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Totaly experimental, possibly useless annotation that logs # of MQ0 reads / total depth, TBD if VQSR can use it. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5905 348d0f76-0448-11de-a6fe-93d51630548a
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delangel 2011-05-30 14:05:39 +00:00
parent 8d294dd6e6
commit 0aef5c0074
1 changed files with 60 additions and 0 deletions
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java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java 100755
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package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.VCFConstants;
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.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
public class MappingQualityZeroFraction implements InfoFieldAnnotation, ExperimentalAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( stratifiedContexts.size() == 0 )
return null;
int mq0 = 0;
int depth = 0;
for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
AlignmentContext context = sample.getValue();
depth += context.size();
ReadBackedPileup pileup = null;
if (context.hasExtendedEventPileup())
pileup = context.getExtendedEventPileup();
else if (context.hasBasePileup())
pileup = context.getBasePileup();
if (pileup != null) {
for (PileupElement p : pileup ) {
if ( p.getMappingQual() == 0 )
mq0++;
}
}
}
if (depth > 0) {
double mq0f = (double)mq0 / (double )depth;
Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%1.4f", mq0f));
return map;
}
else
return null;
}
public List<String> getKeyNames() { return Arrays.asList("MQ0Fraction"); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Integer, "Fraction of Mapping Quality Zero Reads")); }
}