Packages

final case class ReducibleBucket(id: BucketId, supermers: Array[NTBitArray], tags: Array[Array[Int]]) extends KmerBucket with Product with Serializable

A k-mer bucket that reduces (combines) identical k-mers using a supplied method, removing redundant super-mers in the process to keep the bucket compact.

id

The minimizer/ID of this bucket

supermers

Super-mers containing the k-mers of this bucket. Some might not actually be present in the bucket (the super-mers may have gaps) and the tags define which are present. This arranges the k-mers in a 2D grid where rows identify the super-mer and columns identify the offset in the super-mer. (Super-mers may however have different lengths)

tags

Tags for each k-mer, for example k-mer counts in the case of k-mer counting. These follow the 2D coordinate scheme described above.

Linear Supertypes
Serializable, Serializable, Product, Equals, KmerBucket, AnyRef, Any
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. ReducibleBucket
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. KmerBucket
  7. AnyRef
  8. Any
  1. Hide All
  2. Show All
Visibility
  1. Public
  2. All

Instance Constructors

  1. new ReducibleBucket(id: BucketId, supermers: Array[NTBitArray], tags: Array[Array[Int]])

    id

    The minimizer/ID of this bucket

    supermers

    Super-mers containing the k-mers of this bucket. Some might not actually be present in the bucket (the super-mers may have gaps) and the tags define which are present. This arranges the k-mers in a 2D grid where rows identify the super-mer and columns identify the offset in the super-mer. (Super-mers may however have different lengths)

    tags

    Tags for each k-mer, for example k-mer counts in the case of k-mer counting. These follow the 2D coordinate scheme described above.

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 appendAndCompact(other: ReducibleBucket, reducer: Reducer): ReducibleBucket
  5. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  6. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native() @IntrinsicCandidate()
  7. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  8. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @IntrinsicCandidate()
  9. val id: BucketId
  10. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  11. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  12. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @IntrinsicCandidate()
  13. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @IntrinsicCandidate()
  14. def reduceCompact(reducer: Reducer): ReducibleBucket

    Reduce the bucket (combine tags of equal k-mers) and compact it (remove redundant super-mers)

    Reduce the bucket (combine tags of equal k-mers) and compact it (remove redundant super-mers)

    reducer

    the k-mer reducer

  15. def reduceKmers(reducer: Reducer): KmerTable

    Reduce tags of equal k-mers in this bucket (combining them), so that each k-mer appears only once in the result.

    Reduce tags of equal k-mers in this bucket (combining them), so that each k-mer appears only once in the result.

    reducer

    the k-mer reducer

  16. val supermers: Array[NTBitArray]
  17. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  18. val tags: Array[Array[Int]]
  19. def toString(): String
    Definition Classes
    ReducibleBucket → AnyRef → Any
  20. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  21. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  22. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  23. def writeToSortedTable(k: Int, orientation: Orientation): KmerTable
    Definition Classes
    KmerBucket
  24. def writeToSortedTableNoRowCol(k: Int, orientation: Orientation): KmerTable
    Definition Classes
    KmerBucket
  25. def writeToTable(k: Int, orientation: Orientation, sort: Boolean): KmerTable
    Definition Classes
    KmerBucket

Deprecated Value Members

  1. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] ) @Deprecated
    Deprecated

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from KmerBucket

Inherited from AnyRef

Inherited from Any

Ungrouped