GATKVariant (org.broadinstitute.hellbender.utils.variant.GATKVariant)
16
GATKRead (org.broadinstitute.hellbender.utils.read.GATKRead)
10
ReadContextData (org.broadinstitute.hellbender.engine.ReadContextData)
7
SimpleInterval (org.broadinstitute.hellbender.utils.SimpleInterval)
7
JavaSparkContext (org.apache.spark.api.java.JavaSparkContext)
6
ReferenceBases (org.broadinstitute.hellbender.utils.reference.ReferenceBases)
5
BaseTest (org.broadinstitute.hellbender.utils.test.BaseTest)
4
Test (org.testng.annotations.Test)
4
SAMSequenceDictionary (htsjdk.samtools.SAMSequenceDictionary)
3
ArrayList (java.util.ArrayList)
3
ReferenceMultiSource (org.broadinstitute.hellbender.engine.datasources.ReferenceMultiSource)
3
ReadFilter (org.broadinstitute.hellbender.engine.filters.ReadFilter)
3
VariantsSparkSource (org.broadinstitute.hellbender.engine.spark.datasources.VariantsSparkSource)
3
IntervalsSkipList (org.broadinstitute.hellbender.utils.collections.IntervalsSkipList)
3
RecalibrationReport (org.broadinstitute.hellbender.utils.recalibration.RecalibrationReport)
3
Tuple2 (scala.Tuple2)
3
IOException (java.io.IOException)
2
JavaPairRDD (org.apache.spark.api.java.JavaPairRDD)
2
JavaRDD (org.apache.spark.api.java.JavaRDD)
2
ContextShard (org.broadinstitute.hellbender.engine.ContextShard)
2