org.bdgenomics.adam.instrumentation

Timers

object Timers extends Metrics

Contains Timers that are used to instrument ADAM.

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Metrics, Serializable, Serializable, AnyRef, Any
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  1. final def !=(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  2. final def !=(arg0: Any): Boolean

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

  4. final def ==(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  5. final def ==(arg0: Any): Boolean

    Definition Classes
    Any

  6. val BQSRInDriver: Timer

  7. val BroadcastJoinAndGroupByRight: Timer

  8. val BroadcastingKnownSnps: Timer

  9. val BuildingTrees: Timer

  10. val CheckingForMask: Timer

  11. val CollectingSnps: Timer

  12. val ComputeCovariates: Timer

  13. val ComputeQualityScore: Timer

  14. val ComputingCycleCovariate: Timer

  15. val ComputingDinucCovariate: Timer

  16. val ComputingOriginalScores: Timer

  17. val ConvertToSAM: Timer

  18. val ConvertToSAMRecord: Timer

  19. val CreateIndelRealignmentTargets: Timer

  20. val CreateReferencePositionPair: Timer

  21. val CreatingKnownSnpsTable: Timer

  22. val CreatingRecalibrationTable: Timer

  23. val FinalizingRealignments: Timer

  24. val FindTargets: Timer

  25. val FullOuterShuffleJoin: Timer

  26. val GetExtraValues: Timer

  27. val GetReferenceFromFile: Timer

  28. val GetReferenceFromReads: Timer

  29. val GrowingTrees: Timer

  30. val InnerBroadcastJoin: Timer

  31. val InnerShuffleJoin: Timer

  32. val InvertingRecalibrationTable: Timer

  33. val JoinTargets: Timer

  34. val LeftOuterShuffleJoin: Timer

  35. val LoadAlignments: Timer

  36. val LoadBam: Timer

  37. val LoadBed: Timer

  38. val LoadContigFragments: Timer

  39. val LoadCoverage: Timer

  40. val LoadFasta: Timer

  41. val LoadFastq: Timer

  42. val LoadFeatures: Timer

  43. val LoadFragments: Timer

  44. val LoadGenotypes: Timer

  45. val LoadGff3: Timer

  46. val LoadGtf: Timer

  47. val LoadIndexedBam: Timer

  48. val LoadIndexedVcf: Timer

  49. val LoadInterleavedFastq: Timer

  50. val LoadInterleavedFastqFragments: Timer

  51. val LoadIntervalList: Timer

  52. val LoadNarrowPeak: Timer

  53. val LoadPairedFastq: Timer

  54. val LoadParquet: Timer

  55. val LoadReferenceFile: Timer

  56. val LoadSequenceDictionary: Timer

  57. val LoadUnpairedFastq: Timer

  58. val LoadVariants: Timer

  59. val LoadVcf: Timer

  60. val MapTargets: Timer

  61. val MarkDuplicatesInDriver: Timer

  62. val MarkReads: Timer

  63. val ObservationAccumulatorComb: Timer

  64. val ObservationAccumulatorSeq: Timer

  65. val ObservingRead: Timer

  66. val PerformDuplicateMarking: Timer

  67. val QueryingRecalibrationTable: Timer

  68. val ReadCovariates: Timer

  69. val ReadResidues: Timer

  70. val RealignIndelsInDriver: Timer

  71. val RealignTargetGroup: Timer

  72. val RecalibrateRead: Timer

  73. val RightOuterBroadcastJoin: Timer

  74. val RightOuterBroadcastJoinAndGroupByRight: Timer

  75. val RightOuterShuffleJoin: Timer

  76. val RightOuterShuffleJoinAndGroupByLeft: Timer

  77. val RunningMapSideJoin: Timer

  78. val SAMSave: Timer

  79. val SaveAsADAM: Timer

  80. val SaveAsVcf: Timer

  81. val ScoreAndMarkReads: Timer

  82. val ShuffleJoinAndGroupByLeft: Timer

  83. val SortByIndex: Timer

  84. val SortReads: Timer

  85. val SortTargets: Timer

  86. val SortingRightSide: Timer

  87. val SweepReadOverReferenceForQuality: Timer

  88. val SweepReadsOverConsensus: Timer

  89. val TreeJoin: Timer

  90. val TrimCigar: Timer

  91. val TrimLowQualityInDriver: Timer

  92. val TrimMDTag: Timer

  93. val TrimRead: Timer

  94. val TrimReadsInDriver: Timer

  95. val WriteADAMRecord: Timer

  96. val WriteBAMRecord: Timer

  97. val WriteCRAMRecord: Timer

  98. val WriteSAMRecord: Timer

  99. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  100. val clock: Clock

    Definition Classes
    Metrics

  101. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  102. final def eq(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  103. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  104. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
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    Annotations
    @throws( classOf[java.lang.Throwable] )

  105. final def getClass(): Class[_]

    Definition Classes
    AnyRef → Any

  106. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  107. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  108. final def ne(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  109. final def notify(): Unit

    Definition Classes
    AnyRef

  110. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  111. final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
    AnyRef

  112. def timer(name: String): Timer

    Definition Classes
    Metrics

  113. def toString(): String

    Definition Classes
    AnyRef → Any

  114. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  115. final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  116. final def wait(arg0: Long): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Metrics

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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