1. com
   1. com.fulcrumgenomics
      1. (object)
         FgBioDef
      2. (trait)Writer
      1. com.fulcrumgenomics.alignment
         1. (object)(case class)Alignment
         2. (object)(case class)Cigar
         3. (case class)CigarElem
         4. (class)LinearMatrix
         5. (object)(trait)Matrix
         6. (object)(class)NeedlemanWunschAligner
      2. com.fulcrumgenomics.bam
         1. (class)AutoGenerateReadGroupsByName
         2. (object)
            Bams
         3. (object)(case class)BaseCounts
         4. (case class)BaseEntry
         5. (class)ClipBam
         6. (class)ClipOverlappingReads
         7. (case class)DeletionEntry
         8. (class)ErrorRateByReadPosition
         9. (object)(case class)ErrorRateByReadPositionMetric
         10. (class)EstimatePoolingFractions
         11. (class)FilterBam
         12. (class)FindTechnicalReads
         13. (case class)InsertionEntry
         14. (case class)Pileup
         15. (class)PileupBuilder
         16. (trait)PileupEntry
         17. (case class)PoolingFractionMetric
         18. (class)RandomizeBam
         19. (class)RemoveSamTags
         20. (object)(class)SamRecordClipper
         21. (class)SetMateInformation
         22. (class)SortBam
         23. (class)SplitBam
         24. (object)(trait)SplitType
         25. (object)(case class)Template
         26. (class)TrimPrimers
         27. (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)QualityEncoding
         7. (class)QualityEncodingDetector
         8. (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. (object)
            FishersExactTest
      10. com.fulcrumgenomics.personal
          1. com.fulcrumgenomics.personal.nhomer
             1. (class)GenerateRegionsFromFasta
             2. (class)SplitTag
      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)(class)ExtractUmisFromBam
          11. (class)FilterConsensusReads
          12. (object)(class)GroupReadsByUmi
          13. (object)(class)ReviewConsensusVariants
          14. (case class)TagFamilySizeMetric
          15. (object)(trait)UmiConsensusCaller
          16. (case class)VanillaConsensusRead
          17. (class)VanillaUmiConsensusCaller
          18. (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. (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