Moving more tools over to use the standard VC arg collection. Also, while I'm in there, I removed all of the empty references to @Requires given that it's no longer relevant.

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

@@ -50,7 +50,6 @@ import java.util.*;
 /**
  * Annotates variant calls with context information.  Users can specify which of the available annotations to use.
  */
-@Requires(value={})
 @Allows(value={DataSource.READS, DataSource.REFERENCE})
 @Reference(window=@Window(start=-50,stop=50))
 @By(DataSource.REFERENCE)

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

@@ -32,7 +32,6 @@ 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.refdata.features.beagle.BeagleFeature;
-import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
@@ -50,7 +49,6 @@ import static java.lang.Math.log10;
 /**
  * Takes files produced by Beagle imputation engine and creates a vcf with modified annotations.
  */
-@Requires(value={})
 public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
 
     @ArgumentCollection

public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.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.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VQSRCalibrationCurve;
 import org.broadinstitute.sting.utils.GenomeLoc;
@@ -51,7 +50,6 @@ import java.util.*;
 /**
  * Produces an input file to Beagle imputation engine, listing genotype likelihoods for each sample in input variant file
  */
-@Requires(value={})
 public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
 
     @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();

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

@@ -32,7 +32,6 @@ import org.broadinstitute.sting.commandline.RodBinding;
 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.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
@@ -55,7 +54,6 @@ import java.util.Set;
  * in input variant file.  Will additional hold back a fraction of the sites for evaluation, marking the
  * genotypes at that sites as missing, and writing the truth of these sites to a second VCF file
  */
-@Requires(value={})
 public class VariantsToBeagleUnphasedWalker extends RodWalker<Integer, Integer> {
     @Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
     public RodBinding<VariantContext> variants;

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

@@ -29,7 +29,6 @@ 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.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 
 import java.io.File;
@@ -131,7 +130,6 @@ import java.util.List;
  * @author Mark DePristo
  * @since 7/4/11
  */
-@Requires(value={})
 public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
     /**
      * Writes out a file of the DiffEngine format:

public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java

@@ -46,7 +46,6 @@ import java.util.*;
 /**
  * Filters variant calls using a number of user-selectable, parameterizable criteria.
  */
-@Requires(value={})
 @Reference(window=@Window(start=-50,stop=50))
 public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
 

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

@@ -49,7 +49,6 @@ import java.util.TreeSet;
  * the name 'allele' so we know which alternate allele to use at each site.
  */
 @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_INPUT)
-@Requires(value={})
 @Reference(window=@Window(start=-200,stop=200))
 @By(DataSource.READS)
 @Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=250)

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

@@ -24,9 +24,9 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broadinstitute.sting.commandline.Input;
+import org.broadinstitute.sting.commandline.ArgumentCollection;
 import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.commandline.RodBinding;
+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;
@@ -46,10 +46,10 @@ import java.util.Set;
  * Filters a lifted-over VCF file for ref bases that have been changed.
  */
 @Reference(window=@Window(start=0,stop=100))
-@Requires(value={})
 public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
-    @Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
+
-    public RodBinding<VariantContext> variants;
+    @ArgumentCollection
+    protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
 
     private static final int MAX_VARIANT_SIZE = 100;
 
@@ -59,10 +59,11 @@ public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
     private long failedLocs = 0, totalLocs = 0;
 
     public void initialize() {
-        Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getName()));
+        String trackName = variantCollection.variants.getName();
-        Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(variants.getName()));
+        Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName));
+        Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));
 
-        final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey(variants.getName()) ? vcfHeaders.get(variants.getName()).getMetaData() : null, samples);
+        final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey(trackName) ? vcfHeaders.get(trackName).getMetaData() : null, samples);
         writer.writeHeader(vcfHeader);
     }
 
@@ -89,7 +90,7 @@ public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
         if ( tracker == null )
             return 0;
 
-        Collection<VariantContext> VCs = tracker.getValues(variants, context.getLocation());
+        Collection<VariantContext> VCs = tracker.getValues(variantCollection.variants, context.getLocation());
         for ( VariantContext vc : VCs )
             filterAndWrite(ref.getBases(), vc);
 

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

@@ -48,7 +48,6 @@ import java.util.*;
  * Left-aligns indels from a variants file.
  */
 @Reference(window=@Window(start=-200,stop=200))
-@Requires(value={})
 public class LeftAlignVariants extends RodWalker<Integer, Integer> {
 
     @ArgumentCollection

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

@@ -34,7 +34,6 @@ 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.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
@@ -48,7 +47,6 @@ import java.util.*;
 /**
  * Lifts a VCF file over from one build to another.  Note that the resulting VCF could be mis-sorted.
  */
-@Requires(value={})
 public class LiftoverVariants extends RodWalker<Integer, Integer> {
 
     @ArgumentCollection

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

@@ -24,15 +24,12 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.commandline.Input;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+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.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
@@ -45,10 +42,10 @@ import java.util.*;
 /**
  * Takes a VCF file, randomly splits variants into two different sets, and outputs 2 new VCFs with the results.
  */
-@Requires(value={})
 public class RandomlySplitVariants extends RodWalker<Integer, Integer> {
-    @Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
+
-    public RodBinding<VariantContext> variants;
+    @ArgumentCollection
+    protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
 
     @Output(fullName="out1", shortName="o1", doc="File #1 to which variants should be written", required=true)
     protected VCFWriter vcfWriter1 = null;
@@ -72,7 +69,7 @@ public class RandomlySplitVariants extends RodWalker<Integer, Integer> {
         iFraction = (int)(fraction * 1000.0);
 
         // setup the header info
-        final List<String> inputNames = Arrays.asList(variants.getName());
+        final List<String> inputNames = Arrays.asList(variantCollection.variants.getName());
         Set<String> samples = SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames);
         Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
         hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames));
@@ -94,7 +91,7 @@ public class RandomlySplitVariants extends RodWalker<Integer, Integer> {
         if ( tracker == null )
             return 0;
 
-        Collection<VariantContext> vcs = tracker.getValues(variants, context.getLocation());
+        Collection<VariantContext> vcs = tracker.getValues(variantCollection.variants, context.getLocation());
         for ( VariantContext vc : vcs ) {
             int random = GenomeAnalysisEngine.getRandomGenerator().nextInt(1000);
             if ( random < iFraction )

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

@@ -38,7 +38,6 @@ 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.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
@@ -54,7 +53,6 @@ import java.util.*;
  * Takes a VCF file, selects variants based on sample(s) in which it was found and/or on various annotation criteria,
  * recompute the value of certain annotations based on the new sample set, and output a new VCF with the results.
  */
-@Requires(value={})
 public class SelectVariants extends RodWalker<Integer, Integer> {
     /**
      * The VCF file we are selecting variants from.

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

@@ -50,7 +50,6 @@ import java.util.Set;
  * Validates a variants file.
  */
 @Reference(window=@Window(start=0,stop=100))
-@Requires(value={})
 public class ValidateVariants extends RodWalker<Integer, Integer> {
 
     @ArgumentCollection

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

@@ -36,7 +36,6 @@ import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
@@ -47,7 +46,6 @@ import java.util.*;
  * Converts Sequenom files to a VCF annotated with QC metrics (HW-equilibrium, % failed probes)
  */
 @Reference(window=@Window(start=0,stop=40))
-@Requires(value={})
 public class VariantValidationAssessor extends RodWalker<VariantContext,Integer> {
     @Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
     public RodBinding<VariantContext> variants;

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

@@ -31,7 +31,6 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 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.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -43,7 +42,6 @@ import java.util.*;
 /**
  * Emits specific fields as dictated by the user from one or more VCF files.
  */
-@Requires(value={})
 public class VariantsToTable extends RodWalker<Integer, Integer> {
 
     @ArgumentCollection

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

@@ -56,7 +56,6 @@ import java.util.*;
 /**
  * Converts variants from other file formats to VCF format.
  */
-@Requires(value={})
 @Reference(window=@Window(start=-40,stop=40))
 public class VariantsToVCF extends RodWalker<Integer, Integer> {
 

public/java/test/org/broadinstitute/sting/gatk/WalkerManagerUnitTest.java

@@ -26,7 +26,6 @@ package org.broadinstitute.sting.gatk;
 
 import org.testng.Assert;
 import org.broadinstitute.sting.commandline.Hidden;
-import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
@@ -64,7 +63,6 @@ public class WalkerManagerUnitTest {
 }
 
 @Hidden
-@Requires(value={})
 class UninstantiableWalker extends Walker<Integer,Long> {
     // Private constructor will generate uninstantiable message
     private UninstantiableWalker() {}