1. breeze
   1. breeze.stats
2. org
   1. org.hammerlab
      1. org.hammerlab.guacamole
         1. (object)
            Main
         1. org.hammerlab.guacamole.alignment
            1. (object)
               AffineGapPenaltyAlignment
            2. (object)
               AlignmentState
            3. (case class)ReadAlignment
         2. org.hammerlab.guacamole.assembly
            1. (trait)AssemblyArgs
            2. (object)
               AssemblyUtils
            3. (object)(class)DeBruijnGraph
         3. org.hammerlab.guacamole.commands
            1. (trait)Args
            2. (class)Command
            3. (object)
               GermlineAssemblyCaller
            4. (object)
               PartitionLoci
            5. (class)PartitionLociArgs
            6. (object)
               PartitionReads
            7. (class)PartitionReadsArgs
            8. (object)
               SomaticJoint
            9. (object)
               SomaticStandard
            10. (class)SparkCommand
            11. (object)
                VAFHistogram
            12. (object)(case class)VariantLocus
            13. (object)
                VariantSupport
         4. org.hammerlab.guacamole.distributed
            1. (object)
               PileupFlatMapUtils
            2. (class)RegionsByContig
            3. (class)SingleContigRegionIterator
            4. (object)
               WindowFlatMapUtils
         5. org.hammerlab.guacamole.filters
            1. (object)
               FishersExactTest
            1. org.hammerlab.guacamole.filters.genotype
               1. (object)
                  AverageBaseQualityFilter
               2. (object)
                  AverageMappingQualityFilter
               3. (object)
                  GenotypeFilter
               4. (object)
                  MinimumAlternateReadDepthFilter
               5. (object)
                  MinimumLikelihoodFilter
               6. (object)
                  ReadDepthFilter
            2. org.hammerlab.guacamole.filters.somatic
               1. (object)
                  SomaticAlternateReadDepthFilter
               2. (object)
                  SomaticAverageBaseQualityFilter
               3. (object)
                  SomaticAverageMappingQualityFilter
               4. (object)
                  SomaticGenotypeFilter
               5. (object)
                  SomaticLogOddsFilter
               6. (object)
                  SomaticMedianMismatchFilter
               7. (object)
                  SomaticMinimumLikelihoodFilter
               8. (object)
                  SomaticReadDepthFilter
               9. (object)
                  SomaticVAFFilter
         6. org.hammerlab.guacamole.jointcaller
            1. (object)(case class)AlleleAtLocus
            2. (object)(case class)Input
            3. (object)(case class)InputCollection
            4. (object)(case class)Parameters
            5. (object)
               VCFOutput
            1. org.hammerlab.guacamole.jointcaller.annotation
               1. (object)(case class)InsufficientNormal
               2. (object)(case class)MultiSampleAnnotations
               3. (object)(case class)SingleSampleAnnotations
               4. (object)(case class)StrandBias
               5. (object)(case class)TooManyCallsAtSite
            2. org.hammerlab.guacamole.jointcaller.evidence
               1. (object)(case class)MultiSampleMultiAlleleEvidence
               2. (object)(case class)MultiSampleSingleAlleleEvidence
               3. (object)(case class)NormalDNASingleSampleSingleAlleleEvidence
               4. (trait)SingleSampleSingleAlleleEvidence
               5. (object)(case class)TumorDNASingleSampleSingleAlleleEvidence
               6. (object)(case class)TumorRNASingleSampleSingleAlleleEvidence
            3. org.hammerlab.guacamole.jointcaller.kryo
               1. (class)Registrar
            4. org.hammerlab.guacamole.jointcaller.pileup_summarization
               1. (case class)MultiplePileupStats
               2. (object)(class)PileupStats
               3. (object)(case class)ReadSubsequence
         7. org.hammerlab.guacamole.kryo
            1. (class)Registrar
         8. org.hammerlab.guacamole.likelihood
            1. (object)
               Likelihood
         9. org.hammerlab.guacamole.loci
            1. (case class)Coverage
            1. org.hammerlab.guacamole.loci.args
               1. (trait)CallLociArgs
               2. (trait)ForceCallLociArgs
            2. org.hammerlab.guacamole.loci.iterator
               1. (class)SkippableLociIterator
               2. (class)SkippableLocusKeyedIterator
            3. org.hammerlab.guacamole.loci.map
               1. (object)(case class)Contig
               2. (class)ContigSerializer
               3. (object)(case class)LociMap
               4. (class)Serializer
            4. org.hammerlab.guacamole.loci.parsing
               1. (object)
                  All
               2. (object)
                  AllRange
               3. (object)(case class)LociRange
               4. (case class)LociRanges
               5. (object)(class)ParsedLoci
               6. (object)(trait)ParsedLociRange
               7. (object)(trait)ParsedLociRanges
            5. org.hammerlab.guacamole.loci.partitioning
               1. (class)CappedRegionsPartitioner
               2. (trait)CappedRegionsPartitionerArgs
               3. (trait)HalfWindowArgs
               4. (trait)HalfWindowConfig
               5. (object)(trait)LociPartitioner
               6. (trait)LociPartitionerArgs
               7. (object)
                  LociPartitionerType
               8. (object)(case class)LociPartitioning
               9. (object)(class)MicroRegionPartitioner
               10. (trait)MicroRegionPartitionerArgs
               11. (case class)UniformMicroPartitioner
               12. (case class)UniformPartitioner
               13. (trait)UniformPartitionerArgs
            6. org.hammerlab.guacamole.loci.set
               1. (case class)Contig
               2. (class)ContigSerializer
               3. (class)LociIterator
               4. (object)(case class)LociSet
               5. (class)Serializer
               6. (class)TakeLociIterator
         10. org.hammerlab.guacamole.logging
             1. (object)(class)DelayedMessages
             2. (object)
                LoggingUtils
         11. org.hammerlab.guacamole.pileup
             1. (object)
                Clipped
             2. (object)(case class)Deletion
             3. (case class)Insertion
             4. (case class)InvalidCigarElementException
             5. (case class)Match
             6. (object)(class)MatchOrMisMatch
             7. (case class)MidDeletion
             8. (case class)Mismatch
             9. (object)(case class)Pileup
             10. (object)(case class)PileupElement
         12. org.hammerlab.guacamole.reads
             1. (trait)HasSampleId
             2. (case class)MappedRead
             3. (class)MappedReadSerializer
             4. (object)(case class)MateAlignmentProperties
             5. (case class)PairedRead
             6. (object)(trait)Read
             7. (case class)UnmappedRead
             8. (class)UnmappedReadSerializer
         13. org.hammerlab.guacamole.readsets
             1. (object)(case class)ReadSets
             1. org.hammerlab.guacamole.readsets.args
                1. (trait)Arguments
                2. (trait)Base
                3. (trait)GermlineCallerArgs
                4. (trait)HasReference
                5. (trait)NoSequenceDictionaryArgs
                6. (trait)ReferenceArgs
                7. (trait)SingleSampleArgs
                8. (trait)TumorNormalReadsArgs
             2. org.hammerlab.guacamole.readsets.io
                1. (object)(class)Input
                2. (object)(case class)InputFilters
                3. (trait)ReadFilterArgs
             3. org.hammerlab.guacamole.readsets.iterator
                1. (case class)ContigCoverageIterator
                2. (object)(class)ContigsIterator
                3. (case class)RegionsNotSortedException
                4. (case class)RepeatedContigException
             4. org.hammerlab.guacamole.readsets.rdd
                1. (object)(class)CoverageRDD
                2. (object)(class)PartitionedRegions
                3. (trait)PartitionedRegionsArgs
                4. (case class)ReadsRDD
         14. org.hammerlab.guacamole.reference
             1. (object)(class)ContigIterator
             2. (object)
                ContigName
             3. (case class)ContigNotFound
             4. (trait)ContigSequence
             5. (trait)HasContig
             6. (object)(trait)HasLocus
             7. (object)(trait)Interval
             8. (object)(trait)Position
             9. (object)(case class)ReferenceBroadcast
             10. (trait)ReferenceGenome
             11. (object)(trait)ReferenceRegion
         15. org.hammerlab.guacamole.strings
             1. (object)(trait)TruncatedToString
         16. org.hammerlab.guacamole.util
             1. (object)
                Bases
             2. (object)
                CigarUtils
         17. org.hammerlab.guacamole.variants
             1. (object)(case class)Allele
             2. (object)(case class)AlleleEvidence
             3. (class)AlleleSerializer
             4. (case class)CalledAllele
             5. (case class)CalledSomaticAllele
             6. (object)
                Concordance
             7. (case class)Genotype
             8. (trait)GenotypeOutputArgs
             9. (trait)GenotypeOutputCaller
             10. (trait)HasAlleleSerializer
             11. (trait)ReferenceVariant
             12. (object)
                 VariantContext
         18. org.hammerlab.guacamole.windowing
             1. (object)(case class)SlidingWindow
             2. (object)
                SplitIterator