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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 2010-08-08 07:07:42 +00:00
parent 758ab428f5
commit 9aa70d9c7c
1 changed files with 0 additions and 106 deletions
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106
java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSubset.java
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/*
* Copyright (c) 2010.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.gatk.walkers.vcftools;
import org.broad.tribble.util.variantcontext.Genotype;
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.walkers.RodWalker;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broad.tribble.vcf.VCFHeader;
import org.broad.tribble.vcf.VCFHeaderLine;
import java.util.*;
/**
* Extracts subsets of a VCF file like one or more samples, all or only variant loci, all or filtered loci.
*/
public class VariantSubset extends RodWalker<Integer, Integer> {
@Argument(fullName="sample", shortName="SN", doc="Sample to include (or nothing to specify all samples)", required=false)
private ArrayList<String> SAMPLES = null;
@Argument(fullName="includeNonVariants", shortName="INV", doc="Include non-variant loci", required=false)
private boolean INCLUDE_NON_VARIANTS = false;
@Argument(fullName="includeFiltered", shortName="IF", doc="Include filtered loci", required=false)
private boolean INCLUDE_FILTERED = false;
private VCFWriter writer;
public void initialize() {
Set<VCFHeaderLine> metaData = new HashSet<VCFHeaderLine>();
metaData.add(new VCFHeaderLine("source", "VariantsToVCF"));
metaData.add(new VCFHeaderLine("reference", this.getToolkit().getArguments().referenceFile.getAbsolutePath()));
writer = new VCFWriter(out);
Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList("variant"));
final VCFHeader vcfHeader = new VCFHeader(metaData, samples);
writer.writeHeader(vcfHeader);
}
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
Collection<VariantContext> VCs = tracker.getAllVariantContexts(ref, null, context.getLocation(), true, false);
for (VariantContext vc : VCs) {
VariantContext subset = subsetRecord(vc);
if ( (vc.isPolymorphic() || INCLUDE_NON_VARIANTS) &&
(!subset.isFiltered() || INCLUDE_FILTERED) )
writer.add(subset, ref.getBase());
}
return 1;
}
public Integer reduceInit() {
return 0;
}
private VariantContext subsetRecord(VariantContext vc) {
if ( SAMPLES == null || SAMPLES.isEmpty() )
return vc;
ArrayList<Genotype> genotypes = new ArrayList<Genotype>();
for ( Map.Entry<String, Genotype> genotypePair : vc.getGenotypes().entrySet() ) {
if ( SAMPLES.contains(genotypePair.getKey()) )
genotypes.add(genotypePair.getValue());
}
return vc.subContextFromGenotypes(genotypes);
}
public Integer reduce(Integer sum, Integer value) {
return 1;
}
public void onTraversalDone(Integer sum) {
writer.close();
}
}