From fc7fab5f3b0798671d10b3371c87e62eb50c0ffe Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Thu, 29 Nov 2012 22:10:25 -0500
Subject: [PATCH] Fixed ReadBackedPileup downsampling

Downsampling in the PerSampleReadBackedPileup was broken, it didn't downsample anything, always returning a copy the original pileup.
---
 .../utils/pileup/AbstractReadBackedPileup.java     | 14 +++++---------
 1 file changed, 5 insertions(+), 9 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java b/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
index 42938d2a6..25f0bfa6d 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
@@ -652,23 +652,19 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
             PerSamplePileupElementTracker<PE> tracker = (PerSamplePileupElementTracker<PE>) pileupElementTracker;
             PerSamplePileupElementTracker<PE> filteredTracker = new PerSamplePileupElementTracker<PE>();
 
-            int current = 0;
 
             for (final String sample : tracker.getSamples()) {
                 PileupElementTracker<PE> perSampleElements = tracker.getElements(sample);
 
-                List<PileupElement> filteredPileup = new ArrayList<PileupElement>();
-                for (PileupElement p : perSampleElements) {
+                int current = 0;
+                UnifiedPileupElementTracker<PE> filteredPileup = new UnifiedPileupElementTracker<PE>();
+                for (PE p : perSampleElements) {
                     if (positions.contains(current))
                         filteredPileup.add(p);
-                }
+                    current++;
 
-                if (!filteredPileup.isEmpty()) {
-                    AbstractReadBackedPileup<RBP, PE> pileup = createNewPileup(loc, perSampleElements);
-                    filteredTracker.addElements(sample, pileup.pileupElementTracker);
                 }
-
-                current++;
+                filteredTracker.addElements(sample, filteredPileup);
             }
 
             return (RBP) createNewPileup(loc, filteredTracker);