diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java
index 03af27f26..a224bc5a3 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java
@@ -65,12 +65,6 @@ public class TribbleRMDTrackBuilder extends PluginManager<FeatureCodec> implemen
      */
     private static Logger logger = Logger.getLogger(TribbleRMDTrackBuilder.class);
 
-    // what index to use
-    static boolean useLinearIndex = true;
-
-    // our bin size
-    static int binSize = 1600;
-
     // the linear index extension
     public static final String indexExtension = ".idx";
 
@@ -197,11 +191,8 @@ public class TribbleRMDTrackBuilder extends PluginManager<FeatureCodec> implemen
 
         // create the index file name, locking on the index file name
         File indexFile = null;
-        if (useLinearIndex)
-            indexFile = new File(inputFile.getAbsoluteFile() + indexExtension);
-        else
-            indexFile = new File(inputFile.getAbsoluteFile() + ".tdx");
-        
+        indexFile = new File(inputFile.getAbsoluteFile() + indexExtension);
+
         FSLockWithShared lock = new FSLockWithShared(indexFile);
 
         // acquire a lock on the file
@@ -317,13 +308,7 @@ public class TribbleRMDTrackBuilder extends PluginManager<FeatureCodec> implemen
         // this can take a while, let them know what we're doing
         logger.info("Creating Tribble index in memory for file " + inputFile);
         IndexCreator creator;
-        if (useLinearIndex) {
-            creator = new LinearIndexCreator(inputFile,codec,null);
-            ((LinearIndexCreator)creator).setBinWidth(binSize);
-        } else {
-            creator = new IntervalIndexCreator(inputFile, codec, null);
-            ((IntervalIndexCreator)creator).setFeaturesPerInterval(binSize);  
-        }
+        creator = new LinearIndexCreator(inputFile, codec, null);
         return creator.createIndex();
     }
 
diff --git a/java/test/org/broadinstitute/sting/WalkerTest.java b/java/test/org/broadinstitute/sting/WalkerTest.java
index f090c7b52..089630e8b 100755
--- a/java/test/org/broadinstitute/sting/WalkerTest.java
+++ b/java/test/org/broadinstitute/sting/WalkerTest.java
@@ -284,7 +284,9 @@ public class WalkerTest extends BaseTest {
         if (CommandLineExecutable.result != 0) {
             throw new RuntimeException("Error running the GATK with arguments: " + args);
         }
-
+        // clean up some memory
+        instance = null;
+        cmd2 = null;
         return new Pair<List<File>, List<String>>(tmpFiles, assertMatchingMD5s(name, tmpFiles, md5s));
     }
 
diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSelectIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSelectIntegrationTest.java
deleted file mode 100755
index edefa76f2..000000000
--- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSelectIntegrationTest.java
+++ /dev/null
@@ -1,71 +0,0 @@
-/*
- * Copyright (c) 2010.
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.playground.gatk.walkers.vcftools;
-
-import org.broadinstitute.sting.WalkerTest;
-import org.junit.Test;
-
-import java.util.Arrays;
-
-public class VariantSelectIntegrationTest extends WalkerTest {
-
-    public static String baseTestString() {
-        return "-T VariantSelect -o %s -R " + b36KGReference;
-    }
-
-
-    @Test
-    public void testVCFSelect1() {
-        WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample3.vcf -match 'AF == 0.50' -L 1:10001290-10048590 ", 1,
-                Arrays.asList("8fd97a99174483920f84aaf54eeb9dd9"));
-        executeTest("testVCFSelect1", spec);
-    }
-
-    @Test
-    public void testVCFSelect2() {
-        WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample3.vcf -match 'HomopolymerRun == 6' -L 1:10001290-10048590 ", 1,
-                Arrays.asList("ecb61d798ff5e0b003d2986500bf4462"));
-        executeTest("testVCFSelect2", spec);
-    }
-
-    @Test
-    public void testVCFSelectOr() {
-        WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample3.vcf -match 'HomopolymerRun == 6' -match 'AF == 0.50' -L 1:10001290-10048590 ", 1,
-                Arrays.asList("7c23412a0abe28057a78cd532b752019"));
-        executeTest("testVCFSelectOr", spec);
-    }
-
-    @Test
-    public void testVCFSelectAnd() {
-        WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample3.vcf -match 'HomopolymerRun == 6 && AF == 0.50' -L 1:10001290-10048590 ", 1,
-                Arrays.asList("71cc18348a9d5de7270613bedb79880a"));
-        executeTest("testVCFSelectAnd", spec);
-    }
-}
\ No newline at end of file