From ff4a0764df9a479246bd227c167c66ac7c9165aa Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 27 May 2010 19:00:09 +0000
Subject: [PATCH] Read error rate is now parallelizable

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3447 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/ReadErrorRateWalker.java          | 31 ++++++++++++++++++-
 1 file changed, 30 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReadErrorRateWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReadErrorRateWalker.java
index 92aca4643..a159f821d 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReadErrorRateWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReadErrorRateWalker.java
@@ -29,11 +29,13 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.BaseUtils;
 import net.sf.samtools.SAMRecord;
 
 import java.util.HashMap;
+import java.util.Map;
 import java.util.Random;
 
 /**
@@ -45,7 +47,7 @@ import java.util.Random;
  *
  * @author Kiran Garimella
  */
-public class ReadErrorRateWalker extends ReadWalker<boolean[], ReadErrorRateCollection> {
+public class ReadErrorRateWalker extends ReadWalker<boolean[], ReadErrorRateCollection> implements TreeReducible<ReadErrorRateCollection> {
     @Argument(fullName="printVisualHits",   shortName="v",  doc="print visual hits",    required=false) public boolean printVisualHits = false;
     @Argument(fullName="useNextBestBase",   shortName="nb", doc="use next best base",   required=false) public boolean useNextBestBase = false;
     @Argument(fullName="useNonNextBestBase",shortName="nnb",doc="use nonnext best base",required=false) public boolean useNonNextBestBase = false;
@@ -180,6 +182,17 @@ public class ReadErrorRateWalker extends ReadWalker<boolean[], ReadErrorRateColl
         return collection;
     }
 
+    /**
+     * For multithreading - take two read error rate collections and put them together
+     * @param left   one collection
+     * @param right   another collection
+     * @return left updated with the counts from right
+     */
+    public ReadErrorRateCollection treeReduce(ReadErrorRateCollection left, ReadErrorRateCollection right) {
+        left.merge(right);
+        return left;
+    }
+
     /**
      * We've processed all the reads.  Emit the final, normalized error rate data.
      *
@@ -222,6 +235,16 @@ class ReadErrorRateCollection {
         return builder.toString();
     }
 
+    public void merge(ReadErrorRateCollection other) {
+        for ( Map.Entry<Integer,int[]> errorCounts : other.readsByReadLength.entrySet() ) {
+            if ( this.readsByReadLength.keySet().contains(errorCounts.getKey()) ) {
+                mergeCounts(readsByReadLength.get(errorCounts.getKey()),errorCounts.getValue());
+            } else {
+                readsByReadLength.put(errorCounts.getKey(),errorCounts.getValue());
+            }
+        }
+    }
+
     private static int[] zeroArray( int length ) {
         int[] array = new int[length];
         for ( int ii = 0; ii < length; ii ++ ) {
@@ -231,6 +254,12 @@ class ReadErrorRateCollection {
         return array;
     }
 
+    private static void mergeCounts ( int[] addToMe, int[] dontTouchMe ) {
+        for ( int index = 0; index < addToMe.length; index ++ ) {
+            addToMe[index] += dontTouchMe[index];
+        }
+    }
+
     public static void updateErrorCounts(int[] sum, boolean[] value) {
 
         for (int cycle = 0; cycle < value.length; cycle++) {