The debug command line argument is now passed correctly in Haplotype caller -- fixed issue #4943

src/main/java/org/broadinstitute/hellbender/engine/filters/CountingVariantFilter.java

@@ -17,7 +17,7 @@
  * (ie., not all variant filters in a compound predicate will necessarily be evaluated every time). Also note
  * that the count for a compound predicate does not always equal the sum of the counts of it's component
  * predicates, i.e. an "or" filter will report a filter count of 1 in the case where both component predicates
- * are evaluated and both fail, but the the individual component filters will report a count of 1 at the next
+ * are evaluated and both fail, but the individual component filters will report a count of 1 at the next
  * level.
  */
 public class CountingVariantFilter implements VariantFilter {

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

@@ -266,6 +266,7 @@ public static AssemblyResultSet assembleReads(final AssemblyRegion region,
             final AssemblyResultSet assemblyResultSet = assemblyEngine.runLocalAssembly(region, referenceHaplotype, fullReferenceWithPadding,
                                                                                         paddedReferenceLoc, givenAlleles, readErrorCorrector, header,
                                                                                         aligner);
+            assemblyResultSet.setDebug(argumentCollection.debug);
             assemblyResultSet.debugDump(logger);
             return assemblyResultSet;
         } catch (final Exception e){

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

@@ -518,4 +518,8 @@ public SortedSet<VariantContext> getVariationEvents(final int maxMnpDistance) {
         }
         return variationEvents;
     }
+
+    public void setDebug(boolean debug) {
+        this.debug = debug;
+    }
 }

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

@@ -536,7 +536,7 @@ public List<VariantContext> callRegion(final AssemblyRegion region, final Featur
 
         // run the local assembler, getting back a collection of information on how we should proceed
         final AssemblyResultSet untrimmedAssemblyResult =  AssemblyBasedCallerUtils.assembleReads(region, givenAlleles, hcArgs, readsHeader, samplesList, logger, referenceReader, assemblyEngine, aligner);
-
+        
         final SortedSet<VariantContext> allVariationEvents = untrimmedAssemblyResult.getVariationEvents(hcArgs.maxMnpDistance);
         // TODO - line bellow might be unnecessary : it might be that assemblyResult will always have those alleles anyway
         // TODO - so check and remove if that is the case:

src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2Engine.java

@@ -193,6 +193,7 @@ public List<VariantContext> callRegion(final AssemblyRegion originalAssemblyRegi
 
         final AssemblyRegion assemblyActiveRegion = AssemblyBasedCallerUtils.assemblyRegionWithWellMappedReads(originalAssemblyRegion, READ_QUALITY_FILTER_THRESHOLD, header);
         final AssemblyResultSet untrimmedAssemblyResult = AssemblyBasedCallerUtils.assembleReads(assemblyActiveRegion, givenAlleles, MTAC, header, samplesList, logger, referenceReader, assemblyEngine, aligner);
+
         final SortedSet<VariantContext> allVariationEvents = untrimmedAssemblyResult.getVariationEvents(MTAC.maxMnpDistance);
         final AssemblyRegionTrimmer.Result trimmingResult = trimmer.trim(originalAssemblyRegion, allVariationEvents);
         if (!trimmingResult.isVariationPresent()) {