1. org
   1. org.bdgenomics
      1. org.bdgenomics.adam
         1. org.bdgenomics.adam.cli
            1. (object)(class)ADAM2Vcf
            2. (class)ADAM2VcfArgs
            3. (trait)ADAMCommand
            4. (trait)ADAMCommandCompanion
            5. (object)
               ADAMMain
            6. (trait)ADAMSparkCommand
            7. (object)(class)AlleleCount
            8. (class)AlleleCountArgs
            9. (object)
               AlleleCountHelper
            10. (object)
                Args4j
            11. (class)Args4jBase
            12. (object)(class)Bam2ADAM
            13. (class)Bam2ADAMArgs
            14. (object)(class)BuildInformation
            15. (object)(class)CalculateDepth
            16. (class)CalculateDepthArgs
            17. (object)(class)CompareADAM
            18. (class)CompareADAMArgs
            19. (object)(class)CountKmers
            20. (class)CountKmersArgs
            21. (trait)DictionaryCommand
            22. (object)(class)Fasta2ADAM
            23. (class)Fasta2ADAMArgs
            24. (object)(class)Features2ADAM
            25. (class)Features2ADAMArgs
            26. (object)(class)FindReads
            27. (class)FindReadsArgs
            28. (object)(class)FlagStat
            29. (class)FlagStatArgs
            30. (case class)FreqJson
            31. (object)(class)GenotypeConcordance
            32. (class)GenotypeConcordanceArgs
            33. (object)(class)IndexFlatGenotype
            34. (class)IndexFlatGenotypeArgs
            35. (object)(class)ListDict
            36. (class)ListDictArgs
            37. (class)MpileupArgs
            38. (object)(class)MpileupCommand
            39. (trait)ParquetArgs
            40. (object)(class)PileupAggregator
            41. (class)PileupAggregatorArgs
            42. (object)(class)PluginExecutor
            43. (class)PluginExecutorArgs
            44. (object)(class)PrintADAM
            45. (class)PrintADAMArgs
            46. (object)(class)PrintParquet
            47. (class)PrintParquetArgs
            48. (object)(class)PrintTags
            49. (class)PrintTagsArgs
            50. (object)(class)Reads2Ref
            51. (object)(class)Reads2RefArgs
            52. (trait)SparkArgs
            53. (trait)SparkCommand
            54. (object)(class)SummarizeGenotypes
            55. (class)SummarizeGenotypesArgs
            56. (case class)TrackJson
            57. (object)(class)Transform
            58. (class)TransformArgs
            59. (object)(class)Vcf2ADAM
            60. (class)Vcf2ADAMArgs
            61. (object)(class)Vcf2FlatGenotype
            62. (class)Vcf2FlatGenotypeArgs
            63. (object)(class)VcfAnnotation2ADAM
            64. (class)VcfAnnotation2ADAMArgs
            65. (object)(class)VizReads
            66. (class)VizReadsArgs
            67. (class)VizServlet