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Gotta include the changes i made to get an init function into the contexts 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5368 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2011-03-03 15:45:51 +00:00
parent 835a26d145
commit 9e12cd1312
3 changed files with 12 additions and 2 deletions
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3
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/AssociationContext.java
View File

@ -41,6 +41,9 @@ public abstract class AssociationContext<X> {
// do we filter the current location (e.g. omit from window)
public boolean filter(MapExtender m) { return true; }
// a basic initialization of the context (give the walker for access to object?)
public void init(RegionalAssociationWalker walker) { }
public Map<Sample,Object> mapLocus(MapExtender extender) {
Map<Sample,ReadBackedPileup> pileups;
if ( ! usePreviouslySeenReads() ) {

1
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/MapExtender.java
View File

@ -55,7 +55,6 @@ public class MapExtender {
filtElems.add(e);
}
}
readFilteredPileup.put(sac.getKey(),new ReadBackedPileupImpl(current.getRef().getLocus(),filtElems));
} else {
readFilteredPileup = fullPileup;

10
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/RegionalAssociationWalker.java
View File

@ -4,9 +4,11 @@ import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.sample.Sample;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
@ -65,7 +67,9 @@ public class RegionalAssociationWalker extends LocusWalker<MapHolder, RegionalAs
// todo -- this should use the package handler like variant eval
Set<AssociationContext> validAssociations = new HashSet<AssociationContext>();
for ( String s : associationsToUse ) {
validAssociations.add(stringToAssociationContext(s));
AssociationContext context = stringToAssociationContext(s);
context.init(this);
validAssociations.add(context);
}
return validAssociations;
}
@ -79,4 +83,8 @@ public class RegionalAssociationWalker extends LocusWalker<MapHolder, RegionalAs
public void onTraversalDone(RegionalAssociationHandler rac) {
// do nothing
}
public Set<Sample> getSamples() {
return getToolkit().getSAMFileSamples();
}
}