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Following Eric's awesome update to change the VQSR recal file into a VCF file, the ApplyRecalibration step is now scatter/gather-able and tree reducible.

This commit is contained in:
Ryan Poplin 2012-04-18 11:24:04 -04:00
parent 333ae3bc2c
commit 8a84456626
1 changed files with 7 additions and 2 deletions
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9
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
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@ -35,6 +35,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.PartitionBy; import org.broadinstitute.sting.gatk.walkers.PartitionBy;
import org.broadinstitute.sting.gatk.walkers.PartitionType; import org.broadinstitute.sting.gatk.walkers.PartitionType;
import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
@ -83,8 +84,8 @@ import java.util.*;
* *
*/ */
@PartitionBy(PartitionType.NONE) @PartitionBy(PartitionType.LOCUS)
public class ApplyRecalibration extends RodWalker<Integer, Integer> { public class ApplyRecalibration extends RodWalker<Integer, Integer> implements TreeReducible<Integer> {
///////////////////////////// /////////////////////////////
// Inputs // Inputs
@ -266,6 +267,10 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> {
return 1; // This value isn't used for anything return 1; // This value isn't used for anything
} }
public Integer treeReduce( final Integer lhs, final Integer rhs ) {
return 1; // This value isn't used for anything
}
public void onTraversalDone( final Integer reduceSum ) { public void onTraversalDone( final Integer reduceSum ) {
} }
} }