From 566b556b50e2c4304b3d1b45b4de979d6e283fad Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 20 Dec 2009 03:20:22 +0000
Subject: [PATCH] Give user ability to turn off max allowed interval size

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2414 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/indels/IntervalMergerWalker.java       | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java
index 3ad0284f6..eb6d716ff 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java
@@ -70,7 +70,7 @@ public class IntervalMergerWalker extends ReadWalker<Integer,Integer> {
 
         // ignore all intervals which we've passed
         while ( loc.isPast(currentInterval) ) {
-            if ( currentIntervalIsUsed && currentInterval.getStop() - currentInterval.getStart() < maxIntervalSize) {
+            if ( currentIntervalIsUsed && (maxIntervalSize <= 0 || currentInterval.getStop() - currentInterval.getStart() <= maxIntervalSize) ) {
                 out.println(currentInterval);
                 currentIntervalIsUsed = false;
             }
@@ -106,7 +106,7 @@ public class IntervalMergerWalker extends ReadWalker<Integer,Integer> {
     @Override
     public void onTraversalDone( Integer value ) {
         if ( currentInterval != null && currentIntervalIsUsed &&
-             currentInterval.getStop() - currentInterval.getStart() < maxIntervalSize)
+             (maxIntervalSize <= 0 || currentInterval.getStop() - currentInterval.getStart() < maxIntervalSize) )
             out.println(currentInterval);
     }
 }