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broadinstitute · May 14, 2018 · df35942 · df35942
1 parent da9afa2
commit df35942
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Showing 3 changed files with 15 additions and 4 deletions.
diff --git a/...ellbender/cmdline/argumentcollections/SequenceDictionaryValidationArgumentCollection.java b/...ellbender/cmdline/argumentcollections/SequenceDictionaryValidationArgumentCollection.java
@@ -4,7 +4,7 @@
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
 
 /**
- * interface for argument collections that control
+ * interface for argument collections that control how sequence dictionary validation should be handled
  */
 public interface SequenceDictionaryValidationArgumentCollection {
 

diff --git a/src/main/java/org/broadinstitute/hellbender/engine/GATKTool.java b/src/main/java/org/broadinstitute/hellbender/engine/GATKTool.java
@@ -68,7 +68,7 @@ public abstract class GATKTool extends CommandLineProgram {
     private double secondsBetweenProgressUpdates = ProgressMeter.DEFAULT_SECONDS_BETWEEN_UPDATES;
 
     @ArgumentCollection
-    SequenceDictionaryValidationArgumentCollection seqValidationArguments = new SequenceDictionaryValidationArgumentCollection.StandardValidationCollection();
+    SequenceDictionaryValidationArgumentCollection seqValidationArguments = getSequenceDictionaryValidationArgumentCollection();
 
     @Argument(fullName=StandardArgumentDefinitions.CREATE_OUTPUT_BAM_INDEX_LONG_NAME,
             shortName=StandardArgumentDefinitions.CREATE_OUTPUT_BAM_INDEX_SHORT_NAME,
@@ -449,6 +449,17 @@ public boolean requiresIntervals() {
         return false;
     }
 
+
+    /**
+     * Get the {@link SequenceDictionaryValidationArgumentCollection} for the tool.
+     * Subclasses may override this method in order to customize validation options.
+     *
+     * @return a SequenceDictionaryValidationArgumentCollection
+     */
+    protected SequenceDictionaryValidationArgumentCollection getSequenceDictionaryValidationArgumentCollection() {
+        return new SequenceDictionaryValidationArgumentCollection.StandardValidationCollection();
+    }
+
     /**
      * Load the master sequence dictionary as specified in {@code masterSequenceDictionaryFilename}.
      * Will only load the master sequence dictionary if it has not already been loaded.

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/spark/bwa/BwaSpark.java b/src/main/java/org/broadinstitute/hellbender/tools/spark/bwa/BwaSpark.java
@@ -23,8 +23,8 @@
 import java.util.List;
 
 @DocumentedFeature
-@CommandLineProgramProperties(summary = "align reads using BWA",
-        oneLineSummary = "align reads to a given reference using BWA on Spark",
+@CommandLineProgramProperties(summary = "Align reads using BWA",
+        oneLineSummary = "Align reads to a given reference using BWA on Spark",
         programGroup = ReadDataManipulationProgramGroup.class)
 @BetaFeature
 public final class BwaSpark extends GATKSparkTool {