1. org
   1. org.bdgenomics
      1. org.bdgenomics.adam
         1. org.bdgenomics.adam.cli
            1. (object)(class)Adam2Fastq
            2. (class)Adam2FastqArgs
            3. (object)(class)ADAM2Vcf
            4. (class)ADAM2VcfArgs
            5. (trait)ADAMCommand
            6. (trait)ADAMCommandCompanion
            7. (object)
               ADAMMain
            8. (trait)ADAMSparkCommand
            9. (object)(class)AlleleCount
            10. (class)AlleleCountArgs
            11. (object)
                AlleleCountHelper
            12. (object)
                Args4j
            13. (class)Args4jBase
            14. (object)(class)Bam2ADAM
            15. (class)Bam2ADAMArgs
            16. (object)(class)BuildInformation
            17. (object)(class)CalculateDepth
            18. (class)CalculateDepthArgs
            19. (object)(class)CompareADAM
            20. (class)CompareADAMArgs
            21. (object)(class)CountKmers
            22. (class)CountKmersArgs
            23. (trait)DictionaryCommand
            24. (object)(class)Fasta2ADAM
            25. (class)Fasta2ADAMArgs
            26. (object)(class)Features2ADAM
            27. (class)Features2ADAMArgs
            28. (object)(class)FindReads
            29. (class)FindReadsArgs
            30. (object)(class)FlagStat
            31. (class)FlagStatArgs
            32. (case class)FreqJson
            33. (object)(class)GenotypeConcordance
            34. (class)GenotypeConcordanceArgs
            35. (object)(class)ListDict
            36. (class)ListDictArgs
            37. (trait)LoadFileArgs
            38. (class)MpileupArgs
            39. (object)(class)MpileupCommand
            40. (trait)ParquetArgs
            41. (trait)ParquetLoadSaveArgs
            42. (trait)ParquetSaveArgs
            43. (object)(class)PluginExecutor
            44. (class)PluginExecutorArgs
            45. (object)(class)PrintADAM
            46. (class)PrintADAMArgs
            47. (object)(class)PrintGenes
            48. (class)PrintGenesArgs
            49. (object)(class)PrintTags
            50. (class)PrintTagsArgs
            51. (object)(class)Reads2Ref
            52. (class)Reads2RefArgs
            53. (trait)SaveFileArgs
            54. (object)(class)SummarizeGenotypes
            55. (class)SummarizeGenotypesArgs
            56. (case class)TrackJson
            57. (object)(class)Transform
            58. (class)TransformArgs
            59. (case class)VariationJson
            60. (object)(class)Vcf2ADAM
            61. (class)Vcf2ADAMArgs
            62. (object)(class)VcfAnnotation2ADAM
            63. (class)VcfAnnotation2ADAMArgs
            64. (object)(class)View
            65. (class)ViewArgs
            66. (object)(class)VizReads
            67. (class)VizReadsArgs
            68. (class)VizServlet
            69. (class)Wig2BedArgs
            70. (object)(class)WigFix2Bed