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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.GenotypeAnnotation;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import htsjdk.variant.vcf.VCFConstants;
import htsjdk.variant.vcf.VCFFormatHeaderLine;
import htsjdk.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.gatk.utils.pileup.PileupElement;
import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
import htsjdk.variant.variantcontext.Genotype;
import htsjdk.variant.variantcontext.GenotypeBuilder;
import htsjdk.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.List;
/**
* Count of reads with mapping quality zero for each sample
*
* <p>This annotation gives you the count of all reads that have MAPQ = 0 for each sample. The count of reads with MAPQ0 can be used for quality control; high counts typically indicate regions where it is difficult to make confident calls.</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_LowMQ.php">LowMQ</a></b> gives the proportion of reads with low mapping quality (MAPQ below 10, including 0).</li>
* </ul>
*/
public class MappingQualityZeroBySample extends GenotypeAnnotation {
public void annotate(final RefMetaDataTracker tracker,
final AnnotatorCompatible walker,
final ReferenceContext ref,
final AlignmentContext stratifiedContext,
final VariantContext vc,
final Genotype g,
final GenotypeBuilder gb,
final PerReadAlleleLikelihoodMap alleleLikelihoodMap){
if ( g == null || !g.isCalled() || stratifiedContext == null )
return;
int mq0 = 0;
final ReadBackedPileup pileup = stratifiedContext.getBasePileup();
for (PileupElement p : pileup ) {
if ( p.getMappingQual() == 0 )
mq0++;
}
gb.attribute(getKeyNames().get(0), mq0);
}
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")); }
}