30 lines
1.0 KiB
Java
Executable File
30 lines
1.0 KiB
Java
Executable File
package org.broadinstitute.sting.gatk.walkers;
|
|
|
|
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
|
import org.broadinstitute.sting.utils.GenomeLoc;
|
|
|
|
import java.util.List;
|
|
import java.util.Set;
|
|
|
|
import net.sf.samtools.SAMRecord;
|
|
|
|
/**
|
|
* Created by IntelliJ IDEA.
|
|
* User: mdepristo
|
|
* Date: Feb 22, 2009
|
|
* Time: 2:52:28 PM
|
|
* To change this template use File | Settings | File Templates.
|
|
*/
|
|
@Requires({DataSource.READS,DataSource.REFERENCE})
|
|
public abstract class DuplicateWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> {
|
|
// Do we actually want to operate on the context?
|
|
public boolean filter(GenomeLoc loc, AlignmentContext context, Set<List<SAMRecord>> readSets ) {
|
|
return true; // We are keeping all the reads
|
|
}
|
|
|
|
public abstract MapType map(GenomeLoc loc, AlignmentContext context, Set<List<SAMRecord>> readSets );
|
|
|
|
// Given result of map function
|
|
public abstract ReduceType reduceInit();
|
|
public abstract ReduceType reduce(MapType value, ReduceType sum);
|
|
} |