4;
+
+    private void checkForLongEventsThatMightCauseFailures(final List<Civar.ElementOffset> read, final List<Civar.ElementOffset> a1, final List<Civar.ElementOffset> a2) {
+
+        int sequenceLength = Math.max(a1.get(a1.size() - 1).templateTo, a2.get(a2.size() - 1).templateTo) + 1;
+
+        boolean tai1 = thereAreIndels(a1);
+        boolean tai2 = thereAreIndels(a2);
+        boolean tair = thereAreIndels(read);
+        boolean thereAreIndels = tai1 || tai2 || tair;
+        if (!thereAreIndels) return;
+
+        final boolean[] inserts = new boolean[sequenceLength];
+        final boolean[] deletions = new boolean[sequenceLength];
+        final int[] range = new int[2];
+
+        int refStart = Integer.MAX_VALUE;
+        int refEnd = -1;
+
+        for (final Civar.ElementOffset ce : read) {
+            if (refStart > ce.templateFrom)
+                refStart = ce.templateFrom;
+            if (refEnd < ce.templateTo)
+                refEnd = ce.templateTo;
+            switch (ce.element.operator()) {
+                case DELETION:
+                    deletions[ce.templateFrom] = deletions[ce.templateTo] = true;
+                    break;
+                case INSERTION:
+                    inserts[ce.templateFrom] = inserts[ce.templateTo] = true;
+                    break;
+                case MATCH:
+                    break;
+            }
+        }
+
+        range[0] = refStart;
+        range[1] = refEnd;
+
+        checkForLongEventsThatMightCauseFailures_allele(refStart,refEnd,inserts,deletions,a1);
+        checkForLongEventsThatMightCauseFailures_allele(refStart,refEnd,inserts,deletions,a2);
+    }
+
+    private void checkForLongEventsThatMightCauseFailures_allele(final int refStart, final int refEnd, final boolean[] inserts, final boolean[] deletions, final List<Civar.ElementOffset> a1) {
+        for (final Civar.ElementOffset ce : a1) {
+            if (ce.templateFrom <= refStart) continue;
+            if (ce.templateTo >= refEnd) continue;
+            int size;
+            switch (ce.element.operator()) {
+                case DELETION:
+                    size = ce.templateTo - ce.templateFrom;
+                    if (deletions[ce.templateFrom] || deletions[ce.templateTo]) continue;
+                    break;
+                case INSERTION:
+                    size = ce.sequenceTo - ce.sequenceFrom;
+                    if (inserts[ce.templateFrom] || inserts[ce.templateTo]) continue;
+                    break;
+                default:
+                    continue;
+            }
+            int minMargin = (int) Math.ceil(size * MIN_READ_ACROSS_SIZE_FOR_INDEL_EVENTS);
+            if (ce.templateFrom - refStart < minMargin)
+                throw new SkipException("Large Indel");
+            if (refEnd - ce.templateTo < minMargin)
+                throw new SkipException("Large Indel");
+        }
+
+    }
+
+    private boolean thereAreIndels(final List<Civar.ElementOffset> a1) {
+        for (final Civar.ElementOffset ce : a1)  {
+             switch (ce.element.operator()) {
+                 case DELETION:
+                     if (ce.templateTo - ce.templateFrom >= MIN_LARGE_INDEL) return true;
+                     break;
+                 case INSERTION:
+                     if (ce.sequenceTo - ce.sequenceFrom >= MIN_LARGE_INDEL) return true;
+                     break;
+             }
+        }
+        return false;
+    }
+
+    private void dumpLikelihoods(final GATKSAMRecord read, final Double loglessA1lk, final Double loglessA2lk, final Double a1lk, final Double a2lk, final String hapString) {
+        if (!DUMP_LIKELIHOODS) return;
+        likelihoodDumpWriter.println(Utils.join("\t","" + loglessA1lk,"" + loglessA2lk,"" + a1lk,"" + a2lk,read.getReadName(),read.getReadString(),hapString));
+        likelihoodDumpWriter.flush();
+    }
+
+    @DataProvider(name="readLikekihoodRatioTestData")
+    public Iterator<Object[]> readLikelihoodRatioTestDataSets() {
+           final Iterator<Object[]> activeRegionTestDataSetIterator = super.activeRegionTestDataSets();
+           return new java.util.Iterator<Object[]>() {
+
+               public static final boolean INTRODUCE_READ_ERRORS = true;
+
+               private List<Pair<Allele,Allele>> allelePairs;
+               private Iterator<Pair<Allele,Allele>> allelePairsIt;
+               private Iterator<GATKSAMRecord> readIt;
+               private GATKSAMRecord read;
+               private Iterator<List<Civar.ElementOffset>> civarEventOffsetsIt;
+               private List<Civar.ElementOffset> civarEventOffsets;
+               private ActiveRegionTestDataSet dataSet;
+               private GraphBasedLikelihoodCalculationEngineInstance graphEngine;
+               private PerReadAlleleLikelihoodMap graphLks;
+               private PerReadAlleleLikelihoodMap loglessLks;
+               private Map<Allele,Civar> civarByAllele;
+               private String reference;
+
+               @Override
+               public boolean hasNext() {
+                   return activeRegionTestDataSetIterator.hasNext()  || (readIt != null && readIt.hasNext()) || (allelePairsIt != null && allelePairsIt.hasNext());
+               }
+
+               @Override
+               public Object[] next() {
+                   if (allelePairsIt != null && allelePairsIt.hasNext()) {
+                       final Pair<Allele,Allele> allelePair = allelePairsIt.next();
+                       return new Object[] { dataSet, read, allelePair.getFirst(), allelePair.getSecond(), loglessLks, graphLks, civarEventOffsets, civarByAllele.get(allelePair.getFirst()).eventOffsets(reference,0,Integer.MAX_VALUE), civarByAllele.get(allelePair.getSecond()).eventOffsets(reference,0,Integer.MAX_VALUE)};
+                   }
+                   if (readIt != null && readIt.hasNext()) {
+                        allelePairsIt = allelePairs.iterator();
+                        final Pair<Allele,Allele> allelePair = allelePairsIt.next();
+                        return new Object[] {dataSet, read = readIt.next(), allelePair.getFirst(), allelePair.getSecond(), loglessLks, graphLks, civarEventOffsets = civarEventOffsetsIt.next(), civarByAllele.get(allelePair.getFirst()).eventOffsets(reference,0,Integer.MAX_VALUE), civarByAllele.get(allelePair.getSecond()).eventOffsets(reference,0,Integer.MAX_VALUE) };
+                   }
+                   final Object[] params = activeRegionTestDataSetIterator.next();
+                   dataSet = (ActiveRegionTestDataSet) params[0];
+                   if (INTRODUCE_READ_ERRORS) dataSet.introduceErrors(new Random(13));
+                   graphEngine = new GraphBasedLikelihoodCalculationEngineInstance(dataSet.assemblyResultSet(),hmm,Double.NEGATIVE_INFINITY, HeterogeneousKmerSizeResolution.COMBO_MAX);
+                   graphLks = graphEngine.computeReadLikelihoods(dataSet.haplotypeList(),Collections.singletonMap("anonymous",dataSet.readList())).get("anonymous");
+
+                   // clip reads at the anchors.
+                   final Map<GATKSAMRecord,GATKSAMRecord> clippedReads = anchorClippedReads(graphEngine.getHaplotypeGraph(),dataSet.readList());
+                   final List<GATKSAMRecord> clippedReadList = new ArrayList<>(dataSet.readList().size());
+
+                   for (final GATKSAMRecord r : dataSet.readList()) {
+                       clippedReadList.add(clippedReads.containsKey(r) ? clippedReads.get(r) : r);
+                   }
+
+                   loglessLks = fullPairHMM.computeReadLikelihoods(dataSet.assemblyResultSet(),Collections.singletonMap("anonymous",clippedReadList)).get("anonymous");
+
+                   // Change clipped by unclipped in the resulting likelihood map.
+                   for (final GATKSAMRecord r : clippedReads.keySet()) {
+                       loglessLks.getLikelihoodReadMap().put(r,loglessLks.getLikelihoodReadMap().remove(clippedReads.get(r)));
+                   }
+                   final List<Haplotype> haplotypes = dataSet.haplotypeList();
+                   final Map<Haplotype,Allele> alleleByHaplotype = new HashMap<>(haplotypes.size());
+                   final Map<String,Civar> civarBySequence = new HashMap<>(haplotypes.size());
+                   final Map<String,Haplotype> haplotypeBySequence = new HashMap<>(haplotypes.size());
+                   civarByAllele = new HashMap<>(haplotypes.size());
+                   final List<Civar> unrolledCivars = dataSet.unrolledCivars();
+                   for (int i = 0; i < haplotypes.size(); i++)  {
+                       final Haplotype h = haplotypes.get(i);
+                       haplotypeBySequence.put(h.getBaseString(),h);
+                       civarBySequence.put(h.getBaseString(),unrolledCivars.get(i));
+                   }
+                   for (final Allele a : loglessLks.getAllelesSet()) {
+                       alleleByHaplotype.put(haplotypeBySequence.get(a.getBaseString()),a);
+                       civarByAllele.put(a,civarBySequence.get(a.getBaseString()));
+                   }
+                   allelePairs = new ArrayList<>(haplotypes.size() * 2);
+                   final Haplotype[] haplotypeArray = haplotypes.toArray(new Haplotype[haplotypes.size()]);
+                   for (int i = 0; i < haplotypeArray.length; i++)
+                       for (int j = i + 1; j < haplotypeArray.length; j++)
+                           allelePairs.add(new Pair<>(alleleByHaplotype.get(haplotypeArray[i]),alleleByHaplotype.get(haplotypeArray[j])));
+                   allelePairsIt = allelePairs.iterator();
+                   readIt = dataSet.readList().iterator();
+                   final Pair<Allele,Allele> allelePair = allelePairsIt.next();
+                   civarEventOffsetsIt = dataSet.readEventOffsetList().iterator();
+                   reference = dataSet.getReference();
+                   return new Object[] { dataSet , read = readIt.next(), allelePair.getFirst(), allelePair.getSecond(), loglessLks, graphLks, civarEventOffsets = civarEventOffsetsIt.next(), civarByAllele.get(allelePair.getFirst()).eventOffsets(reference,0,Integer.MAX_VALUE), civarByAllele.get(allelePair.getSecond()).eventOffsets(reference,0,Integer.MAX_VALUE)};
+               }
+
+               @Override
+               public void remove() {
+                   throw new UnsupportedOperationException();
+               }
+           };
+    }
+
+
+    /**
+     * Returns the reads clipped at their anchors.
+     *
+     * @param reads target reads.
+     * @return never {@code null}.
+     */
+    protected Map<GATKSAMRecord, GATKSAMRecord> anchorClippedReads(final HaplotypeGraph haplotypeGraph, final List<GATKSAMRecord> reads) {
+        final Map<GATKSAMRecord, GATKSAMRecord> result = new HashMap<>(reads.size());
+        for (final GATKSAMRecord r : reads) {
+            final ReadAnchoring anchoring = new ReadAnchoring(r,haplotypeGraph);
+            if (anchoring.isAnchoredSomewhere())
+                continue;
+            final int start = anchoring.leftAnchorIndex;
+            final int end = anchoring.rightAnchorIndex + haplotypeGraph.getKmerSize();
+            final GATKSAMRecord clipped = new ClippedGATKSAMRecord(r, start, end);
+            result.put(r, clipped);
+        }
+        return result;
+    }
+
+
+
+}
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java
index e07adc0f6..5e91ad4f7 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java
@@ -60,7 +60,7 @@ public class BaseGraphUnitTest extends BaseTest {
 
     @BeforeMethod
     public void setUp() throws Exception {
-        graph = new SeqGraph();
+        graph = new SeqGraph(11);
 
         v1 = new SeqVertex("A");
         v2 = new SeqVertex("C");
@@ -118,7 +118,7 @@ public class BaseGraphUnitTest extends BaseTest {
 
     @Test
     public void testRemoveSingletonOrphanVerticesOnSingleRefNode() throws Exception {
-        final SeqGraph original = new SeqGraph();
+        final SeqGraph original = new SeqGraph(11);
         original.addVertex(v1);
         original.removeSingletonOrphanVertices();
         Assert.assertTrue(original.containsVertex(v1));
@@ -128,7 +128,7 @@ public class BaseGraphUnitTest extends BaseTest {
     @Test
     public void testIsRefSourceAndSink() throws Exception {
 
-        final SeqGraph g = new SeqGraph();
+        final SeqGraph g = new SeqGraph(11);
         g.addVertex(v1);
         Assert.assertTrue(g.isRefSource(v1));
         Assert.assertTrue(g.isRefSink(v1));
@@ -164,7 +164,7 @@ public class BaseGraphUnitTest extends BaseTest {
 
     @Test
     public void testRemovePathsNotConnectedToRef() throws Exception {
-        final SeqGraph graph = new SeqGraph();
+        final SeqGraph graph = new SeqGraph(11);
 
         SeqVertex src = new SeqVertex("A");
         SeqVertex end = new SeqVertex("A");
@@ -216,7 +216,7 @@ public class BaseGraphUnitTest extends BaseTest {
 
     @Test
     public void testRemoveVerticesNotConnectedToRefRegardlessOfEdgeDirection() throws Exception {
-        final SeqGraph graph = new SeqGraph();
+        final SeqGraph graph = new SeqGraph(11);
 
         SeqVertex src = new SeqVertex("A");
         SeqVertex end = new SeqVertex("A");
@@ -275,7 +275,7 @@ public class BaseGraphUnitTest extends BaseTest {
     public void testPrintEmptyGraph() throws Exception {
         final File tmp = File.createTempFile("tmp", "dot");
         tmp.deleteOnExit();
-        new SeqGraph().printGraph(tmp, 10);
+        new SeqGraph(11).printGraph(tmp, 10);
         new TestGraph().printGraph(tmp, 10);
     }
 
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixMergerUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixMergerUnitTest.java
index e1398e119..63fd21d8f 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixMergerUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixMergerUnitTest.java
@@ -93,7 +93,7 @@ public class CommonSuffixMergerUnitTest extends BaseTest {
                     for ( int nTops = 0; nTops < nMids; nTops++ ) {
                         for ( int nTopConnections = 1; nTopConnections <= nMids; nTopConnections++ ) {
                             int multi = 1;
-                            final SeqGraph graph = new SeqGraph();
+                            final SeqGraph graph = new SeqGraph(11);
                             final SeqVertex v = new SeqVertex("GGGG");
                             graph.addVertex(v);
 
@@ -169,7 +169,7 @@ public class CommonSuffixMergerUnitTest extends BaseTest {
 
     @Test
     public void testDoesntMergeSourceNodes() {
-        final SeqGraph g = new SeqGraph();
+        final SeqGraph g = new SeqGraph(11);
         final SeqVertex v1 = new SeqVertex("A");
         final SeqVertex v2 = new SeqVertex("A");
         final SeqVertex v3 = new SeqVertex("A");
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixSplitterUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixSplitterUnitTest.java
index 9703d76cb..cae39d26a 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixSplitterUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixSplitterUnitTest.java
@@ -81,7 +81,7 @@ public class CommonSuffixSplitterUnitTest extends BaseTest {
 
     @Test(enabled = !DEBUG)
     public void testSplitPrevHaveMultipleEdges() {
-        final SeqGraph original = new SeqGraph();
+        final SeqGraph original = new SeqGraph(11);
         final SeqVertex v1 = new SeqVertex("A");
         final SeqVertex v2 = new SeqVertex("A");
         final SeqVertex v3 = new SeqVertex("A");
@@ -100,7 +100,7 @@ public class CommonSuffixSplitterUnitTest extends BaseTest {
 
     @Test(enabled = !DEBUG)
     public void testSplitNoCycles() {
-        final SeqGraph original = new SeqGraph();
+        final SeqGraph original = new SeqGraph(11);
         final SeqVertex v1 = new SeqVertex("A");
         final SeqVertex v2 = new SeqVertex("AC");
         final SeqVertex v3 = new SeqVertex("TC");
@@ -118,7 +118,7 @@ public class CommonSuffixSplitterUnitTest extends BaseTest {
 
     @Test(timeOut = 10000, enabled = !DEBUG)
     public void testSplitComplexCycle() {
-        final SeqGraph original = new SeqGraph();
+        final SeqGraph original = new SeqGraph(11);
         final SeqVertex r1 = new SeqVertex("ACTG");
         final SeqVertex r2 = new SeqVertex("ATGC");
         final SeqVertex cat1 = new SeqVertex("CAT");
@@ -142,7 +142,7 @@ public class CommonSuffixSplitterUnitTest extends BaseTest {
 
     @Test(timeOut = 10000)
     public void testSplitInfiniteCycleFailure() {
-        final SeqGraph original = new SeqGraph();
+        final SeqGraph original = new SeqGraph(11);
         final SeqVertex v1 = new SeqVertex("GC");
         final SeqVertex v2 = new SeqVertex("X");
         final SeqVertex v3 = new SeqVertex("N");
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/HaplotypeGraphUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/HaplotypeGraphUnitTest.java
new file mode 100644
index 000000000..e756737a2
--- /dev/null
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/HaplotypeGraphUnitTest.java
@@ -0,0 +1,238 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+*
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs;
+
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.Kmer;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.HaplotypeGraph;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex;
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.*;
+
+/**
+ * Tests for {@link HaplotypeGraph}
+ *
+ * @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.org&gt;
+ */
+public class HaplotypeGraphUnitTest extends BaseTest {
+
+   @Test(dataProvider="buildByStringDataProvider")
+   public void testBuildByString(final String string, final int kmerSize, final int vertexCount, final int edgeCount) {
+       final HaplotypeGraph g = new HaplotypeGraph(string);
+       Assert.assertEquals(g.getKmerSize(),kmerSize,g.toString());
+       Assert.assertEquals(g.vertexSet().size(),vertexCount,g.toString());
+       Assert.assertEquals(g.edgeSet().size(),edgeCount,g.toString());
+   }
+
+   @Test(dataProvider="equalTestDataProvider")
+   public void testEquals(final HaplotypeGraph one, final HaplotypeGraph two, final boolean expected) {
+      Assert.assertEquals(one.equals(two),expected);
+   }
+
+   @Test(dataProvider="equalTestDataProvider")
+   public void testEqualReciprocal(final HaplotypeGraph one, final HaplotypeGraph two, final boolean expected) {
+       Assert.assertEquals(two.equals(one),expected);
+   }
+
+
+   @Test(dataProvider="equalTestDataProvider")
+   public void testReflexibeEquals(final HaplotypeGraph one, final HaplotypeGraph two,
+                                   @SuppressWarnings("unused") final boolean expected) {
+       Assert.assertTrue(one.equals(one));
+       Assert.assertTrue(two.equals(two));
+   }
+
+   @Test(dataProvider="mergingCommonChainsDataProvider")
+   public void testMergingCommonChains(final HaplotypeGraph actual, HaplotypeGraph expected) {
+
+
+        final Map<Kmer,MultiDeBruijnVertex> beforeMap = new HashMap<>(actual.uniqueKmerMap());
+        actual.mergeCommonChains();
+        final Map<Kmer,MultiDeBruijnVertex> afterMap = new HashMap<>(actual.uniqueKmerMap());
+        final Map<Kmer,MultiDeBruijnVertex> mergedMap = new HashMap<>(expected.uniqueKmerMap());
+
+        Assert.assertEquals(actual, expected,""+actual.vertexSet() + " EDGES " + actual.edgeSet());
+        Assert.assertEquals(beforeMap.size(),afterMap.size());
+        Assert.assertEquals(afterMap.size(),mergedMap.size());
+        for (final Kmer k : beforeMap.keySet()) {
+            Assert.assertTrue(afterMap.containsKey(k));
+            Assert.assertTrue(mergedMap.containsKey(k));
+            final byte[] seq1 = beforeMap.get(k).getSequence();
+            final byte[] seq2 = afterMap.get(k).getSequence();
+            final byte[] seq3 = mergedMap.get(k).getSequence();
+            Assert.assertEquals(seq1.length,seq2.length);
+            Assert.assertEquals(seq2.length,seq3.length);
+            for (int i = 0; i < seq3.length; i++) {
+                final byte bk = k.base(i);
+                final byte b1 = seq1[i];
+                final byte b2 = seq2[i];
+                final byte b3 = seq3[i];
+                final byte theByte = b1 == 'N' || b2 == 'N' || b3 == 'N' ? (byte)'N' : b1;
+                if (theByte == 'N') continue;
+                Assert.assertEquals(b1,b2);
+                Assert.assertEquals(b2,b3);
+                Assert.assertEquals(bk,b1);
+            }
+        }
+   }
+
+
+   @DataProvider(name="mergingCommonChainsDataProvider")
+   public Iterator<Object[]> mergingCommonChainsDataProvider() {
+      final List<Object[]> list = new LinkedList<>();
+      for (int i = 0; i < MERGING_COMMON_CHAINS_DATA.length; i += 2) {
+          final HaplotypeGraph before = new HaplotypeGraph(MERGING_COMMON_CHAINS_DATA[i]);
+          final HaplotypeGraph after = new HaplotypeGraph(MERGING_COMMON_CHAINS_DATA[i+1]);
+          list.add(new Object[] { before , after});
+      }
+      return list.iterator();
+   }
+
+   @DataProvider(name="equalTestDataProvider")
+   public Iterator<Object[]> equalsTestDataProvider() {
+      final List<Object[]> result = new LinkedList<>();
+      for (int i = 0; i < EQUAL_TEST_DATA.length; i += 3) {
+          final HaplotypeGraph g1 = new HaplotypeGraph(EQUAL_TEST_DATA[i]);
+          final HaplotypeGraph g2 = new HaplotypeGraph(EQUAL_TEST_DATA[i+1]);
+          final boolean outcome = Boolean.parseBoolean(EQUAL_TEST_DATA[i+2]);
+          result.add(new Object[] { g1, g2, outcome});
+      }
+      return result.iterator();
+   }
+
+   @DataProvider(name="buildByStringDataProvider")
+   public Iterator<Object[]> buildByStringDataProvider() {
+      return Arrays.asList(BUILD_BY_STRING_TEST_DATA).iterator();
+   }
+
+   private static final Object[][] BUILD_BY_STRING_TEST_DATA = new Object[][] {
+           {"[ks=3]{REF: ACT}",3,1,0},
+           {"[ks=3]{REF: ACT(3) -> T(1)      ->      G(2) -> A}" +
+                         "{ (3) -> A -> G ->          (2) }" +
+                                "{  (1) -> A -> G ->  (2) }",3,8,9},
+           {"[ks=3]{REF: ACT -> C(1) -> G}{ACT -> C(1) -> G}{ACT -> C(1) -> G}",3,5,4} ,
+           {"[ks=3]{REF: ACT -> A(1) -> G -> A(2) -> C -> G -> T }" +
+                              "{A(1) -> T -> A(2) }",3,8,8}  ,
+           {"[ks=3]{REF: ACT -> A -> T(2) -> C -> A -> G -> T -> A -> C -> G -> T -> A(1) -> T}" +
+                   "{ ACT -> A -> T(2) -> C -> A -> G -> T -> A -> C -> G -> T -> A(1) -> T}",3,15,14} ,
+           {"[ks=3]{REF: ACT -> A -> T    -> C -> A -> G -> T -> A -> C -> G -> T -> A    -> T}",3,13,12},
+           {"[ks=3]{REF: ACT -> A -> T(1) }" +
+                   "{ ACT -> A -> T(1) }",3,5,4},
+           {"[ks=3]{REF: TTT -> A(1) -> C -> T(2)}{ A(1) -> T(2) } ",3,4,4}
+   };
+
+   private static final String[] EQUAL_TEST_DATA = new String[] {
+           "[ks=3]{REF: ACT}","[ks=3]{REF: ACT}", "true",
+           "[ks=3]{REF: TCA}","[ks=3]{REF: ACT}", "false",
+           "[ks=4]{REF: ACTG}","[ks=3]{REF: ACT}", "false",
+           "[ks=3]{REF: ACT(3) -> T(1)      ->      G(2) -> A}" +
+                        "{ (3) -> A -> G ->          (2) }" +
+                               "{  (1) -> A -> G ->  (2) }"
+                   ,"[ks=3]{REF: ACT(3) -> T(1)      ->      G(2) -> A}" +
+                                                                 "{  (1) -> A -> G ->  (2) }" +
+                                                          "{ (3) -> A -> G ->          (2) }", "true",
+           "[ks=3]{REF: ACT(3) -> T(1)      ->      G(2) -> A}" +
+                        "{ (3) -> A -> T ->          (2) }" +
+                              "{  (1) -> A -> G ->  (2) }"
+                    ,"[ks=3]{REF: ACT(3) -> T(1)      ->      G(2) -> A}" +
+                     "{  (1) -> A -> G ->  (2) }" +
+                     "{ (3) -> A -> G ->          (2) }", "true",
+           "[ks=3]{REF: ACT -> G -> C(2) }{ ACT -> T -> C(2) }","[ks=3]{REF: ACT -> T -> C(2) }{ ACT -> G -> C(2) }","false",
+
+   };
+
+   private static final String[] MERGING_COMMON_CHAINS_DATA = new String[] {  // pairs before and after.
+           "[ks=3]{REF: ACT -> A(1) -> G -> A -> G(2) -> T }" +
+                             "{A(1) -> T -> A -> G(2) }",
+           "[ks=3]{REF: ACT -> A(1) -> G -> A(2) -> G -> T }" +
+                             "{A(1) -> T -> A(2) }",
+
+           "[ks=3]{REF: ACT -> A(1) -> G -> A -> C -> G(2) -> T }" +
+                             "{A(1) -> T -> A -> C -> G(2) }",
+           "[ks=3]{REF: ACT -> A(1) -> G -> A(2) -> C -> G -> T }" +
+                             "{A(1) -> T -> A(2) }",
+
+           "[ks=3]{REF: ACT -> A -> T(1) -> C -> A -> G -> T -> A -> C(2) -> G -> T -> A}" +
+                                 "{ T(1) -> A -> A -> G -> T -> A -> C(2) }",
+           "[ks=3]{REF: ACT -> A -> T(1) -> C -> A(2) -> G -> T -> A -> C -> G -> T -> A}" +
+                                 "{ T(1) -> A -> A(2) } ",
+
+//           "[ks=3]{REF: ACT -> A -> T -> C -> A -> G -> T -> A -> C -> G -> T -> A(1)}" +
+//                     "{ ACT -> A -> T -> C -> A -> G -> T -> A -> C -> G -> T -> A(1)}" ,
+//           "[ks=3]{REF: ACT -> A -> T -> C -> A -> G -> T -> A -> C -> G -> T -> A}" ,
+
+           "[ks=3]{REF: ACT -> A -> T(1) }" +
+                     "{ AGT -> A -> T(1) }" ,
+           "[ks=3]{REF: ACT -> A(1) -> T }" +
+                   "{ AGT -> A(1)  }"  ,
+           "[ks=3]{REF: ACT -> A -> T -> C -> A -> G -> T -> A -> C -> G -> T -> A -> T}" ,
+           "[ks=3]{REF: ACT -> A -> T -> C -> A -> G -> T -> A -> C -> G -> T -> A -> T}" ,
+           "[ks=3]{REF: ACT -> A -> T -> C -> A -> G -> T -> A -> C -> G -> T -> A -> T(1)}" + "{ACT -> A -> T -> C -> A -> G -> T -> A -> C -> G -> T -> A -> T(1)}" ,
+           "[ks=3]{REF: ACT -> A -> T -> C -> A -> G -> T -> A -> C -> G -> T -> A -> T}" ,
+
+           "[ks=3]{REF: TTT -> T -> T -> T -> T -> T -> T -> T -> T -> T -> T(1) -> T -> T -> T(2) -> T -> T}"
+                  + "{  TTT -> T -> T -> T -> T -> T -> T -> T -> T -> T -> T(1) -> G -> T -> T -> T -> T -> T(2) -> T -> T}",
+           "[ks=3]{REF: TTT -> T -> T -> T -> T -> T -> T -> T -> T -> T -> T(1) -> T(2) -> T -> T -> T -> T}"
+                  +                                                      "{ T(1) -> G -> T -> T -> T(2) }",
+
+           "[ks=3]{REF: TTT -> T -> G(1) -> A -> C -> C -> T(2)}" +
+                                 "{ G(1) -> T -> C -> C -> T(2)}" +
+                                 "{ G(1) -> G -> C -> C -> T(2)}" +
+                                 "{ G(1) -> C -> T(2)} ",
+           "[ks=3]{REF: TTT -> T -> G(1) -> A -> C(2) -> C(3) -> T }" +
+                                 "{  G(1) -> T -> C(2) }" +
+                                 "{  G(1) -> G -> C(2) }" +
+                                 "{  G(1) -> C(3) }",
+
+           "[ks=3]{REF: TTT -> T -> G(1) -> A -> C -> G}{ TTT -> T -> G(1) -> G -> C -> G}",
+           "[ks=3]{REF: TTT -> T -> G(1) -> A -> C -> G}{ G(1) -> G -> C -> G}",
+
+   };
+
+}
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestPathsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestPathsUnitTest.java
index d6709672a..fa7ad9a3d 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestPathsUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestPathsUnitTest.java
@@ -102,7 +102,7 @@ public class KBestPathsUnitTest extends BaseTest {
 
     @Test(dataProvider = "BasicPathFindingData", enabled = !DEBUG)
     public void testBasicPathFinding(final int nStartNodes, final int nBranchesPerBubble, final int nEndNodes, final boolean addCycle, final boolean allowCycles) {
-        SeqGraph graph = new SeqGraph();
+        SeqGraph graph = new SeqGraph(11);
 
         final SeqVertex middleTop = new SeqVertex("GTAC");
         final SeqVertex middleBottom = new SeqVertex("ACTG");
@@ -134,7 +134,7 @@ public class KBestPathsUnitTest extends BaseTest {
 
     @Test(enabled = !DEBUG)
     public void testPathFindingComplexCycle() {
-        SeqGraph graph = new SeqGraph();
+        SeqGraph graph = new SeqGraph(11);
 
         final SeqVertex v1 = new SeqVertex("A");
         final SeqVertex v2 = new SeqVertex("C");
@@ -154,7 +154,7 @@ public class KBestPathsUnitTest extends BaseTest {
 
     @Test(enabled = !DEBUG)
     public void testPathFindingCycleLastNode() {
-        SeqGraph graph = new SeqGraph();
+        SeqGraph graph = new SeqGraph(11);
 
         final SeqVertex v1 = new SeqVertex("A");
         final SeqVertex v2 = new SeqVertex("C");
@@ -276,7 +276,7 @@ public class KBestPathsUnitTest extends BaseTest {
     @Test(dataProvider = "TripleBubbleDataProvider", enabled = !DEBUG)
     public void testTripleBubbleData(final int refBubbleLength, final int altBubbleLength, final boolean offRefBeginning, final boolean offRefEnding) {
         // Construct the assembly graph
-        SeqGraph graph = new SeqGraph();
+        SeqGraph graph = new SeqGraph(11);
         final String preAltOption = "ATCGATCGATCGATCGATCG";
         final String postAltOption = "CCCC";
         final String preRef = "ATGG";
@@ -384,7 +384,7 @@ public class KBestPathsUnitTest extends BaseTest {
     @Test(enabled = !DEBUG)
     public void testIntraNodeInsertionDeletion() {
         // Construct the assembly graph
-        SeqGraph graph = new SeqGraph();
+        SeqGraph graph = new SeqGraph(11);
         final SeqVertex top = new SeqVertex("T");
         final SeqVertex bot = new SeqVertex("T");
         final SeqVertex alt = new SeqVertex("AAACCCCC");
@@ -410,7 +410,7 @@ public class KBestPathsUnitTest extends BaseTest {
     @Test(enabled = !DEBUG)
     public void testHardSWPath() {
         // Construct the assembly graph
-        SeqGraph graph = new SeqGraph();
+        SeqGraph graph = new SeqGraph(11);
         final SeqVertex top = new SeqVertex( "NNN" );
         final SeqVertex bot = new SeqVertex( "NNN" );
         final SeqVertex alt = new SeqVertex(               "ACAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA" );
@@ -472,7 +472,7 @@ public class KBestPathsUnitTest extends BaseTest {
     @Test(dataProvider = "SystematicRefAltSWTestData", enabled = !DEBUG)
     public void testRefAltSW(final String prefix, final String end, final String refMid, final String altMid, final String midCigar) {
         // Construct the assembly graph
-        SeqGraph graph = new SeqGraph();
+        SeqGraph graph = new SeqGraph(11);
 
         final int padSize = 0;
         SeqVertex top = new SeqVertex(Utils.dupString("N", padSize));
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/LowWeightChainPrunerUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/LowWeightChainPrunerUnitTest.java
index 06d81499c..a4c0464a5 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/LowWeightChainPrunerUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/LowWeightChainPrunerUnitTest.java
@@ -51,7 +51,6 @@ import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
-import java.io.File;
 import java.util.*;
 
 public class LowWeightChainPrunerUnitTest extends BaseTest {
@@ -71,7 +70,7 @@ public class LowWeightChainPrunerUnitTest extends BaseTest {
                 for ( final boolean isRef : Arrays.asList(true, false)) {
                     { // just an isolated chain
                         final int nExpected = edgeWeight < pruneFactor && ! isRef ? 3 : 0;
-                        SeqGraph graph = new SeqGraph();
+                        SeqGraph graph = new SeqGraph(11);
                         graph.addVertices(v1, v2, v3);
                         graph.addEdges(new BaseEdge(isRef, edgeWeight), v1, v2, v3);
                         tests.add(new Object[]{"combinatorial", graph, pruneFactor, nExpected > 0 ? Collections.emptySet() : graph.vertexSet()});
@@ -81,7 +80,7 @@ public class LowWeightChainPrunerUnitTest extends BaseTest {
         }
 
         { // connects to ref chain
-            SeqGraph graph = new SeqGraph();
+            SeqGraph graph = new SeqGraph(11);
             graph.addVertices(v1, v2, v3);
             graph.addVertices(v4, v5);
             graph.addEdges(new BaseEdge(true, 1), v4, v5);
@@ -90,7 +89,7 @@ public class LowWeightChainPrunerUnitTest extends BaseTest {
         }
 
         { // has bad cycle
-            SeqGraph graph = new SeqGraph();
+            SeqGraph graph = new SeqGraph(11);
             graph.addVertices(v1, v2, v3, v4);
             graph.addEdges(new BaseEdge(false, 1), v4, v1, v2, v3, v1);
             // note that we'll remove v4 because it's low weight
@@ -98,7 +97,7 @@ public class LowWeightChainPrunerUnitTest extends BaseTest {
         }
 
         { // has good cycle
-            SeqGraph graph = new SeqGraph();
+            SeqGraph graph = new SeqGraph(111);
             graph.addVertices(v1, v2, v3, v4);
             graph.addEdges(new BaseEdge(false, 3), v4, v1, v2, v3, v1);
             // note that we'll remove v4 because it's low weight
@@ -106,7 +105,7 @@ public class LowWeightChainPrunerUnitTest extends BaseTest {
         }
 
         { // has branch
-            SeqGraph graph = new SeqGraph();
+            SeqGraph graph = new SeqGraph(11);
             graph.addVertices(v1, v2, v3, v4, v5, v6);
             graph.addEdges(new BaseEdge(false, 1), v1, v2, v3, v4, v6);
             graph.addEdges(new BaseEdge(false, 1), v1, v2, v3, v5, v6);
@@ -114,7 +113,7 @@ public class LowWeightChainPrunerUnitTest extends BaseTest {
         }
 
         { // middle vertex above threshold => no one can be removed
-            SeqGraph graph = new SeqGraph();
+            SeqGraph graph = new SeqGraph(11);
             graph.addVertices(v1, v2, v3, v4, v5);
             graph.addEdges(new BaseEdge(false, 1), v1, v2);
             graph.addEdges(new BaseEdge(false, 3), v2, v3);
@@ -123,7 +122,7 @@ public class LowWeightChainPrunerUnitTest extends BaseTest {
         }
 
         { // the branching node has value > pruneFactor
-            SeqGraph graph = new SeqGraph();
+            SeqGraph graph = new SeqGraph(11);
             graph.addVertices(v1, v2, v3, v4, v5, v6);
             graph.addEdges(new BaseEdge(false, 3), v1, v2);
             graph.addEdges(new BaseEdge(false, 3), v2, v3);
@@ -133,7 +132,7 @@ public class LowWeightChainPrunerUnitTest extends BaseTest {
         }
 
         { // A single isolated chain with weights all below pruning should be pruned
-            SeqGraph graph = new SeqGraph();
+            SeqGraph graph = new SeqGraph(11);
             graph.addVertices(v1, v2, v3, v4, v5);
             graph.addEdges(new BaseEdge(false, 1), v1, v2, v3);
             graph.addEdges(new BaseEdge(false, 5), v4, v5);
@@ -141,7 +140,7 @@ public class LowWeightChainPrunerUnitTest extends BaseTest {
         }
 
         { // A chain with weights all below pruning should be pruned, even if it connects to another good chain
-            SeqGraph graph = new SeqGraph();
+            SeqGraph graph = new SeqGraph(11);
             graph.addVertices(v1, v2, v3, v4, v5, v6);
             graph.addEdges(new BaseEdge(false, 1), v1, v2, v3, v5);
             graph.addEdges(new BaseEdge(false, 5), v4, v5, v6);
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/PathUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/PathUnitTest.java
index ee07bea33..da59b523a 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/PathUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/PathUnitTest.java
@@ -57,7 +57,7 @@ public class PathUnitTest extends BaseTest {
         final String ref = "ATGGTGGCTCATACCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGAACATCACCTGAGGCCAGGAGTTCAAAACCAGCCTGGCTAACATAGCAAAACCCCATCTCTAATGAAAATACAAAAATTAGCTGGGTGTGGTGGTGTCCGCCTGTAGTCCCAGCTACTCAGGAGACTAAGGCATGAGAATCACTTGAACCCAGGATGCAGAGGCTGTAGTGAGCCGAGATTGCACCACGGCTGCACTCCAGCCTGGGCAACAGAGCGAGACTCTGTCTCAAATAAAATAGCGTAACGTAACATAACATAACATAACATAACATAACATAACATAACATAACATAACATAACATAACACAACAACAAAATAAAATAACATAAATCATGTTGTTAGGAAAAAAATCAGTTATGCAGCTACATGCTATTTACAAGAGATATACCTTAAAATATAAGACACAGAGGCCGGGCGCGGTAGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCAAGCGGATCATGAGGTCAGGAGATCGAGACCATCC";
         final String hap = "ATGGTGGCTCATACCTGTAATCCCAGCACTTTGGGAGGCTGAGGCAAGCGGATCATGAGGTCAGGAGATCGAGACCATCCT";
 
-        final SeqGraph graph = new SeqGraph();
+        final SeqGraph graph = new SeqGraph(11);
         final SeqVertex v = new SeqVertex(hap);
         graph.addVertex(v);
         final Path<SeqVertex,BaseEdge> path = new Path<SeqVertex,BaseEdge>(v, graph);
@@ -70,7 +70,7 @@ public class PathUnitTest extends BaseTest {
         final String ref = "CGGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTGGCCAGGCTGGTCTTGAACTCCTGACCTCAGGTGATCCACTCGCCTCGGTCTCCCAAAGTGTTGGGATTACAGGCATGAACCACTGCACCTGGCCTAGTGTTTGGGAAAACTATACTAGGAAAAGAATAGTTGCTTTAAGTCATTCTTTGATTATTCTGAGAATTGGCATATAGCTGCCATTATAACCTACTTTTGCTAAATATAATAATAATAATCATTATTTTTATTTTTTGAGACAGGGTCTTGTTTTGTCACCCCGGCTGGAGTGAAGTGGCGCAATCTCGGCTCACTGCAACCTCCACCTCCGGGTGCAAGCAATTCTCCTGCCTCAGCCTCTTGAGTAGCTAGGATTACAGGCACAAGCCATCATGCCCAGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTGGTCAGGCTGGTCTTGAACTCCTGACCTCAGGT";
         final String hap = "CGGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTGGTCAGGCTGGTCTTGAACTCCTGACCTCAGGT";
 
-        final SeqGraph graph = new SeqGraph();
+        final SeqGraph graph = new SeqGraph(11);
         final SeqVertex v = new SeqVertex(hap);
         graph.addVertex(v);
         final Path<SeqVertex,BaseEdge> path = new Path<SeqVertex,BaseEdge>(v, graph);
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/RouteUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/RouteUnitTest.java
new file mode 100644
index 000000000..2918501b2
--- /dev/null
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/RouteUnitTest.java
@@ -0,0 +1,261 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+*
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+package org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs;
+
+import org.broadinstitute.sting.BaseTest;
+import org.jgrapht.EdgeFactory;
+import org.testng.Assert;
+import org.testng.Reporter;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.*;
+
+/**
+ * Created with IntelliJ IDEA.
+ * User: valentin
+ * Date: 9/5/13
+ * Time: 11:04 AM
+ * To change this template use File | Settings | File Templates.
+ */
+public class RouteUnitTest extends BaseTest {
+
+
+       @Test(dataProvider="isSuffixTestData")
+       public void testIsSuffix(final Route<BaseVertex,BaseEdge> route, final Path<BaseVertex,BaseEdge> path, final boolean expectedResult) {
+          Assert.assertEquals(route.isSuffix(path), expectedResult);
+       }
+
+       @DataProvider(name="isSuffixTestData")
+       public Iterator<Object[]> isSuffixTestData() {
+           return TEST_DATA.iterator();
+       }
+
+       private static final int[] TEST_EDGE_PAIRS1 = new int[] {
+                      3 , 4,
+                          4 , 5,
+                              5, 7,
+                                 7, 8,
+                                    8, 9,
+                          4 , 6,
+                              6,       9,
+                                       9,     11,
+                                              11, 12,
+       };
+
+
+
+       private static final int[] TEST_EDGE_PAIRS = new int[] {
+              1 , 2,
+                  2 , 3,
+                      3 , 4,
+                          4 , 5,
+                              5, 7,
+                                 7, 8,
+                                    8, 9,
+                          4 , 6,
+                              6,       9,
+                                       9, 10,
+                                          10, 11,
+                                              11, 12,
+                  2,          5,
+                              5,                  12,
+
+                      3,                             13,
+                                                     13, 14,
+                                                         14, 15
+       };
+
+    public static final EdgeFactory<BaseVertex, BaseEdge> TEST_GRAPH_EDGE_FACTORY = new EdgeFactory<BaseVertex, BaseEdge>() {
+        @Override
+        public BaseEdge createEdge(final BaseVertex baseVertex, final BaseVertex baseVertex2) {
+            return new BaseEdge(false, 0);
+        }
+    };
+
+
+    private static Map<Integer, BaseVertex> vertexByInteger = new HashMap<>();
+    private static final BaseGraph<BaseVertex, BaseEdge> TEST_GRAPH = new BaseGraph<>(1, TEST_GRAPH_EDGE_FACTORY);
+    private static final List<Object[]> TEST_DATA;
+
+
+    static {
+        for (int i = 0; i < TEST_EDGE_PAIRS.length; i += 2) {
+            final int sourceInteger = TEST_EDGE_PAIRS[i];
+            final int targetInteger = TEST_EDGE_PAIRS[i + 1];
+            final BaseVertex sourceVertex = resolveVertexByInteger(sourceInteger);
+            final BaseVertex targetVertex = resolveVertexByInteger(targetInteger);
+            TEST_GRAPH.addEdge(sourceVertex, targetVertex);
+        }
+        Assert.assertEquals(1,TEST_GRAPH.getSources().size());
+        final Deque<Path<BaseVertex,BaseEdge>> pendingPaths = new LinkedList<>();
+        final Deque<Route<BaseVertex,BaseEdge>> pendingRoutes = new LinkedList<>();
+        final List<Path<BaseVertex,BaseEdge>> allPossiblePaths = new LinkedList<>();
+        final List<Route<BaseVertex,BaseEdge>> allPossibleRoutes = new LinkedList<>();
+        for (final BaseVertex vertex : TEST_GRAPH.vertexSet()) {
+            pendingPaths.add(new Path(vertex, TEST_GRAPH));
+            pendingRoutes.add(new Route(vertex,TEST_GRAPH));
+        }
+        while (!pendingPaths.isEmpty()) { // !pendingRoutes.isEmpty();
+            final Path<BaseVertex,BaseEdge> path = pendingPaths.remove();
+            final Route<BaseVertex,BaseEdge> route = pendingRoutes.remove();
+            final BaseVertex lastVertex = path.getLastVertex();
+            allPossiblePaths.add(path);
+            allPossibleRoutes.add(route);
+
+            if (allPossiblePaths.size() % 100 == 0)
+                Reporter.log("" + allPossiblePaths.size(), true);
+            for (final BaseEdge edge : TEST_GRAPH.outgoingEdgesOf(lastVertex))
+                pendingPaths.add(new Path<>(path,edge));
+            for (final BaseEdge edge : TEST_GRAPH.outgoingEdgesOf(lastVertex))
+                pendingRoutes.add(new Route<>(route,edge));
+        }
+
+        final int numberOfPaths = allPossiblePaths.size();
+        final boolean[][] isSuffix = buildIsSuffixMatrix(allPossiblePaths, numberOfPaths);
+        TEST_DATA = createTestData(allPossiblePaths,allPossibleRoutes,isSuffix);
+    }
+
+    private static boolean[][] buildIsSuffixMatrix(final List<Path<BaseVertex, BaseEdge>> allPossiblePaths, final int numberOfPaths) {
+        final boolean[][] isSuffix = new boolean[numberOfPaths][numberOfPaths];
+        final ListIterator<Path<BaseVertex,BaseEdge>> iIterator = allPossiblePaths.listIterator();
+        for (int i = 0; i < numberOfPaths; i++) {
+            isSuffix[i][i] = true;
+            final ListIterator<Path<BaseVertex,BaseEdge>> jIterator = allPossiblePaths.listIterator(i + 1);
+            final Path<BaseVertex,BaseEdge> iPath = iIterator.next();
+            for (int j = i + 1; j < numberOfPaths; j++) {
+                final Path<BaseVertex,BaseEdge> jPath = jIterator.next();
+                if (iPath.getLastVertex() != jPath.getLastVertex()) {
+                    isSuffix[i][j] = isSuffix[j][i] = false;
+                } else {
+                    isSuffix[i][j] = isSuffix[j][i] = true; // let assume they are suffix of each other by default.
+                    final Path<BaseVertex,BaseEdge> shortPath;
+                    final Path<BaseVertex,BaseEdge> longPath;
+                    if (iPath.getEdges().size() <= jPath.getEdges().size()) {
+                        shortPath = iPath;
+                        longPath = jPath;
+                    } else {
+                        longPath = iPath;
+                        shortPath = jPath;
+                    }
+                    final ListIterator<BaseEdge> longPathEdgesIterator = longPath.getEdges().listIterator(longPath.getEdges().size());
+                    final ListIterator<BaseEdge> shortPathEdgesIterator = shortPath.getEdges().listIterator(shortPath.getEdges().size());
+
+                    while (shortPathEdgesIterator.hasPrevious()) {
+                        final BaseEdge shortEdge = shortPathEdgesIterator.previous();
+                        final BaseEdge longEdge = longPathEdgesIterator.previous();
+                        if (shortEdge != longEdge) {
+                           isSuffix[i][j] = isSuffix[j][i] = false;
+                            break;
+                        }
+                    }
+                    if (isSuffix[i][j]) {
+                        if (longPathEdgesIterator.hasPrevious()) {
+                            if (longPath == iPath)
+                                isSuffix[j][i] = false;
+                            else
+                                isSuffix[i][j] = false;
+                        }
+                    }
+                }
+
+            }
+        }
+        return isSuffix;
+    }
+
+    private static List<Object[]> createTestData(final List<Path<BaseVertex, BaseEdge>> allPossiblePaths, final List<Route<BaseVertex, BaseEdge>> allPossibleRoutes, final boolean[][] isSuffix) {
+        final List<Object[]> result = new ArrayList<>(allPossiblePaths.size() * allPossiblePaths.size() * 2 );
+        final Path<BaseVertex,BaseEdge>[] allPaths = allPossiblePaths.toArray(new Path[allPossiblePaths.size()]);
+        final Route<BaseVertex,BaseEdge>[] allRoutes = allPossibleRoutes.toArray(new Route[allPossibleRoutes.size()]);
+        final int numberOfPaths = allPaths.length;
+        for (int i = 0; i < numberOfPaths; i++)
+            for (int j = 0; j < numberOfPaths; j++) {
+                result.add(new Object[] { allRoutes[i], allPaths[j], isSuffix[i][j] });
+                result.add(new Object[] { allRoutes[i], allRoutes[j], isSuffix[i][j] });
+                result.add(new Object[] { allRoutes[i], inverseRebuild(allRoutes[j]), isSuffix[i][j]});
+            }
+
+        return result;
+    }
+
+    private static Route<BaseVertex,BaseEdge> inverseRebuild(final Route<BaseVertex,BaseEdge> original) {
+        final ListIterator<BaseEdge> it = original.getEdges().listIterator(original.length());
+        Route<BaseVertex,BaseEdge> result = new Route<>(original.getLastVertex(),original.getGraph());
+        while (it.hasPrevious()) {
+            result = new Route<>(it.previous(),result);
+        }
+        return result;
+    }
+
+    private static BaseVertex resolveVertexByInteger(final int targetInteger) {
+        if (vertexByInteger.containsKey(targetInteger))
+            return vertexByInteger.get(targetInteger);
+        else {
+            int value = targetInteger;
+            final StringBuffer stringBuffer = new StringBuffer();
+            while (value > 0) {
+               int c = value % 4;
+               switch (c) {
+                   case 0: stringBuffer.append('A'); break;
+                   case 1: stringBuffer.append('C'); break;
+                   case 2: stringBuffer.append('G'); break;
+                   case 3: stringBuffer.append('T'); break;
+               }
+               value = value / 4;
+            }
+            if (stringBuffer.length() == 0) stringBuffer.append('A');
+            final byte[] sequence = stringBuffer.reverse().toString().getBytes();
+            final BaseVertex result = new BaseVertex(sequence);
+            vertexByInteger.put(targetInteger, result);
+            TEST_GRAPH.addVertex(result);
+            return result;
+        }
+
+    }
+
+
+}
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java
index 473df8fb0..84b2ee449 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java
@@ -113,6 +113,8 @@ public class SeqGraphUnitTest extends BaseTest {
         Assert.assertEquals(actualV.getSequence(), cfg.sequence);
     }
 
+
+
     @DataProvider(name = "IsDiamondData")
     public Object[][] makeIsDiamondData() throws Exception {
         List<Object[]> tests = new ArrayList<Object[]>();
@@ -120,7 +122,7 @@ public class SeqGraphUnitTest extends BaseTest {
         SeqGraph graph;
         SeqVertex pre1, pre2, top, middle1, middle2, middle3, bottom, tail1, tail2;
 
-        graph = new SeqGraph();
+        graph = new SeqGraph(11);
 
         pre1 = new SeqVertex("ACT");
         pre2 = new SeqVertex("AGT");
@@ -170,7 +172,7 @@ public class SeqGraphUnitTest extends BaseTest {
 
         // top connects to bottom directly as well
         {
-            final SeqGraph topConnectsToBottomToo = new SeqGraph();
+            final SeqGraph topConnectsToBottomToo = new SeqGraph(11);
             final SeqVertex top2 = new SeqVertex("A");
             final SeqVertex middle4 = new SeqVertex("C");
             final SeqVertex bottom2 = new SeqVertex("G");
@@ -194,7 +196,7 @@ public class SeqGraphUnitTest extends BaseTest {
     public Object[][] makeMergingData() throws Exception {
         List<Object[]> tests = new ArrayList<Object[]>();
 
-        final SeqGraph graph = new SeqGraph();
+        final SeqGraph graph = new SeqGraph(11);
 
         SeqVertex pre1 = new SeqVertex(Utils.dupString("A", SeqGraph.MIN_COMMON_SEQUENCE_TO_MERGE_SOURCE_SINK_VERTICES) + "CT");
         SeqVertex pre2 = new SeqVertex(Utils.dupString("A", SeqGraph.MIN_COMMON_SEQUENCE_TO_MERGE_SOURCE_SINK_VERTICES) + "GT");
@@ -216,7 +218,7 @@ public class SeqGraphUnitTest extends BaseTest {
             graph.addVertices(top);
             graph.addEdges(pre1, top);
             final SeqVertex pre1_top = new SeqVertex(pre1.getSequenceString() + top.getSequenceString());
-            final SeqGraph expected = new SeqGraph();
+            final SeqGraph expected = new SeqGraph(11);
             expected.addVertex(pre1_top);
             tests.add(new Object[]{graph.clone(), expected.clone()});
         }
@@ -225,7 +227,7 @@ public class SeqGraphUnitTest extends BaseTest {
         {
             graph.addVertices(middle1);
             graph.addEdges(top, middle1);
-            final SeqGraph expected = new SeqGraph();
+            final SeqGraph expected = new SeqGraph(11);
             final SeqVertex pre1_top_middle1 = new SeqVertex(pre1.getSequenceString() + top.getSequenceString() + middle1.getSequenceString());
             expected.addVertex(pre1_top_middle1);
             tests.add(new Object[]{graph.clone(), expected});
@@ -235,7 +237,7 @@ public class SeqGraphUnitTest extends BaseTest {
         {
             graph.addVertices(middle2);
             graph.addEdges(top, middle2);
-            final SeqGraph expected = new SeqGraph();
+            final SeqGraph expected = new SeqGraph(11);
             final SeqVertex pre1_top = new SeqVertex(pre1.getSequenceString() + top.getSequenceString());
             expected.addVertices(pre1_top, middle1, middle2);
             expected.addEdges(pre1_top, middle1);
@@ -248,7 +250,7 @@ public class SeqGraphUnitTest extends BaseTest {
             graph.addVertices(bottom);
             graph.addEdges(middle1, bottom);
             graph.addEdges(middle2, bottom);
-            final SeqGraph expected = new SeqGraph();
+            final SeqGraph expected = new SeqGraph(11);
             final SeqVertex pre1_top = new SeqVertex(pre1.getSequenceString() + top.getSequenceString());
             final SeqVertex newMiddle1 = new SeqVertex("G");
             final SeqVertex newMiddle2 = new SeqVertex("T");
@@ -274,12 +276,12 @@ public class SeqGraphUnitTest extends BaseTest {
         }
 
         { // all the nodes -> lots of merging and motion of nodes
-            final SeqGraph all = new SeqGraph();
+            final SeqGraph all = new SeqGraph(11);
             all.addVertices(pre1, pre2, top, middle1, middle2, bottom, tail1, tail2);
             all.addEdges(pre1, top, middle1, bottom, tail1);
             all.addEdges(pre2, top, middle2, bottom, tail2);
 
-            final SeqGraph expected = new SeqGraph();
+            final SeqGraph expected = new SeqGraph(11);
             SeqVertex newPre1 = new SeqVertex(Utils.dupString("A", SeqGraph.MIN_COMMON_SEQUENCE_TO_MERGE_SOURCE_SINK_VERTICES) + "C");
             SeqVertex newPre2 = new SeqVertex(Utils.dupString("A", SeqGraph.MIN_COMMON_SEQUENCE_TO_MERGE_SOURCE_SINK_VERTICES) + "G");
             final SeqVertex newTop = new SeqVertex("TA");
@@ -294,7 +296,7 @@ public class SeqGraphUnitTest extends BaseTest {
 
         // test the case where we delete a middle node away because the common sequence is all of its sequence
         {
-            final SeqGraph graph2 = new SeqGraph();
+            final SeqGraph graph2 = new SeqGraph(11);
             final SeqVertex mytop = new SeqVertex("A");
             final SeqVertex mid1 = new SeqVertex("AC");
             final SeqVertex mid2 = new SeqVertex("C");
@@ -303,7 +305,7 @@ public class SeqGraphUnitTest extends BaseTest {
             graph2.addEdges(mytop, mid1, bot);
             graph2.addEdges(mytop, mid2, bot);
 
-            final SeqGraph expected = new SeqGraph();
+            final SeqGraph expected = new SeqGraph(11);
             final SeqVertex newMid1 = new SeqVertex("A");
             final SeqVertex newBottom = new SeqVertex("CG");
             expected.addVertices(mytop, newMid1, newBottom);
@@ -339,7 +341,7 @@ public class SeqGraphUnitTest extends BaseTest {
     //
     @Test(enabled = !DEBUG)
     public void testBubbleSameBasesWithRef() {
-        final SeqGraph graph = new SeqGraph();
+        final SeqGraph graph = new SeqGraph(11);
         final SeqVertex top = new SeqVertex("A");
         final SeqVertex mid1 = new SeqVertex("ACT");
         final SeqVertex mid2 = new SeqVertex("ACT");
@@ -349,7 +351,7 @@ public class SeqGraphUnitTest extends BaseTest {
         graph.addEdge(top, mid1, new BaseEdge(true, 1));
         graph.addEdge(mid1, bot, new BaseEdge(true, 1));
 
-        final SeqGraph expected = new SeqGraph();
+        final SeqGraph expected = new SeqGraph(11);
         expected.addVertex(new SeqVertex("AACTC"));
         final SeqGraph actual = ((SeqGraph)graph.clone());
         actual.simplifyGraph();
@@ -360,8 +362,8 @@ public class SeqGraphUnitTest extends BaseTest {
     public Object[][] makeLinearZipData() throws Exception {
         List<Object[]> tests = new ArrayList<Object[]>();
 
-        SeqGraph graph = new SeqGraph();
-        SeqGraph expected = new SeqGraph();
+        SeqGraph graph = new SeqGraph(11);
+        SeqGraph expected = new SeqGraph(11);
 
         // empty graph => empty graph
         tests.add(new Object[]{graph.clone(), expected.clone()});
@@ -377,7 +379,7 @@ public class SeqGraphUnitTest extends BaseTest {
         tests.add(new Object[]{graph.clone(), expected.clone()});
 
         graph.addEdges(a1, c1);
-        expected = new SeqGraph();
+        expected = new SeqGraph(11);
         expected.addVertices(ac1);
         tests.add(new Object[]{graph.clone(), expected.clone()});
 
@@ -385,25 +387,25 @@ public class SeqGraphUnitTest extends BaseTest {
         SeqVertex g1 = new SeqVertex("G");
         graph.addVertices(g1);
         graph.addEdges(c1, g1);
-        expected = new SeqGraph();
+        expected = new SeqGraph(11);
         expected.addVertex(new SeqVertex("ACG"));
         tests.add(new Object[]{graph.clone(), expected.clone()});
 
         // adding something that isn't connected isn't a problem
         SeqVertex t1 = new SeqVertex("T");
         graph.addVertices(t1);
-        expected = new SeqGraph();
+        expected = new SeqGraph(11);
         expected.addVertices(new SeqVertex("ACG"), new SeqVertex("T"));
         tests.add(new Object[]{graph.clone(), expected.clone()});
 
         // splitting chain with branch produces the correct zipped subgraphs
         final SeqVertex a2 = new SeqVertex("A");
         final SeqVertex c2 = new SeqVertex("C");
-        graph = new SeqGraph();
+        graph = new SeqGraph(11);
         graph.addVertices(a1, c1, g1, t1, a2, c2);
         graph.addEdges(a1, c1, g1, t1, a2);
         graph.addEdges(g1, c2);
-        expected = new SeqGraph();
+        expected = new SeqGraph(11);
         SeqVertex acg = new SeqVertex("ACG");
         SeqVertex ta = new SeqVertex("TA");
         expected.addVertices(acg, ta, c2);
@@ -413,11 +415,11 @@ public class SeqGraphUnitTest extends BaseTest {
 
         // Can merge chains with loops in them
         {
-            graph = new SeqGraph();
+            graph = new SeqGraph(11);
             graph.addVertices(a1, c1, g1);
             graph.addEdges(a1, c1, g1);
             graph.addEdges(a1, a1);
-            expected = new SeqGraph();
+            expected = new SeqGraph(11);
 
             SeqVertex ac = new SeqVertex("AC");
             SeqVertex cg = new SeqVertex("CG");
@@ -433,7 +435,7 @@ public class SeqGraphUnitTest extends BaseTest {
 
             graph.removeEdge(c1, c1);
             graph.addEdges(g1, g1);
-            expected = new SeqGraph();
+            expected = new SeqGraph(11);
             expected.addVertices(ac, g1);
             expected.addEdges(ac, g1, g1);
             tests.add(new Object[]{graph.clone(), expected.clone()});
@@ -443,8 +445,8 @@ public class SeqGraphUnitTest extends BaseTest {
         {
             final List<String> bases = Arrays.asList("A", "C", "G", "T", "TT", "GG", "CC", "AA");
             for ( final int len : Arrays.asList(1, 2, 10, 100, 1000)) {
-                graph = new SeqGraph();
-                expected = new SeqGraph();
+                graph = new SeqGraph(11);
+                expected = new SeqGraph(11);
                 SeqVertex last = null;
                 String expectedBases = "";
                 for ( int i = 0; i < len; i++ ) {
@@ -465,8 +467,8 @@ public class SeqGraphUnitTest extends BaseTest {
             int edgeWeight = 1;
             for ( final int nIncoming : Arrays.asList(0, 2, 5, 10) ) {
                 for ( final int nOutgoing : Arrays.asList(0, 2, 5, 10) ) {
-                    graph = new SeqGraph();
-                    expected = new SeqGraph();
+                    graph = new SeqGraph(11);
+                    expected = new SeqGraph(11);
 
                     graph.addVertices(a1, c1, g1);
                     graph.addEdges(a1, c1, g1);
@@ -530,7 +532,7 @@ public class SeqGraphUnitTest extends BaseTest {
         final SeqVertex v5 = new SeqVertex("CCTCCACCATCCTCCCCTCTAGGCTTCTCCTCCTCCTCCACCATCCTCCCCTCTAGACTTCTCCTCCTCCTCCACCATCCTCCCCTCTAGACTTCTCCTCCTCCTCCACCATC");
         final SeqVertex v6 = new SeqVertex("CTCCCCT");
 
-        final SeqGraph graph = new SeqGraph();
+        final SeqGraph graph = new SeqGraph(11);
         graph.addVertices(v1, v2, v3, v4, v5, v6);
         graph.addEdges(v1, v3, v4, v6, v3);
         graph.addEdges(v2, v4);
@@ -538,4 +540,5 @@ public class SeqGraphUnitTest extends BaseTest {
 
         graph.simplifyGraph();
     }
+
 }
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java
index 5bc13f884..bb504b78c 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java
@@ -125,7 +125,7 @@ public class SharedVertexSequenceSplitterUnitTest extends BaseTest {
 
     @Test(dataProvider = "PrefixSuffixData")
     public void testSplitter(final List<String> strings, int expectedPrefixLen, int expectedSuffixLen) {
-        final SeqGraph graph = new SeqGraph();
+        final SeqGraph graph = new SeqGraph(11);
 
         final List<SeqVertex> v = new ArrayList<SeqVertex>();
         for ( final String s : strings ) {
@@ -202,7 +202,7 @@ public class SharedVertexSequenceSplitterUnitTest extends BaseTest {
 
     @Test(dataProvider = "CompleteCycleData")
     public void testSplitterCompleteCycle(final List<String> strings, final boolean hasTop, final boolean hasBot) {
-        final SeqGraph graph = new SeqGraph();
+        final SeqGraph graph = new SeqGraph(11);
 
         int edgeWeight = 1;
         final SeqVertex top = hasTop ? new SeqVertex("AAAAAAAA") : null;
@@ -276,7 +276,7 @@ public class SharedVertexSequenceSplitterUnitTest extends BaseTest {
 
     @Test(dataProvider = "MeetsMinSequenceData")
     public void testSplitterCompleteCycle(final List<String> mids, final int minSeqLength, final boolean prefixMeets, final boolean suffixMeets) {
-        final SeqGraph graph = new SeqGraph();
+        final SeqGraph graph = new SeqGraph(11);
 
         final SeqVertex top = new SeqVertex("AAAAAAAA");
         final SeqVertex bot = new SeqVertex("GGGGGGGG");
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java
index 1c59f9f7e..0d9c07251 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java
@@ -74,6 +74,20 @@ public class ReadThreadingGraphUnitTest extends BaseTest {
         Assert.assertEquals(actual, expected);
     }
 
+    @Test
+    public void testSimpleHaplotypeRethreading() {
+        final ReadThreadingGraph assembler = new ReadThreadingGraph(11);
+        final String ref   = "CATGCACTTTAAAACTTGCCTTTTTAACAAGACTTCCAGATG";
+        final String alt   = "CATGCACTTTAAAACTTGCCGTTTTAACAAGACTTCCAGATG";
+        assembler.addSequence("anonymous", getBytes(ref), null, true);
+        assembler.addSequence("anonymous", getBytes(alt), null, false);
+        assembler.buildGraphIfNecessary();
+        Assert.assertNotEquals(ref.length() - 11 + 1,assembler.vertexSet().size(),"the number of vertex in the graph is the same as if there was no alternative sequence");
+        Assert.assertEquals(ref.length() - 11 + 1 + 11,assembler.vertexSet().size(),"the number of vertex in the graph is not the same as if there is an alternative sequence");
+        MultiDeBruijnVertex startAlt = assembler.findKmer(new Kmer(alt.getBytes(),20,11));
+        Assert.assertNotNull(startAlt);
+    }
+
     @Test(enabled = ! DEBUG)
     public void testNonUniqueMiddle() {
         final ReadThreadingGraph assembler = new ReadThreadingGraph(3);
diff --git a/protected/java/test/org/broadinstitute/sting/utils/RandomDNA.java b/protected/java/test/org/broadinstitute/sting/utils/RandomDNA.java
new file mode 100644
index 000000000..88f5910f7
--- /dev/null
+++ b/protected/java/test/org/broadinstitute/sting/utils/RandomDNA.java
@@ -0,0 +1,127 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+*
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+package org.broadinstitute.sting.utils;
+
+import com.sun.istack.internal.NotNull;
+
+import java.util.Random;
+
+/**
+ * Random DNA sequence generator.
+ *
+ * <p>
+ *     Returned bases are always in upper case and one of the valid four nocleotides 'A', 'C', 'G' and 'T'.
+ * </p>
+ *
+ * @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.org&gt;
+ */
+public class RandomDNA {
+
+    private Random random;
+
+    /**
+     * Constructs a new random DNA generator.
+     *
+     * <p>
+     *     The seed would be the default which would depend on system properties and the current time as
+     *     described in {@link Random} documentation.
+     * </p>
+     */
+    public RandomDNA() {
+        random = new Random();
+    }
+
+    /**
+     * Constructs a new random DNA generator providing a seed.
+     *
+     * @param seed the random number generator seed.
+     */
+    public RandomDNA(final long seed) {
+        random = new Random(seed);
+    }
+
+    /**
+     * Updates the content of a byte array with a random base sequence.
+     *
+     * <p>
+     *     The whole array will be filled with new base values.
+     * </p>
+     *
+     * @param destination the array to update.
+     *
+     * @throws NullPointerException if {@code destination} is {@code null}.
+     */
+    public void nextBases(final byte[] destination) {
+        random.nextBytes(destination);
+        for (int i = 0; i < destination.length; i++) {
+            final int ord = destination[i] & 0x03;
+            switch (ord) {
+                case 0: destination[i] = 'A'; break;
+                case 1: destination[i] = 'C'; break;
+                case 2: destination[i] = 'G'; break;
+                case 3: destination[i] = 'T'; break;
+                default: throw new IllegalStateException("this cannot be happening!!!");
+            }
+        }
+    }
+
+    /**
+     * Returns a random RNA sequence of bases.
+     * @param size the length of the sequence.
+     *
+     * @throws IllegalArgumentException if {@code size} is negative.
+     * @return never {@code null}.
+     */
+    @NotNull
+    public byte[] nextBases(final int size) {
+        if (size < 0) throw new IllegalArgumentException("the size cannot be negative");
+        final byte[] result = new byte[size];
+        nextBases(result);
+        return result;
+    }
+
+
+}
diff --git a/protected/java/test/org/broadinstitute/sting/utils/collections/CountSetUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/collections/CountSetUnitTest.java
new file mode 100644
index 000000000..ae9ead827
--- /dev/null
+++ b/protected/java/test/org/broadinstitute/sting/utils/collections/CountSetUnitTest.java
@@ -0,0 +1,249 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+*
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt.
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+package org.broadinstitute.sting.utils.collections;
+
+import org.broadinstitute.sting.BaseTest;
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.Random;
+
+/**
+ * Unit tests for {@link CountSet}
+ */
+public class CountSetUnitTest extends BaseTest {
+
+    @Test(dataProvider="capacities")
+    public void testSize(final int capacity) {
+        final CountSet empty = new CountSet(capacity);
+        Assert.assertEquals(empty.size(), 0);
+        CountSet nonEmpty = new CountSet(capacity);
+        for (int i = 0; i < capacity * 3; i++) {
+            nonEmpty.add(i);
+            Assert.assertEquals(nonEmpty.size(),i + 1);
+        }
+    }
+
+    @Test
+    public void testSingleValueAdd() {
+        final int CAPACITY = 10;
+        final CountSet subject = new CountSet(CAPACITY);
+        final HashSet<Integer> reasuranceSet = new HashSet<>(CAPACITY);
+        final int REPEATS = 1000;
+        final Random rnd = new Random(13);
+        for (int i = 0; i < REPEATS; i++) {
+            int newInt = rnd.nextInt(500);
+            boolean expectedResult = reasuranceSet.add(newInt);
+            boolean result = subject.add(newInt);
+            Assert.assertEquals(result,expectedResult);
+            Assert.assertEquals(subject.size(),reasuranceSet.size());
+        }
+        for (final int j : reasuranceSet)
+            Assert.assertTrue(subject.contains(j));
+        for (int j = 0; j < 501; j++)
+            Assert.assertEquals(subject.contains(j),reasuranceSet.contains(j));
+    }
+
+    @Test
+    public void testToIntArray() {
+        final CountSet subject = new CountSet(10);
+        subject.addAll(1,4,7);
+        final int[] intArray = subject.toIntArray();
+        Assert.assertEquals(intArray.length,3);
+        Assert.assertEquals(intArray[0],1);
+        Assert.assertEquals(intArray[1],4);
+        Assert.assertEquals(intArray[2],7);
+    }
+
+    @Test
+    public void testCopyTo() {
+        final CountSet subject = new CountSet(10);
+        subject.addAll(1,4,7);
+        final int[] intArray = new int[3];
+        subject.copyTo(intArray);
+        Assert.assertEquals(intArray[0],1);
+        Assert.assertEquals(intArray[1],4);
+        Assert.assertEquals(intArray[2],7);
+    }
+
+    @Test
+    public void testSetToSingleValue() {
+        final CountSet subject = new CountSet(10);
+        subject.setTo(-31);
+        Assert.assertEquals(subject.size(),1);
+        Assert.assertEquals(subject.min(),-31);
+        Assert.assertEquals(subject.max(),-31);
+        Assert.assertTrue(subject.contains(-31));
+        Assert.assertFalse(subject.contains(-21));
+    }
+
+    @Test void testSetToArrayOfValues() {
+        final int CAPACITY = 10;
+        final CountSet subject = new CountSet(CAPACITY);
+        final int REPEATS = 1000;
+        final Random rnd = new Random(13);
+        final int[] values = new int[REPEATS];
+        for (int i = 0; i < REPEATS; i++) {
+            int newInt = rnd.nextInt(Integer.MAX_VALUE) * (rnd.nextBoolean() ? -1 : 1);
+            values[i] = newInt;
+        }
+        subject.setTo(values);
+        Arrays.sort(values);
+        Assert.assertEquals(subject.size(),REPEATS);
+        Assert.assertEquals(subject.min(),values[0]);
+        Assert.assertEquals(subject.max(),values[REPEATS - 1]);
+    }
+
+    @Test
+    public void testMinMax() {
+        final int CAPACITY = 10;
+        final CountSet subject = new CountSet(CAPACITY);
+        final int REPEATS = 1000;
+        final Random rnd = new Random(13);
+        final int[] values = new int[REPEATS];
+        for (int i = 0; i < REPEATS; i++) {
+            int newInt = rnd.nextInt(Integer.MAX_VALUE) * (rnd.nextBoolean() ? -1 : 1);
+            values[i] = newInt;
+        }
+        subject.addAll(values);
+        Arrays.sort(values);
+        Assert.assertEquals(subject.min(),values[0]);
+        Assert.assertEquals(subject.max(),values[REPEATS - 1]);
+    }
+
+    @Test
+    public void testIncrease() {
+        final int CAPACITY = 10;
+        final CountSet subject = new CountSet(CAPACITY);
+        final HashSet<Integer> reasuranceSet = new HashSet<>(CAPACITY);
+        final int REPEATS = 1000;
+        final Random rnd = new Random(13);
+        final int[] values = new int[REPEATS];
+        final Integer[] valueWrappers = new Integer[REPEATS];
+        for (int i = 0; i < REPEATS; i++) {
+            int newInt = rnd.nextInt(500);
+            values[i] = newInt;
+            valueWrappers[i] = newInt;
+        }
+
+        subject.incAll(3);
+
+        for (final int j : reasuranceSet)
+            Assert.assertTrue(subject.contains(j+3));
+        for (int j = 0; j < 501; j++)
+            Assert.assertEquals(subject.contains(j+3),reasuranceSet.contains(j));
+
+    }
+
+    @Test
+    public void testArrayValueAdd() {
+        final int CAPACITY = 10;
+        final CountSet subject = new CountSet(CAPACITY);
+        final HashSet<Integer> reasuranceSet = new HashSet<>(CAPACITY);
+        final int REPEATS = 1000;
+        final Random rnd = new Random(13);
+        final int[] values = new int[REPEATS];
+        final Integer[] valueWrappers = new Integer[REPEATS];
+        for (int i = 0; i < REPEATS; i++) {
+            int newInt = rnd.nextInt(500);
+            values[i] = newInt;
+            valueWrappers[i] = newInt;
+        }
+
+        boolean expectedResult = reasuranceSet.addAll(Arrays.asList(valueWrappers));
+        boolean result = subject.addAll(values);
+        Assert.assertEquals(result,expectedResult);
+        Assert.assertEquals(subject.size(),reasuranceSet.size());
+
+        for (final int j : reasuranceSet)
+            Assert.assertTrue(subject.contains(j));
+        for (int j = 0; j < 501; j++)
+            Assert.assertEquals(subject.contains(j),reasuranceSet.contains(j));
+
+    }
+
+    @Test
+    public void testAddRange() {
+        final CountSet subject = new CountSet(10);
+        subject.addRange(10,21);
+        Assert.assertEquals(subject.size(),12);
+        for (int i = 10; i < 22; i++)
+            Assert.assertTrue(subject.contains(i));
+        for (int i = -1; i < 10; i++)
+            Assert.assertFalse(subject.contains(i));
+        for (int i = 22; i < 31; i++)
+            Assert.assertFalse(subject.contains(i));
+    }
+
+    @DataProvider(name="capacities")
+    public Iterator<Object[]> capacities() {
+        final int MIN = 0;
+        final int MAX = 255;
+        return new Iterator<Object[]>() {
+                private int current = MIN;
+
+
+            @Override
+            public boolean hasNext() {
+                return current < MAX;
+            }
+
+            @Override
+            public Object[] next() {
+                return new Object[] { Integer.valueOf(current++) };
+            }
+
+            @Override
+            public void remove() {
+                throw new UnsupportedOperationException();
+            }
+        };
+    }
+}
diff --git a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/ActiveRegionTestDataSet.java b/protected/java/test/org/broadinstitute/sting/utils/pairhmm/ActiveRegionTestDataSet.java
new file mode 100644
index 000000000..cee8d358e
--- /dev/null
+++ b/protected/java/test/org/broadinstitute/sting/utils/pairhmm/ActiveRegionTestDataSet.java
@@ -0,0 +1,589 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*  
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*  
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*  
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*  
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*  
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. 
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.  
+*  
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY 
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*  
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*  
+*  5. NO REPRESENTATIONS OR WARRANTIES
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+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*  
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt. 
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. 
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.sting.utils.pairhmm;
+
+import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMSequenceDictionary;
+import net.sf.samtools.SAMSequenceRecord;
+import org.apache.commons.math.MathException;
+import org.apache.commons.math.distribution.ExponentialDistribution;
+import org.apache.commons.math.distribution.ExponentialDistributionImpl;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.AssemblyResult;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.AssemblyResultSet;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.Civar;
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.ReadThreadingGraph;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.QualityUtils;
+import org.broadinstitute.sting.utils.haplotype.Haplotype;
+import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+
+import java.util.*;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+/**
+* Mock-up active region data used in testing.
+*
+* @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.org&gt;
+*/
+public class ActiveRegionTestDataSet {
+
+    private final byte[] referenceBytes;
+    protected String reference;
+    protected String[] haplotypeCigars;
+    protected List<String> haplotypeStrings;
+    protected String[] readCigars;
+    protected byte[] bq;
+    protected byte[] dq;
+    protected byte[] iq;
+    protected int kmerSize;
+    private List<Haplotype> haplotypeList;
+    private List<GATKSAMRecord> readList;
+    private AssemblyResultSet assemblyResultSet;
+    private Map<String,GATKSAMRecord> readBySequence;
+    private String stringRepresentation;
+    private List<List<Civar.ElementOffset>> readEventOffsetList;
+    private GenomeLocParser genomeLocParser;
+
+    /** Create a new active region data test set */
+    public ActiveRegionTestDataSet(final int kmerSize, final String reference, final String[] haplotypes,
+                                   final String[] readCigars, final byte[] bq, final byte[] dq, final byte[] iq) {
+        this.reference = reference;
+        this.referenceBytes = reference.getBytes();
+        this.haplotypeCigars = haplotypes;
+        this.readCigars = readCigars;
+        this.bq = bq;
+        this.dq = dq;
+        this.iq = iq;
+        this.kmerSize = kmerSize;
+        this.genomeLocParser = new GenomeLocParser(ArtificialSAMUtils.createArtificialSamHeader(1,1,reference.length()).getSequenceDictionary());
+    }
+
+    public String getReference() {
+        return reference;
+    }
+
+    public String toString() {
+        if (stringRepresentation == null)
+            return super.toString();
+        else return stringRepresentation;
+    }
+
+    public AssemblyResultSet assemblyResultSet() {
+        if (assemblyResultSet == null) {
+            final ReadThreadingGraph rtg = new ReadThreadingGraph(kmerSize);
+            rtg.addSequence("anonymous", this.getReference().getBytes(), null, true);
+            for (final String haplotype : this.haplotypesStrings()) {
+                rtg.addSequence("anonymous", haplotype.getBytes(), null, false);
+            }
+            rtg.buildGraphIfNecessary();
+            if (rtg.hasCycles())
+                throw new RuntimeException("there is cycles in the reference with kmer size " + kmerSize + ". Don't use this size for the benchmark or change the reference");
+
+            List<Haplotype> haplotypeList = this.haplotypeList();
+
+            assemblyResultSet = new AssemblyResultSet();
+            final AssemblyResult ar = new AssemblyResult((haplotypeList.size() > 1 ?
+                    AssemblyResult.Status.ASSEMBLED_SOME_VARIATION : AssemblyResult.Status.JUST_ASSEMBLED_REFERENCE),rtg.convertToSequenceGraph());
+            ar.setThreadingGraph(rtg);
+
+            for (final Haplotype h : haplotypeList)
+                assemblyResultSet.add(h, ar);
+        }
+        return assemblyResultSet;
+    }
+
+    public List<String> haplotypesStrings() {
+        if (haplotypeStrings != null) {
+            return haplotypeStrings;
+        }
+        final List<String> result = new ArrayList<>(haplotypeCigars.length);
+        String reference = this.reference;
+        for (final String cigar : haplotypeCigars) {
+            if (cigar.matches("^Civar:.*$")) {
+                stringRepresentation = cigar.substring(6);
+                result.addAll(expandAllCombinations(cigar.substring(6),reference));
+            } else if (cigar.matches("^.*\\d+.*$")) {
+                result.add(applyCigar(reference, cigar,0,true));
+            } else {
+                result.add(cigar);
+            }
+        }
+        haplotypeStrings = result;
+        return result;
+    }
+
+    private List<String> expandAllCombinations(final String cigarString, final String reference) {
+        final Civar civar = Civar.fromCharSequence(cigarString);
+        final List<Civar> unrolledCivars = civar.optionalizeAll().unroll();
+        List<String> result = new ArrayList<>(unrolledCivars.size());
+        for (final Civar c : unrolledCivars) {
+            result.add(c.applyTo(reference));
+        }
+        return result;
+    }
+
+    private List<Haplotype> expandAllHaplotypeCombinations(final String civarString, final String reference) {
+        final Civar civar = Civar.fromCharSequence(civarString);
+        final List<Civar> unrolledCivars = civar.optionalizeAll().unroll();
+        List<Haplotype> result = new ArrayList<>(unrolledCivars.size());
+        for (final Civar c : unrolledCivars) {
+            final String baseString = c.applyTo(reference);
+            final Haplotype haplotype = new Haplotype(baseString.getBytes(),baseString.equals(reference));
+            haplotype.setGenomeLocation(genomeLocParser.createGenomeLoc("chr1",1,reference.length()));
+            try {
+            haplotype.setCigar(c.toCigar(reference.length()));
+            } catch (final RuntimeException ex) {
+                c.applyTo(reference);
+                c.toCigar(reference.length());
+                throw new RuntimeException("" + c + " " + ex.getMessage(),ex);
+            }
+            result.add(haplotype);
+        }
+        return result;
+    }
+
+
+    public List<Haplotype> haplotypeList() {
+        if (haplotypeList == null) {
+
+          final List<Haplotype> result = new ArrayList<>(haplotypeCigars.length);
+          final String reference = this.reference;
+          for (final String cigar : haplotypeCigars) {
+              if (cigar.matches("^Civar:.*$")) {
+                  stringRepresentation = cigar.substring(6);
+                  result.addAll(expandAllHaplotypeCombinations(cigar.substring(6), reference));
+              } else if (cigar.matches("^.*\\d+.*$")) {
+                  result.add(cigarToHaplotype(reference, cigar, 0, true));
+              } else {
+                  final Haplotype h = new Haplotype(cigar.getBytes());
+                  h.setGenomeLocation(genomeLocParser.createGenomeLoc("chr1",1,reference.length()));
+                  result.add(h);
+              }
+          }
+          haplotypeList = result;
+        }
+        return haplotypeList;
+    }
+
+
+    protected SAMSequenceDictionary artificialSAMSequenceDictionary() {
+        return new SAMSequenceDictionary(Collections.singletonList(new SAMSequenceRecord("00",reference.length())));
+    }
+
+    protected SAMFileHeader artificialSAMFileHeader() {
+        return ArtificialSAMUtils.createArtificialSamHeader(artificialSAMSequenceDictionary());
+    }
+
+    public List<GATKSAMRecord> readList() {
+        if (readList == null) {
+            final SAMFileHeader header = artificialSAMFileHeader();
+            readList = new ArrayList<>(readCigars.length);
+            final List<String> haplotypes = haplotypesStrings();
+            int count = 0;
+            for (final String descr : readCigars) {
+                String sequence;
+                if (descr.matches("^\\d+:\\d+:.+$")) {
+                    final String[] parts = descr.split(":");
+                    int allele = Integer.valueOf(parts[0]);
+                    int offset = Integer.valueOf(parts[1]);
+                    final String cigar = parts[2];
+                    final String base = allele == 0 ? reference : haplotypes.get(allele - 1);
+                    sequence = applyCigar(base, cigar, offset, false);
+                    final GATKSAMRecord samRecord = ArtificialSAMUtils.createArtificialRead(header, "read_" + count, 0, 1, sequence.getBytes(), Arrays.copyOf(bq, sequence.length()));
+                    readList.add(new MyGATKSAMRecord(samRecord));
+                } else if (descr.matches("^\\*:\\d+:\\d+$")) {
+                    int readCount = Integer.valueOf(descr.split(":")[1]);
+                    int readLength = Integer.valueOf(descr.split(":")[2]);
+                    readList.addAll(generateSamRecords(haplotypes, readCount, readLength, header, count));
+                } else {
+                    sequence = descr;
+                    final GATKSAMRecord samRecord = ArtificialSAMUtils.createArtificialRead(header, "read_" + count, 0, 1, sequence.getBytes(), Arrays.copyOf(bq, sequence.length()));
+                    readList.add(new MyGATKSAMRecord(samRecord));
+                }
+                count = readList.size();
+            }
+        }
+        return readList;
+    }
+
+    public List<List<Civar.ElementOffset>> readEventOffsetList() {
+        if (haplotypeCigars.length != 1 || !haplotypeCigars[0].startsWith("Civar:"))
+            throw new UnsupportedOperationException();
+        if (readEventOffsetList == null) {
+            final Civar civar = Civar.fromCharSequence(haplotypeCigars[0].substring(6));
+            final List<Civar> unrolledCivars = civar.optionalizeAll().unroll();
+
+            readEventOffsetList = new ArrayList<>(readCigars.length);
+            int count = 0;
+            for (final String descr : readCigars) {
+                if (descr.matches("^\\d+:\\d+:.+$")) {
+                    throw new UnsupportedOperationException();
+                } else if (descr.matches("^\\*:\\d+:\\d+$")) {
+                    int readCount = Integer.valueOf(descr.split(":")[1]);
+                    int readLength = Integer.valueOf(descr.split(":")[2]);
+                    readEventOffsetList.addAll(generateElementOffsetRecords(haplotypesStrings(), unrolledCivars, readCount, readLength, count));
+                } else {
+                    throw new UnsupportedOperationException();
+                }
+                count = readEventOffsetList.size();
+            }
+            readEventOffsetList = Collections.unmodifiableList(readEventOffsetList);
+        }
+        return readEventOffsetList;
+    }
+
+
+
+
+    @SuppressWarnings("unused")
+    public String cigarToSequence(final String cigar) {
+            String reference = this.reference;
+            return applyCigar(reference, cigar,0,true);
+    }
+
+    @SuppressWarnings("unused")
+    public GATKSAMRecord readFromString(final String readSequence) {
+        if (readBySequence == null) {
+            final List<GATKSAMRecord> readList = readList();
+            readBySequence = new HashMap<>(readList.size());
+            for (final GATKSAMRecord r : readList)
+                readBySequence.put(r.getReadString(),r);
+        }
+        return readBySequence.get(readSequence);
+    }
+
+    public List<Civar> unrolledCivars() {
+        if (haplotypeCigars.length != 1 || !haplotypeCigars[0].startsWith("Civar:"))
+            throw new UnsupportedOperationException();
+        final Civar civar = Civar.fromCharSequence(haplotypeCigars[0].substring(6));
+        return civar.optionalizeAll().unroll();
+    }
+
+    public void introduceErrors(final Random rnd) {
+        final List<GATKSAMRecord> reads = readList();
+        final ArrayList<GATKSAMRecord> result = new ArrayList<>(reads.size());
+        for (final GATKSAMRecord read : reads) {
+            result.add(new MyGATKSAMRecord(read,rnd));
+        }
+        readList = result;
+    }
+
+    private class MyGATKSAMRecord extends GATKSAMRecord {
+            protected MyGATKSAMRecord(final GATKSAMRecord r) {
+                super(r.getHeader(), r.getReferenceIndex(), r.getAlignmentStart(), (short) r.getReadNameLength(),
+                        (short) 100, -1, r.getCigarLength(), r.getFlags(), r.getReadLength(),
+                        r.getMateReferenceIndex(), r.getMateAlignmentStart(), r.getInferredInsertSize(),
+                        new byte[0]);
+                this.setReadBases(r.getReadBases());
+                this.setBaseQualities(r.getBaseQualities());
+                this.setReadName(r.getReadName());
+            }
+
+        ExponentialDistribution indelLengthDist = new ExponentialDistributionImpl(1.0/0.9);
+
+        public MyGATKSAMRecord(final GATKSAMRecord r, final Random rnd) {
+            super(r.getHeader(), r.getReferenceIndex(), r.getAlignmentStart(), (short) r.getReadNameLength(),
+                    (short) 100, -1, r.getCigarLength(), r.getFlags(), r.getReadLength(),
+                    r.getMateReferenceIndex(), r.getMateAlignmentStart(), r.getInferredInsertSize(),
+                    new byte[0]);
+            final byte[] bases = new byte[r.getReadBases().length];
+
+            final byte[] readBases = r.getReadBases();
+            final byte[] bq = r.getBaseQualities();
+            final byte[] iq = r.getBaseInsertionQualities();
+            final byte[] dq = r.getBaseDeletionQualities();
+            int refOffset = r.getAlignmentStart() - 1;
+            int readOffset = 0;
+            for (int i = 0; i < r.getReadBases().length;) {
+                double p = rnd.nextDouble();
+                double iqp = QualityUtils.qualToErrorProb(iq[i]);
+                if (p < iqp) { // insertion
+                    final int length = Math.min(generateIndelLength(rnd),r.getReadBases().length - i);
+                    final int refStart = rnd.nextInt(reference.length() - length);
+                    System.arraycopy(referenceBytes,refStart,bases,i,length);
+                    i += length;
+                    continue;
+                }
+                p -= iqp;
+                double dqp = QualityUtils.qualToErrorProb(dq[i]);
+                if (p < dqp) {
+                    final int length = generateIndelLength(rnd);
+                    refOffset += length;
+                    refOffset = refOffset % referenceBytes.length;
+                    readOffset += length;
+                    continue;
+                }
+                p -= dqp;
+                double bqp = QualityUtils.qualToErrorProb(bq[i]);
+                byte b = readOffset < readBases.length ? readBases[readOffset] : referenceBytes[refOffset];
+                byte nb;
+                if (p < bqp) {
+                   switch (b) {
+                       case 'A': nb = 'C'; break;
+                       case 'T': nb = 'A'; break;
+                       case 'C': nb = 'G'; break;
+                       case 'G': nb = 'B'; break;
+                       default: nb = 'A';
+                   }
+                } else
+                    nb = b;
+
+                bases[i++] = nb;
+                refOffset++;
+                refOffset = refOffset % referenceBytes.length;
+                readOffset++;
+            }
+            this.setReadBases(bases);
+            this.setBaseQualities(r.getBaseQualities());
+            this.setReadName(r.getReadName());
+
+
+        }
+
+        private int generateIndelLength(final Random rnd) {
+            final int length;
+            try {
+                length = (int) Math.round(indelLengthDist.inverseCumulativeProbability(rnd.nextDouble()) + 1);
+            } catch (MathException e) {
+                throw new RuntimeException(e);
+            }
+            return length;
+        }
+
+        @Override
+            public byte[] getBaseDeletionQualities() {
+                return Arrays.copyOf(dq,getReadLength());
+            }
+
+            @Override
+            public byte[] getBaseInsertionQualities() {
+                return Arrays.copyOf(iq,getReadLength());
+            }
+
+            @Override
+            public int getMappingQuality() {
+                return 100;
+            }
+
+            @Override
+            public int hashCode() {
+                return getReadName().hashCode();
+            }
+
+            @Override
+            public boolean equals(Object o) {
+                if (o instanceof GATKSAMRecord) {
+                    return getReadName().equals(((GATKSAMRecord)o).getReadName());
+                } else {
+                    return false;
+                }
+            }
+
+            public String toString() {
+                return super.toString() + " " + this.getReadString();
+            }
+    }
+
+
+    public List<String> readStrings() {
+        final List<String> result = new ArrayList<>(readCigars.length);
+        final List<String> haplotypes = haplotypesStrings();
+        for (final String descr : readCigars) {
+            String sequence;
+            if (descr.matches("^\\d+:\\d+:.+$")) {
+                final String[] parts = descr.split(":");
+                int allele = Integer.valueOf(parts[0]);
+                int offset = Integer.valueOf(parts[1]);
+                final String cigar = parts[2];
+                final String base = allele == 0 ? reference : haplotypes.get(allele - 1);
+                sequence = applyCigar(base, cigar, offset, false);
+                result.add(sequence);
+            } else if (descr.matches("\\*:^\\d+:\\d+")) {
+                int readCount = Integer.valueOf(descr.split(":")[1]);
+                int readLength = Integer.valueOf(descr.split(":")[2]);
+                result.addAll(generateReads(haplotypes, readCount, readLength));
+            } else {
+                sequence = descr;
+                result.add(sequence);
+            }
+        }
+        return result;
+    }
+
+    private List<String> generateReads(final List<String> haplotypes, final int readCount, final int readLength) {
+        final List<String> result = new ArrayList<>(readCount);
+        for (int i = 0; i < readCount; i++) {
+            int hi = i % haplotypes.size();
+            final String h = haplotypes.get(hi);
+            int offset = i % h.length() - readLength;
+            result.add(h.substring(offset,offset + readLength));
+        }
+        return result;
+    }
+
+    private List<MyGATKSAMRecord> generateSamRecords(final List<String> haplotypes, final int readCount, final int readLength, final SAMFileHeader header, final int idStart) {
+        int id = idStart;
+        final List<MyGATKSAMRecord> result = new ArrayList<>(readCount);
+        for (int i = 0; i < readCount; i++) {
+            int hi = i % haplotypes.size();
+            final String h = haplotypes.get(hi);
+            int offset = h.length() <= readLength ? 0 : i % (h.length() - readLength);
+            int to = Math.min(h.length(),offset + readLength);
+            byte[] bases = h.substring(offset,to).getBytes();
+            byte[] quals = Arrays.copyOf(bq,to - offset);
+            final GATKSAMRecord samRecord = ArtificialSAMUtils.createArtificialRead(header,"read_" + id++,0,offset + 1,bases, quals);
+            result.add(new MyGATKSAMRecord(samRecord));
+        }
+        return result;
+    }
+
+
+    private List<List<Civar.ElementOffset>> generateElementOffsetRecords(final List<String> haplotypes, final List<Civar> unrolledCivars, final int readCount, final int readLength, final int count) {
+
+        final List<List<Civar.ElementOffset>> result = new ArrayList<>(readCount);
+        for (int i = 0; i < readCount; i++) {
+            int hi = i % unrolledCivars.size();
+            final Civar c = unrolledCivars.get(hi);
+            final String h = haplotypes.get(hi);
+            int offset = h.length() <= readLength ? 0 : i % (h.length() - readLength);
+            int to = Math.min(h.length(),offset + readLength);
+            result.add(c.eventOffsets(reference,offset,to));
+        }
+        return result;
+    }
+
+    private static final Pattern cigarPattern = Pattern.compile("(\\d+)([=A-Z])");
+
+
+    private Haplotype cigarToHaplotype(final String reference, final String cigar, final int offset, final boolean global) {
+        final String sequence = applyCigar(reference,cigar,offset,global);
+        final Haplotype haplotype = new Haplotype(sequence.getBytes(),reference.equals(sequence));
+        haplotype.setGenomeLocation(genomeLocParser.createGenomeLoc("chr1",1,reference.length()));
+        haplotype.setCigar(Civar.fromCharSequence(cigar).toCigar(reference.length()));
+        return haplotype;
+    }
+
+    private String applyCigar(final String reference, final String cigar, final int offset, final boolean global) {
+        final Matcher pm = cigarPattern.matcher(cigar);
+        StringBuffer sb = new StringBuffer();
+        int index = offset;
+        while (pm.find()) {
+            int length = Integer.valueOf(pm.group(1));
+            char operator = pm.group(2).charAt(0);
+            switch (operator) {
+                case '=' :
+                    try {
+                      sb.append(reference.substring(index, index + length));
+                    } catch (Exception e) {
+                      throw new RuntimeException(" " + index + " " + (index + length) + " " + reference.length() + " " + cigar,e);
+                    }
+                    index += length; break;
+                case 'D' :
+                    index += length; break;
+                case 'I' :
+                    String insert = cigar.substring(pm.end(),pm.end() + length).toUpperCase();
+                    sb.append(insert); break;
+                case 'V' :
+                    sb.append(transversionV(reference.charAt(index))); index++; break;
+                case 'W' :
+                        sb.append(transversionW(reference.charAt(index))); index++; break;
+                case 'T' :
+                    sb.append(transition(reference.charAt(index))); index++; break;
+                default:
+                    throw new UnsupportedOperationException("cigar operator " + operator + " not supported.");
+            }
+        }
+        if (global && index != reference.length()) {
+            throw new RuntimeException(" haplotype cigar does not explain reference length (" + index + " != " + reference.length() + ") on cigar " + cigar);
+        } else if (index > reference.length()) {
+            throw new RuntimeException(" index beyond end ");
+        }
+        return sb.toString();
+    }
+
+    protected int kmerSize() {
+        return kmerSize;
+    }
+
+    private char transversionV(final char c) {
+        switch (Character.toUpperCase(c)) {
+            case 'A': return 'C';
+            case 'G': return 'T';
+            case 'C': return 'A';
+            case 'T': return 'G';
+            default:
+                return c;
+        }
+
+    }
+
+    private char transversionW(final char c) {
+        switch (Character.toUpperCase(c)) {
+            case 'A': return 'T';
+            case 'G': return 'C';
+            case 'T': return 'A';
+            case 'C': return 'G';
+            default:
+                return c;
+        }
+
+    }
+
+    private char transition(final char c) {
+        switch (Character.toUpperCase(c)) {
+            case 'A': return 'G';
+            case 'G': return 'A';
+            case 'T': return 'C';
+            case 'C': return 'T';
+            default:
+                return c;
+        }
+
+    }
+}
diff --git a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/FastLoglessPairHMMUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/pairhmm/FastLoglessPairHMMUnitTest.java
new file mode 100644
index 000000000..18817c9de
--- /dev/null
+++ b/protected/java/test/org/broadinstitute/sting/utils/pairhmm/FastLoglessPairHMMUnitTest.java
@@ -0,0 +1,177 @@
+/*
+*  By downloading the PROGRAM you agree to the following terms of use:
+*  
+*  BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+*  
+*  This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
+*  
+*  WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+*  WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+*  NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+*  
+*  1. DEFINITIONS
+*  1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
+*  
+*  2. LICENSE
+*  2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. 
+*  The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only.  For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+*  2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD.  LICENSEE shall ensure that all of its users agree to the terms of this Agreement.  LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+*  2.3  License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.  
+*  
+*  3. OWNERSHIP OF INTELLECTUAL PROPERTY 
+*  LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies.  LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+*  Copyright 2012 Broad Institute, Inc.
+*  Notice of attribution:  The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+*  LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+*  
+*  4. INDEMNIFICATION
+*  LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+*  
+*  5. NO REPRESENTATIONS OR WARRANTIES
+*  THE PROGRAM IS DELIVERED AS IS.  BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+*  IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+*  
+*  6. ASSIGNMENT
+*  This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+*  
+*  7. MISCELLANEOUS
+*  7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+*  7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+*  7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+*  7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested.  All notices under this Agreement shall be deemed effective upon receipt. 
+*  7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. 
+*  7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+*  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.sting.utils.pairhmm;
+
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.ActiveRegionTestDataSetUnitTest;
+import org.broadinstitute.sting.utils.haplotype.Haplotype;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+import java.util.*;
+
+
+/**
+ * Created with IntelliJ IDEA.
+ * User: valentin
+ * Date: 10/13/13
+ * Time: 12:55 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class FastLoglessPairHMMUnitTest extends ActiveRegionTestDataSetUnitTest {
+
+    private FastLoglessPairHMM unsorted = new FastLoglessPairHMM((byte)10);
+    private FastLoglessPairHMM sorted = new FastLoglessPairHMM((byte)10);
+
+    @Test(enabled=false,dataProvider="activeRegionTestDataSets")
+    public void testActiveRegionsDataSet(final ActiveRegionTestDataSet as, final int kmerSize, final int readLength, final String variation, final int readCount, final int regionSize, final byte bq, final byte iq, final byte dq) {
+
+    }
+
+    @Test(enabled=true,dataProvider="activeRegionTestDataSets")
+    public void testHaplotypeGrouped(final ActiveRegionTestDataSet as, final int kmerSize, final int readLength, final String variation, final int readCount, final int regionSize, final byte bq, final byte iq, final byte dq) {
+        final List<GATKSAMRecord> reads = as.readList();
+        final List<Haplotype> haplotypes = as.haplotypeList();
+        PairHMMReadyHaplotypes haplotypeCollection = new PairHMMReadyHaplotypes(haplotypes.size());
+        final List<Haplotype> sortedHaplotypes = new ArrayList<>(haplotypes);
+        Collections.sort(sortedHaplotypes, HAPLOTYPE_COMPARATOR);
+        Map<byte[],Integer> basesToPos = new HashMap<>(sortedHaplotypes.size());
+        int nextIdx = 0;
+
+        for (final Haplotype h : sortedHaplotypes) {
+            final byte[] bases = h.getBases();
+            haplotypeCollection.add(bases);
+            basesToPos.put(bases,nextIdx++);
+        }
+        for (GATKSAMRecord read : reads) {
+            final double[] unsortedLikelihoods = new double[sortedHaplotypes.size()];
+            final double[] sortedLikelihoods = new double[sortedHaplotypes.size()];
+            unsorted.loadRead(read);
+            sorted.loadRead(read);
+            final Map<Haplotype,Double> unsortedResults = new HashMap<>(haplotypes.size());
+            for (int i = 0; i < sortedHaplotypes.size(); i++) {
+                final Haplotype h = sortedHaplotypes.get(i);
+                final byte[] haplotypeBases = h.getBases().clone();
+                unsorted.loadHaplotypeBases(haplotypeBases);
+                double lk = unsorted.calculateLocalLikelihood(0, read.getReadLength(), 0, haplotypeBases.length, false);
+                unsortedLikelihoods[i] = lk;
+            }
+            sorted.calculateLocalLikelihoods(0, read.getReadLength(), haplotypeCollection);
+            for (final PairHMMReadyHaplotypes.Entry entry : haplotypeCollection) {
+                final byte[] bases = entry.getBases();
+                final double lk = entry.getLikelihood();
+                final int haplotypePos = basesToPos.get(bases);
+                sortedLikelihoods[haplotypePos] = lk;
+            }
+            for (int i = 0; i < unsortedLikelihoods.length; i++)
+                Assert.assertEquals(unsortedLikelihoods[i],sortedLikelihoods[i],0.00000001,Arrays.toString(unsortedLikelihoods) + Arrays.toString(sortedLikelihoods));
+        }
+    }
+
+    @Test(enabled=true,dataProvider="activeRegionTestDataSets")
+    public void testSortedVsUnsorted(final ActiveRegionTestDataSet as, final int kmerSize, final int readLength, final String variation, final int readCount, final int regionSize, final byte bq, final byte iq, final byte dq) {
+        final List<GATKSAMRecord> reads = as.readList();
+        final List<Haplotype> haplotypes = as.haplotypeList();
+        final List<Haplotype> sortedHaplotypes = new ArrayList<>(haplotypes);
+        Collections.sort(sortedHaplotypes, HAPLOTYPE_COMPARATOR);
+
+        byte[] lastHaplotypeBases = null;
+        for (GATKSAMRecord read : reads) {
+            final double[] unsortedLikelihoods = new double[sortedHaplotypes.size()];
+            final double[] sortedLikelihoods = new double[sortedHaplotypes.size()];
+            unsorted.loadRead(read);
+            sorted.loadRead(read);
+            for (int i = 0; i < sortedHaplotypes.size(); i++) {
+                final Haplotype h = sortedHaplotypes.get(i);
+                final byte[] haplotypeBases = h.getBases().clone();
+                final byte[] haplotypeBases2 = haplotypeBases.clone();
+                int commonPrefixEnd = 0;
+
+
+                if (lastHaplotypeBases != null) {
+                   final int prefixEndLimit = Math.min(lastHaplotypeBases.length,haplotypeBases.length);
+                   for (commonPrefixEnd = 0; commonPrefixEnd < prefixEndLimit; commonPrefixEnd++)
+                       if (lastHaplotypeBases[commonPrefixEnd] != haplotypeBases[commonPrefixEnd])
+                           break;
+                }
+
+                unsorted.loadHaplotypeBases(haplotypeBases);
+                sorted.changeHaplotypeSuffix(commonPrefixEnd, haplotypeBases, commonPrefixEnd, haplotypeBases.length);
+                Assert.assertTrue(Arrays.equals(haplotypeBases2, unsorted.getHaplotypeBases()));
+                Assert.assertTrue(Arrays.equals(haplotypeBases2, sorted.getHaplotypeBases()));
+                unsortedLikelihoods[i] = unsorted.calculateLocalLikelihood(0, read.getReadLength(), 0, haplotypeBases.length, false);
+                sortedLikelihoods[i] = sorted.calculateLocalLikelihood(0, read.getReadLength(), 0, haplotypeBases.length, false);
+                Assert.assertTrue(Arrays.equals(haplotypeBases2,unsorted.getHaplotypeBases()));
+                Assert.assertTrue(Arrays.equals(haplotypeBases2,sorted.getHaplotypeBases()));
+                Assert.assertEquals((double)unsortedLikelihoods[i], (double) sortedLikelihoods[i],0.00000001);
+                lastHaplotypeBases = haplotypeBases;
+            }
+        }
+    }
+
+    public static final Comparator<Haplotype> HAPLOTYPE_COMPARATOR = new Comparator<Haplotype>() {
+
+        @Override
+        public int compare(final Haplotype o1, final Haplotype o2) {
+            if (o1 == o2)
+                return 0;
+            final byte[] bases1 = o1.getBases();
+            final byte[] bases2 = o2.getBases();
+            final int ilimit = Math.min(bases1.length,bases2.length);
+            for (int i = 0; i < ilimit; i++) {
+                final int cmp = Byte.compare(bases1[i],bases2[i]);
+                if (cmp != 0) return cmp;
+            }
+            if (bases1.length == bases2.length) return 0;
+            return (bases1.length > bases2.length) ? -1 : 1; // is a bit better to get the longest haplotypes first.
+        }
+    };
+
+
+
+
+}
diff --git a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java
index b235f95c8..4a224e0be 100644
--- a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java
@@ -73,6 +73,7 @@ public class PairHMMUnitTest extends BaseTest {
     final N2MemoryPairHMM originalHMM = new Log10PairHMM(false); // the reference implementation
     final N2MemoryPairHMM loglessHMM = new LoglessPairHMM();
     final PairHMM arrayHMM = new ArrayLoglessPairHMM();
+    final N2MemoryPairHMM fastloglessHMM = new FastLoglessPairHMM((byte) 10);
 
     @BeforeClass
     public void initialize() {
@@ -80,10 +81,11 @@ public class PairHMMUnitTest extends BaseTest {
         originalHMM.doNotUseTristateCorrection();
         loglessHMM.doNotUseTristateCorrection();
         arrayHMM.doNotUseTristateCorrection();
+        fastloglessHMM.doNotUseTristateCorrection();
     }
 
-    private List<PairHMM> getHMMs() {
-        return Arrays.asList(exactHMM, originalHMM, loglessHMM, arrayHMM);
+    private List<N2MemoryPairHMM> getHMMs() {
+        return Arrays.asList(exactHMM, originalHMM, loglessHMM, fastloglessHMM);
     }
 
     // --------------------------------------------------------------------------------
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
index 793877396..f60b7de54 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
@@ -180,4 +180,6 @@ public abstract class ActiveRegionWalker<MapType, ReduceType> extends Walker<Map
         }
         return IntervalUtils.sortAndMergeIntervals(genomeLocParser, allIntervals, IntervalMergingRule.ALL);
     }
+
+
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java b/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java
index 46f8f2a84..1bbf481b1 100644
--- a/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java
@@ -138,6 +138,48 @@ public class BaseUtils {
         return simpleBaseToBaseIndex(base1) == simpleBaseToBaseIndex(base2);
     }
 
+    /**
+     * Checks whether to bases are the same in fact ignore ambiguous 'N' bases.
+     *
+     * @param base1 first base to compare.
+     * @param base2 second base to compare.
+     * @return true if {@code base1 == base2} or either is an 'N', false otherwise.
+     */
+    static public boolean basesAreEqualIgnoreAmbiguous(final byte base1, final byte base2) {
+        if (base1 == base2) return true;
+        else if (base1 == 'n' || base1 == 'N' || base2 == 'N' || base2 == 'n') return true;
+        else return false;
+    }
+
+    /**
+     * Compare to base arrays ranges checking whether they contain the same bases.
+     *
+     * <p>
+     *     By default two array have equal bases, i.e. {@code length == 0} results results in {@code true}.
+     * </p>
+     *
+     * @param bases1 first base array to compare.
+     * @param offset1 position of the first base in bases1 to compare.
+     * @param bases2 second base array to compare.
+     * @param offset2 position of the first base in bases2 to compare.
+     * @param length number of bases to compare.
+     *
+     * @throws NullPointerException if {@code bases1} or {@code bases2} is {@code null}.
+     * @throws ArrayIndexOutOfBoundsException if:
+     * <ul>
+     *      <li>{@code offset1} is not within the range [0,{@code bases1.length}) or</li>
+     *     <li>{@code offset2} is not within the range [0,{@code bases2.length}) or</li>
+     *     <li>{@code offset1 + length} is not within the range [0,{@code bases1.length}) or </li>
+     *     <li>{@code offset2 + length} is not within the range [0,{@code bases2.length})</li>
+     * </ul>
+     * @return
+     */
+    static public boolean basesAreEqualIgnoreAmbiguous(final byte[] bases1, final int offset1, final byte[] bases2, final int offset2, final int length) {
+        for (int i = 0; i < length; i++)
+            if (!basesAreEqualIgnoreAmbiguous(bases1[offset1 + i],bases2[offset2 + i])) return false;
+        return true;
+    }
+
     static public boolean extendedBasesAreEqual(byte base1, byte base2) {
         return extendedBaseToBaseIndex(base1) == extendedBaseToBaseIndex(base2);
     }
diff --git a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
index 8697fcab6..06d3d8fd8 100644
--- a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
@@ -30,7 +30,6 @@ import com.google.java.contract.Requires;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import javax.annotation.Nullable;
 import java.math.BigDecimal;
 import java.util.*;
 
@@ -425,7 +424,6 @@ public class MathUtils {
      * happen when: any value is negative or larger than a short.  This method is optimized for speed; it is not intended to serve as a 
      * utility function.
      */
-    @Nullable
     static Long fastGenerateUniqueHashFromThreeIntegers(final int one, final int two, final int three) {
         if (one < 0 || two < 0 || three < 0 || Short.MAX_VALUE < one || Short.MAX_VALUE < two || Short.MAX_VALUE < three) {
             return null;
diff --git a/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java b/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java
index fe782bc31..c0d1df09d 100644
--- a/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java
@@ -63,6 +63,7 @@ public class QualityUtils {
     private static double qualToErrorProbCache[] = new double[256];
     private static double qualToProbLog10Cache[] = new double[256];
 
+
     static {
         for (int i = 0; i < 256; i++) {
             qualToErrorProbCache[i] = qualToErrorProb((double) i);
diff --git a/public/java/src/org/broadinstitute/sting/utils/Utils.java b/public/java/src/org/broadinstitute/sting/utils/Utils.java
index 5cb141074..41a36c235 100644
--- a/public/java/src/org/broadinstitute/sting/utils/Utils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/Utils.java
@@ -27,7 +27,6 @@ package org.broadinstitute.sting.utils;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
-import net.sf.samtools.CigarOperator;
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMProgramRecord;
 import org.apache.log4j.Logger;
diff --git a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java
index bb74619a7..8f6af0158 100644
--- a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java
+++ b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java
@@ -32,9 +32,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 import org.broadinstitute.sting.utils.HasGenomeLocation;
-import org.broadinstitute.sting.utils.clipping.ReadClipper;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 import java.util.*;
 
@@ -109,6 +107,12 @@ public class ActiveRegion implements HasGenomeLocation {
      */
     private GenomeLoc spanIncludingReads;
 
+
+    /**
+     * Indicates whether the active region has been finalized
+     */
+    private boolean hasBeenFinalized;
+
     /**
      * Create a new ActiveRegion containing no reads
      *
@@ -205,7 +209,7 @@ public class ActiveRegion implements HasGenomeLocation {
      * @return a non-null array of bytes holding the reference bases in referenceReader
      */
     @Ensures("result != null")
-    private byte[] getReference( final IndexedFastaSequenceFile referenceReader, final int padding, final GenomeLoc genomeLoc ) {
+    public byte[] getReference( final IndexedFastaSequenceFile referenceReader, final int padding, final GenomeLoc genomeLoc ) {
         if ( referenceReader == null ) throw new IllegalArgumentException("referenceReader cannot be null");
         if ( padding < 0 ) throw new IllegalArgumentException("padding must be a positive integer but got " + padding);
         if ( genomeLoc == null ) throw new IllegalArgumentException("genomeLoc cannot be null");
@@ -451,4 +455,12 @@ public class ActiveRegion implements HasGenomeLocation {
 
         return new ActiveRegion( subActive, Collections.<ActivityProfileState>emptyList(), isActive, genomeLocParser, requiredExtension );
     }
+
+    public void setFinalized(final boolean value) {
+        hasBeenFinalized = value;
+    }
+
+    public boolean isFinalized() {
+        return hasBeenFinalized;
+    }
 }
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/utils/genotyper/MostLikelyAllele.java b/public/java/src/org/broadinstitute/sting/utils/genotyper/MostLikelyAllele.java
index 03a2b8077..9b12a58d5 100644
--- a/public/java/src/org/broadinstitute/sting/utils/genotyper/MostLikelyAllele.java
+++ b/public/java/src/org/broadinstitute/sting/utils/genotyper/MostLikelyAllele.java
@@ -65,7 +65,7 @@ public final class MostLikelyAllele {
      * @param log10LikelihoodOfMostLikely the log10 likelihood of the most likely allele
      * @param log10LikelihoodOfSecondBest the log10 likelihood of the next most likely allele (should be NEGATIVE_INFINITY if none is available)
      */
-    public MostLikelyAllele(Allele mostLikely, Allele secondMostLikely, double log10LikelihoodOfMostLikely, double log10LikelihoodOfSecondBest) {
+    public MostLikelyAllele(final Allele mostLikely, final Allele secondMostLikely, double log10LikelihoodOfMostLikely, double log10LikelihoodOfSecondBest) {
         if ( mostLikely == null ) throw new IllegalArgumentException("mostLikely allele cannot be null");
         if ( log10LikelihoodOfMostLikely != Double.NEGATIVE_INFINITY && ! MathUtils.goodLog10Probability(log10LikelihoodOfMostLikely) )
             throw new IllegalArgumentException("log10LikelihoodOfMostLikely must be either -Infinity or a good log10 prob but got " + log10LikelihoodOfMostLikely);
diff --git a/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java b/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java
index af22eb7f9..b7cd03919 100644
--- a/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java
+++ b/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java
@@ -305,18 +305,16 @@ public class PerReadAlleleLikelihoodMap {
     /**
      * Debug method to dump contents of object into string for display
      */
-    @Override
     public String toString() {
-        StringBuilder sb = new StringBuilder();
+        final StringBuilder sb = new StringBuilder();
 
         sb.append("Alelles in map:");
-        for (Allele a:alleles) {
+        for (final Allele a:alleles) {
             sb.append(a.getDisplayString()+",");
-
         }
         sb.append("\n");
-        for (Map.Entry <GATKSAMRecord, Map<Allele, Double>> el : getLikelihoodReadMap().entrySet() ) {
-            for (Map.Entry<Allele,Double> eli : el.getValue().entrySet()) {
+        for (final Map.Entry <GATKSAMRecord, Map<Allele, Double>> el : getLikelihoodReadMap().entrySet() ) {
+            for (final Map.Entry<Allele,Double> eli : el.getValue().entrySet()) {
                 sb.append("Read "+el.getKey().getReadName()+". Allele:"+eli.getKey().getDisplayString()+" has likelihood="+Double.toString(eli.getValue())+"\n");
             }
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/haplotype/Haplotype.java b/public/java/src/org/broadinstitute/sting/utils/haplotype/Haplotype.java
index 1f932b222..a381e1b2f 100644
--- a/public/java/src/org/broadinstitute/sting/utils/haplotype/Haplotype.java
+++ b/public/java/src/org/broadinstitute/sting/utils/haplotype/Haplotype.java
@@ -38,10 +38,13 @@ import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.broadinstitute.variant.variantcontext.Allele;
 
 import java.util.Arrays;
+import java.util.Comparator;
 import java.util.LinkedHashMap;
 import java.util.List;
 
 public class Haplotype extends Allele {
+
+
     private GenomeLoc genomeLocation = null;
     private EventMap eventMap = null;
     private Cigar cigar;
@@ -214,7 +217,7 @@ public class Haplotype extends Allele {
     public void setCigar( final Cigar cigar ) {
         this.cigar = AlignmentUtils.consolidateCigar(cigar);
         if ( this.cigar.getReadLength() != length() )
-            throw new IllegalArgumentException("Read length " + length() + " not equal to the read length of the cigar " + cigar.getReadLength());
+            throw new IllegalArgumentException("Read length " + length() + " not equal to the read length of the cigar " + cigar.getReadLength() + " " + this.cigar);
     }
 
     @Requires({"refInsertLocation >= 0"})
@@ -311,4 +314,30 @@ public class Haplotype extends Allele {
     public void setScore(double score) {
         this.score = this.isReference() ? Double.MAX_VALUE : score;
     }
+
+    /**
+     * Comparator used to sort haplotypes, alphanumerically.
+     *
+     * <p>
+     *     If one haplotype is the prefix of the other, the shorter one comes first.
+     * </p>
+     */
+    public static final Comparator<Haplotype> ALPHANUMERICAL_COMPARATOR = new Comparator<Haplotype>() {
+
+        @Override
+        public int compare(final Haplotype o1, final Haplotype o2) {
+            if (o1 == o2)
+                return 0;
+            final byte[] bases1 = o1.getBases();
+            final byte[] bases2 = o2.getBases();
+            final int iLimit = Math.min(bases1.length, bases2.length);
+            for (int i = 0; i < iLimit; i++) {
+                final int cmp = Byte.compare(bases1[i], bases2[i]);
+                if (cmp != 0) return cmp;
+            }
+            if (bases1.length == bases2.length) return 0;
+            return (bases1.length > bases2.length) ? -1 : 1; // is a bit better to get the longest haplotypes first.
+        }
+    };
+
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/pairhmm/Log10PairHMM.java b/public/java/src/org/broadinstitute/sting/utils/pairhmm/Log10PairHMM.java
index 83b87da95..b83a15d6d 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pairhmm/Log10PairHMM.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pairhmm/Log10PairHMM.java
@@ -1,27 +1,27 @@
 /*
- * Copyright (c) 2012 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.
- */
+* Copyright (c) 2012 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.pairhmm;
 
@@ -40,18 +40,18 @@ import static java.lang.Math.log10;
  * User: rpoplin, carneiro
  * Date: 3/1/12
  */
-public final class Log10PairHMM extends N2MemoryPairHMM {
+public class Log10PairHMM extends N2MemoryPairHMM {
     /**
      * Should we use exact log10 calculation (true), or an approximation (false)?
      */
     private final boolean doExactLog10;
 
-    private static final int matchToMatch = 0;
-    private static final int indelToMatch = 1;
-    private static final int matchToInsertion = 2;
-    private static final int insertionToInsertion = 3;
-    private static final int matchToDeletion = 4;
-    private static final int deletionToDeletion = 5;
+    protected static final int matchToMatch = 0;
+    protected static final int indelToMatch = 1;
+    protected static final int matchToInsertion = 2;
+    protected static final int insertionToInsertion = 3;
+    protected static final int matchToDeletion = 4;
+    protected static final int deletionToDeletion = 5;
 
     // we divide e by 3 because the observed base could have come from any of the non-observed alleles
     protected final static double log10_3 = log10(3.0);
@@ -101,17 +101,14 @@ public final class Log10PairHMM extends N2MemoryPairHMM {
                                                                final boolean recacheReadValues,
                                                                final int nextHapStartIndex) {
 
-        if (previousHaplotypeBases == null || previousHaplotypeBases.length != haplotypeBases.length) {
-            // set the initial value (free deletions in the beginning) for the first row in the deletion matrix
-            final double initialValue = Math.log10(1.0 / haplotypeBases.length);
-            for( int j = 0; j < paddedHaplotypeLength; j++ ) {
-                deletionMatrix[0][j] = initialValue;
-            }
-        }
 
         if ( ! constantsAreInitialized || recacheReadValues )
             initializeProbabilities(insertionGOP, deletionGOP, overallGCP);
         initializePriors(haplotypeBases, readBases, readQuals, hapStartIndex);
+        if (previousHaplotypeBases == null || previousHaplotypeBases.length != haplotypeBases.length) {
+            // set the initial value (free deletions in the beginning) for the first row in the deletion matrix
+            initializeMatrixValues(haplotypeBases);
+        }
 
         for (int i = 1; i < paddedReadLength; i++) {
             // +1 here is because hapStartIndex is 0-based, but our matrices are 1 based
@@ -123,14 +120,27 @@ public final class Log10PairHMM extends N2MemoryPairHMM {
         // final probability is the log10 sum of the last element in the Match and Insertion state arrays
         // this way we ignore all paths that ended in deletions! (huge)
         // but we have to sum all the paths ending in the M and I matrices, because they're no longer extended.
+        double finalSumProbabilities = finalLikelihoodCalculation();
+
+        return finalSumProbabilities;
+    }
+
+    protected void initializeMatrixValues(final byte[] haplotypeBases) {
+        final double initialValue = Math.log10(1.0 / haplotypeBases.length);
+        for( int j = 0; j < paddedHaplotypeLength; j++ ) {
+            deletionMatrix[0][j] = initialValue;
+        }
+    }
+
+    protected double finalLikelihoodCalculation() {
         final int endI = paddedReadLength - 1;
         double finalSumProbabilities = myLog10SumLog10(new double[]{matchMatrix[endI][1], insertionMatrix[endI][1]});
         for (int j = 2; j < paddedHaplotypeLength; j++)
             finalSumProbabilities = myLog10SumLog10(new double[]{finalSumProbabilities, matchMatrix[endI][j], insertionMatrix[endI][j]});
-
         return finalSumProbabilities;
     }
 
+
     /**
      * Initializes the matrix that holds all the constants related to the editing
      * distance between the read and the haplotype.
@@ -169,7 +179,7 @@ public final class Log10PairHMM extends N2MemoryPairHMM {
             "overallGCP != null"
     })
     @Ensures("constantsAreInitialized")
-    private void initializeProbabilities(final byte[] insertionGOP, final byte[] deletionGOP, final byte[] overallGCP) {
+    protected void initializeProbabilities(final byte[] insertionGOP, final byte[] deletionGOP, final byte[] overallGCP) {
         for (int i = 0; i < insertionGOP.length; i++) {
             final int qualIndexGOP = Math.min(insertionGOP[i] + deletionGOP[i], Byte.MAX_VALUE);
             transition[i+1][matchToMatch] = QualityUtils.qualToProbLog10((byte) qualIndexGOP);
@@ -199,7 +209,7 @@ public final class Log10PairHMM extends N2MemoryPairHMM {
      * @return the log10 of the sum of the probabilities
      */
     @Requires("values != null")
-    private double myLog10SumLog10(final double[] values) {
+    protected double myLog10SumLog10(final double[] values) {
         return doExactLog10 ? MathUtils.log10sumLog10(values) : MathUtils.approximateLog10SumLog10(values);
     }
 
@@ -214,7 +224,7 @@ public final class Log10PairHMM extends N2MemoryPairHMM {
      * @param prior            the likelihood editing distance matrix for the read x haplotype
      * @param transition        an array with the six transition relevant to this location
      */
-    private void updateCell( final int indI, final int indJ, final double prior, final double[] transition) {
+    protected void updateCell( final int indI, final int indJ, final double prior, final double[] transition) {
 
         matchMatrix[indI][indJ] = prior +
                 myLog10SumLog10(new double[]{matchMatrix[indI - 1][indJ - 1] + transition[matchToMatch],
diff --git a/public/java/src/org/broadinstitute/sting/utils/pairhmm/N2MemoryPairHMM.java b/public/java/src/org/broadinstitute/sting/utils/pairhmm/N2MemoryPairHMM.java
index c02461c03..18cb9054b 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pairhmm/N2MemoryPairHMM.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pairhmm/N2MemoryPairHMM.java
@@ -40,6 +40,13 @@ abstract class N2MemoryPairHMM extends PairHMM {
     protected double[][] insertionMatrix = null;
     protected double[][] deletionMatrix = null;
 
+    // only used for debugging purposes
+    protected boolean doNotUseTristateCorrection = false;
+
+    public void doNotUseTristateCorrection() {
+        doNotUseTristateCorrection = true;
+    }
+
     /**
      * Initialize this PairHMM, making it suitable to run against a read and haplotype with given lengths
      *
diff --git a/public/java/src/org/broadinstitute/sting/utils/pairhmm/PairHMM.java b/public/java/src/org/broadinstitute/sting/utils/pairhmm/PairHMM.java
index ce3d43a06..ff883c5ae 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pairhmm/PairHMM.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pairhmm/PairHMM.java
@@ -78,7 +78,7 @@ public abstract class PairHMM {
      * @param haplotypeMaxLength the max length of haplotypes we want to use with this PairHMM
      * @param readMaxLength the max length of reads we want to use with this PairHMM
      */
-    protected void initialize( final int readMaxLength, final int haplotypeMaxLength ) {
+    public void initialize( final int readMaxLength, final int haplotypeMaxLength ) {
         if ( readMaxLength <= 0 ) throw new IllegalArgumentException("READ_MAX_LENGTH must be > 0 but got " + readMaxLength);
         if ( haplotypeMaxLength <= 0 ) throw new IllegalArgumentException("HAPLOTYPE_MAX_LENGTH must be > 0 but got " + haplotypeMaxLength);
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/pairhmm/PairHMMReadyHaplotypes.java b/public/java/src/org/broadinstitute/sting/utils/pairhmm/PairHMMReadyHaplotypes.java
new file mode 100644
index 000000000..125fee36c
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/utils/pairhmm/PairHMMReadyHaplotypes.java
@@ -0,0 +1,182 @@
+/*
+* Copyright (c) 2012 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.pairhmm;
+
+import java.util.*;
+
+/**
+ * Collection of haplotypes sorted in a conveniently way to be run efficiently by the PairHMM.
+ *
+ * TODO not yet in use but likely to be as part of making graph-base likelihood run faster.
+ * TODO this could be extended to the classical PairHMM implementation simplifyling the PairHMM API.
+ */
+public class PairHMMReadyHaplotypes implements Iterable<PairHMMReadyHaplotypes.Entry> {
+
+
+    public class Entry {
+
+        private final byte[] bases;
+
+        private double likelihood = Double.NaN;
+
+        protected Entry(final byte[] bases) {
+            this.bases = bases;
+        }
+
+        protected byte[] getBases() {
+            return bases;
+        }
+
+        public void setLikelihood(final double lk) {
+            likelihood = lk;
+        }
+
+        public double getLikelihood() {
+            return likelihood;
+        }
+
+    }
+
+    private Map<Entry,Map<Entry,Integer>> commonPrefixLength;
+
+    private SortedSet<Entry> entries;
+
+    private int capacity;
+
+    private final Comparator<Entry> comparator = new Comparator<Entry>() {
+        @Override
+        public int compare(final Entry o1, final Entry o2) {
+            final byte[] b1 = o1.bases;
+            final byte[] b2 = o2.bases;
+            Map<Entry,Integer> b1map = commonPrefixLength.get(o1);
+            if (b1map == null)
+                commonPrefixLength.put(o1, b1map = new HashMap<>(capacity));
+            Map<Entry,Integer> b2map = commonPrefixLength.get(o2);
+            if (b2map == null)
+                commonPrefixLength.put(o2, b2map = new HashMap<>(capacity));
+            final Integer previousI = b1map.get(o2) == null ? null : b1map.get(o2);
+            int i;
+            int result;
+            final int iLimit = Math.min(b1.length,b2.length);
+            if (previousI == null) {
+                for (i = 0; i < iLimit; i++)
+                    if (b1[i] != b2[i])
+                        break;
+                b1map.put(o2,i);
+                b2map.put(o1,i);
+            } else
+                i = previousI;
+
+            if (i < iLimit)
+                result = Byte.compare(b1[i],b2[i]);
+            else if (b1.length == b2.length)
+                result = 0;
+            else
+                result = b1.length < b2.length ? -1 : 1;
+            return result;
+        }
+    };
+
+    public PairHMMReadyHaplotypes(final int capacity) {
+        commonPrefixLength = new HashMap<>(capacity);
+        entries = new TreeSet<>(comparator);
+    }
+
+    public void add(final byte[] bases) {
+        final Entry entry = new Entry(bases);
+        entries.add(entry);
+    }
+
+    public int size() {
+        return entries.size();
+    }
+
+    @Override
+    public Iterator iterator() {
+        return new Iterator();
+    }
+
+    public class Iterator implements java.util.Iterator<Entry> {
+
+        private java.util.Iterator<Entry> actualIterator;
+        private Entry previousEntry;
+        private Entry currentEntry;
+        private int startIndex;
+        private int cmp;
+
+        private Iterator() {
+            actualIterator = entries.iterator();
+        }
+
+        public boolean hasNext() {
+            return actualIterator.hasNext();
+        }
+
+        public Entry next() {
+            previousEntry = currentEntry;
+            final Entry result = currentEntry = actualIterator.next();
+            startIndex = -1;
+            return result;
+        }
+
+        @Override
+        public void remove() {
+            throw new UnsupportedOperationException();
+        }
+
+        public byte[] bases() {
+            if (currentEntry == null)
+                throw new NoSuchElementException();
+            return currentEntry.bases;
+        }
+
+        public int startIndex() {
+            if (startIndex >= 0)
+                return startIndex;
+            else if (previousEntry == null)
+                return startIndex = 0;
+            else {
+                // The comparator will make sure the common-prefix-length is updated.
+                // The result in a field so that we avoid dead code elimination.
+                // perhaps I a bit paranohic but it does not harm to prevent.
+                cmp = comparator.compare(previousEntry,currentEntry);
+                return startIndex = commonPrefixLength.get(previousEntry).get(currentEntry);
+            }
+        }
+
+        @Override
+        public String toString() {
+            return super.toString() + " cmp = " + cmp;
+        }
+
+        public void setLikelihood(final double likelihood) {
+            if (currentEntry == null)
+                throw new NoSuchElementException();
+            currentEntry.setLikelihood(likelihood);
+        }
+    }
+
+}
diff --git a/public/java/test/org/broadinstitute/sting/BaseTest.java b/public/java/test/org/broadinstitute/sting/BaseTest.java
index 9d23062c0..c1e11e2ce 100644
--- a/public/java/test/org/broadinstitute/sting/BaseTest.java
+++ b/public/java/test/org/broadinstitute/sting/BaseTest.java
@@ -90,6 +90,7 @@ public abstract class BaseTest {
     public static final String b36KGReference = "/humgen/1kg/reference/human_b36_both.fasta";
     //public static final String b37KGReference = "/Users/depristo/Desktop/broadLocal/localData/human_g1k_v37.fasta";
     public static final String b37KGReference = "/humgen/1kg/reference/human_g1k_v37.fasta";
+    public static final String b37KGReferenceWithDecoy = "/humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37_decoy.fasta";
     public static final String GATKDataLocation = "/humgen/gsa-hpprojects/GATK/data/";
     public static final String validationDataLocation = GATKDataLocation + "Validation_Data/";
     public static final String evaluationDataLocation = GATKDataLocation + "Evaluation_Data/";
diff --git a/public/java/test/org/broadinstitute/sting/TestNGTestTransformer.java b/public/java/test/org/broadinstitute/sting/TestNGTestTransformer.java
index 772c86563..ae7e41dfe 100644
--- a/public/java/test/org/broadinstitute/sting/TestNGTestTransformer.java
+++ b/public/java/test/org/broadinstitute/sting/TestNGTestTransformer.java
@@ -54,7 +54,7 @@ public class TestNGTestTransformer implements IAnnotationTransformer {
                           Method testMethod)
     {
         if ( annotation.getTimeOut() == 0 ) {
-            logger.warn("test " + testMethod.toString() + " has no specified timeout, adding default timeout " + DEFAULT_TIMEOUT / 1000 / 60 + " minutes");
+            logger.warn("test " + (testMethod == null ? "<null>" : testMethod.toString()) + " has no specified timeout, adding default timeout " + DEFAULT_TIMEOUT / 1000 / 60 + " minutes");
             annotation.setTimeOut(DEFAULT_TIMEOUT);
         }
     }
diff --git a/public/java/test/org/broadinstitute/sting/WalkerTest.java b/public/java/test/org/broadinstitute/sting/WalkerTest.java
index 78f67967b..e8e791a8a 100644
--- a/public/java/test/org/broadinstitute/sting/WalkerTest.java
+++ b/public/java/test/org/broadinstitute/sting/WalkerTest.java
@@ -388,7 +388,6 @@ public class WalkerTest extends BaseTest {
     private void executeTest(String testName, String testClassName, String args, Class expectedException) {
         CommandLineGATK instance = new CommandLineGATK();
         String[] command = Utils.escapeExpressions(args);
-
         // run the executable
         boolean gotAnException = false;
         try {
diff --git a/public/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java
index 9621aecda..b94b6cda1 100644
--- a/public/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java
@@ -66,7 +66,7 @@ public class GenomeLocParserUnitTest extends BaseTest {
     private SAMFileHeader header;
 
     @BeforeClass
-    public void init() {
+         public void init() {
         header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 10);
         genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
     }

From 6bee6a1b5359bda50258a7f745f95bc87e51861d Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 2 Dec 2013 12:46:51 -0500
Subject: [PATCH 64/77] Change the behavior of SelectVariants for PL/AD when it
 encounters a record that has lost one or more alternate alleles.

Previously, we would strip out the PLs and AD values since they were no longer accurate.  However, this is not ideal because
then that information is just lost and 1) users complain on the forum and post it as a bug and 2) it gives us problems in both
the current and future (single sample) calling pipelines because we subset samples/alleles all the time and lose info.

Now the PLs and AD get correctly selected down.

While I was in there I also refactored some related code in subsetDiploidAlleles().  There were no real changes there - I just
broke it out into smaller chunks as per our best practices.

Added unit tests and updated integration tests.
Addressed reviews.
---
 .../SelectVariantsIntegrationTest.java        |   2 +-
 .../walkers/variantutils/SelectVariants.java  |  19 +-
 .../broadinstitute/sting/utils/MathUtils.java |  10 +
 .../variant/GATKVariantContextUtils.java      | 248 +++++++++++++++---
 .../GATKVariantContextUtilsUnitTest.java      | 108 ++++++++
 5 files changed, 336 insertions(+), 51 deletions(-)

diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
index 4b1483cb6..884b46692 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
@@ -316,7 +316,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b37KGReference + " -o %s --no_cmdline_in_header -sf " + samplesFile + " --excludeNonVariants --variant " + testfile,
                 1,
-                Arrays.asList("f14d75892b99547d8e9ba3a03bfb04ea")
+                Arrays.asList("69862fb97e8e895fe65c7abb14b03cee")
         );
         executeTest("test select from multi allelic with excludeNonVariants --" + testfile, spec);
     }
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 1f2b6d09b..e688b7f17 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -299,7 +299,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
     @Argument(doc="indel size select",required=false,fullName="maxIndelSize")
     private int maxIndelSize = Integer.MAX_VALUE;
 
-    @Argument(doc="Allow a samples other than those in the VCF to be specified on the command line. These samples will be ignored.",required=false,fullName="ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES")
+    @Argument(doc="Allow samples other than those in the VCF to be specified on the command line. These samples will be ignored.",required=false,fullName="ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES")
     private boolean ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES = false;
 
 
@@ -657,6 +657,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
      * Helper method to subset a VC record, modifying some metadata stored in the INFO field (i.e. AN, AC, AF).
      *
      * @param vc       the VariantContext record to subset
+     * @param excludeNonVariants should we exclude sites that have AC=0 for any alternate alleles?
      * @return the subsetted VariantContext
      */
     private VariantContext subsetRecord(final VariantContext vc, final boolean excludeNonVariants) {
@@ -665,14 +666,10 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
 
         final VariantContext sub = vc.subContextFromSamples(samples, excludeNonVariants); // strip out the alternate alleles that aren't being used
 
-        VariantContextBuilder builder = new VariantContextBuilder(sub);
+        final VariantContextBuilder builder = new VariantContextBuilder(sub);
 
-        GenotypesContext newGC = sub.getGenotypes();
-
-        // if we have fewer alternate alleles in the selected VC than in the original VC, we need to strip out the GL/PLs and AD (because they are no longer accurate)
-        final boolean lostAllelesInSelection = vc.getAlleles().size() != sub.getAlleles().size();
-        if ( lostAllelesInSelection )
-            newGC = GATKVariantContextUtils.stripPLsAndAD(sub.getGenotypes());
+        // if there are fewer alternate alleles now in the selected VC, we need to fix the PL and AD values
+        GenotypesContext newGC = GATKVariantContextUtils.updatePLsAndAD(sub, vc);
 
         // if we have fewer samples in the selected VC than in the original VC, we need to strip out the MLE tags
         if ( vc.getNSamples() != sub.getNSamples() ) {
@@ -682,11 +679,11 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
 
         // Remove a fraction of the genotypes if needed
         if ( fractionGenotypes > 0 ){
-            ArrayList<Genotype> genotypes = new ArrayList<Genotype>();
+            final ArrayList<Genotype> genotypes = new ArrayList<>();
             for ( Genotype genotype : newGC ) {
                 //Set genotype to no call if it falls in the fraction.
                 if(fractionGenotypes>0 && randomGenotypes.nextDouble()<fractionGenotypes){
-                    List<Allele> alleles = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL);
+                    final List<Allele> alleles = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL);
                     genotypes.add(new GenotypeBuilder(genotype).alleles(alleles).noGQ().make());
                 }
                 else{
@@ -698,7 +695,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
 
         builder.genotypes(newGC);
 
-        addAnnotations(builder, sub, lostAllelesInSelection);
+        addAnnotations(builder, sub, vc.getAlleles().size() != sub.getAlleles().size());
 
         return builder.make();
     }
diff --git a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
index 06d3d8fd8..0b6cd4b1d 100644
--- a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
@@ -976,6 +976,16 @@ public class MathUtils {
         return count;
     }
 
+    public static int countOccurrences(final boolean element, final boolean[] array) {
+        int count = 0;
+        for (final boolean b : array) {
+            if (element == b)
+                count++;
+        }
+
+        return count;
+    }
+
 
     /**
      * Returns n random indices drawn with replacement from the range 0..(k-1)
diff --git a/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
index 03bb9763c..1ae34e268 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
@@ -453,7 +453,12 @@ public class GATKVariantContextUtils {
          * rather than the undetermined behavior when using the PLs to assign, which could result
          * in hom-var or hom-ref for each, depending on the exact PL values.
          */
-        BEST_MATCH_TO_ORIGINAL
+        BEST_MATCH_TO_ORIGINAL,
+
+        /**
+         * do not even bother changing the GTs
+         */
+        DO_NOT_ASSIGN_GENOTYPES
     }
 
     /**
@@ -461,8 +466,8 @@ public class GATKVariantContextUtils {
      *
      * @param vc                 variant context with genotype likelihoods
      * @param allelesToUse       which alleles from the vc are okay to use; *** must be in the same relative order as those in the original VC ***
-     * @param assignGenotypes    true if we should update the genotypes based on the (subsetted) PLs
-     * @return genotypes
+     * @param assignGenotypes    assignment strategy for the (subsetted) PLs
+     * @return a new non-null GenotypesContext
      */
     public static GenotypesContext subsetDiploidAlleles(final VariantContext vc,
                                                         final List<Allele> allelesToUse,
@@ -470,50 +475,109 @@ public class GATKVariantContextUtils {
         if ( allelesToUse.get(0).isNonReference() ) throw new IllegalArgumentException("First allele must be the reference allele");
         if ( allelesToUse.size() == 1 ) throw new IllegalArgumentException("Cannot subset to only 1 alt allele");
 
-        // the genotypes with PLs
-        final GenotypesContext oldGTs = vc.getGenotypes();
-
-        // the new genotypes to create
-        final GenotypesContext newGTs = GenotypesContext.create();
-
         // optimization: if no input genotypes, just exit
-        if (oldGTs.isEmpty()) return newGTs;
-
-        // samples
-        final List<String> sampleIndices = oldGTs.getSampleNamesOrderedByName();
+        if (vc.getGenotypes().isEmpty()) return GenotypesContext.create();
 
         // we need to determine which of the alternate alleles (and hence the likelihoods) to use and carry forward
-        final int numOriginalAltAlleles = vc.getAlternateAlleles().size();
-        final int expectedNumLikelihoods = GenotypeLikelihoods.numLikelihoods(vc.getNAlleles(), 2);
-        final int numNewAltAlleles = allelesToUse.size() - 1;
+        final List<Integer> likelihoodIndexesToUse = determineLikelihoodIndexesToUse(vc, allelesToUse);
 
-        // which PLs should be carried forward?
-        ArrayList<Integer> likelihoodIndexesToUse = null;
+        // create the new genotypes
+        return createGenotypesWithSubsettedLikelihoods(vc.getGenotypes(), vc, allelesToUse, likelihoodIndexesToUse, assignGenotypes);
+    }
+
+    /**
+     * Figure out which likelihood indexes to use for a selected down set of alleles
+     *
+     * @param originalVC        the original VariantContext
+     * @param allelesToUse      the subset of alleles to use
+     * @return a list of PL indexes to use or null if none
+     */
+    private static List<Integer> determineLikelihoodIndexesToUse(final VariantContext originalVC, final List<Allele> allelesToUse) {
+
+        // the bitset representing the allele indexes we want to keep
+        final boolean[] alleleIndexesToUse = getAlleleIndexBitset(originalVC, allelesToUse);
 
         // an optimization: if we are supposed to use all (or none in the case of a ref call) of the alleles,
         // then we can keep the PLs as is; otherwise, we determine which ones to keep
-        if ( numNewAltAlleles != numOriginalAltAlleles ) {
-            likelihoodIndexesToUse = new ArrayList<>(30);
+        if ( MathUtils.countOccurrences(true, alleleIndexesToUse) == alleleIndexesToUse.length )
+            return null;
 
-            final boolean[] altAlleleIndexToUse = new boolean[numOriginalAltAlleles];
-            for ( int i = 0; i < numOriginalAltAlleles; i++ ) {
-                if ( allelesToUse.contains(vc.getAlternateAllele(i)) )
-                    altAlleleIndexToUse[i] = true;
-            }
+        return getLikelihoodIndexes(originalVC, alleleIndexesToUse);
+    }
 
-            // numLikelihoods takes total # of alleles. Use default # of chromosomes (ploidy) = 2
-            final int numLikelihoods = GenotypeLikelihoods.numLikelihoods(1 + numOriginalAltAlleles, DEFAULT_PLOIDY);
-            for ( int PLindex = 0; PLindex < numLikelihoods; PLindex++ ) {
-                final GenotypeLikelihoods.GenotypeLikelihoodsAllelePair alleles = GenotypeLikelihoods.getAllelePair(PLindex);
-                // consider this entry only if both of the alleles are good
-                if ( (alleles.alleleIndex1 == 0 || altAlleleIndexToUse[alleles.alleleIndex1 - 1]) && (alleles.alleleIndex2 == 0 || altAlleleIndexToUse[alleles.alleleIndex2 - 1]) )
-                    likelihoodIndexesToUse.add(PLindex);
-            }
+    /**
+     * Get the actual likelihoods indexes to use given the corresponding allele indexes
+     *
+     * @param originalVC           the original VariantContext
+     * @param alleleIndexesToUse   the bitset representing the alleles to use (@see #getAlleleIndexBitset)
+     * @return a non-null List
+     */
+    private static List<Integer> getLikelihoodIndexes(final VariantContext originalVC, final boolean[] alleleIndexesToUse) {
+
+        final List<Integer> result = new ArrayList<>(30);
+
+        // numLikelihoods takes total # of alleles. Use default # of chromosomes (ploidy) = 2
+        final int numLikelihoods = GenotypeLikelihoods.numLikelihoods(originalVC.getNAlleles(), DEFAULT_PLOIDY);
+
+        for ( int PLindex = 0; PLindex < numLikelihoods; PLindex++ ) {
+            final GenotypeLikelihoods.GenotypeLikelihoodsAllelePair alleles = GenotypeLikelihoods.getAllelePair(PLindex);
+            // consider this entry only if both of the alleles are good
+            if ( alleleIndexesToUse[alleles.alleleIndex1] && alleleIndexesToUse[alleles.alleleIndex2] )
+                result.add(PLindex);
         }
 
+        return result;
+    }
+
+    /**
+     * Given an original VariantContext and a list of alleles from that VC to keep,
+     * returns a bitset representing which allele indexes should be kept
+     *
+     * @param originalVC      the original VC
+     * @param allelesToKeep   the list of alleles to keep
+     * @return non-null bitset
+     */
+    private static boolean[] getAlleleIndexBitset(final VariantContext originalVC, final List<Allele> allelesToKeep) {
+        final int numOriginalAltAlleles = originalVC.getNAlleles() - 1;
+        final boolean[] alleleIndexesToKeep = new boolean[numOriginalAltAlleles + 1];
+
+        // the reference Allele is definitely still used
+        alleleIndexesToKeep[0] = true;
+        for ( int i = 0; i < numOriginalAltAlleles; i++ ) {
+            if ( allelesToKeep.contains(originalVC.getAlternateAllele(i)) )
+                alleleIndexesToKeep[i+1] = true;
+        }
+
+        return alleleIndexesToKeep;
+    }
+
+    /**
+     * Create the new GenotypesContext with the subsetted PLs
+     *
+     * @param originalGs               the original GenotypesContext
+     * @param vc                       the original VariantContext
+     * @param allelesToUse             the actual alleles to use with the new Genotypes
+     * @param likelihoodIndexesToUse   the indexes in the PL to use given the allelesToUse (@see #determineLikelihoodIndexesToUse())
+     * @param assignGenotypes          assignment strategy for the (subsetted) PLs
+     * @return a new non-null GenotypesContext
+     */
+    private static GenotypesContext createGenotypesWithSubsettedLikelihoods(final GenotypesContext originalGs,
+                                                                            final VariantContext vc,
+                                                                            final List<Allele> allelesToUse,
+                                                                            final List<Integer> likelihoodIndexesToUse,
+                                                                            final GenotypeAssignmentMethod assignGenotypes) {
+        // the new genotypes to create
+        final GenotypesContext newGTs = GenotypesContext.create(originalGs.size());
+
+        // make sure we are seeing the expected number of likelihoods per sample
+        final int expectedNumLikelihoods = GenotypeLikelihoods.numLikelihoods(vc.getNAlleles(), 2);
+
+        // the samples
+        final List<String> sampleIndices = originalGs.getSampleNamesOrderedByName();
+
         // create the new genotypes
-        for ( int k = 0; k < oldGTs.size(); k++ ) {
-            final Genotype g = oldGTs.get(sampleIndices.get(k));
+        for ( int k = 0; k < originalGs.size(); k++ ) {
+            final Genotype g = originalGs.get(sampleIndices.get(k));
             final GenotypeBuilder gb = new GenotypeBuilder(g);
 
             // create the new likelihoods array from the alleles we are allowed to use
@@ -570,13 +634,16 @@ public class GATKVariantContextUtils {
                                                      final GenotypeAssignmentMethod assignmentMethod,
                                                      final double[] newLikelihoods,
                                                      final List<Allele> allelesToUse) {
-        gb.noAD();
         switch ( assignmentMethod ) {
+            case DO_NOT_ASSIGN_GENOTYPES:
+                break;
             case SET_TO_NO_CALL:
                 gb.alleles(NO_CALL_ALLELES);
+                gb.noAD();
                 gb.noGQ();
                 break;
             case USE_PLS_TO_ASSIGN:
+                gb.noAD();
                 if ( newLikelihoods == null || likelihoodsAreUninformative(newLikelihoods) ) {
                     // if there is no mass on the (new) likelihoods, then just no-call the sample
                     gb.alleles(NO_CALL_ALLELES);
@@ -597,6 +664,7 @@ public class GATKVariantContextUtils {
                 }
                 gb.noGQ();
                 gb.noPL();
+                gb.noAD();
                 gb.alleles(best);
                 break;
         }
@@ -622,7 +690,7 @@ public class GATKVariantContextUtils {
         if (oldGTs.isEmpty()) return oldGTs;
 
         // the new genotypes to create
-        final GenotypesContext newGTs = GenotypesContext.create();
+        final GenotypesContext newGTs = GenotypesContext.create(oldGTs.size());
 
         final Allele ref = vc.getReference();
         final List<Allele> diploidRefAlleles = Arrays.asList(ref, ref);
@@ -1083,7 +1151,7 @@ public class GATKVariantContextUtils {
     }
 
     public static GenotypesContext stripPLsAndAD(GenotypesContext genotypes) {
-        GenotypesContext newGs = GenotypesContext.create(genotypes.size());
+        final GenotypesContext newGs = GenotypesContext.create(genotypes.size());
 
         for ( final Genotype g : genotypes ) {
             newGs.add(removePLsAndAD(g));
@@ -1092,6 +1160,108 @@ public class GATKVariantContextUtils {
         return newGs;
     }
 
+    /**
+     * Updates the PLs and AD of the Genotypes in the newly selected VariantContext to reflect the fact that some alleles
+     * from the original VariantContext are no longer present.
+     *
+     * @param selectedVC  the selected (new) VariantContext
+     * @param originalVC  the original VariantContext
+     * @return a new non-null GenotypesContext
+     */
+    public static GenotypesContext updatePLsAndAD(final VariantContext selectedVC, final VariantContext originalVC) {
+        final int numNewAlleles = selectedVC.getAlleles().size();
+        final int numOriginalAlleles = originalVC.getAlleles().size();
+
+        // if we have more alternate alleles in the selected VC than in the original VC, then something is wrong
+        if ( numNewAlleles > numOriginalAlleles )
+            throw new IllegalArgumentException("Attempting to fix PLs and AD from what appears to be a *combined* VCF and not a selected one");
+
+        final GenotypesContext oldGs = selectedVC.getGenotypes();
+
+        // if we have the same number of alternate alleles in the selected VC as in the original VC, then we don't need to fix anything
+        if ( numNewAlleles == numOriginalAlleles )
+            return oldGs;
+
+        final GenotypesContext newGs = fixPLsFromSubsettedAlleles(oldGs, originalVC, selectedVC.getAlleles());
+
+        return fixADFromSubsettedAlleles(newGs, originalVC, selectedVC.getAlleles());
+    }
+
+    /**
+     * Fix the PLs for the GenotypesContext of a VariantContext that has been subset
+     *
+     * @param originalGs       the original GenotypesContext
+     * @param originalVC       the original VariantContext
+     * @param allelesToUse     the new (sub)set of alleles to use
+     * @return a new non-null GenotypesContext
+     */
+    static private GenotypesContext fixPLsFromSubsettedAlleles(final GenotypesContext originalGs, final VariantContext originalVC, final List<Allele> allelesToUse) {
+
+        // we need to determine which of the alternate alleles (and hence the likelihoods) to use and carry forward
+        final List<Integer> likelihoodIndexesToUse = determineLikelihoodIndexesToUse(originalVC, allelesToUse);
+
+        // create the new genotypes
+        return createGenotypesWithSubsettedLikelihoods(originalGs, originalVC, allelesToUse, likelihoodIndexesToUse, GenotypeAssignmentMethod.DO_NOT_ASSIGN_GENOTYPES);
+    }
+
+    /**
+     * Fix the AD for the GenotypesContext of a VariantContext that has been subset
+     *
+     * @param originalGs       the original GenotypesContext
+     * @param originalVC       the original VariantContext
+     * @param allelesToUse     the new (sub)set of alleles to use
+     * @return a new non-null GenotypesContext
+     */
+    static private GenotypesContext fixADFromSubsettedAlleles(final GenotypesContext originalGs, final VariantContext originalVC, final List<Allele> allelesToUse) {
+
+        // the bitset representing the allele indexes we want to keep
+        final boolean[] alleleIndexesToUse = getAlleleIndexBitset(originalVC, allelesToUse);
+
+        // the new genotypes to create
+        final GenotypesContext newGTs = GenotypesContext.create(originalGs.size());
+
+        // the samples
+        final List<String> sampleIndices = originalGs.getSampleNamesOrderedByName();
+
+        // create the new genotypes
+        for ( int k = 0; k < originalGs.size(); k++ ) {
+            final Genotype g = originalGs.get(sampleIndices.get(k));
+            newGTs.add(fixAD(g, alleleIndexesToUse, allelesToUse.size()));
+        }
+
+        return newGTs;
+    }
+
+    /**
+     * Fix the AD for the given Genotype
+     *
+     * @param genotype              the original Genotype
+     * @param alleleIndexesToUse    a bitset describing whether or not to keep a given index
+     * @param nAllelesToUse         how many alleles we are keeping
+     * @return a non-null Genotype
+     */
+    private static Genotype fixAD(final Genotype genotype, final boolean[] alleleIndexesToUse, final int nAllelesToUse) {
+        // if it ain't broke don't fix it
+        if ( !genotype.hasAD() )
+            return genotype;
+
+        final GenotypeBuilder builder = new GenotypeBuilder(genotype);
+
+        final int[] oldAD = genotype.getAD();
+        if ( oldAD.length != alleleIndexesToUse.length ) {
+            builder.noAD();
+        } else {
+            final int[] newAD = new int[nAllelesToUse];
+            int currentIndex = 0;
+            for ( int i = 0; i < oldAD.length; i++ ) {
+                if ( alleleIndexesToUse[i] )
+                    newAD[currentIndex++] = oldAD[i];
+            }
+            builder.AD(newAD);
+        }
+        return builder.make();
+    }
+
     static private Allele determineReferenceAllele(List<VariantContext> VCs) {
         Allele ref = null;
 
@@ -1277,7 +1447,7 @@ public class GATKVariantContextUtils {
 
     @Requires("originalGenotypes != null && alleleMapper != null")
     protected static GenotypesContext updateGenotypesWithMappedAlleles(final GenotypesContext originalGenotypes, final AlleleMapper alleleMapper) {
-        final GenotypesContext updatedGenotypes = GenotypesContext.create();
+        final GenotypesContext updatedGenotypes = GenotypesContext.create(originalGenotypes.size());
 
         for ( final Genotype genotype : originalGenotypes ) {
             final List<Allele> updatedAlleles = alleleMapper.remap(genotype.getAlleles());
diff --git a/public/java/test/org/broadinstitute/sting/utils/variant/GATKVariantContextUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variant/GATKVariantContextUtilsUnitTest.java
index 575fe4936..30f112241 100644
--- a/public/java/test/org/broadinstitute/sting/utils/variant/GATKVariantContextUtilsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variant/GATKVariantContextUtilsUnitTest.java
@@ -1320,4 +1320,112 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
             }
         }
     }
+
+    // --------------------------------------------------------------------------------
+    //
+    // Test updatePLsAndAD
+    //
+    // --------------------------------------------------------------------------------
+
+    @DataProvider(name = "updatePLsAndADData")
+    public Object[][] makeUpdatePLsAndADData() {
+        List<Object[]> tests = new ArrayList<>();
+
+        final Allele A = Allele.create("A", true);
+        final Allele C = Allele.create("C");
+        final Allele G = Allele.create("G");
+
+        final List<Allele> AA = Arrays.asList(A,A);
+        final List<Allele> AC = Arrays.asList(A,C);
+        final List<Allele> CC = Arrays.asList(C,C);
+        final List<Allele> AG = Arrays.asList(A,G);
+        final List<Allele> CG = Arrays.asList(C,G);
+        final List<Allele> GG = Arrays.asList(G,G);
+        final List<Allele> ACG = Arrays.asList(A,C,G);
+
+        final VariantContext vcBase = new VariantContextBuilder("test", "20", 10, 10, AC).make();
+
+        final double[] homRefPL = MathUtils.normalizeFromRealSpace(new double[]{0.9, 0.09, 0.01});
+        final double[] hetPL = MathUtils.normalizeFromRealSpace(new double[]{0.09, 0.9, 0.01});
+        final double[] homVarPL = MathUtils.normalizeFromRealSpace(new double[]{0.01, 0.09, 0.9});
+        final double[] uninformative = new double[]{0, 0, 0};
+
+        final Genotype base = new GenotypeBuilder("NA12878").DP(10).GQ(100).make();
+
+        // make sure we don't screw up the simple case where no selection happens
+        final Genotype aaGT = new GenotypeBuilder(base).alleles(AA).AD(new int[]{10,2}).PL(homRefPL).GQ(8).make();
+        final Genotype acGT = new GenotypeBuilder(base).alleles(AC).AD(new int[]{10,2}).PL(hetPL).GQ(8).make();
+        final Genotype ccGT = new GenotypeBuilder(base).alleles(CC).AD(new int[]{10,2}).PL(homVarPL).GQ(8).make();
+
+        tests.add(new Object[]{new VariantContextBuilder(vcBase).genotypes(aaGT).make(), new VariantContextBuilder(vcBase).alleles(AC).make(), Arrays.asList(new GenotypeBuilder(aaGT).make())});
+        tests.add(new Object[]{new VariantContextBuilder(vcBase).genotypes(acGT).make(), new VariantContextBuilder(vcBase).alleles(AC).make(), Arrays.asList(new GenotypeBuilder(acGT).make())});
+        tests.add(new Object[]{new VariantContextBuilder(vcBase).genotypes(ccGT).make(), new VariantContextBuilder(vcBase).alleles(AC).make(), Arrays.asList(new GenotypeBuilder(ccGT).make())});
+
+        // uninformative test cases
+        final Genotype uninformativeGT = new GenotypeBuilder(base).alleles(CC).noAD().PL(uninformative).GQ(0).make();
+        tests.add(new Object[]{new VariantContextBuilder(vcBase).genotypes(uninformativeGT).make(), new VariantContextBuilder(vcBase).alleles(AC).make(), Arrays.asList(uninformativeGT)});
+        final Genotype emptyGT = new GenotypeBuilder(base).alleles(GATKVariantContextUtils.NO_CALL_ALLELES).noAD().noPL().noGQ().make();
+        tests.add(new Object[]{new VariantContextBuilder(vcBase).genotypes(emptyGT).make(), new VariantContextBuilder(vcBase).alleles(AC).make(), Arrays.asList(emptyGT)});
+
+        // actually subsetting down from multiple alt values
+        final double[] homRef3AllelesPL = new double[]{0, -10, -20, -30, -40, -50};
+        final double[] hetRefC3AllelesPL = new double[]{-10, 0, -20, -30, -40, -50};
+        final double[] homC3AllelesPL = new double[]{-20, -10, 0, -30, -40, -50};
+        final double[] hetRefG3AllelesPL = new double[]{-20, -10, -30, 0, -40, -50};
+        final double[] hetCG3AllelesPL = new double[]{-20, -10, -30, -40, 0, -50}; // AA, AC, CC, AG, CG, GG
+        final double[] homG3AllelesPL = new double[]{-20, -10, -30, -40, -50, 0};  // AA, AC, CC, AG, CG, GG
+
+        final int[] homRef3AllelesAD = new int[]{20, 0, 1};
+        final int[] hetRefC3AllelesAD = new int[]{10, 10, 1};
+        final int[] homC3AllelesAD = new int[]{0, 20, 1};
+        final int[] hetRefG3AllelesAD = new int[]{10, 0, 11};
+        final int[] hetCG3AllelesAD = new int[]{0, 12, 11}; // AA, AC, CC, AG, CG, GG
+        final int[] homG3AllelesAD = new int[]{0, 1, 21};  // AA, AC, CC, AG, CG, GG
+
+        tests.add(new Object[]{
+                new VariantContextBuilder(vcBase).alleles(ACG).genotypes(new GenotypeBuilder(base).alleles(AA).AD(homRef3AllelesAD).PL(homRef3AllelesPL).make()).make(),
+                new VariantContextBuilder(vcBase).alleles(AC).make(),
+                Arrays.asList(new GenotypeBuilder(base).alleles(AA).PL(new double[]{0, -10, -20}).AD(new int[]{20, 0}).GQ(100).make())});
+
+        tests.add(new Object[]{
+                new VariantContextBuilder(vcBase).alleles(ACG).genotypes(new GenotypeBuilder(base).alleles(AA).AD(hetRefC3AllelesAD).PL(hetRefC3AllelesPL).make()).make(),
+                new VariantContextBuilder(vcBase).alleles(AC).make(),
+                Arrays.asList(new GenotypeBuilder(base).alleles(AA).PL(new double[]{-10, 0, -20}).AD(new int[]{10, 10}).GQ(100).make())});
+
+        tests.add(new Object[]{
+                new VariantContextBuilder(vcBase).alleles(ACG).genotypes(new GenotypeBuilder(base).alleles(AA).AD(homC3AllelesAD).PL(homC3AllelesPL).make()).make(),
+                new VariantContextBuilder(vcBase).alleles(AC).make(),
+                Arrays.asList(new GenotypeBuilder(base).alleles(AA).PL(new double[]{-20, -10, 0}).AD(new int[]{0, 20}).GQ(100).make())});
+        tests.add(new Object[]{
+                new VariantContextBuilder(vcBase).alleles(ACG).genotypes(new GenotypeBuilder(base).alleles(AA).AD(hetRefG3AllelesAD).PL(hetRefG3AllelesPL).make()).make(),
+                new VariantContextBuilder(vcBase).alleles(AG).make(),
+                Arrays.asList(new GenotypeBuilder(base).alleles(AA).PL(new double[]{-20, 0, -50}).AD(new int[]{10, 11}).GQ(100).make())});
+
+        tests.add(new Object[]{
+                new VariantContextBuilder(vcBase).alleles(ACG).genotypes(new GenotypeBuilder(base).alleles(AA).AD(hetCG3AllelesAD).PL(hetCG3AllelesPL).make()).make(),
+                new VariantContextBuilder(vcBase).alleles(AG).make(),
+                Arrays.asList(new GenotypeBuilder(base).alleles(AA).PL(new double[]{0, -20, -30}).AD(new int[]{0, 11}).GQ(100).make())});
+
+        tests.add(new Object[]{
+                new VariantContextBuilder(vcBase).alleles(ACG).genotypes(new GenotypeBuilder(base).alleles(AA).AD(homG3AllelesAD).PL(homG3AllelesPL).make()).make(),
+                new VariantContextBuilder(vcBase).alleles(AG).make(),
+                Arrays.asList(new GenotypeBuilder(base).alleles(AA).PL(new double[]{-20, -40, 0}).AD(new int[]{0, 21}).GQ(100).make())});
+
+        return tests.toArray(new Object[][]{});
+    }
+
+    @Test(dataProvider = "updatePLsAndADData")
+    public void testUpdatePLsAndADData(final VariantContext originalVC,
+                                       final VariantContext selectedVC,
+                                       final List<Genotype> expectedGenotypes) {
+        final VariantContext selectedVCwithGTs = new VariantContextBuilder(selectedVC).genotypes(originalVC.getGenotypes()).make();
+        final GenotypesContext actual = GATKVariantContextUtils.updatePLsAndAD(selectedVCwithGTs, originalVC);
+
+        Assert.assertEquals(actual.size(), expectedGenotypes.size());
+        for ( final Genotype expected : expectedGenotypes ) {
+            final Genotype actualGT = actual.get(expected.getSampleName());
+            Assert.assertNotNull(actualGT);
+            assertGenotypesAreEqual(actualGT, expected);
+        }
+    }
 }
\ No newline at end of file

From ed6f06919108a278c10a3e2724266728c0f8bf16 Mon Sep 17 00:00:00 2001
From: Joel Thibault <thibault@broadinstitute.org>
Date: Wed, 13 Nov 2013 15:31:41 -0500
Subject: [PATCH 66/77] Rev Picard 1.102.1595

---
 ...rd-1.96.1534.jar => picard-1.102.1595.jar} | Bin 1689713 -> 1717977 bytes
 .../repository/net.sf/picard-1.102.1595.xml   |   3 +++
 .../repository/net.sf/picard-1.96.1534.xml    |   3 ---
 .../{sam-1.96.1534.jar => sam-1.102.1595.jar} | Bin 636983 -> 645027 bytes
 settings/repository/net.sf/sam-1.102.1595.xml |   3 +++
 settings/repository/net.sf/sam-1.96.1534.xml  |   3 ---
 ...e-1.96.1534.jar => tribble-1.102.1595.jar} | Bin 300089 -> 300395 bytes
 ...e-1.96.1534.xml => tribble-1.102.1595.xml} |   2 +-
 ...t-1.96.1534.jar => variant-1.102.1595.jar} | Bin 557066 -> 580439 bytes
 ...t-1.96.1534.xml => variant-1.102.1595.xml} |   2 +-
 10 files changed, 8 insertions(+), 8 deletions(-)
 rename settings/repository/net.sf/{picard-1.96.1534.jar => picard-1.102.1595.jar} (88%)
 create mode 100644 settings/repository/net.sf/picard-1.102.1595.xml
 delete mode 100644 settings/repository/net.sf/picard-1.96.1534.xml
 rename settings/repository/net.sf/{sam-1.96.1534.jar => sam-1.102.1595.jar} (89%)
 create mode 100644 settings/repository/net.sf/sam-1.102.1595.xml
 delete mode 100644 settings/repository/net.sf/sam-1.96.1534.xml
 rename settings/repository/org.broad/{tribble-1.96.1534.jar => tribble-1.102.1595.jar} (89%)
 rename settings/repository/org.broad/{tribble-1.96.1534.xml => tribble-1.102.1595.xml} (75%)
 rename settings/repository/org.broadinstitute/{variant-1.96.1534.jar => variant-1.102.1595.jar} (75%)
 rename settings/repository/org.broadinstitute/{variant-1.96.1534.xml => variant-1.102.1595.xml} (70%)

diff --git a/settings/repository/net.sf/picard-1.96.1534.jar b/settings/repository/net.sf/picard-1.102.1595.jar
similarity index 88%
rename from settings/repository/net.sf/picard-1.96.1534.jar
rename to settings/repository/net.sf/picard-1.102.1595.jar
index 8be3e01a30c9d74fa0d53b0be6fb666e4ad943c5..314b1db6ad3f69fde9d03ccac932bc9a2f0990ee 100644
GIT binary patch
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diff --git a/settings/repository/net.sf/picard-1.102.1595.xml b/settings/repository/net.sf/picard-1.102.1595.xml
new file mode 100644
index 000000000..e4370e4cd
--- /dev/null
+++ b/settings/repository/net.sf/picard-1.102.1595.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="picard" revision="1.102.1595" status="release" />
+</ivy-module>
diff --git a/settings/repository/net.sf/picard-1.96.1534.xml b/settings/repository/net.sf/picard-1.96.1534.xml
deleted file mode 100644
index 651193f22..000000000
--- a/settings/repository/net.sf/picard-1.96.1534.xml
+++ /dev/null
@@ -1,3 +0,0 @@
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-    <info organisation="net.sf" module="picard" revision="1.96.1534" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.96.1534.jar b/settings/repository/net.sf/sam-1.102.1595.jar
similarity index 89%
rename from settings/repository/net.sf/sam-1.96.1534.jar
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diff --git a/settings/repository/net.sf/sam-1.102.1595.xml b/settings/repository/net.sf/sam-1.102.1595.xml
new file mode 100644
index 000000000..44fc06d58
--- /dev/null
+++ b/settings/repository/net.sf/sam-1.102.1595.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.102.1595" status="release" />
+</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.96.1534.xml b/settings/repository/net.sf/sam-1.96.1534.xml
deleted file mode 100644
index f72556cfb..000000000
--- a/settings/repository/net.sf/sam-1.96.1534.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.96.1534" status="release" />
-</ivy-module>
diff --git a/settings/repository/org.broad/tribble-1.96.1534.jar b/settings/repository/org.broad/tribble-1.102.1595.jar
similarity index 89%
rename from settings/repository/org.broad/tribble-1.96.1534.jar
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index c414565bf01374e5083f6dc3b254d7757826bb51..4afeb3366e4a57c7cd62d2a9e092ee86e4dd5318 100644
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diff --git a/settings/repository/org.broad/tribble-1.96.1534.xml b/settings/repository/org.broad/tribble-1.102.1595.xml
similarity index 75%
rename from settings/repository/org.broad/tribble-1.96.1534.xml
rename to settings/repository/org.broad/tribble-1.102.1595.xml
index 7bbb7d27b..3500c3b08 100644
--- a/settings/repository/org.broad/tribble-1.96.1534.xml
+++ b/settings/repository/org.broad/tribble-1.102.1595.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="org.broad" module="tribble" revision="1.96.1534" status="integration" />
+    <info organisation="org.broad" module="tribble" revision="1.102.1595" status="integration" />
 </ivy-module>
diff --git a/settings/repository/org.broadinstitute/variant-1.96.1534.jar b/settings/repository/org.broadinstitute/variant-1.102.1595.jar
similarity index 75%
rename from settings/repository/org.broadinstitute/variant-1.96.1534.jar
rename to settings/repository/org.broadinstitute/variant-1.102.1595.jar
index 1e34967fa024de73ab6b4def1315573e092a15cc..18118bfae6de5ad8a60eec7ced2243980200cee8 100644
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AF8}}l

diff --git a/settings/repository/org.broadinstitute/variant-1.96.1534.xml b/settings/repository/org.broadinstitute/variant-1.102.1595.xml
similarity index 70%
rename from settings/repository/org.broadinstitute/variant-1.96.1534.xml
rename to settings/repository/org.broadinstitute/variant-1.102.1595.xml
index 0784e4891..aa348fc84 100644
--- a/settings/repository/org.broadinstitute/variant-1.96.1534.xml
+++ b/settings/repository/org.broadinstitute/variant-1.102.1595.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="org.broadinstitute" module="variant" revision="1.96.1534" status="integration" />
+    <info organisation="org.broadinstitute" module="variant" revision="1.102.1595" status="integration" />
 </ivy-module>

From cd3ee2ae7e5f4d6a8071542362ca8cc6e69376dc Mon Sep 17 00:00:00 2001
From: Joel Thibault <thibault@broadinstitute.org>
Date: Fri, 15 Nov 2013 16:50:26 -0500
Subject: [PATCH 67/77] whitespace

---
 .../broadinstitute/sting/gatk/io/storage/StorageFactory.java    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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 35aba8114..231f46f10 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
@@ -62,7 +62,7 @@ public class StorageFactory {
      * @param <T> Type of the stream to create.
      * @return Storage object with a facade of type T.
      */
-        public static <T> Storage<T> createStorage( Stub<T> stub, File file ) {
+     public static <T> Storage<T> createStorage( Stub<T> stub, File file ) {
         Storage storage;
 
         if(stub instanceof OutputStreamStub) {

From 42f78bdb3ab77c5a6910f094d6b41b05e7f67721 Mon Sep 17 00:00:00 2001
From: Joel Thibault <thibault@broadinstitute.org>
Date: Wed, 27 Nov 2013 11:45:58 -0500
Subject: [PATCH 68/77] Add a class-based DataProvider

---
 .../sting/ExampleToCopyUnitTest.java          | 36 +++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/public/java/test/org/broadinstitute/sting/ExampleToCopyUnitTest.java b/public/java/test/org/broadinstitute/sting/ExampleToCopyUnitTest.java
index 8a8faee8b..06bab8fc0 100644
--- a/public/java/test/org/broadinstitute/sting/ExampleToCopyUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/ExampleToCopyUnitTest.java
@@ -104,6 +104,42 @@ public class ExampleToCopyUnitTest extends BaseTest {
         Assert.assertTrue(size >= 0);
     }
 
+    /**
+     * DataProvider example using a class-based data structure
+     */
+    private class MyDataProviderClass extends TestDataProvider {
+        private int start;
+        private int size;
+
+        private MyDataProviderClass(int start, int size) {
+            super(MyDataProviderClass.class);
+            this.start = start;
+            this.size = size;
+        }
+    }
+
+    @DataProvider(name = "MyClassBasedDataProvider")
+    public Object[][] makeMyDataProviderClass() {
+        // this functionality can be adapted to provide input data for whatever you might want in your data
+        for ( final int start : Arrays.asList(1, 10, 100) ) {
+            for ( final int size : Arrays.asList(1, 10, 100, 1000) ) {
+                new MyDataProviderClass(start, size);
+            }
+        }
+
+        return TestDataProvider.getTests(MyDataProviderClass.class);
+    }
+
+    /**
+     * Example testng test using MyClassBasedDataProvider
+     */
+    @Test(dataProvider = "MyClassBasedDataProvider")
+    public void testMyDataProviderClass(MyDataProviderClass testSpec) {
+        // adaptor this code to do whatever testing you want given the arguments start and size
+        Assert.assertTrue(testSpec.start >= 0);
+        Assert.assertTrue(testSpec.size >= 0);
+    }
+
     /**
      * A unit test that creates an artificial read for testing some code that uses reads
      */

From fd0a02e52e7afe28518a7158d57159109a9ca874 Mon Sep 17 00:00:00 2001
From: Joel Thibault <thibault@broadinstitute.org>
Date: Thu, 7 Nov 2013 11:49:13 -0500
Subject: [PATCH 69/77] New VCF engine arguments to specify an alternate
 IndexCreator - CatVariants updates to use custom VCF indices - Scala scripts
 for VCF index testing

---
 .../arguments/GATKArgumentCollection.java     |  23 +++
 .../storage/VariantContextWriterStorage.java  |  11 +-
 .../io/stubs/VariantContextWriterStub.java    |  24 +++-
 .../sting/tools/CatVariants.java              |  12 +-
 .../sting/utils/variant/GATKVCFIndexType.java |  39 ++++++
 .../sting/utils/variant/GATKVCFUtils.java     |  30 ++++
 .../utils/variant/GATKVCFUtilsUnitTest.java   |  43 ++++++
 .../utils/variant/VCFIntegrationTest.java     | 131 ++++++++++++++++++
 .../extensions/gatk/CatVariantsGatherer.scala |   3 +
 9 files changed, 307 insertions(+), 9 deletions(-)
 create mode 100644 public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFIndexType.java

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 17849749e..1dc760709 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
@@ -35,6 +35,8 @@ import org.broadinstitute.sting.gatk.samples.PedigreeValidationType;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variant.GATKVCFIndexType;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
 
 import java.io.File;
 import java.util.ArrayList;
@@ -454,5 +456,26 @@ public class GATKArgumentCollection {
     @Hidden
     public boolean generateShadowBCF = false;
     // TODO -- remove all code tagged with TODO -- remove me when argument generateShadowBCF is removed
+
+    // --------------------------------------------------------------------------------------------------------------
+    //
+    // VCF/BCF index parameters
+    //
+    // --------------------------------------------------------------------------------------------------------------
+
+    /**
+     * Specify the Tribble indexing strategy to use for VCFs.
+     *
+     * LINEAR creates a LinearIndex with bins of equal width, specified by the Bin Width parameter
+     * INTERVAL creates an IntervalTreeIndex with bins with an equal amount of features, specified by the Features Per Bin parameter
+     * DYNAMIC_SEEK attempts to optimize for minimal seek time by choosing an appropriate strategy and parameter (user-supplied parameter is ignored)
+     * DYNAMIC_SIZE attempts to optimize for minimal index size by choosing an appropriate strategy and parameter (user-supplied parameter is ignored)
+     */
+
+    @Argument(fullName="variant_index_type",shortName = "variant_index_type",doc="which type of IndexCreator to use for VCF/BCF indices",required=false)
+    public GATKVCFIndexType variant_index_type = GATKVCFUtils.DEFAULT_INDEX_TYPE;
+
+    @Argument(fullName="variant_index_parameter",shortName = "variant_index_parameter",doc="the parameter (bin width or features per bin) to pass to the VCF/BCF IndexCreator",required=false)
+    public int variant_index_parameter = GATKVCFUtils.DEFAULT_INDEX_PARAMETER;
 }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
index e1dc36f5c..de203e59f 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
@@ -133,14 +133,21 @@ public class VariantContextWriterStorage implements Storage<VariantContextWriter
 
         // The GATK/Tribble can't currently index block-compressed files on the fly.  Disable OTF indexing even if the user explicitly asked for it.
         EnumSet<Options> options = stub.getWriterOptions(indexOnTheFly);
-        VariantContextWriter writer = VariantContextWriterFactory.create(file, this.stream, stub.getMasterSequenceDictionary(), options);
+        VariantContextWriter writer = VariantContextWriterFactory.create(file, this.stream, stub.getMasterSequenceDictionary(), stub.getIndexCreator(), options);
 
         // if the stub says to test BCF, create a secondary writer to BCF and an 2 way out writer to send to both
         // TODO -- remove me when argument generateShadowBCF is removed
         if ( stub.alsoWriteBCFForTest() && ! VariantContextWriterFactory.isBCFOutput(file, options)) {
             final File bcfFile = BCF2Utils.shadowBCF(file);
             if ( bcfFile != null ) {
-                VariantContextWriter bcfWriter = VariantContextWriterFactory.create(bcfFile, stub.getMasterSequenceDictionary(), options);
+                FileOutputStream bcfStream;
+                try {
+                    bcfStream = new FileOutputStream(bcfFile);
+                } catch (FileNotFoundException e) {
+                    throw new RuntimeException(bcfFile + ": Unable to create BCF writer", e);
+                }
+
+                VariantContextWriter bcfWriter = VariantContextWriterFactory.create(bcfFile, bcfStream, stub.getMasterSequenceDictionary(), stub.getIndexCreator(), options);
                 writer = new TestWriter(writer, bcfWriter);
             }
         }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java
index 3e3d6de41..9ad388adf 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java
@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.gatk.io.stubs;
 
 import net.sf.samtools.SAMSequenceDictionary;
+import org.broad.tribble.index.IndexCreator;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.io.OutputTracker;
 import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
@@ -70,6 +71,17 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
      */
     private final PrintStream genotypeStream;
 
+    /**
+     * A hack: push the argument sources into the VCF header so that the VCF header
+     * can rebuild the command-line arguments.
+     */
+    private final Collection<Object> argumentSources;
+
+    /**
+     * Which IndexCreator to use
+     */
+    private final IndexCreator indexCreator;
+
     /**
      * The cached VCF header (initialized to null)
      */
@@ -80,12 +92,6 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
      */
     private boolean isCompressed = false;
 
-    /**
-     * A hack: push the argument sources into the VCF header so that the VCF header
-     * can rebuild the command-line arguments.
-     */
-    private final Collection<Object> argumentSources;
-
     /**
      * Should the header be written out?  A hidden argument.
      */
@@ -118,6 +124,7 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
         this.engine = engine;
         this.genotypeFile = genotypeFile;
         this.genotypeStream = null;
+        this.indexCreator = GATKVCFUtils.getIndexCreator(engine.getArguments().variant_index_type, engine.getArguments().variant_index_parameter, genotypeFile);
         this.argumentSources = argumentSources;
     }
 
@@ -132,6 +139,7 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
         this.engine = engine;
         this.genotypeFile = null;
         this.genotypeStream = new PrintStream(genotypeStream);
+        this.indexCreator = null;
         this.argumentSources = argumentSources;
     }
 
@@ -175,6 +183,10 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
         this.forceBCF = forceBCF;
     }
 
+    public IndexCreator getIndexCreator() {
+        return indexCreator;
+    }
+
     /**
      * Gets the master sequence dictionary from the engine associated with this stub
      * @link GenomeAnalysisEngine.getMasterSequenceDictionary
diff --git a/public/java/src/org/broadinstitute/sting/tools/CatVariants.java b/public/java/src/org/broadinstitute/sting/tools/CatVariants.java
index b59786d15..8e5078f1f 100644
--- a/public/java/src/org/broadinstitute/sting/tools/CatVariants.java
+++ b/public/java/src/org/broadinstitute/sting/tools/CatVariants.java
@@ -31,12 +31,15 @@ import org.apache.log4j.BasicConfigurator;
 import org.apache.log4j.Level;
 import org.broad.tribble.AbstractFeatureReader;
 import org.broad.tribble.FeatureReader;
+import org.broad.tribble.index.IndexCreator;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.commandline.CommandLineProgram;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.help.HelpConstants;
+import org.broadinstitute.sting.utils.variant.GATKVCFIndexType;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
 import org.broadinstitute.variant.bcf2.BCF2Codec;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.variant.vcf.VCFCodec;
@@ -123,6 +126,12 @@ public class CatVariants extends CommandLineProgram {
     @Argument(fullName = "assumeSorted", shortName = "assumeSorted", doc = "assumeSorted should be true if he input files are already sorted (based on the position of the variants", required = false)
     private Boolean assumeSorted = false;
 
+    @Argument(fullName = "variant_index_type", doc = "which type of IndexCreator to use for VCF/BCF indices", required = false)
+    private GATKVCFIndexType variant_index_type = GATKVCFUtils.DEFAULT_INDEX_TYPE;
+
+    @Argument(fullName = "variant_index_parameter", doc = "the parameter (bin width or features per bin) to pass to the VCF/BCF IndexCreator", required = false)
+    private Integer variant_index_parameter = GATKVCFUtils.DEFAULT_INDEX_PARAMETER;
+
     /*
      * print usage information
      */
@@ -204,7 +213,8 @@ public class CatVariants extends CommandLineProgram {
 
         FileOutputStream outputStream = new FileOutputStream(outputFile);
         EnumSet<Options> options = EnumSet.of(Options.INDEX_ON_THE_FLY);
-        final VariantContextWriter outputWriter = VariantContextWriterFactory.create(outputFile, outputStream, ref.getSequenceDictionary(), options);
+        final IndexCreator idxCreator = GATKVCFUtils.getIndexCreator(variant_index_type, variant_index_parameter, outputFile);
+        final VariantContextWriter outputWriter = VariantContextWriterFactory.create(outputFile, outputStream, ref.getSequenceDictionary(), idxCreator, options);
 
         boolean firstFile = true;
         int count =0;
diff --git a/public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFIndexType.java b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFIndexType.java
new file mode 100644
index 000000000..3f00d9fe5
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFIndexType.java
@@ -0,0 +1,39 @@
+/*
+* Copyright (c) 2012 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.variant;
+
+import org.broadinstitute.sting.commandline.EnumerationArgumentDefault;
+
+/**
+ * Choose the Tribble indexing strategy
+ */
+public enum GATKVCFIndexType {
+    @EnumerationArgumentDefault
+    DYNAMIC_SEEK,       // use DynamicIndexCreator(IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME)
+    DYNAMIC_SIZE,       // use DynamicIndexCreator(IndexFactory.IndexBalanceApproach.FOR_SIZE)
+    LINEAR,             // use LinearIndexCreator()
+    INTERVAL            // use IntervalIndexCreator()
+}
diff --git a/public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java
index d1ba990fd..5a160566e 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java
@@ -28,6 +28,11 @@ package org.broadinstitute.sting.utils.variant;
 import org.broad.tribble.Feature;
 import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.FeatureCodecHeader;
+import org.broad.tribble.index.DynamicIndexCreator;
+import org.broad.tribble.index.IndexCreator;
+import org.broad.tribble.index.IndexFactory;
+import org.broad.tribble.index.interval.IntervalIndexCreator;
+import org.broad.tribble.index.linear.LinearIndexCreator;
 import org.broad.tribble.readers.LineIterator;
 import org.broad.tribble.readers.PositionalBufferedStream;
 import org.broadinstitute.sting.commandline.RodBinding;
@@ -43,6 +48,7 @@ import java.io.FileInputStream;
 import java.io.IOException;
 import java.util.*;
 
+
 /**
  * A set of GATK-specific static utility methods for common operations on VCF files/records.
  */
@@ -55,6 +61,9 @@ public class GATKVCFUtils {
 
     public final static String GATK_COMMAND_LINE_KEY = "GATKCommandLine";
 
+    public final static GATKVCFIndexType DEFAULT_INDEX_TYPE = GATKVCFIndexType.DYNAMIC_SEEK;  // by default, optimize for seek time.  All indices prior to Nov 2013 used this type.
+    public final static Integer DEFAULT_INDEX_PARAMETER = -1;           // the default DYNAMIC_SEEK does not use a parameter
+
     /**
      * Gets the appropriately formatted header for a VCF file describing this GATK run
      *
@@ -175,6 +184,27 @@ public class GATKVCFUtils {
         return VCFUtils.withUpdatedContigs(header, engine.getArguments().referenceFile, engine.getMasterSequenceDictionary());
     }
 
+    /**
+     * Create and return an IndexCreator
+     * @param type
+     * @param parameter
+     * @param outFile
+     * @return
+     */
+    public static IndexCreator getIndexCreator(GATKVCFIndexType type, int parameter, File outFile) {
+        IndexCreator idxCreator;
+        switch (type) {
+            case DYNAMIC_SEEK: idxCreator = new DynamicIndexCreator(IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME); break;
+            case DYNAMIC_SIZE: idxCreator = new DynamicIndexCreator(IndexFactory.IndexBalanceApproach.FOR_SIZE); break;
+            case LINEAR: idxCreator = new LinearIndexCreator(); break;
+            case INTERVAL: idxCreator = new IntervalIndexCreator(); break;
+            default: throw new IllegalArgumentException("Unknown IndexCreator type: " + type);
+        }
+
+        idxCreator.initialize(outFile, parameter);
+        return idxCreator;
+    }
+
     /**
      * Utility class to read all of the VC records from a file
      *
diff --git a/public/java/test/org/broadinstitute/sting/utils/variant/GATKVCFUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variant/GATKVCFUtilsUnitTest.java
index 051d0bcec..57020424c 100644
--- a/public/java/test/org/broadinstitute/sting/utils/variant/GATKVCFUtilsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variant/GATKVCFUtilsUnitTest.java
@@ -25,6 +25,10 @@
 
 package org.broadinstitute.sting.utils.variant;
 
+import org.broad.tribble.index.DynamicIndexCreator;
+import org.broad.tribble.index.IndexCreator;
+import org.broad.tribble.index.interval.IntervalIndexCreator;
+import org.broad.tribble.index.linear.LinearIndexCreator;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -35,8 +39,10 @@ import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.variant.vcf.VCFHeader;
 import org.broadinstitute.variant.vcf.VCFHeaderLine;
 import org.testng.Assert;
+import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
+import java.io.File;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.Set;
@@ -83,4 +89,41 @@ public class GATKVCFUtilsUnitTest extends BaseTest {
         Assert.assertTrue(lines2.contains(line1));
         Assert.assertTrue(lines2.contains(line2));
     }
+
+    private class IndexCreatorTest extends TestDataProvider {
+        private final GATKVCFIndexType type;
+        private final int parameter;
+        private final Class expectedClass;
+        private final int expectedDefaultBinSize;
+        private final int expectedBinSize;
+
+        private IndexCreatorTest(GATKVCFIndexType type, int parameter, Class expectedClass, int expectedDefaultBinSize, int expectedBinSize) {
+            super(IndexCreatorTest.class);
+
+            this.type = type;
+            this.parameter = parameter;
+            this.expectedClass = expectedClass;
+            this.expectedDefaultBinSize = expectedDefaultBinSize;
+            this.expectedBinSize = expectedBinSize;
+        }
+    }
+
+    @DataProvider(name = "indexCreator")
+    public Object[][] indexCreatorData() {
+        new IndexCreatorTest(GATKVCFIndexType.DYNAMIC_SEEK, 0, DynamicIndexCreator.class, -1, -1);
+        new IndexCreatorTest(GATKVCFIndexType.DYNAMIC_SIZE, 0, DynamicIndexCreator.class, -1, -1);
+        new IndexCreatorTest(GATKVCFIndexType.LINEAR, 100, LinearIndexCreator.class, LinearIndexCreator.DEFAULT_BIN_WIDTH, 100);
+        new IndexCreatorTest(GATKVCFIndexType.INTERVAL, 200, IntervalIndexCreator.class, IntervalIndexCreator.DEFAULT_FEATURE_COUNT, 200);
+
+        return IndexCreatorTest.getTests(IndexCreatorTest.class);
+    }
+
+    @Test(dataProvider = "indexCreator")
+    public void testGetIndexCreator(IndexCreatorTest spec) {
+        File dummy = new File("");
+        IndexCreator ic = GATKVCFUtils.getIndexCreator(spec.type, spec.parameter, dummy);
+        Assert.assertEquals(ic.getClass(), spec.expectedClass, "Wrong IndexCreator type");
+        Assert.assertEquals(ic.defaultBinSize(), spec.expectedDefaultBinSize, "Wrong default bin size");
+        Assert.assertEquals(ic.getBinSize(), spec.expectedBinSize, "Wrong bin size");
+    }
 }
\ No newline at end of file
diff --git a/public/java/test/org/broadinstitute/sting/utils/variant/VCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/variant/VCFIntegrationTest.java
index f4cef7730..f29a1106c 100644
--- a/public/java/test/org/broadinstitute/sting/utils/variant/VCFIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variant/VCFIntegrationTest.java
@@ -25,11 +25,24 @@
 
 package org.broadinstitute.sting.utils.variant;
 
+import org.broad.tribble.index.AbstractIndex;
+import org.broad.tribble.index.ChrIndex;
+import org.broad.tribble.index.Index;
+import org.broad.tribble.index.IndexFactory;
+import org.broad.tribble.index.interval.IntervalTreeIndex;
+import org.broad.tribble.index.linear.LinearIndex;
 import org.broadinstitute.sting.WalkerTest;
+import org.broadinstitute.variant.vcf.VCFCodec;
+import org.testng.Assert;
+import org.testng.TestException;
+import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
 import java.io.File;
+import java.lang.reflect.Field;
 import java.util.Arrays;
+import java.util.Collections;
+import java.util.LinkedHashMap;
 import java.util.List;
 
 public class VCFIntegrationTest extends WalkerTest {
@@ -141,4 +154,122 @@ public class VCFIntegrationTest extends WalkerTest {
             spec1.disableShadowBCF();
         executeTest("Test reading VCF without header lines with additional args " + moreArgs, spec1);
     }
+
+    //
+    //
+    // IndexCreator tests
+    //
+    //
+
+    private class VCFIndexCreatorTest extends TestDataProvider {
+        private final GATKVCFIndexType type;
+        private final int parameter;
+
+        private VCFIndexCreatorTest(GATKVCFIndexType type, int parameter) {
+            super(VCFIndexCreatorTest.class);
+
+            this.type = type;
+            this.parameter = parameter;
+        }
+
+        public String toString() {
+            return String.format("Index Type %s, Index Parameter %s", type, parameter);
+        }
+
+        public Index getIndex(final File vcfFile) {
+            switch (type) {
+                case DYNAMIC_SEEK : return IndexFactory.createDynamicIndex(vcfFile, new VCFCodec(), IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME);
+                case DYNAMIC_SIZE : return IndexFactory.createDynamicIndex(vcfFile, new VCFCodec(), IndexFactory.IndexBalanceApproach.FOR_SIZE);
+                case LINEAR : return IndexFactory.createLinearIndex(vcfFile, new VCFCodec(), parameter);
+                case INTERVAL : return IndexFactory.createIntervalIndex(vcfFile, new VCFCodec(), parameter);
+                default : throw new TestException("Invalid index type");
+            }
+        }
+    }
+
+    @DataProvider(name = "IndexDataProvider")
+    public Object[][] indexCreatorData() {
+        new VCFIndexCreatorTest(GATKVCFIndexType.DYNAMIC_SEEK, 0);
+        new VCFIndexCreatorTest(GATKVCFIndexType.DYNAMIC_SIZE, 0);
+        new VCFIndexCreatorTest(GATKVCFIndexType.LINEAR, 100);
+        new VCFIndexCreatorTest(GATKVCFIndexType.LINEAR, 10000);
+        new VCFIndexCreatorTest(GATKVCFIndexType.INTERVAL, 20);
+        new VCFIndexCreatorTest(GATKVCFIndexType.INTERVAL, 2000);
+
+        return TestDataProvider.getTests(VCFIndexCreatorTest.class);
+    }
+
+    @Test(dataProvider = "IndexDataProvider")
+    public void testVCFIndexCreation(VCFIndexCreatorTest testSpec) throws NoSuchFieldException, IllegalAccessException {
+
+        final String commandLine = " -T SelectVariants" +
+                " -R " + b37KGReference +
+                " --no_cmdline_in_header" +
+                " -L 20" +
+                " -V " + b37_NA12878_OMNI +
+                " --variant_index_type " + testSpec.type +
+                " --variant_index_parameter " + testSpec.parameter +
+                " -o %s ";
+        final String name = "testVCFIndexCreation: " + testSpec.toString();
+
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine, 1, Arrays.asList(""));
+        spec.disableShadowBCF();
+
+        File outVCF = executeTest(name, spec).first.get(0);
+        File outIdx = new File(outVCF.getAbsolutePath() + ".idx");
+
+        final Index actualIndex = IndexFactory.loadIndex(outIdx.getAbsolutePath());
+        final Index expectedIndex = testSpec.getIndex(outVCF);
+
+        if (testSpec.type.equals("LINEAR"))
+            Assert.assertTrue(actualIndex instanceof LinearIndex, "Index is not a LinearIndex");
+        else if (testSpec.type.equals("INTERVAL"))
+            Assert.assertTrue(actualIndex instanceof IntervalTreeIndex, "Index is not a IntervalTreeIndex");
+        // dynamic indices ultimately resolve to one of LinearIndex or IntervalTreeIndex
+
+        Assert.assertTrue(equivalentAbstractIndices((AbstractIndex)actualIndex, (AbstractIndex)expectedIndex), "Indices are not equivalent");
+
+        if (actualIndex instanceof LinearIndex && expectedIndex instanceof LinearIndex) {
+            Assert.assertTrue(equivalentLinearIndices((LinearIndex)actualIndex, (LinearIndex)expectedIndex, "20"), "Linear indices are not equivalent");
+        }
+        else if (actualIndex instanceof IntervalTreeIndex && expectedIndex instanceof IntervalTreeIndex) {
+            Assert.assertTrue(equivalentIntervalIndices((IntervalTreeIndex)actualIndex, (IntervalTreeIndex)expectedIndex, "20"), "Interval indices are not equivalent");
+        }
+        else {
+            Assert.fail("Indices are not of the same type");
+        }
+    }
+
+    private static boolean equivalentAbstractIndices(AbstractIndex thisIndex, AbstractIndex otherIndex){
+        return thisIndex.getVersion() == otherIndex.getVersion() &&
+                thisIndex.getIndexedFile().equals(otherIndex.getIndexedFile()) &&
+                thisIndex.getIndexedFileSize() == otherIndex.getIndexedFileSize() &&
+                thisIndex.getIndexedFileMD5().equals(otherIndex.getIndexedFileMD5()) &&
+                thisIndex.getFlags() == otherIndex.getFlags();
+     }
+
+    private static boolean equivalentLinearIndices(LinearIndex thisIndex, LinearIndex otherIndex, String chr) throws NoSuchFieldException, IllegalAccessException {
+        org.broad.tribble.index.linear.LinearIndex.ChrIndex thisChr = (org.broad.tribble.index.linear.LinearIndex.ChrIndex)getChrIndex(thisIndex, chr);
+        org.broad.tribble.index.linear.LinearIndex.ChrIndex otherChr = (org.broad.tribble.index.linear.LinearIndex.ChrIndex)getChrIndex(otherIndex, chr);
+
+        return  thisChr.getName().equals(otherChr.getName()) &&
+                //thisChr.getTotalSize() == otherChr.getTotalSize() &&      TODO: why does this differ?
+                thisChr.getNFeatures() == otherChr.getNFeatures() &&
+                thisChr.getNBlocks() == otherChr.getNBlocks();
+    }
+
+    private static boolean equivalentIntervalIndices(IntervalTreeIndex thisIndex, IntervalTreeIndex otherIndex, String chr) throws NoSuchFieldException, IllegalAccessException {
+        org.broad.tribble.index.interval.IntervalTreeIndex.ChrIndex thisChr = (org.broad.tribble.index.interval.IntervalTreeIndex.ChrIndex)getChrIndex(thisIndex, chr);
+        org.broad.tribble.index.interval.IntervalTreeIndex.ChrIndex otherChr = (org.broad.tribble.index.interval.IntervalTreeIndex.ChrIndex)getChrIndex(otherIndex, chr);
+
+        // TODO: compare trees?
+        return thisChr.getName().equals(otherChr.getName());
+    }
+
+    private static ChrIndex getChrIndex(AbstractIndex index, String chr) throws NoSuchFieldException, IllegalAccessException {
+        Field f = AbstractIndex.class.getDeclaredField("chrIndices");
+        f.setAccessible(true);
+        LinkedHashMap<String, ChrIndex> chrIndices = (LinkedHashMap<String, ChrIndex>) f.get(index);
+        return chrIndices.get(chr);
+    }
 }
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala
index 30fd4c81f..940d98860 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala
@@ -48,6 +48,9 @@ class CatVariantsGatherer extends CatVariants with GatherFunction with RetryMemo
     this.variant = this.gatherParts.zipWithIndex map { case (input, index) => new TaggedFile(input, "input"+index) }
     this.outputFile = this.originalOutput
     this.assumeSorted = true
+    this.variant_index_type = originalGATK.variant_index_type
+    this.variant_index_parameter = originalGATK.variant_index_parameter
+
     super.freezeFieldValues()
   }
 

From 701ede2817372b6b2f65c18e40101b059c058c5c Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Wed, 27 Nov 2013 11:53:49 -0500
Subject: [PATCH 70/77] Add GC Content to DiagnoseTargets

---
 .../diagnosetargets/DiagnoseTargets.java           | 12 ++++++++++--
 .../diagnosetargets/IntervalStratification.java    | 14 +++++++++++++-
 .../DiagnoseTargetsIntegrationTest.java            |  4 ++--
 3 files changed, 25 insertions(+), 5 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java
index bde324e3c..fbf4b23c6 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java
@@ -89,7 +89,12 @@ import java.util.*;
  * <p/>
  * <h3>Output</h3>
  * <p>
- * A modified VCF detailing each interval by sample
+ * A modified VCF detailing each interval by sample and information for each interval according to the thresholds used.
+ * Interval information includes GC Content, average interval depth, callable status among others.
+ *
+ * If you use the --missing option, you can get as a second output a intervals file with the loci that have missing data.
+ * This file can then be used as input to QualifyMissingIntervals for full qualification and interpretation of why
+ * the data is missing.
  * </p>
  * <p/>
  * <h3>Examples</h3>
@@ -117,6 +122,7 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
     private static final String AVG_INTERVAL_DP_KEY = "IDP";
     private static final String LOW_COVERAGE_LOCI = "LL";
     private static final String ZERO_COVERAGE_LOCI = "ZL";
+    private static final String GC_CONTENT_KEY = "GC";
 
 
     @Output(doc = "File to which interval statistics should be written")
@@ -161,7 +167,7 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
 
         // at this point, all intervals in intervalMap overlap with this locus, so update all of them
         for (IntervalStratification intervalStratification : intervalMap.values())
-            intervalStratification.addLocus(context);
+            intervalStratification.addLocus(context, ref);
 
         return 1L;
     }
@@ -276,6 +282,7 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
 
         attributes.put(VCFConstants.END_KEY, interval.getStop());
         attributes.put(AVG_INTERVAL_DP_KEY, stats.averageCoverage(interval.size()));
+        attributes.put(GC_CONTENT_KEY, stats.gcContent());
 
         vcb = vcb.attributes(attributes);
         vcb = vcb.genotypes(genotypes);
@@ -391,6 +398,7 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
         // INFO fields for overall data
         headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.END_KEY));
         headerLines.add(new VCFInfoHeaderLine(AVG_INTERVAL_DP_KEY, 1, VCFHeaderLineType.Float, "Average depth across the interval. Sum of the depth in a loci divided by interval size."));
+        headerLines.add(new VCFInfoHeaderLine(GC_CONTENT_KEY, 1, VCFHeaderLineType.Float, "GC Content of the interval"));
         headerLines.add(new VCFInfoHeaderLine("Diagnose Targets", 0, VCFHeaderLineType.Flag, "DiagnoseTargets mode"));
 
         // FORMAT fields for each genotype
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/IntervalStratification.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/IntervalStratification.java
index 3b5a23d51..cd38d28c6 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/IntervalStratification.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/IntervalStratification.java
@@ -47,6 +47,7 @@
 package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@@ -57,9 +58,13 @@ final class IntervalStratification extends AbstractStratification {
     private final Map<String, AbstractStratification> samples;
     private final GenomeLoc interval;
     private List<CallableStatus> callableStatuses;
+    private long gcCount = 0;
 
     public IntervalStratification(Set<String> samples, GenomeLoc interval, ThresHolder thresholds) {
         super(thresholds);
+
+        assert interval != null && interval.size() > 0;  // contracts
+
         this.interval = interval;
         this.samples = new HashMap<String, AbstractStratification>(samples.size());
         for (String sample : samples)
@@ -83,8 +88,11 @@ final class IntervalStratification extends AbstractStratification {
      * This takes the input and manages passing the data to the SampleStatistics and Locus Statistics
      *
      * @param context    The alignment context given from the walker
+     * @param ref        The reference context given from the walker
      */
-    public void addLocus(AlignmentContext context) {
+    public void addLocus(final AlignmentContext context,  final ReferenceContext ref) {
+        assert ref != null;  // contracts
+
         ReadBackedPileup pileup = context.getBasePileup();
 
         Map<String, ReadBackedPileup> samplePileups = pileup.getPileupsForSamples(samples.keySet());
@@ -99,7 +107,11 @@ final class IntervalStratification extends AbstractStratification {
 
             sampleStratification.addLocus(context.getLocation(), samplePileup);
         }
+        gcCount += (ref.getBase() == 'G' || ref.getBase() == 'C') ? 1 : 0;
+    }
 
+    public double gcContent() {
+        return (double) gcCount / interval.size();
     }
 
     /**
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java
index 52e385957..0259e9685 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java
@@ -66,11 +66,11 @@ public class DiagnoseTargetsIntegrationTest extends WalkerTest {
 
     @Test(enabled = true)
     public void testSingleSample() {
-        DTTest("testSingleSample ", "-I " + singleSample + " -max 75", "1771e95aed2b3b240dc353f84e19847d");
+        DTTest("testSingleSample ", "-I " + singleSample + " -max 75", "6ca3d3917a7b65eaa877aa3658d80912");
     }
 
     @Test(enabled = true)
     public void testMultiSample() {
-        DTTest("testMultiSample ", "-I " + multiSample, "c7f1691dbe5f121c4a79be823d3057e5");
+        DTTest("testMultiSample ", "-I " + multiSample, "f50c6b9bef9f63f0a8b32ae9a9bdd51a");
     }
 }

From 8571a641bf5a0c1d35551f7cb0255e65fbdc1d35 Mon Sep 17 00:00:00 2001
From: Joel Thibault <thibault@broadinstitute.org>
Date: Tue, 3 Dec 2013 16:40:31 -0500
Subject: [PATCH 71/77] Add @Advanced to variant_index_type and
 variant_index_parameter

---
 .../sting/gatk/arguments/GATKArgumentCollection.java            | 2 ++
 1 file changed, 2 insertions(+)

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 1dc760709..08f892f97 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
@@ -473,9 +473,11 @@ public class GATKArgumentCollection {
      */
 
     @Argument(fullName="variant_index_type",shortName = "variant_index_type",doc="which type of IndexCreator to use for VCF/BCF indices",required=false)
+    @Advanced
     public GATKVCFIndexType variant_index_type = GATKVCFUtils.DEFAULT_INDEX_TYPE;
 
     @Argument(fullName="variant_index_parameter",shortName = "variant_index_parameter",doc="the parameter (bin width or features per bin) to pass to the VCF/BCF IndexCreator",required=false)
+    @Advanced
     public int variant_index_parameter = GATKVCFUtils.DEFAULT_INDEX_PARAMETER;
 }
 

From 5fe0531b4de73c9ab0c362bd8ac890c8d89d599f Mon Sep 17 00:00:00 2001
From: Joel Thibault <thibault@broadinstitute.org>
Date: Tue, 3 Dec 2013 16:36:23 -0500
Subject: [PATCH 72/77] Throw a GVCFIndexException when the user doesn't
 specify the optimal indexing strategy

---
 .../haplotypecaller/HaplotypeCaller.java      | 11 +++++
 .../HaplotypeCallerGVCFIntegrationTest.java   | 42 +++++++++++++++++--
 .../sting/utils/exceptions/UserException.java |  9 ++++
 .../org/broadinstitute/sting/WalkerTest.java  |  1 +
 4 files changed, 59 insertions(+), 4 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
index d795f5b90..6b7373273 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
@@ -92,6 +92,7 @@ import org.broadinstitute.sting.utils.help.HelpConstants;
 import org.broadinstitute.sting.utils.pairhmm.PairHMM;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
+import org.broadinstitute.sting.utils.variant.GATKVCFIndexType;
 import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
 import org.broadinstitute.variant.variantcontext.*;
 import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
@@ -536,6 +537,10 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
 
     ReferenceConfidenceModel referenceConfidenceModel = null;
 
+    // as determined experimentally Nov-Dec 2013
+    protected final static GATKVCFIndexType OPTIMAL_GVCF_INDEX_TYPE = GATKVCFIndexType.LINEAR;
+    protected final static int OPTIMAL_GVCF_INDEX_PARAMETER = 128000;
+
     //---------------------------------------------------------------------------------------------------------------
     //
     // initialize
@@ -601,6 +606,12 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
             if ( samples.size() != 1 ) throw new UserException.BadArgumentValue("emitRefConfidence", "Can only be used in single sample mode currently");
             headerInfo.addAll(referenceConfidenceModel.getVCFHeaderLines());
             if ( emitReferenceConfidence == ReferenceConfidenceMode.GVCF ) {
+                // a kluge to enforce the use of this indexing strategy
+                if (getToolkit().getArguments().variant_index_type != OPTIMAL_GVCF_INDEX_TYPE ||
+                        getToolkit().getArguments().variant_index_parameter != OPTIMAL_GVCF_INDEX_PARAMETER) {
+                    throw new UserException.GVCFIndexException(OPTIMAL_GVCF_INDEX_TYPE, OPTIMAL_GVCF_INDEX_PARAMETER);
+                }
+
                 try {
                     vcfWriter = new GVCFWriter(vcfWriter, GVCFGQBands);
                 } catch ( IllegalArgumentException e ) {
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
index e430cd8d1..97744f126 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
@@ -47,6 +47,8 @@
 package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
 
 import org.broadinstitute.sting.WalkerTest;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variant.GATKVCFIndexType;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
@@ -79,8 +81,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
      */
     @Test(dataProvider = "MyDataProvider")
     public void testHCWithGVCF(String bam, HaplotypeCaller.ReferenceConfidenceMode mode, String intervals, String md5) {
-        final String commandLine = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R %s -I %s %s -ERC %s --no_cmdline_in_header",
-                b37KGReference, bam, intervals, mode);
+        final String commandLine = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R %s -I %s %s -ERC %s --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
+                b37KGReference, bam, intervals, mode, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
         final String name = "testHCWithGVCF bam=" + bam + " intervals= " + intervals + " gvcf= " + mode;
         final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(md5));
         executeTest(name, spec);
@@ -88,10 +90,42 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
 
     @Test
     public void testERCRegionWithNoCalledHaplotypes() {
-        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF",
-                b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001");
+        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF -variant_index_type %s -variant_index_parameter %d",
+                b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001", HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
         final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(""));
         spec.disableShadowBCF();
         executeTest("testERCRegionWithNoCalledHaplotypes", spec);
     }
+
+    @Test()
+    public void testMissingGVCFIndexException() {
+        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF",
+                b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001");
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", 1, UserException.GVCFIndexException.class);
+        spec.disableShadowBCF();
+        executeTest("testMissingGVCFIndexingStrategyException", spec);
+    }
+
+    @Test()
+    public void testWrongParameterGVCFIndexException() {
+        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF -variant_index_type %s -variant_index_parameter %d",
+                b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001", HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER + 1);
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", 1, UserException.GVCFIndexException.class);
+        spec.disableShadowBCF();
+        executeTest("testMissingGVCFIndexingStrategyException", spec);
+    }
+
+    @Test()
+    public void testWrongTypeGVCFIndexException() {
+        // ensure non-optimal, if optimal changes
+        GATKVCFIndexType type = GATKVCFIndexType.DYNAMIC_SEEK;
+        if (HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE == GATKVCFIndexType.DYNAMIC_SEEK)
+            type = GATKVCFIndexType.DYNAMIC_SIZE;
+
+        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF -variant_index_type %s -variant_index_parameter %d",
+                b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001", type, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", 1, UserException.GVCFIndexException.class);
+        spec.disableShadowBCF();
+        executeTest("testMissingGVCFIndexingStrategyException", spec);
+    }
 }
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 6126116c2..40a730029 100644
--- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
+++ b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
@@ -33,6 +33,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.help.HelpConstants;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
+import org.broadinstitute.sting.utils.variant.GATKVCFIndexType;
 import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.io.File;
@@ -455,6 +456,14 @@ public class UserException extends ReviewedStingException {
         }
     }
 
+    public static class GVCFIndexException extends UserException {
+        public GVCFIndexException (GATKVCFIndexType indexType, int indexParameter) {
+            super(String.format("GVCF output requires a specific indexing strategy.  Please re-run including the arguments " +
+                    "-variant_index_type %s -variant_index_parameter %d.",
+                    indexType, indexParameter));
+        }
+    }
+
     /**
      * A special exception that happens only in the case where
      * the filesystem, by design or configuration, is completely unable
diff --git a/public/java/test/org/broadinstitute/sting/WalkerTest.java b/public/java/test/org/broadinstitute/sting/WalkerTest.java
index e8e791a8a..994a2419c 100644
--- a/public/java/test/org/broadinstitute/sting/WalkerTest.java
+++ b/public/java/test/org/broadinstitute/sting/WalkerTest.java
@@ -201,6 +201,7 @@ public class WalkerTest extends BaseTest {
             this.testClass = getCallingTestClass();
         }
 
+        // @Test(expectedExceptions) doesn't work in integration tests, so use this instead
         public WalkerTestSpec(String args, int nOutputFiles, Class expectedException) {
             this.args = args;
             this.nOutputFiles = nOutputFiles;

From 3ab2f4edb2e7fd4903ddd8f680e37f49e5c4a1d8 Mon Sep 17 00:00:00 2001
From: Geraldine Van der Auwera <vdauwera@broadinstitute.org>
Date: Wed, 4 Dec 2013 19:55:24 -0500
Subject: [PATCH 73/77] Fixed documentation for -deletions argument in the UAC

---
 .../gatk/walkers/genotyper/UnifiedArgumentCollection.java   | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
index 4fae3d6e3..04c5587c3 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
@@ -95,7 +95,11 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection
     @Argument(fullName = "min_base_quality_score", shortName = "mbq", doc = "Minimum base quality required to consider a base for calling", required = false)
     public int MIN_BASE_QUALTY_SCORE = 17;
 
-    @Argument(fullName = "max_deletion_fraction", shortName = "deletions", doc = "Maximum fraction of reads with deletions spanning this locus for it to be callable [to disable, set to < 0 or > 1; default:0.05]", required = false)
+    /**
+     * If the fraction of reads with deletions spanning a locus is greater than this value, the site will not be considered callable and will be skipped.
+     * To disable the use of this parameter, set its value to >1.
+     */
+    @Argument(fullName = "max_deletion_fraction", shortName = "deletions", doc = "Maximum fraction of reads with deletions spanning this locus for it to be callable", required = false)
     public Double MAX_DELETION_FRACTION = 0.05;
 
     /**

From e022db46901ab9953a50bd12b019783a6879e9c4 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 5 Dec 2013 11:50:56 -0500
Subject: [PATCH 74/77] Added docs for the minPruning argument in the HC

---
 .../gatk/walkers/haplotypecaller/HaplotypeCaller.java      | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
index 6b7373273..82015d153 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
@@ -335,6 +335,13 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
     // general advanced arguments to control haplotype caller behavior
     // -----------------------------------------------------------------------------------------------
 
+    /**
+     * Users should be aware that this argument can really affect the results of the variant calling and should exercise caution.
+     * Using a prune factor of 1 (or below) will prevent any pruning from the graph which is generally not ideal; it can make the
+     * calling much slower and even less accurate (because it can prevent effective merging of "tails" in the graph).  Higher values
+     * tend to make the calling much faster, but also lowers the sensitivity of the results (because it ultimately requires higher
+     * depth to produce calls).
+     */
     @Advanced
     @Argument(fullName="minPruning", shortName="minPruning", doc = "The minimum allowed pruning factor in assembly graph. Paths with < X supporting kmers are pruned from the graph", required = false)
     protected int MIN_PRUNE_FACTOR = 2;

From 0e65296efbd65f39c48e76c3bfe652dd1630eb02 Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Thu, 5 Dec 2013 12:25:33 -0500
Subject: [PATCH 75/77] Rev picard, sam-jdk, tribble, and variant jars to
 1.104.1628

-update VariantFiltration to work with new Lazy wrapper around the
 JexlEngine in VariantContextUtils
---
 .../walkers/filters/VariantFiltration.java    |   2 +-
 .../repository/net.sf/picard-1.102.1595.xml   |   3 ---
 ...d-1.102.1595.jar => picard-1.104.1628.jar} | Bin 1717977 -> 1725289 bytes
 .../repository/net.sf/picard-1.104.1628.xml   |   3 +++
 settings/repository/net.sf/sam-1.102.1595.xml |   3 ---
 ...{sam-1.102.1595.jar => sam-1.104.1628.jar} | Bin 645027 -> 660527 bytes
 settings/repository/net.sf/sam-1.104.1628.xml |   3 +++
 ...-1.102.1595.jar => tribble-1.104.1628.jar} | Bin 300395 -> 303987 bytes
 ...-1.102.1595.xml => tribble-1.104.1628.xml} |   2 +-
 ...-1.102.1595.jar => variant-1.104.1628.jar} | Bin 580439 -> 582844 bytes
 ...-1.102.1595.xml => variant-1.104.1628.xml} |   2 +-
 11 files changed, 9 insertions(+), 9 deletions(-)
 delete mode 100644 settings/repository/net.sf/picard-1.102.1595.xml
 rename settings/repository/net.sf/{picard-1.102.1595.jar => picard-1.104.1628.jar} (91%)
 create mode 100644 settings/repository/net.sf/picard-1.104.1628.xml
 delete mode 100644 settings/repository/net.sf/sam-1.102.1595.xml
 rename settings/repository/net.sf/{sam-1.102.1595.jar => sam-1.104.1628.jar} (90%)
 create mode 100644 settings/repository/net.sf/sam-1.104.1628.xml
 rename settings/repository/org.broad/{tribble-1.102.1595.jar => tribble-1.104.1628.jar} (83%)
 rename settings/repository/org.broad/{tribble-1.102.1595.xml => tribble-1.104.1628.xml} (75%)
 rename settings/repository/org.broadinstitute/{variant-1.102.1595.jar => variant-1.104.1628.jar} (94%)
 rename settings/repository/org.broadinstitute/{variant-1.102.1595.xml => variant-1.104.1628.xml} (70%)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
index 1d07215ad..5ef1f0cf0 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
@@ -230,7 +230,7 @@ public class VariantFiltration extends RodWalker<Integer, Integer> {
         filterExps = VariantContextUtils.initializeMatchExps(FILTER_NAMES, FILTER_EXPS);
         genotypeFilterExps = VariantContextUtils.initializeMatchExps(GENOTYPE_FILTER_NAMES, GENOTYPE_FILTER_EXPS);
 
-        VariantContextUtils.engine.setSilent(true);
+        VariantContextUtils.engine.get().setSilent(true);
 
         initializeVcfWriter();
     }
diff --git a/settings/repository/net.sf/picard-1.102.1595.xml b/settings/repository/net.sf/picard-1.102.1595.xml
deleted file mode 100644
index e4370e4cd..000000000
--- a/settings/repository/net.sf/picard-1.102.1595.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.102.1595" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/picard-1.102.1595.jar b/settings/repository/net.sf/picard-1.104.1628.jar
similarity index 91%
rename from settings/repository/net.sf/picard-1.102.1595.jar
rename to settings/repository/net.sf/picard-1.104.1628.jar
index 314b1db6ad3f69fde9d03ccac932bc9a2f0990ee..0a24f339ec9df44334c8e9538b6f2ce0a4fe409e 100644
GIT binary patch
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diff --git a/settings/repository/net.sf/picard-1.104.1628.xml b/settings/repository/net.sf/picard-1.104.1628.xml
new file mode 100644
index 000000000..bd0c9fbcd
--- /dev/null
+++ b/settings/repository/net.sf/picard-1.104.1628.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="picard" revision="1.104.1628" status="release" />
+</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.102.1595.xml b/settings/repository/net.sf/sam-1.102.1595.xml
deleted file mode 100644
index 44fc06d58..000000000
--- a/settings/repository/net.sf/sam-1.102.1595.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.102.1595" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.102.1595.jar b/settings/repository/net.sf/sam-1.104.1628.jar
similarity index 90%
rename from settings/repository/net.sf/sam-1.102.1595.jar
rename to settings/repository/net.sf/sam-1.104.1628.jar
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diff --git a/settings/repository/net.sf/sam-1.104.1628.xml b/settings/repository/net.sf/sam-1.104.1628.xml
new file mode 100644
index 000000000..0b0cba93f
--- /dev/null
+++ b/settings/repository/net.sf/sam-1.104.1628.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.104.1628" status="release" />
+</ivy-module>
diff --git a/settings/repository/org.broad/tribble-1.102.1595.jar b/settings/repository/org.broad/tribble-1.104.1628.jar
similarity index 83%
rename from settings/repository/org.broad/tribble-1.102.1595.jar
rename to settings/repository/org.broad/tribble-1.104.1628.jar
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diff --git a/settings/repository/org.broad/tribble-1.102.1595.xml b/settings/repository/org.broad/tribble-1.104.1628.xml
similarity index 75%
rename from settings/repository/org.broad/tribble-1.102.1595.xml
rename to settings/repository/org.broad/tribble-1.104.1628.xml
index 3500c3b08..c2158e974 100644
--- a/settings/repository/org.broad/tribble-1.102.1595.xml
+++ b/settings/repository/org.broad/tribble-1.104.1628.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="org.broad" module="tribble" revision="1.102.1595" status="integration" />
+    <info organisation="org.broad" module="tribble" revision="1.104.1628" status="integration" />
 </ivy-module>
diff --git a/settings/repository/org.broadinstitute/variant-1.102.1595.jar b/settings/repository/org.broadinstitute/variant-1.104.1628.jar
similarity index 94%
rename from settings/repository/org.broadinstitute/variant-1.102.1595.jar
rename to settings/repository/org.broadinstitute/variant-1.104.1628.jar
index 18118bfae6de5ad8a60eec7ced2243980200cee8..59f4f10d723552135f9223e98e8e5ca869fe9d9c 100644
GIT binary patch
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diff --git a/settings/repository/org.broadinstitute/variant-1.102.1595.xml b/settings/repository/org.broadinstitute/variant-1.104.1628.xml
similarity index 70%
rename from settings/repository/org.broadinstitute/variant-1.102.1595.xml
rename to settings/repository/org.broadinstitute/variant-1.104.1628.xml
index aa348fc84..527223bfb 100644
--- a/settings/repository/org.broadinstitute/variant-1.102.1595.xml
+++ b/settings/repository/org.broadinstitute/variant-1.104.1628.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="org.broadinstitute" module="variant" revision="1.102.1595" status="integration" />
+    <info organisation="org.broadinstitute" module="variant" revision="1.104.1628" status="integration" />
 </ivy-module>

From 10dc038a247822475c2a2764d90716bc95662e2b Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Thu, 5 Dec 2013 17:31:32 -0500
Subject: [PATCH 77/77] Separate tests that access the knowledge base from
 other tests

The tests that access the knowledge base are interfering with the basic
ability to run the unit/integration test suite to completion -- these
few tests often take hours to complete.

Created a new class of test ("KnowledgeBaseTest") that runs separately
from the unit/integration test suite, with corresponding build target.
A new bamboo plan will be set up to run these tests independently so
that they don't interfere with unit/integration testing.

With this change, plus the recent changes to the parallel test runner,
unit/integration test suite runtime should be back down to ~30 minutes
on average.
---
 build.xml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/build.xml b/build.xml
index 16cfa9a61..fd0801bfb 100644
--- a/build.xml
+++ b/build.xml
@@ -1415,6 +1415,13 @@
         <run-test testtype="${pipetype}" outputdir="${report}/${pipetype}" runfailed="false"/>
     </target>
 
+    <target name="knowledgebasetest" depends="test.compile,test.init" description="Run knowledge base tests">
+        <condition property="ktype" value="*KnowledgeBaseTest" else="${single}">
+            <not><isset property="single"/></not>
+        </condition>
+        <run-test testtype="${ktype}" outputdir="${report}/${ktype}" runfailed="false"/>
+    </target>
+
     <target name="failed-unit" depends="test.compile,test.init">
         <run-test testtype="${report}/*UnitTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
     </target>