From eb200e4cce7fd94adb641e7a13233a59faba3dd8 Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 18 May 2010 17:13:44 +0000
Subject: [PATCH] Hrumph. Don't just add pointers to the same objects, actually
 clone the underlying arrays.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3379 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../coverage/DepthOfCoverageStats.java        | 26 +++++++++++++------
 1 file changed, 18 insertions(+), 8 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java
index 6114a4024..5926baf99 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java
@@ -86,15 +86,25 @@ public class DepthOfCoverageStats {
 
     public DepthOfCoverageStats(DepthOfCoverageStats cloneMe) {
         this.binLeftEndpoints = cloneMe.binLeftEndpoints;
-        this.granularHistogramBySample = cloneMe.granularHistogramBySample;
-        this.totalCoverages = cloneMe.totalCoverages;
-        this.nLoci = cloneMe.nLoci;
-        this.totalLocusDepth = cloneMe.totalLocusDepth;
-        this.totalDepthOfCoverage = cloneMe.totalDepthOfCoverage;
-        this.locusHistogram = cloneMe.locusHistogram;
-        this.locusCoverageCounts = cloneMe.locusCoverageCounts;
-        this.tabulateLocusCounts = cloneMe.tabulateLocusCounts;
+        granularHistogramBySample = new HashMap<String,int[]>();
+        totalCoverages = new HashMap<String,Long>();
+        for ( String s : cloneMe.getAllSamples() ) {
+            granularHistogramBySample.put(s,new int[cloneMe.getHistograms().get(s).length]);
+            for ( int i = 0; i < granularHistogramBySample.get(s).length; i++ ) {
+                granularHistogramBySample.get(s)[i] = cloneMe.getHistograms().get(s)[i];
+            }
+            totalCoverages.put(s,cloneMe.totalCoverages.get(s));
+        }
+
         this.includeDeletions = cloneMe.includeDeletions;
+        if ( cloneMe.tabulateLocusCounts ) {
+            this.locusCoverageCounts = new int[cloneMe.locusCoverageCounts.length][cloneMe.locusCoverageCounts[0].length];
+        }
+        //this.granularHistogramBySample = cloneMe.granularHistogramBySample;
+        //this.totalCoverages = cloneMe.totalCoverages;
+        this.nLoci = cloneMe.nLoci;
+        this.totalDepthOfCoverage = cloneMe.totalDepthOfCoverage;
+        this.tabulateLocusCounts = cloneMe.tabulateLocusCounts;
     }
 
     public void addSample(String sample) {