org.bdgenomics.adam.algorithms.consensus

# ConsensusGeneratorFromSmithWaterman

#### class ConsensusGeneratorFromSmithWaterman extends ConsensusGeneratorFromReads

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ConsensusGeneratorFromReads, ConsensusGenerator, Serializable, Serializable, AnyRef, Any
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1. ConsensusGeneratorFromSmithWaterman
2. ConsensusGeneratorFromReads
3. ConsensusGenerator
4. Serializable
5. Serializable
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### Instance Constructors

1. #### new ConsensusGeneratorFromSmithWaterman(wMatch: Double, wMismatch: Double, wInsert: Double, wDelete: Double)

### Value Members

1. #### final def !=(arg0: Any): Boolean

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     AnyRef → Any

2. #### final def ##(): Int

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

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4. #### final def asInstanceOf[T0]: T0

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5. #### def clone(): AnyRef

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6. #### final def eq(arg0: AnyRef): Boolean

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7. #### def equals(arg0: Any): Boolean

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8. #### def finalize(): Unit

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

9. #### def findConsensus(reads: Iterable[RichAlignmentRecord]): Iterable[Consensus]

   Generates concensus sequences from reads with indels.

   Generates concensus sequences from reads with indels.

   reads

     Reads to generate consensus sequences from.

   returns

     Consensus sequences to use for realignment.

   Definition Classes
     ConsensusGeneratorFromReads → ConsensusGenerator

10. #### final def getClass(): Class[_]

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11. #### def hashCode(): Int

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12. #### final def isInstanceOf[T0]: Boolean

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13. #### final def ne(arg0: AnyRef): Boolean

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14. #### final def notify(): Unit

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15. #### final def notifyAll(): Unit

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16. #### def preprocessReadsForRealignment(reads: Iterable[RichAlignmentRecord], reference: String, region: ReferenceRegion): Iterable[RichAlignmentRecord]

    Attempts realignment of all reads using Smith-Waterman.

    Attempts realignment of all reads using Smith-Waterman. Accepts all realignments that have one or fewer indels.

    reads

      Reads to process.

    returns

      Reads with indels normalized if they contain a single indel.

    Definition Classes
      ConsensusGeneratorFromSmithWaterman → ConsensusGeneratorFromReads → ConsensusGenerator

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

    Definition Classes
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18. #### def targetsToAdd(): Option[RDD[IndelRealignmentTarget]]

    No targets to add if generating consensus targets from reads.

    No targets to add if generating consensus targets from reads.

    returns

      Returns a None.

    Definition Classes
      ConsensusGeneratorFromReads → ConsensusGenerator

19. #### def toString(): String

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20. #### final def wait(): Unit

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

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22. #### final def wait(arg0: Long): Unit

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### Inherited from ConsensusGeneratorFromReads

### Inherited from ConsensusGenerator

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

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