{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/46600258","id":46600258,"diff_hunk":"@@ -0,0 +1,230 @@\n+package org.broadinstitute.hellbender.tools.spark.validation;\n+\n+import com.google.common.collect.Lists;\n+import org.apache.avro.io.parsing.Symbol;\n+import org.apache.spark.api.java.JavaPairRDD;\n+import org.apache.spark.api.java.JavaRDD;\n+import org.apache.spark.api.java.JavaSparkContext;\n+import org.apache.spark.api.java.function.Function2;\n+import org.apache.spark.api.java.function.PairFunction;\n+import org.broadinstitute.hellbender.cmdline.Argument;\n+import org.broadinstitute.hellbender.cmdline.CommandLineProgramProperties;\n+import org.broadinstitute.hellbender.cmdline.programgroups.SparkProgramGroup;\n+import org.broadinstitute.hellbender.engine.spark.GATKSparkTool;\n+import org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSource;\n+import org.broadinstitute.hellbender.exceptions.GATKException;\n+import org.broadinstitute.hellbender.exceptions.UserException;\n+import org.broadinstitute.hellbender.utils.QualityUtils;\n+import org.broadinstitute.hellbender.utils.read.GATKRead;\n+import scala.Tuple2;\n+\n+import java.io.Serializable;\n+import java.util.Arrays;\n+import java.util.List;\n+import java.util.Map;\n+import java.util.Set;\n+\n+@CommandLineProgramProperties(summary = \"Compares two the quality scores of BAMs\", oneLineSummary = \"Diff qs of two BAMs\",\n+        programGroup = SparkProgramGroup.class)\n+\n+public class BqsrRecalBasesCompare extends GATKSparkTool  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