From c2c0c1f57ce5992b98536d64391529642f3bddf1 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 9 Aug 2010 22:27:13 +0000
Subject: [PATCH] Removing used --enable_overlap_filters argument; Eric assures
 me this won't break the currently broken tests

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3992 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/arguments/GATKArgumentCollection.java       | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
index f6143c5ac..fe8821a61 100755
--- a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
@@ -174,10 +174,6 @@ public class GATKArgumentCollection {
     @Argument(fullName = "read_group_black_list", shortName="rgbl", doc="Filters out read groups matching <TAG>:<STRING> or a .txt file containing the filter strings one per line.", required = false)
     public List<String> readGroupBlackList = null;
 
-    @Element(required = false)
-    @Argument(fullName = "enable_overlap_filters",shortName="eof", doc="Enable automatic removal of bases that overlap adaptor sequence or that overlap their mate pair", required = false)
-    public boolean enableOverlapFilters = false;
-
     /**
      * marshal the data out to a object
      *
@@ -344,9 +340,6 @@ public class GATKArgumentCollection {
         if (other.intervalMerging != this.intervalMerging) {
             return false;
         }
-        if (enableOverlapFilters != other.enableOverlapFilters) {
-            return false;
-        }
         if ((other.RODToInterval == null && RODToInterval != null) ||
             (other.RODToInterval != null && !other.RODToInterval.equals(RODToInterval))) {
             return false;