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

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

@@ -185,7 +185,7 @@ public class ArgumentSource {
      * @return A default value for the given type.
      */
     public Object createTypeDefault(ParsingEngine parsingEngine) {
-        return typeDescriptor.createTypeDefault(parsingEngine,this,field.getType());
+        return typeDescriptor.createTypeDefault(parsingEngine,this,field.getGenericType());
     }
 
     /**

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

@@ -96,12 +96,13 @@ public abstract class ArgumentTypeDescriptor {
 
     /**
      * Generates a default for the given type.
+     *
      * @param parsingEngine the parsing engine used to validate this argument type descriptor.
      * @param source Source of the command-line argument.
      * @param type Type of value to create, in case the command-line argument system wants influence.
      * @return A default value for the given type.
      */
-    public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source,Class<?> type) { throw new UnsupportedOperationException("Unable to create default for type " + getClass()); }
+    public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source, Type type) { throw new UnsupportedOperationException("Unable to create default for type " + getClass()); }
 
     /**
      * Given the given argument source and attributes, synthesize argument definitions for command-line arguments.
@@ -323,8 +324,9 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
     public boolean createsTypeDefault(ArgumentSource source) { return ! source.isRequired(); }
 
     @Override
-    public Object createTypeDefault(ParsingEngine parsingEngine, ArgumentSource source, Class<?> type) {
+    public Object createTypeDefault(ParsingEngine parsingEngine, ArgumentSource source, Type type) {
-        return RodBinding.makeUnbound((Class<? extends Feature>)type);
+        Class parameterType = getParameterizedTypeClass(type);
+        return RodBinding.makeUnbound((Class<? extends Feature>)parameterType);
     }
 
     @Override
@@ -646,7 +648,7 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor {
     }
 
     @Override
-    public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source,Class<?> type) {
+    public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source, Type type) {
         if(multiplexer == null || multiplexedIds == null)
             throw new ReviewedStingException("No multiplexed ids available");
 

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

@@ -364,7 +364,7 @@ public class ParsingEngine {
      */
     private void loadValueIntoObject( ArgumentSource source, Object instance, ArgumentMatches argumentMatches ) {
         // Nothing to load
-        if( argumentMatches.size() == 0 && !(source.createsTypeDefault() && source.isRequired()))
+        if( argumentMatches.size() == 0 && ! source.createsTypeDefault() )
             return;
 
         // Target instance into which to inject the value.

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

@@ -0,0 +1,82 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.examples;
+
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.ArgumentCollection;
+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.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
+
+/**
+ * [Short one sentence description of this walker]
+ *
+ * <p>
+ * [Functionality of this walker]
+ * </p>
+ *
+ * <h2>Input</h2>
+ * <p>
+ * [Input description]
+ * </p>
+ *
+ * <h2>Output</h2>
+ * <p>
+ * [Output description]
+ * </p>
+ *
+ * <h2>Examples</h2>
+ * <pre>
+ *    java
+ *      -jar GenomeAnalysisTK.jar
+ *      -T $WalkerName
+ *  </pre>
+ *
+ * @author Your Name
+ * @since Date created
+ */
+public class GATKDocsExample extends RodWalker<Integer, Integer> {
+    /**
+     * Put detailed documentation about the argument here.  No need to duplicate the summary information
+     * in doc annotation field, as that will be added before this text in the documentation page.
+     *
+     * Notes:
+     * <ul>
+     *     <li>This field can contain HTML as a normal javadoc</li>
+     *     <li>Don't include information about the default value, as gatkdocs adds this automatically</li>
+     *     <li>Try your best to describe in detail the behavior of the argument, as ultimately confusing
+     *          docs here will just result in user posts on the forum</li>
+     * </ul>
+     */
+    @Argument(fullName="full", shortName="short", doc="Brief summary of argument [~ 80 characters of text]", required=false)
+    private boolean myWalkerArgument = false;
+
+    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { return 0; }
+    public Integer reduceInit() { return 0; }
+    public Integer reduce(Integer value, Integer sum) { return value + sum; }
+    public void onTraversalDone(Integer result) { }
+}

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

@@ -75,12 +75,12 @@ public class OutputStreamArgumentTypeDescriptor extends ArgumentTypeDescriptor {
     }
 
     @Override
-    public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source,Class type) {
+    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.");
         OutputStreamStub stub = new OutputStreamStub(defaultOutputStream);
         engine.addOutput(stub);
-        return createInstanceOfClass(type,stub);        
+        return createInstanceOfClass((Class)type,stub);
     }
 
     @Override

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

@@ -99,7 +99,7 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
     }
 
     @Override
-    public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source,Class<?> type) {
+    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.");
         SAMFileWriterStub stub = new SAMFileWriterStub(engine,defaultOutputStream);

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

@@ -114,7 +114,7 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
     }
 
     @Override
-    public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source,Class<?> type) {
+    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.");        
         VCFWriterStub stub = new VCFWriterStub(engine, defaultOutputStream, false, argumentSources, false, false);

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

@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.apache.log4j.Logger;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -35,6 +36,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.Map;
 

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

@@ -321,7 +321,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
             haplotypeMap.clear();
 
             if (getAlleleListFromVCF) {
-                 for( final VariantContext vc_input : tracker.getValues(VariantContext.class, "alleles") ) {
+                 for( final VariantContext vc_input : tracker.getValues(UAC.alleles) ) {
                       if( vc_input != null &&
                               allowableTypes.contains(vc_input.getType()) &&
                               ref.getLocus().getStart() == vc_input.getStart()) {

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

@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.apache.log4j.Logger;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -57,13 +58,13 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
         useAlleleFromVCF = UAC.GenotypingMode == GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
     }
 
-    public static VariantContext getSNPVCFromAllelesRod(RefMetaDataTracker tracker, ReferenceContext ref, boolean requireSNP, Logger logger) {
+    public static VariantContext getSNPVCFromAllelesRod(RefMetaDataTracker tracker, ReferenceContext ref, boolean requireSNP, Logger logger, final RodBinding<VariantContext> allelesBinding) {
         if ( tracker == null || ref == null || logger == null )
             throw new ReviewedStingException("Bad arguments: tracker=" + tracker + " ref=" + ref + " logger=" + logger);
         VariantContext vc = null;
 
         // search for usable record
-        for( final VariantContext vc_input : tracker.getValues(VariantContext.class, "alleles", ref.getLocus()) ) {
+        for( final VariantContext vc_input : tracker.getValues(allelesBinding) ) {
             if ( vc_input != null && ! vc_input.isFiltered() && (! requireSNP || vc_input.isSNP() )) {
                 if ( vc == null ) {
                     vc = vc_input;
@@ -95,7 +96,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
         if ( alternateAlleleToUse != null ) {
             bestAlternateAllele = alternateAlleleToUse.getBases()[0];
         } else if ( useAlleleFromVCF ) {
-            VariantContext vc = getSNPVCFromAllelesRod(tracker, ref, true, logger);
+            VariantContext vc = getSNPVCFromAllelesRod(tracker, ref, true, logger, UAC.alleles);
 
             // ignore places where we don't have a variant
             if ( vc == null )

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

@@ -27,6 +27,9 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Hidden;
+import org.broadinstitute.sting.commandline.Input;
+import org.broadinstitute.sting.commandline.RodBinding;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
 
@@ -61,6 +64,11 @@ public class UnifiedArgumentCollection {
     @Argument(fullName = "computeSLOD", shortName = "sl", doc = "If provided, we will calculate the SLOD", required = false)
     public boolean COMPUTE_SLOD = false;
 
+    /**
+     * When the UnifiedGenotyper is put into GENOTYPE_GIVEN_ALLELES mode it will genotype the samples using only the alleles provide in this rod binding
+     */
+    @Input(fullName="alleles", shortName = "alleles", doc="The set of alleles at which to genotype when in GENOTYPE_MODE = GENOTYPE_GIVEN_ALLELES", required=false)
+    public RodBinding<VariantContext> alleles;
 
     // control the error modes
     @Hidden
@@ -168,6 +176,7 @@ public class UnifiedArgumentCollection {
         uac.OUTPUT_DEBUG_INDEL_INFO = OUTPUT_DEBUG_INDEL_INFO;
         uac.INDEL_HAPLOTYPE_SIZE = INDEL_HAPLOTYPE_SIZE;
         uac.DO_CONTEXT_DEPENDENT_PENALTIES = DO_CONTEXT_DEPENDENT_PENALTIES;
+        uac.alleles = alleles;
 
         uac.GET_GAP_PENALTIES_FROM_DATA = GET_GAP_PENALTIES_FROM_DATA;
         uac.INDEL_RECAL_FILE = INDEL_RECAL_FILE;

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

@@ -25,10 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
-import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.commandline.ArgumentCollection;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.DownsampleType;
 import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;

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

@@ -58,6 +58,7 @@ public class UnifiedGenotyperEngine {
 
     // the unified argument collection
     private final UnifiedArgumentCollection UAC;
+    public UnifiedArgumentCollection getUAC() { return UAC; }
 
     // the annotation engine
     private final VariantAnnotatorEngine annotationEngine;
@@ -232,7 +233,7 @@ public class UnifiedGenotyperEngine {
     private VariantCallContext generateEmptyContext(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, AlignmentContext rawContext) {
         VariantContext vc;
         if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) {
-            VariantContext vcInput = SNPGenotypeLikelihoodsCalculationModel.getSNPVCFromAllelesRod(tracker, ref, false, logger);
+            VariantContext vcInput = SNPGenotypeLikelihoodsCalculationModel.getSNPVCFromAllelesRod(tracker, ref, false, logger, UAC.alleles);
             if ( vcInput == null )
                 return null;
             vc = new VariantContext("UG_call", vcInput.getChr(), vcInput.getStart(), vcInput.getEnd(), vcInput.getAlleles());
@@ -630,7 +631,7 @@ public class UnifiedGenotyperEngine {
             // no extended event pileup
             // 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) {
-                VariantContext vcInput = SNPGenotypeLikelihoodsCalculationModel.getSNPVCFromAllelesRod(tracker, refContext, false, logger);
+                VariantContext vcInput = SNPGenotypeLikelihoodsCalculationModel.getSNPVCFromAllelesRod(tracker, refContext, false, logger, UAC.alleles);
                 if (vcInput == null)
                     return null;
 

public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java

@@ -25,15 +25,10 @@
 
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
-import org.broad.tribble.bed.BEDCodec;
+import org.broad.tribble.Feature;
-import org.broad.tribble.dbsnp.DbSNPCodec;
+import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.ArgumentCollection;
-import org.broadinstitute.sting.commandline.Gather;
-import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableReadFilter;
 import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -42,8 +37,6 @@ import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
-import org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
 import org.broadinstitute.sting.utils.collections.NestedHashMap;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -94,13 +87,18 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
     /////////////////////////////
     @ArgumentCollection private RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();
 
-    @Output
-    PrintStream out;
-
     /////////////////////////////
     // Command Line Arguments
     /////////////////////////////
-    @Output(fullName="recal_file", shortName="recalFile", required=true, doc="Filename for the outputted covariates table recalibration file")
+    /**
+     * This algorithm treats every reference mismatch as an indication of error. However, real genetic variation is expected to mismatch the reference,
+     * so it is critical that a database of known polymorphic sites is given to the tool in order to skip over those sites.
+     */
+    @Input(fullName="knownSites", shortName = "knownSites", doc="A database of known polymorphic sites to skip over in the recalibration algorithm", required=false)
+    public List<RodBinding<Feature>> knownSites = Collections.emptyList();
+    @Output
+    PrintStream out;
+    @Output(fullName="recal_file", shortName="recalFile", required=true, doc="Filename for the output covariates table recalibration file")
     @Gather(CountCovariatesGatherer.class)
     public PrintStream RECAL_FILE;
 
@@ -124,8 +122,8 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
     /////////////////////////////
     private final RecalDataManager dataManager = new RecalDataManager(); // Holds the data HashMap, mostly used by TableRecalibrationWalker to create collapsed data hashmaps
     private final ArrayList<Covariate> requestedCovariates = new ArrayList<Covariate>(); // A list to hold the covariate objects that were requested
-    private static final double DBSNP_VS_NOVEL_MISMATCH_RATE = 2.0;        // rate at which dbSNP sites (on an individual level) mismatch relative to novel sites (determined by looking at NA12878)
+    private static final double DBSNP_VS_NOVEL_MISMATCH_RATE = 2.0;      // rate at which dbSNP sites (on an individual level) mismatch relative to novel sites (determined by looking at NA12878)
-    private static int DBSNP_VALIDATION_CHECK_FREQUENCY = 1000000;                // how often to validate dbsnp mismatch rate (in terms of loci seen)
+    private static int DBSNP_VALIDATION_CHECK_FREQUENCY = 1000000;       // how often to validate dbsnp mismatch rate (in terms of loci seen)
 
     public static class CountedData {
         private long countedSites = 0; // Number of loci used in the calculations, used for reporting in the output file
@@ -136,7 +134,7 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
 
         private long dbSNPCountsMM = 0, dbSNPCountsBases = 0;  // mismatch/base counts for dbSNP loci
         private long novelCountsMM = 0, novelCountsBases = 0;  // mismatch/base counts for non-dbSNP loci
-        private int lociSinceLastDbsnpCheck = 0;                               // loci since last dbsnp validation
+        private int lociSinceLastDbsnpCheck = 0;               // loci since last dbsnp validation
 
         /**
          * Adds the values of other to this, returning this
@@ -190,20 +188,8 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
         }
 
         // Warn the user if no dbSNP file or other variant mask was specified
-        boolean foundDBSNP = false;
+        if( knownSites.isEmpty() && !RUN_WITHOUT_DBSNP ) {
-        for( ReferenceOrderedDataSource rod : this.getToolkit().getRodDataSources() ) {
+            throw new UserException.CommandLineException("This calculation is critically dependent on being able to skip over known variant sites. Please provide a VCF file containing known sites of genetic variation.");
-            if( rod != null ) {
-                if( rod.getType().equals(DbSNPCodec.class) ||
-                        rod.getType().equals(VCFCodec.class) ||
-                        rod.getType().equals(VCF3Codec.class) ||
-                        rod.getType().equals(BEDCodec.class) ) {
-                    foundDBSNP = true;
-                    break;
-                }
-            }
-        }
-        if( !foundDBSNP && !RUN_WITHOUT_DBSNP ) {
-            throw new UserException.CommandLineException("This calculation is critically dependent on being able to skip over known variant sites. Please provide a dbSNP ROD or a VCF file containing known sites of genetic variation.");
         }
 
         // Initialize the requested covariates by parsing the -cov argument
@@ -266,12 +252,6 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
             logger.info( "\t" + cov.getClass().getSimpleName() );
             cov.initialize( RAC ); // Initialize any covariate member variables using the shared argument collection
         }
-
-//        try {
-//            stream = new PrintStream( RAC.RECAL_FILE );
-//        } catch ( FileNotFoundException e ) {
-//            throw new RuntimeException( "Couldn't open output file: ", e );
-//        }
     }
 
 
@@ -290,16 +270,13 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
      * @return Returns 1, but this value isn't used in the reduce step
      */
     public CountedData map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
-        // If any ROD covers this site then we assume it is a site of known genetic variation and we skip it
-        boolean isSNP = tracker.getNTracksWithBoundFeatures() > 0;
-        
         // Only use data from non-dbsnp sites
         // Assume every mismatch at a non-dbsnp site is indicative of poor quality
         CountedData counter = new CountedData();
-        if( !isSNP ) {
+        if( tracker.getValues(knownSites).size() == 0 ) { // If something here is in one of the knownSites tracks then skip over it, otherwise proceed
             // For each read at this locus
-            for( PileupElement p : context.getBasePileup() ) {
+            for( final PileupElement p : context.getBasePileup() ) {
-                GATKSAMRecord gatkRead = (GATKSAMRecord) p.getRead();
+                final GATKSAMRecord gatkRead = (GATKSAMRecord) p.getRead();
                 int offset = p.getOffset();
 
                 if( gatkRead.containsTemporaryAttribute( SKIP_RECORD_ATTRIBUTE  ) ) {
@@ -358,8 +335,6 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
         return counter;
     }
 
-
-
    /**
      * Update the mismatch / total_base counts for a given class of loci.
      *

public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java

@@ -93,8 +93,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
 
     @Output(doc="The output BAM file", required=true)
     private StingSAMFileWriter OUTPUT_BAM = null;
-    @Argument(fullName="preserve_qscores_less_than", shortName="pQ",
+    @Argument(fullName="preserve_qscores_less_than", shortName="pQ", doc="Bases with quality scores less than this threshold won't be recalibrated, default=5. In general it's unsafe to change qualities scores below < 5, since base callers use these values to indicate random or bad bases", required=false)
-        doc="Bases with quality scores less than this threshold won't be recalibrated, default=5. In general it's unsafe to change qualities scores below < 5, since base callers use these values to indicate random or bad bases", required=false)
     private int PRESERVE_QSCORES_LESS_THAN = 5;
     @Argument(fullName="smoothing", shortName="sm", required = false, doc="Number of imaginary counts to add to each bin in order to smooth out bins with few data points, default=1")
     private int SMOOTHING = 1;

public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java

@@ -632,8 +632,8 @@ public class ParsingEngineUnitTest extends BaseTest {
     // --------------------------------------------------------------------------------
 
     private class SingleRodBindingArgProvider {
-        @Input(fullName="binding", shortName="V", required=false)
+        @Input(fullName="binding", shortName="V", required=true)
-        public RodBinding<Feature> binding = RodBinding.makeUnbound(Feature.class);
+        public RodBinding<Feature> binding;
     }
 
     @Test
@@ -656,7 +656,7 @@ public class ParsingEngineUnitTest extends BaseTest {
 
     private class ShortNameOnlyRodBindingArgProvider {
         @Input(shortName="short", required=false)
-        public RodBinding<Feature> binding = RodBinding.makeUnbound(Feature.class);
+        public RodBinding<Feature> binding; // = RodBinding.makeUnbound(Feature.class);
     }
 
     @Test
@@ -677,22 +677,38 @@ public class ParsingEngineUnitTest extends BaseTest {
         Assert.assertEquals(argProvider.binding.getTags().getPositionalTags().size(), 1, "Tags aren't correctly set");
     }
 
+    private class OptionalRodBindingArgProvider {
+        @Input(fullName="binding", shortName="V", required=false)
+        public RodBinding<Feature> binding;
+
+        @Input(fullName="bindingNull", shortName="VN", required=false)
+        public RodBinding<VariantContext> bindingNull = null;
+    }
+
     @Test
-    public void unbasicRodBindingArgumentTest() {
+    public void optionalRodBindingArgumentTest() {
         final String[] commandLine = new String[] {};
 
-        parsingEngine.addArgumentSource( SingleRodBindingArgProvider.class );
+        parsingEngine.addArgumentSource( OptionalRodBindingArgProvider.class );
         parsingEngine.parse( commandLine );
         parsingEngine.validate();
 
-        SingleRodBindingArgProvider argProvider = new SingleRodBindingArgProvider();
+        OptionalRodBindingArgProvider argProvider = new OptionalRodBindingArgProvider();
         parsingEngine.loadArgumentsIntoObject( argProvider );
 
+        Assert.assertNotNull(argProvider.binding, "Default value not applied corrected to RodBinding");
         Assert.assertEquals(argProvider.binding.getName(), RodBinding.UNBOUND_VARIABLE_NAME, "Name isn't set properly");
         Assert.assertEquals(argProvider.binding.getSource(), RodBinding.UNBOUND_SOURCE, "Source isn't set to its expected value");
         Assert.assertEquals(argProvider.binding.getType(), Feature.class, "Type isn't set to its expected value");
         Assert.assertEquals(argProvider.binding.isBound(), false, "Bound() isn't returning its expected value");
         Assert.assertEquals(argProvider.binding.getTags().getPositionalTags().size(), 0, "Tags aren't correctly set");
+
+        Assert.assertNotNull(argProvider.bindingNull, "Default value not applied corrected to RodBinding");
+        Assert.assertEquals(argProvider.bindingNull.getName(), RodBinding.UNBOUND_VARIABLE_NAME, "Name isn't set properly");
+        Assert.assertEquals(argProvider.bindingNull.getSource(), RodBinding.UNBOUND_SOURCE, "Source isn't set to its expected value");
+        Assert.assertEquals(argProvider.bindingNull.getType(), VariantContext.class, "Type isn't set to its expected value");
+        Assert.assertEquals(argProvider.bindingNull.isBound(), false, "Bound() isn't returning its expected value");
+        Assert.assertEquals(argProvider.bindingNull.getTags().getPositionalTags().size(), 0, "Tags aren't correctly set");
     }
 
     @Test(expectedExceptions = UserException.class)

public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java

@@ -45,7 +45,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
         GenomeAnalysisEngine.resetRandomGenerator();
 
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
-                baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,050,000", 1,
+                baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,050,000", 1,
                 Arrays.asList(md5));
         executeTest("test MultiSample Pilot2 with alleles passed in", spec2);       
     }
@@ -53,12 +53,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testWithAllelesPassedIn() {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
-                baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
+                baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
                 Arrays.asList("811ddc0bd8322b14f14f58df8c627aa9"));
         executeTest("test MultiSample Pilot2 with alleles passed in", spec1);
 
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
-                baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
+                baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
                 Arrays.asList("5cf08dd7ac3d218082f7be3915ce0b15"));
         executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2);
     }
@@ -286,13 +286,13 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testWithIndelAllelesPassedIn() {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
-                baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
+                baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
                 Arrays.asList("69b0b3f089c80b9864294d838a061336"));
         executeTest("test MultiSample Pilot2 indels with alleles passed in", spec1);
 
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
-                baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf "
+                baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
                         + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
                 Arrays.asList("c90174cfd7dd68bdef36fe2c60145e10"));

public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java

@@ -54,7 +54,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
-                        " -B:dbsnp,vcf " + b36dbSNP129 +
+                        " -knownSites " + b36dbSNP129 +
                         " -T CountCovariates" +
                         " -I " + bam +
                         ( bam.equals( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" )
@@ -135,7 +135,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
                             " -standard" +
                             " -OQ" +
                             " -recalFile %s" +
-                            " -B:dbsnp,vcf " + b36dbSNP129,
+                            " -knownSites " + b36dbSNP129,
                     1, // just one output file
                     Arrays.asList(md5));
             executeTest("testCountCovariatesUseOriginalQuals", spec);
@@ -182,7 +182,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
 
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                     "-R " + b36KGReference +
-                            " -B:dbsnp,vcf " + b36dbSNP129 +
+                            " -knownSites " + b36dbSNP129 +
                             " -T CountCovariates" +
                             " -I " + bam +
                             " -standard" +
@@ -225,30 +225,6 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
         }
     }
 
-    @Test
-    public void testCountCovariatesVCF() {
-        HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "170f0c3cc4b8d72c539136effeec9a16");
-
-        for ( Map.Entry<String, String> entry : e.entrySet() ) {
-            String bam = entry.getKey();
-            String md5 = entry.getValue();
-
-            WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                    "-R " + b36KGReference +
-                            " -B:dbsnp,VCF3 " + validationDataLocation + "vcfexample3.vcf" +
-                            " -T CountCovariates" +
-                            " -I " + bam +
-                            " -L 1:10,000,000-10,200,000" +
-                            " -standard" +
-                            " --solid_recal_mode SET_Q_ZERO" +
-                            " -recalFile %s",
-                    1, // just one output file
-                    Arrays.asList(md5));
-            executeTest("testCountCovariatesVCF", spec);
-        }
-    }
-
     @Test
     public void testCountCovariatesBED() {
         HashMap<String, String> e = new HashMap<String, String>();
@@ -260,7 +236,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
 
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                     "-R " + b36KGReference +
-                            " -B:bed,bed " + validationDataLocation + "recalibrationTest.bed" +
+                            " -knownSites:bed " + validationDataLocation + "recalibrationTest.bed" +
                             " -T CountCovariates" +
                             " -I " + bam +
                             " -L 1:10,000,000-10,200,000" +
@@ -284,10 +260,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
 
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                     "-R " + b36KGReference +
-                            " -B:anyNameABCD,VCF3 " + validationDataLocation + "vcfexample3.vcf" +
+                            " -knownSites:anyNameABCD,VCF3 " + validationDataLocation + "vcfexample3.vcf" +
                             " -T CountCovariates" +
                             " -I " + bam +
-                            " -B:dbsnp,vcf " + b36dbSNP129 +
+                            " -knownSites " + b36dbSNP129 +
                             " -L 1:10,000,000-10,200,000" +
                             " -cov ReadGroupCovariate" +
                             " -cov QualityScoreCovariate" +
@@ -312,7 +288,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
 
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                     "-R " + b36KGReference +
-                            " -B:dbsnp,vcf " + b36dbSNP129 +
+                            " -knownSites " + b36dbSNP129 +
                             " -T CountCovariates" +
                             " -I " + bam +
                             " -cov ReadGroupCovariate" +