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A walker that moves annotations from the filter field to the info field of truth annotated vcfs. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5458 348d0f76-0448-11de-a6fe-93d51630548a
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carneiro 2011-03-17 17:11:28 +00:00
parent 55e5971b3b
commit 3de300e504
1 changed files with 136 additions and 0 deletions
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java/src/org/broadinstitute/sting/oneoffprojects/walkers/AnnotateTruthROD.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.oneoffprojects.walkers;
import org.broad.tribble.util.variantcontext.MutableVariantContext;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.VCFHeader;
import org.broad.tribble.vcf.VCFHeaderLine;
import org.broad.tribble.vcf.VCFWriter;
import org.broadinstitute.sting.commandline.Output;
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.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.Set;
import static org.broadinstitute.sting.utils.IndelUtils.isInsideExtendedIndel;
/**
* Changes annotation in the truth dataset from the filter field to the INFO field.
*
* @author carneiro
* @since Mar 15, 2011
* @help.summary Changes annotation in the truth dataset from the filter field to the INFO field.
*/
public class AnnotateTruthROD extends RodWalker<Integer, Integer> {
@Output(doc="File to which validated variants should be written", required=true)
protected VCFWriter vcfWriter = null;
List<String> rodNames;
//---------------------------------------------------------------------------------------------------------------
//
// initialize
//
//---------------------------------------------------------------------------------------------------------------
public void initialize() {
List<ReferenceOrderedDataSource> rodList = getToolkit().getRodDataSources();
rodNames = new ArrayList<String>();
// Initialize VCF header
Set<VCFHeaderLine> headerLines = null;
Set<String> samples = null;
for (ReferenceOrderedDataSource rod : rodList) {
rodNames.add(rod.getName());
Map<String, VCFHeader> header = VCFUtils.getVCFHeadersFromRodPrefix(getToolkit(), rod.getName());
samples = SampleUtils.getSampleList(header, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
headerLines = VCFUtils.smartMergeHeaders(header.values(), logger);
headerLines.add(new VCFHeaderLine("source", "GenotypeAndValidate"));
}
if (headerLines == null|| samples == null)
throw new UserException.BadInput("You need to provide at least one ROD file to annotate");
vcfWriter.writeHeader(new VCFHeader(headerLines, samples));
}
//---------------------------------------------------------------------------------------------------------------
//
// map
//
//---------------------------------------------------------------------------------------------------------------
public Integer map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
int linesWritten = 0;
// For some reason RodWalkers get map calls with null trackers
if( tracker == null )
return linesWritten;
for (String rod : rodNames) {
VariantContext vc = tracker.getVariantContext(ref, rod, null, context.getLocation(), false);
if (!isInsideExtendedIndel(vc, ref)) {
MutableVariantContext mvc = new MutableVariantContext(vc);
mvc.putAttribute("GV", vc.getFilters().contains("TP") ? "T":"F");
mvc.clearFilters();
vcfWriter.add(mvc, ref.getBase());
linesWritten++;
}
}
return linesWritten;
}
//---------------------------------------------------------------------------------------------------------------
//
// reduce
//
//---------------------------------------------------------------------------------------------------------------
public Integer reduceInit() {
return 0;
}
public Integer reduce( Integer mapValue, Integer reduceSum ) {
return reduceSum + mapValue;
}
public void onTraversalDone( Integer reduceSum ) {
logger.info(reduceSum + " lines written.");
}
}