From a6dc8cd44e051c0e4a7ef2616e114d335cd07ffd Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 22 Oct 2009 23:19:29 +0000
Subject: [PATCH] BTTC is now Tree Reducible allowing for parallelization.

Integration test comment changed to reflect actual date of last md5 update.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1901 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/BaseTransitionTableCalculatorJavaWalker.java    | 6 +++++-
 .../BaseTransitionTableCalculatorJavaIntegrationTest.java   | 2 +-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
index 3ff55bab6..dd8cd1c26 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
@@ -24,7 +24,7 @@ import net.sf.samtools.SAMRecord;
  */
 @By(DataSource.REFERENCE)
 @Reference(window=@Window(start=-3,stop=3))
-public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<BaseTransitionTable>,Set<BaseTransitionTable>> {
+public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<BaseTransitionTable>,Set<BaseTransitionTable>> implements TreeReducible<Set<BaseTransitionTable>> {
     @Argument(fullName="usePreviousBases", doc="Use previous bases of the reference as part of the calculation, uses the specified number, defaults to 0", required=false)
     int nPreviousBases = 0;
     @Argument(fullName="useSecondaryBase",doc="Use the secondary base of a read as part of the calculation", required=false)
@@ -111,6 +111,10 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
         return reduce;
     }
 
+    public Set<BaseTransitionTable> treeReduce( Set<BaseTransitionTable> reduce1, Set<BaseTransitionTable> reduce2 ) {
+        return reduce(reduce1,reduce2);
+    }
+
     public void onTraversalDone( Set<BaseTransitionTable> conditionalTables ) {
         out.print(createHeaderFromConditions());
         for ( BaseTransitionTable t : conditionalTables )
diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaIntegrationTest.java
index 5b787dc5d..e908ae339 100644
--- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaIntegrationTest.java
@@ -13,7 +13,7 @@ import java.util.Arrays;
  * To change this template use File | Settings | File Templates.
  */
 public class BaseTransitionTableCalculatorJavaIntegrationTest extends WalkerTest{
-    // MD5s last computed 10/20 at revision 1877
+    // MD5s last computed 10/21 at revision 1897
     public static final String OUTPUT_MD5_STANDARD = "e88f010ea842bcdb6503a4da24b90edc";
     public static final String OUTPUT_MD5_3MISMATCHES = "46f9aadbfe260a286fb6c8cac137dddd";
     public static final String OUTPUT_MD5_LOWMAPPINGQUALITY = "0b7447e0a271ffa5c8ff1719db3585e6";