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object KmerTable

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  1. final case class BuildParams(k: Int, orientation: Orientation = Unchanged, sort: Boolean = true) extends Product with Serializable

    Parameters for KmerTable construction

    Parameters for KmerTable construction

    k

    k

    orientation

    Orientation filter for k-mers

    sort

    Whether to sort the k-mers

Value Members

  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. final def asInstanceOf[T0]: T0
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  5. def builder(k: Int, sizeEstimate: Int = 100, tagWidth: Int = 0): KmerTableBuilder

    Obtain a new KmerTableBuilder

  6. def clone(): AnyRef
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    @throws( ... ) @native() @IntrinsicCandidate()
  7. final def eq(arg0: AnyRef): Boolean
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  8. def equals(arg0: Any): Boolean
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  9. def fromSegment(segment: NTBitArray, bpar: BuildParams): KmerTable

    Obtain a KmerTable from a single segment/superkmer

  10. def fromSegments(segments: Iterable[NTBitArray], abundances: Array[Int], bpar: BuildParams): KmerTable

    Construct a KmerTable from super k-mers.

    Construct a KmerTable from super k-mers.

    segments

    Super-mers

    abundances

    Abundances for each super-mer

    bpar

    Build parameters

  11. def fromSupermers(supermers: Iterator[NTBitArray], bpar: BuildParams, tagData: TagProvider, sizeEstimate: Int): KmerTable
  12. def fromSupermers(supermers: Iterable[NTBitArray], bpar: BuildParams, tagData: TagProvider): KmerTable

    Write super-mers as k-mers, along with tag data, to a new KmerTable.

    Write super-mers as k-mers, along with tag data, to a new KmerTable.

    supermers

    Super k-mers

    bpar

    Build parameters

    tagData

    Extra (tag) data for the given row and column, to be appended after the k-mer data

    returns

    The resulting KmerTable

  13. final def getClass(): Class[_]
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  14. def hashCode(): Int
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  15. final def isInstanceOf[T0]: Boolean
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  16. def longsForK(k: Int): Int

    Number of longs required to represent a k-mer of length k

  17. final def ne(arg0: AnyRef): Boolean
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  18. final def notify(): Unit
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  19. final def notifyAll(): Unit
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  20. final def synchronized[T0](arg0: ⇒ T0): T0
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  22. final def wait(arg0: Long, arg1: Int): Unit
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  23. final def wait(arg0: Long): Unit
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  24. final def wait(): Unit
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  1. def finalize(): Unit
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    Deprecated

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