Limiting access to the DT classes

* Make most classes final, others package local
    * Move to diagnostics.diagnosetargets package
    * Aggregate statistics and walker classes on the same package for simplified visibility.
    * Make status list a LinkedList instead of a HashSet

protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/BaseCoverageDistribution.java

@@ -44,7 +44,7 @@
 *  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
 */
 
-package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
+package org.broadinstitute.sting.gatk.walkers.diagnostics;
 
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;

protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/FindCoveredIntervals.java

@@ -44,7 +44,7 @@
 *  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
 */
 
-package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
+package org.broadinstitute.sting.gatk.walkers.diagnostics;
 
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;

protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/CallableStatus.java

@@ -44,7 +44,7 @@
 *  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
 */
 
-package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
+package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
 
 /**
  * Short one line description of the walker.
@@ -52,7 +52,7 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
  * @author Mauricio Carneiro
  * @since 2/1/12
  */
-public enum CallableStatus {
+enum CallableStatus {
 
     PASS("the base satisfied the min. depth for calling but had less than maxDepth to avoid having EXCESSIVE_COVERAGE"),
 

protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java

@@ -44,7 +44,7 @@
 *  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
 */
 
-package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
+package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
 
 import net.sf.picard.util.PeekableIterator;
 import org.broadinstitute.sting.commandline.ArgumentCollection;
@@ -54,9 +54,6 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.statistics.Interval;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.statistics.Locus;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.statistics.Sample;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
@@ -259,7 +256,7 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
         VariantContextBuilder vcb = new VariantContextBuilder("DiagnoseTargets", interval.getContig(), interval.getStart(), interval.getStop(), alleles);
 
         vcb = vcb.log10PError(VariantContext.NO_LOG10_PERROR);
-        vcb.filters(new HashSet<String>(statusesToStrings(stats.callableStatuses(), true)));
+        vcb.filters(new LinkedHashSet<String>(statusToStrings(stats.callableStatuses(), true)));
 
         attributes.put(VCFConstants.END_KEY, interval.getStop());
         attributes.put(AVG_INTERVAL_DP_KEY, stats.averageCoverage());
@@ -268,10 +265,10 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
         for (String sample : samples) {
             final GenotypeBuilder gb = new GenotypeBuilder(sample);
 
-            SampleStatistics sampleStat = stats.getSampleStatics(sample);
+            SampleStatistics sampleStat = stats.getSampleStatistics(sample);
             gb.attribute(AVG_INTERVAL_DP_KEY, sampleStat.averageCoverage());
 
-            gb.filters(statusesToStrings(stats.getSampleStatics(sample).getCallableStatuses(), false));
+            gb.filters(statusToStrings(stats.getSampleStatistics(sample).callableStatuses(), false));
 
             genotypes.add(gb.make());
         }
@@ -286,7 +283,7 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
      * @param statuses the set of statuses to be converted
      * @return a matching set of strings
      */
-    private List<String> statusesToStrings(Set<CallableStatus> statuses, final boolean isInfoField) {
+    private List<String> statusToStrings(List<CallableStatus> statuses, final boolean isInfoField) {
         List<String> output = new ArrayList<String>(statuses.size());
 
         for (CallableStatus status : statuses)

protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/Interval.java

@@ -44,11 +44,7 @@
 *  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
 */
 
-package org.broadinstitute.sting.gatk.walkers.diagnostics.targets.statistics;
+package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
-
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.CallableStatus;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.IntervalStatistics;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.ThresHolder;
 
 /**
  * Created with IntelliJ IDEA.
@@ -57,7 +53,7 @@ import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.ThresHolder;
  * Time: 11:30 PM
  * To change this template use File | Settings | File Templates.
  */
-public interface Interval {
+interface Interval {
     public void initialize(ThresHolder thresholds);
     public CallableStatus status (IntervalStatistics intervalStatistics);
 }

protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/IntervalStatistics.java

@@ -44,21 +44,16 @@
 *  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
 */
 
-package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
+package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.statistics.Interval;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
-import java.util.HashMap;
+import java.util.*;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
-
-public class IntervalStatistics {
 
+final class IntervalStatistics {
     private final Map<String, SampleStatistics> samples;
     private final GenomeLoc interval;
     private final ThresHolder thresholds;
@@ -73,7 +68,7 @@ public class IntervalStatistics {
             this.samples.put(sample, new SampleStatistics(interval, thresholds));
     }
 
-    public SampleStatistics getSampleStatics(String sample) {
+    public SampleStatistics getSampleStatistics(String sample) {
         return samples.get(sample);
     }
 
@@ -126,13 +121,13 @@ public class IntervalStatistics {
      *
      * @return the callable status(es) for the whole interval
      */
-    public Set<CallableStatus> callableStatuses() {
+    public List<CallableStatus> callableStatuses() {
-        final Set<CallableStatus> output = new HashSet<CallableStatus>();
+        final List<CallableStatus> output = new LinkedList<CallableStatus>();
 
         // sum up all the callable status for each sample
         final Map<CallableStatus, Integer> sampleStatusTally = new HashMap<CallableStatus, Integer>(CallableStatus.values().length);
         for (SampleStatistics sampleStatistics : samples.values()) {
-            for (CallableStatus status : sampleStatistics.getCallableStatuses()) {
+            for (CallableStatus status : sampleStatistics.callableStatuses()) {
                 sampleStatusTally.put(status, !sampleStatusTally.containsKey(status) ? 1 : sampleStatusTally.get(status) + 1);
             }
         }

protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/Locus.java

@@ -44,12 +44,7 @@
 *  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
 */
 
-package org.broadinstitute.sting.gatk.walkers.diagnostics.targets.statistics;
+package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
-
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.CallableStatus;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.LocusStatistics;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.SampleStatistics;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.ThresHolder;
 
 /**
  * Created with IntelliJ IDEA.
@@ -58,7 +53,7 @@ import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.ThresHolder;
  * Time: 11:29 PM
  * To change this template use File | Settings | File Templates.
  */
-public interface Locus {
+interface Locus {
     public void initialize(ThresHolder thresholds);
     public CallableStatus status (LocusStatistics locusStatistics);
     public CallableStatus sampleStatus (SampleStatistics sampleStatistics);

protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusCoverageGap.java

@@ -44,19 +44,14 @@
 *  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
 */
 
-package org.broadinstitute.sting.gatk.walkers.diagnostics.targets.statistics;
+package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
-
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.CallableStatus;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.LocusStatistics;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.SampleStatistics;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.ThresHolder;
 
 /**
  * User: carneiro
  * Date: 4/20/13
  * Time: 11:44 PM
  */
-public class LocusCoverageGap implements Locus {
+final class LocusCoverageGap implements Locus {
     private double threshold;
     private static final CallableStatus CALL = CallableStatus.COVERAGE_GAPS;
 

protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusExcessiveCoverage.java

@@ -44,19 +44,14 @@
 *  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
 */
 
-package org.broadinstitute.sting.gatk.walkers.diagnostics.targets.statistics;
+package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
-
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.CallableStatus;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.LocusStatistics;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.SampleStatistics;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.ThresHolder;
 
 /**
  * User: carneiro
  * Date: 4/20/13
  * Time: 11:44 PM
  */
-public class LocusExcessiveCoverage implements Locus {
+final class LocusExcessiveCoverage implements Locus {
     private int excessiveCoverage;
     private double threshold;
     private static final CallableStatus CALL = CallableStatus.EXCESSIVE_COVERAGE ;

protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusLowCoverage.java

@@ -44,19 +44,14 @@
 *  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
 */
 
-package org.broadinstitute.sting.gatk.walkers.diagnostics.targets.statistics;
+package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
-
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.CallableStatus;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.LocusStatistics;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.SampleStatistics;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.ThresHolder;
 
 /**
  * User: carneiro
  * Date: 4/20/13
  * Time: 11:44 PM
  */
-public class LocusLowCoverage implements Locus {
+final class LocusLowCoverage implements Locus {
     private int minCoverage;
     private double threshold;
     private static final CallableStatus CALL = CallableStatus.LOW_COVERAGE ;

protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusPoorQuality.java

@@ -44,19 +44,14 @@
 *  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
 */
 
-package org.broadinstitute.sting.gatk.walkers.diagnostics.targets.statistics;
+package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
-
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.CallableStatus;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.LocusStatistics;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.SampleStatistics;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.ThresHolder;
 
 /**
  * User: carneiro
  * Date: 4/20/13
  * Time: 11:44 PM
  */
-public class LocusPoorQuality implements Locus {
+final class LocusPoorQuality implements Locus {
     private int minCoverage;
     private double threshold;
     private static final CallableStatus CALL = CallableStatus.POOR_QUALITY ;

protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusStatistics.java

@@ -44,15 +44,12 @@
 *  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
 */
 
-package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
+package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
 
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.statistics.Locus;
+import java.util.LinkedList;
-
-import java.util.HashSet;
 import java.util.List;
-import java.util.Set;
 
-public class LocusStatistics {
+final class LocusStatistics {
     private int coverage;
     private int rawCoverage;
     private final List<Locus> locusStatisticsList;
@@ -80,8 +77,8 @@ public class LocusStatistics {
      *
      * @return a set of all statuses that apply
      */
-    public Set<CallableStatus> callableStatuses() {
+    public List<CallableStatus> callableStatuses() {
-        Set<CallableStatus> output = new HashSet<CallableStatus>();
+        List<CallableStatus> output = new LinkedList<CallableStatus>();
         for (Locus stats : locusStatisticsList) {
             CallableStatus status = stats.status(this);
             if (status != null) {

protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/PluginUtils.java

@@ -44,10 +44,7 @@
 *  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
 */
 
-package org.broadinstitute.sting.gatk.walkers.diagnostics.targets.statistics;
+package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
-
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.CallableStatus;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.SampleStatistics;
 
 import java.util.Map;
 
@@ -56,7 +53,7 @@ import java.util.Map;
  * Date: 4/21/13
  * Time: 11:23 AM
  */
-public class PluginUtils {
+final class PluginUtils {
     public static CallableStatus genericSampleStatus (final SampleStatistics sampleStatistics, final CallableStatus CALL, final double threshold) {
         final Map<CallableStatus, Integer> totals = sampleStatistics.getLocusStatusTally();
         final int size = sampleStatistics.getIntervalSize();

protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/Sample.java

@@ -44,11 +44,7 @@
 *  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
 */
 
-package org.broadinstitute.sting.gatk.walkers.diagnostics.targets.statistics;
+package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
-
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.CallableStatus;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.SampleStatistics;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.ThresHolder;
 
 /**
  * Created with IntelliJ IDEA.
@@ -57,7 +53,7 @@ import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.ThresHolder;
  * Time: 11:30 PM
  * To change this template use File | Settings | File Templates.
  */
-public interface Sample {
+interface Sample {
     public void initialize(ThresHolder thresholds);
     public CallableStatus status (SampleStatistics sampleStatistics);
 }

protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleBadMates.java

@@ -44,18 +44,14 @@
 *  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
 */
 
-package org.broadinstitute.sting.gatk.walkers.diagnostics.targets.statistics;
+package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
-
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.CallableStatus;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.SampleStatistics;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.ThresHolder;
 
 /**
  * User: carneiro
  * Date: 4/20/13
  * Time: 11:44 PM
  */
-public class SampleBadMates implements Sample {
+final class SampleBadMates implements Sample {
     private static final CallableStatus CALL = CallableStatus.NO_READS ;
 
     private double threshold;

protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleNoReads.java

@@ -44,18 +44,14 @@
 *  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
 */
 
-package org.broadinstitute.sting.gatk.walkers.diagnostics.targets.statistics;
+package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
-
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.CallableStatus;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.SampleStatistics;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.ThresHolder;
 
 /**
  * User: carneiro
  * Date: 4/20/13
  * Time: 11:44 PM
  */
-public class SampleNoReads implements Sample {
+final class SampleNoReads implements Sample {
     private static final CallableStatus CALL = CallableStatus.NO_READS;
 
     private double votingThreshold;

protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleStatistics.java

@@ -44,10 +44,8 @@
 *  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
 */
 
-package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
+package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
 
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.statistics.Locus;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.statistics.Sample;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@@ -58,7 +56,7 @@ import java.util.*;
 /**
  * The statistics calculator for a specific sample given the interval
  */
-public class SampleStatistics {
+final class SampleStatistics {
     private final GenomeLoc interval;
     private final ArrayList<LocusStatistics> loci;
     private final ThresHolder thresholds;
@@ -129,8 +127,8 @@ public class SampleStatistics {
      *
      * @return the callable statuses of the entire sample
      */
-    public Set<CallableStatus> getCallableStatuses() {
+    public List<CallableStatus> callableStatuses() {
-        final Set<CallableStatus> output = new HashSet<CallableStatus>();
+        final List<CallableStatus> output = new LinkedList<CallableStatus>();
 
         // get the tally of all the locus callable statuses
         for (Locus locusStat : thresholds.locusStatisticList) {

protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java

@@ -44,17 +44,14 @@
 *  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
 */
 
-package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
+package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
 
 import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.statistics.Interval;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.statistics.Locus;
-import org.broadinstitute.sting.gatk.walkers.diagnostics.targets.statistics.Sample;
 
 import java.util.LinkedList;
 import java.util.List;
 
-public class ThresHolder {
+final class ThresHolder {
 
     /**
      * Only bases with quality greater than this will be considered in the coverage metrics.

protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/BaseCoverageDistributionIntegrationTest.java

@@ -44,7 +44,7 @@
 *  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
 */
 
-package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
+package org.broadinstitute.sting.gatk.walkers.diagnostics;
 
 import org.broadinstitute.sting.WalkerTest;
 import org.testng.annotations.DataProvider;

protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java

@@ -44,23 +44,23 @@
 *  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
 */
 
-package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
+package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
 
+import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.WalkerTest;
 import org.testng.annotations.Test;
 
 import java.util.Arrays;
 
 public class DiagnoseTargetsIntegrationTest extends WalkerTest {
-    final static String REF = b37KGReference;
+    final static String REF = BaseTest.b37KGReference;
-    final String singleSample = validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.bam";
+    final String singleSample = BaseTest.validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.bam";
-    final String multiSample = validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam";
+    final String multiSample = BaseTest.validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam";
-    final String L = validationDataLocation + "DT-itest.interval_list";
+    final String L = BaseTest.validationDataLocation + "DT-itest.interval_list";
 
     private void DTTest(String testName, String args, String md5) {
         String base = String.format("-T DiagnoseTargets  --no_cmdline_in_header -R %s -L %s", REF, L) + " -o %s ";
         WalkerTestSpec spec = new WalkerTestSpec(base + args, Arrays.asList(md5));
-        //spec.disableShadowBCF();
         executeTest(testName, spec);
     }
 

protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusStatisticsUnitTest.java

@@ -44,14 +44,14 @@
 *  7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
 */
 
-package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
+package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
 
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
-import java.util.Set;
+import java.util.List;
 
 public class LocusStatisticsUnitTest {
 
@@ -64,7 +64,7 @@ public class LocusStatisticsUnitTest {
 
     @Test(dataProvider = "StatusTestValues")
     public void testCallableStatuses(int coverage, int rawCoverage, CallableStatus status) {
-        Set<CallableStatus> statuses = new LocusStatistics(coverage, rawCoverage, thresholds).callableStatuses();
+        List<CallableStatus> statuses = new LocusStatistics(coverage, rawCoverage, thresholds).callableStatuses();
         Assert.assertTrue((status == null) ? statuses.isEmpty() : (statuses.contains(status) && statuses.size() == 1));
     }