Package org.broadinstitute.gatk.engine.samples

Examples of org.broadinstitute.gatk.engine.samples.Sample

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        violationFamilies.clear();
        clearInheritanceMap();

        for(Set<Sample> family : families.values()){
            Iterator<Sample> sampleIterator = family.iterator();
            Sample sample;
            while(sampleIterator.hasNext()){
                sample = sampleIterator.next();
                if(sample.getParents().size() > 0)
                    updateViolations(sample.getFamilyID(),sample.getMaternalID(), sample.getPaternalID(), sample.getID() ,vc);
            }
        }
        return violations_total;
    }
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public class CountMales extends ReadWalker<Integer, Integer> {
    @Output
    public PrintStream out;

    public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) {
        Sample sample = getSampleDB().getSample(read);
        return sample.getGender() == Gender.MALE ? 1 : 0;
    }
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Related Classes of org.broadinstitute.gatk.engine.samples.Sample

  • org.broadinstitute.gatk.tools.walkers.qc.CountMales
  • org.broadinstitute.gatk.utils.MendelianViolation
  • org.broadinstitute.gatk.utils.exceptions.UserException
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