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 CreateSequenceDictionary: Timer

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  20. val CreatingKnownSnpsTable: Timer

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  21. val CreatingRecalibrationTable: Timer

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  22. val FinalizingRealignments: Timer

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  23. val FindTargets: Timer

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  24. val FullOuterShuffleJoin: Timer

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  25. val GetExtraValues: Timer

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  26. val GetReferenceFromFile: Timer

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  27. val GetReferenceFromReads: Timer

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  28. val GrowingTrees: Timer

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  29. val InnerBroadcastJoin: Timer

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  30. val InnerShuffleJoin: Timer

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  31. val InvertingRecalibrationTable: Timer

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  32. val JoinTargets: Timer

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  33. val LeftOuterShuffleJoin: Timer

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  34. val LoadAlignments: Timer

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  35. val LoadBam: Timer

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  36. val LoadBed: Timer

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  37. val LoadCoverage: Timer

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  38. val LoadFasta: Timer

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  39. val LoadFastaSequences: Timer

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  40. val LoadFastaSlices: Timer

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  41. val LoadFastq: Timer

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  42. val LoadFeatures: Timer

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  43. val LoadFragments: Timer

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  44. val LoadGenotypes: Timer

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  45. val LoadGff3: Timer

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  46. val LoadGtf: Timer

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  47. val LoadIndexedBam: Timer

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  48. val LoadIndexedVcf: Timer

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  49. val LoadInterleavedFastq: Timer

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  50. val LoadInterleavedFastqFragments: Timer

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  51. val LoadIntervalList: Timer

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  52. val LoadNarrowPeak: Timer

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  53. val LoadPairedFastq: Timer

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  54. val LoadPairedFastqFragments: Timer

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  55. val LoadParquet: Timer

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  56. val LoadReferenceFile: Timer

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  57. val LoadSequenceDictionary: Timer

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  58. val LoadSequences: Timer

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  59. val LoadSlices: Timer

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  60. val LoadUnpairedFastq: Timer

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  61. val LoadVariants: Timer

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  62. val LoadVcf: Timer

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  63. val MapTargets: Timer

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  64. val MarkDuplicatesInDriver: Timer

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  65. val MarkReads: Timer

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  66. val ObservationAccumulatorComb: Timer

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  67. val ObservationAccumulatorSeq: Timer

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  68. val ObservingRead: Timer

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  69. val PerformDuplicateMarking: Timer

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  70. val QueryingRecalibrationTable: Timer

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  71. val ReadCovariates: Timer

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  72. val ReadResidues: Timer

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  73. val RealignIndelsInDriver: Timer

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  74. val RealignTargetGroup: Timer

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  75. val RecalibrateRead: Timer

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  76. val RightOuterBroadcastJoin: Timer

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  77. val RightOuterBroadcastJoinAndGroupByRight: Timer

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  78. val RightOuterShuffleJoin: Timer

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  79. val RightOuterShuffleJoinAndGroupByLeft: Timer

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  80. val RunningMapSideJoin: Timer

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  81. val SAMSave: Timer

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  82. val SaveAsADAM: Timer

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  83. val SaveAsVcf: Timer

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  84. val ScoreAndMarkReads: Timer

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  85. val ShuffleJoinAndGroupByLeft: Timer

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  86. val SortAlignments: Timer

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  87. val SortAlignmentsByIndex: Timer

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  88. val SortTargets: Timer

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  89. val SortingRightSide: Timer

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  90. val SweepReadOverReferenceForQuality: Timer

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  91. val SweepReadsOverConsensus: Timer

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  92. val TreeJoin: Timer

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  93. val TrimCigar: Timer

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  94. val TrimLowQualityInDriver: Timer

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  95. val TrimMDTag: Timer

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  96. val TrimRead: Timer

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  97. val TrimReadsInDriver: Timer

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  98. val WriteADAMRecord: Timer

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  99. val WriteBAMRecord: Timer

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  100. val WriteCRAMRecord: Timer

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  101. val WriteSAMRecord: Timer

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  102. final def asInstanceOf[T0]: T0

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  103. val clock: Clock

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  104. def clone(): AnyRef

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

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  106. def equals(arg0: Any): Boolean

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  107. def finalize(): Unit

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

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  109. def hashCode(): Int

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  110. final def isInstanceOf[T0]: Boolean

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

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  112. final def notify(): Unit

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  113. final def notifyAll(): Unit

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

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  115. def timer(name: String): Timer

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    Metrics

  116. def toString(): String

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  117. final def wait(): Unit

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

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

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Inherited from Metrics

Inherited from Serializable

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