Replaced by SelectVariants
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3979 348d0f76-0448-11de-a6fe-93d51630548a
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kiran
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/*
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* Copyright (c) 2010.
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.playground.gatk.walkers.vcftools;
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import org.broad.tribble.util.variantcontext.Genotype;
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import org.broad.tribble.util.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.RodWalker;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broad.tribble.vcf.VCFHeader;
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import org.broad.tribble.vcf.VCFHeaderLine;
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import java.util.*;
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/**
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* Extracts subsets of a VCF file like one or more samples, all or only variant loci, all or filtered loci.
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*/
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public class VariantSubset extends RodWalker<Integer, Integer> {
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@Argument(fullName="sample", shortName="SN", doc="Sample to include (or nothing to specify all samples)", required=false)
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private ArrayList<String> SAMPLES = null;
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@Argument(fullName="includeNonVariants", shortName="INV", doc="Include non-variant loci", required=false)
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private boolean INCLUDE_NON_VARIANTS = false;
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@Argument(fullName="includeFiltered", shortName="IF", doc="Include filtered loci", required=false)
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private boolean INCLUDE_FILTERED = false;
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private VCFWriter writer;
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public void initialize() {
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Set<VCFHeaderLine> metaData = new HashSet<VCFHeaderLine>();
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metaData.add(new VCFHeaderLine("source", "VariantsToVCF"));
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metaData.add(new VCFHeaderLine("reference", this.getToolkit().getArguments().referenceFile.getAbsolutePath()));
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writer = new VCFWriter(out);
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Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList("variant"));
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final VCFHeader vcfHeader = new VCFHeader(metaData, samples);
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writer.writeHeader(vcfHeader);
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}
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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Collection<VariantContext> VCs = tracker.getAllVariantContexts(ref, null, context.getLocation(), true, false);
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for (VariantContext vc : VCs) {
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VariantContext subset = subsetRecord(vc);
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if ( (vc.isPolymorphic() || INCLUDE_NON_VARIANTS) &&
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(!subset.isFiltered() || INCLUDE_FILTERED) )
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writer.add(subset, ref.getBase());
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}
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return 1;
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}
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public Integer reduceInit() {
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return 0;
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}
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private VariantContext subsetRecord(VariantContext vc) {
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if ( SAMPLES == null || SAMPLES.isEmpty() )
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return vc;
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ArrayList<Genotype> genotypes = new ArrayList<Genotype>();
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for ( Map.Entry<String, Genotype> genotypePair : vc.getGenotypes().entrySet() ) {
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if ( SAMPLES.contains(genotypePair.getKey()) )
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genotypes.add(genotypePair.getValue());
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}
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return vc.subContextFromGenotypes(genotypes);
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}
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public Integer reduce(Integer sum, Integer value) {
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return 1;
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}
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public void onTraversalDone(Integer sum) {
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writer.close();
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}
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}
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