diff --git a/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisTKTest.java b/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisTKTest.java
new file mode 100755
index 000000000..2708d9f4a
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+++ b/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisTKTest.java
@@ -0,0 +1,170 @@
+package org.broadinstitute.sting.gatk;
+
+import net.sf.samtools.SAMSequenceRecord;
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
+import static org.junit.Assert.fail;
+import org.junit.Test;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ *
+ * User: aaron
+ * Date: Apr 28, 2009
+ * Time: 5:21:29 PM
+ *
+ * The Broad Institute
+ * SOFTWARE COPYRIGHT NOTICE AGREEMENT 
+ * This software and its documentation are copyright 2009 by the
+ * Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
+ *
+ * This software is supplied without any warranty or guaranteed support whatsoever. Neither
+ * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
+ *
+ */
+
+
+/**
+ * @author aaron
+ * @version 1.0
+ * @date Apr 28, 2009
+ * <p/>
+ * Class GenomeAnalysisTKTest
+ * <p/>
+ * A quick move of the unit test cases that were stuffed into GenomeAnalysisTK.
+ */
+public class GenomeAnalysisTKTest extends BaseTest {
+
+    // our sequence dictionary to check
+    private final File refFileName = new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/Homo_sapiens_assembly17.fasta");
+
+    // skip n number of chromesomes when we do a chromesome by chromesome jumping
+    private final int skipChrome = 8;
+    /**
+     * This has been blindly moved out of the GenomeAnalysisTK.java where it was hanging on,
+     * but the author makes very limited promises of any functionality 
+     *
+     */
+    @Test
+    public void testNewReferenceFeatures() {
+
+        final FastaSequenceFile2 refFile = new FastaSequenceFile2(refFileName);
+        GenomeLoc.setupRefContigOrdering(refFile);
+
+        List<SAMSequenceRecord> refContigs = refFile.getSequenceDictionary().getSequences();
+
+        /*
+        for ( SAMSequenceRecord refContig: refContigs ) {
+            System.out.printf("  Traversing from chr1 to %s would require jumping %d bytes%n",
+                    refContig.getSequenceName(), refFile.getDistanceBetweenContigs("chr1", refContig.getSequenceName()));
+        }
+        */
+        String lastContig = null;
+        List<Double> timings = new ArrayList<Double>();
+        for ( SAMSequenceRecord startContig : refFile.getSequenceDictionary().getSequences() ) {
+            final String startContigName = startContig.getSequenceName();
+            int skip = 1;
+            for ( SAMSequenceRecord targetContig : refFile.getSequenceDictionary().getSequences() ) {
+                if (skipChrome != skip) {
+                    ++skip;
+                    continue;
+                } else {
+                    skip = 1;
+                }
+
+                refFile.seekToContig(startContigName, true);
+                logger.warn(String.format("Seeking: current=%s, target=%s", startContigName, targetContig.getSequenceName()));
+                long lastTime = System.currentTimeMillis();
+                final boolean success = refFile.seekToContig(targetContig.getSequenceName(), true);
+                long curTime = System.currentTimeMillis();
+                final double elapsed = (curTime - lastTime) / 1000.0;
+                timings.add(elapsed);
+                logger.warn(String.format("  -> Elapsed time %.2f, averaging %.2f sec / seek for %d seeks",
+                        elapsed, Utils.averageDouble(timings), timings.size()));
+
+                if ( ! success ) {
+                    fail(String.format("Failured to seek to %s from %s", targetContig.getSequenceName(), lastContig ));
+
+                }
+                //System.exit(1);
+            }
+        }
+
+        // code for randomly sampling the seeks
+//        Random rnd = new Random();
+//        String lastContig = null;
+//        List<Double> timings = new ArrayList<Double>();
+//        final int N_SAMPLES = 1000;
+//        //try { refFile.seekToContig("chr3"); } catch ( IOException e ) {}
+//        for ( int i = 0; i < N_SAMPLES; i++ ) {
+//            final int nextIndex = rnd.nextInt(refContigs.size());
+//            String nextContig = refFile.getSequenceDictionary().getSequence(nextIndex).getSequenceName();
+//            //nextContig = "chr2";
+//            try {
+//                System.out.printf("Seeking: current=%s, target=%s%n", refFile.getContigName(), nextContig);
+//                long lastTime = System.currentTimeMillis();
+//                final boolean success = refFile.seekToContig(nextContig, true);
+//                long curTime = System.currentTimeMillis();
+//                final double elapsed = (curTime - lastTime) / 1000.0;
+//                timings.add(elapsed);
+//                System.out.printf("  -> Elapsed time %.2f, averaging %.2f sec / seek for %d seeks%n",
+//                        elapsed, Utils.averageDouble(timings), timings.size());
+//
+//                if ( ! success ) {
+//                    System.out.printf("Failured to seek to %s from %s%n", nextContig, lastContig );
+//                }
+//                //System.exit(1);
+//            } catch ( IOException e ) {
+//                System.out.printf("Failured to seek to %s from %s%n", nextContig, lastContig );
+//                e.printStackTrace();
+//            }
+//
+//            lastContig = nextContig;
+//        }
+//        System.exit(1);
+
+/*
+        final String targetChr = "chr10";
+        try {
+            refFile.seekToContig(targetChr);
+        } catch ( IOException e ){
+            System.out.printf("Failured to seek to %s%n", targetChr);
+            e.printStackTrace();
+        }
+        System.exit(1);
+
+
+        //List<Double> timings = new ArrayList<Double>();
+        final long startTime = System.currentTimeMillis();
+        long lastTime = System.currentTimeMillis();
+
+        int i = 0;
+        String prevNextContigName = null;
+        logger.info(String.format("Walking reference sequence:%n"));
+        for ( SAMSequenceRecord refContig: refContigs ) {
+            long curTime = System.currentTimeMillis();
+            ReferenceSequence contig = refFile.nextSequence();
+            final double elapsed = (curTime - lastTime) / 1000.0;
+            timings.add(elapsed);
+            logger.info(String.format("%2d : expected %s contig, found %s with next of %s after %.2f seconds, average is %.2f", i,
+                    refContig.getSequenceName(), contig.getName(), refFile.getNextContigName(), elapsed, Utils.averageDouble(timings)));
+            if ( prevNextContigName != null && contig.getName() != null && ! prevNextContigName.equals(contig.getName()) )
+                throw new RuntimeIOException(String.format("Unexpected contig ordering %s was expected next, but I found %s?",
+                        prevNextContigName, contig.getName()));
+
+            prevNextContigName = refFile.getNextContigName();
+            lastTime = curTime;
+            i++;
+
+            logger.info(String.format("  Traversing from chr1 to %s would require jumping %d bytes",
+                    contig.getName(), refFile.getDistanceBetweenContigs("chr1", contig.getName())));
+        }
+        */
+    }
+
+}