org.bdgenomics.avocado.realigner

Aligner

object Aligner

Core code for aliging two sequences (read and ref) against each other.

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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. def align(ref: String, alt: String, kmerLength: Int): Seq[ObservationOperator]

    Aligns two sequences against each other.

    Aligns two sequences against each other.

    Performs trimming and partitioning before aligning the two sequences.

    ref

    Reference sequence to align against.

    alt

    Alternate sequence to align against ref.

    kmerLength

    Length k to use for cutting up k-mers.

    returns

    Returns a sequence of alignment operators describing the pairwise alignment of the two sequences.

  5. final def asInstanceOf[T0]: T0

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  6. def clone(): AnyRef

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

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

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  18. final def wait(): Unit

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

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