Some minor misc engine changes (#7744)

.gitignore

@@ -34,6 +34,12 @@ funcotator_tmp
 #Eclipse files
 /bin/
 .project
+*.jar
 
 #JENV local file
 .java-version
+
+.run/
+
+#Test generated dot files
+test*.dot

build.gradle

@@ -319,7 +319,8 @@ dependencies {
         exclude module: 'hadoop-bam'
     }
 
-    implementation 'org.jgrapht:jgrapht-core:0.9.1'
+    implementation 'org.jgrapht:jgrapht-core:1.1.0'
+    implementation 'org.jgrapht:jgrapht-io:1.1.0'
 
     implementation('org.disq-bio:disq:' + disqVersion)
     implementation('org.apache.hadoop:hadoop-client:' + hadoopVersion) // should be a 'provided' dependency

src/main/java/org/broadinstitute/hellbender/engine/AssemblyRegionIterator.java

@@ -122,6 +122,8 @@ private AssemblyRegion loadNextAssemblyRegion() {
         while ( locusIterator.hasNext() && nextRegion == null ) {
             final AlignmentContext pileup = locusIterator.next();
 
+            logger.debug(()->"AssemblyRegionIterator pileup: " + pileup);
+
             // Pop any new pending regions off of the activity profile. These pending regions will not become ready
             // until we've traversed all the reads that belong in them.
             //
@@ -140,6 +142,7 @@ private AssemblyRegion loadNextAssemblyRegion() {
             }
 
             final ActivityProfileState profile = evaluator.isActive(pileup, pileupRefContext, pileupFeatureContext);
+            logger.debug(() -> profile.toString());
             activityProfile.add(profile);
 
             // A pending region only becomes ready once our locus iterator has advanced beyond the end of its extended span