org.opencb.biodata.tools.variant.tasks.VariantStatsTask Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of biodata-tools Show documentation
There is a newer version: 3.4.0
/*
 * 
 *
 */

package org.opencb.biodata.tools.variant.tasks;

import java.io.IOException;
import java.util.List;
import java.util.Map;

import org.opencb.biodata.formats.variant.io.VariantReader;
import org.opencb.biodata.models.variant.StudyEntry;
import org.opencb.biodata.models.variant.Variant;
import org.opencb.biodata.models.variant.VariantSource;
import org.opencb.biodata.models.variant.stats.VariantSourceStats;
import org.opencb.biodata.models.variant.stats.VariantStats;
import org.opencb.biodata.tools.variant.stats.VariantAggregatedEVSStatsCalculator;
import org.opencb.biodata.tools.variant.stats.VariantAggregatedExacStatsCalculator;
import org.opencb.biodata.tools.variant.stats.VariantAggregatedStatsCalculator;
import org.opencb.biodata.tools.variant.stats.VariantStatsCalculator;
import org.opencb.commons.run.Task;

/**
 * @author Alejandro Aleman Ramos <[email protected]>
 * @author Cristina Yenyxe Gonzalez Garcia <[email protected]>
 */
public class VariantStatsTask extends Task {

    @Deprecated
    private VariantReader reader;
    private VariantSource source;
    private VariantSourceStats stats;

    public VariantStatsTask(VariantSource study) {
        super();
        this.source = study;
        stats = new VariantSourceStats(study.getFileId(), study.getStudyId());
    }

    public VariantStatsTask(VariantReader reader, VariantSource study) {
        super();
        this.reader = reader;
        this.source = study;
        stats = new VariantSourceStats(study.getFileId(), study.getStudyId());
    }

    public VariantStatsTask(VariantReader reader, VariantSource study, int priority) {
        super(priority);
        this.reader = reader;
        this.source = study;
        stats = new VariantSourceStats(study.getFileId(), study.getStudyId());
    }

    @Override
    public boolean apply(List batch) {
//        VariantStats.calculateStatsForVariantsList(batch, source.getPedigree());
        for (Variant variant : batch) {
            for (StudyEntry study : variant.getSourceEntries().values()) {
                VariantStats variantStats = new VariantStats(variant);
                study.setStats(StudyEntry.DEFAULT_COHORT, variantStats);
                Map attributes = study.getFile(source.getFileId()).getAttributes();
                switch (source.getAggregation()) {
                    case NONE:
                        VariantStatsCalculator.calculate(study, attributes, source.getPedigree(), variantStats);
                        break;
                    case BASIC:
                        new VariantAggregatedStatsCalculator().calculate(variant, study);
                        break;
                    case EVS:
                        new VariantAggregatedEVSStatsCalculator().calculate(variant, study);
                        break;
                    case EXAC:
                        new VariantAggregatedExacStatsCalculator().calculate(variant, study);
                        break;
                }
            }
        }
        
        stats.updateFileStats(batch);
        stats.updateSampleStats(batch, source.getPedigree());
        return true;
    }

    @Override
    public boolean post() {
        source.setStats(stats.getFileStats());
        return true;
    }
}