ADAM_2.12: Core 0.30.0 API < Back
 

# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package adam
  Definition Classes
    bdgenomics
-  package instrumentation
  Definition Classes
    adam
- Timers

o

org.bdgenomics.adam.instrumentation

# Timers 

###

#### object Timers extends Metrics

Contains Timers that are used to instrument ADAM.

Linear Supertypes
Metrics, Serializable, Serializable, AnyRef, Any
 
Ordering

1. Alphabetic
2. By Inheritance

Inherited

1. Timers
2. Metrics
3. Serializable
4. Serializable
5. AnyRef
6. Any

1. Hide All
2. Show All

Visibility

1. Public
2. All

### 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 AnyRef

### Inherited from Any

### Ungrouped