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Number of MQ0 reads in each sample (format field) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5229 348d0f76-0448-11de-a6fe-93d51630548a
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asivache 2011-02-11 17:16:26 +00:00
parent 8560bb290b
commit 03482bf7c4
1 changed files with 86 additions and 0 deletions
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java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java 100644
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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.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.util.variantcontext.Genotype;
import org.broad.tribble.vcf.VCFConstants;
import org.broad.tribble.vcf.VCFHeaderLineType;
import org.broad.tribble.vcf.VCFFormatHeaderLine;
import java.util.Map;
import java.util.HashMap;
import java.util.List;
import java.util.Arrays;
/**
* Created by IntelliJ IDEA.
* User: asivache
* Date: Feb 4, 2011
* Time: 6:46:25 PM
* To change this template use File | Settings | File Templates.
*/
public class MappingQualityZeroBySample implements GenotypeAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref,
StratifiedAlignmentContext stratifiedContext, VariantContext vc, Genotype g) {
if ( g == null || !g.isCalled() )
return null;
int mq0 = 0;
AlignmentContext context = stratifiedContext.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE);
ReadBackedPileup pileup = null;
if (vc.isIndel() && context.hasExtendedEventPileup())
pileup = context.getExtendedEventPileup();
else if (context.hasBasePileup())
pileup = context.getBasePileup();
else return null;
if (pileup != null) {
for (PileupElement p : pileup ) {
if ( p.getMappingQual() == 0 )
mq0++;
}
}
Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%d", mq0));
return map;
}
public List<String> getKeyNames() { return Arrays.asList(VCFConstants.MAPPING_QUALITY_ZERO_KEY); }
public List<VCFFormatHeaderLine> getDescriptions() { return Arrays.asList(
new VCFFormatHeaderLine(getKeyNames().get(0), 1,
VCFHeaderLineType.Integer, "Number of Mapping Quality Zero Reads per sample")); }
}