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Annotation that adds a list of samples who are polymorphic at a site based on the GTs. Very useful if you are looking at rare variants among many samples, esp. in Evoker 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5868 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2011-05-24 20:12:27 +00:00
parent 1bd1404aa9
commit 6ed71cf683
1 changed files with 71 additions and 0 deletions
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java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java 100755
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/*
* Copyright (c) 2010 The Broad Institute
*
* 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.gatk.walkers.annotator;
import org.broad.tribble.util.variantcontext.Genotype;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.VCFHeaderLineType;
import org.broad.tribble.vcf.VCFInfoHeaderLine;
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.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
public class SampleList implements InfoFieldAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( vc.isMonomorphic() || !vc.hasGenotypes() )
return null;
StringBuffer samples = new StringBuffer();
for ( Genotype genotype : vc.getGenotypesSortedByName() ) {
if ( genotype.isCalled() && !genotype.isHomRef() ){
if ( samples.length() > 0 )
samples.append(",");
samples.append(genotype.getSampleName());
}
}
if ( samples.length() == 0 )
return null;
Map<String, Object> map = new HashMap<String, Object>();
map.put("Samples", samples.toString());
return map;
}
public List<String> getKeyNames() { return Arrays.asList("Samples"); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("Samples", VCFInfoHeaderLine.UNBOUNDED, VCFHeaderLineType.String, "List of polymorphic samples")); }
}