Packages

object Timers extends Metrics

Contains Timers that are used to instrument ADAM.

Linear Supertypes
Metrics, Serializable, Serializable, AnyRef, Any
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  1. Timers
  2. Metrics
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  4. Serializable
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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. val BQSRInDriver: Timer
  5. val BroadcastJoinAndGroupByRight: Timer
  6. val BroadcastingKnownSnps: Timer
  7. val BuildingTrees: Timer
  8. val CheckingForMask: Timer
  9. val CollectingSnps: Timer
  10. val ComputeCovariates: Timer
  11. val ComputeQualityScore: Timer
  12. val ComputingCycleCovariate: Timer
  13. val ComputingDinucCovariate: Timer
  14. val ComputingOriginalScores: Timer
  15. val ConvertToSAM: Timer
  16. val ConvertToSAMRecord: Timer
  17. val ConvertToVcf: Timer
  18. val CreateIndelRealignmentTargets: Timer
  19. val CreateReferencePositionPair: Timer
  20. val CreateSequenceDictionary: 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 LoadCoverage: Timer
  39. val LoadFasta: Timer
  40. val LoadFastaSequences: Timer
  41. val LoadFastaSlices: Timer
  42. val LoadFastq: Timer
  43. val LoadFeatures: Timer
  44. val LoadFragments: Timer
  45. val LoadGenotypes: Timer
  46. val LoadGff3: Timer
  47. val LoadGtf: Timer
  48. val LoadIndexedBam: Timer
  49. val LoadIndexedVcf: Timer
  50. val LoadInterleavedFastq: Timer
  51. val LoadInterleavedFastqFragments: Timer
  52. val LoadIntervalList: Timer
  53. val LoadNarrowPeak: Timer
  54. val LoadPairedFastq: Timer
  55. val LoadPairedFastqFragments: Timer
  56. val LoadParquet: Timer
  57. val LoadReferenceFile: Timer
  58. val LoadSequenceDictionary: Timer
  59. val LoadSequences: Timer
  60. val LoadSlices: Timer
  61. val LoadUnpairedFastq: Timer
  62. val LoadVariants: Timer
  63. val LoadVcf: Timer
  64. val MapTargets: Timer
  65. val MarkDuplicatesInDriver: Timer
  66. val MarkReads: Timer
  67. val ObservationAccumulatorComb: Timer
  68. val ObservationAccumulatorSeq: Timer
  69. val ObservingRead: Timer
  70. val PerformDuplicateMarking: Timer
  71. val QueryingRecalibrationTable: Timer
  72. val ReadCovariates: Timer
  73. val ReadResidues: Timer
  74. val RealignIndelsInDriver: Timer
  75. val RealignTargetGroup: Timer
  76. val RecalibrateRead: Timer
  77. val RightOuterBroadcastJoin: Timer
  78. val RightOuterBroadcastJoinAndGroupByRight: Timer
  79. val RightOuterShuffleJoin: Timer
  80. val RightOuterShuffleJoinAndGroupByLeft: Timer
  81. val RunningMapSideJoin: Timer
  82. val SAMSave: Timer
  83. val SaveAsADAM: Timer
  84. val SaveAsVcf: Timer
  85. val ScoreAndMarkReads: Timer
  86. val ShuffleJoinAndGroupByLeft: Timer
  87. val SortAlignments: Timer
  88. val SortAlignmentsByIndex: Timer
  89. val SortTargets: Timer
  90. val SortingRightSide: Timer
  91. val SweepReadOverReferenceForQuality: Timer
  92. val SweepReadsOverConsensus: Timer
  93. val TreeJoin: Timer
  94. val TrimCigar: Timer
  95. val TrimLowQualityInDriver: Timer
  96. val TrimMDTag: Timer
  97. val TrimRead: Timer
  98. val TrimReadsInDriver: Timer
  99. val WriteADAMRecord: Timer
  100. val WriteBAMRecord: Timer
  101. val WriteCRAMRecord: Timer
  102. val WriteSAMRecord: Timer
  103. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  104. val clock: Clock
    Definition Classes
    Metrics
  105. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  106. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  107. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  108. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  109. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  110. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  111. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  112. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  113. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  114. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  115. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  116. def timer(name: String): Timer
    Definition Classes
    Metrics
  117. def toString(): String
    Definition Classes
    AnyRef → Any
  118. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  119. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  120. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )

Inherited from Metrics

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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