From 1ea5ec276bea63c485ff2b8cd4cf31265682ba25 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 9 Aug 2011 23:28:59 -0400
Subject: [PATCH] Minor cleanup

---
 .../gatk/walkers/indels/IndelRealigner.java      | 16 ----------------
 .../indels/IndelRealignerIntegrationTest.java    |  1 -
 2 files changed, 17 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index cb7627888..dcd4f5dec 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -36,7 +36,6 @@ import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.walkers.BAQMode;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
@@ -159,21 +158,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
     protected boolean CHECKEARLY = false;
 
 
-    // DEPRECATED
-
-    @Deprecated
-    @Argument(fullName="sortInCoordinateOrderEvenThoughItIsHighlyUnsafe", doc="This argument is no longer used.", required=false)
-    protected boolean DEPRECATED_SORT_IN_COORDINATE_ORDER = false;
-
-    @Deprecated
-    @Argument(fullName="realignReadsWithBadMates", doc="This argument is no longer used.", required=false)
-    protected boolean DEPRECATED_REALIGN_MATES = false;
-
-    @Deprecated
-    @Argument(fullName="useOnlyKnownIndels", shortName="knownsOnly", doc="This argument is no longer used. See --consensusDeterminationModel instead.", required=false)
-    protected boolean DEPRECATED_KNOWNS_ONLY = false;
-
-
     // DEBUGGING OPTIONS FOLLOW
 
     @Hidden
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
index 28e5a15de..0ff6fc244 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.indels;
 
 import org.broadinstitute.sting.WalkerTest;
-import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.testng.annotations.Test;
 
 import java.util.Arrays;