c

org.bdgenomics.adam.cli

TransformAlignmentsArgs

class TransformAlignmentsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs with CramArgs

Linear Supertypes
CramArgs, ParquetArgs, ADAMSaveAnyArgs, SaveArgs, ParquetRDDArgs, Args4jBase, AnyRef, Any
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  2. By Inheritance
Inherited
  1. TransformAlignmentsArgs
  2. CramArgs
  3. ParquetArgs
  4. ADAMSaveAnyArgs
  5. SaveArgs
  6. ParquetRDDArgs
  7. Args4jBase
  8. AnyRef
  9. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new TransformAlignmentsArgs()

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  4. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  5. var asSingleFile: Boolean
    Definition Classes
    TransformAlignmentsArgs → ADAMSaveAnyArgs
  6. var binQualityScores: String
  7. val blockSize: Int
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  8. var cache: Boolean
  9. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native() @HotSpotIntrinsicCandidate()
  10. var coalesce: Int
  11. var command: String
  12. val compressionCodec: CompressionCodecName
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  13. var concatFilename: String
  14. def configureCramFormat(sc: SparkContext): Option[Unit]

    Configure CRAM format.

    Configure CRAM format.

    sc

    Spark context to configure

    Definition Classes
    CramArgs
  15. val cramReference: String
    Definition Classes
    CramArgs
    Annotations
    @Option()
  16. var deferMerging: Boolean
    Definition Classes
    TransformAlignmentsArgs → ADAMSaveAnyArgs
  17. val disableDictionaryEncoding: Boolean
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  18. var disableFastConcat: Boolean
    Definition Classes
    TransformAlignmentsArgs → ADAMSaveAnyArgs
  19. var disableProcessingStep: Boolean
  20. var doPrintUsage: Boolean
    Definition Classes
    Args4jBase
  21. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  22. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  23. var fastqReadGroup: String
  24. var forceLoadBam: Boolean
  25. var forceLoadFastq: Boolean
  26. var forceLoadIFastq: Boolean
  27. var forceLoadParquet: Boolean
  28. var forceShuffle: Boolean
  29. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  30. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  31. var inputPath: String
  32. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  33. var knownIndelsFile: String
  34. var knownSnpsFile: String
  35. var limitProjection: Boolean
  36. var locallyRealign: Boolean
  37. var lodThreshold: Double
  38. val logLevel: String
    Definition Classes
    ParquetArgs
    Annotations
    @Option()
  39. var markDuplicates: Boolean
  40. var maxConsensusNumber: Int
  41. var maxIndelSize: Int
  42. var maxReadLength: Int
  43. var maxReadsPerTarget: Int
  44. var maxTargetSize: Int
  45. var mdTagsFragmentSize: Long
  46. var mdTagsOverwrite: Boolean
  47. var mdTagsReferenceFile: String
  48. var minAcceptableQuality: Int
  49. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  50. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  51. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  52. var outputPath: String
    Definition Classes
    TransformAlignmentsArgs → SaveArgs
  53. val pageSize: Int
    Definition Classes
    ParquetArgs → ParquetRDDArgs
    Annotations
    @Option()
  54. var pairedFastqFile: String
  55. var partitionByStartPos: Boolean
  56. var partitionedBinSize: Int
  57. var recalibrateBaseQualities: Boolean
  58. var reference: String
  59. var regionPredicate: String
  60. var repartition: Int
  61. var samplingFraction: Double
  62. var samplingSeed: Long
  63. var sortByReadName: Boolean
  64. var sortByReferencePosition: Boolean
  65. var sortByReferencePositionAndIndex: Boolean
  66. var sortFastqOutput: Boolean
    Definition Classes
    TransformAlignmentsArgs → ADAMSaveAnyArgs
  67. var storageLevel: String
  68. var stringency: String
  69. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  70. def toString(): String
    Definition Classes
    AnyRef → Any
  71. var unclipReads: Boolean
  72. var useAlignedReadPredicate: Boolean
  73. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  74. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  75. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Deprecated Value Members

  1. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] ) @Deprecated @deprecated
    Deprecated

    (Since version ) see corresponding Javadoc for more information.

Inherited from CramArgs

Inherited from ParquetArgs

Inherited from ADAMSaveAnyArgs

Inherited from SaveArgs

Inherited from ParquetRDDArgs

Inherited from Args4jBase

Inherited from AnyRef

Inherited from Any

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