1. htsjdk
   1. htsjdk.samtools
      1. (class)BAMBDGRecord
      2. (class)SAMRecordHelper
2. magic_rdds
3. org
   1. org.apache
      1. org.apache.spark
         1. org.apache.spark.sql
            1. (object)(case class)BDGCoverage
            2. (object)(case class)GenomicInterval
            3. (object)(case class)PileupTemplate
            4. (object)
               ResolveTableValuedFunctionsSeq
            5. (case class)SequilaSession
            6. (case class)SequilaSessionState
            7. (object)
               UTVFRegister
            1. org.apache.spark.sql.catalyst
               1. org.apache.spark.sql.catalyst.analysis
                  1. (class)SeQuiLaAnalyzer
            2. org.apache.spark.sql.execution
               1. org.apache.spark.sql.execution.datasources
                  1. (object)(case class)SequilaDataSourceStrategy
            3. org.apache.spark.sql.hive
               1. org.apache.spark.sql.hive.thriftserver
                  1. (object)
                     HiveThriftServer2Seq
                  2. (trait)ReflectedCompositeService
                  3. (object)
                     SequilaThriftServer
                  4. (object)
                     SparkExecuteStatementOperation
                  5. (class)SparkSQLCLIServiceSeq
   2. org.biodatageeks
      1. org.biodatageeks.formats
         1. (case class)Alignment
         2. (case class)BrowserExtensibleData
         3. (case class)Interval
         4. (case class)SequencedFragment
      2. org.biodatageeks.sequila
         1. org.biodatageeks.sequila.apps
            1. (object)
               Benchmark
            2. (object)
               CovRun
            3. (object)
               DepthOfCoverage
            4. (object)
               FeatureCounts
            5. (object)
               PileupApp
         2. org.biodatageeks.sequila.coverage
            1. (class)AbstractCovRecord
            2. (case class)BDGCoveragePlan
            3. (case class)ContigRange
            4. (class)CoverageAccumulatorV2
            5. (object)
               CoverageMethodsMos
            6. (class)CoverageStrategy
            7. (case class)CovRecord
            8. (case class)CovRecordWindow
            9. (class)CovUpdate
            10. (case class)RightCovEdge
            11. (case class)UpdateStruct
         3. org.biodatageeks.sequila.datasources
            1. (object)
               InputDataType
            1. org.biodatageeks.sequila.datasources.ADAM
               1. (class)ADAMDataSource
               2. (class)ADAMRelation
            2. org.biodatageeks.sequila.datasources.BAM
               1. (class)BAMDataSource
               2. (trait)BDGAlignFileReaderWriter
               3. (class)BDGAlignmentRelation
               4. (class)CRAMDataSource
            3. org.biodatageeks.sequila.datasources.BED
               1. (class)BEDDataSource
               2. (class)BEDRelation
            4. org.biodatageeks.sequila.datasources.FASTQ
               1. (class)FASTQDataSource
               2. (class)SequencedFragmentRelation
            5. org.biodatageeks.sequila.datasources.VCF
               1. (class)VCFDataSource
               2. (class)VCFRelation
         4. org.biodatageeks.sequila.inputformats
            1. (class)BDGAlignInputFormat
         5. org.biodatageeks.sequila.outputformats
            1. (class)BAMOutputFormat
         6. org.biodatageeks.sequila.pileup
            1. (case class)MDOperator
            2. (object)
               MDTagParser
            3. (class)Pileup
            4. (object)
               PileupMethods
            5. (case class)PileupPlan
            6. (class)PileupStrategy
            1. org.biodatageeks.sequila.pileup.broadcast
               1. (object)(case class)Correction
               2. (case class)FullCorrections
               3. (class)PileupAccumulator
               4. (class)PileupUpdate
               5. (case class)Range
               6. (object)(case class)Shrink
               7. (case class)Tail
            2. org.biodatageeks.sequila.pileup.conf
               1. (object)
                  Conf
               2. (object)
                  QualityConstants
            3. org.biodatageeks.sequila.pileup.converters
               1. (class)DelContext
               2. (case class)DelTransfer
               3. (class)PileupConverter
               4. (object)
                  PileupStringUtils
            4. org.biodatageeks.sequila.pileup.model
               1. (case class)AggregateRDD
               2. (object)
                  AggregateRDDOperations
               3. (case class)AlignmentsRDD
               4. (object)
                  AlignmentsRDDOperations
               5. (object)
                  Alts
               6. (class)BlockProperties
               7. (object)(case class)CigarDerivedConf
               8. (case class)ContigAggregate
               9. (case class)ExtendedReads
               10. (class)GenericPileupRecord
               11. (case class)InDelPositions
               12. (case class)PileupRecord
               13. (class)QualityCache
               14. (object)
                   Quals
               15. (object)
                   ReadOperations
               16. (case class)ReadQualSummary
               17. (class)Reference
            5. org.biodatageeks.sequila.pileup.serializers
               1. (class)CustomKryoRegistrator
               2. (class)IntMapSerializer
               3. (class)LinkedHashSetSerializer
               4. (class)LongMapSerializer
               5. (object)
                  PileupProjection
            6. org.biodatageeks.sequila.pileup.timers
               1. (object)
                  PileupTimers
            7. org.biodatageeks.sequila.pileup.udfs
               1. (object)
                  AltFunctions
               2. (object)
                  CoverageFunctions
               3. (object)
                  QualityFunctions
         7. org.biodatageeks.sequila.R
            1. (class)SequilaR
         8. org.biodatageeks.sequila.rangejoins
            1. org.biodatageeks.sequila.rangejoins.common
               1. (object)
                  ExtractRangeJoinKeys
               2. (object)
                  ExtractRangeJoinKeysWithEquality
               3. (object)
                  Main
               1. org.biodatageeks.sequila.rangejoins.common.metrics
                  1. (class)MetricsCollector
                  2. (case class)TestMetaRecord
               2. org.biodatageeks.sequila.rangejoins.common.performance
                  1. org.biodatageeks.sequila.rangejoins.common.performance.timers
                     1. (object)
                        IntervalTreeTimer
            2. org.biodatageeks.sequila.rangejoins.genApp
               1. (case class)Interval
               2. (class)IntervalTree
               3. (case class)IntervalTreeJoin
               4. (object)
                  IntervalTreeJoinImpl
               5. (class)IntervalTreeJoinStrategy
            3. org.biodatageeks.sequila.rangejoins.IntervalTree
               1. (case class)Interval
               2. (case class)IntervalTreeJoinOptim
               3. (object)
                  IntervalTreeJoinOptimImpl
               4. (class)IntervalTreeJoinStrategyOptim
               5. (case class)IntervalWithRow
            4. org.biodatageeks.sequila.rangejoins.methods
               1. org.biodatageeks.sequila.rangejoins.methods.genApp
                  1. (class)IntervalTreeChromosome
                  2. (case class)IntervalTreeJoinChromosome
                  3. (object)
                     IntervalTreeJoinChromosomeImpl
               2. org.biodatageeks.sequila.rangejoins.methods.IntervalTree
                  1. (case class)InternalRowPacker
                  2. (class)IntervalTreeHTS
                  3. (class)IntervalTreeHTSChromosome
                  4. (case class)IntervalTreeJoinOptimChromosome
                  5. (object)
                     IntervalTreeJoinOptimChromosomeImpl
               3. org.biodatageeks.sequila.rangejoins.methods.transformations
                  1. (object)
                     RangeMethods
            5. org.biodatageeks.sequila.rangejoins.optimizer
               1. (class)JoinOptimizer
               2. (class)JoinOptimizerChromosome
               3. (object)
                  RangeJoinMethod
         9. org.biodatageeks.sequila.utils
            1. (object)
               Columns
            2. (object)
               DataQualityFuncs
            3. (object)
               FastMath
            4. (class)FastSerializer
            5. (object)
               InternalParams
            6. (trait)Interval
            7. (object)
               ScalaFuncs
            8. (object)
               SequilaRegister
            9. (object)
               TableFuncs
            10. (object)
                UDFRegister
            1. org.biodatageeks.sequila.utils.schema
               1. (object)
                  CSVToJsonTags
         10. org.biodatageeks.sequila.utvf
             1. (case class)GenomicIntervalPlan
             2. (class)GenomicIntervalStrategy
             3. (case class)GIntervalRow
   3. org.seqdoop
      1. org.seqdoop.hadoop_bam
         1. (class)BAMBDGInputFormat
         2. (class)BAMBDGRecordReader
         3. (class)BAMBDGSplitGuesser
         4. (class)CRAMBDGInputFormat
4. scala
   1. scala.collection
      1. scala.collection.mutable
         1. (object)(class)IntMap
         2. (trait)ReusableBuilder