Make a few changes and refactors based on comments

src/main/java/org/broadinstitute/hellbender/tools/copynumber/formats/records/SimpleCount.java

@@ -21,20 +21,14 @@ public class SimpleCount implements Locatable, Feature {
     public SimpleCount(final SimpleInterval interval,
                        final int count) {
         this.interval = Utils.nonNull(interval);
-        this.count = ParamUtils.isPositiveOrZero(count, "Can't construct SimpleCount with negative count.");
+        this.count = ParamUtils.isPositiveOrZero(count, "Can't construct SimpleCount with negative count at " + interval.getContig() + ":" + interval.getStart() + "-" + interval.getEnd() + ".");
     }
 
     public SimpleCount(final NamedFeature namedFeature) {
-        this.interval = new SimpleInterval(namedFeature.getContig(), namedFeature.getStart(), namedFeature.getEnd());
         try {
-            int count = Integer.parseInt(namedFeature.getName());
-            if (count > 0) {
-                this.count = count;
-            } else {
-                throw new UserException("Error parsing name into positive integer for feature at " + namedFeature.getContig() + "\t" + namedFeature.getStart() + "\t" + namedFeature.getEnd());
-            }
+            this(new SimpleInterval(namedFeature), Integer.parseInt(namedFeature.getName()));
         } catch (NumberFormatException e) {
-            throw new UserException("Error parsing name into positive integer for feature at " + namedFeature.getContig() + "\t" + namedFeature.getStart() + "\t" + namedFeature.getEnd());
+            throw new IllegalArgumentException("Error parsing name into integer for feature at " + namedFeature.getContig() + ":" + namedFeature.getStart() + "-" + namedFeature.getEnd());
         }
     }
 

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java

@@ -65,7 +65,7 @@ protected ReadThreadingAssemblerArgumentCollection getReadThreadingAssemblerArgu
         return new HaplotypeCallerReadThreadingAssemblerArgumentCollection();
     }
 
-    @Argument(fullName = PLOIDY_REGIONS_NAME, shortName = PLOIDY_REGIONS_NAME, doc = "Interval file with column specifying desired ploidy for genotyping models.", optional = true)
+    @Argument(fullName = PLOIDY_REGIONS_NAME, shortName = PLOIDY_REGIONS_NAME, doc = "Interval file with column specifying desired ploidy for genotyping models. Overrides default ploidy and user-provided --ploidy argument in specific regions.", optional = true)
     public FeatureDataSource<NamedFeature> ploidyRegions = null;
 
     /**

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java

@@ -588,11 +588,11 @@ public void writeHeader( final VariantContextWriter vcfWriter, final SAMSequence
     }
 
     /**
-     * Selects appropriate active region genotyping engine for given region
+     * Determines the appropriate ploidy to use at given site for different genotyping engines.
      * @param region Current region of interest
-     * @return Active genotyping engine with correct ploidy setting for given region
+     * @return Ploidy value to use here given user inputs, or -1 if fall back to default
      */
-    private MinimalGenotypingEngine getLocalActiveGenotyper(Locatable region) {
+    private int getPloidyToUseAtThisSite(Locatable region) {
         Set<SimpleCount> overlaps = this.ploidyRegionsOverlapDetector.getOverlaps(region);
         // Return first engine for interval overlapping this region
         if (!overlaps.isEmpty()) {
@@ -604,9 +604,23 @@ private MinimalGenotypingEngine getLocalActiveGenotyper(Locatable region) {
                     max = next;
                 }
             }
-            return this.ploidyToActiveEvaluationGenotyper.get(max);
+            return max;
         } else {
+            return -1; // Sentinel value to fall back to default genotyper
+        }
+    }
+
+    /**
+     * Selects appropriate active region genotyping engine for given region
+     * @param region Current region of interest
+     * @return Active genotyping engine with correct ploidy setting for given region
+     */
+    private MinimalGenotypingEngine getLocalActiveGenotyper(Locatable region) {
+        int currentPloidy = getPloidyToUseAtThisSite(region);
+        if (currentPloidy == -1) {
             return this.defaultActiveRegionEvaluationGenotyperEngine;
+        } else {
+            return this.ploidyToActiveEvaluationGenotyper.get(currentPloidy);
         }
     }
 
@@ -616,42 +630,14 @@ private MinimalGenotypingEngine getLocalActiveGenotyper(Locatable region) {
      * @return Genotyping engine with correct ploidy setting for given region
      */
     protected HaplotypeCallerGenotypingEngine getLocalGenotypingEngine(Locatable region) {
-        Set<SimpleCount> overlaps = this.ploidyRegionsOverlapDetector.getOverlaps(region);
-        // Return first engine for interval overlapping this region
-        if (!overlaps.isEmpty()) {
-            Iterator<SimpleCount> intervals = overlaps.iterator();
-            int max = intervals.next().getCount();
-            while (intervals.hasNext()) {
-                int next = intervals.next().getCount();
-                if (next > max) {
-                    max = next;
-                }
-            }
-            return this.ploidyToGenotyperMap.get(max);
-        } else {
+        int currentPloidy = getPloidyToUseAtThisSite(region);
+        if (currentPloidy == -1) {
             return this.defaultGenotypingEngine;
+        } else {
+            return this.ploidyToGenotyperMap.get(currentPloidy);
         }
     }
 
-//    /**
-//     * Selects appropriate genotyping engine for given region, either for active region determination or full genotyping.
-//     * @param ploidyEngineMap A HashMap of ploidy values to appropriate genotyping engines to choose from
-//     * @param defaultEngine The backup default engine to use if no overlap detected
-//     * @param ploidyOverlapDetector OverlapDetector to use for checking if region overlaps the given ploidy regions
-//     * @param region Current region of interest, e.g. AssemblyRegion
-//     * @return Genotyping engine with correct ploidy setting for given region
-//     */
-//    protected GenotypingEngine<StandardCallerArgumentCollection> getEngineForOverlap(HashMap<Integer, GenotypingEngine<StandardCallerArgumentCollection>> ploidyEngineMap,
-//                                                                                     GenotypingEngine<StandardCallerArgumentCollection> defaultEngine, OverlapDetector ploidyOverlapDetector, Locatable region) {
-//        Set<SimpleCount> overlaps = ploidyOverlapDetector.getOverlaps(region);
-//        // Return first engine for interval overlapping this region
-//        if (overlaps.size() > 0) {
-//            return ploidyEngineMap.get(overlaps.iterator().next());
-//        } else {
-//            return defaultEngine;
-//        }
-//    }
-
     /**
      * Given a pileup, returns an ActivityProfileState containing the probability (0.0 to 1.0) that it's an "active" site.
      *