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Add a RemoveProgramRecords annotation 

* Add the RemoveProgramRecords annotation to LocusWalker
This commit is contained in:
Joel Thibault 2012-08-02 14:21:30 -04:00
parent 524d7ea306
commit addbfd6437
3 changed files with 23 additions and 2 deletions
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3
public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -800,8 +800,7 @@ public class GenomeAnalysisEngine {
if (argCollection.removeProgramRecords && argCollection.keepProgramRecords) if (argCollection.removeProgramRecords && argCollection.keepProgramRecords)
throw new UserException.BadArgumentValue("rpr / kpr", "Cannot enable both options"); throw new UserException.BadArgumentValue("rpr / kpr", "Cannot enable both options");
// LocusWalkers don't use program records, so remove them by default to save memory boolean removeProgramRecords = argCollection.removeProgramRecords || walker.getClass().isAnnotationPresent(RemoveProgramRecords.class);
boolean removeProgramRecords = (this.walker instanceof LocusWalker) || argCollection.removeProgramRecords;
if (argCollection.keepProgramRecords) if (argCollection.keepProgramRecords)
removeProgramRecords = false; removeProgramRecords = false;

1
public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java
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@ -19,6 +19,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@Requires({DataSource.READS,DataSource.REFERENCE, DataSource.REFERENCE_BASES}) @Requires({DataSource.READS,DataSource.REFERENCE, DataSource.REFERENCE_BASES})
@PartitionBy(PartitionType.LOCUS) @PartitionBy(PartitionType.LOCUS)
@ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentFilter.class,DuplicateReadFilter.class,FailsVendorQualityCheckFilter.class}) @ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentFilter.class,DuplicateReadFilter.class,FailsVendorQualityCheckFilter.class})
@RemoveProgramRecords
public abstract class LocusWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> { public abstract class LocusWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> {
// Do we actually want to operate on the context? // Do we actually want to operate on the context?
public boolean filter(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { public boolean filter(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {

21
public/java/src/org/broadinstitute/sting/gatk/walkers/RemoveProgramRecords.java 100644
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@ -0,0 +1,21 @@
package org.broadinstitute.sting.gatk.walkers;
/**
* Created with IntelliJ IDEA.
* User: thibault
* Date: 8/2/12
* Time: 1:58 PM
* To change this template use File | Settings | File Templates.
*/
import java.lang.annotation.*;
/**
* Indicates that program records should be removed from SAM headers by default for this walker
*/
@Documented
@Inherited
@Retention(RetentionPolicy.RUNTIME)
@Target(ElementType.TYPE)
public @interface RemoveProgramRecords {
}