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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
This commit is contained in:
ebanks 2010-08-23 17:49:37 +00:00
parent 35b9883dd6
commit 55a8306a0d
14 changed files with 15 additions and 27 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java
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@ -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

3
java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
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@ -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)

3
java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
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@ -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

3
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java
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@ -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();

4
java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java
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@ -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;

3
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
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@ -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;

3
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
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@ -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;

3
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -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;

5
java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java
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@ -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) {

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java
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@ -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> {

3
java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java
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@ -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> {

3
java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java
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@ -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";

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java
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@ -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)

3
java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java
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@ -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;