From 9e12cd13120df6994c60d8334fa8628080fa212c Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 3 Mar 2011 15:45:51 +0000
Subject: [PATCH] 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
---
 .../walkers/association/AssociationContext.java        |  3 +++
 .../walkers/association/MapExtender.java               |  1 -
 .../walkers/association/RegionalAssociationWalker.java | 10 +++++++++-
 3 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/AssociationContext.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/AssociationContext.java
index cfd0c249f..33d23e33d 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/AssociationContext.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/AssociationContext.java
@@ -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() ) {
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/MapExtender.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/MapExtender.java
index c731aaa7a..7ca1f8a0d 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/MapExtender.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/MapExtender.java
@@ -55,7 +55,6 @@ public class MapExtender {
                             filtElems.add(e);
                         }
                     }
-
                     readFilteredPileup.put(sac.getKey(),new ReadBackedPileupImpl(current.getRef().getLocus(),filtElems));
                 } else {
                     readFilteredPileup = fullPileup;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/RegionalAssociationWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/RegionalAssociationWalker.java
index 387298ca3..70a8d2ff4 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/RegionalAssociationWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/RegionalAssociationWalker.java
@@ -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();
+    }
 }
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