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trait NTBitArray extends AnyRef

A bit-packed array of nucleotides, where each letter is represented by two bits.

Linear Supertypes
AnyRef, Any
Known Subclasses
OffsetNTBitArray, ZeroNTBitArray
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Abstract Value Members

  1. abstract def data: Array[Long]

    Array of longs, each storing up to 16 nts, with optional padding at the end.

  2. abstract def offset: Int

    Offset into the array where data starts (in NTs)

  3. abstract def size: Int

    Size of the data represented (in NTs)

Concrete Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  4. def apply(pos: Int): Byte

    Obtain the (twobit) NT at a given position.

    Obtain the (twobit) NT at a given position. Only the lowest two bits of the byte are valid. The others will be zeroed out.

  5. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  6. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  7. def copyPartAsLongArray(writeTo: Array[Long], offset: Int, size: Int): Unit

    Write a subsequence of this sequence to the provided long array.

    Write a subsequence of this sequence to the provided long array.

    writeTo

    destination to write to (at offset zero)

    offset

    offset to read from (0-based)

    size

    amount to write

  8. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  9. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  10. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  11. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  12. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  13. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  14. def kmers(k: Int, onlyForwardOrientation: Boolean = false): Iterator[NTBitArray]

    Obtain all k-mers from this bit array as NTBitArrays.

    Obtain all k-mers from this bit array as NTBitArrays.

    k

    Length of k-mers

    onlyForwardOrientation

    If this flag is true, only k-mers with forward orientation will be returned.

    returns

    All k-mers as an iterator

  15. def kmersAsLongArrays(k: Int, onlyForwardOrientation: Boolean = false): Iterator[Array[Long]]

    Obtain all k-mers from this bit array as long arrays.

    Obtain all k-mers from this bit array as long arrays.

    k

    length of k-mers

    onlyForwardOrientation

    If this flag is true, only k-mers with forward orientation will be returned.

    returns

    All k-mers as an iterator

  16. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  17. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  18. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  19. final def partAsLongArray(offset: Int, size: Int): Array[Long]

    Create a long array representing a subsequence of this sequence.

    Create a long array representing a subsequence of this sequence.

    offset

    0-based offset

    size

    size

  20. def slice(from: Int, length: Int): NTBitArray

    Construct a new NTBitArray from a subsequence of this one, sharing data with this object.

  21. def sliceAsCopy(offset: Int, length: Int): ZeroNTBitArray

    Construct a new NTBitArray from a subsequence of this one, copying data from this object.

  22. def sliceIsForwardOrientation(pos: Int, size: Int): Boolean

    Test the orientation of a slice of this buffer.

    Test the orientation of a slice of this buffer.

    pos

    Start position

    size

    Length of slice (must be an odd number)

    returns

    True iff this slice has forward orientation.

  23. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  24. def toString(): String
    Definition Classes
    NTBitArray → AnyRef → Any
  25. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  26. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  27. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  28. def writeKmersToBuilder(destination: KmerTableBuilder, k: Int, forwardOnly: Boolean, provider: RowTagProvider = EmptyRowTagProvider): Unit

    Write all k-mers from this bit array into a KmerTableBuilder.

    Write all k-mers from this bit array into a KmerTableBuilder.

    destination

    builder to write to

    k

    k

    forwardOnly

    if this flag is true, only k-mers with forward orientation will be written.

    provider

    function to generate extra (tag) data for the k-mer starting at each column (offset). By default no extra data is generated.

Inherited from AnyRef

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