From 95f2899f0586a8b3415e8ccaab9a5b6373652f5d Mon Sep 17 00:00:00 2001
From: Geraldine Van der Auwera <vdauwera@broadinstitute.org>
Date: Tue, 2 Jun 2015 00:34:34 -0400
Subject: [PATCH] User (mnw21cam) patch to fix DoC slowdown in 3.4

---
 .../tools/walkers/coverage/CoverageUtils.java | 19 ++++++++++++++++---
 1 file changed, 16 insertions(+), 3 deletions(-)

diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CoverageUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CoverageUtils.java
index e71860794..e027464d4 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CoverageUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CoverageUtils.java
@@ -137,6 +137,9 @@ public class CoverageUtils {
     public static Map<SAMReadGroupRecord,int[]> getBaseCountsByReadGroup(AlignmentContext context, int minMapQ, int maxMapQ, byte minBaseQ, byte maxBaseQ, CountPileupType countType) {
         Map<SAMReadGroupRecord, int[]> countsByRG = new HashMap<SAMReadGroupRecord,int[]>();
 
+        Map<String, int[]> countsByRGName = new HashMap<String, int[]>();
+        Map<String, SAMReadGroupRecord> RGByName = new HashMap<String, SAMReadGroupRecord>();
+
         List<PileupElement> countPileup = new LinkedList<PileupElement>();
         FragmentCollection<PileupElement> fpile;
 
@@ -202,10 +205,20 @@ public class CoverageUtils {
 
         for (PileupElement e : countPileup) {
             SAMReadGroupRecord readGroup = getReadGroup(e.getRead());
-            if (!countsByRG.keySet().contains(readGroup))
-                countsByRG.put(readGroup, new int[6]);
 
-            updateCounts(countsByRG.get(readGroup), e);
+            String readGroupId = readGroup.getSample() + "_" + readGroup.getReadGroupId();
+            int[] counts = countsByRGName.get(readGroupId);
+            if (counts == null) {
+                counts = new int[6];
+                countsByRGName.put(readGroupId, counts);
+                RGByName.put(readGroupId, readGroup);
+            }
+
+            updateCounts(counts, e);
+        }
+
+        for (String readGroupId : RGByName.keySet()) {
+            countsByRG.put(RGByName.get(readGroupId), countsByRGName.get(readGroupId));
         }
 
         return countsByRG;