Value Members

1.  final def !=(arg0: Any): Boolean

   Definition Classes

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2.  final def ##(): Int

   Definition Classes

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3.  final def ==(arg0: Any): Boolean

   Definition Classes

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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 CreateIndelRealignmentTargets: Timer
18.  val CreateReferencePositionPair: Timer
19.  val CreateSequenceDictionary: Timer
20.  val CreatingKnownSnpsTable: Timer
21.  val CreatingRecalibrationTable: Timer
22.  val FinalizingRealignments: Timer
23.  val FindTargets: Timer
24.  val FullOuterShuffleJoin: Timer
25.  val GetExtraValues: Timer
26.  val GetReferenceFromFile: Timer
27.  val GetReferenceFromReads: Timer
28.  val GrowingTrees: Timer
29.  val InnerBroadcastJoin: Timer
30.  val InnerShuffleJoin: Timer
31.  val InvertingRecalibrationTable: Timer
32.  val JoinTargets: Timer
33.  val LeftOuterShuffleJoin: Timer
34.  val LoadAlignments: Timer
35.  val LoadBam: Timer
36.  val LoadBed: Timer
37.  val LoadCoverage: Timer
38.  val LoadFasta: Timer
39.  val LoadFastaSequences: Timer
40.  val LoadFastaSlices: 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 LoadPairedFastqFragments: Timer
55.  val LoadParquet: Timer
56.  val LoadReferenceFile: Timer
57.  val LoadSequenceDictionary: Timer
58.  val LoadSequences: Timer
59.  val LoadSlices: Timer
60.  val LoadUnpairedFastq: Timer
61.  val LoadVariants: Timer
62.  val LoadVcf: Timer
63.  val MapTargets: Timer
64.  val MarkDuplicatesInDriver: Timer
65.  val MarkReads: Timer
66.  val ObservationAccumulatorComb: Timer
67.  val ObservationAccumulatorSeq: Timer
68.  val ObservingRead: Timer
69.  val PerformDuplicateMarking: Timer
70.  val QueryingRecalibrationTable: Timer
71.  val ReadCovariates: Timer
72.  val ReadResidues: Timer
73.  val RealignIndelsInDriver: Timer
74.  val RealignTargetGroup: Timer
75.  val RecalibrateRead: Timer
76.  val RightOuterBroadcastJoin: Timer
77.  val RightOuterBroadcastJoinAndGroupByRight: Timer
78.  val RightOuterShuffleJoin: Timer
79.  val RightOuterShuffleJoinAndGroupByLeft: Timer
80.  val RunningMapSideJoin: Timer
81.  val SAMSave: Timer
82.  val SaveAsADAM: Timer
83.  val SaveAsVcf: Timer
84.  val ScoreAndMarkReads: Timer
85.  val ShuffleJoinAndGroupByLeft: Timer
86.  val SortAlignments: Timer
87.  val SortAlignmentsByIndex: Timer
88.  val SortTargets: Timer
89.  val SortingRightSide: Timer
90.  val SweepReadOverReferenceForQuality: Timer
91.  val SweepReadsOverConsensus: Timer
92.  val TreeJoin: Timer
93.  val TrimCigar: Timer
94.  val TrimLowQualityInDriver: Timer
95.  val TrimMDTag: Timer
96.  val TrimRead: Timer
97.  val TrimReadsInDriver: Timer
98.  val WriteADAMRecord: Timer
99.  val WriteBAMRecord: Timer
100.  val WriteCRAMRecord: Timer
101.  val WriteSAMRecord: Timer
102.  final def asInstanceOf[T0]: T0

     Definition Classes

     Any

103.  val clock: Clock

     Definition Classes

     Metrics

104.  def clone(): AnyRef

     Attributes

     protected[java.lang]

     Definition Classes

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     Annotations

     @native() @throws( ... )

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

     Definition Classes

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106.  def equals(arg0: Any): Boolean

     Definition Classes

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107.  def finalize(): Unit

     Attributes

     protected[java.lang]

     Definition Classes

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     Annotations

     @throws( classOf[java.lang.Throwable] )

108.  final def getClass(): Class[_]

     Definition Classes

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     Annotations

     @native()

109.  def hashCode(): Int

     Definition Classes

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     Annotations

     @native()

110.  final def isInstanceOf[T0]: Boolean

     Definition Classes

     Any

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

     Definition Classes

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112.  final def notify(): Unit

     Definition Classes

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     @native()

113.  final def notifyAll(): Unit

     Definition Classes

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     @native()

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

     Definition Classes

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115.  def timer(name: String): Timer

     Definition Classes

     Metrics

116.  def toString(): String

     Definition Classes

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117.  final def wait(): Unit

     Definition Classes

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     Annotations

     @throws( ... )

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

     Definition Classes

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     Annotations

     @throws( ... )

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

     Definition Classes

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     Annotations

     @native() @throws( ... )