From 008d677bea5a05bc236857cc2c3a4fe73d3826d2 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sat, 23 May 2009 20:50:28 +0000
Subject: [PATCH] Fixed ValidatingPileup to work with Andrey's new rodSAMPileup
 -> GenotypeList type hierarchy. Fixed reference-ordered data validation
 system to validate class hierarchies instead of specific class types.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@811 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/refdata/ReferenceOrderedData.java     |  7 ++++---
 .../gatk/walkers/ValidatingPileupWalker.java   | 18 +++++++++++++++++-
 2 files changed, 21 insertions(+), 4 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java b/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
index 26085aa18..7cdaf53b8 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
@@ -140,14 +140,15 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
     public String getName() { return name; }
 
     /**
-     * Special equals override to see if this ROD is of type name, type.
-     * Implemented to preserve data hiding whenever possible.
+     * Special equals override to see if this ROD is compatible with the given
+     * name and type.  'Compatible' means that this ROD has the name that's passed
+     * in and its data can fit into the container specified by type.
      * @param name Name to check.
      * @param type Type to check.
      * @return True if these parameters imply this rod.  False otherwise.
      */
     public boolean matches( String name, Class<? extends ReferenceOrderedDatum> type ) {
-        return this.name.equals(name) && this.type.equals(type);
+        return this.name.equals(name) && type.isAssignableFrom(this.type);
     }
 
     public RODIterator iterator() {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java
index 7115a2580..397cd02e1 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java
@@ -24,7 +24,7 @@ public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats
 
     public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {
         Pileup pileup = new ReadBackedPileup(ref, context);
-        Pileup truePileup = (Pileup)tracker.lookup("pileup", null);
+        Pileup truePileup = getTruePileup( tracker );
 
         if ( truePileup == null ) {
             System.out.printf("No truth pileup data available at %s%n", pileup.getPileupString());
@@ -59,6 +59,22 @@ public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats
         combined.nBases = lhs.nBases + rhs.nBases;
         return combined;
     }
+
+    /**
+     * Extracts the true pileup data from the given rodSAMPileup.  Note that this implementation
+     * assumes that the genotype will only be point or indel.
+     * @param tracker ROD tracker from which to extract pileup data.
+     * @return True pileup data.
+     */
+    private Pileup getTruePileup( RefMetaDataTracker tracker ) {
+        rodSAMPileup pileup = (rodSAMPileup)tracker.lookup("pileup", null);
+        if( pileup.hasPointGenotype() )
+            return (Pileup)pileup.getPointGenotype();
+        else if( pileup.hasIndelGenotype() )
+            return (Pileup)pileup.getIndelGenotype();
+        else
+            throw new StingException("Unsupported pileup type: " + pileup);
+    }
 }
 
 class ValidationStats {