Object

org.bdgenomics.adam.instrumentation

Timers

Related Doc: package instrumentation

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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: Any): Boolean

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  2. final def ##(): Int

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

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  4. val BQSRInDriver: Timer

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  5. val BroadcastJoinAndGroupByRight: Timer

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  6. val BroadcastingKnownSnps: Timer

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  7. val BuildingTrees: Timer

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  8. val CheckingForMask: Timer

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  9. val CollectingSnps: Timer

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  10. val ComputeCovariates: Timer

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  11. val ComputeQualityScore: Timer

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  12. val ComputingCycleCovariate: Timer

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  13. val ComputingDinucCovariate: Timer

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  14. val ComputingOriginalScores: Timer

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  15. val ConvertToSAM: Timer

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  16. val ConvertToSAMRecord: Timer

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  17. val CreateIndelRealignmentTargets: Timer

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  18. val CreateReferencePositionPair: Timer

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  19. val CreatingKnownSnpsTable: Timer

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  20. val CreatingRecalibrationTable: Timer

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  21. val FinalizingRealignments: Timer

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  22. val FindTargets: Timer

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  23. val FullOuterShuffleJoin: Timer

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  24. val GetExtraValues: Timer

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  25. val GetReferenceFromFile: Timer

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  26. val GetReferenceFromReads: Timer

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  27. val GrowingTrees: Timer

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  28. val InnerBroadcastJoin: Timer

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  29. val InnerShuffleJoin: Timer

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  30. val InvertingRecalibrationTable: Timer

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  31. val JoinTargets: Timer

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  32. val LeftOuterShuffleJoin: Timer

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  33. val LoadAlignments: Timer

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  34. val LoadBam: Timer

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  35. val LoadBed: Timer

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  36. val LoadContigFragments: Timer

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  37. val LoadCoverage: Timer

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  38. val LoadFasta: Timer

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  39. val LoadFastq: Timer

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  40. val LoadFeatures: Timer

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  41. val LoadFragments: Timer

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  42. val LoadGenotypes: Timer

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  43. val LoadGff3: Timer

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  44. val LoadGtf: Timer

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  45. val LoadIndexedBam: Timer

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  46. val LoadIndexedVcf: Timer

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  47. val LoadInterleavedFastq: Timer

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  48. val LoadInterleavedFastqFragments: Timer

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  49. val LoadIntervalList: Timer

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  50. val LoadNarrowPeak: Timer

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  51. val LoadPairedFastq: Timer

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  52. val LoadParquet: Timer

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  53. val LoadReferenceFile: Timer

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  54. val LoadSequenceDictionary: Timer

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  55. val LoadUnpairedFastq: Timer

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  56. val LoadVariants: Timer

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  57. val LoadVcf: Timer

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  58. val MapTargets: Timer

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  59. val MarkDuplicatesInDriver: Timer

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  60. val MarkReads: Timer

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  61. val ObservationAccumulatorComb: Timer

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  62. val ObservationAccumulatorSeq: Timer

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  63. val ObservingRead: Timer

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  64. val PerformDuplicateMarking: Timer

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  65. val QueryingRecalibrationTable: Timer

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  66. val ReadCovariates: Timer

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  67. val ReadResidues: Timer

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  68. val RealignIndelsInDriver: Timer

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  69. val RealignTargetGroup: Timer

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  70. val RecalibrateRead: Timer

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  71. val RightOuterBroadcastJoin: Timer

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  72. val RightOuterBroadcastJoinAndGroupByRight: Timer

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  73. val RightOuterShuffleJoin: Timer

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  74. val RightOuterShuffleJoinAndGroupByLeft: Timer

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  75. val RunningMapSideJoin: Timer

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  76. val SAMSave: Timer

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  77. val SaveAsADAM: Timer

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  78. val SaveAsVcf: Timer

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  79. val ScoreAndMarkReads: Timer

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  80. val ShuffleJoinAndGroupByLeft: Timer

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  81. val SortByIndex: Timer

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  82. val SortReads: Timer

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  83. val SortTargets: Timer

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  84. val SortingRightSide: Timer

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  85. val SweepReadOverReferenceForQuality: Timer

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  86. val SweepReadsOverConsensus: Timer

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  87. val TreeJoin: Timer

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  88. val TrimCigar: Timer

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  89. val TrimLowQualityInDriver: Timer

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  90. val TrimMDTag: Timer

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  91. val TrimRead: Timer

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  92. val TrimReadsInDriver: Timer

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  93. val WriteADAMRecord: Timer

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  94. val WriteBAMRecord: Timer

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  95. val WriteCRAMRecord: Timer

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  96. val WriteSAMRecord: Timer

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  97. final def asInstanceOf[T0]: T0

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  98. val clock: Clock

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    Metrics
  99. def clone(): AnyRef

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

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  101. def equals(arg0: Any): Boolean

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  102. def finalize(): Unit

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

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  104. def hashCode(): Int

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  105. final def isInstanceOf[T0]: Boolean

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

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  107. final def notify(): Unit

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  108. final def notifyAll(): Unit

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

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  110. def timer(name: String): Timer

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  111. def toString(): String

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  112. final def wait(): Unit

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

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

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Inherited from Metrics

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