Added a new Walker abstract class to be used for all built-in walkers.

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

@@ -14,7 +14,6 @@
 import org.broadinstitute.hellbender.utils.SimpleInterval;
 import org.broadinstitute.hellbender.utils.Utils;
 import org.broadinstitute.hellbender.utils.gcs.BucketUtils;
-import org.broadinstitute.hellbender.utils.io.IOUtils;
 
 import java.io.File;
 import java.util.Iterator;
@@ -34,7 +33,7 @@
  * Created by Takuto Sato 1/30/17, abstractified by David Benjamin on 2/22/17.
  * {@link #onTraversalStart}, {@link #onTraversalSuccess} and/or {@link #closeTool}.
  */
-public abstract class AbstractConcordanceWalker extends GATKTool {
+public abstract class AbstractConcordanceWalker extends Walker {
 
     public static final String TRUTH_VARIANTS_LONG_NAME = "truth";
     public static final String EVAL_VARIANTS_SHORT_NAME = "eval";

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

@@ -1,6 +1,5 @@
 package org.broadinstitute.hellbender.engine;
 
-import htsjdk.samtools.util.Locatable;
 import org.broadinstitute.barclay.argparser.Advanced;
 import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.barclay.argparser.CommandLineException;
@@ -12,13 +11,10 @@
 import org.broadinstitute.hellbender.utils.IGVUtils;
 import org.broadinstitute.hellbender.utils.IntervalUtils;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
-import org.broadinstitute.hellbender.utils.Utils;
 import org.broadinstitute.hellbender.utils.activityprofile.ActivityProfileState;
 import org.broadinstitute.hellbender.utils.downsampling.PositionalDownsampler;
 import org.broadinstitute.hellbender.utils.downsampling.ReadsDownsampler;
-import org.broadinstitute.hellbender.utils.read.GATKRead;
 
-import java.io.File;
 import java.io.IOException;
 import java.io.PrintStream;
 import java.util.ArrayList;
@@ -43,7 +39,7 @@
  * Internally, the reads are loaded in chunks called read shards, which are then subdivided into active/inactive regions
  * for processing by the tool implementation. One read shard is created per contig.
  */
-public abstract class AssemblyRegionWalker extends GATKTool {
+public abstract class AssemblyRegionWalker extends Walker {
 
     //NOTE: these argument names are referenced by HaplotypeCallerSpark
     public static final String MIN_ASSEMBLY_LONG_NAME = "min-assembly-region-size";

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

@@ -8,7 +8,6 @@
 import org.broadinstitute.hellbender.utils.Utils;
 
 import java.io.File;
-import java.nio.file.Path;
 
 /**
  * A FeatureWalker is a tool that processes a {@link Feature} at a time from a source of Features, with
@@ -21,7 +20,7 @@
  *
  * @param <F> the driving feature type.
  */
-public abstract class FeatureWalker<F extends Feature> extends GATKTool {
+public abstract class FeatureWalker<F extends Feature> extends Walker {
 
     private FeatureDataSource<F> drivingFeatures;
 
@@ -79,7 +78,7 @@ private void initializeDrivingFeatures() {
      * Subclasses can override to provide their own behavior but default implementation should be suitable for most uses.
      */
     @Override
-    public void traverse() {
+    public final void traverse() {
         CountingReadFilter readFilter = makeReadFilter();
         // Process each feature in the input stream.
         Utils.stream(drivingFeatures).forEach(feature -> {

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

@@ -10,11 +10,6 @@
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
 import htsjdk.variant.vcf.VCFHeaderLine;
 import htsjdk.variant.vcf.VCFSimpleHeaderLine;
-import java.io.File;
-import java.nio.file.Path;
-import java.time.ZonedDateTime;
-import java.util.*;
-import java.util.stream.Stream;
 import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.barclay.argparser.ArgumentCollection;
 import org.broadinstitute.barclay.argparser.CommandLinePluginDescriptor;
@@ -43,6 +38,12 @@
 import org.broadinstitute.hellbender.utils.reference.ReferenceUtils;
 import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils;
 
+import java.io.File;
+import java.nio.file.Path;
+import java.time.ZonedDateTime;
+import java.util.*;
+import java.util.stream.Stream;
+
 /**
  * Base class for all GATK tools. Tool authors that wish to write a "GATK" tool but not use one of
  * the pre-packaged Walker traversals should feel free to extend this class directly. All other
@@ -157,6 +158,45 @@ public abstract class GATKTool extends CommandLineProgram {
      */
     List<SimpleInterval> intervalsForTraversal;
 
+    /**
+     * Get the {@link ReferenceDataSource} for this {@link GATKTool}.
+     * Will throw a {@link GATKException} if the reference is null.
+     * Clients are expected to call the {@link #hasReference()} method prior to calling this.
+     * @return the {@link ReferenceDataSource} for this {@link GATKTool}.  Never {@code null}.
+     */
+    protected ReferenceDataSource getReferenceDataSource() {
+        if ( reference == null ) {
+            throw new GATKException("Attempted to retrieve null reference!");
+        }
+        return reference;
+    }
+
+    /**
+     * Get the {@link ReadsDataSource} for this {@link GATKTool}.
+     * Will throw a {@link GATKException} if the reads are null.
+     * Clients are expected to call the {@link #hasReads()} method prior to calling this.
+     * @return the {@link ReadsDataSource} for this {@link GATKTool}.  Never {@code null}.
+     */
+    protected ReadsDataSource getReadsDataSource() {
+        if ( reads == null ) {
+            throw new GATKException("Attempted to retrieve null reads!");
+        }
+        return reads;
+    }
+
+    /**
+     * Get the {@link FeatureManager} for this {@link GATKTool}.
+     * Will throw a {@link GATKException} if the features are null.
+     * Clients are expected to call the {@link #hasFeatures()} method prior to calling this.
+     * @return the {@link FeatureManager} for this {@link GATKTool}.  Never {@code null}.
+     */
+    protected FeatureManager getFeatureManager() {
+        if ( features == null ) {
+            throw new GATKException("Attempted to retrieve null features!");
+        }
+        return features;
+    }
+
     /**
      * Progress meter to print out traversal statistics. Subclasses must invoke
      * {@link ProgressMeter#update(Locatable)} after each record processed from

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

@@ -3,8 +3,6 @@
 import org.broadinstitute.hellbender.engine.filters.ReadFilter;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
 
-import java.nio.file.Path;
-
 /**
  * An IntervalWalker is a tool that processes a single interval at a time, with the ability to query
  * optional overlapping sources of reads, reference data, and/or variants/features.
@@ -18,7 +16,7 @@
  * onTraversalStart() and/or onTraversalSuccess(). See the {@link org.broadinstitute.hellbender.tools.examples.ExampleIntervalWalker}
  * tool for an example.
  */
-public abstract class IntervalWalker extends GATKTool {
+public abstract class IntervalWalker extends Walker {
 
     @Override
     public boolean requiresIntervals() {
@@ -56,7 +54,7 @@ protected final void onStartup() {
     }
 
     @Override
-    public void traverse() {
+    public final void traverse() {
         final ReadFilter readFilter = makeReadFilter();
         for ( final SimpleInterval interval : intervalsForTraversal ) {
             apply(interval,

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

@@ -34,7 +34,7 @@
  *
  * @author Daniel Gomez-Sanchez (magicDGS)
  */
-public abstract class LocusWalker extends GATKTool {
+public abstract class LocusWalker extends Walker {
 
     @Argument(fullName = "maxDepthPerSample", shortName = "maxDepthPerSample", doc = "Maximum number of reads to retain per sample per locus. Reads above this threshold will be downsampled. Set to 0 to disable.", optional = true)
     protected int maxDepthPerSample = defaultMaxDepthPerSample();
@@ -146,7 +146,7 @@ protected final void onStartup() {
      * and including deletions only if {@link #includeDeletions()} returns {@code true}.
      */
     @Override
-    public void traverse() {
+    public final void traverse() {
         final SAMFileHeader header = getHeaderForReads();
         // get the samples from the read groups
         final Set<String> samples = header.getReadGroups().stream()

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

@@ -1,16 +1,11 @@
 package org.broadinstitute.hellbender.engine;
 
-import org.broadinstitute.barclay.argparser.CommandLinePluginDescriptor;
-import org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterPluginDescriptor;
+import org.broadinstitute.hellbender.engine.filters.CountingReadFilter;
 import org.broadinstitute.hellbender.engine.filters.ReadFilter;
 import org.broadinstitute.hellbender.engine.filters.WellformedReadFilter;
-import org.broadinstitute.hellbender.transformers.ReadTransformer;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
-import org.broadinstitute.hellbender.engine.filters.CountingReadFilter;
-import org.broadinstitute.hellbender.utils.Utils;
 import org.broadinstitute.hellbender.utils.read.GATKRead;
 
-import java.nio.file.Path;
 import java.util.Collections;
 import java.util.List;
 
@@ -29,7 +24,7 @@
  * ReadWalker authors must implement the apply() method to process each read, and may optionally implement
  * onTraversalStart() and/or onTraversalSuccess(). See the PrintReadsWithReference walker for an example.
  */
-public abstract class ReadWalker extends GATKTool {
+public abstract class ReadWalker extends Walker {
 
     @Override
     public boolean requiresReads() {

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

@@ -22,7 +22,7 @@
  * {@link #getSpliteratorForDrivingVariants}, and may optionally implement {@link #onTraversalStart},
  * {@link #onTraversalSuccess} and/or {@link #closeTool}.
  */
-public abstract class VariantWalkerBase extends GATKTool {
+public abstract class VariantWalkerBase extends Walker {
 
     /**
      * This number controls the size of the cache for our primary and auxiliary FeatureInputs

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

@@ -0,0 +1,27 @@
+package org.broadinstitute.hellbender.engine;
+
+import org.broadinstitute.hellbender.exceptions.GATKException;
+
+/**
+ * An abstract class to represent built-in walkers that inherit directly from {@link GATKTool}.
+ * Created by jonn on 6/28/18.
+ */
+public abstract class Walker extends GATKTool {
+
+    @Override
+    final protected ReferenceDataSource getReferenceDataSource() {
+        throw new GATKException("Should never access ReferenceDataSource in child classes of AssemblyRegionWalker.");
+    }
+
+    @Override
+    final protected ReadsDataSource getReadsDataSource() {
+        throw new GATKException("Should never access ReadsDataSource in child classes of AssemblyRegionWalker.");
+    }
+
+    @Override
+    final protected FeatureManager getFeatureManager() {
+        throw new GATKException("Should never access FeatureManager in child classes of AssemblyRegionWalker.");
+    }
+
+
+}