1. com
   1. com.fulcrumgenomics
      1. (object)(class)FgBioDef
      1. com.fulcrumgenomics.bam
         1. (class)AutoGenerateReadGroupsByName
         2. (class)ErrorRateByReadPosition
         3. (object)(case class)ErrorRateByReadPositionMetric
         4. (class)FilterBam
         5. (class)FindTechnicalReads
         6. (class)RandomizeBam
         7. (object)(trait)SamRecordClipper
         8. (class)SetMateInformation
         9. (class)TrimPrimers
         10. (class)UpdateReadGroups
      2. com.fulcrumgenomics.cmdline
         1. (object)
            ClpGroups
         2. (object)(class)FgBioMain
         3. (trait)FgBioTool
      3. com.fulcrumgenomics.fasta
         1. (class)HardMaskFasta
         2. (object)(class)ReferenceSequenceIterator
      4. com.fulcrumgenomics.fastq
         1. (case class)FastqRecord
         2. (object)(class)FastqSource
         3. (object)(class)FastqWriter
         4. (class)TrimFastq
      5. com.fulcrumgenomics.personal
         1. com.fulcrumgenomics.personal.nhomer
            1. (class)GenerateRegionsFromFasta
            2. (class)HasSequence
            3. (class)SplitTag
      6. com.fulcrumgenomics.testing
         1. (object)(class)SamRecordSetBuilder
         2. (object)(class)VariantContextSetBuilder
      7. com.fulcrumgenomics.umi
         1. (class)AnnotateBamWithUmis
         2. (class)CallMolecularConsensusReads
         3. (object)(class)ConsensusCaller
         4. (case class)ConsensusRead
         5. (object)(class)ExtractUmisFromBam
         6. (object)(class)GroupReadsByUmi
         7. (class)ReviewConsensusVariants
         8. (case class)SourceRead
         9. (case class)TagFamilySizeMetric
         10. (object)(class)VanillaUmiConsensusCaller
         11. (object)(case class)VanillaUmiConsensusCallerOptions
      8. com.fulcrumgenomics.util
         1. (class)BetterBufferedIterator
         2. (object)(class)DelimitedDataParser
         3. (class)DnaFoldPrediction
         4. (class)DnaFoldPredictor
         5. (trait)GenomicSpan
         6. (object)
            IlluminaAdapters
         7. (case class)IndexMetric
         8. (object)(class)Io
         9. (object)
            MathUtil
         10. (object)(trait)Metric
         11. (case class)MolecularBarcode
         12. (object)(class)NumericCounter
         13. (object)
             NumericTypes
         14. (class)PickIlluminaIndices
         15. (object)(class)PickLongIndices
         16. (class)ProgressLogger
         17. (object)(trait)ReadSegment
         18. (object)(class)ReadStructure
         19. (class)Row
         20. (case class)SampleBarcode
         21. (object)(case class)SampleBarcodeMetric
         22. (object)
             Sequences
         23. (object)(class)SimpleCounter
         24. (case class)Skip
         25. (case class)Template
         1. com.fulcrumgenomics.util.miseq
            1. (class)Sample
            2. (object)(class)SampleBarcode
            3. (object)(class)SampleSheet
      9. 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. (class)HapCutToVcf
         9. (object)
            HapCutType
         10. (object)(trait)HeaderLines
         11. (object)(class)JointVariantContextIterator
         12. (object)(class)MakeTwoSampleMixtureVcf
         13. (object)(case class)PhaseBlock
         14. (object)(case class)PhaseBlockLengthMetric