Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable

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

@@ -26,6 +26,7 @@ package org.broadinstitute.sting.gatk.examples;
 
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.ArgumentCollection;
+import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -59,6 +60,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
  * @author Your Name
  * @since Date created
  */
+@Hidden
 public class GATKDocsExample extends RodWalker<Integer, Integer> {
     /**
      * Put detailed documentation about the argument here.  No need to duplicate the summary information

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java

@@ -43,6 +43,9 @@ import java.util.List;
 import java.util.Map;
 
 
+/**
+ * The allele balance (fraction of ref bases over ref + alt bases) across all bialleleic het-called samples
+ */
 public class AlleleBalance extends InfoFieldAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java

@@ -16,6 +16,9 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import java.util.*;
 
 
+/**
+ * The allele balance (fraction of ref bases over ref + alt bases) separately for each bialleleic het-called sample
+ */
 public class AlleleBalanceBySample extends GenotypeAnnotation implements ExperimentalAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g) {

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java

@@ -6,8 +6,9 @@ import org.broadinstitute.sting.utils.variantcontext.Genotype;
 
 import java.util.Map;
 
-
+/**
-
+ * Abstract base class for all annotations that are normalized by depth
+ */
 public abstract class AnnotationByDepth extends InfoFieldAnnotation {
 
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java

@@ -47,6 +47,9 @@ import java.util.List;
 import java.util.Map;
 
 
+/**
+ * Count of A, C, G, T bases across all samples
+ */
 public class BaseCounts extends InfoFieldAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java

@@ -13,6 +13,9 @@ import java.util.LinkedHashMap;
 import java.util.List;
 
 
+/**
+ * The phred-scaled p-value (u-based z-approximation) from the Mann-Whitney Rank Sum Test for base qualities (ref bases vs. bases of the alternate allele)
+ */
 public class BaseQualityRankSumTest extends RankSumTest {
     public List<String> getKeyNames() { return Arrays.asList("BaseQRankSum"); }
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java

@@ -44,6 +44,11 @@ import java.util.List;
 import java.util.Map;
 
 
+/**
+ * Allele count in genotypes, for each ALT allele, in the same order as listed;
+ * allele Frequency, for each ALT allele, in the same order as listed; total number
+ * of alleles in called genotypes.
+ */
 public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnnotation {
 
     private String[] keyNames = { VCFConstants.ALLELE_NUMBER_KEY, VCFConstants.ALLELE_COUNT_KEY, VCFConstants.ALLELE_FREQUENCY_KEY };

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java

@@ -16,7 +16,12 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-
+/**
+ * Total (unfiltered) depth over all samples.
+ *
+ * Affected by downsampling (-dcov) though, so the max value one can obtain for N samples with -dcov D
+ * is N * D
+ */
 public class DepthOfCoverage extends InfoFieldAnnotation implements StandardAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java

@@ -23,6 +23,25 @@ import java.util.List;
 import java.util.Map;
 
 
+/**
+ * The depth of coverage of each VCF allele in this sample
+ *
+ * Complementary fields that two important ways of thinking about the depth of the data for this sample
+ * at this site. The DP field describe the total depth of reads that passed the Unified Genotypers internal
+ * quality control metrics (like MAPQ > 17, for example), whatever base was present in the read at this site.
+ * The AD values (one for each of REF and ALT fields) is the count of all reads that carried with them the
+ * REF and ALT alleles. The reason for this distinction is that the DP is in some sense reflective of the
+ * power I have to determine the genotype of the sample at this site, while the AD tells me how many times
+ * I saw each of the REF and ALT alleles in the reads, free of any bias potentially introduced by filtering
+ * the reads. If, for example, I believe there really is a an A/T polymorphism at a site, then I would like
+ * to know the counts of A and T bases in this sample, even for reads with poor mapping quality that would
+ * normally be excluded from the statistical calculations going into GQ and QUAL. Please note, however, that
+ * the AD isn't necessarily calculated exactly for indels (it counts as non-reference only those indels that
+ * are actually present and correctly left-aligned in the alignments themselves). Because of this fact and
+ * because the AD includes reads and bases that were filtered by the Unified Genotyper, one should not base
+ * assumptions about the underlying genotype based on it; instead, the genotype likelihoods (PLs) are what
+ * determine the genotype calls (see below).
+ */
 public class DepthPerAlleleBySample extends GenotypeAnnotation implements StandardAnnotation {
 
     private static String REF_ALLELE = "REF";

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java

@@ -43,6 +43,11 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import java.util.*;
 
 
+/**
+ * Phred-scaled p-value using Fisher's Exact Test to detect strand bias (the variation
+ * being seen on only the forward or only the reverse strand) in the reads? More bias is
+ * indicative of false positive calls.
+ */
 public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotation {
     private static final String FS = "FS";
     private static final double MIN_PVALUE = 1E-320;

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java

@@ -17,6 +17,9 @@ import java.util.List;
 import java.util.Map;
 
 
+/**
+ * The GC content (# GC bases / # all bases) of the reference within 50 bp +/- this site
+ */
 public class GCContent extends InfoFieldAnnotation implements ExperimentalAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java

@@ -49,6 +49,10 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.*;
 
+/**
+ * Consistency of the site with two (and only two) segregating haplotypes. Higher scores
+ * are indicative of regions with bad alignments, often leading to artifactual SNP and indel calls.
+ */
 public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnotation {
     private final static boolean DEBUG = false;
     private final static int MIN_CONTEXT_WING_SIZE = 10;

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java

@@ -19,6 +19,9 @@ import java.util.List;
 import java.util.Map;
 
 
+/**
+ * Phred-scaled P value of genotype-based (using GT field) test for Hardy-Weinberg test for disequilibrium
+ */
 public class HardyWeinberg extends InfoFieldAnnotation implements WorkInProgressAnnotation {
 
     private static final int MIN_SAMPLES = 10;

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java

@@ -16,7 +16,9 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-
+/**
+ * Largest contiguous homopolymer run of the variant allele in either direction on the reference.
+ */
 public class HomopolymerRun extends InfoFieldAnnotation implements StandardAnnotation {
 
     private boolean ANNOTATE_INDELS = true;

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java

@@ -17,14 +17,15 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-/**
- * Created by IntelliJ IDEA.
- * User: rpoplin
- * Date: 5/16/11
- */
 
-// A set of annotations calculated directly from the GLs
+/**
-public class GLstats extends InfoFieldAnnotation implements StandardAnnotation {
+ * Likelihood-based (using PL field) test for the inbreeding among samples.
+ *
+ * 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.
+ */
+public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnnotation {
 
     private static final int MIN_SAMPLES = 10;
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java

@@ -14,11 +14,7 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import java.util.*;
 
 /**
- * Created by IntelliJ IDEA.
+ * Rough category of indel type (insertion, deletion, multi-allelic, other)
- * User: delangel
- * Date: Mar 11, 2011
- * Time: 11:47:33 AM
- * To change this template use File | Settings | File Templates.
  */
 public class IndelType extends InfoFieldAnnotation implements ExperimentalAnnotation {
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java

@@ -17,6 +17,9 @@ import java.util.List;
 import java.util.Map;
 
 
+/**
+ * Triplet annotation: fraction of MAQP == 0, MAPQ < 10, and count of all mapped reads
+ */
 public class LowMQ extends InfoFieldAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java

@@ -14,6 +14,9 @@ import java.util.LinkedHashMap;
 import java.util.List;
 
 
+/**
+ * The phred-scaled p-value (u-based z-approximation) from the Mann-Whitney Rank Sum Test for mapping qualities (reads with ref bases vs. those with the alternate allele)
+ */
 public class MappingQualityRankSumTest extends RankSumTest {
 
     public List<String> getKeyNames() { return Arrays.asList("MQRankSum"); }

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java

@@ -19,6 +19,9 @@ import java.util.List;
 import java.util.Map;
 
 
+/**
+ * Total count across all samples of mapping quality zero reads
+ */
 public class MappingQualityZero extends InfoFieldAnnotation implements StandardAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java

@@ -44,11 +44,7 @@ import java.util.List;
 import java.util.Map;
 
 /**
- * Created by IntelliJ IDEA.
+ * Count for each sample of mapping quality zero reads
- * User: asivache
- * Date: Feb 4, 2011
- * Time: 6:46:25 PM
- * To change this template use File | Settings | File Templates.
  */
 public class MappingQualityZeroBySample extends GenotypeAnnotation {
     public Map<String, Object> annotate(RefMetaDataTracker tracker,

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java

@@ -17,8 +17,9 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-
+/**
-
+ * Fraction of all reads across samples that have mapping quality zero
+ */
 public class MappingQualityZeroFraction extends InfoFieldAnnotation implements ExperimentalAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java

@@ -17,11 +17,8 @@ import java.util.List;
 import java.util.Map;
 
 /**
- * Created by IntelliJ IDEA.
+ * The number of N bases, counting only SOLiD data
- * User: rpoplin
- * Date: 5/16/11
  */
-
 public class NBaseCount extends InfoFieldAnnotation {
     public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if( stratifiedContexts.size() == 0 )

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -15,7 +16,11 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-
+/**
+ * Variant confidence (given as (AB+BB)/AA from the PLs) / unfiltered depth.
+ *
+ * Low scores are indicative of false positive calls and artifacts.
+ */
 public class QualByDepth extends AnnotationByDepth implements StandardAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java

@@ -21,6 +21,9 @@ import java.util.List;
 import java.util.Map;
 
 
+/**
+ * Root Mean Square of the mapping quality of the reads across all samples.
+ */
 public class RMSMappingQuality extends InfoFieldAnnotation implements StandardAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java

@@ -21,7 +21,9 @@ import java.util.List;
 import java.util.Map;
 
 
-
+/**
+ * Abstract root for all RankSum based annotations
+ */
 public abstract class RankSumTest extends InfoFieldAnnotation implements StandardAnnotation {
     static final double INDEL_LIKELIHOOD_THRESH = 0.1;
     static final boolean DEBUG = false;

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java

@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -47,12 +48,9 @@ import java.util.List;
 import java.util.Map;
 
 /**
- * Created by IntelliJ IDEA.
+ * Unsupported
- * User: asivache
- * Date: Feb 4, 2011
- * Time: 3:59:27 PM
- * To change this template use File | Settings | File Templates.
  */
+@Hidden
 public class ReadDepthAndAllelicFractionBySample extends GenotypeAnnotation {
 
         private static String REF_ALLELE = "REF";

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java

@@ -19,11 +19,8 @@ import java.util.LinkedHashMap;
 import java.util.List;
 
 /**
- * Created by IntelliJ IDEA.
+ * The phred-scaled p-value (u-based z-approximation) from the Mann-Whitney Rank Sum Test for the distance from the end of the read for reads with the alternate allele; if the alternate allele is only seen near the ends of reads this is indicative of error).
- * User: rpoplin
- * Date: 3/30/11
  */
-
 public class ReadPosRankSumTest extends RankSumTest {
 
     public List<String> getKeyNames() { return Arrays.asList("ReadPosRankSum"); }

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java

@@ -15,8 +15,9 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-
+/**
-
+ * SB annotation value by depth of alt containing samples
+ */
 public class SBByDepth extends AnnotationByDepth {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java

@@ -41,7 +41,9 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-
+/**
+ * List all of the samples in the info field
+ */
 public class SampleList extends InfoFieldAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java

@@ -17,6 +17,9 @@ import java.util.List;
 import java.util.Map;
 
 
+/**
+ * Fraction of reads containing spanning deletions at this site.
+ */
 public class SpanningDeletions extends InfoFieldAnnotation implements StandardAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -19,12 +20,9 @@ import java.util.List;
 import java.util.Map;
 
 /**
- * Created by IntelliJ IDEA.
+ * Counts of bases from SLX, 454, and SOLiD at this site
- * User: delangel
- * Date: 6/29/11
- * Time: 3:14 PM
- * To change this template use File | Settings | File Templates.
  */
+@Hidden
 public class TechnologyComposition extends InfoFieldAnnotation implements ExperimentalAnnotation {
     private String nSLX = "NumSLX";
     private String n454 ="Num454";

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java

@@ -48,27 +48,12 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
     // code for testing purposes
     //
     private final static boolean DEBUG = false;
-    private final static boolean PRINT_LIKELIHOODS = false;
-    private final static int N_CYCLES = 1;
-    private SimpleTimer timerExpt = new SimpleTimer("linearExactBanded");
-    private SimpleTimer timerGS = new SimpleTimer("linearExactGS");
-    private final static boolean COMPARE_TO_GS = false;
-
-    public enum ExactCalculation {
-        N2_GOLD_STANDARD,
-        LINEAR_EXPERIMENTAL
-    }
-
     private final static double MAX_LOG10_ERROR_TO_STOP_EARLY = 6; // we want the calculation to be accurate to 1 / 10^6
-
+    private final boolean SIMPLE_GREEDY_GENOTYPER = false;
-    private boolean SIMPLE_GREEDY_GENOTYPER = false;
-
     private final static double SUM_GL_THRESH_NOCALL = -0.001; // if sum(gl) is bigger than this threshold, we treat GL's as non-informative and will force a no-call.
 
-    final private ExactCalculation calcToUse;
     protected ExactAFCalculationModel(UnifiedArgumentCollection UAC, int N, Logger logger, PrintStream verboseWriter) {
         super(UAC, N, logger, verboseWriter);
-        calcToUse = UAC.EXACT_CALCULATION_TYPE;
     }
 
     public void getLog10PNonRef(RefMetaDataTracker tracker,
@@ -76,43 +61,12 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
                                 Map<String, Genotype> GLs, Set<Allele>alleles,
                                 double[] log10AlleleFrequencyPriors,
                                 double[] log10AlleleFrequencyPosteriors) {
-        // todo -- REMOVE ME AFTER TESTING
+        final int numAlleles = alleles.size();
-        // todo -- REMOVE ME AFTER TESTING
+        final double[][] posteriorCache = numAlleles > 2 ? new double[numAlleles-1][] : null;
-        // todo -- REMOVE ME AFTER TESTING
+        final double[] bestAFguess = numAlleles > 2 ? new double[numAlleles-1] : null;
-        double[] gsPosteriors;
-        if ( COMPARE_TO_GS ) // due to annoying special values in incoming array, we have to clone up here
-            gsPosteriors = log10AlleleFrequencyPosteriors.clone();
-
-        int idxAA = GenotypeType.AA.ordinal();
-        int idxAB = GenotypeType.AB.ordinal();
-        int idxBB = GenotypeType.BB.ordinal();
-
-        // todo -- remove me after testing
-        if ( N_CYCLES > 1 ) {
-            for ( int i = 0; i < N_CYCLES; i++) {
-                timerGS.restart();
-                linearExact(GLs, log10AlleleFrequencyPriors, log10AlleleFrequencyPosteriors.clone(), idxAA, idxAB, idxBB);
-                timerGS.stop();
-
-                timerExpt.restart();
-                linearExactBanded(GLs, log10AlleleFrequencyPriors, log10AlleleFrequencyPosteriors.clone());
-                timerExpt.stop();
-            }
-
-            System.out.printf("good = %.2f, expt = %.2f, delta = %.2f%n",
-                    timerGS.getElapsedTime(), timerExpt.getElapsedTime(), timerExpt.getElapsedTime()-timerGS.getElapsedTime());
-        }
-
-        int lastK = -1;
-
-        int numAlleles = alleles.size();
 
         int idxDiag = numAlleles;
         int incr = numAlleles - 1;
-
-        double[][] posteriorCache = new double[numAlleles-1][];
-        double[] bestAFguess = new double[numAlleles-1];
-
         for (int k=1; k < numAlleles; k++) {
             // multi-allelic approximation, part 1: Ideally
             // for each alt allele compute marginal (suboptimal) posteriors -
@@ -121,24 +75,17 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
             // So, for example, with 2 alt alleles, likelihoods have AA,AB,AC,BB,BC,CC.
             // 3 alt alleles: AA,AB,AC,AD BB BC BD CC CD DD
 
-            idxAA = 0;
+            final int idxAA = 0;
-            idxAB = k;
+            final int idxAB = k;
             // yy is always element on the diagonal.
             // 2 alleles: BBelement 2
             // 3 alleles: BB element  3. CC element 5
             // 4 alleles:
-            idxBB = idxDiag;
+            final int idxBB = idxDiag;
             idxDiag += incr--;
 
-            // todo - possible cleanup
+            final int lastK = linearExact(GLs, log10AlleleFrequencyPriors, log10AlleleFrequencyPosteriors, idxAA, idxAB, idxBB);
-            switch ( calcToUse ) {
+
-                case N2_GOLD_STANDARD:
-                    lastK = gdaN2GoldStandard(GLs, log10AlleleFrequencyPriors, log10AlleleFrequencyPosteriors, idxAA, idxAB, idxBB);
-                    break;
-                case LINEAR_EXPERIMENTAL:
-                    lastK = linearExact(GLs, log10AlleleFrequencyPriors, log10AlleleFrequencyPosteriors, idxAA, idxAB, idxBB);
-                    break;
-            }
             if (numAlleles > 2) {
                 posteriorCache[k-1] = log10AlleleFrequencyPosteriors.clone();
                 bestAFguess[k-1] = (double)MathUtils.maxElementIndex(log10AlleleFrequencyPosteriors);
@@ -153,39 +100,14 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
                 log10AlleleFrequencyPosteriors[k] = (posteriorCache[mostLikelyAlleleIdx][k]);
 
         }
-        // todo -- REMOVE ME AFTER TESTING
-        // todo -- REMOVE ME AFTER TESTING
-        // todo -- REMOVE ME AFTER TESTING
-        if ( COMPARE_TO_GS ) {
-            gdaN2GoldStandard(GLs, log10AlleleFrequencyPriors, gsPosteriors, idxAA, idxAB, idxBB);
-
-            double log10thisPVar = Math.log10(MathUtils.normalizeFromLog10(log10AlleleFrequencyPosteriors)[0]);
-            double log10gsPVar = Math.log10(MathUtils.normalizeFromLog10(gsPosteriors)[0]);
-            boolean eq = (log10thisPVar == Double.NEGATIVE_INFINITY && log10gsPVar == Double.NEGATIVE_INFINITY) || MathUtils.compareDoubles(log10thisPVar, log10gsPVar, 1e-4) == 0;
-
-            if ( ! eq || PRINT_LIKELIHOODS ) {
-                System.out.printf("----------------------------------------%n");
-                for (int k=0; k < log10AlleleFrequencyPosteriors.length; k++) {
-                    double x = log10AlleleFrequencyPosteriors[k];
-                    System.out.printf("  %d\t%.2f\t%.2f\t%b%n", k,
-                            x < -1e10 ? Double.NEGATIVE_INFINITY : x, gsPosteriors[k],
-                            log10AlleleFrequencyPosteriors[k] == gsPosteriors[k]);
-                }
-                System.out.printf("MAD_AC\t%d\t%d\t%.2f\t%.2f\t%.6f%n",
-                        ref.getLocus().getStart(), lastK, log10thisPVar, log10gsPVar, log10thisPVar - log10gsPVar);
-            }
-        }
-
     }
 
     private static final ArrayList<double[]> getGLs(Map<String, Genotype> GLs) {
         ArrayList<double[]> genotypeLikelihoods = new ArrayList<double[]>();
 
-        //int j = 0;
         genotypeLikelihoods.add(new double[]{0.0,0.0,0.0}); // dummy
         for ( Genotype sample : GLs.values() ) {
             if ( sample.hasLikelihoods() ) {
-                //double[] genotypeLikelihoods = MathUtils.normalizeFromLog10(GLs.get(sample).getLikelihoods());
                 double[] gls = sample.getLikelihoods().getAsVector();
 
                 if (MathUtils.sum(gls) < SUM_GL_THRESH_NOCALL)
@@ -240,84 +162,6 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
         }
     }
 
-    // now with banding
-    public int linearExactBanded(Map<String, Genotype> GLs,
-                                 double[] log10AlleleFrequencyPriors,
-                                 double[] log10AlleleFrequencyPosteriors) {
-        throw new NotImplementedException();
-//        final int numSamples = GLs.size();
-//        final int numChr = 2*numSamples;
-//        final double[][] genotypeLikelihoods = getGLs(GLs);
-//
-//        final ExactACCache logY = new ExactACCache(numSamples+1);
-//        logY.getkMinus0()[0] = 0.0; // the zero case
-//
-//        double maxLog10L = Double.NEGATIVE_INFINITY;
-//        boolean done = false;
-//        int lastK = -1;
-//        final int BAND_SIZE = 10;
-//
-//        for (int k=0; k <= numChr && ! done; k++ ) {
-//            final double[] kMinus0 = logY.getkMinus0();
-//            int jStart = Math.max(k - BAND_SIZE, 1);
-//            int jStop = Math.min(k + BAND_SIZE, numSamples);
-//
-//            if ( k == 0 ) { // special case for k = 0
-//                for ( int j=1; j <= numSamples; j++ ) {
-//                    kMinus0[j] = kMinus0[j-1] + genotypeLikelihoods[j][GenotypeType.AA.ordinal()];
-//                }
-//            } else { // k > 0
-//                final double[] kMinus1 = logY.getkMinus1();
-//                final double[] kMinus2 = logY.getkMinus2();
-//                Arrays.fill(kMinus0,0);
-//
-//                for ( int j = jStart; j <= jStop; j++ ) {
-//                    final double[] gl = genotypeLikelihoods[j];
-//                    final double logDenominator = log10Cache[2*j] + log10Cache[2*j-1];
-//
-//                    double aa = Double.NEGATIVE_INFINITY;
-//                    double ab = Double.NEGATIVE_INFINITY;
-//                    if (k < 2*j-1)
-//                        aa = log10Cache[2*j-k] + log10Cache[2*j-k-1] + kMinus0[j-1] + gl[GenotypeType.AA.ordinal()];
-//
-//                    if (k < 2*j)
-//                        ab = log10Cache[2*k] + log10Cache[2*j-k]+ kMinus1[j-1] + gl[GenotypeType.AB.ordinal()];
-//
-//                    double log10Max;
-//                    if (k > 1) {
-//                        final double bb = log10Cache[k] + log10Cache[k-1] + kMinus2[j-1] + gl[GenotypeType.BB.ordinal()];
-//                        log10Max = approximateLog10SumLog10(aa, ab, bb);
-//                    } else {
-//                        // we know we aren't considering the BB case, so we can use an optimized log10 function
-//                        log10Max = approximateLog10SumLog10(aa, ab);
-//                    }
-//
-//                    // finally, update the L(j,k) value
-//                    kMinus0[j] = log10Max - logDenominator;
-//
-//                    String offset = Utils.dupString(' ',k);
-//                    System.out.printf("%s%3d %3d %.2f%n", offset, k, j, kMinus0[j]);
-//                }
-//            }
-//
-//            // update the posteriors vector
-//            final double log10LofK = kMinus0[jStop];
-//            log10AlleleFrequencyPosteriors[k] = log10LofK + log10AlleleFrequencyPriors[k];
-//
-//            // can we abort early?
-//            lastK = k;
-//            maxLog10L = Math.max(maxLog10L, log10LofK);
-//            if ( log10LofK < maxLog10L - MAX_LOG10_ERROR_TO_STOP_EARLY ) {
-//                if ( DEBUG ) System.out.printf("  *** breaking early k=%d log10L=%.2f maxLog10L=%.2f%n", k, log10LofK, maxLog10L);
-//                done = true;
-//            }
-//
-//            logY.rotate();
-//        }
-//
-//        return lastK;
-    }
-
     public int linearExact(Map<String, Genotype> GLs,
                            double[] log10AlleleFrequencyPriors,
                            double[] log10AlleleFrequencyPosteriors, int idxAA, int idxAB, int idxBB) {
@@ -605,82 +449,6 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
         return calls;
     }
 
-    // -------------------------------------------------------------------------------------
-    //
-    // Gold standard, but O(N^2), implementation.
-    //
-    // TODO -- remove me for clarity in this code
-    //
-    // -------------------------------------------------------------------------------------
-    public int gdaN2GoldStandard(Map<String, Genotype> GLs,
-                                 double[] log10AlleleFrequencyPriors,
-                                 double[] log10AlleleFrequencyPosteriors, int idxAA, int idxAB, int idxBB) {
-        int numSamples = GLs.size();
-        int numChr = 2*numSamples;
-
-        double[][] logYMatrix = new double[1+numSamples][1+numChr];
-
-        for (int i=0; i <=numSamples; i++)
-            for (int j=0; j <=numChr; j++)
-                logYMatrix[i][j] = Double.NEGATIVE_INFINITY;
-
-        //YMatrix[0][0] = 1.0;
-        logYMatrix[0][0] = 0.0;
-        int j=0;
-
-        for ( Map.Entry<String, Genotype> sample : GLs.entrySet() ) {
-            j++;
-
-            if ( !sample.getValue().hasLikelihoods() )
-                continue;
-
-            //double[] genotypeLikelihoods = MathUtils.normalizeFromLog10(GLs.get(sample).getLikelihoods());
-            double[] genotypeLikelihoods = sample.getValue().getLikelihoods().getAsVector();
-            //double logDenominator = Math.log10(2.0*j*(2.0*j-1));
-            double logDenominator = MathUtils.log10Cache[2*j] + MathUtils.log10Cache[2*j-1];
-
-            // special treatment for k=0: iteration reduces to:
-            //YMatrix[j][0] = YMatrix[j-1][0]*genotypeLikelihoods[GenotypeType.AA.ordinal()];
-            logYMatrix[j][0] = logYMatrix[j-1][0] + genotypeLikelihoods[idxAA];
-
-            for (int k=1; k <= 2*j; k++ ) {
-
-                //double num = (2.0*j-k)*(2.0*j-k-1)*YMatrix[j-1][k] * genotypeLikelihoods[GenotypeType.AA.ordinal()];
-                double logNumerator[];
-                logNumerator = new double[3];
-                if (k < 2*j-1)
-                    logNumerator[0] = MathUtils.log10Cache[2*j-k] + MathUtils.log10Cache[2*j-k-1] + logYMatrix[j-1][k] +
-                            genotypeLikelihoods[idxAA];
-                else
-                    logNumerator[0] = Double.NEGATIVE_INFINITY;
-
-
-                if (k < 2*j)
-                    logNumerator[1] = MathUtils.log10Cache[2*k] + MathUtils.log10Cache[2*j-k]+ logYMatrix[j-1][k-1] +
-                            genotypeLikelihoods[idxAB];
-                else
-                    logNumerator[1] = Double.NEGATIVE_INFINITY;
-
-                if (k > 1)
-                    logNumerator[2] = MathUtils.log10Cache[k] + MathUtils.log10Cache[k-1] + logYMatrix[j-1][k-2] +
-                            genotypeLikelihoods[idxBB];
-                else
-                    logNumerator[2] = Double.NEGATIVE_INFINITY;
-
-                double logNum = MathUtils.softMax(logNumerator);
-
-                //YMatrix[j][k] = num/den;
-                logYMatrix[j][k] = logNum - logDenominator;
-            }
-
-        }
-
-        for (int k=0; k <= numChr; k++)
-            log10AlleleFrequencyPosteriors[k] = logYMatrix[j][k] + log10AlleleFrequencyPriors[k];
-
-        return numChr;
-    }
-
     private final static void printLikelihoods(int numChr, double[][] logYMatrix, double[] log10AlleleFrequencyPriors) {
         int j = logYMatrix.length - 1;
         System.out.printf("-----------------------------------%n");
@@ -689,5 +457,4 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
             System.out.printf("  %4d\t%8.2f\t%8.2f\t%8.2f%n", k, logYMatrix[j][k], log10AlleleFrequencyPriors[k], posterior);
         }
     }
-
 }

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java

@@ -168,10 +168,6 @@ public class UnifiedArgumentCollection {
     @Argument(fullName = "GSA_PRODUCTION_ONLY", shortName = "GSA_PRODUCTION_ONLY", doc = "don't ever use me", required = false)
     public boolean GSA_PRODUCTION_ONLY = false;
 
-    @Hidden
-    @Argument(fullName = "exactCalculation", shortName = "exactCalculation", doc = "expt", required = false)
-    public ExactAFCalculationModel.ExactCalculation EXACT_CALCULATION_TYPE = ExactAFCalculationModel.ExactCalculation.LINEAR_EXPERIMENTAL;
-
     @Hidden
     @Argument(fullName = "ignoreSNPAlleles", shortName = "ignoreSNPAlleles", doc = "expt", required = false)
     public boolean IGNORE_SNP_ALLELES = false;
@@ -191,7 +187,6 @@ public class UnifiedArgumentCollection {
 
         uac.GLmodel = GLmodel;
         uac.AFmodel = AFmodel;
-        uac.EXACT_CALCULATION_TYPE = EXACT_CALCULATION_TYPE;
         uac.heterozygosity = heterozygosity;
         uac.PCR_error = PCR_error;
         uac.GenotypingMode = GenotypingMode;

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/DocumentationTest.java

@@ -42,6 +42,7 @@ import java.util.*;
  *
  * <p>Body test</p>
  */
+@Hidden
 public class DocumentationTest extends RodWalker<Integer, Integer> {
     // the docs for the arguments are in the collection
     @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();

public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java

@@ -432,25 +432,37 @@ public class ClippingOp {
     }
 
     private int calculateAlignmentStartShift(Cigar oldCigar, Cigar newCigar) {
-        int shift = 0;
+        int newShift = 0;
+        int oldShift = 0;
+        int deletionShift = 0;
 
-        // Rewind to previous start (by counting everything that was already clipped in this read)
-        for (CigarElement cigarElement : oldCigar.getCigarElements()) {
-            if (!cigarElement.getOperator().consumesReferenceBases())
-                shift -= cigarElement.getLength();
-            else
-                break;
-        }
-
-        // Advance to new start (by counting everything new that has been clipped )
         for (CigarElement cigarElement : newCigar.getCigarElements()) {
-            if (!cigarElement.getOperator().consumesReferenceBases())
+            if (cigarElement.getOperator() == CigarOperator.HARD_CLIP || cigarElement.getOperator() == CigarOperator.SOFT_CLIP)
-                shift += cigarElement.getLength();
+                newShift += cigarElement.getLength();
             else
                 break;
         }
 
-        return shift;
+        for (CigarElement cigarElement : oldCigar.getCigarElements()) {
+            if (cigarElement.getOperator() == CigarOperator.HARD_CLIP || cigarElement.getOperator() == CigarOperator.SOFT_CLIP )
+                oldShift += Math.min(cigarElement.getLength(), newShift - oldShift);
+            else
+                break;
+        }
+
+        int basesClipped = 0;
+        for (CigarElement cigarElement : oldCigar.getCigarElements()) {
+            if (basesClipped > newShift)                                        // are we beyond the clipped region?
+                break;
+
+            else if (cigarElement.getOperator() == CigarOperator.DELETION)      // if this is a deletion, we have to adjust the starting shift
+                deletionShift += cigarElement.getLength();
+
+            else
+                basesClipped += cigarElement.getLength();
+        }
+
+        return newShift - oldShift + deletionShift;
     }
 
     private int calculateHardClippingAlignmentShift(CigarElement cigarElement, int clippedLength) {
@@ -462,8 +474,8 @@ public class ClippingOp {
                 return -clippedLength;
         }
 
-        if (cigarElement.getOperator() == CigarOperator.DELETION)
+//        if (cigarElement.getOperator() == CigarOperator.DELETION)
-            return cigarElement.getLength();
+//            return cigarElement.getLength();
 
         return 0;
     }

public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java

@@ -71,21 +71,21 @@ public class ReadClipper {
 
     private SAMRecord hardClipByReferenceCoordinates(int refStart, int refStop) {
         int start = (refStart < 0) ? 0 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStart);
-        int stop =  (refStop  < 0) ? read.getReadLength() - 1: ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStop);
+        int stop =  (refStop  < 0) ? read.getReadLength() - 1 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStop);
 
-        if (start < 0 || stop > read.getReadLength() - 1 + numDeletions(read))
+        if (start < 0 || stop > read.getReadLength() - 1)
             throw new ReviewedStingException("Trying to clip before the start or after the end of a read");
 
-        // TODO add check in the Hardclip function
+        if ( start > stop ) {
-        if ( start > stop )
+//            stop = ReadUtils.getReadCoordinateForReferenceCoordinate(read, ReadUtils.getRefCoordSoftUnclippedEnd(read));
-            stop = ReadUtils.getReadCoordinateForReferenceCoordinate(read, ReadUtils.getRefCoordSoftUnclippedEnd(read));
+            throw new ReviewedStingException("START > STOP -- this should never happen -- call Mauricio!");
-
+        }
 
         //This tries to fix the bug where the deletion is counted a read base and as a result, the hardCLipper runs into
         //an endless loop when hard clipping the cigar string because the read coordinates are not covered by the read
-        stop -= numDeletions(read);
+//        stop -= numDeletions(read);
-        if ( start > stop )
+//        if ( start > stop )
-            start -= numDeletions(read);
+//            start -= numDeletions(read);
 
 
         //System.out.println("Clipping start/stop: " + start + "/" + stop);
@@ -145,7 +145,7 @@ public class ReadClipper {
                     cutLeft = readIndex + cigarElement.getLength() - 1;
                 }
             }
-            else
+            else if (cigarElement.getOperator() != CigarOperator.HARD_CLIP)
                 rightTail = true;
 
             if (cigarElement.getOperator().consumesReadBases())

public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java

@@ -66,7 +66,8 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
     public boolean includeInDocs(ClassDoc doc) {
         try {
             Class type = HelpUtils.getClassForDoc(doc);
-            return JVMUtils.isConcrete(type);
+            boolean hidden = ! getDoclet().showHiddenFeatures() && type.isAnnotationPresent(Hidden.class);
+            return ! hidden && JVMUtils.isConcrete(type);
         } catch ( ClassNotFoundException e ) {
             return false;
         }

public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java

@@ -74,13 +74,6 @@ public class Genotype {
         return new Genotype(g.getSampleName(), g.getAlleles(), g.getNegLog10PError(), g.filtersWereApplied() ? g.getFilters() : null, attributes, g.isPhased());
     }
 
-    public static Genotype removePLs(Genotype g) {
-        Map<String, Object> attrs = new HashMap<String, Object>(g.getAttributes());
-        attrs.remove(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY);
-        attrs.remove(VCFConstants.GENOTYPE_LIKELIHOODS_KEY);
-        return new Genotype(g.getSampleName(), g.getAlleles(), g.getNegLog10PError(), g.filtersWereApplied() ? g.getFilters() : null, attrs, g.isPhased());
-    }
-
     public static Genotype modifyAlleles(Genotype g, List<Allele> alleles) {
         return new Genotype(g.getSampleName(), alleles, g.getNegLog10PError(), g.filtersWereApplied() ? g.getFilters() : null, g.getAttributes(), g.isPhased());
     }

public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java

@@ -44,6 +44,11 @@ import java.io.Serializable;
 import java.util.*;
 
 public class VariantContextUtils {
+    public final static String MERGE_INTERSECTION = "Intersection";
+    public final static String MERGE_FILTER_IN_ALL = "FilteredInAll";
+    public final static String MERGE_REF_IN_ALL = "ReferenceInAll";
+    public final static String MERGE_FILTER_PREFIX = "filterIn";
+
     final public static JexlEngine engine = new JexlEngine();
     static {
         engine.setSilent(false); // will throw errors now for selects that don't evaluate properly
@@ -154,6 +159,13 @@ public class VariantContextUtils {
         return "%." + precision + "f";
     }
 
+    public static Genotype removePLs(Genotype g) {
+        Map<String, Object> attrs = new HashMap<String, Object>(g.getAttributes());
+        attrs.remove(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY);
+        attrs.remove(VCFConstants.GENOTYPE_LIKELIHOODS_KEY);
+        return new Genotype(g.getSampleName(), g.getAlleles(), g.getNegLog10PError(), g.filtersWereApplied() ? g.getFilters() : null, attrs, g.isPhased());
+    }
+
     /**
      * A simple but common wrapper for matching VariantContext objects using JEXL expressions
      */
@@ -609,19 +621,20 @@ public class VariantContextUtils {
         if ( filteredRecordMergeType == FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED && nFiltered != VCs.size() )
             filters.clear();
 
+
         if ( annotateOrigin ) { // we care about where the call came from
             String setValue;
             if ( nFiltered == 0 && variantSources.size() == priorityListOfVCs.size() ) // nothing was unfiltered
-                setValue = "Intersection";
+                setValue = MERGE_INTERSECTION;
             else if ( nFiltered == VCs.size() )     // everything was filtered out
-                setValue = "FilteredInAll";
+                setValue = MERGE_FILTER_IN_ALL;
             else if ( variantSources.isEmpty() )               // everyone was reference
-                setValue = "ReferenceInAll";
+                setValue = MERGE_REF_IN_ALL;
             else {
                 LinkedHashSet<String> s = new LinkedHashSet<String>();
                 for ( VariantContext vc : VCs )
                     if ( vc.isVariant() )
-                        s.add( vc.isFiltered() ? "filterIn" + vc.getSource() : vc.getSource() );
+                        s.add( vc.isFiltered() ? MERGE_FILTER_PREFIX + vc.getSource() : vc.getSource() );
                 setValue = Utils.join("-", s);
             }
 
@@ -734,7 +747,7 @@ public class VariantContextUtils {
         Map<String, Genotype> newGs = new HashMap<String, Genotype>(genotypes.size());
 
         for ( Map.Entry<String, Genotype> g : genotypes.entrySet() ) {
-            newGs.put(g.getKey(), g.getValue().hasLikelihoods() ? Genotype.removePLs(g.getValue()) : g.getValue());
+            newGs.put(g.getKey(), g.getValue().hasLikelihoods() ? removePLs(g.getValue()) : g.getValue());
         }
 
         return newGs;

public/java/test/org/broadinstitute/sting/BaseTest.java

@@ -132,15 +132,21 @@ public abstract class BaseTest {
      */
     public static class TestDataProvider {
         private static final Map<Class, List<Object>> tests = new HashMap<Class, List<Object>>();
+        private final String name;
 
         /**
          * Create a new TestDataProvider instance bound to the class variable C
          * @param c
          */
-        public TestDataProvider(Class c) {
+        public TestDataProvider(Class c, String name) {
             if ( ! tests.containsKey(c) )
                 tests.put(c, new ArrayList<Object>());
             tests.get(c).add(this);
+            this.name = name;
+        }
+
+        public TestDataProvider(Class c) {
+            this(c, "");
         }
 
         /**
@@ -153,6 +159,11 @@ public abstract class BaseTest {
             for ( Object x : tests.get(c) ) params2.add(new Object[]{x});
             return params2.toArray(new Object[][]{});
         }
+
+        @Override
+        public String toString() {
+            return "TestDataProvider("+name+")";
+        }
     }
 
     /**

public/java/test/org/broadinstitute/sting/gatk/walkers/CNV/SymbolicAllelesIntegrationTest.java

@@ -33,7 +33,7 @@ public class SymbolicAllelesIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(b36KGReference, "symbolic_alleles_2.vcf"),
                 1,
-                Arrays.asList("6645babc8c7d46be0da223477c7b1291"));
+                Arrays.asList("3008d6f5044bc14801e5c58d985dec72"));
         executeTest("Test symbolic alleles mixed in with non-symbolic alleles", spec);
     }
 }

public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java

@@ -21,37 +21,25 @@
  * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
  * OTHER DEALINGS IN THE SOFTWARE.
  */
-
-// our package
 package org.broadinstitute.sting.utils.variantcontext;
 
-
-// the imports for unit testing.
-
-
 import net.sf.picard.reference.IndexedFastaSequenceFile;
-import org.apache.log4j.Priority;
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.testng.Assert;
 import org.testng.annotations.BeforeSuite;
-import org.testng.annotations.Test;
 import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
 
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.util.*;
 
-
 public class VariantContextUtilsUnitTest extends BaseTest {
-    Allele Aref, T, delRef, ATC;
+    Allele Aref, T, C, delRef, ATC, ATCATC;
-    Genotype ref1, snp1, snp2, indel1, indelref;
     private GenomeLocParser genomeLocParser;
-    VariantContext refVC, snpVC1, snpVC2, snpVC3, snpVC4, indelVC1, indelVC2, indelVC3;
 
     @BeforeSuite
     public void setup() {
@@ -68,28 +56,35 @@ public class VariantContextUtilsUnitTest extends BaseTest {
         Aref = Allele.create("A", true);
         delRef = Allele.create("-", true);
         T = Allele.create("T");
+        C = Allele.create("C");
         ATC = Allele.create("ATC");
+        ATCATC = Allele.create("ATCATC");
+    }
 
-        ref1 = new Genotype("ref1", Arrays.asList(Aref, Aref), 5, new double[]{0, 5, 10});
+    private Genotype makeG(String sample, Allele a1, Allele a2) {
-        snp1 = new Genotype("snp1", Arrays.asList(Aref,T), 10, new double[]{10, 0, 20});
+        return new Genotype(sample, Arrays.asList(a1, a2));
-        snp2 = new Genotype("snp2", Arrays.asList(T,T), 15, new double[]{25, 15, 0});
+    }
-        indelref = new Genotype("indelref", Arrays.asList(delRef,delRef), 25, new double[]{0, 25, 30});
-        indel1 = new Genotype("indel1", Arrays.asList(delRef,ATC), 20, new double[]{20, 0, 30});
 
-        refVC = makeVC("refvc", Arrays.asList(Aref), Arrays.asList(ref1));
+    private Genotype makeG(String sample, Allele a1, Allele a2, double log10pError) {
-        snpVC1 = makeVC("snpvc1", Arrays.asList(Aref, T), Arrays.asList(snp1));
+        return new Genotype(sample, Arrays.asList(a1, a2), log10pError);
-        snpVC2 = makeVC("snpvc2", Arrays.asList(Aref, T), Arrays.asList(snp1, snp2));
-        snpVC3 = makeVC("snpvc3", Arrays.asList(Aref, T), Arrays.asList(ref1, snp1));
-        snpVC4 = makeVC("snpvc4", Arrays.asList(Aref, T), Arrays.asList(ref1, snp1, snp2));
-        indelVC1 = makeVC("indelvc1", Arrays.asList(delRef), Arrays.asList(indelref));
-        indelVC2 = makeVC("indelvc2", Arrays.asList(delRef, ATC), Arrays.asList(indel1));
-        indelVC3 = makeVC("indelvc3", Arrays.asList(delRef, ATC), Arrays.asList(indelref, indel1));
     }
 
     private VariantContext makeVC(String source, List<Allele> alleles) {
         return makeVC(source, alleles, null, null);
     }
 
+    private VariantContext makeVC(String source, List<Allele> alleles, Genotype... g1) {
+        return makeVC(source, alleles, Arrays.asList(g1));
+    }
+
+    private VariantContext makeVC(String source, List<Allele> alleles, String filter) {
+        return makeVC(source, alleles, filter.equals(".") ? null : new HashSet<String>(Arrays.asList(filter)));
+    }
+
+    private VariantContext makeVC(String source, List<Allele> alleles, Set<String> filters) {
+        return makeVC(source, alleles, null, filters);
+    }
+
     private VariantContext makeVC(String source, List<Allele> alleles, Collection<Genotype> genotypes) {
         return makeVC(source, alleles, genotypes, null);
     }
@@ -98,45 +93,108 @@ public class VariantContextUtilsUnitTest extends BaseTest {
         int start = 10;
         int stop = start; // alleles.contains(ATC) ? start + 3 : start;
         return new VariantContext(source, "1", start, stop, alleles,
-                VariantContext.genotypeCollectionToMap(new TreeMap<String, Genotype>(), genotypes),
+                genotypes == null ? null : VariantContext.genotypeCollectionToMap(new TreeMap<String, Genotype>(), genotypes),
                 1.0, filters, null, (byte)'C');
     }
 
-    private class SimpleMergeTest extends TestDataProvider {
+    // --------------------------------------------------------------------------------
-        List<VariantContext> inputVCs;
+    //
-        VariantContext expectedVC;
+    // Test allele merging
+    //
+    // --------------------------------------------------------------------------------
 
-        private SimpleMergeTest(VariantContext... vcsArg) {
+    private class MergeAllelesTest extends TestDataProvider {
-            super(SimpleMergeTest.class);
+        List<List<Allele>> inputs;
-            LinkedList<VariantContext> allVCs = new LinkedList<VariantContext>(Arrays.asList(vcsArg));
+        List<Allele> expected;
-            expectedVC = allVCs.pollLast();
+
-            inputVCs = allVCs;
+        private MergeAllelesTest(List<Allele>... arg) {
+            super(MergeAllelesTest.class);
+            LinkedList<List<Allele>> all = new LinkedList<List<Allele>>(Arrays.asList(arg));
+            expected = all.pollLast();
+            inputs = all;
         }
 
         public String toString() {
-            return String.format("SimpleMergeTest vc=%s expected=%s", inputVCs, expectedVC);
+            return String.format("MergeAllelesTest input=%s expected=%s", inputs, expected);
         }
     }
-
+    @DataProvider(name = "mergeAlleles")
-    @DataProvider(name = "simplemergedata")
+    public Object[][] mergeAllelesData() {
-    public Object[][] createSimpleMergeData() {
         // first, do no harm
-        new SimpleMergeTest(refVC,    refVC);
+        new MergeAllelesTest(Arrays.asList(Aref),
-        new SimpleMergeTest(snpVC1,   snpVC1);
+                Arrays.asList(Aref));
-        new SimpleMergeTest(indelVC1, indelVC1);
-        new SimpleMergeTest(indelVC3, indelVC3);
 
-        new SimpleMergeTest(refVC,  snpVC1, snpVC3);
+        new MergeAllelesTest(Arrays.asList(Aref),
-        new SimpleMergeTest(snpVC1, snpVC2, snpVC2);
+                Arrays.asList(Aref),
-        new SimpleMergeTest(refVC,  snpVC2, snpVC4);
+                Arrays.asList(Aref));
 
-        new SimpleMergeTest(indelVC1,  indelVC2, indelVC3);
+        new MergeAllelesTest(Arrays.asList(Aref),
-        new SimpleMergeTest(indelVC1,  indelVC3, indelVC3);
+                Arrays.asList(Aref, T),
-        new SimpleMergeTest(indelVC2,  indelVC3, indelVC3);
+                Arrays.asList(Aref, T));
 
-        return SimpleMergeTest.getTests(SimpleMergeTest.class);
+        new MergeAllelesTest(Arrays.asList(Aref, C),
+                Arrays.asList(Aref, T),
+                Arrays.asList(Aref, C, T));
+
+        new MergeAllelesTest(Arrays.asList(Aref, T),
+                Arrays.asList(Aref, C),
+                Arrays.asList(Aref, C, T)); // sorted by allele
+
+        new MergeAllelesTest(Arrays.asList(Aref, C, T),
+                Arrays.asList(Aref, C),
+                Arrays.asList(Aref, C, T));
+
+        new MergeAllelesTest(Arrays.asList(Aref, T, C),
+                Arrays.asList(Aref, C),
+                Arrays.asList(Aref, C, T)); // sorted by allele
+
+        new MergeAllelesTest(Arrays.asList(delRef),
+                Arrays.asList(delRef)); // todo -- FIXME me GdA
+
+        new MergeAllelesTest(Arrays.asList(delRef),
+                Arrays.asList(delRef, ATC),
+                Arrays.asList(delRef, ATC));
+
+        new MergeAllelesTest(Arrays.asList(delRef),
+                Arrays.asList(delRef, ATC, ATCATC),
+                Arrays.asList(delRef, ATC, ATCATC));
+
+        new MergeAllelesTest(Arrays.asList(delRef, ATCATC),
+                Arrays.asList(delRef, ATC, ATCATC),
+                Arrays.asList(delRef, ATC, ATCATC));
+
+        new MergeAllelesTest(Arrays.asList(delRef, ATC),
+                Arrays.asList(delRef, ATCATC),
+                Arrays.asList(delRef, ATC, ATCATC));
+
+        return MergeAllelesTest.getTests(MergeAllelesTest.class);
     }
 
+    @Test(dataProvider = "mergeAlleles")
+    public void testMergeAlleles(MergeAllelesTest cfg) {
+        final List<VariantContext> inputs = new ArrayList<VariantContext>();
+
+        int i = 0;
+        for ( final List<Allele> alleles : cfg.inputs ) {
+            final String name = "vcf" + ++i;
+            inputs.add(makeVC(name, alleles));
+        }
+
+        final List<String> priority = vcs2priority(inputs);
+
+        final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser,
+                inputs, priority,
+                VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
+                VariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, "set", false, false);
+        Assert.assertEquals(merged.getAlleles(), cfg.expected);
+    }
+
+    // --------------------------------------------------------------------------------
+    //
+    // Test rsID merging
+    //
+    // --------------------------------------------------------------------------------
+
     private class SimpleMergeRSIDTest extends TestDataProvider {
         List<String> inputs;
         String expected;
@@ -156,10 +214,13 @@ public class VariantContextUtilsUnitTest extends BaseTest {
     @DataProvider(name = "simplemergersiddata")
     public Object[][] createSimpleMergeRSIDData() {
         new SimpleMergeRSIDTest(".", ".");
+        new SimpleMergeRSIDTest(".", ".", ".");
         new SimpleMergeRSIDTest("rs1", "rs1");
+        new SimpleMergeRSIDTest("rs1", "rs1", "rs1");
         new SimpleMergeRSIDTest(".", "rs1", "rs1");
         new SimpleMergeRSIDTest("rs1", ".", "rs1");
         new SimpleMergeRSIDTest("rs1", "rs2", "rs1,rs2");
+        new SimpleMergeRSIDTest("rs1", "rs2", "rs1", "rs1,rs2"); // duplicates
         new SimpleMergeRSIDTest("rs2", "rs1", "rs2,rs1");
         new SimpleMergeRSIDTest("rs2", "rs1", ".", "rs2,rs1");
         new SimpleMergeRSIDTest("rs2", ".", "rs1", "rs2,rs1");
@@ -171,32 +232,312 @@ public class VariantContextUtilsUnitTest extends BaseTest {
 
     @Test(dataProvider = "simplemergersiddata")
     public void testRSIDMerge(SimpleMergeRSIDTest cfg) {
-        List<VariantContext> inputs = new ArrayList<VariantContext>();
+        final VariantContext snpVC1 = makeVC("snpvc1", Arrays.asList(Aref, T));
-        for ( String id : cfg.inputs ) {
+        final List<VariantContext> inputs = new ArrayList<VariantContext>();
+
+        for ( final String id : cfg.inputs ) {
             MutableVariantContext vc = new MutableVariantContext(snpVC1);
             if ( ! id.equals(".") ) vc.setID(id);
             inputs.add(vc);
-
         }
 
-        VariantContext merged = myMerge(inputs);
+        final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser,
+                inputs, null,
+                VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
+                VariantContextUtils.GenotypeMergeType.UNSORTED, false, false, "set", false, false);
         Assert.assertEquals(merged.getID(), cfg.expected.equals(".") ? null : cfg.expected);
     }
 
-    private VariantContext myMerge(List<VariantContext> inputs) {
+    // --------------------------------------------------------------------------------
-        List<String> priority = new ArrayList<String>();
+    //
-        for ( VariantContext vc : inputs ) priority.add(vc.getSource());
+    // Test filtered merging
+    //
+    // --------------------------------------------------------------------------------
 
-        return VariantContextUtils.simpleMerge(genomeLocParser,
+    private class MergeFilteredTest extends TestDataProvider {
-                inputs, priority,
+        List<VariantContext> inputs;
-                VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
+        VariantContext expected;
-                VariantContextUtils.GenotypeMergeType.PRIORITIZE, true, false, "set", false, false);
+        String setExpected;
+        VariantContextUtils.FilteredRecordMergeType type;
+
+
+        private MergeFilteredTest(String name, VariantContext input1, VariantContext input2, VariantContext expected, String setExpected) {
+            this(name, input1, input2, expected, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, setExpected);
+        }
+
+        private MergeFilteredTest(String name, VariantContext input1, VariantContext input2, VariantContext expected, VariantContextUtils.FilteredRecordMergeType type, String setExpected) {
+            super(MergeFilteredTest.class, name);
+            LinkedList<VariantContext> all = new LinkedList<VariantContext>(Arrays.asList(input1, input2));
+            this.expected = expected;
+            this.type = type;
+            inputs = all;
+            this.setExpected = setExpected;
+        }
+
+        public String toString() {
+            return String.format("%s input=%s expected=%s", super.toString(), inputs, expected);
+        }
     }
 
-    // todo -- add tests for subset merging, especially with correct PLs
+    @DataProvider(name = "mergeFiltered")
-    // todo -- test priority list
+    public Object[][] mergeFilteredData() {
-    // todo -- test FilteredRecordMergeType
+        new MergeFilteredTest("AllPass",
-    // todo -- no annotate origin
+                makeVC("1", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
-    // todo -- test set key
+                makeVC("2", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
-    // todo -- test filtered are uncalled
+                makeVC("3", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
+                VariantContextUtils.MERGE_INTERSECTION);
+
+        new MergeFilteredTest("noFilters",
+                makeVC("1", Arrays.asList(Aref, T), "."),
+                makeVC("2", Arrays.asList(Aref, T), "."),
+                makeVC("3", Arrays.asList(Aref, T), "."),
+                VariantContextUtils.MERGE_INTERSECTION);
+
+        new MergeFilteredTest("oneFiltered",
+                makeVC("1", Arrays.asList(Aref, T), "."),
+                makeVC("2", Arrays.asList(Aref, T), "FAIL"),
+                makeVC("3", Arrays.asList(Aref, T), "."),
+                String.format("1-%s2", VariantContextUtils.MERGE_FILTER_PREFIX));
+
+        new MergeFilteredTest("onePassOneFail",
+                makeVC("1", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
+                makeVC("2", Arrays.asList(Aref, T), "FAIL"),
+                makeVC("3", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
+                String.format("1-%s2", VariantContextUtils.MERGE_FILTER_PREFIX));
+
+        new MergeFilteredTest("AllFiltered",
+                makeVC("1", Arrays.asList(Aref, T), "FAIL"),
+                makeVC("2", Arrays.asList(Aref, T), "FAIL"),
+                makeVC("3", Arrays.asList(Aref, T), "FAIL"),
+                VariantContextUtils.MERGE_FILTER_IN_ALL);
+
+        // test ALL vs. ANY
+        new MergeFilteredTest("FailOneUnfiltered",
+                makeVC("1", Arrays.asList(Aref, T), "FAIL"),
+                makeVC("2", Arrays.asList(Aref, T), "."),
+                makeVC("3", Arrays.asList(Aref, T), "."),
+                VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
+                String.format("%s1-2", VariantContextUtils.MERGE_FILTER_PREFIX));
+
+        new MergeFilteredTest("OneFailAllUnfilteredArg",
+                makeVC("1", Arrays.asList(Aref, T), "FAIL"),
+                makeVC("2", Arrays.asList(Aref, T), "."),
+                makeVC("3", Arrays.asList(Aref, T), "FAIL"),
+                VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ALL_UNFILTERED,
+                String.format("%s1-2", VariantContextUtils.MERGE_FILTER_PREFIX));
+
+        // test excluding allele in filtered record
+        new MergeFilteredTest("DontIncludeAlleleOfFilteredRecords",
+                makeVC("1", Arrays.asList(Aref, T), "."),
+                makeVC("2", Arrays.asList(Aref, T), "FAIL"),
+                makeVC("3", Arrays.asList(Aref, T), "."),
+                String.format("1-%s2", VariantContextUtils.MERGE_FILTER_PREFIX));
+
+        // promotion of site from unfiltered to PASSES
+        new MergeFilteredTest("UnfilteredPlusPassIsPass",
+                makeVC("1", Arrays.asList(Aref, T), "."),
+                makeVC("2", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
+                makeVC("3", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
+                VariantContextUtils.MERGE_INTERSECTION);
+
+        new MergeFilteredTest("RefInAll",
+                makeVC("1", Arrays.asList(Aref), VariantContext.PASSES_FILTERS),
+                makeVC("2", Arrays.asList(Aref), VariantContext.PASSES_FILTERS),
+                makeVC("3", Arrays.asList(Aref), VariantContext.PASSES_FILTERS),
+                VariantContextUtils.MERGE_REF_IN_ALL);
+
+        new MergeFilteredTest("RefInOne",
+                makeVC("1", Arrays.asList(Aref), VariantContext.PASSES_FILTERS),
+                makeVC("2", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
+                makeVC("3", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
+                "2");
+
+        return MergeFilteredTest.getTests(MergeFilteredTest.class);
+    }
+
+    @Test(dataProvider = "mergeFiltered")
+    public void testMergeFiltered(MergeFilteredTest cfg) {
+        final List<String> priority = vcs2priority(cfg.inputs);
+        final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser,
+                cfg.inputs, priority, cfg.type, VariantContextUtils.GenotypeMergeType.PRIORITIZE, true, false, "set", false, false);
+
+        // test alleles are equal
+        Assert.assertEquals(merged.getAlleles(), cfg.expected.getAlleles());
+
+        // test set field
+        Assert.assertEquals(merged.getAttribute("set"), cfg.setExpected);
+
+        // test filter field
+        Assert.assertEquals(merged.getFilters(), cfg.expected.getFilters());
+    }
+
+    // --------------------------------------------------------------------------------
+    //
+    // Test genotype merging
+    //
+    // --------------------------------------------------------------------------------
+
+    private class MergeGenotypesTest extends TestDataProvider {
+        List<VariantContext> inputs;
+        VariantContext expected;
+        List<String> priority;
+
+        private MergeGenotypesTest(String name, String priority, VariantContext... arg) {
+            super(MergeGenotypesTest.class, name);
+            LinkedList<VariantContext> all = new LinkedList<VariantContext>(Arrays.asList(arg));
+            this.expected = all.pollLast();
+            inputs = all;
+            this.priority = Arrays.asList(priority.split(","));
+        }
+
+        public String toString() {
+            return String.format("%s input=%s expected=%s", super.toString(), inputs, expected);
+        }
+    }
+
+    @DataProvider(name = "mergeGenotypes")
+    public Object[][] mergeGenotypesData() {
+        new MergeGenotypesTest("TakeGenotypeByPriority-1,2", "1,2",
+                makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1)),
+                makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2)),
+                makeVC("3", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1)));
+
+        new MergeGenotypesTest("TakeGenotypeByPriority-1,2-nocall", "1,2",
+                makeVC("1", Arrays.asList(Aref, T), makeG("s1", Allele.NO_CALL, Allele.NO_CALL, 1)),
+                makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2)),
+                makeVC("3", Arrays.asList(Aref, T), makeG("s1", Allele.NO_CALL, Allele.NO_CALL, 1)));
+
+        new MergeGenotypesTest("TakeGenotypeByPriority-2,1", "2,1",
+                makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1)),
+                makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2)),
+                makeVC("3", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2)));
+
+        new MergeGenotypesTest("NonOverlappingGenotypes", "1,2",
+                makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1)),
+                makeVC("2", Arrays.asList(Aref, T), makeG("s2", Aref, T, 2)),
+                makeVC("3", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1), makeG("s2", Aref, T, 2)));
+
+        new MergeGenotypesTest("PreserveNoCall", "1,2",
+                makeVC("1", Arrays.asList(Aref, T), makeG("s1", Allele.NO_CALL, Allele.NO_CALL, 1)),
+                makeVC("2", Arrays.asList(Aref, T), makeG("s2", Aref, T, 2)),
+                makeVC("3", Arrays.asList(Aref, T), makeG("s1", Allele.NO_CALL, Allele.NO_CALL, 1), makeG("s2", Aref, T, 2)));
+
+        new MergeGenotypesTest("PerserveAlleles", "1,2",
+                makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1)),
+                makeVC("2", Arrays.asList(Aref, C), makeG("s2", Aref, C, 2)),
+                makeVC("3", Arrays.asList(Aref, C, T), makeG("s1", Aref, T, 1), makeG("s2", Aref, C, 2)));
+
+        new MergeGenotypesTest("TakeGenotypePartialOverlap-1,2", "1,2",
+                makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1)),
+                makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2), makeG("s3", Aref, T, 3)),
+                makeVC("3", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1), makeG("s3", Aref, T, 3)));
+
+        new MergeGenotypesTest("TakeGenotypePartialOverlap-2,1", "2,1",
+                makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1)),
+                makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2), makeG("s3", Aref, T, 3)),
+                makeVC("3", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2), makeG("s3", Aref, T, 3)));
+
+        // todo -- GDA -- add tests for merging correct PLs
+
+        return MergeGenotypesTest.getTests(MergeGenotypesTest.class);
+    }
+
+    @Test(dataProvider = "mergeGenotypes")
+    public void testMergeGenotypes(MergeGenotypesTest cfg) {
+        final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser,
+                cfg.inputs, cfg.priority, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
+                VariantContextUtils.GenotypeMergeType.PRIORITIZE, true, false, "set", false, false);
+
+        // test alleles are equal
+        Assert.assertEquals(merged.getAlleles(), cfg.expected.getAlleles());
+
+        // test genotypes
+        assertGenotypesAreMostlyEqual(merged.getGenotypes(), cfg.expected.getGenotypes());
+    }
+
+    // necessary to not overload equals for genotypes
+    private void assertGenotypesAreMostlyEqual(Map<String, Genotype> actual, Map<String, Genotype> expected) {
+        if (actual == expected) {
+            return;
+        }
+
+        if (actual == null || expected == null) {
+            Assert.fail("Maps not equal: expected: " + expected + " and actual: " + actual);
+        }
+
+        if (actual.size() != expected.size()) {
+            Assert.fail("Maps do not have the same size:" + actual.size() + " != " + expected.size());
+        }
+
+        for (Map.Entry<String, Genotype> entry : actual.entrySet()) {
+            String key = entry.getKey();
+            Genotype value = entry.getValue();
+            Genotype expectedValue = expected.get(key);
+
+            Assert.assertEquals(value.alleles, expectedValue.alleles);
+            Assert.assertEquals(value.getNegLog10PError(), expectedValue.getNegLog10PError());
+            Assert.assertEquals(value.hasLikelihoods(), expectedValue.hasLikelihoods());
+            if ( value.hasLikelihoods() )
+                Assert.assertEquals(value.getLikelihoods(), expectedValue.getLikelihoods());
+        }
+    }
+
+    @Test
+    public void testMergeGenotypesUniquify() {
+        final VariantContext vc1 = makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1));
+        final VariantContext vc2 = makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2));
+
+        final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser,
+                Arrays.asList(vc1, vc2), null, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
+                VariantContextUtils.GenotypeMergeType.UNIQUIFY, false, false, "set", false, false);
+
+        // test genotypes
+        Assert.assertEquals(merged.getGenotypes().keySet(), new HashSet<String>(Arrays.asList("s1.1", "s1.2")));
+    }
+
+    @Test(expectedExceptions = UserException.class)
+    public void testMergeGenotypesRequireUnique() {
+        final VariantContext vc1 = makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1));
+        final VariantContext vc2 = makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2));
+
+        final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser,
+                Arrays.asList(vc1, vc2), null, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
+                VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE, false, false, "set", false, false);
+    }
+
+    // --------------------------------------------------------------------------------
+    //
+    // Misc. tests
+    //
+    // --------------------------------------------------------------------------------
+
+    @Test
+    public void testAnnotationSet() {
+        for ( final boolean annotate : Arrays.asList(true, false)) {
+            for ( final String set : Arrays.asList("set", "combine", "x")) {
+                final List<String> priority = Arrays.asList("1", "2");
+                VariantContext vc1 = makeVC("1", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS);
+                VariantContext vc2 = makeVC("2", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS);
+
+                final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser,
+                        Arrays.asList(vc1, vc2), priority, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
+                        VariantContextUtils.GenotypeMergeType.PRIORITIZE, annotate, false, set, false, false);
+
+                if ( annotate )
+                    Assert.assertEquals(merged.getAttribute(set), VariantContextUtils.MERGE_INTERSECTION);
+                else
+                    Assert.assertFalse(merged.hasAttribute(set));
+            }
+        }
+    }
+
+    private static final List<String> vcs2priority(final Collection<VariantContext> vcs) {
+        final List<String> priority = new ArrayList<String>();
+
+        for ( final VariantContext vc : vcs ) {
+            priority.add(vc.getSource());
+        }
+
+        return priority;
+    }
 }