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* Copyright (c) 2012 The Broad Institute
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* The above copyright notice and this permission notice shall be
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package org.broadinstitute.gatk.tools.walkers.annotator;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.gatk.utils.pileup.PileupElement;
import htsjdk.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* Proportion of low quality reads
*
* <p>This annotation tells you what fraction of reads have a mapping quality of less than the given threshold of 10 (including 0). Note that certain tools may impose a different minimum mapping quality threshold. For example, HaplotypeCaller excludes reads with MAPQ<20.</p>
*
* <h3>Calculation</h3>
* <p> $$ LowMQ = \frac{# reads with MAPQ=0 + # reads with MAPQ<10}{total # reads} $$
* </p>
*
* <h3>Related annotations</h3>
* <ul>
* <li><b><a href="https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_annotator_MappingQualityZero.php">MappingQualityZero</a></b> gives the count of reads with MAPQ=0 across all samples.</li>
* <li><b><a href="https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_annotator_MappingQualityZeroBySample.php">MappingQualityZeroBySample</a></b> gives the count of reads with MAPQ=0 for each individual sample.</li>
* </ul>
*/
public class LowMQ extends InfoFieldAnnotation {
public Map<String, Object> annotate(final RefMetaDataTracker tracker,
final AnnotatorCompatible walker,
final ReferenceContext ref,
final Map<String, AlignmentContext> stratifiedContexts,
final VariantContext vc,
final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
if ( stratifiedContexts.size() == 0 )
return null;
double mq0 = 0;
double mq10 = 0;
double total = 0;
for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() )
{
for ( PileupElement p : sample.getValue().getBasePileup() )
{
if ( p.getMappingQual() == 0 ) { mq0 += 1; }
if ( p.getMappingQual() <= 10 ) { mq10 += 1; }
total += 1;
}
}
Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%.04f,%.04f,%.00f", mq0/total, mq10/total, total));
return map;
}
public List<String> getKeyNames() { return Arrays.asList("LowMQ"); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 3, VCFHeaderLineType.Float, "3-tuple: <fraction of reads with MQ=0>,<fraction of reads with MQ<=10>,<total number of reads>")); }
}