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object NTBitArray extends Serializable

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  1. NTBitArray
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  1. final def !=(arg0: Any): Boolean
    Definition Classes
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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
    Definition Classes
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  5. def blank(size: Int): NTBitArray

    Fill an NTBitArray with all zeroes (the nucleotide A)

  6. def builder(capacity: Int): NTBitArrayBuilder

    Create a new builder with the given capacity.

  7. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
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    @throws( ... ) @native() @IntrinsicCandidate()
  8. def decoder: NTBitDecoder

    A decoder that can decode NT sequences of a fixed max length.

  9. val empty: NTBitArray
  10. def encode(data: NTSeq): NTBitArray

    Reversibly encode a nucleotide sequence as an array of 64-bit longs.

    Reversibly encode a nucleotide sequence as an array of 64-bit longs. The 2*length leftmost bits in the array will be populated.

  11. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  12. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  13. def fill(data: Long, size: Int): NTBitArray

    Populate an NTBitArray with a fixed pattern repeatedly to reach a given size.

    Populate an NTBitArray with a fixed pattern repeatedly to reach a given size. No shifting will be performed.

  14. def fromLong(data: Long, size: Int): NTBitArray

    Populate a new NTBitArray with a single right-aligned long, shifting it to be left-aligned.

    Populate a new NTBitArray with a single right-aligned long, shifting it to be left-aligned. Only well-defined when the data fits inside a positive long, i.e. size <= 31. The inverse mapping is NTBitArray.toLong.

  15. final def getClass(): Class[_]
    Definition Classes
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    @native() @IntrinsicCandidate()
  16. def hashCode(): Int
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    @native() @IntrinsicCandidate()
  17. final def isInstanceOf[T0]: Boolean
    Definition Classes
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  18. def longBuffer(size: Int, fill: Long): Array[Long]
  19. def longBuffer(size: Int): Array[Long]
  20. def longsForSize(size: Int): Int
  21. def longsToString(data: Array[Long], offset: Int, size: Int): NTSeq

    Decode a previously encoded NT sequence to human-readable string form.

    Decode a previously encoded NT sequence to human-readable string form.

    data

    encoded data

    offset

    0-based offset in the data array to start from

    size

    number of letters to decode

    returns

    decoded string

  22. final def ne(arg0: AnyRef): Boolean
    Definition Classes
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  23. final def notify(): Unit
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    @native() @IntrinsicCandidate()
  24. final def notifyAll(): Unit
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    @native() @IntrinsicCandidate()
  25. def shiftLongArrayKmerLeft(data: Array[Long], addRight: Byte, k: Int): Unit

    Shift an array of two-bits one step to the left, dropping one bp, and inserting another on the right.

    Shift an array of two-bits one step to the left, dropping one bp, and inserting another on the right.

    data

    The sequence to shift

    addRight

    New two-bit nucleotide to insert on the right

    k

    k

  26. def shiftLongKmerAndWrite(data: Array[Long], addRight: Byte, k: Int, destination: KmerTableBuilder): Unit

    Shift an array of two-bits one step to the left, dropping one bp, and inserting another on the right.

    Shift an array of two-bits one step to the left, dropping one bp, and inserting another on the right. Write the result to a KmerTableBuilder.

    data

    The sequence to shift

    addRight

    New two-bit nucleotide to insert on the right

    k

    k

    destination

    KmerTableBuilder where the result should be inserted

  27. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
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  28. def toString(): String
    Definition Classes
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  29. final def wait(arg0: Long, arg1: Int): Unit
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    @throws( ... )
  30. final def wait(arg0: Long): Unit
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    @throws( ... ) @native()
  31. final def wait(): Unit
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    @throws( ... )

Deprecated Value Members

  1. def finalize(): Unit
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    @throws( classOf[java.lang.Throwable] ) @Deprecated
    Deprecated

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