1. com
   1. com.fulcrumgenomics
      1. (object)
         FgBioDef
      2. (trait)Writer
      1. com.fulcrumgenomics.alignment
         1. (object)(class)Aligner
         2. (object)(case class)Alignment
         3. (object)(case class)Cigar
         4. (case class)CigarElem
         5. (class)LinearMatrix
         6. (object)(trait)Matrix
         7. (object)(trait)Mode
         8. (class)SimpleIntMatrix
      2. com.fulcrumgenomics.bam
         1. (class)AutoGenerateReadGroupsByName
         2. (object)
            Bams
         3. (object)(case class)BaseCounts
         4. (case class)BaseEntry
         5. (class)ClipBam
         6. (case class)ClippingMetrics
         7. (object)(trait)ClippingMode
         8. (case class)DeletionEntry
         9. (class)ErrorRateByReadPosition
         10. (object)(case class)ErrorRateByReadPositionMetric
         11. (class)EstimatePoolingFractions
         12. (class)FilterBam
         13. (object)(class)FindSwitchbackReads
         14. (class)FindTechnicalReads
         15. (case class)InsertionEntry
         16. (case class)Pileup
         17. (class)PileupBuilder
         18. (trait)PileupEntry
         19. (case class)PoolingFractionMetric
         20. (class)RandomizeBam
         21. (object)(trait)ReadType
         22. (class)RemoveSamTags
         23. (object)(class)SamRecordClipper
         24. (class)SetMateInformation
         25. (class)SortBam
         26. (class)SplitBam
         27. (object)(trait)SplitType
         28. (object)(case class)Template
         29. (object)(class)TrimPrimers
         30. (class)UpdateReadGroups
         1. com.fulcrumgenomics.bam.api
            1. (object)
               QueryType
            2. (class)SamIterator
            3. (object)(trait)SamOrder
            4. (object)(trait)SamRecord
            5. (class)SamRecordCodec
            6. (object)(class)SamSource
            7. (object)(class)SamWriter
            8. (class)TransientAttrs
      3. com.fulcrumgenomics.basecalling
         1. (object)(case class)BasecallingParams
         2. (class)ExtractBasecallingParamsForPicard
         3. (class)ExtractIlluminaRunInfo
      4. com.fulcrumgenomics.cmdline
         1. (object)
            ClpGroups
         2. (class)FgBioCommonArgs
         3. (object)(class)FgBioMain
         4. (trait)FgBioTool
      5. com.fulcrumgenomics.fasta
         1. (class)HardMaskFasta
         2. (object)(class)ReferenceSequenceIterator
      6. com.fulcrumgenomics.fastq
         1. (object)(class)DemuxFastqs
         2. (case class)FastqRecord
         3. (object)(class)FastqSource
         4. (class)FastqToBam
         5. (object)(class)FastqWriter
         6. (object)(trait)OutputType
         7. (object)(trait)QualityEncoding
         8. (class)QualityEncodingDetector
         9. (object)(class)SortFastq
         10. (class)TrimFastq
      7. com.fulcrumgenomics.illumina
         1. (object)(case class)RunInfo
         2. (object)(case class)Sample
         3. (object)(class)SampleSheet
      8. com.fulcrumgenomics.internal
         1. (class)BuildToolDocs
         2. (case class)ColumnDescription
         3. (class)FgMetricsDoclet
         4. (trait)InternalTool
         5. (object)
            InternalTools
         6. (case class)MetricDescription
      9. com.fulcrumgenomics.math
         1. (class)BinomialDistribution
         2. (object)
            FishersExactTest
      10. com.fulcrumgenomics.personal
          1. com.fulcrumgenomics.personal.nhomer
             1. (class)GenerateRegionsFromFasta
             2. (class)SplitTag
          2. com.fulcrumgenomics.personal.tfenne
             1. (class)StripFastqReadNumbers
      11. com.fulcrumgenomics.rnaseq
          1. (object)(class)CollectErccMetrics
          2. (case class)ErccDetailedMetric
          3. (object)(trait)ErccMixture
          4. (case class)ErccSummaryMetrics
          5. (object)(class)EstimateRnaSeqInsertSize
          6. (case class)InsertSizeMetric
      12. com.fulcrumgenomics.testing
          1. (class)ReferenceSetBuilder
          2. (object)(class)SamBuilder
          3. (object)(class)VariantContextSetBuilder
      13. com.fulcrumgenomics.umi
          1. (class)AnnotateBamWithUmis
          2. (class)CallDuplexConsensusReads
          3. (class)CallMolecularConsensusReads
          4. (object)(class)CollectDuplexSeqMetrics
          5. (object)(class)ConsensusCaller
          6. (class)ConsensusCallingIterator
          7. (object)
             ConsensusTags
          8. (object)(class)CorrectUmis
          9. (object)(class)DuplexConsensusCaller
          10. (object)(case class)DuplexConsensusPerBaseValues
          11. (object)(class)ExtractUmisFromBam
          12. (class)FilterConsensusReads
          13. (object)(class)GroupReadsByUmi
          14. (object)(class)ReviewConsensusVariants
          15. (object)(trait)Strategy
          16. (case class)TagFamilySizeMetric
          17. (object)(trait)UmiConsensusCaller
          18. (case class)VanillaConsensusRead
          19. (class)VanillaUmiConsensusCaller
          20. (object)(case class)VanillaUmiConsensusCallerOptions
      14. com.fulcrumgenomics.util
          1. (class)DnaFoldPrediction
          2. (class)DnaFoldPredictor
          3. (object)
             GeneAnnotations
          4. (trait)GenomicSpan
          5. (object)
             IlluminaAdapters
          6. (case class)IndexMetric
          7. (object)(class)Io
          8. (object)
             MathUtil
          9. (object)(trait)Metric
          10. (object)
              NumericTypes
          11. (class)PickIlluminaIndices
          12. (object)(class)PickLongIndices
          13. (case class)ProgressLogger
          14. (object)(case class)ReadSegment
          15. (object)(class)ReadStructure
          16. (object)(class)RefFlatSource
          17. (object)
              Rscript
          18. (object)(case class)SampleBarcodeMetric
          19. (object)(class)SegmentType
          20. (object)
              Sequences
          21. (object)(class)Sorter
      15. com.fulcrumgenomics.vcf
          1. (object)(class)AssessPhasing
          2. (object)(case class)AssessPhasingMetric
          3. (trait)BlockInfo
          4. (object)
             ByIntervalListVariantContextIterator
          5. (object)
             HapCut1VcfHeaderLines
          6. (object)
             HapCut2VcfHeaderLines
          7. (object)
             HapCutReader
          8. (object)(class)HapCutToVcf
          9. (object)
             HapCutType
          10. (object)(trait)HeaderLines
          11. (object)(class)JointVariantContextIterator
          12. (object)(class)MakeMixtureVcf
          13. (object)(class)MakeTwoSampleMixtureVcf
          14. (object)(case class)PhaseBlock
          15. (object)(case class)PhaseBlockLengthMetric
          16. (object)(class)VariantMask
          1. com.fulcrumgenomics.vcf.filtration
             1. (class)EndRepairArtifactLikelihoodFilter
             2. (class)FilterSomaticVcf
             3. (trait)SomaticVariantFilter