creates multiple enginges to handle different ploidies

Finish changes to HaplotypeCaller to add ploidy-regions flag allowing variable ploidy

Change IntervalFileFeature interface to NamedFeature for htsjdk dependency

Address comments for draft PR

Make a few changes and refactors based on comments

Add some tests and small tweaks

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

@@ -2,6 +2,8 @@
 
 import htsjdk.samtools.util.Locatable;
 import htsjdk.tribble.Feature;
+import htsjdk.tribble.NamedFeature;
+import org.broadinstitute.hellbender.exceptions.UserException;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
 import org.broadinstitute.hellbender.utils.Utils;
 import org.broadinstitute.hellbender.utils.param.ParamUtils;
@@ -19,7 +21,17 @@ 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) {
+        try {
+            int count = Integer.parseInt(namedFeature.getName());
+            this.interval = new SimpleInterval(namedFeature);
+            this.count = ParamUtils.isPositiveOrZero(count, "Can't construct SimpleCount with negative count at " + namedFeature.getContig() + ":" + namedFeature.getStart() + "-" + namedFeature.getEnd() + ".");
+        } catch (NumberFormatException e) {
+            throw new IllegalArgumentException("Error parsing name into integer for feature at " + namedFeature.getContig() + ":" + namedFeature.getStart() + "-" + namedFeature.getEnd() + ".");
+        }
     }
 
     @Override

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

@@ -127,6 +127,21 @@
  * argument. Note however that very high ploidies (such as are encountered in large pooled experiments) may cause
  * performance challenges including excessive slowness. We are working on resolving these limitations.</p>
  *
+ * <p>For having variable ploidy in different regions, like making haploid calls outside the PAR on chrX or chrY,
+ * see the --ploidy-regions flag. The -ploidy flag sets the default ploidy to use everywhere, and --ploidy-regions
+ * should be a .bed or .interval_list with "name" column containing the desired ploidy to use in that region
+ * when genotyping. Note that variants near the boundary may not have the matching ploidy since the ploidy used will
+ * be determined using the following precedence: </p>
+ * <ol>
+ *     <li>ploidy given in --ploidy-regions for all intervals overlapping the active region when calling your variant
+ *     (with ties broken by using largest ploidy); note ploidy interval may only overlap the active region and determine
+ *     the ploidy of your variant even if the end coordinate written for your variant lies outside the given region;</li>
+ *     <li>ploidy given via global -ploidy flag;</li>
+ *     <li>ploidy determined by the default global built-in constant for humans (2).</li>
+ * </ol>
+ *
+ * <p>Coordinates for the PAR for CRCh38 can be found <a href='http://useast.ensembl.org/info/genome/genebuild/human_PARS.html'>here</a>.</p>
+ *
  * <h3>Additional Notes</h3>
  * <ul>
  *     <li>When working with PCR-free data, be sure to set `-pcr_indel_model NONE` (see argument below).</li>

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

@@ -1,6 +1,8 @@
 package org.broadinstitute.hellbender.tools.walkers.haplotypecaller;
 
+import htsjdk.tribble.NamedFeature;
 import htsjdk.variant.variantcontext.VariantContext;
+import org.apache.arrow.util.VisibleForTesting;
 import org.apache.commons.lang3.ArrayUtils;
 import org.broadinstitute.barclay.argparser.Advanced;
 import org.broadinstitute.barclay.argparser.Argument;
@@ -9,6 +11,7 @@
 import org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
 import org.broadinstitute.hellbender.cmdline.argumentcollections.DbsnpArgumentCollection;
+import org.broadinstitute.hellbender.engine.FeatureDataSource;
 import org.broadinstitute.hellbender.engine.FeatureInput;
 import org.broadinstitute.hellbender.engine.GATKPath;
 import org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection;
@@ -23,9 +26,11 @@
 /**
  * Set of arguments for the {@link HaplotypeCallerEngine}
  */
-public class HaplotypeCallerArgumentCollection extends AssemblyBasedCallerArgumentCollection implements Serializable{
+public class HaplotypeCallerArgumentCollection extends AssemblyBasedCallerArgumentCollection implements Serializable {
     private static final long serialVersionUID = 1L;
 
+    public static final String PLOIDY_REGIONS_NAME = "ploidy-regions";
+
     public static final String GQ_BAND_LONG_NAME = "gvcf-gq-bands";
     public static final String GQ_BAND_SHORT_NAME = "GQB";
     public static final String DO_NOT_CORRECT_OVERLAPPING_BASE_QUALITIES_LONG_NAME = "do-not-correct-overlapping-quality";
@@ -61,6 +66,9 @@ 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. Overrides default ploidy and user-provided --ploidy argument in specific regions.", optional = true)
+    public FeatureDataSource<NamedFeature> ploidyRegions = null;
+
     /**
      * You can use this argument to specify that HC should process a single sample out of a multisample BAM file. This
      * is especially useful if your samples are all in the same file but you need to run them individually through HC
@@ -312,6 +320,21 @@ boolean isFlowBasedCallingMode() {
         return flowMode != FlowMode.NONE;
     }
 
+    // Default constructor
+    public HaplotypeCallerArgumentCollection() {
+        super();
+    }
+
+    // Private constructor for use in copyWithNewPloidy
+    // Allows you to make new instances of hcArgs with identical fields except for genotyper ploidy
+    private HaplotypeCallerArgumentCollection(int ploidy) {
+        this.standardArgs.genotypeArgs.samplePloidy = ploidy;
+    }
+
+    // Copy method used to create new hcArgs with same fields except input ploidy model
+    public HaplotypeCallerArgumentCollection copyWithNewPloidy(int ploidy) {
+        return new HaplotypeCallerArgumentCollection(ploidy);
+    }
 
     /**
      * the different flow modes, in terms of their parameters and their values