Update the @RMD tags to look for VariantContext.class instead of ReferenceOrderedDatum.class. Since the test for rod type is broken this won't affect anything right now.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4084 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -47,7 +47,7 @@ import java.io.PrintStream;
 /**
  * Converts variants from other file formats to VCF format.
  */
-@Requires(value={},referenceMetaData=@RMD(name=VariantsToVCF.INPUT_ROD_NAME,type= ReferenceOrderedDatum.class))
+@Requires(value={},referenceMetaData=@RMD(name=VariantsToVCF.INPUT_ROD_NAME, type=VariantContext.class))
 @Reference(window=@Window(start=0,stop=40))
 public class VariantsToVCF extends RodWalker<Integer, Integer> {
     @Output

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

@@ -32,7 +32,6 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationType;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
@@ -52,7 +51,7 @@ import java.io.PrintStream;
 /**
  * Annotates variant calls with context information.  Users can specify which of the available annotations to use.
  */
-@Requires(value={},referenceMetaData=@RMD(name="variant",type=ReferenceOrderedDatum.class))
+@Requires(value={},referenceMetaData=@RMD(name="variant",type=VariantContext.class))
 @Allows(value={DataSource.READS, DataSource.REFERENCE})
 @Reference(window=@Window(start=-50,stop=50))
 @By(DataSource.REFERENCE)

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

@@ -33,7 +33,6 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.commandline.Argument;
@@ -48,7 +47,7 @@ import java.io.PrintStream;
 /**
  * Filters variant calls using a number of user-selectable, parameterizable criteria.
  */
-@Requires(value={},referenceMetaData=@RMD(name="variant", type=ReferenceOrderedDatum.class))
+@Requires(value={},referenceMetaData=@RMD(name="variant", type=VariantContext.class))
 @Reference(window=@Window(start=-50,stop=50))
 public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
     @Output

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java

@@ -29,7 +29,6 @@ import org.broad.tribble.vcf.VCFWriter;
 import org.broadinstitute.sting.gatk.contexts.*;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
@@ -51,7 +50,7 @@ import net.sf.samtools.SAMReadGroupRecord;
  */
 @Reference(window=@Window(start=-20,stop=20))
 @By(DataSource.REFERENCE)
-@Requires(value={},referenceMetaData=@RMD(name="trigger", type=ReferenceOrderedData.class))
+@Requires(value={},referenceMetaData=@RMD(name="trigger", type=VariantContext.class))
 public class BatchedCallsMerger extends LocusWalker<VariantContext, Integer> implements TreeReducible<Integer> {
     @ArgumentCollection private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
 

java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java

@@ -28,13 +28,13 @@ package org.broadinstitute.sting.gatk.walkers.sequenom;
 import org.broad.tribble.util.variantcontext.Allele;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broad.tribble.vcf.*;
+import org.broad.tribble.Feature;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.PlinkRod;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
@@ -48,7 +48,7 @@ import java.io.PrintStream;
  * Converts Sequenom files to a VCF annotated with QC metrics (HW-equilibrium, % failed probes)
  */
 @Reference(window=@Window(start=0,stop=40))
-@Requires(value={},referenceMetaData=@RMD(name="sequenom",type= ReferenceOrderedDatum.class))
+@Requires(value={},referenceMetaData=@RMD(name="sequenom",type= Feature.class))
 public class SequenomValidationConverter extends RodWalker<Pair<VariantContext, Byte>,Integer> {
     @Output
     protected PrintStream out;

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

@@ -30,7 +30,6 @@ import org.broad.tribble.vcf.VCFWriter;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -43,7 +42,7 @@ import java.io.PrintStream;
 /**
  * Filters a lifted-over VCF file for ref bases that have been changed.
  */
-@Requires(value={},referenceMetaData=@RMD(name="variant",type= ReferenceOrderedDatum.class))
+@Requires(value={},referenceMetaData=@RMD(name="variant",type= VariantContext.class))
 public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
     @Output
     PrintStream out;

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

@@ -33,7 +33,6 @@ import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -52,7 +51,7 @@ import net.sf.samtools.SAMFileReader;
 /**
  * Lifts a VCF file over from one build to another.  Note that the resulting VCF could be mis-sorted.
  */
-@Requires(value={},referenceMetaData=@RMD(name="variant", type=ReferenceOrderedDatum.class))
+@Requires(value={},referenceMetaData=@RMD(name="variant", type=VariantContext.class))
 public class LiftoverVariants extends RodWalker<Integer, Integer> {
     @Output
     protected PrintStream out;

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

@@ -36,7 +36,6 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.walkers.RMD;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
@@ -55,7 +54,7 @@ import java.io.FileNotFoundException;
  * 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={},referenceMetaData=@RMD(name="variant", type=ReferenceOrderedDatum.class))
+@Requires(value={},referenceMetaData=@RMD(name="variant", type=VariantContext.class))
 public class SelectVariants extends RodWalker<Integer, Integer> {
     @Output
     private PrintStream out;

java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java

@@ -45,7 +45,6 @@ import java.util.*;
  * Produces an input file to Beagle imputation engine, listing genotype likelihoods for each sample in input VCF file
  * @help.summary Produces an input file to Beagle imputation engine, listing genotype likelihoods for each sample in input VCF file
  */
-//@Requires(value={},referenceMetaData=@RMD(name=BeagleOutputByDepthWalker.INPUT_EVAL_ROD_NAME,type= VCFRecord.class))
 public class BeagleOutputByDepthWalker extends RodWalker<Integer, Integer> {
 
 
@@ -54,8 +53,6 @@ public class BeagleOutputByDepthWalker extends RodWalker<Integer, Integer> {
     public static final String INPUT_HAPMAP_ROD_NAME = "hapmap";
     public static final String INPUT_COMP_ROD_NAME = "comp";
 
-    private boolean newLine = true;
-
     @Output
     public PrintStream out;
 
@@ -87,7 +84,7 @@ public class BeagleOutputByDepthWalker extends RodWalker<Integer, Integer> {
                 return 0;
 
             Map<String, Genotype> compGenotypes = vc_comp.getGenotypes();
-            Integer alleleCountH = 0, chrCountH = 0, alleleCountEmp=0, chrCountEmp=0;
+            Integer alleleCountH = 0, chrCountH = 0, alleleCountEmp=0, chrCountEmp;
 
             // Get Hapmap AC and AF
             if (vc_hapmap != null) {

java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java

@@ -36,7 +36,7 @@ import org.broad.tribble.util.variantcontext.VariantContext;
 import java.util.*;
 
 @By(DataSource.READS)
-@Requires(value={},referenceMetaData=@RMD(name="indels", type=ReferenceOrderedDatum.class))
+@Requires(value={},referenceMetaData=@RMD(name="indels", type=VariantContext.class))
 // walker to count reads that are and are not consistent with homozygous indels
 public class IndelConsistencyReadCounter extends ReadWalker<Integer, Integer> {
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java

@@ -36,7 +36,6 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.*;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.features.beagle.BeagleFeature;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.RMD;
@@ -54,7 +53,7 @@ import static java.lang.Math.log10;
 /**
  * Takes files produced by Beagle imputation engine and creates a vcf with modified annotations.
  */
-@Requires(value={},referenceMetaData=@RMD(name=BeagleOutputToVCFWalker.INPUT_ROD_NAME, type=ReferenceOrderedDatum.class))
+@Requires(value={},referenceMetaData=@RMD(name=BeagleOutputToVCFWalker.INPUT_ROD_NAME, type=VariantContext.class))
 
 public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java

@@ -34,7 +34,6 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.RMD;
 import org.broadinstitute.sting.gatk.walkers.Requires;
@@ -48,7 +47,7 @@ import java.util.*;
 /**
  * Produces an input file to Beagle imputation engine, listing genotype likelihoods for each sample in input variant file
  */
-@Requires(value={},referenceMetaData=@RMD(name=ProduceBeagleInputWalker.ROD_NAME, type=ReferenceOrderedDatum.class))
+@Requires(value={},referenceMetaData=@RMD(name=ProduceBeagleInputWalker.ROD_NAME, type=VariantContext.class))
 public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
 
     public static final String ROD_NAME = "variant";

java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java

@@ -72,7 +72,7 @@ import org.broadinstitute.sting.utils.vcf.VCFUtils;
  *
  * For details, see:  http://www.broadinstitute.org/gsa/wiki/index.php/GenomicAnnotator
  */
-//@Requires(value={DataSource.READS, DataSource.REFERENCE},referenceMetaData=@RMD(name="variant",type=VariationRod.class))
+//@Requires(value={DataSource.READS, DataSource.REFERENCE},referenceMetaData=@RMD(name="variant",type=VariantContext.class))
 //@Allows(value={DataSource.READS, DataSource.REFERENCE})
 //@Reference(window=@Window(start=-50,stop=50))
 @By(DataSource.REFERENCE)

java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java

@@ -29,7 +29,6 @@ import org.broad.tribble.util.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.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
@@ -43,7 +42,7 @@ import java.io.PrintStream;
  * Computes the density of SNPs passing and failing filters in intervals on the genome and emits a table for display
  */
 @By(DataSource.REFERENCE)
-@Requires(value={},referenceMetaData=@RMD(name="eval",type=ReferenceOrderedDatum.class))
+@Requires(value={},referenceMetaData=@RMD(name="eval",type=VariantContext.class))
 public class SNPDensity extends RefWalker<Pair<VariantContext, GenomeLoc>, SNPDensity.Counter> {
     @Output
     private PrintStream out;