Fix merge conflicts

protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java

@@ -262,18 +262,19 @@ public class ErrorModel  {
     }
 
     public String toString() {
-        String result = "(";
+        StringBuilder result = new StringBuilder("(");
         boolean skipComma = true;
         for (double v : probabilityVector.getProbabilityVector()) {
             if (skipComma) {
                 skipComma = false;
             }
             else {
-                result += ",";
+                result.append(",");
             }
-            result += String.format("%.4f", v);
+            result.append(String.format("%.4f", v));
         }
-        return result + ")";
+        result.append(")");
+        return result.toString();
     }
     
     public static int getTotalReferenceDepth(HashMap<String, ErrorModel>  perLaneErrorModels) {

protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java

@@ -145,7 +145,7 @@ public class GeneralPloidyIndelGenotypeLikelihoods extends GeneralPloidyGenotype
         List<Integer> numSeenBases = new ArrayList<Integer>(this.alleles.size());
 
         if (!hasReferenceSampleData) {
-
+ 
             final int readCounts[] = new int[pileup.getNumberOfElements()];
             readHaplotypeLikelihoods = pairModel.computeGeneralReadHaplotypeLikelihoods(pileup, haplotypeMap, refContext, eventLength, perReadAlleleLikelihoodMap, readCounts);
             n = readHaplotypeLikelihoods.length;

protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java

@@ -45,32 +45,32 @@ public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest {
         executeTest("testPoolCaller:"+name+" args=" + args, spec);
     }
 
-    @Test(enabled = false)
+    @Test(enabled = true)
     public void testBOTH_GGA_Pools() {
         PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","BOTH","0934f72865388999efec64bd9d4a9b93");
     }
 
-    @Test(enabled = false)
+    @Test(enabled = true)
     public void testINDEL_GGA_Pools() {
         PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_INDEL_GGA","INDEL","126581c72d287722437274d41b6fed7b");
     }
 
-    @Test(enabled = false)
+    @Test(enabled = true)
     public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() {
         PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","b543aa1c3efedb301e525c1d6c50ed8d");
     }
 
-    @Test(enabled = false)
+    @Test(enabled = true)
     public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() {
         PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","55b20557a836bb92688e68f12d7f5dc4");
     }
 
-    @Test(enabled = false)
+    @Test(enabled = true)
     public void testMT_SNP_DISCOVERY_sp4() {
          PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","7eb889e8e07182f4c3d64609591f9459");
     }
 
-    @Test(enabled = false)
+    @Test(enabled = true)
     public void testMT_SNP_GGA_sp10() {
         PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "db8114877b99b14f7180fdcd24b040a7");
     }

public/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java

@@ -208,6 +208,7 @@ public class FastaSequenceIndexBuilder {
                         break;
                 }
             }
+            in.close();
             return sequenceIndex;
         }
         catch (IOException e) {

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

@@ -12,10 +12,10 @@ import java.util.*;
  */
 public class Bases implements Iterable<Byte>
 {
-    public static byte A = 'A';
+    public static final byte A = 'A';
-    public static byte C = 'C';
+    public static final byte C = 'C';
-    public static byte G = 'G';
+    public static final byte G = 'G';
-    public static byte T = 'T';
+    public static final byte T = 'T';
 
     public static final Bases instance = new Bases();
 

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

@@ -55,10 +55,8 @@ public class ArgumentDefinitionGroup implements Iterable<ArgumentDefinition> {
      * Does the name of this argument group match the name of another?
      */
     public boolean groupNameMatches( ArgumentDefinitionGroup other ) {
-        if( this.groupName == null && other.groupName == null )
+        if( this.groupName == null )
-            return true;
+            return other.groupName == null;
-        if( this.groupName == null && other.groupName != null )
-            return false;
         return this.groupName.equals(other.groupName);
     }
 

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

@@ -53,7 +53,7 @@ public abstract class ArgumentTypeDescriptor {
     /**
      * our log, which we want to capture anything from org.broadinstitute.sting
      */
-    protected static Logger logger = Logger.getLogger(ArgumentTypeDescriptor.class);
+    protected static final Logger logger = Logger.getLogger(ArgumentTypeDescriptor.class);
 
     /**
      * Fetch the given descriptor from the descriptor repository.

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

@@ -120,8 +120,8 @@ public abstract class ParsingMethod {
      */
     private static final String TAG_TEXT = "[\\w\\-\\.\\=]*";
 
-    public static ParsingMethod FullNameParsingMethod = new ParsingMethod(Pattern.compile(String.format("\\s*--(%1$s)(?:\\:(%2$s(?:,%2$s)*))?\\s*",ARGUMENT_TEXT,TAG_TEXT)),
+    public static final ParsingMethod FullNameParsingMethod = new ParsingMethod(Pattern.compile(String.format("\\s*--(%1$s)(?:\\:(%2$s(?:,%2$s)*))?\\s*",ARGUMENT_TEXT,TAG_TEXT)),
                                                                           ArgumentDefinitions.FullNameDefinitionMatcher) {};
-    public static ParsingMethod ShortNameParsingMethod = new ParsingMethod(Pattern.compile(String.format("\\s*-(%1$s)(?:\\:(%2$s(?:,%2$s)*))?\\s*",ARGUMENT_TEXT,TAG_TEXT)),
+    public static final ParsingMethod ShortNameParsingMethod = new ParsingMethod(Pattern.compile(String.format("\\s*-(%1$s)(?:\\:(%2$s(?:,%2$s)*))?\\s*",ARGUMENT_TEXT,TAG_TEXT)),
                                                                            ArgumentDefinitions.ShortNameDefinitionMatcher) {};
 }

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

@@ -233,10 +233,6 @@ public class GenomeAnalysisEngine {
         if (args.nonDeterministicRandomSeed)
             resetRandomGenerator(System.currentTimeMillis());
 
-        // TODO -- REMOVE ME WHEN WE STOP BCF testing
-        if ( args.USE_SLOW_GENOTYPES )
-            GenotypeBuilder.MAKE_FAST_BY_DEFAULT = false;
-
         // if the use specified an input BQSR recalibration table then enable on the fly recalibration
         if (args.BQSR_RECAL_FILE != null)
             setBaseRecalibration(args.BQSR_RECAL_FILE, args.quantizationLevels, args.disableIndelQuals, args.PRESERVE_QSCORES_LESS_THAN, args.emitOriginalQuals);
@@ -849,20 +845,9 @@ public class GenomeAnalysisEngine {
                                                                             SAMSequenceDictionary sequenceDictionary,
                                                                             GenomeLocParser genomeLocParser,
                                                                             ValidationExclusion.TYPE validationExclusionType) {
-        VCFHeader header = null;
+        final RMDTrackBuilder builder = new RMDTrackBuilder(sequenceDictionary,genomeLocParser, validationExclusionType);
-        if ( getArguments().repairVCFHeader != null ) {
-            try {
-                final PositionalBufferedStream pbs = new PositionalBufferedStream(new FileInputStream(getArguments().repairVCFHeader));
-                header = (VCFHeader)new VCFCodec().readHeader(pbs).getHeaderValue();
-                pbs.close();
-            } catch ( IOException e ) {
-                throw new UserException.CouldNotReadInputFile(getArguments().repairVCFHeader, e);
-            }
-        }
 
-        RMDTrackBuilder builder = new RMDTrackBuilder(sequenceDictionary,genomeLocParser, header, validationExclusionType);
+        final List<ReferenceOrderedDataSource> dataSources = new ArrayList<ReferenceOrderedDataSource>();
-
-        List<ReferenceOrderedDataSource> dataSources = new ArrayList<ReferenceOrderedDataSource>();
         for (RMDTriplet fileDescriptor : referenceMetaDataFiles)
             dataSources.add(new ReferenceOrderedDataSource(fileDescriptor,
                                                            builder,

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

@@ -379,19 +379,5 @@ public class GATKArgumentCollection {
     @Hidden
     public boolean generateShadowBCF = false;
     // TODO -- remove all code tagged with TODO -- remove me when argument generateShadowBCF is removed
-
-    @Argument(fullName="useSlowGenotypes",shortName = "useSlowGenotypes",doc="",required=false)
-    @Hidden
-    public boolean USE_SLOW_GENOTYPES = false;
-    // TODO -- remove all code tagged with TODO -- remove me when argument generateShadowBCF is removed
-
-    /**
-     * The file pointed to by this argument must be a VCF file. The GATK will read in just the header of this file
-     * and then use the INFO, FORMAT, and FILTER field values from this file to repair the header file of any other
-     * VCF file that GATK reads in.  This allows us to have in effect a master set of header records and use these
-     * to fill in any missing ones in input VCF files.
-     */
-    @Argument(fullName="repairVCFHeader", shortName = "repairVCFHeader", doc="If provided, whenever we read a VCF file we will use the header in this file to repair the header of the input VCF files", required=false)
-    public File repairVCFHeader = null;
 }
 

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

@@ -118,7 +118,7 @@ class WindowedData {
                 rec.getAlignmentStart(),
                 stop);
         states = new ArrayList<RMDDataState>();
-        if (provider != null && provider.getReferenceOrderedData() != null)
+        if (provider.getReferenceOrderedData() != null)
             for (ReferenceOrderedDataSource dataSource : provider.getReferenceOrderedData())
                 states.add(new RMDDataState(dataSource, dataSource.seek(range)));
     }

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

@@ -45,7 +45,6 @@ import org.broadinstitute.sting.utils.file.FileSystemInabilityToLockException;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Collections;
-import java.util.LinkedList;
 import java.util.List;
 
 /**
@@ -56,7 +55,7 @@ public class ReferenceDataSource {
     private IndexedFastaSequenceFile reference;
 
     /** our log, which we want to capture anything from this class */
-    protected static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(ReferenceDataSource.class);
+    protected static final org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(ReferenceDataSource.class);
 
     /**
      * Create reference data source from fasta file

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

@@ -58,7 +58,7 @@ import java.util.Collection;
 
 /** Shards and schedules data in manageable chunks. */
 public abstract class MicroScheduler implements MicroSchedulerMBean {
-    protected static Logger logger = Logger.getLogger(MicroScheduler.class);
+    protected static final Logger logger = Logger.getLogger(MicroScheduler.class);
 
     /**
      * Counts the number of instances of the class that are currently alive.

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

@@ -66,13 +66,13 @@ public class TreeReducer implements Callable {
      * @return Result of the reduce.
      */
     public Object call() {
-        Object result = null;
+        Object result;
 
         final long startTime = System.currentTimeMillis();
 
         try {
             if( lhs == null )
-                result = lhs.get();
+                result = null;
                 // todo -- what the hell is this above line?  Shouldn't it be the two below?
 //            if( lhs == null )
 //                throw new IllegalStateException(String.format("Insufficient data on which to reduce; lhs = %s, rhs = %s", lhs, rhs) );

public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java

@@ -119,7 +119,7 @@ public class ThreadLocalOutputTracker extends OutputTracker {
 
         try {
             tempFile = File.createTempFile( stub.getClass().getName(), null );
-            tempFile.deleteOnExit();
+            //tempFile.deleteOnExit();
         }
         catch( IOException ex ) {
             throw new UserException.BadTmpDir("Unable to create temporary file for stub: " + stub.getClass().getName() );

public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java

@@ -61,6 +61,7 @@ public class VariantContextWriterStorage implements Storage<VariantContextWriter
     protected final File file;
     protected OutputStream stream;
     protected final VariantContextWriter writer;
+    boolean closed = false;
 
     /**
      * Constructs an object which will write directly into the output file provided by the stub.
@@ -172,10 +173,13 @@ public class VariantContextWriterStorage implements Storage<VariantContextWriter
         if(file != null)
             logger.debug("Closing temporary file " + file.getAbsolutePath());
         writer.close();
+        closed = true;
     }
 
     public void mergeInto(VariantContextWriterStorage target) {
         try {
+            if ( ! closed )
+                throw new ReviewedStingException("Writer not closed, but we are merging into the file!");
             final String targetFilePath = target.file != null ? target.file.getAbsolutePath() : "/dev/stdin";
             logger.debug(String.format("Merging %s into %s",file.getAbsolutePath(),targetFilePath));
 
@@ -194,6 +198,9 @@ public class VariantContextWriterStorage implements Storage<VariantContextWriter
             }
 
             source.close();
+            file.delete(); // this should be last to aid in debugging when the process fails
+        } catch (UserException e) {
+            throw new ReviewedStingException("BUG: intermediate file " + file + " is malformed, got error while reading", e);
         } catch (IOException e) {
             throw new UserException.CouldNotReadInputFile(file, "Error reading file in VCFWriterStorage: ", e);
         }

public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java

@@ -47,6 +47,7 @@ import java.util.List;
 public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
     public static final String NO_HEADER_ARG_NAME = "no_cmdline_in_header";
     public static final String SITES_ONLY_ARG_NAME = "sites_only";
+    public static final String FORCE_BCF = "bcf";
     public static final HashSet<String> SUPPORTED_ZIPPED_SUFFIXES = new HashSet<String>();
 
     //
@@ -96,7 +97,11 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
 
     @Override
     public List<ArgumentDefinition> createArgumentDefinitions( ArgumentSource source ) {
-        return Arrays.asList( createDefaultArgumentDefinition(source), createNoCommandLineHeaderArgumentDefinition(),createSitesOnlyArgumentDefinition());
+        return Arrays.asList(
+                createDefaultArgumentDefinition(source),
+                createNoCommandLineHeaderArgumentDefinition(),
+                createSitesOnlyArgumentDefinition(),
+                createBCFArgumentDefinition() );
     }
 
     /**
@@ -117,7 +122,7 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
     public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source, Type type) {
         if(!source.isRequired())
             throw new ReviewedStingException("BUG: tried to create type default for argument type descriptor that can't support a type default.");        
-        VariantContextWriterStub stub = new VariantContextWriterStub(engine, defaultOutputStream, false, argumentSources, false, false);
+        VariantContextWriterStub stub = new VariantContextWriterStub(engine, defaultOutputStream, argumentSources);
         engine.addOutput(stub);
         return stub;
     }
@@ -141,15 +146,15 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
         if(writerFile == null && !source.isRequired())
             throw new MissingArgumentValueException(defaultArgumentDefinition);
 
-        // Should we compress the output stream?
-        boolean compress = isCompressed(writerFileName);
-
-        boolean skipWritingCmdLineHeader = argumentIsPresent(createNoCommandLineHeaderArgumentDefinition(),matches);
-        boolean doNotWriteGenotypes = argumentIsPresent(createSitesOnlyArgumentDefinition(),matches);
-
         // Create a stub for the given object.
-        VariantContextWriterStub stub = (writerFile != null) ? new VariantContextWriterStub(engine, writerFile, compress, argumentSources, skipWritingCmdLineHeader, doNotWriteGenotypes)
+        final VariantContextWriterStub stub = (writerFile != null)
-                                                  : new VariantContextWriterStub(engine, defaultOutputStream, compress, argumentSources, skipWritingCmdLineHeader, doNotWriteGenotypes);
+                ? new VariantContextWriterStub(engine, writerFile, argumentSources)
+                : new VariantContextWriterStub(engine, defaultOutputStream, argumentSources);
+
+        stub.setCompressed(isCompressed(writerFileName));
+        stub.setDoNotWriteGenotypes(argumentIsPresent(createSitesOnlyArgumentDefinition(),matches));
+        stub.setSkipWritingCommandLineHeader(argumentIsPresent(createNoCommandLineHeaderArgumentDefinition(),matches));
+        stub.setForceBCF(argumentIsPresent(createBCFArgumentDefinition(),matches));
 
         // WARNING: Side effects required by engine!
         parsingEngine.addTags(stub,getArgumentTags(matches));
@@ -159,8 +164,8 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
     }
 
     /**
-     * Creates the optional compression level argument for the BAM file.
+     * Creates the optional no_header argument for the VCF file.
-     * @return Argument definition for the BAM file itself.  Will not be null.
+     * @return Argument definition for the VCF file itself.  Will not be null.
      */
     private ArgumentDefinition createNoCommandLineHeaderArgumentDefinition() {
         return new ArgumentDefinition( ArgumentIOType.ARGUMENT,
@@ -179,8 +184,8 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
     }
 
     /**
-     * Creates the optional compression level argument for the BAM file.
+     * Creates the optional sites_only argument definition
-     * @return Argument definition for the BAM file itself.  Will not be null.
+     * @return Argument definition for the VCF file itself.  Will not be null.
      */
     private ArgumentDefinition createSitesOnlyArgumentDefinition() {
         return new ArgumentDefinition( ArgumentIOType.ARGUMENT,
@@ -198,6 +203,26 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
                                        null );
     }
 
+    /**
+     * Creates the optional bcf argument definition
+     * @return Argument definition for the VCF file itself.  Will not be null.
+     */
+    private ArgumentDefinition createBCFArgumentDefinition() {
+        return new ArgumentDefinition( ArgumentIOType.ARGUMENT,
+                boolean.class,
+                FORCE_BCF,
+                FORCE_BCF,
+                "force BCF output, regardless of the file's extension",
+                false,
+                true,
+                false,
+                true,
+                null,
+                null,
+                null,
+                null );
+    }
+
     /**
      * Returns true if the file will be compressed.
      * @param writerFileName Name of the file

public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java

@@ -79,7 +79,7 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
     /**
      * Should we emit a compressed output stream?
      */
-    private final boolean isCompressed;
+    private boolean isCompressed = false;
 
     /**
      * A hack: push the argument sources into the VCF header so that the VCF header
@@ -90,12 +90,17 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
     /**
      * Should the header be written out?  A hidden argument.
      */
-    private final boolean skipWritingCommandLineHeader;
+    private boolean skipWritingCommandLineHeader = false;
 
     /**
      * Should we not write genotypes even when provided?
      */
-    private final boolean doNotWriteGenotypes;
+    private boolean doNotWriteGenotypes = false;
+
+    /**
+     * Should we force BCF writing regardless of the file extension?
+     */
+    private boolean forceBCF = false;
 
     /**
      * Connects this stub with an external stream capable of serving the
@@ -108,19 +113,13 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
      *
      * @param engine engine.
      * @param genotypeFile  file to (ultimately) create.
-     * @param isCompressed  should we compress the output stream?
      * @param argumentSources sources.
-     * @param skipWritingCommandLineHeader skip writing header.
-     * @param doNotWriteGenotypes do not write genotypes.
      */
-    public VariantContextWriterStub(GenomeAnalysisEngine engine, File genotypeFile, boolean isCompressed, Collection<Object> argumentSources, boolean skipWritingCommandLineHeader, boolean doNotWriteGenotypes) {
+    public VariantContextWriterStub(GenomeAnalysisEngine engine, File genotypeFile, Collection<Object> argumentSources) {
         this.engine = engine;
         this.genotypeFile = genotypeFile;
         this.genotypeStream = null;
-        this.isCompressed = isCompressed;
         this.argumentSources = argumentSources;
-        this.skipWritingCommandLineHeader = skipWritingCommandLineHeader;
-        this.doNotWriteGenotypes = doNotWriteGenotypes;
     }
 
     /**
@@ -128,19 +127,13 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
      *
      * @param engine engine.
      * @param genotypeStream  stream to (ultimately) write.
-     * @param isCompressed  should we compress the output stream?
      * @param argumentSources sources.
-     * @param skipWritingCommandLineHeader skip writing header.
-     * @param doNotWriteGenotypes do not write genotypes.
      */
-    public VariantContextWriterStub(GenomeAnalysisEngine engine, OutputStream genotypeStream, boolean isCompressed, Collection<Object> argumentSources, boolean skipWritingCommandLineHeader, boolean doNotWriteGenotypes) {
+    public VariantContextWriterStub(GenomeAnalysisEngine engine, OutputStream genotypeStream, Collection<Object> argumentSources) {
         this.engine = engine;
         this.genotypeFile = null;
         this.genotypeStream = new PrintStream(genotypeStream);
-        this.isCompressed = isCompressed;
         this.argumentSources = argumentSources;
-        this.skipWritingCommandLineHeader = skipWritingCommandLineHeader;
-        this.doNotWriteGenotypes = doNotWriteGenotypes;
     }
 
     /**
@@ -167,6 +160,22 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
         return isCompressed;
     }
 
+    public void setCompressed(boolean compressed) {
+        isCompressed = compressed;
+    }
+
+    public void setSkipWritingCommandLineHeader(boolean skipWritingCommandLineHeader) {
+        this.skipWritingCommandLineHeader = skipWritingCommandLineHeader;
+    }
+
+    public void setDoNotWriteGenotypes(boolean doNotWriteGenotypes) {
+        this.doNotWriteGenotypes = doNotWriteGenotypes;
+    }
+
+    public void setForceBCF(boolean forceBCF) {
+        this.forceBCF = forceBCF;
+    }
+
     /**
      * Gets the master sequence dictionary from the engine associated with this stub
      * @link GenomeAnalysisEngine.getMasterSequenceDictionary
@@ -187,7 +196,7 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
         if ( engine.lenientVCFProcessing() ) options.add(Options.ALLOW_MISSING_FIELDS_IN_HEADER);
         if ( indexOnTheFly && ! isCompressed() ) options.add(Options.INDEX_ON_THE_FLY);
 
-        if ( getFile() != null && VariantContextWriterFactory.isBCFOutput(getFile()) )
+        if ( forceBCF || (getFile() != null && VariantContextWriterFactory.isBCFOutput(getFile())) )
             options.add(Options.FORCE_BCF);
 
         return options.isEmpty() ? EnumSet.noneOf(Options.class) : EnumSet.copyOf(options);

public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java

@@ -93,7 +93,7 @@ public class GATKRunReport {
     /**
      * our log
      */
-    protected static Logger logger = Logger.getLogger(GATKRunReport.class);
+    protected static final Logger logger = Logger.getLogger(GATKRunReport.class);
 
 
     @Element(required = false, name = "id")

public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java

@@ -85,18 +85,16 @@ public class FeatureManager  {
 
     private final PluginManager<FeatureCodec> pluginManager;
     private final Collection<FeatureDescriptor> featureDescriptors = new TreeSet<FeatureDescriptor>();
-    private final VCFHeader headerForRepairs;
     private final boolean lenientVCFProcessing;
 
     /**
      * Construct a FeatureManager without a master VCF header
      */
     public FeatureManager() {
-        this(null, false);
+        this(false);
     }
 
-    public FeatureManager(final VCFHeader headerForRepairs, final boolean lenientVCFProcessing) {
+    public FeatureManager(final boolean lenientVCFProcessing) {
-        this.headerForRepairs = headerForRepairs;
         this.lenientVCFProcessing = lenientVCFProcessing;
         pluginManager = new PluginManager<FeatureCodec>(FeatureCodec.class, "Codecs", "Codec");
 
@@ -255,8 +253,6 @@ public class FeatureManager  {
             ((NameAwareCodec)codex).setName(name);
         if ( codex instanceof ReferenceDependentFeatureCodec )
             ((ReferenceDependentFeatureCodec)codex).setGenomeLocParser(genomeLocParser);
-        if ( codex instanceof VCFCodec )
-            ((VCFCodec)codex).setHeaderForRepairs(headerForRepairs);
         if ( codex instanceof AbstractVCFCodec && lenientVCFProcessing )
             ((AbstractVCFCodec)codex).disableOnTheFlyModifications();
 

public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java

@@ -89,17 +89,15 @@ public class RMDTrackBuilder { // extends PluginManager<FeatureCodec> {
      * please talk through your approach with the SE team.
      * @param dict Sequence dictionary to use.
      * @param genomeLocParser Location parser to use.
-     * @param headerForRepairs a VCF header that should be used to repair VCF headers.  Can be null
      * @param validationExclusionType Types of validations to exclude, for sequence dictionary verification.
      */
     public RMDTrackBuilder(final SAMSequenceDictionary dict,
                            final GenomeLocParser genomeLocParser,
-                           final VCFHeader headerForRepairs,
                            ValidationExclusion.TYPE validationExclusionType) {
         this.dict = dict;
         this.validationExclusionType = validationExclusionType;
         this.genomeLocParser = genomeLocParser;
-        this.featureManager = new FeatureManager(headerForRepairs, GenomeAnalysisEngine.lenientVCFProcessing(validationExclusionType));
+        this.featureManager = new FeatureManager(GenomeAnalysisEngine.lenientVCFProcessing(validationExclusionType));
     }
 
     /**
@@ -111,18 +109,6 @@ public class RMDTrackBuilder { // extends PluginManager<FeatureCodec> {
         return featureManager;
     }
 
-    /**
-     * Same as full constructor but makes one without a header for repairs
-     * @param dict
-     * @param genomeLocParser
-     * @param validationExclusionType
-     */
-    public RMDTrackBuilder(final SAMSequenceDictionary dict,
-                           final GenomeLocParser genomeLocParser,
-                           ValidationExclusion.TYPE validationExclusionType) {
-        this(dict, genomeLocParser, null, validationExclusionType);
-    }
-
     /**
      * create a RMDTrack of the specified type
      *

public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java

@@ -92,7 +92,7 @@ public abstract class TraversalEngine<M,T,WalkerType extends Walker<M,T>,Provide
     GenomeLocSortedSet targetIntervals = null;
 
     /** our log, which we want to capture anything from this class */
-    protected static Logger logger = Logger.getLogger(TraversalEngine.class);
+    protected static final Logger logger = Logger.getLogger(TraversalEngine.class);
 
     protected GenomeAnalysisEngine engine;
 
@@ -354,7 +354,7 @@ public abstract class TraversalEngine<M,T,WalkerType extends Walker<M,T>,Provide
 
         synchronized(performanceLogLock) {
             // Ignore multiple calls to reset the same lock.
-            if(performanceLogFile != null && performanceLogFile.equals(fileName))
+            if(performanceLogFile != null && performanceLogFile.equals(file))
                 return;
 
             // Close an existing log

public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java

@@ -19,7 +19,7 @@ public class TraverseLoci<M,T> extends TraversalEngine<M,T,LocusWalker<M,T>,Locu
     /**
      * our log, which we want to capture anything from this class
      */
-    protected static Logger logger = Logger.getLogger(TraversalEngine.class);
+    protected static final Logger logger = Logger.getLogger(TraversalEngine.class);
 
     @Override
     protected String getTraversalType() {

public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java

@@ -24,7 +24,7 @@ import java.util.List;
 public class TraverseReadPairs<M,T> extends TraversalEngine<M,T, ReadPairWalker<M,T>,ReadShardDataProvider> {
 
     /** our log, which we want to capture anything from this class */
-    protected static Logger logger = Logger.getLogger(TraverseReadPairs.class);
+    protected static final Logger logger = Logger.getLogger(TraverseReadPairs.class);
 
     @Override
     protected String getTraversalType() {

public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java

@@ -51,7 +51,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
  */
 public class TraverseReads<M,T> extends TraversalEngine<M,T,ReadWalker<M,T>,ReadShardDataProvider> {    
     /** our log, which we want to capture anything from this class */
-    protected static Logger logger = Logger.getLogger(TraverseReads.class);
+    protected static final Logger logger = Logger.getLogger(TraverseReads.class);
 
     @Override
     protected String getTraversalType() {

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

@@ -72,8 +72,8 @@ public class TandemRepeatAnnotator extends InfoFieldAnnotation implements Standa
         return map;
     }
 
-    public static final String[] keyNames = {STR_PRESENT, REPEAT_UNIT_KEY,REPEATS_PER_ALLELE_KEY };
+    protected static final String[] keyNames = {STR_PRESENT, REPEAT_UNIT_KEY,REPEATS_PER_ALLELE_KEY };
-    public static final VCFInfoHeaderLine[] descriptions = {
+    protected static final VCFInfoHeaderLine[] descriptions = {
             new VCFInfoHeaderLine(STR_PRESENT, 0, VCFHeaderLineType.Flag, "Variant is a short tandem repeat"),
             new VCFInfoHeaderLine(REPEAT_UNIT_KEY, 1, VCFHeaderLineType.String, "Tandem repeat unit (bases)"),
             new VCFInfoHeaderLine(REPEATS_PER_ALLELE_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "Number of times tandem repeat unit is repeated, for each allele (including reference)") };

public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java

@@ -30,7 +30,6 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.GenomeLoc;
@@ -142,9 +141,6 @@ public class BeagleOutputToVCF extends RodWalker<Integer, Integer> {
         hInfo.add(new VCFFilterHeaderLine("BGL_RM_WAS_G", "This 'G' site was set to monomorphic by Beagle"));
         hInfo.add(new VCFFilterHeaderLine("BGL_RM_WAS_T", "This 'T' site was set to monomorphic by Beagle"));
 
-        // Open output file specified by output VCF ROD
-        final List<ReferenceOrderedDataSource> dataSources = this.getToolkit().getRodDataSources();
-
         if ( comp.isBound() ) {
             hInfo.add(new VCFInfoHeaderLine("ACH", 1, VCFHeaderLineType.Integer, "Allele Count from Comparison ROD at this site"));
             hInfo.add(new VCFInfoHeaderLine("ANH", 1, VCFHeaderLineType.Integer, "Allele Frequency from Comparison ROD at this site"));

public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java

@@ -351,7 +351,6 @@ public class ProduceBeagleInput extends RodWalker<Integer, Integer> {
     }
 
     public static class CachingFormatter {
-        private int maxCacheSize = 0;
         private String format;
         private LRUCache<Double, String> cache;
 
@@ -379,7 +378,6 @@ public class ProduceBeagleInput extends RodWalker<Integer, Integer> {
         }
 
         public CachingFormatter(String format, int maxCacheSize) {
-            this.maxCacheSize = maxCacheSize;
             this.format = format;
             this.cache = new LRUCache<Double, String>(maxCacheSize);
         }

public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java

@@ -78,9 +78,9 @@ public class FindCoveredIntervals extends ActiveRegionWalker<GenomeLoc, Long> {
     public Long reduce(final GenomeLoc value, Long reduce) {
         if (value != null) {
             out.println(value.toString());
-            return ++reduce;
+            reduce++;
-        } else
+        }
-            return reduce;
+        return reduce;
     }
 
     @Override

public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatistics.java

@@ -264,7 +264,7 @@ class SampleStatistics {
             return false;
 
         // different contigs
-        if (read.getMateReferenceIndex() != read.getReferenceIndex())
+        if (!read.getMateReferenceIndex().equals(read.getReferenceIndex()))
             return false;
 
         // unmapped

public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java

@@ -104,7 +104,9 @@ public class BAMDiffableReader implements DiffableReader {
             InputStream fstream = new BufferedInputStream(new FileInputStream(file));
             if ( !BlockCompressedInputStream.isValidFile(fstream) )
                 return false;
-            new BlockCompressedInputStream(fstream).read(buffer, 0, BAM_MAGIC.length);
+            final BlockCompressedInputStream BCIS = new BlockCompressedInputStream(fstream);
+            BCIS.read(buffer, 0, BAM_MAGIC.length);
+            BCIS.close();
             return Arrays.equals(buffer, BAM_MAGIC);
         } catch ( IOException e ) {
             return false;

public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java

@@ -224,7 +224,7 @@ public class DiffNode extends DiffValue {
         // X=(A=A B=B C=(D=D))
         String[] parts = tree.split("=", 2);
         if ( parts.length != 2 )
-            throw new ReviewedStingException("Unexpected tree structure: " + tree + " parts=" + parts);
+            throw new ReviewedStingException("Unexpected tree structure: " + tree);
         String name = parts[0];
         String value = parts[1];
 

public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java

@@ -90,8 +90,10 @@ public class GATKReportDiffableReader implements DiffableReader {
     public boolean canRead(File file) {
         try {
             final String HEADER = GATKReport.GATKREPORT_HEADER_PREFIX;
-            char[] buff = new char[HEADER.length()];
+            final char[] buff = new char[HEADER.length()];
-            new FileReader(file).read(buff, 0, HEADER.length());
+            final FileReader FR = new FileReader(file);
+            FR.read(buff, 0, HEADER.length());
+            FR.close();
             String firstLine = new String(buff);
             return firstLine.startsWith(HEADER);
         } catch (IOException e) {

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

@@ -188,7 +188,7 @@ public class UnifiedGenotyperEngine {
                 perReadAlleleLikelihoodMap.clear();
                 final Map<String, AlignmentContext> stratifiedContexts = getFilteredAndStratifiedContexts(UAC, refContext, rawContext, model);
                 if ( stratifiedContexts == null ) {
-                    results.add(UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ? generateEmptyContext(tracker, refContext, stratifiedContexts, rawContext) : null);
+                    results.add(UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ? generateEmptyContext(tracker, refContext, null, rawContext) : null);
                 }
                 else {
                     final VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, null, true, model, perReadAlleleLikelihoodMap);
@@ -207,7 +207,7 @@ public class UnifiedGenotyperEngine {
         final List<VariantCallContext> withAllSamples = new ArrayList<VariantCallContext>(calls.size());
         for ( final VariantCallContext call : calls ) {
             if ( call == null )
-                withAllSamples.add(call);
+                withAllSamples.add(null);
             else {
                 final VariantContext withoutMissing = VariantContextUtils.addMissingSamples(call, allSamples);
                 withAllSamples.add(new VariantCallContext(withoutMissing, call.confidentlyCalled, call.shouldEmit));
@@ -258,8 +258,7 @@ public class UnifiedGenotyperEngine {
     public VariantCallContext calculateGenotypes(final RefMetaDataTracker tracker,
                                                  final ReferenceContext refContext,
                                                  final AlignmentContext rawContext,
-                                                 final VariantContext vc,
+                                                 final VariantContext vc) {
-                                                 final Map<String,PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
         final List<GenotypeLikelihoodsCalculationModel.Model> models = getGLModelsToUse(tracker, refContext, rawContext);
         if ( models.isEmpty() ) {
             return null;
@@ -268,16 +267,21 @@ public class UnifiedGenotyperEngine {
         // return the first one
         final GenotypeLikelihoodsCalculationModel.Model model = models.get(0);
         final Map<String, AlignmentContext> stratifiedContexts = getFilteredAndStratifiedContexts(UAC, refContext, rawContext, model);
-        return calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model, perReadAlleleLikelihoodMap);
+        return calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model, null);
     }
 
-    public VariantCallContext calculateGenotypes(final RefMetaDataTracker tracker,
+    /**
-                                                 final ReferenceContext refContext,
+     * Compute genotypes at a given locus.
-                                                 final AlignmentContext rawContext,
+     *
-                                                 final VariantContext vc) {
+     * @param vc         the GL-annotated variant context
-        return calculateGenotypes(tracker, refContext, rawContext, vc, null);
+     * @return the VariantCallContext object
+     */
+    public VariantCallContext calculateGenotypes(VariantContext vc) {
+        return calculateGenotypes(null, null, null, null, vc, GenotypeLikelihoodsCalculationModel.Model.valueOf("SNP"), null);
     }
-        // ---------------------------------------------------------------------------------------------------------
+
+
+    // ---------------------------------------------------------------------------------------------------------
     //
     // Private implementation helpers
     //
@@ -684,10 +688,8 @@ public class UnifiedGenotyperEngine {
         // if we're genotyping given alleles and we have a requested SNP at this position, do SNP
         if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) {
             final VariantContext vcInput = getVCFromAllelesRod(tracker, refContext, rawContext.getLocation(), false, logger, UAC.alleles);
-            if ( vcInput == null ) {
+            if ( vcInput == null )
-                models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix+"SNP"));
                 return models;
-            }
 
             if ( vcInput.isSNP() )  {
                 // ignore SNPs if the user chose INDEL mode only

public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java

@@ -305,7 +305,7 @@ public class ConstrainedMateFixingManager {
     }
 
     public static boolean iSizeTooBigToMove(SAMRecord read, int maxInsertSizeForMovingReadPairs) {
-        return ( read.getReadPairedFlag() && ! read.getMateUnmappedFlag() && read.getReferenceName() != read.getMateReferenceName() ) // maps to different chromosomes
+        return ( read.getReadPairedFlag() && ! read.getMateUnmappedFlag() && !read.getReferenceName().equals(read.getMateReferenceName()) ) // maps to different chromosomes
                 || Math.abs(read.getInferredInsertSize()) > maxInsertSizeForMovingReadPairs;     // we won't try to move such a read
     }
 

public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java

@@ -645,7 +645,7 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
                                 bestChildGenotype.clear();
                                 bestChildGenotype.add(childGenotype.getKey());
                             }
-                            else if(configurationLikelihood == bestConfigurationLikelihood) {
+                            else if(MathUtils.compareDoubles(configurationLikelihood, bestConfigurationLikelihood) == 0) {
                                 bestFirstParentGenotype.add(firstParentGenotype.getKey());
                                 bestSecondParentGenotype.add(secondParentGenotype.getKey());
                                 bestChildGenotype.add(childGenotype.getKey());

public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java

@@ -86,7 +86,7 @@ class PreciseNonNegativeDouble implements Comparable<PreciseNonNegativeDouble> {
         if (Math.abs(logValDiff) <= EQUALS_THRESH)
             return 0; // this.equals(other)
 
-        return new Double(Math.signum(logValDiff)).intValue();
+        return (int)Math.signum(logValDiff);
     }
 
     public boolean equals(PreciseNonNegativeDouble other) {

public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java

@@ -870,7 +870,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
 
             int useOnLeft, useOnRight;
             if (numOnLeft <= numOnRight) {
-                int halfToUse = new Double(Math.floor(numToUse / 2.0)).intValue(); // skimp on the left [floor], and be generous with the right side
+                int halfToUse = numToUse / 2; // skimp on the left [floor], and be generous with the right side
                 useOnLeft = Math.min(halfToUse, numOnLeft);
                 useOnRight = Math.min(numToUse - useOnLeft, numOnRight);
             }

public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java

@@ -41,7 +41,7 @@ public class ThetaVariantEvaluator extends VariantEvaluator {
         ConcurrentMap<String, Integer> alleleCounts = new ConcurrentHashMap<String, Integer>();
 
         int numHetsHere = 0;
-        float numGenosHere = 0;
+        int numGenosHere = 0;
         int numIndsHere = 0;
 
         for (final Genotype genotype : vc.getGenotypes()) {
@@ -68,7 +68,7 @@ public class ThetaVariantEvaluator extends VariantEvaluator {
             //only if have one called genotype at least
             this.numSites++;
 
-            this.totalHet += numHetsHere / numGenosHere;
+            this.totalHet += numHetsHere / (double)numGenosHere;
 
             //compute based on num sites
             float harmonicFactor = 0;
@@ -79,7 +79,7 @@ public class ThetaVariantEvaluator extends VariantEvaluator {
 
             //now compute pairwise mismatches
             float numPairwise = 0;
-            float numDiffs = 0;
+            int numDiffs = 0;
             for (String allele1 : alleleCounts.keySet()) {
                 int allele1Count = alleleCounts.get(allele1);
 

public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java

@@ -19,6 +19,8 @@ import java.util.*;
  * it computes the AC from the genotypes themselves.  If no AC can be computed, 0 is used.
  */
 public class AlleleCount extends VariantStratifier {
+    int nchrom;
+
     @Override
     public void initialize() {
         // we can only work with a single eval VCF, and it must have genotypes
@@ -26,7 +28,8 @@ public class AlleleCount extends VariantStratifier {
             throw new UserException.BadArgumentValue("AlleleCount", "AlleleCount stratification only works with a single eval vcf");
 
         // There are 2 x n sample chromosomes for diploids
-        int nchrom = getVariantEvalWalker().getSampleNamesForEvaluation().size() * 2;
+        // TODO -- generalize to handle multiple ploidy
+        nchrom = getVariantEvalWalker().getSampleNamesForEvaluation().size() * 2;
         if ( nchrom < 2 )
             throw new UserException.BadArgumentValue("AlleleCount", "AlleleCount stratification requires an eval vcf with at least one sample");
 
@@ -52,8 +55,10 @@ public class AlleleCount extends VariantStratifier {
             }
 
             // make sure that the AC isn't invalid
-            if ( AC > eval.getCalledChrCount() )
+            if ( AC > nchrom )
-                throw new UserException.MalformedVCF(String.format("The AC or MLEAC value (%d) at position %s:%d is larger than the possible called chromosome count (%d)", AC, eval.getChr(), eval.getStart(), eval.getCalledChrCount()));
+                throw new UserException.MalformedVCF(String.format("The AC or MLEAC value (%d) at position %s:%d " +
+                        "is larger than the number of chromosomes over all samples (%d)", AC,
+                        eval.getChr(), eval.getStart(), nchrom));
 
             return Collections.singletonList((Object) AC);
         } else {

public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java

@@ -177,6 +177,7 @@ public class TrancheManager {
                 double runningValue = metric.getRunningMetric(i);
                 out.printf("%.4f %d %.4f%n", d.lod, score, runningValue);
             }
+            out.close();
         } catch (FileNotFoundException e) {
             throw new UserException.CouldNotCreateOutputFile(f, e);
         }

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java

@@ -31,7 +31,6 @@ import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgume
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.samples.Sample;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCounts;
@@ -311,10 +310,6 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
     private File rsIDFile = null;
 
 
-    @Hidden
-    @Argument(fullName="outMVFile", shortName="outMVFile", doc="", required=false)
-    private String outMVFile = null;
-
     @Hidden
     @Argument(fullName="fullyDecode", doc="If true, the incoming VariantContext will be fully decoded", required=false)
     private boolean fullyDecode = false;
@@ -369,8 +364,6 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
     private int positionToAdd = 0;
     private RandomVariantStructure [] variantArray;
 
-    private PrintStream outMVFileStream = null;
-
     //Random number generator for the genotypes to remove
     private Random randomGenotypes = new Random();
 
@@ -528,23 +521,6 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
             if (MENDELIAN_VIOLATIONS && mv.countViolations(this.getSampleDB().getFamilies(samples),vc) < 1)
                 break;
 
-            if (outMVFile != null){
-                for( String familyId : mv.getViolationFamilies()){
-                    for(Sample sample : this.getSampleDB().getFamily(familyId)){
-                        if(sample.getParents().size() > 0){
-                            outMVFileStream.format("MV@%s:%d. REF=%s, ALT=%s, AC=%d, momID=%s, dadID=%s, childID=%s, momG=%s, momGL=%s, dadG=%s, dadGL=%s, " +
-                                    "childG=%s childGL=%s\n",vc.getChr(), vc.getStart(),
-                                    vc.getReference().getDisplayString(), vc.getAlternateAllele(0).getDisplayString(),  vc.getCalledChrCount(vc.getAlternateAllele(0)),
-                                    sample.getMaternalID(), sample.getPaternalID(), sample.getID(),
-                                    vc.getGenotype(sample.getMaternalID()).toBriefString(), vc.getGenotype(sample.getMaternalID()).getLikelihoods().getAsString(),
-                                    vc.getGenotype(sample.getPaternalID()).toBriefString(), vc.getGenotype(sample.getPaternalID()).getLikelihoods().getAsString(),
-                                    vc.getGenotype(sample.getID()).toBriefString(),vc.getGenotype(sample.getID()).getLikelihoods().getAsString()  );
-
-                        }
-                    }
-                }
-            }
-
             if (DISCORDANCE_ONLY) {
                 Collection<VariantContext> compVCs = tracker.getValues(discordanceTrack, context.getLocation());
                 if (!isDiscordant(vc, compVCs))
@@ -568,7 +544,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
             VariantContext sub = subsetRecord(vc, EXCLUDE_NON_VARIANTS);
 
             if ( REGENOTYPE && sub.isPolymorphicInSamples() && hasPLs(sub) ) {
-                final VariantContextBuilder builder = new VariantContextBuilder(UG_engine.calculateGenotypes(null, ref, context, sub)).filters(sub.getFiltersMaybeNull());
+                final VariantContextBuilder builder = new VariantContextBuilder(UG_engine.calculateGenotypes(sub)).filters(sub.getFiltersMaybeNull());
                 addAnnotations(builder, sub);
                 sub = builder.make();
             }

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java

@@ -8,8 +8,6 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.R.RScriptExecutorException;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@@ -18,7 +16,6 @@ import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.text.XReadLines;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.io.*;
@@ -95,7 +92,6 @@ public class VariantsToBinaryPed extends RodWalker<Integer,Integer> {
         // write to the fam file, the first six columns of the standard ped file
         // first, load data from the input meta data file
         Map<String,Map<String,String>> metaValues = new HashMap<String,Map<String,String>>();
-        Set<String> samplesToUse = new HashSet<String>();
         logger.debug("Reading in metadata...");
         try {
             if ( metaDataFile.getAbsolutePath().endsWith(".fam") ) {
@@ -274,6 +270,7 @@ public class VariantsToBinaryPed extends RodWalker<Integer,Integer> {
                     inStream.read(readGenotypes);
                     outBed.write(readGenotypes);
                 }
+                inStream.close();
             } catch (IOException e) {
                 throw new ReviewedStingException("Error reading form temp file for input.",e);
             }

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java

@@ -372,7 +372,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
     // ----------------------------------------------------------------------------------------------------
 
     public static abstract class Getter { public abstract String get(VariantContext vc); }
-    public static Map<String, Getter> getters = new HashMap<String, Getter>();
+    public static final Map<String, Getter> getters = new HashMap<String, Getter>();
 
     static {
         // #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT

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

@@ -67,10 +67,10 @@ public class BaseUtils {
     public static final byte DELETION_INDEX = 4;
     public static final byte NO_CALL_INDEX = 5; // (this is 'N')
 
-    public static int gIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'G');
+    public static final int aIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'A');
-    public static int cIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'C');
+    public static final int cIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'C');
-    public static int aIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'A');
+    public static final int gIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'G');
-    public static int tIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'T');
+    public static final int tIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'T');
 
     /// In genetics, a transition is a mutation changing a purine to another purine nucleotide (A <-> G) or
     // a pyrimidine to another pyrimidine nucleotide (C <-> T).

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

@@ -199,9 +199,9 @@ public class MannWhitneyU {
         else if ( z > n ) { return 0.0; }
         else {
             if ( z > ((double) n) /2 ) {
-                return 1.0-1/((double)Arithmetic.factorial(n))*uniformSumHelper(z, (int) Math.floor(z), n, 0);
+                return 1.0-1/(Arithmetic.factorial(n))*uniformSumHelper(z, (int) Math.floor(z), n, 0);
             } else {
-                return 1/((double)Arithmetic.factorial(n))*uniformSumHelper(z, (int) Math.floor(z), n, 0);
+                return 1/(Arithmetic.factorial(n))*uniformSumHelper(z, (int) Math.floor(z), n, 0);
             }
         }
     }

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

@@ -789,7 +789,7 @@ public class MathUtils {
         for (byte v : vals) {
             sum += v;
         }
-        return (byte) Math.floor(sum / vals.length);
+        return (byte) (sum / vals.length);
     }
 
     public static double averageDouble(List<Double> vals) {
@@ -1066,7 +1066,6 @@ public class MathUtils {
         // the list is assumed *not* to be sorted
 
         final Comparable x = list.get(orderStat);
-        ListIterator iterator = list.listIterator();
         ArrayList lessThanX = new ArrayList();
         ArrayList equalToX = new ArrayList();
         ArrayList greaterThanX = new ArrayList();

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

@@ -377,59 +377,6 @@ public class SWPairwiseAlignment {
         return w_open+(k-1)*w_extend; // gap
     }
 
-    private void print(int[][] s) {
-        for ( int i = 0 ; i < s.length ; i++) {
-            for ( int j = 0; j < s[i].length ; j++ ) {
-                System.out.printf(" %4d",s[i][j]);
-            }
-            System.out.println();
-        }
-    }
-
-    private void print(double[][] s) {
-        for ( int i = 0 ; i < s.length ; i++) {
-            for ( int j = 0; j < s[i].length ; j++ ) {
-                System.out.printf(" %4g",s[i][j]);
-            }
-            System.out.println();
-        }
-    }
-
-    private void print(int[][] s, String a, String b) {
-
-        System.out.print("        ");
-        for ( int j = 1 ; j < s[0].length ; j++) System.out.printf(" %4c",b.charAt(j-1)) ;
-        System.out.println();
-
-        for ( int i = 0 ; i < s.length ; i++) {
-            if ( i > 0 ) System.out.print(a.charAt(i-1));
-            else System.out.print(' ');
-            System.out.print("  ");
-            for ( int j = 0; j < s[i].length ; j++ ) {
-                System.out.printf(" %4d",s[i][j]);
-            }
-            System.out.println();
-        }
-    }
-
-
-    private void print(double[][] s, String a, String b) {
-
-        System.out.print("");
-        for ( int j = 1 ; j < s[0].length ; j++) System.out.printf(" %4c",b.charAt(j-1)) ;
-        System.out.println();
-
-        for ( int i = 0 ; i < s.length ; i++) {
-            if ( i > 0 ) System.out.print(a.charAt(i-1));
-            else System.out.print(' ');
-            System.out.print("  ");
-            for ( int j = 0; j < s[i].length ; j++ ) {
-                System.out.printf(" %2.1f",s[i][j]);
-            }
-            System.out.println();
-        }
-    }
-
     private void print(double[] s, byte[] a, byte[] b) {
            int n = a.length+1;
            int m = b.length+1;

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

@@ -563,7 +563,6 @@ public class Utils {
         List<T> t = new ArrayList<T>(c.keySet());
         Collections.sort(t);
 
-        List<V> l = new ArrayList<V>();
         List<String> pairs = new ArrayList<String>();
         for ( T k : t ) {
             pairs.add(k + "=" + c.get(k));

public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java

@@ -51,7 +51,6 @@ import java.util.Map;
  */
 public final class BCF2Codec implements FeatureCodec<VariantContext> {
     final protected static Logger logger = Logger.getLogger(BCF2Codec.class);
-    private final static boolean FORBID_SYMBOLICS = false;
 
     private final static int ALLOWED_MAJOR_VERSION = 2;
     private final static int MIN_MINOR_VERSION = 1;
@@ -178,7 +177,7 @@ public final class BCF2Codec implements FeatureCodec<VariantContext> {
                 contigNames.add(contig.getID());
             }
         } else {
-            throw new UserException.MalformedBCF2("Didn't find any contig lines in BCF2 file header");
+            error("Didn't find any contig lines in BCF2 file header");
         }
 
         // create the string dictionary
@@ -271,7 +270,7 @@ public final class BCF2Codec implements FeatureCodec<VariantContext> {
         final int nSamples = nFormatSamples & 0x00FFFFF;
 
         if ( header.getNGenotypeSamples() != nSamples )
-            throw new UserException.MalformedBCF2("GATK currently doesn't support reading BCF2 files with " +
+            error("GATK currently doesn't support reading BCF2 files with " +
                     "different numbers of samples per record.  Saw " + header.getNGenotypeSamples() +
                     " samples in header but have a record with " + nSamples + " samples");
 
@@ -343,9 +342,6 @@ public final class BCF2Codec implements FeatureCodec<VariantContext> {
             if ( isRef ) ref = alleleBases;
 
             alleles.add(allele);
-
-            if ( FORBID_SYMBOLICS && allele.isSymbolic() )
-                throw new ReviewedStingException("LIMITATION: GATK BCF2 codec does not yet support symbolic alleles");
         }
         assert ref != null;
 
@@ -496,7 +492,7 @@ public final class BCF2Codec implements FeatureCodec<VariantContext> {
         return gtFieldDecoders.getDecoder(field);
     }
 
-    private final void error(final String message) throws RuntimeException {
+    private void error(final String message) throws RuntimeException {
         throw new UserException.MalformedBCF2(String.format("%s, at record %d with position %d:", message, recordNo, pos));
     }
 }

public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java

@@ -49,13 +49,6 @@ public class VCFCodec extends AbstractVCFCodec {
     // Our aim is to read in the records and convert to VariantContext as quickly as possible, relying on VariantContext to do the validation of any contradictory (or malformed) record parameters.
     public final static String VCF4_MAGIC_HEADER = "##fileformat=VCFv4";
 
-    /**
-     * A VCF header the contains master info/filter/format records that we use to 'fill in'
-     * any missing records from our input VCF header.  This allows us to repair headers on
-     * the fly
-     */
-    private VCFHeader headerForRepairs = null;
-
     /**
      * @param reader the line reader to take header lines from
      * @return the number of header lines
@@ -88,8 +81,6 @@ public class VCFCodec extends AbstractVCFCodec {
                     }
                     headerStrings.add(line);
                     super.parseHeaderFromLines(headerStrings, version);
-                    if ( headerForRepairs != null )
-                        this.header = repairHeader(this.header, headerForRepairs);
                     return this.header;
                 }
                 else {
@@ -103,24 +94,6 @@ public class VCFCodec extends AbstractVCFCodec {
         throw new TribbleException.InvalidHeader("We never saw the required CHROM header line (starting with one #) for the input VCF file");
     }
 
-    private final VCFHeader repairHeader(final VCFHeader readHeader, final VCFHeader masterHeader) {
-        final Set<VCFHeaderLine> lines = VCFUtils.smartMergeHeaders(Arrays.asList(readHeader, masterHeader), log);
-        return new VCFHeader(lines, readHeader.getGenotypeSamples());
-    }
-
-    /**
-     * Tells this VCFCodec to repair the incoming header files with the information in masterHeader
-     *
-     * @param headerForRepairs
-     */
-    public void setHeaderForRepairs(final VCFHeader headerForRepairs) {
-        if ( headerForRepairs != null )
-            log.info("Using master VCF header to repair missing files from incoming VCFs");
-        this.headerForRepairs = headerForRepairs;
-    }
-
-
-
     /**
      * parse the filter string, first checking to see if we already have parsed it in a previous attempt
      *

public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java

@@ -38,8 +38,8 @@ import java.util.Map;
  *         A class representing a key=value entry in the VCF header
  */
 public class VCFHeaderLine implements Comparable {
-    protected static boolean ALLOW_UNBOUND_DESCRIPTIONS = true;
+    protected static final boolean ALLOW_UNBOUND_DESCRIPTIONS = true;
-    protected static String UNBOUND_DESCRIPTION = "Not provided in original VCF header";
+    protected static final String UNBOUND_DESCRIPTION = "Not provided in original VCF header";
 
     private String mKey = null;
     private String mValue = null;
@@ -53,7 +53,7 @@ public class VCFHeaderLine implements Comparable {
      */
     public VCFHeaderLine(String key, String value) {
         if ( key == null )
-            throw new IllegalArgumentException("VCFHeaderLine: key cannot be null: key = " + key);
+            throw new IllegalArgumentException("VCFHeaderLine: key cannot be null");
         mKey = key;
         mValue = value;
     }

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

@@ -135,6 +135,7 @@ public class ForumAPIUtils {
                 System.out.println(line);
             }
 
+            br.close();
             httpClient.getConnectionManager().shutdown();
             return output;
 

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

@@ -584,20 +584,39 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
      * @return
      */
     @Requires("enumClass.isEnum()")
-    private List<Map<String, Object>> docForEnumArgument(Class enumClass) {
+    private List<Map<String, Object>> docForEnumArgument(final Class enumClass) {
-        ClassDoc doc = this.getDoclet().getClassDocForClass(enumClass);
+        final ClassDoc doc = this.getDoclet().getClassDocForClass(enumClass);
-        if (doc == null) //  || ! doc.isEnum() )
+        if ( doc == null )
-            throw new RuntimeException("Tried to get docs for enum " + enumClass + " but got instead: " + doc);
+            throw new RuntimeException("Tried to get docs for enum " + enumClass + " but got null instead");
 
-        List<Map<String, Object>> bindings = new ArrayList<Map<String, Object>>();
+        final Set<String> enumConstantFieldNames = enumConstantsNames(enumClass);
-        for (final FieldDoc field : doc.fields(false)) {
+
-            bindings.add(
+        final List<Map<String, Object>> bindings = new ArrayList<Map<String, Object>>();
-                    new HashMap<String, Object>() {{
+        for (final FieldDoc fieldDoc : doc.fields(false)) {
-                        put("name", field.name());
+            if (enumConstantFieldNames.contains(fieldDoc.name()) )
-                        put("summary", field.commentText());
+                bindings.add(
-                    }});
+                        new HashMap<String, Object>() {{
+                            put("name", fieldDoc.name());
+                            put("summary", fieldDoc.commentText());
+                        }});
         }
 
         return bindings;
     }
+
+    /**
+     * Returns the name of the fields that are enum constants according to reflection
+     *
+     * @return a non-null set of fields that are enum constants
+     */
+    private Set<String> enumConstantsNames(final Class enumClass) {
+        final Set<String> enumConstantFieldNames = new HashSet<String>();
+
+        for ( final Field field : enumClass.getFields() ) {
+            if ( field.isEnumConstant() )
+                enumConstantFieldNames.add(field.getName());
+        }
+
+        return enumConstantFieldNames;
+    }
 }

public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.utils.pileup;
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@@ -220,7 +221,7 @@ public class PileupElement implements Comparable<PileupElement> {
             if (isDeletion() && (offset + 1 >= read.getReadLength()) )  // deletion in the end of the read
                 throw new UserException.MalformedBAM(read, String.format("Adjacent I/D events in read %s -- cigar: %s", read.getReadName(), read.getCigarString()));
 
-            representativeCount = (isDeletion()) ? Math.round((read.getReducedCount(offset) + read.getReducedCount(offset + 1)) / 2) : read.getReducedCount(offset);
+            representativeCount = (isDeletion()) ? MathUtils.fastRound((read.getReducedCount(offset) + read.getReducedCount(offset + 1)) / 2.0) : read.getReducedCount(offset);
         }
         return representativeCount;
     }

public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java

@@ -94,8 +94,8 @@ public class RecalDatum {
      * @param reportedQuality
      */
     public RecalDatum(final long _numObservations, final long _numMismatches, final byte reportedQuality) {
-        if ( numObservations < 0 ) throw new IllegalArgumentException("numObservations < 0");
+        if ( _numObservations < 0 ) throw new IllegalArgumentException("numObservations < 0");
-        if ( numMismatches < 0 ) throw new IllegalArgumentException("numMismatches < 0");
+        if ( _numMismatches < 0 ) throw new IllegalArgumentException("numMismatches < 0");
         if ( reportedQuality < 0 ) throw new IllegalArgumentException("reportedQuality < 0");
 
         numObservations = _numObservations;

public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java

@@ -21,7 +21,7 @@ import java.util.Set;
  */
 public class RecalDatumNode<T extends RecalDatum> {
     private final static double SMALLEST_CHI2_PVALUE = 1e-300;
-    protected static Logger logger = Logger.getLogger(RecalDatumNode.class);
+    protected static final Logger logger = Logger.getLogger(RecalDatumNode.class);
 
     /**
      * fixedPenalty is this value if it's considered fixed

public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java

@@ -51,7 +51,7 @@ public class CycleCovariate implements StandardCovariate {
 
     private static final int MAXIMUM_CYCLE_VALUE = 1000;
     private static final int CUSHION_FOR_INDELS = 4;
-    private static String default_platform = null;
+    private String default_platform = null;
 
     private static final EnumSet<NGSPlatform> DISCRETE_CYCLE_PLATFORMS = EnumSet.of(NGSPlatform.ILLUMINA, NGSPlatform.SOLID, NGSPlatform.PACBIO, NGSPlatform.COMPLETE_GENOMICS);
     private static final EnumSet<NGSPlatform> FLOW_CYCLE_PLATFORMS = EnumSet.of(NGSPlatform.LS454, NGSPlatform.ION_TORRENT);

public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java

@@ -13,7 +13,7 @@ import org.broadinstitute.sting.utils.NGSPlatform;
  */
 public class GATKSAMReadGroupRecord extends SAMReadGroupRecord {
 
-    public static String LANE_TAG = "LN";
+    public static final String LANE_TAG = "LN";
     
     // the SAMReadGroupRecord data we're caching
     private String mSample = null;

public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java

@@ -53,8 +53,8 @@ public class ReadUtils {
     private ReadUtils() {
     }
 
-    private static int DEFAULT_ADAPTOR_SIZE = 100;
+    private static final int DEFAULT_ADAPTOR_SIZE = 100;
-    public static int CLIPPING_GOAL_NOT_REACHED = -1;
+    public static final int CLIPPING_GOAL_NOT_REACHED = -1;
 
     public static int getMeanRepresentativeReadCount(GATKSAMRecord read) {
         if (!read.isReducedRead())

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

@@ -172,7 +172,7 @@ public final class FastGenotype extends Genotype {
      * @param values
      * @return
      */
-    private final static boolean validADorPLField(final int[] values) {
+    private static boolean validADorPLField(final int[] values) {
         if ( values != null )
             for ( int v : values )
                 if ( v < 0 )

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

@@ -53,8 +53,6 @@ import java.util.*;
  */
 @Invariant({"alleles != null"})
 public final class GenotypeBuilder {
-    public static boolean MAKE_FAST_BY_DEFAULT = true;
-
     private String sampleName = null;
     private List<Allele> alleles = Collections.emptyList();
 
@@ -67,8 +65,6 @@ public final class GenotypeBuilder {
     private String filters = null;
     private int initialAttributeMapSize = 5;
 
-    private boolean useFast = MAKE_FAST_BY_DEFAULT;
-
     private final static Map<String, Object> NO_ATTRIBUTES =
             Collections.unmodifiableMap(new HashMap<String, Object>(0));
 
@@ -78,31 +74,22 @@ public final class GenotypeBuilder {
     //
     // -----------------------------------------------------------------
 
-    public final static Genotype create(final String sampleName, final List<Allele> alleles) {
+    public static Genotype create(final String sampleName, final List<Allele> alleles) {
         return new GenotypeBuilder(sampleName, alleles).make();
     }
 
-    public final static Genotype create(final String sampleName,
+    public static Genotype create(final String sampleName,
                                         final List<Allele> alleles,
                                         final Map<String, Object> attributes) {
         return new GenotypeBuilder(sampleName, alleles).attributes(attributes).make();
     }
 
-    protected final static Genotype create(final String sampleName,
+    protected static Genotype create(final String sampleName,
                                            final List<Allele> alleles,
                                            final double[] gls) {
         return new GenotypeBuilder(sampleName, alleles).PL(gls).make();
     }
 
-    public final static Genotype create(final String sampleName,
-                                        final List<Allele> alleles,
-                                        final double log10Perror,
-                                        final Map<String, Object> attributes) {
-        return new GenotypeBuilder(sampleName, alleles)
-                .GQ(log10Perror == SlowGenotype.NO_LOG10_PERROR ? -1 : (int)(log10Perror * -10))
-                .attributes(attributes).make();
-    }
-
     /**
      * Create a empty builder.  Both a sampleName and alleles must be provided
      * before trying to make a Genotype from this builder.
@@ -182,23 +169,8 @@ public final class GenotypeBuilder {
      */
     @Ensures({"result != null"})
     public Genotype make() {
-        if ( useFast ) {
+        final Map<String, Object> ea = extendedAttributes == null ? NO_ATTRIBUTES : extendedAttributes;
-            final Map<String, Object> ea = extendedAttributes == null ? NO_ATTRIBUTES : extendedAttributes;
+        return new FastGenotype(sampleName, alleles, isPhased, GQ, DP, AD, PL, filters, ea);
-            return new FastGenotype(sampleName, alleles, isPhased, GQ, DP, AD, PL, filters, ea);
-        } else {
-            final Map<String, Object> attributes = new LinkedHashMap<String, Object>();
-            if ( extendedAttributes != null ) attributes.putAll(extendedAttributes);
-            final double log10PError = GQ == -1 ? SlowGenotype.NO_LOG10_PERROR : (GQ == 0 ? 0 : GQ / -10.0);
-            if ( DP != -1 ) attributes.put(VCFConstants.DEPTH_KEY, DP);
-            if ( AD != null ) attributes.put(VCFConstants.GENOTYPE_ALLELE_DEPTHS, AD);
-            final double[] log10likelihoods = PL != null ? GenotypeLikelihoods.fromPLs(PL).getAsVector() : null;
-            return new SlowGenotype(sampleName, alleles, log10PError, filters, attributes, isPhased, log10likelihoods);
-        }
-    }
-
-    public GenotypeBuilder useFast(boolean useFast) {
-        this.useFast = useFast;
-        return this;
     }
 
     /**

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

@@ -401,7 +401,7 @@ public class GenotypeLikelihoods {
     }
 
     // An index conversion from the deprecated PL ordering to the new VCF-based ordering for up to 3 alternate alleles
-    protected static int[] PLindexConversion = new int[]{0, 1, 3, 6, 2, 4, 7, 5, 8, 9};
+    protected static final int[] PLindexConversion = new int[]{0, 1, 3, 6, 2, 4, 7, 5, 8, 9};
 
     /**
      * get the allele index pair for the given PL using the deprecated PL ordering:

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

@@ -1,193 +0,0 @@
-/*
- * Copyright (c) 2012, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.utils.variantcontext;
-
-
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-
-import java.util.*;
-
-/**
- * This class encompasses all the basic information about a genotype.  It is immutable.
- *
- * @author Mark DePristo
- */
-@Deprecated
-public class SlowGenotype extends Genotype {
-    protected CommonInfo commonInfo;
-    public final static double NO_LOG10_PERROR = CommonInfo.NO_LOG10_PERROR;
-    protected List<Allele> alleles = null;
-    protected boolean isPhased = false;
-
-    protected SlowGenotype(final String sampleName,
-                           final List<Allele> alleles,
-                           final double log10PError,
-                           final String filters,
-                           final Map<String, Object> attributes,
-                           final boolean isPhased,
-                           final double[] log10Likelihoods) {
-        super(sampleName, filters);
-
-        if ( alleles == null || alleles.isEmpty() )
-            this.alleles = Collections.emptyList();
-        else
-            this.alleles = Collections.unmodifiableList(alleles);
-        commonInfo = new CommonInfo(sampleName, log10PError, Collections.<String>emptySet(), attributes);
-        if ( log10Likelihoods != null )
-            commonInfo.putAttribute(VCFConstants.GENOTYPE_PL_KEY, GenotypeLikelihoods.fromLog10Likelihoods(log10Likelihoods));
-        this.isPhased = isPhased;
-        validate();
-    }
-
-    @Override public List<Allele> getAlleles() {
-        return alleles;
-    }
-
-    @Override public Allele getAllele(int i) {
-        if ( getType() == GenotypeType.UNAVAILABLE )
-            throw new ReviewedStingException("Requesting alleles for an UNAVAILABLE genotype");
-        return alleles.get(i);
-    }
-
-    @Override public boolean isPhased() { return isPhased; }
-
-    //
-    // Useful methods for getting genotype likelihoods for a genotype object, if present
-    //
-    @Override public boolean hasLikelihoods() {
-        return (commonInfo.hasAttribute(VCFConstants.GENOTYPE_PL_KEY) && !commonInfo.getAttribute(VCFConstants.GENOTYPE_PL_KEY).equals(VCFConstants.MISSING_VALUE_v4)) ||
-                (commonInfo.hasAttribute(VCFConstants.GENOTYPE_LIKELIHOODS_KEY) && !commonInfo.getAttribute(VCFConstants.GENOTYPE_LIKELIHOODS_KEY).equals(VCFConstants.MISSING_VALUE_v4));
-    }
-
-    @Override public GenotypeLikelihoods getLikelihoods() {
-        GenotypeLikelihoods x = getLikelihoods(VCFConstants.GENOTYPE_PL_KEY, true);
-        if ( x != null )
-            return x;
-        else {
-            x = getLikelihoods(VCFConstants.GENOTYPE_LIKELIHOODS_KEY, false);
-            return x;
-        }
-    }
-
-    private GenotypeLikelihoods getLikelihoods(String key, boolean asPL) {
-        Object x = commonInfo.getAttribute(key);
-        if ( x instanceof String ) {
-            if ( asPL )
-                return GenotypeLikelihoods.fromPLField((String)x);
-            else
-                return GenotypeLikelihoods.fromGLField((String)x);
-        }
-        else if ( x instanceof GenotypeLikelihoods ) return (GenotypeLikelihoods)x;
-        else return null;
-    }
-
-    private final void validate() {
-        if ( alleles.size() == 0) return;
-
-        for ( Allele allele : alleles ) {
-            if ( allele == null )
-                throw new IllegalArgumentException("BUG: allele cannot be null in Genotype");
-        }
-    }
-
-    // ---------------------------------------------------------------------------------------------------------
-    // 
-    // get routines to access context info fields
-    //
-    // ---------------------------------------------------------------------------------------------------------
-    @Override public boolean hasLog10PError()     { return commonInfo.hasLog10PError(); }
-    @Override public double getLog10PError()      { return commonInfo.getLog10PError(); }
-
-    @Override
-    public boolean hasExtendedAttribute(String key)     { return commonInfo.hasAttribute(key); }
-
-    @Override
-    public Object getExtendedAttribute(String key)      { return commonInfo.getAttribute(key); }
-
-    @Override
-    public Object getExtendedAttribute(String key, Object defaultValue) {
-        return commonInfo.getAttribute(key, defaultValue); 
-    }
-
-//    public String getAttributeAsString(String key, String defaultValue)   { return commonInfo.getAttributeAsString(key, defaultValue); }
-//    public int getAttributeAsInt(String key, int defaultValue)            { return commonInfo.getAttributeAsInt(key, defaultValue); }
-//    public double getAttributeAsDouble(String key, double  defaultValue)  { return commonInfo.getAttributeAsDouble(key, defaultValue); }
-//    public boolean getAttributeAsBoolean(String key, boolean  defaultValue)  { return commonInfo.getAttributeAsBoolean(key, defaultValue); }
-
-    @Override
-    public int[] getPL() {
-        return hasPL() ? getLikelihoods().getAsPLs() : null;
-    }
-
-    @Override
-    public boolean hasPL() {
-        return hasLikelihoods();
-    }
-
-    @Override
-    public int getDP() {
-        return commonInfo.getAttributeAsInt(VCFConstants.DEPTH_KEY, -1);
-    }
-
-    @Override
-    public boolean hasDP() {
-        return commonInfo.hasAttribute(VCFConstants.DEPTH_KEY);
-    }
-
-    @Override
-    public int[] getAD() {
-        if ( hasAD() ) {
-            return (int[])commonInfo.getAttribute(VCFConstants.GENOTYPE_ALLELE_DEPTHS);
-        } else
-            return null;
-    }
-
-    @Override
-    public boolean hasAD() {
-        return commonInfo.hasAttribute(VCFConstants.GENOTYPE_ALLELE_DEPTHS);
-    }
-
-    @Override
-    public int getGQ() {
-        if ( commonInfo.hasLog10PError() )
-            return (int)Math.round(commonInfo.getPhredScaledQual());
-        else
-            return -1;
-    }
-
-    @Override
-    public boolean hasGQ() {
-        return hasLog10PError();
-    }
-
-    @Override
-    public Map<String, Object> getExtendedAttributes() {
-        final Map<String, Object> ea = new LinkedHashMap<String, Object>(commonInfo.getAttributes());
-        for ( final String primary : FastGenotype.PRIMARY_KEYS )
-            ea.remove(primary);
-        return ea;
-    }
-}

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

@@ -730,7 +730,7 @@ public class VariantContextUtils {
                         vcList.remove(k);
                         // avoid having empty lists
                         if (vcList.size() == 0)
-                            mappedVCs.remove(vcList);
+                            mappedVCs.remove(type);
                         if ( !mappedVCs.containsKey(vc.getType()) )
                             mappedVCs.put(vc.getType(), new ArrayList<VariantContext>());
                         mappedVCs.get(vc.getType()).add(otherVC);

public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java

@@ -563,6 +563,6 @@ class VCFWriter extends IndexingVariantContextWriter {
                     + " at " + vc.getChr() + ":" + vc.getStart()
                     + " but this key isn't defined in the VCFHeader.  The GATK now requires all VCFs to have"
                     + " complete VCF headers by default.  This error can be disabled with the engine argument"
-                    + " -U LENIENT_VCF_PROCESSING or repair the VCF file header using repairVCFHeader");
+                    + " -U LENIENT_VCF_PROCESSING");
     }
 }

public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java

@@ -76,7 +76,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
 
     VRTest bcfTest = new VRTest(privateTestDir + "vqsr.bcf_test.snps.unfiltered.bcf",
             "a8ce3cd3dccafdf7d580bcce7d660a9a",  // tranches
-            "1cdf8c9ee77d91d1ba7f002573108bad",  // recal file
+            "74c10fc15f9739a938b7138909fbde04",  // recal file
             "62fda105e14b619a1c263855cf56af1d"); // cut VCF
 
     @DataProvider(name = "VRBCFTest")

public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java

@@ -148,7 +148,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("52cb2f150559ca1457e9df7ec153dbb452cb2f150559ca1457e9df7ec153dbb4")
+                Arrays.asList("52cb2f150559ca1457e9df7ec153dbb4")
         );
 
         executeTest("testRegenotype--" + testFile, spec);

public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java

@@ -92,7 +92,7 @@ public class VCFIntegrationTest extends WalkerTest {
 
     //
     //
-    // Tests to ensure that -U LENIENT_VCF_PROCESS and header repairs are working
+    // Tests to ensure that -U LENIENT_VCF_PROCESS
     //
     //
 
@@ -106,11 +106,6 @@ public class VCFIntegrationTest extends WalkerTest {
         runVCFWithoutHeaders("-U LENIENT_VCF_PROCESSING", "6de8cb7457154dd355aa55befb943f88", null, true);
     }
 
-    @Test
-    public void testPassingOnVCFWithoutHeadersRepairingHeaders() {
-        runVCFWithoutHeaders("-repairVCFHeader " + privateTestDir + "vcfexample2.justHeader.vcf", "ff61e9cad6653c7f93d82d391f7ecdcb", null, false);
-    }
-
     private void runVCFWithoutHeaders(final String moreArgs, final String expectedMD5, final Class expectedException, final boolean disableBCF) {
         final String testVCF = privateTestDir + "vcfexample2.noHeader.vcf";
         final String baseCommand = "-R " + b37KGReference