gatk-3.8/java/src/org/broadinstitute/sting/utils/ReadBackedPileup.java

package org.broadinstitute.sting.utils;

import org.broadinstitute.sting.gatk.LocusContext;
import net.sf.samtools.SAMRecord;

import java.util.List;
import java.util.ArrayList;

/**
 * Created by IntelliJ IDEA.
 * User: depristo
 * Date: Apr 14, 2009
 * Time: 8:54:05 AM
 * To change this template use File | Settings | File Templates.
 */
public class ReadBackedPileup extends BasicPileup {
    GenomeLoc loc;
    char ref;
    List<SAMRecord> reads;
    List<Integer> offsets;

    public ReadBackedPileup(GenomeLoc loc, char ref, LocusContext context ) {
        this(loc, ref, context.getReads(), context.getOffsets());
    }

    public ReadBackedPileup(GenomeLoc loc, char ref, List<SAMRecord> reads, List<Integer> offsets ) {
        assert reads != null;
        assert offsets != null;
        assert reads.size() == offsets.size();
        
        this.loc = loc;
        this.ref = ref;
        this.reads = reads;
        this.offsets = offsets;
    }

    public int size()                 { return reads.size(); }
    public List<SAMRecord> getReads() { return reads; }
    public List<Integer> getOffsets() { return offsets; }

    public GenomeLoc getLocation() {
        return loc;
    }

    public char getRef() {
        return ref;
    }

    public String getBases() {
        return basePileupAsString(reads, offsets);
    }

    public String getQuals() {
        return qualPileupAsString(reads, offsets);
    }

    public String getQualsAsInts() {
        return Utils.join(",", qualPileup(reads, offsets));
    }

    public String getMappingQualsAsInts() {
        return Utils.join(",", mappingQualPileup(reads));
    }

    public String getSecondaryBasePileup() {
        return secondaryBasePileupAsString(reads, offsets);
    }

    public String getSecondaryQualPileup() {
        return secondaryQualPileupAsString(reads, offsets);
    }
    
    public String getPileupString()
    {
        return String.format("%s: %s %s %s", getLocation(), getRef(), getBases(), getQuals());
    }
}