From 3fca23cd16b1dc15d7f25cf51927efb10bc49dc4 Mon Sep 17 00:00:00 2001
From: andrewk <andrewk@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 24 Nov 2009 18:51:19 +0000
Subject: [PATCH] Added a stub treeReduce function for debugging multi-threaded
 execution.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2146 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../playground/gatk/walkers/HybSelPerformanceWalker.java  | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java
index 522cfcb17..5636db94f 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java
@@ -25,7 +25,7 @@ import edu.mit.broad.picard.util.OverlapDetector;
 import edu.mit.broad.picard.directed.IntervalList;
 
 @By(DataSource.REFERENCE)
-public class HybSelPerformanceWalker extends LocusWalker<Integer, HybSelPerformanceWalker.TargetInfo> {
+public class HybSelPerformanceWalker extends LocusWalker<Integer, HybSelPerformanceWalker.TargetInfo> implements TreeReducible<HybSelPerformanceWalker.TargetInfo> {
     @Argument(fullName="min_mapq", shortName="mmq", required=false, doc="Minimum mapping quality of reads to consider")
     public Integer MIN_MAPQ = 1;
 
@@ -123,6 +123,10 @@ public class HybSelPerformanceWalker extends LocusWalker<Integer, HybSelPerforma
         return sum;
     }
 
+    public TargetInfo treeReduce(TargetInfo lhs, TargetInfo rhs) {
+        return lhs; // dummy function to test if tree reduce by interval is working
+    }
+
     public void onTraversalDone(TargetInfo result) {
     }
 
@@ -204,7 +208,7 @@ public class HybSelPerformanceWalker extends LocusWalker<Integer, HybSelPerforma
 
             Collection<Interval> bait_quant_hits = bait_quant.getOverlaps(targetInterval);
             String bait_quant_string = (bait_quant_hits.size() == 1) ? bait_quant_hits.iterator().next().getName() : "0";
-            if (bait_quant_hits.size() <= 1) { out.printf("Warning: multiple bait quantity intervals detected; perhaps bait quantity interval lengths don't match primary interval list specified with -L"); }
+            if (bait_quant_hits.size() > 1) { out.printf("Warning: multiple bait quantity intervals detected; perhaps bait quantity interval lengths don't match primary interval list specified with -L\n"); }
             int adjacent_baits = adjacent_bait_detector.getOverlaps(targetInterval).size() - 1;
 
             out.printf("%s:%d-%d\t%d\t%6.4f\t%6.4f\t%6.4f\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%s\t%s\t%d\n",