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.
This commit is contained in:
Eric Banks
parent
c884b6bf1f
commit
a42f90db11
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@ -50,7 +50,6 @@ import java.util.*;
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/**
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* Annotates variant calls with context information. Users can specify which of the available annotations to use.
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*/
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@Requires(value={})
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@Allows(value={DataSource.READS, DataSource.REFERENCE})
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@Reference(window=@Window(start=-50,stop=50))
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@By(DataSource.REFERENCE)
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@ -32,7 +32,6 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.refdata.features.beagle.BeagleFeature;
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import org.broadinstitute.sting.gatk.walkers.Requires;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.SampleUtils;
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@ -50,7 +49,6 @@ import static java.lang.Math.log10;
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/**
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* Takes files produced by Beagle imputation engine and creates a vcf with modified annotations.
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*/
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@Requires(value={})
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public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
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@ArgumentCollection
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@ -31,7 +31,6 @@ import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgume
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.Requires;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VQSRCalibrationCurve;
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import org.broadinstitute.sting.utils.GenomeLoc;
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@ -51,7 +50,6 @@ import java.util.*;
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/**
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* Produces an input file to Beagle imputation engine, listing genotype likelihoods for each sample in input variant file
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*/
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@Requires(value={})
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public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
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@ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
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@ -32,7 +32,6 @@ import org.broadinstitute.sting.commandline.RodBinding;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.Requires;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.SampleUtils;
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@ -55,7 +54,6 @@ import java.util.Set;
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* in input variant file. Will additional hold back a fraction of the sites for evaluation, marking the
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* genotypes at that sites as missing, and writing the truth of these sites to a second VCF file
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*/
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@Requires(value={})
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public class VariantsToBeagleUnphasedWalker extends RodWalker<Integer, Integer> {
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@Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
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public RodBinding<VariantContext> variants;
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@ -29,7 +29,6 @@ import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.Requires;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import java.io.File;
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@ -131,7 +130,6 @@ import java.util.List;
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* @author Mark DePristo
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* @since 7/4/11
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*/
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@Requires(value={})
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public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
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/**
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* Writes out a file of the DiffEngine format:
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@ -46,7 +46,6 @@ import java.util.*;
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/**
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* Filters variant calls using a number of user-selectable, parameterizable criteria.
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*/
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@Requires(value={})
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@Reference(window=@Window(start=-50,stop=50))
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public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
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@ -49,7 +49,6 @@ import java.util.TreeSet;
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* the name 'allele' so we know which alternate allele to use at each site.
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*/
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@BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_INPUT)
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@Requires(value={})
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@Reference(window=@Window(start=-200,stop=200))
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@By(DataSource.READS)
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@Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=250)
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@ -24,9 +24,9 @@
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package org.broadinstitute.sting.gatk.walkers.variantutils;
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import org.broadinstitute.sting.commandline.Input;
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import org.broadinstitute.sting.commandline.ArgumentCollection;
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import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.commandline.RodBinding;
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import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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@ -46,10 +46,10 @@ import java.util.Set;
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* Filters a lifted-over VCF file for ref bases that have been changed.
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*/
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@Reference(window=@Window(start=0,stop=100))
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@Requires(value={})
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public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
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@Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
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public RodBinding<VariantContext> variants;
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@ArgumentCollection
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protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
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private static final int MAX_VARIANT_SIZE = 100;
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@ -59,10 +59,11 @@ public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
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private long failedLocs = 0, totalLocs = 0;
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public void initialize() {
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Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getName()));
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Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(variants.getName()));
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String trackName = variantCollection.variants.getName();
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Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName));
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Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));
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final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey(variants.getName()) ? vcfHeaders.get(variants.getName()).getMetaData() : null, samples);
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final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey(trackName) ? vcfHeaders.get(trackName).getMetaData() : null, samples);
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writer.writeHeader(vcfHeader);
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}
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@ -89,7 +90,7 @@ public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
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if ( tracker == null )
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return 0;
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Collection<VariantContext> VCs = tracker.getValues(variants, context.getLocation());
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Collection<VariantContext> VCs = tracker.getValues(variantCollection.variants, context.getLocation());
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for ( VariantContext vc : VCs )
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filterAndWrite(ref.getBases(), vc);
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@ -48,7 +48,6 @@ import java.util.*;
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* Left-aligns indels from a variants file.
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*/
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@Reference(window=@Window(start=-200,stop=200))
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@Requires(value={})
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public class LeftAlignVariants extends RodWalker<Integer, Integer> {
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@ArgumentCollection
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@ -34,7 +34,6 @@ import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgume
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.Requires;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.codecs.vcf.*;
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@ -48,7 +47,6 @@ import java.util.*;
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/**
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* Lifts a VCF file over from one build to another. Note that the resulting VCF could be mis-sorted.
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*/
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@Requires(value={})
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public class LiftoverVariants extends RodWalker<Integer, Integer> {
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@ArgumentCollection
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@ -24,15 +24,12 @@
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package org.broadinstitute.sting.gatk.walkers.variantutils;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.commandline.Input;
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import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.commandline.RodBinding;
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import org.broadinstitute.sting.commandline.*;
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import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
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import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.Requires;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.codecs.vcf.*;
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@ -45,10 +42,10 @@ import java.util.*;
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/**
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* Takes a VCF file, randomly splits variants into two different sets, and outputs 2 new VCFs with the results.
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*/
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@Requires(value={})
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public class RandomlySplitVariants extends RodWalker<Integer, Integer> {
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@Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
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public RodBinding<VariantContext> variants;
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@ArgumentCollection
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protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
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@Output(fullName="out1", shortName="o1", doc="File #1 to which variants should be written", required=true)
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protected VCFWriter vcfWriter1 = null;
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@ -72,7 +69,7 @@ public class RandomlySplitVariants extends RodWalker<Integer, Integer> {
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iFraction = (int)(fraction * 1000.0);
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// setup the header info
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final List<String> inputNames = Arrays.asList(variants.getName());
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final List<String> inputNames = Arrays.asList(variantCollection.variants.getName());
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Set<String> samples = SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames);
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Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
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hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames));
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@ -94,7 +91,7 @@ public class RandomlySplitVariants extends RodWalker<Integer, Integer> {
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if ( tracker == null )
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return 0;
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Collection<VariantContext> vcs = tracker.getValues(variants, context.getLocation());
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Collection<VariantContext> vcs = tracker.getValues(variantCollection.variants, context.getLocation());
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for ( VariantContext vc : vcs ) {
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int random = GenomeAnalysisEngine.getRandomGenerator().nextInt(1000);
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if ( random < iFraction )
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@ -38,7 +38,6 @@ import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.Requires;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.variantcontext.Allele;
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@ -54,7 +53,6 @@ import java.util.*;
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* Takes a VCF file, selects variants based on sample(s) in which it was found and/or on various annotation criteria,
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* recompute the value of certain annotations based on the new sample set, and output a new VCF with the results.
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*/
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@Requires(value={})
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public class SelectVariants extends RodWalker<Integer, Integer> {
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/**
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* The VCF file we are selecting variants from.
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@ -50,7 +50,6 @@ import java.util.Set;
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* Validates a variants file.
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*/
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@Reference(window=@Window(start=0,stop=100))
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@Requires(value={})
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public class ValidateVariants extends RodWalker<Integer, Integer> {
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@ArgumentCollection
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@ -36,7 +36,6 @@ import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.utils.QualityUtils;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.codecs.vcf.*;
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import org.broadinstitute.sting.utils.collections.Pair;
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import org.broadinstitute.sting.utils.variantcontext.Allele;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
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@ -47,7 +46,6 @@ import java.util.*;
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* Converts Sequenom files to a VCF annotated with QC metrics (HW-equilibrium, % failed probes)
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*/
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@Reference(window=@Window(start=0,stop=40))
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@Requires(value={})
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public class VariantValidationAssessor extends RodWalker<VariantContext,Integer> {
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@Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
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public RodBinding<VariantContext> variants;
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@ -31,7 +31,6 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.Requires;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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@ -43,7 +42,6 @@ import java.util.*;
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/**
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* Emits specific fields as dictated by the user from one or more VCF files.
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*/
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@Requires(value={})
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public class VariantsToTable extends RodWalker<Integer, Integer> {
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@ArgumentCollection
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@ -56,7 +56,6 @@ import java.util.*;
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/**
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* Converts variants from other file formats to VCF format.
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*/
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@Requires(value={})
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@Reference(window=@Window(start=-40,stop=40))
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public class VariantsToVCF extends RodWalker<Integer, Integer> {
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@ -26,7 +26,6 @@ package org.broadinstitute.sting.gatk;
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import org.testng.Assert;
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import org.broadinstitute.sting.commandline.Hidden;
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import org.broadinstitute.sting.gatk.walkers.Requires;
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import org.broadinstitute.sting.gatk.walkers.Walker;
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import org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker;
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import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
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@ -64,7 +63,6 @@ public class WalkerManagerUnitTest {
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}
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@Hidden
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@Requires(value={})
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class UninstantiableWalker extends Walker<Integer,Long> {
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// Private constructor will generate uninstantiable message
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private UninstantiableWalker() {}
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