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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.  final def asInstanceOf[T0]: T0

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5.  def clone(): AnyRef

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6.  def encode(data: NTSeq): ZeroNTBitArray

   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.

7.  final def eq(arg0: AnyRef): Boolean

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8.  def equals(arg0: Any): Boolean

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9.  def finalize(): Unit

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10.  def fixedSizeDecoder(size: Int): NTBitDecoder

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

11.  final def getClass(): Class[_]

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12.  def hashCode(): Int

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13.  final def isInstanceOf[T0]: Boolean

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14.  def longsToString(buffer: ByteBuffer, builder: StringBuilder, 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. Optimized version for repeated calls (avoids repeatedly allocating new buffers)

    buffer

    buffer to reuse repeatedly

    data

    encoded data

    offset

    offset in the data array to start from

    size

    number of letters to decode

    returns

    decoded string

15.  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

16.  final def ne(arg0: AnyRef): Boolean

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17.  final def notify(): Unit

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18.  final def notifyAll(): Unit

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19.  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

20.  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

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

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22.  def toString(): String

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23.  final def wait(): Unit

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

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25.  final def wait(arg0: Long): Unit

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