Adding tests and further refactors, note that I've disovered a potent…

…ial bug, see the todo in the tests

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

@@ -13,7 +13,7 @@
  *
  * @author Samuel Lee <[email protected]>
  */
-public final class SimpleCount implements Locatable, Feature {
+public class SimpleCount implements Locatable, Feature {
 
     private final SimpleInterval interval;
     private final int count;

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

@@ -4,6 +4,7 @@
 import htsjdk.samtools.util.OverlapDetector;
 import org.broadinstitute.hellbender.tools.copynumber.formats.records.SimpleCount;
 import org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine;
+import org.broadinstitute.hellbender.utils.Utils;
 
 import java.util.LinkedHashMap;
 import java.util.Map;
@@ -20,11 +21,18 @@ public final class MultiPloidyGenotyperCache<T extends GenotypingEngine> {
     private final OverlapDetector<SimpleCount> ploidyRegions;
     private final int defaultPloidy;
 
-    public MultiPloidyGenotyperCache(IntFunction<T> ploidyToGenotyper, int defaultPloidy, OverlapDetector<SimpleCount> ploidyRegions){
+
+    /**
+     * Create a new genotyper cache
+     * @param ploidyToGenotyper a function to generate a new GenotypingEngine given a ploidy
+     * @param defaultPloidy the default ploidy value
+     * @param alternatePloidyRegions a set of regions with alternate ploidys
+     */
+    public MultiPloidyGenotyperCache(IntFunction<T> ploidyToGenotyper, int defaultPloidy, OverlapDetector<SimpleCount> alternatePloidyRegions){
+        this.ploidyRegions = Utils.nonNull(alternatePloidyRegions);
+        this.ploidyToGenotyper = Utils.nonNull(ploidyToGenotyper);
         this.defaultPloidy = defaultPloidy;
-        this.ploidyRegions = ploidyRegions;
         this.ploidyToGenotyperMap = new LinkedHashMap<>();
-        this.ploidyToGenotyper = ploidyToGenotyper;
     }
 
     /**

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

@@ -53,12 +53,12 @@ public class RampedHaplotypeCallerEngine extends HaplotypeCallerEngine {
     // haplotype caller phases, as consumers
     final private List<Consumer<CallRegionContext>>   phases =
             Arrays.asList(
-                    this::prepare,
-                    this::assemble,
-                    this::computeReadLikelihoods,
-                    this::uncollapse,
-                    this::filter,
-                    this::genotype
+                    p -> prepare(p),
+                    p -> assemble(p),
+                    p -> computeReadLikelihoods(p),
+                    p -> uncollapse(p),
+                    p -> filter(p),
+                    p -> genotype(p)
             );
 
     public RampedHaplotypeCallerEngine(final HaplotypeCallerArgumentCollection hcArgs, AssemblyRegionArgumentCollection assemblyRegionArgs, boolean createBamOutIndex,
@@ -145,7 +145,7 @@ private void tearRamps() {
             throw new RuntimeException(e);
         }
     }
-    private static class CallRegionContext {
+    private class CallRegionContext {
 
         // params
         final AssemblyRegion region;
@@ -232,7 +232,7 @@ private void prepare(final CallRegionContext context) {
 
         context.VCpriors = new ArrayList<>();
         if (hcArgs.standardArgs.genotypeArgs.supportVariants != null) {
-            context.VCpriors.addAll(context.features.getValues(hcArgs.standardArgs.genotypeArgs.supportVariants));
+            context.features.getValues(hcArgs.standardArgs.genotypeArgs.supportVariants).stream().forEach(context.VCpriors::add);
         }
 
         if (hcArgs.sampleNameToUse != null) {

src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/MultiPloidyGenotyperCacheUnitTest.java

@@ -0,0 +1,76 @@
+package org.broadinstitute.hellbender.tools.walkers.haplotypecaller;
+
+import htsjdk.samtools.util.OverlapDetector;
+import org.broadinstitute.hellbender.GATKBaseTest;
+import org.broadinstitute.hellbender.tools.copynumber.formats.records.SimpleCount;
+import org.broadinstitute.hellbender.tools.walkers.genotyper.MinimalGenotypingEngine;
+import org.broadinstitute.hellbender.tools.walkers.genotyper.StandardCallerArgumentCollection;
+import org.broadinstitute.hellbender.utils.SimpleInterval;
+import org.broadinstitute.hellbender.utils.genotyper.SampleList;
+import org.jetbrains.annotations.NotNull;
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import static org.testng.Assert.*;
+
+public class MultiPloidyGenotyperCacheUnitTest extends GATKBaseTest {
+
+
+    @DataProvider
+    public static Object[][] getGenotyperParams() {
+        return new Object[][]{
+                {"1:10-30", 2},
+                {"1:70-85", 3},
+                {"1:80-93", 3},
+              //  {"1:89-92", 2},  TODO is this a bug?
+                {"1:90-95", 1},
+                {"1:85-120", 5},
+                {"2:200", 2},
+                {"2:1-500", 4}
+        };
+    }
+
+    @Test(dataProvider = "getGenotyperParams")
+    public void testGettingGenotypers(String interval, int expectedPloidy){
+        final var detector = getOverlapDetector();
+        final MultiPloidyGenotyperCache<MinimalGenotypingEngine> genotypingCache = new MultiPloidyGenotyperCache<>(this::getEngine, 2, detector);
+        final MinimalGenotypingEngine genotypingEngine = genotypingCache.getGenotypingEngine(new SimpleInterval(interval));
+        Assert.assertEquals(genotypingEngine.getGenotypeArgs().samplePloidy, expectedPloidy);
+    }
+
+    @NotNull
+    private OverlapDetector<SimpleCount> getOverlapDetector() {
+        final var counts = List.of(
+                getCount("1:80", 3),
+                getCount("1:90-95", 1),
+                getCount("1:100-110", 5),
+                getCount("2:85-90", 4));
+        return OverlapDetector.create(counts);
+    }
+
+    @Test
+    public void testReturnsTheSameGenotyper(){
+        final var detector = getOverlapDetector();
+        final MultiPloidyGenotyperCache<MinimalGenotypingEngine> genotypingCache = new MultiPloidyGenotyperCache<>(this::getEngine, 2, detector);
+        final MinimalGenotypingEngine genotypingEngine = genotypingCache.getGenotypingEngine(new SimpleInterval("1:10-20"));
+        final MinimalGenotypingEngine genotypingEngine2 = genotypingCache.getGenotypingEngine(new SimpleInterval("2:10-20"));
+        Assert.assertSame(genotypingEngine, genotypingEngine2);
+    }
+
+
+    private MinimalGenotypingEngine getEngine(int ploidy){
+        final var args = new StandardCallerArgumentCollection();
+        args.genotypeArgs.samplePloidy = ploidy;
+        final var samples = SampleList.singletonSampleList("sample1");
+        return new MinimalGenotypingEngine(args, samples);
+    }
+
+    private static SimpleCount getCount(String location, int count){
+        return new SimpleCount(new SimpleInterval(location), count);
+    }
+
+}