Removing WellformedReadFilter from CountReadsSpark (#5329)

broadinstitute · Oct 19, 2018 · ec59e1e · ec59e1e
1 parent 05860f7
commit ec59e1e
Showing 1 changed file with 9 additions and 0 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/CountReadsSpark.java b/src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/CountReadsSpark.java
@@ -8,11 +8,15 @@
 import org.broadinstitute.barclay.help.DocumentedFeature;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
 import org.broadinstitute.hellbender.cmdline.programgroups.CoverageAnalysisProgramGroup;
+import org.broadinstitute.hellbender.engine.filters.ReadFilter;
+import org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary;
 import org.broadinstitute.hellbender.engine.spark.GATKSparkTool;
 import org.broadinstitute.hellbender.utils.gcs.BucketUtils;
 import org.broadinstitute.hellbender.utils.read.GATKRead;
 
 import java.io.PrintStream;
+import java.util.Collections;
+import java.util.List;
 
 /**
  * Calculate the overall number of reads in a SAM/BAM file
@@ -64,6 +68,11 @@ public final class CountReadsSpark extends GATKSparkTool {
     )
     public String out;
 
+    @Override
+    public List<ReadFilter> getDefaultReadFilters() {
+        return Collections.singletonList(ReadFilterLibrary.ALLOW_ALL_READS);
+    }
+
     @Override
     protected void runTool(final JavaSparkContext ctx) {
         final JavaRDD<GATKRead> reads = getReads();