From e5e65ecfbe5c4084c5434ae146eb2010719aee7a Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 1 Feb 2011 06:40:42 +0000
Subject: [PATCH] Bugfix for GetSatisfaction: ensure that the two statistics
 objects (the map, and the pair) are actually pointers to the very same
 object.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5156 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/coverage/DepthOfCoverageWalker.java     | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
index d35eaea2c..91ae81cd5 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
@@ -363,17 +363,22 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
     }
 
     private void printGeneStats(List<Pair<GenomeLoc, CoveragePartitioner>> statsByTarget) {
+        logger.debug("statsByTarget size is "+Integer.toString(statsByTarget.size()));
+        logger.debug("Initializing refseq...");
         LocationAwareSeekableRODIterator refseqIterator = initializeRefSeq();
+        logger.debug("Refseq init done.");
         List<Pair<String,DepthOfCoverageStats>> statsByGene = new ArrayList<Pair<String,DepthOfCoverageStats>>();// maintains order
         Map<String,DepthOfCoverageStats> geneNamesToStats = new HashMap<String,DepthOfCoverageStats>(); // allows indirect updating of objects in list
 
         for ( Pair<GenomeLoc, CoveragePartitioner> targetStats : statsByTarget ) {
             String gene = getGeneName(targetStats.first,refseqIterator);
             if ( geneNamesToStats.keySet().contains(gene) ) {
+                logger.debug("Merging "+geneNamesToStats.get(gene).toString()+" and "+targetStats.second.getCoverageByAggregationType(DoCOutputType.Partition.sample).toString());
                 geneNamesToStats.get(gene).merge(targetStats.second.getCoverageByAggregationType(DoCOutputType.Partition.sample));
             } else {
-                geneNamesToStats.put(gene,new DepthOfCoverageStats(targetStats.second.getCoverageByAggregationType(DoCOutputType.Partition.sample)));
-                statsByGene.add(new Pair<String,DepthOfCoverageStats>(gene,new DepthOfCoverageStats(targetStats.second.getCoverageByAggregationType(DoCOutputType.Partition.sample))));
+                DepthOfCoverageStats merger = new DepthOfCoverageStats(targetStats.second.getCoverageByAggregationType(DoCOutputType.Partition.sample));
+                geneNamesToStats.put(gene,merger);
+                statsByGene.add(new Pair<String,DepthOfCoverageStats>(gene,merger));
             }
         }
 
@@ -386,15 +391,19 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
 
     //blatantly stolen from Andrew Kernytsky
     private String getGeneName(GenomeLoc target, LocationAwareSeekableRODIterator refseqIterator) {
+        logger.debug("Examining "+target.toString());
         if (refseqIterator == null) { return "UNKNOWN"; }
 
         RODRecordList annotationList = refseqIterator.seekForward(target);
+        logger.debug("Annotation list is " + (annotationList == null ? "null" : annotationList.getName()));
         if (annotationList == null) { return "UNKNOWN"; }
 
         for(GATKFeature rec : annotationList) {
             if ( ((RefSeqFeature)rec.getUnderlyingObject()).overlapsExonP(target) ) {
+                logger.debug("We do overlap "+ rec.getUnderlyingObject().toString());
                 return ((RefSeqFeature)rec.getUnderlyingObject()).getGeneName();
             }
+            logger.debug("No overlap");
         }
 
         return "UNKNOWN";