Split class names into stratification and metrics

Calling everything statistics was very confusing. Diagnose Targets stratifies the data three ways: Interval, Sample and Locus. Each stratification then has it's own set of metrics (plugin system) to calculate -- LocusMetric, SampleMetric, IntervalMetric.

 Metrics are generalized by the Metric interface. (for generic access)
 Stratifications are generalized by the AbstractStratification abstract class. (to aggressively limit code duplication)

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

@@ -57,7 +57,7 @@ import java.util.Map;
  * @author Mauricio Carneiro
  * @since 4/23/13
  */
-abstract class AbstractStatistics {
+abstract class AbstractStratification {
 
     private long preComputedTotalCoverage = -1;
     private Map<CallableStatus, Integer> statusTally = null;
@@ -93,9 +93,9 @@ abstract class AbstractStatistics {
      *
      * @return the total coverage
      */
-    private long calculateTotalCoverage(Iterable<AbstractStatistics> elements) {
+    private long calculateTotalCoverage(Iterable<AbstractStratification> elements) {
         long cov = 0;
-        for (AbstractStatistics element : elements) {
+        for (AbstractStratification element : elements) {
             cov += element.getCoverage();
         }
         return cov;
@@ -109,7 +109,7 @@ abstract class AbstractStatistics {
      *
      * @return the corresponding list of elements of the extending class
      */
-    public abstract Iterable<AbstractStatistics> getElements();
+    public abstract Iterable<AbstractStratification> getElements();
 
     /**
      * Calculates the Callable statuses for the statistic as a whole (interval, sample or locus)
@@ -127,7 +127,7 @@ abstract class AbstractStatistics {
     public Map<CallableStatus, Integer> getStatusTally() {
         if (statusTally == null) {
             statusTally = new HashMap<CallableStatus, Integer>(CallableStatus.values().length);
-            for (AbstractStatistics stats : getElements()) {
+            for (AbstractStratification stats : getElements()) {
                 for (CallableStatus status : stats.callableStatuses()) {
                     statusTally.put(status, !statusTally.containsKey(status) ? 1 : statusTally.get(status) + 1);
                 }
@@ -136,9 +136,9 @@ abstract class AbstractStatistics {
         return statusTally;
     }
 
-    public static List<CallableStatus> queryStatus(List<Statistic> statList, AbstractStatistics stratification) {
+    public static List<CallableStatus> queryStatus(List<Metric> statList, AbstractStratification stratification) {
         List<CallableStatus> output = new LinkedList<CallableStatus>();
-        for (Statistic stat : statList) {
+        for (Metric stat : statList) {
             final CallableStatus status = stat.status(stratification);
             if (status != null) {
                 output.add(status);

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

@@ -119,7 +119,7 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
     @ArgumentCollection
     private ThresHolder thresholds = new ThresHolder();
 
-    private Map<GenomeLoc, IntervalStatistics> intervalMap = null;              // maps each interval => statistics
+    private Map<GenomeLoc, IntervalStratification> intervalMap = null;              // maps each interval => statistics
     private PeekableIterator<GenomeLoc> intervalListIterator;                   // an iterator to go over all the intervals provided as we traverse the genome
     private Set<String> samples = null;                                         // all the samples being processed
     private static final Allele SYMBOLIC_ALLELE = Allele.create("<DT>", false); // avoid creating the symbolic allele multiple times
@@ -134,7 +134,7 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
         if (getToolkit().getIntervals() == null || getToolkit().getIntervals().isEmpty())
             throw new UserException("This tool only works if you provide one or more intervals (use the -L argument). If you want to run whole genome, use -T DepthOfCoverage instead.");
 
-        intervalMap = new HashMap<GenomeLoc, IntervalStatistics>(INITIAL_HASH_SIZE);
+        intervalMap = new HashMap<GenomeLoc, IntervalStratification>(INITIAL_HASH_SIZE);
         intervalListIterator = new PeekableIterator<GenomeLoc>(getToolkit().getIntervals().iterator());
 
         // get all of the unique sample names for the VCF Header
@@ -155,8 +155,8 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
         addNewOverlappingIntervals(refLocus);
 
         // at this point, all intervals in intervalMap overlap with this locus, so update all of them
-        for (IntervalStatistics intervalStatistics : intervalMap.values())
+        for (IntervalStratification intervalStratification : intervalMap.values())
-            intervalStatistics.addLocus(context);
+            intervalStratification.addLocus(context);
 
         return 1L;
     }
@@ -207,7 +207,7 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
 
         // output empty statistics for uncovered intervals
         while (interval != null && interval.isBefore(refLocus)) {
-            final IntervalStatistics stats = intervalMap.get(interval);
+            final IntervalStratification stats = intervalMap.get(interval);
             outputStatsToVCF(stats != null ? stats : createIntervalStatistic(interval), UNCOVERED_ALLELE);
             if (stats != null) intervalMap.remove(interval);
             intervalListIterator.next();
@@ -243,7 +243,7 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
      * @param stats     The statistics of the interval
      * @param refAllele the reference allele
      */
-    private void outputStatsToVCF(IntervalStatistics stats, Allele refAllele) {
+    private void outputStatsToVCF(IntervalStratification stats, Allele refAllele) {
         GenomeLoc interval = stats.getInterval();
 
 
@@ -265,7 +265,7 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
         for (String sample : samples) {
             final GenotypeBuilder gb = new GenotypeBuilder(sample);
 
-            SampleStatistics sampleStat = stats.getSampleStatistics(sample);
+            SampleStratification sampleStat = stats.getSampleStatistics(sample);
             gb.attribute(AVG_INTERVAL_DP_KEY, sampleStat.averageCoverage(interval.size()));
 
             gb.filters(statusToStrings(stats.getSampleStatistics(sample).callableStatuses(), false));
@@ -293,36 +293,36 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
         return output;
     }
 
-    private IntervalStatistics createIntervalStatistic(GenomeLoc interval) {
+    private IntervalStratification createIntervalStatistic(GenomeLoc interval) {
-        return new IntervalStatistics(samples, interval, thresholds);
+        return new IntervalStratification(samples, interval, thresholds);
     }
 
     protected static void loadAllPlugins(final ThresHolder thresholds) {
-        for (Class<?> stat : new PluginManager<Locus>(Locus.class).getPlugins()) {
+        for (Class<?> stat : new PluginManager<LocusMetric>(LocusMetric.class).getPlugins()) {
             try {
-                final Locus stats = (Locus) stat.newInstance();
+                final LocusMetric stats = (LocusMetric) stat.newInstance();
                 stats.initialize(thresholds);
-                thresholds.locusStatisticList.add(stats);
+                thresholds.locusMetricList.add(stats);
             } catch (Exception e) {
                 throw new DynamicClassResolutionException(stat, e);
             }
         }
 
-        for (Class<?> stat : new PluginManager<Sample>(Sample.class).getPlugins()) {
+        for (Class<?> stat : new PluginManager<SampleMetric>(SampleMetric.class).getPlugins()) {
             try {
-                final Sample stats = (Sample) stat.newInstance();
+                final SampleMetric stats = (SampleMetric) stat.newInstance();
                 stats.initialize(thresholds);
-                thresholds.sampleStatisticList.add(stats);
+                thresholds.sampleMetricList.add(stats);
             } catch (Exception e) {
                 throw new DynamicClassResolutionException(stat, e);
             }
         }
 
-        for (Class<?> stat : new PluginManager<Interval>(Interval.class).getPlugins()) {
+        for (Class<?> stat : new PluginManager<IntervalMetric>(IntervalMetric.class).getPlugins()) {
             try {
-                final Interval stats = (Interval) stat.newInstance();
+                final IntervalMetric stats = (IntervalMetric) stat.newInstance();
                 stats.initialize(thresholds);
-                thresholds.intervalStatisticList.add(stats);
+                thresholds.intervalMetricList.add(stats);
             } catch (Exception e) {
                 throw new DynamicClassResolutionException(stat, e);
             }

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

@@ -53,5 +53,5 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
  * Time: 11:30 PM
  * To change this template use File | Settings | File Templates.
  */
-interface Sample extends Statistic {
+interface IntervalMetric extends Metric {
 }

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

@@ -53,21 +53,21 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
 import java.util.*;
 
-final class IntervalStatistics extends AbstractStatistics{
+final class IntervalStratification extends AbstractStratification {
-    private final Map<String, AbstractStatistics> samples;
+    private final Map<String, AbstractStratification> samples;
     private final GenomeLoc interval;
     private final ThresHolder thresholds;
 
-    public IntervalStatistics(Set<String> samples, GenomeLoc interval, ThresHolder thresholds) {
+    public IntervalStratification(Set<String> samples, GenomeLoc interval, ThresHolder thresholds) {
         this.interval = interval;
         this.thresholds = thresholds;
-        this.samples = new HashMap<String, AbstractStatistics>(samples.size());
+        this.samples = new HashMap<String, AbstractStratification>(samples.size());
         for (String sample : samples)
-            this.samples.put(sample, new SampleStatistics(interval, thresholds));
+            this.samples.put(sample, new SampleStratification(interval, thresholds));
     }
 
-    public SampleStatistics getSampleStatistics(String sample) {
+    public SampleStratification getSampleStatistics(String sample) {
-        return (SampleStatistics) samples.get(sample);
+        return (SampleStratification) samples.get(sample);
     }
 
     public GenomeLoc getInterval() {
@@ -92,12 +92,12 @@ final class IntervalStatistics extends AbstractStatistics{
         for (Map.Entry<String, ReadBackedPileup> entry : samplePileups.entrySet()) {
             String sample = entry.getKey();
             ReadBackedPileup samplePileup = entry.getValue();
-            SampleStatistics sampleStatistics = (SampleStatistics) samples.get(sample);
+            SampleStratification sampleStratification = (SampleStratification) samples.get(sample);
 
-            if (sampleStatistics == null)
+            if (sampleStratification == null)
                 throw new ReviewedStingException(String.format("Trying to add locus statistics to a sample (%s) that doesn't exist in the Interval.", sample));
 
-            sampleStatistics.addLocus(context.getLocation(), samplePileup);
+            sampleStratification.addLocus(context.getLocation(), samplePileup);
         }
 
     }
@@ -106,7 +106,7 @@ final class IntervalStatistics extends AbstractStatistics{
      * {@inheritDoc}
      */
     @Override
-    public Iterable<AbstractStatistics> getElements() {
+    public Iterable<AbstractStratification> getElements() {
         return samples.values();
     }
 
@@ -125,7 +125,7 @@ final class IntervalStatistics extends AbstractStatistics{
             }
         }
 
-        output.addAll(queryStatus(thresholds.intervalStatisticList, this));
+        output.addAll(queryStatus(thresholds.intervalMetricList, this));
 
         return output;
     }

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

@@ -53,6 +53,6 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
  * Time: 11:29 PM
  * To change this template use File | Settings | File Templates.
  */
-interface Locus extends Statistic {
+interface LocusMetric extends Metric {
-    public CallableStatus sampleStatus (SampleStatistics sampleStatistics);
+    public CallableStatus sampleStatus (SampleStratification sampleStratification);
 }

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

@@ -51,7 +51,7 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
  * Date: 4/20/13
  * Time: 11:44 PM
  */
-final class LocusCoverageGap implements Locus {
+final class LocusMetricCoverageGap implements LocusMetric {
     private double threshold;
     private static final CallableStatus CALL = CallableStatus.COVERAGE_GAPS;
 
@@ -61,13 +61,13 @@ final class LocusCoverageGap implements Locus {
     }
 
     @Override
-    public CallableStatus status(AbstractStatistics statistics) {
+    public CallableStatus status(AbstractStratification statistics) {
-        final LocusStatistics locusStatistics = (LocusStatistics) statistics;
+        final LocusStratification locusStratification = (LocusStratification) statistics;
-        return locusStatistics.getRawCoverage() == 0 ? CALL : null;
+        return locusStratification.getRawCoverage() == 0 ? CALL : null;
     }
 
     @Override
-    public CallableStatus sampleStatus(SampleStatistics sampleStatistics) {
+    public CallableStatus sampleStatus(SampleStratification sampleStratification) {
-        return PluginUtils.genericSampleStatus(sampleStatistics, CALL, threshold);
+        return PluginUtils.genericSampleStatus(sampleStratification, CALL, threshold);
     }
 }

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

@@ -51,7 +51,7 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
  * Date: 4/20/13
  * Time: 11:44 PM
  */
-final class LocusExcessiveCoverage implements Locus {
+final class LocusMetricExcessiveCoverage implements LocusMetric {
     private int excessiveCoverage;
     private double threshold;
     private static final CallableStatus CALL = CallableStatus.EXCESSIVE_COVERAGE ;
@@ -63,13 +63,13 @@ final class LocusExcessiveCoverage implements Locus {
     }
 
     @Override
-    public CallableStatus status(AbstractStatistics statistics) {
+    public CallableStatus status(AbstractStratification statistics) {
-        final LocusStatistics locusStatistics = (LocusStatistics) statistics;
+        final LocusStratification locusStratification = (LocusStratification) statistics;
-        return locusStatistics.getCoverage() > excessiveCoverage ? CALL : null;
+        return locusStratification.getCoverage() > excessiveCoverage ? CALL : null;
     }
 
     @Override
-    public CallableStatus sampleStatus(SampleStatistics sampleStatistics) {
+    public CallableStatus sampleStatus(SampleStratification sampleStratification) {
-        return PluginUtils.genericSampleStatus(sampleStatistics, CALL, threshold);
+        return PluginUtils.genericSampleStatus(sampleStratification, CALL, threshold);
     }
 }

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

@@ -51,7 +51,7 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
  * Date: 4/20/13
  * Time: 11:44 PM
  */
-final class LocusLowCoverage implements Locus {
+final class LocusMetricLowCoverage implements LocusMetric {
     private int minCoverage;
     private double threshold;
     private static final CallableStatus CALL = CallableStatus.LOW_COVERAGE ;
@@ -63,14 +63,14 @@ final class LocusLowCoverage implements Locus {
     }
 
     @Override
-    public CallableStatus status(AbstractStatistics statistics) {
+    public CallableStatus status(AbstractStratification statistics) {
-        final LocusStatistics locusStatistics = (LocusStatistics) statistics;
+        final LocusStratification locusStratification = (LocusStratification) statistics;
-        final long raw = locusStatistics.getRawCoverage();
+        final long raw = locusStratification.getRawCoverage();
         return raw > 0 && raw < minCoverage ? CALL: null;
     }
 
     @Override
-    public CallableStatus sampleStatus(SampleStatistics sampleStatistics) {
+    public CallableStatus sampleStatus(SampleStratification sampleStratification) {
-        return PluginUtils.genericSampleStatus(sampleStatistics, CALL, threshold);
+        return PluginUtils.genericSampleStatus(sampleStratification, CALL, threshold);
     }
 }

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

@@ -51,7 +51,7 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
  * Date: 4/20/13
  * Time: 11:44 PM
  */
-final class LocusPoorQuality implements Locus {
+final class LocusMetricPoorQuality implements LocusMetric {
     private int minCoverage;
     private double threshold;
     private static final CallableStatus CALL = CallableStatus.POOR_QUALITY ;
@@ -63,13 +63,13 @@ final class LocusPoorQuality implements Locus {
     }
 
     @Override
-    public CallableStatus status(AbstractStatistics statistics) {
+    public CallableStatus status(AbstractStratification statistics) {
-        final LocusStatistics locusStatistics = (LocusStatistics) statistics;
+        final LocusStratification locusStratification = (LocusStratification) statistics;
-        return locusStatistics.getCoverage() < minCoverage && locusStatistics.getRawCoverage() >= minCoverage ? CALL: null;
+        return locusStratification.getCoverage() < minCoverage && locusStratification.getRawCoverage() >= minCoverage ? CALL: null;
     }
 
     @Override
-    public CallableStatus sampleStatus(SampleStatistics sampleStatistics) {
+    public CallableStatus sampleStatus(SampleStratification sampleStratification) {
-        return PluginUtils.genericSampleStatus(sampleStatistics, CALL, threshold);
+        return PluginUtils.genericSampleStatus(sampleStratification, CALL, threshold);
     }
 }

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

@@ -49,19 +49,19 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
 import java.util.LinkedList;
 import java.util.List;
 
-final class LocusStatistics extends AbstractStatistics{
+final class LocusStratification extends AbstractStratification {
     private long coverage;
     private long rawCoverage;
-    private final List<Statistic> locusStatisticsList;
+    private final List<Metric> locusStatisticsList;
 
-    public LocusStatistics(ThresHolder thresholds) {
+    public LocusStratification(ThresHolder thresholds) {
         this(0,0,thresholds);
     }
 
-    protected LocusStatistics(int coverage, int rawCoverage, ThresHolder thresholds) {
+    protected LocusStratification(int coverage, int rawCoverage, ThresHolder thresholds) {
         this.coverage = coverage;
         this.rawCoverage = rawCoverage;
-        this.locusStatisticsList = thresholds.locusStatisticList;
+        this.locusStatisticsList = thresholds.locusMetricList;
     }
 
     @Override
@@ -80,7 +80,7 @@ final class LocusStatistics extends AbstractStatistics{
      */
     public List<CallableStatus> callableStatuses() {
         List<CallableStatus> output = new LinkedList<CallableStatus>();
-        for (Statistic stats : locusStatisticsList) {
+        for (Metric stats : locusStatisticsList) {
             CallableStatus status = stats.status(this);
             if (status != null) {
                 output.add(status);
@@ -90,7 +90,7 @@ final class LocusStatistics extends AbstractStatistics{
     }
 
     @Override
-    public Iterable<AbstractStatistics> getElements() {
+    public Iterable<AbstractStratification> getElements() {
         return null;
     }
 

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

@@ -51,7 +51,7 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
  * @author Mauricio Carneiro
  * @since 4/23/13
  */
-interface Statistic {
+interface Metric {
     public void initialize(ThresHolder thresholds);
-    public CallableStatus status (AbstractStatistics statistic);
+    public CallableStatus status (AbstractStratification statistic);
 }

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

@@ -54,9 +54,9 @@ import java.util.Map;
  * Time: 11:23 AM
  */
 final class PluginUtils {
-    public static CallableStatus genericSampleStatus (final SampleStatistics sampleStatistics, final CallableStatus CALL, final double threshold) {
+    public static CallableStatus genericSampleStatus (final SampleStratification sampleStratification, final CallableStatus CALL, final double threshold) {
-        final Map<CallableStatus, Integer> totals = sampleStatistics.getStatusTally();
+        final Map<CallableStatus, Integer> totals = sampleStratification.getStatusTally();
-        final int size = sampleStatistics.getIntervalSize();
+        final int size = sampleStratification.getIntervalSize();
         final int statusCount = totals.containsKey(CALL) ? totals.get(CALL) : 0;
         return ( (double) statusCount / size) >= threshold ? CALL: null;
     }

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

@@ -53,5 +53,5 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
  * Time: 11:30 PM
  * To change this template use File | Settings | File Templates.
  */
-interface Interval extends Statistic {
+interface SampleMetric extends Metric {
 }

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

@@ -51,7 +51,7 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
  * Date: 4/20/13
  * Time: 11:44 PM
  */
-final class SampleBadMates implements Sample {
+final class SampleMetricBadMates implements SampleMetric {
     private static final CallableStatus CALL = CallableStatus.NO_READS ;
 
     private double threshold;
@@ -64,10 +64,10 @@ final class SampleBadMates implements Sample {
     }
 
     @Override
-    public CallableStatus status(AbstractStatistics statistics) {
+    public CallableStatus status(AbstractStratification statistics) {
-        final SampleStatistics sampleStatistics = (SampleStatistics) statistics;
+        final SampleStratification sampleStratification = (SampleStratification) statistics;
-        final int nReads = sampleStatistics.getnReads();
+        final int nReads = sampleStratification.getnReads();
-        return  nReads > 0 && (double) sampleStatistics.getnBadMates() / nReads > threshold ? CALL : null;
+        return  nReads > 0 && (double) sampleStratification.getnBadMates() / nReads > threshold ? CALL : null;
     }
 
 }

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

@@ -51,16 +51,16 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets;
  * Date: 4/20/13
  * Time: 11:44 PM
  */
-final class SampleNoReads implements Sample {
+final class SampleMetricNoReads implements SampleMetric {
     private static final CallableStatus CALL = CallableStatus.NO_READS;
 @Override
     public void initialize(ThresHolder thresholds) {
     }
 
     @Override
-    public CallableStatus status(AbstractStatistics statistics) {
+    public CallableStatus status(AbstractStratification statistics) {
-        final SampleStatistics sampleStatistics = (SampleStatistics) statistics;
+        final SampleStratification sampleStratification = (SampleStratification) statistics;
-        return sampleStatistics.getnReads() == 0 ? CALL : null;
+        return sampleStratification.getnReads() == 0 ? CALL : null;
     }
 
 }

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

@@ -51,30 +51,31 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.LinkedList;
+import java.util.List;
 
 /**
  * The statistics calculator for a specific sample given the interval
  */
-final class SampleStatistics extends AbstractStatistics {
+final class SampleStratification extends AbstractStratification {
     private final GenomeLoc interval;
-    private final ArrayList<AbstractStatistics> loci;
+    private final ArrayList<AbstractStratification> loci;
     private final ThresHolder thresholds;
 
-    private Map<CallableStatus, Integer> locusStatusTally = null;
     private int nReads = -1;
     private int nBadMates = -1;
 
-    public SampleStatistics(final GenomeLoc interval, final ThresHolder thresholds) {
+    public SampleStratification(final GenomeLoc interval, final ThresHolder thresholds) {
         this.interval = interval;
-        this.loci = new ArrayList<AbstractStatistics>(interval.size());
+        this.loci = new ArrayList<AbstractStratification>(interval.size());
         this.thresholds = thresholds;
         nReads = 0;
         nBadMates = 0;
 
         // Initialize every loci (this way we don't have to worry about non-existent loci in the object
         for (int i = 0; i < interval.size(); i++)
-            this.loci.add(new LocusStatistics(thresholds));
+            this.loci.add(new LocusStratification(thresholds));
     }
 
     /**
@@ -99,7 +100,7 @@ final class SampleStatistics extends AbstractStatistics {
             final int locusIndex = locus.getStart() - interval.getStart();
             final int rawCoverage = pileup.depthOfCoverage();
             final int coverage = pileup.getBaseAndMappingFilteredPileup(thresholds.minimumBaseQuality, thresholds.minimumMappingQuality).depthOfCoverage();
-            final LocusStatistics locusData = (LocusStatistics) loci.get(locusIndex);
+            final LocusStratification locusData = (LocusStratification) loci.get(locusIndex);
             locusData.addLocus(coverage, rawCoverage);
 
             // process all the reads in this pileup (tallying number of reads and bad mates)
@@ -109,7 +110,7 @@ final class SampleStatistics extends AbstractStatistics {
     }
 
     @Override
-    public Iterable<AbstractStatistics> getElements() {
+    public Iterable<AbstractStratification> getElements() {
         return loci;
     }
 
@@ -121,15 +122,15 @@ final class SampleStatistics extends AbstractStatistics {
         final List<CallableStatus> output = new LinkedList<CallableStatus>();
 
         // get the tally of all the locus callable statuses
-        for (Statistic locusStat : thresholds.locusStatisticList) {
+        for (Metric locusStat : thresholds.locusMetricList) {
-            final CallableStatus status = ((Locus) locusStat).sampleStatus(this);
+            final CallableStatus status = ((LocusMetric) locusStat).sampleStatus(this);
             if (status != null) {
                 output.add(status);
             }
         }
 
         // get the sample specific statitics statuses
-        for (Statistic sampleStat : thresholds.sampleStatisticList) {
+        for (Metric sampleStat : thresholds.sampleMetricList) {
             final CallableStatus status = sampleStat.status(this);
             if (status != null) {
                 output.add(status);

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

@@ -114,9 +114,9 @@ final class ThresHolder {
     @Argument(fullName = "quality_status_threshold", shortName = "stQ", doc = "The proportion of the loci needed for calling POOR_QUALITY", required = false)
     public double qualityStatusThreshold = 0.50;
 
-    public final List<Statistic> locusStatisticList = new LinkedList<Statistic>();
+    public final List<Metric> locusMetricList = new LinkedList<Metric>();
-    public final List<Statistic> sampleStatisticList = new LinkedList<Statistic>();
+    public final List<Metric> sampleMetricList = new LinkedList<Metric>();
-    public final List<Statistic> intervalStatisticList = new LinkedList<Statistic>();
+    public final List<Metric> intervalMetricList = new LinkedList<Metric>();
 
     public ThresHolder() {}
 

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

@@ -64,7 +64,7 @@ public class LocusStatisticsUnitTest {
 
     @Test(dataProvider = "StatusTestValues")
     public void testCallableStatuses(int coverage, int rawCoverage, CallableStatus status) {
-        List<CallableStatus> statuses = new LocusStatistics(coverage, rawCoverage, thresholds).callableStatuses();
+        List<CallableStatus> statuses = new LocusStratification(coverage, rawCoverage, thresholds).callableStatuses();
         Assert.assertTrue((status == null) ? statuses.isEmpty() : (statuses.contains(status) && statuses.size() == 1));
     }