ConsensusGeneratorFromSmithWaterman

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1. final def !=(arg0: AnyRef): Boolean

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2. final def !=(arg0: Any): Boolean

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3. final def ##(): Int

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4. final def ==(arg0: AnyRef): Boolean

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

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6. final def asInstanceOf[T0]: T0

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7. def clone(): AnyRef

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

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9. def equals(arg0: Any): Boolean

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10. def finalize(): Unit

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11. 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

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

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13. def hashCode(): Int

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14. final def isInstanceOf[T0]: Boolean

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

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16. final def notify(): Unit

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17. final def notifyAll(): Unit

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18. 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

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

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20. 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

21. def toString(): String

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22. final def wait(): Unit

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

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

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