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.

   Definition Classes

   NTBitArray

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

   Definition Classes

   NTBitArray

8.  val data: Array[Long]

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

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

   Definition Classes

   ZeroNTBitArray → NTBitArray

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

   Definition Classes

   AnyRef

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.  final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

13.  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

    Definition Classes

    NTBitArray

14.  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

    Definition Classes

    NTBitArray

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

    Definition Classes

    AnyRef

16.  final def notify(): Unit

    Definition Classes

    AnyRef

    Annotations

    @native()

17.  final def notifyAll(): Unit

    Definition Classes

    AnyRef

    Annotations

    @native()

18.  def offset: Int

    Offset into the array where data starts (in NTs)

    Offset into the array where data starts (in NTs)

    Definition Classes

    ZeroNTBitArray → NTBitArray

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

    Definition Classes

    NTBitArray

20.  val size: Int

    Size of the data represented (in NTs)

    Size of the data represented (in NTs)

    Definition Classes

    ZeroNTBitArray → NTBitArray

21.  def slice(from: Int, length: Int): NTBitArray

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

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

    Definition Classes

    NTBitArray

22.  def sliceAsCopy(offset: Int, length: Int): ZeroNTBitArray

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

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

    Definition Classes

    NTBitArray

23.  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.

    Definition Classes

    NTBitArray

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

    Definition Classes

    AnyRef

25.  def toString(): String

    Definition Classes

    NTBitArray → AnyRef → Any

26.  final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... ) @native()

29.  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.

    Definition Classes

    NTBitArray