name

src/main/java/org/broadinstitute/hellbender/engine/spark/SparkCommandLineProgram.java

@@ -20,6 +20,14 @@ public abstract class SparkCommandLineProgram extends CommandLineProgram impleme
     @Argument(fullName = "sparkMaster", doc="URL of the Spark Master to submit jobs to when using the Spark pipeline runner.", optional = true)
     protected String sparkMaster = "local[2]";
 
+    @Argument(
+            doc = "Name of the program running",
+            shortName = "N",
+            fullName = "programName",
+            optional = true
+    )
+    public String programName;
+
     @Override
     protected Object doWork() {
         final JavaSparkContext ctx = SparkContextFactory.getSparkContext(getProgramName(), sparkMaster);
@@ -65,5 +73,13 @@ protected void afterPipeline(final JavaSparkContext ctx) {
         SparkContextFactory.stopSparkContext(ctx);
     }
 
-    protected abstract String getProgramName();
+    /**
+     * Returns the program's name.
+     * If programName argument is provided, returns that. Otherwise, returns the simple name of the class.
+     *
+     * Subclasses can override if desired.
+     */
+    protected String getProgramName(){
+       return programName == null ? getClass().getSimpleName() : programName;
+    }
 }

src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/ComputeCoveragePerIntervalSpark.java

@@ -58,7 +58,7 @@ public final class ComputeCoveragePerIntervalSpark extends SparkCommandLineProgr
     public File targetIntervalFile;
 
     @ArgumentCollection
-    private IntervalArgumentCollection intervalArgumentCollection = new OptionalIntervalArgumentCollection();
+    public IntervalArgumentCollection intervalArgumentCollection = new OptionalIntervalArgumentCollection();
 
     @Argument(doc = "uri for the output file: a local file path",
             shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME, fullName = StandardArgumentDefinitions.OUTPUT_LONG_NAME,
@@ -90,7 +90,7 @@ protected void runPipeline(final JavaSparkContext ctx) {
         //so for now we'll write some filters out explicitly.
 //        final ReadFilter readFilter = ctx.broadcast(new WellformedReadFilter(readsHeader));
         final JavaRDD<GATKRead> rawReads = readSource.getParallelReads(bam, intervals);
-        final JavaRDD<GATKRead> reads = rawReads.filter(read -> !read.isUnmapped() && read.getStart() <= read.getEnd());//.filter(read -> readFilter.getValue().test(read));
+        final JavaRDD<GATKRead> reads = rawReads.filter(read -> !read.isUnmapped() && read.getStart() <= read.getEnd());
         final Map<Locatable, Long> byKey = reads.flatMap(read -> islBroad.getValue().getOverlapping(new SimpleInterval(read))).countByValue();
 
         final SortedMap<Locatable, Object> byKeySorted = new TreeMap<>(IntervalUtils.LEXICOGRAPHICAL_ORDER_COMPARATOR);
@@ -134,9 +134,4 @@ private TargetCollection<Locatable> getTargetCollection() {
         final List<Locatable> targets = result.targets().stream().collect(Collectors.toList());
         return new HashedListTargetCollection<>(targets);
     }
-
-    @Override
-    protected String getProgramName() {
-        return getClass().getSimpleName();
-    }
 }