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

build.xml

@@ -955,8 +955,8 @@
                 <jvmarg value="-Dpipeline.run=${pipeline.run}" />
                 <jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
                 <jvmarg line="${cofoja.jvm.args}"/>
-<!--                 <jvmarg value="-Xdebug"/> -->
+                <!-- <jvmarg value="-Xdebug"/> --> 
-<!--                 <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> -->
+                <!-- <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5678"/> -->  
 
                 <classfileset dir="${java.public.test.classes}" includes="**/@{testtype}.class"/>
                 <classfileset dir="${java.private.test.classes}" erroronmissingdir="false">

public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java

@@ -177,11 +177,8 @@ public class GATKReport {
      */
     public void print(PrintStream out) {
         out.println(GATKREPORT_HEADER_PREFIX + getVersion().toString() + SEPARATOR + getTables().size());
-        for (GATKReportTable table : tables.values()) {
+        for (GATKReportTable table : tables.values())
-            if (table.getNumRows() > 0) {
+            table.write(out);
-                table.write(out);
-            }
-        }
     }
 
     public Collection<GATKReportTable> getTables() {

public/java/src/org/broadinstitute/sting/gatk/report/GATKReportDataType.java

@@ -48,9 +48,9 @@ public enum GATKReportDataType {
     Boolean("%[Bb]"),
 
     /**
-     * Used for byte and char value. Will display as a char so use printable values!
+     * Used for char values. Will display as a char so use printable values!
      */
-    Byte("%[Cc]"),
+    Character("%[Cc]"),
 
     /**
      * Used for float and double values. Will output a decimal with format %.8f unless otherwise specified.
@@ -58,7 +58,7 @@ public enum GATKReportDataType {
     Decimal("%.*[EeFf]"),
 
     /**
-     * Used for int, and long values. Will display the full number by default.
+     * Used for int, byte, short, and long values. Will display the full number by default.
      */
     Integer("%[Dd]"),
 
@@ -97,17 +97,26 @@ public enum GATKReportDataType {
         GATKReportDataType value;
         if (object instanceof Boolean) {
             value = GATKReportDataType.Boolean;
-        } else if (object instanceof Byte || object instanceof Character) {
+
-            value = GATKReportDataType.Byte;
+        } else if (object instanceof Character) {
-        } else if (object instanceof Float || object instanceof Double) {
+            value = GATKReportDataType.Character;
+
+        } else if (object instanceof Float ||
+                object instanceof Double) {
             value = GATKReportDataType.Decimal;
-        } else if (object instanceof Integer || object instanceof Long) {
+
+        } else if (object instanceof Integer ||
+                object instanceof Long ||
+                object instanceof Short ||
+                object instanceof Byte ) {
             value = GATKReportDataType.Integer;
+
         } else if (object instanceof String) {
             value = GATKReportDataType.String;
+
         } else {
             value = GATKReportDataType.Unknown;
-            //throw new ReviewedStingException("GATKReport could not convert the data object into a GATKReportDataType. Acceptable data objects are found in the documentation.");
+            //throw new UserException("GATKReport could not convert the data object into a GATKReportDataType. Acceptable data objects are found in the documentation.");
         }
         return value;
     }
@@ -140,8 +149,8 @@ public enum GATKReportDataType {
                 return 0.0D;
             case Boolean:
                 return false;
-            case Byte:
+            case Character:
-                return (byte) 0;
+                return '0';
             case Integer:
                 return 0L;
             case String:
@@ -166,16 +175,7 @@ public enum GATKReportDataType {
             case Boolean:
             case Integer:
                 return a.toString().equals(b.toString());
-            case Byte:
+            case Character:
-                // A mess that checks if the bytes and characters contain the same value
-                if ((a instanceof Character && b instanceof Character) ||
-                        (a instanceof Byte && b instanceof Byte))
-                    return a.toString().equals(b.toString());
-                else if (a instanceof Character && b instanceof Byte) {
-                    return ((Character) a).charValue() == ((Byte) b).byteValue();
-                } else if (a instanceof Byte && b instanceof Character) {
-                    return ((Byte) a).byteValue() == ((Character) b).charValue();
-                }
             case String:
             default:
                 return a.equals(b);
@@ -201,8 +201,8 @@ public enum GATKReportDataType {
                     return Long.parseLong(str);
                 case String:
                     return str;
-                case Byte:
+                case Character:
-                    return (byte) str.toCharArray()[0];
+                    return str.toCharArray()[0];
                 default:
                     return str;
             }
@@ -225,7 +225,7 @@ public enum GATKReportDataType {
                 return "%d";
             case String:
                 return "%s";
-            case Byte:
+            case Character:
                 return "%c";
             case Null:
             default:

public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java

@@ -254,7 +254,7 @@ public class GATKReportTable {
      * @param dottedColumnValues Period concatenated values.
      * @return The first primary key matching the column values or throws an exception.
      */
-    public Object getPrimaryKey(String dottedColumnValues) {
+    public Object getPrimaryKeyByData(String dottedColumnValues) {
         Object key = findPrimaryKey(dottedColumnValues);
         if (key == null)
             throw new ReviewedStingException("Attempted to get non-existent GATKReportTable key for values: " + dottedColumnValues);
@@ -411,9 +411,8 @@ public class GATKReportTable {
         if (value == null)
             value = "null";
 
-        // This code is bs. Why am do I have to conform to bad code
+        // This code below is bs. Why am do I have to conform to bad code
-        // Below is some ode to convert a string into its appropriate type.
+        // Below is some code to convert a string into its appropriate type.
-        // This is just Roger ranting
 
         // If we got a string but the column is not a String type
         Object newValue = null;
@@ -431,7 +430,7 @@ public class GATKReportTable {
                 } catch (Exception e) {
                 }
             }
-            if (column.getDataType().equals(GATKReportDataType.Byte) && ((String) value).length() == 1) {
+            if (column.getDataType().equals(GATKReportDataType.Character) && ((String) value).length() == 1) {
                 newValue = ((String) value).charAt(0);
 
             }
@@ -816,7 +815,7 @@ public class GATKReportTable {
             out.println();
         }
 
-        out.println();
+         out.println();
     }
 
     public int getNumRows() {
@@ -877,8 +876,6 @@ public class GATKReportTable {
                     this.set(rowKey, columnKey, toAdd.get(rowKey));
                     //System.out.printf("Putting row with PK: %s \n", rowKey);
                 } else {
-
-                    // TODO we should be able to handle combining data by adding, averaging, etc.
                     this.set(rowKey, columnKey, toAdd.get(rowKey));
 
                     System.out.printf("OVERWRITING Row with PK: %s \n", rowKey);

public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReport.java

@@ -94,8 +94,11 @@ public class RecalibrationReport {
                 BitSet key = entry.getKey();
                 RecalDatum otherDatum = entry.getValue();
                 RecalDatum thisDatum = thisTable.get(key);
-                thisDatum.increment(otherDatum);                                                                          // add the two datum objects into 'this'
+                if (thisDatum == null)
-                thisDatum.resetCalculatedQualities();                                                                      // reset the empirical quality to make sure the user doesn't forget to recalculate it
+                    thisDatum = otherDatum;                                                                             // sometimes the datum in other won't be present in 'this'. So just assign it!
+                else
+                    thisDatum.increment(otherDatum);                                                                    // add the two datum objects into 'this'
+                thisDatum.resetCalculatedQualities();                                                                   // reset the empirical quality to make sure the user doesn't forget to recalculate it
             }            
         }
     }

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

@@ -41,7 +41,8 @@ public abstract class AlleleFrequencyCalculationModel implements Cloneable {
 
     public enum Model {
         /** The default model with the best performance in all cases */
-        EXACT
+        EXACT,
+        POOL
     }
 
     protected int N;

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

@@ -152,7 +152,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
 
         @Override
         public boolean equals(Object obj) {
-            return (obj instanceof ExactACcounts) ? Arrays.equals(counts, ((ExactACcounts)obj).counts) : false;
+            return (obj instanceof ExactACcounts) && Arrays.equals(counts, ((ExactACcounts)obj).counts);
         }
 
         @Override
@@ -202,7 +202,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
         }
 
         public boolean equals(Object obj) {
-            return (obj instanceof ExactACset) ? ACcounts.equals(((ExactACset)obj).ACcounts) : false;
+            return (obj instanceof ExactACset) && ACcounts.equals(((ExactACset)obj).ACcounts);
         }
     }
 

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

@@ -47,9 +47,17 @@ import java.util.Map;
  */
 public abstract class GenotypeLikelihoodsCalculationModel implements Cloneable {
 
+/*    public enum Model {
+        SNP,
+        INDEL,
+        BOTH
+    }
+  */
     public enum Model {
         SNP,
         INDEL,
+        POOLSNP,
+        POOLINDEL,
         BOTH
     }
 
@@ -60,7 +68,7 @@ public abstract class GenotypeLikelihoodsCalculationModel implements Cloneable {
         GENOTYPE_GIVEN_ALLELES
     }
 
-    protected UnifiedArgumentCollection UAC;
+    protected final UnifiedArgumentCollection UAC;
     protected Logger logger;
 
     /**
@@ -70,7 +78,7 @@ public abstract class GenotypeLikelihoodsCalculationModel implements Cloneable {
      */
     protected GenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) {
         if ( logger == null || UAC == null ) throw new ReviewedStingException("Bad arguments");
-        this.UAC = UAC.clone();
+        this.UAC = UAC;
         this.logger = logger;
     }
 

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

@@ -38,7 +38,7 @@ public class UnifiedArgumentCollection {
      * Controls the model used to calculate the probability that a site is variant plus the various sample genotypes in the data at a given locus.
      */
     @Argument(fullName = "p_nonref_model", shortName = "pnrm", doc = "Non-reference probability calculation model to employ -- EXACT is the default option, while GRID_SEARCH is also available.", required = false)
-    public AlleleFrequencyCalculationModel.Model AFmodel = AlleleFrequencyCalculationModel.Model.EXACT;
+    protected AlleleFrequencyCalculationModel.Model AFmodel = AlleleFrequencyCalculationModel.Model.EXACT;
 
     /**
      * The expected heterozygosity value used to compute prior likelihoods for any locus. The default priors are:

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

@@ -222,7 +222,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
             verboseWriter.println("AFINFO\tLOC\tREF\tALT\tMAF\tF\tAFprior\tMLE\tMAP");
 
         annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit());
-        UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, verboseWriter, annotationEngine, samples);
+        UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, verboseWriter, annotationEngine, samples, 2*samples.size());
 
         // initialize the header
         Set<VCFHeaderLine> headerInfo = getHeaderInfo();

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

@@ -36,14 +36,17 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.baq.BAQ;
+import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.variantcontext.*;
 
 import java.io.PrintStream;
+import java.lang.reflect.Constructor;
 import java.util.*;
 
 public class UnifiedGenotyperEngine {
@@ -71,7 +74,7 @@ public class UnifiedGenotyperEngine {
     private final VariantAnnotatorEngine annotationEngine;
 
     // the model used for calculating genotypes
-    private ThreadLocal<Map<GenotypeLikelihoodsCalculationModel.Model, GenotypeLikelihoodsCalculationModel>> glcm = new ThreadLocal<Map<GenotypeLikelihoodsCalculationModel.Model, GenotypeLikelihoodsCalculationModel>>();
+    private ThreadLocal<Map<String, GenotypeLikelihoodsCalculationModel>> glcm = new ThreadLocal<Map<String, GenotypeLikelihoodsCalculationModel>>();
 
     // the model used for calculating p(non-ref)
     private ThreadLocal<AlleleFrequencyCalculationModel> afcm = new ThreadLocal<AlleleFrequencyCalculationModel>();
@@ -112,22 +115,22 @@ public class UnifiedGenotyperEngine {
     // ---------------------------------------------------------------------------------------------------------
     @Requires({"toolkit != null", "UAC != null"})
     public UnifiedGenotyperEngine(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC) {
-        this(toolkit, UAC, Logger.getLogger(UnifiedGenotyperEngine.class), null, null, SampleUtils.getSAMFileSamples(toolkit.getSAMFileHeader()));
+        this(toolkit, UAC, Logger.getLogger(UnifiedGenotyperEngine.class), null, null, SampleUtils.getSAMFileSamples(toolkit.getSAMFileHeader()), 2*(SampleUtils.getSAMFileSamples(toolkit.getSAMFileHeader()).size()));
     }
 
-    @Requires({"toolkit != null", "UAC != null", "logger != null", "samples != null && samples.size() > 0"})
+    @Requires({"toolkit != null", "UAC != null", "logger != null", "samples != null && samples.size() > 0","N>0"})
-    public UnifiedGenotyperEngine(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC, Logger logger, PrintStream verboseWriter, VariantAnnotatorEngine engine, Set<String> samples) {
+    public UnifiedGenotyperEngine(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC, Logger logger, PrintStream verboseWriter, VariantAnnotatorEngine engine, Set<String> samples, int N) {
         this.BAQEnabledOnCMDLine = toolkit.getArguments().BAQMode != BAQ.CalculationMode.OFF;
         genomeLocParser = toolkit.getGenomeLocParser();
         this.samples = new TreeSet<String>(samples);
         // note that, because we cap the base quality by the mapping quality, minMQ cannot be less than minBQ
-        this.UAC = UAC.clone();
+        this.UAC = UAC;
 
         this.logger = logger;
         this.verboseWriter = verboseWriter;
         this.annotationEngine = engine;
 
-        N = 2 * this.samples.size();
+        this.N = N;
         log10AlleleFrequencyPriorsSNPs = new double[N+1];
         log10AlleleFrequencyPriorsIndels = new double[N+1];
         computeAlleleFrequencyPriors(N, log10AlleleFrequencyPriorsSNPs, UAC.heterozygosity);
@@ -219,7 +222,7 @@ public class UnifiedGenotyperEngine {
             glcm.set(getGenotypeLikelihoodsCalculationObject(logger, UAC));
         }
 
-        return glcm.get().get(model).getLikelihoods(tracker, refContext, stratifiedContexts, type, getGenotypePriors(model), alternateAllelesToUse, useBAQedPileup && BAQEnabledOnCMDLine, genomeLocParser);
+        return glcm.get().get(model.name()).getLikelihoods(tracker, refContext, stratifiedContexts, type, getGenotypePriors(model), alternateAllelesToUse, useBAQedPileup && BAQEnabledOnCMDLine, genomeLocParser);
     }
 
     private VariantCallContext generateEmptyContext(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, AlignmentContext rawContext) {
@@ -433,7 +436,7 @@ public class UnifiedGenotyperEngine {
         if ( !BaseUtils.isRegularBase( refContext.getBase() ) )
             return null;
 
-        if ( model == GenotypeLikelihoodsCalculationModel.Model.INDEL ) {
+        if ( model.name().toUpperCase().contains("INDEL")) {
 
             if (UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) {
                 // regular pileup in this case
@@ -463,7 +466,7 @@ public class UnifiedGenotyperEngine {
                 // stratify the AlignmentContext and cut by sample
                 stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup);
             }
-        } else if ( model == GenotypeLikelihoodsCalculationModel.Model.SNP ) {
+        } else if ( model.name().toUpperCase().contains("SNP") ) {
 
             // stratify the AlignmentContext and cut by sample
             stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(rawContext.getBasePileup());
@@ -594,21 +597,27 @@ public class UnifiedGenotyperEngine {
                     return null;
 
                 if (vcInput.isSNP())  {
-                    if (( UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH || UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.SNP))
+                    if ( UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH )
                         return GenotypeLikelihoodsCalculationModel.Model.SNP;
+                    else if ( UAC.GLmodel.name().toUpperCase().contains("SNP"))
+                        return UAC.GLmodel;
                     else
                         // ignore SNP's if user chose INDEL mode
                         return null;
                 }
-                else if ((vcInput.isIndel() || vcInput.isMixed()) && (UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH || UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.INDEL))
+                else if ((vcInput.isIndel() || vcInput.isMixed())) {
-                    return GenotypeLikelihoodsCalculationModel.Model.INDEL;
+                    if ( UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH )
+                        return GenotypeLikelihoodsCalculationModel.Model.INDEL;
+                    else if (UAC.GLmodel.name().toUpperCase().contains("INDEL"))
+                        return UAC.GLmodel;
+                }
             }
             else {
                 // todo - this assumes SNP's take priority when BOTH is selected, should do a smarter way once extended events are removed
-                if( UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH || UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.SNP)
+                if( UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH )
                     return GenotypeLikelihoodsCalculationModel.Model.SNP;
-                else if (UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.INDEL)
+                else if (UAC.GLmodel.name().toUpperCase().contains("SNP") || UAC.GLmodel.name().toUpperCase().contains("INDEL"))
-                    return GenotypeLikelihoodsCalculationModel.Model.INDEL;
+                    return UAC.GLmodel;
             }
         }
         return null;
@@ -630,58 +639,77 @@ public class UnifiedGenotyperEngine {
     }
 
     protected double[] getAlleleFrequencyPriors( final GenotypeLikelihoodsCalculationModel.Model model ) {
-        switch( model ) {
+        if (model.name().toUpperCase().contains("SNP"))
-            case SNP:
+            return log10AlleleFrequencyPriorsSNPs;
-                return log10AlleleFrequencyPriorsSNPs;
+        else if (model.name().toUpperCase().contains("INDEL"))
-            case INDEL:
+            return log10AlleleFrequencyPriorsIndels;
-                return log10AlleleFrequencyPriorsIndels;
+        else
-            default: throw new IllegalArgumentException("Unexpected GenotypeCalculationModel " + model);
+            throw new IllegalArgumentException("Unexpected GenotypeCalculationModel " + model);
-        }
+
     }
 
     private static GenotypePriors createGenotypePriors( final GenotypeLikelihoodsCalculationModel.Model model ) {
         GenotypePriors priors;
-        switch ( model ) {
+        if( model.name().contains("SNP") )
-            case SNP:
+            priors = new DiploidSNPGenotypePriors();
-                // use flat priors for GLs
+        else if( model.name().contains("INDEL") )
-                priors = new DiploidSNPGenotypePriors();
+            priors = new DiploidIndelGenotypePriors();
-                break;
+        else throw new IllegalArgumentException("Unexpected GenotypeCalculationModel " + model);
-            case INDEL:
+
-                // create flat priors for Indels, actual priors will depend on event length to be genotyped
-                priors = new DiploidIndelGenotypePriors();
-                break;
-            default: throw new IllegalArgumentException("Unexpected GenotypeCalculationModel " + model);
-        }
         return priors;
     }
 
     protected GenotypePriors getGenotypePriors( final GenotypeLikelihoodsCalculationModel.Model model ) {
-        switch( model ) {
+        if( model.name().contains("SNP") )
-            case SNP:
+            return genotypePriorsSNPs;
-                return genotypePriorsSNPs;
+        if( model.name().contains("INDEL") )
-            case INDEL:
+            return genotypePriorsIndels;
-                return genotypePriorsIndels;
+        else throw new IllegalArgumentException("Unexpected GenotypeCalculationModel " + model);
-            default: throw new IllegalArgumentException("Unexpected GenotypeCalculationModel " + model);
-        }
     }
 
-    private static Map<GenotypeLikelihoodsCalculationModel.Model, GenotypeLikelihoodsCalculationModel> getGenotypeLikelihoodsCalculationObject(Logger logger, UnifiedArgumentCollection UAC) {
+    private static Map<String,GenotypeLikelihoodsCalculationModel> getGenotypeLikelihoodsCalculationObject(Logger logger, UnifiedArgumentCollection UAC) {
-        Map<GenotypeLikelihoodsCalculationModel.Model, GenotypeLikelihoodsCalculationModel> glcm = new HashMap<GenotypeLikelihoodsCalculationModel.Model, GenotypeLikelihoodsCalculationModel>();
+
-        glcm.put(GenotypeLikelihoodsCalculationModel.Model.SNP, new SNPGenotypeLikelihoodsCalculationModel(UAC, logger));
+
-        glcm.put(GenotypeLikelihoodsCalculationModel.Model.INDEL, new IndelGenotypeLikelihoodsCalculationModel(UAC, logger));
+        Map<String, GenotypeLikelihoodsCalculationModel> glcm = new HashMap<String, GenotypeLikelihoodsCalculationModel>();
+       // GenotypeLikelihoodsCalculationModel.Model.
+        List<Class<? extends GenotypeLikelihoodsCalculationModel>> glmClasses = new PluginManager<GenotypeLikelihoodsCalculationModel>(GenotypeLikelihoodsCalculationModel.class).getPlugins();
+
+        for (int i = 0; i < glmClasses.size(); i++) {
+            Class<? extends GenotypeLikelihoodsCalculationModel> glmClass = glmClasses.get(i);
+            String key = glmClass.getSimpleName().replaceAll("GenotypeLikelihoodsCalculationModel","").toUpperCase();
+            //System.out.println("KEY:"+key+"\t" + glmClass.getSimpleName());
+            try {
+                Object args[] = new Object[]{UAC,logger};
+                Constructor c = glmClass.getDeclaredConstructor(UnifiedArgumentCollection.class, Logger.class);
+                glcm.put(key, (GenotypeLikelihoodsCalculationModel)c.newInstance(args));
+            }
+            catch (Exception e) {
+                throw new UserException("Incorrect specification for argument glm:"+UAC.GLmodel+e.getMessage());
+            }
+         }
+
         return glcm;
     }
 
     private static AlleleFrequencyCalculationModel getAlleleFrequencyCalculationObject(int N, Logger logger, PrintStream verboseWriter, UnifiedArgumentCollection UAC) {
-        AlleleFrequencyCalculationModel afcm;
+        List<Class<? extends AlleleFrequencyCalculationModel>> afClasses = new PluginManager<AlleleFrequencyCalculationModel>(AlleleFrequencyCalculationModel.class).getPlugins();
-        switch ( UAC.AFmodel ) {
-            case EXACT:
-                afcm = new ExactAFCalculationModel(UAC, N, logger, verboseWriter);
-                break;
-            default: throw new IllegalArgumentException("Unexpected AlleleFrequencyCalculationModel " + UAC.AFmodel);
-        }
 
-        return afcm;
+        for (int i = 0; i < afClasses.size(); i++) {
+            Class<? extends AlleleFrequencyCalculationModel> afClass = afClasses.get(i);
+            String key = afClass.getSimpleName().replace("AFCalculationModel","").toUpperCase();
+            if (UAC.AFmodel.name().equalsIgnoreCase(key)) {
+                try {
+                    Object args[] = new Object[]{UAC,N,logger,verboseWriter};
+                    Constructor c = afClass.getDeclaredConstructor(UnifiedArgumentCollection.class, int.class, Logger.class, PrintStream.class);
+
+                    return (AlleleFrequencyCalculationModel)c.newInstance(args);
+                }
+                catch (Exception e) {
+                    throw new IllegalArgumentException("Unexpected AlleleFrequencyCalculationModel " + UAC.AFmodel);
+                }
+            }
+        }
+        throw new IllegalArgumentException("Unexpected AlleleFrequencyCalculationModel " + UAC.AFmodel);
     }
 
     public static VariantContext getVCFromAllelesRod(RefMetaDataTracker tracker, ReferenceContext ref, GenomeLoc loc, boolean requireSNP, Logger logger, final RodBinding<VariantContext> allelesBinding) {

public/java/src/org/broadinstitute/sting/utils/MathUtils.java

@@ -29,6 +29,7 @@ import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.math.BigDecimal;
@@ -48,6 +49,7 @@ public class MathUtils {
     }
 
     public static final double[] log10Cache;
+    public static final double[] log10FactorialCache;
     private static final double[] jacobianLogTable;
     private static final double JACOBIAN_LOG_TABLE_STEP = 0.001;
     private static final double JACOBIAN_LOG_TABLE_INV_STEP = 1.0 / 0.001;
@@ -58,11 +60,14 @@ public class MathUtils {
 
     static {
         log10Cache = new double[LOG10_CACHE_SIZE];
+        log10FactorialCache = new double[LOG10_CACHE_SIZE];
         jacobianLogTable = new double[JACOBIAN_LOG_TABLE_SIZE];
 
         log10Cache[0] = Double.NEGATIVE_INFINITY;
-        for (int k = 1; k < LOG10_CACHE_SIZE; k++)
+        for (int k = 1; k < LOG10_CACHE_SIZE; k++) {
             log10Cache[k] = Math.log10(k);
+            log10FactorialCache[k] = log10FactorialCache[k-1] + log10Cache[k];
+        }
 
         for (int k = 0; k < JACOBIAN_LOG_TABLE_SIZE; k++) {
             jacobianLogTable[k] = Math.log10(1.0 + Math.pow(10.0, -((double) k) * JACOBIAN_LOG_TABLE_STEP));
@@ -233,6 +238,9 @@ public class MathUtils {
         double sum = 0.0;
 
         double maxValue = Utils.findMaxEntry(log10p);
+        if(maxValue == Double.NEGATIVE_INFINITY)
+            return sum;
+
         for (int i = start; i < finish; i++) {
             sum += Math.pow(10.0, log10p[i] - maxValue);
         }
@@ -1046,6 +1054,28 @@ public class MathUtils {
 
     }
 
+    /**
+     * Given two log-probability vectors, compute log of vector product of them:
+     * in Matlab notation, return log10(10.*x'*10.^y)
+     * @param x vector 1
+     * @param y vector 2
+     * @return a double representing log (dotProd(10.^x,10.^y)
+     */
+    public static double logDotProduct(double [] x, double[] y) {
+        if (x.length != y.length)
+            throw new ReviewedStingException("BUG: Vectors of different lengths");
+
+        double tmpVec[] = new double[x.length];
+
+        for (int k=0; k < tmpVec.length; k++ ) {
+            tmpVec[k] = x[k]+y[k];
+        }
+
+        return log10sumLog10(tmpVec);
+
+
+
+    }
     public static Object getMedian(List<Comparable> list) {
         return orderStatisticSearch((int) Math.ceil(list.size() / 2), list);
     }
@@ -1485,6 +1515,24 @@ public class MathUtils {
         return result;
     }
 
+    /** Same routine, unboxed types for efficiency
+     *
+     * @param x
+     * @param y
+     * @return Vector of same length as x and y so that z[k] = x[k]+y[k]
+     */
+    public static double[] vectorSum(double[]x, double[] y) {
+        if (x.length != y.length)
+            throw new ReviewedStingException("BUG: Lengths of x and y must be the same");
+
+        double[] result = new double[x.length];
+        for (int k=0; k <x.length; k++)
+            result[k] = x[k]+y[k];
+
+        return result;
+    }
+
+
     public static <E extends Number> Double[] scalarTimesVector(E a, E[] v1) {
 
         Double result[] = new Double[v1.length];

public/java/test/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java

@@ -34,21 +34,22 @@ import java.io.IOException;
 import java.io.PrintStream;
 
 public class GATKReportUnitTest extends BaseTest {
-    @Test(enabled = false)
+    @Test
     public void testParse() throws Exception {
         String reportPath = validationDataLocation + "exampleGATKReportv1.tbl";
         GATKReport report = new GATKReport(reportPath);
+        Assert.assertEquals(report.getVersion(), GATKReportVersion.V1_0);
+        Assert.assertEquals(report.getTables().size(), 5);
 
         GATKReportTable countVariants = report.getTable("CountVariants");
-        //Assert.assertEquals(countVariants.getVersion(), GATKReportVersion.V0_1);
+        Object countVariantsPK = countVariants.getPrimaryKeyByData("dbsnp.eval.none.all");
-        Object countVariantsPK = countVariants.getPrimaryKey("none.eval.none.all");
+        Assert.assertEquals(countVariants.get(countVariantsPK, "nProcessedLoci"), "63025520");
-        Assert.assertEquals(countVariants.get(countVariantsPK, "nProcessedLoci"), "100000");
+        Assert.assertEquals(countVariants.get(countVariantsPK, "nNoCalls"), "0");
-        Assert.assertEquals(countVariants.get(countVariantsPK, "nNoCalls"), "99872");
+        Assert.assertEquals(countVariants.get(countVariantsPK, "heterozygosity"), 4.73e-06);
 
         GATKReportTable validationReport = report.getTable("ValidationReport");
-        //Assert.assertEquals(validationReport.getVersion(), GATKReportVersion.V0_1);
+        Object validationReportPK = countVariants.getPrimaryKeyByData("dbsnp.eval.none.novel");
-        Object validationReportPK = countVariants.getPrimaryKey("none.eval.none.known");
+        Assert.assertEquals(validationReport.get(validationReportPK, "PPV"), Double.NaN);
-        Assert.assertEquals(validationReport.get(validationReportPK, "sensitivity"), "NaN");
     }
 
     @DataProvider(name = "rightAlignValues")
@@ -117,15 +118,15 @@ public class GATKReportUnitTest extends BaseTest {
         report1.addTable("TableName", "Description");
         report1.getTable("TableName").addPrimaryKey("id", displayPK);
         report1.getTable("TableName").addColumn("colA", GATKReportDataType.String.getDefaultValue(), "%s");
-        report1.getTable("TableName").addColumn("colB", GATKReportDataType.Byte.getDefaultValue(), "%c");
+        report1.getTable("TableName").addColumn("colB", GATKReportDataType.Character.getDefaultValue(), "%c");
         report1.getTable("TableName").set(1, "colA", "NotNum");
-        report1.getTable("TableName").set(1, "colB", (byte) 64);
+        report1.getTable("TableName").set(1, "colB", (char) 64);
 
         report2 = new GATKReport();
         report2.addTable("TableName", "Description");
         report2.getTable("TableName").addPrimaryKey("id", displayPK);
         report2.getTable("TableName").addColumn("colA", GATKReportDataType.String.getDefaultValue(), "%s");
-        report2.getTable("TableName").addColumn("colB", GATKReportDataType.Byte.getDefaultValue(), "%c");
+        report2.getTable("TableName").addColumn("colB", GATKReportDataType.Character.getDefaultValue(), "%c");
         report2.getTable("TableName").set(2, "colA", "df3");
         report2.getTable("TableName").set(2, "colB", 'A');
 
@@ -133,7 +134,7 @@ public class GATKReportUnitTest extends BaseTest {
         report3.addTable("TableName", "Description");
         report3.getTable("TableName").addPrimaryKey("id", displayPK);
         report3.getTable("TableName").addColumn("colA", GATKReportDataType.String.getDefaultValue(), "%s");
-        report3.getTable("TableName").addColumn("colB", GATKReportDataType.Byte.getDefaultValue(), "%c");
+        report3.getTable("TableName").addColumn("colB", GATKReportDataType.Character.getDefaultValue(), "%c");
         report3.getTable("TableName").set(3, "colA", "df5f");
         report3.getTable("TableName").set(3, "colB", 'c');
 
@@ -146,13 +147,13 @@ public class GATKReportUnitTest extends BaseTest {
         table.addColumn("SomeInt", GATKReportDataType.Integer.getDefaultValue(), true, "%d");
         table.addColumn("SomeFloat", GATKReportDataType.Decimal.getDefaultValue(), true, "%.16E");
         table.addColumn("TrueFalse", false, true, "%B");
-        table.set("12df", "SomeInt", 34);
+        table.set("12df", "SomeInt", Byte.MAX_VALUE);
         table.set("12df", "SomeFloat", 34.0);
         table.set("12df", "TrueFalse", true);
-        table.set("5f", "SomeInt", -1);
+        table.set("5f", "SomeInt", Short.MAX_VALUE);
-        table.set("5f", "SomeFloat", 0.000003);
+        table.set("5f", "SomeFloat", Double.MAX_VALUE);
         table.set("5f", "TrueFalse", false);
-        table.set("RZ", "SomeInt", 904948230958203958L);
+        table.set("RZ", "SomeInt", Long.MAX_VALUE);
         table.set("RZ", "SomeFloat", 535646345.657453464576);
         table.set("RZ", "TrueFalse", true);
 

public/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java

@@ -284,6 +284,18 @@ public class MathUtilsUnitTest extends BaseTest {
         Assert.assertTrue(compareDoubleArrays(MathUtils.normalizeFromLog10(new double[] {-1.0, -3.0, -1.0, -2.0}), new double[] {0.1 * 1.0 / 0.211, 0.001 * 1.0 / 0.211, 0.1 * 1.0 / 0.211, 0.01 * 1.0 / 0.211}));
     }
 
+    @Test
+    public void testDotProduct() {
+        Assert.assertEquals(MathUtils.dotProduct(new Double[]{-5.0,-3.0,2.0}, new Double[]{6.0,7.0,8.0}),-35.0,1e-3);
+        Assert.assertEquals(MathUtils.dotProduct(new Double[]{-5.0}, new Double[]{6.0}),-30.0,1e-3);
+    }
+
+    @Test
+    public void testLogDotProduct() {
+        Assert.assertEquals(MathUtils.logDotProduct(new double[]{-5.0,-3.0,2.0}, new double[]{6.0,7.0,8.0}),10.0,1e-3);
+        Assert.assertEquals(MathUtils.logDotProduct(new double[]{-5.0}, new double[]{6.0}),1.0,1e-3);
+    }
+
     /**
      * Private function used by testNormalizeFromLog10()
      */

public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala

@@ -136,7 +136,7 @@ object PipelineTest extends BaseTest with Logging {
     println("    value (min,target,max) table key metric")
     for (validation <- evalSpec.validations) {
       val table = report.getTable(validation.table)
-      val key = table.getPrimaryKey(validation.key)
+      val key = table.getPrimaryKeyByData(validation.key)
       val value = String.valueOf(table.get(key, validation.metric))
       val inRange = if (value == null) false else validation.inRange(value)
       val flag = if (!inRange) "*" else " "