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)IndexFlatGenotype
            36. (class)IndexFlatGenotypeArgs
            37. (object)(class)ListDict
            38. (class)ListDictArgs
            39. (trait)LoadFileArgs
            40. (class)MpileupArgs
            41. (object)(class)MpileupCommand
            42. (trait)ParquetArgs
            43. (trait)ParquetLoadSaveArgs
            44. (trait)ParquetSaveArgs
            45. (object)(class)PluginExecutor
            46. (class)PluginExecutorArgs
            47. (object)(class)PrintADAM
            48. (class)PrintADAMArgs
            49. (object)(class)PrintGenes
            50. (class)PrintGenesArgs
            51. (object)(class)PrintParquet
            52. (class)PrintParquetArgs
            53. (object)(class)PrintTags
            54. (class)PrintTagsArgs
            55. (object)(class)Reads2Ref
            56. (class)Reads2RefArgs
            57. (trait)SaveFileArgs
            58. (object)(class)SummarizeGenotypes
            59. (class)SummarizeGenotypesArgs
            60. (case class)TrackJson
            61. (object)(class)Transform
            62. (class)TransformArgs
            63. (object)(class)Vcf2ADAM
            64. (class)Vcf2ADAMArgs
            65. (object)(class)Vcf2FlatGenotype
            66. (class)Vcf2FlatGenotypeArgs
            67. (object)(class)VcfAnnotation2ADAM
            68. (class)VcfAnnotation2ADAMArgs
            69. (object)(class)View
            70. (class)ViewArgs
            71. (object)(class)VizReads
            72. (class)VizReadsArgs
            73. (class)VizServlet