Packages

trait CountReducer extends Reducer

A reducer that handles k-mer count values stored in the longsForK(k) + 1 tag position.

Linear Supertypes
Reducer, AnyRef, Any
Known Subclasses
CountersSubtractReducer, KmerSubtractReducer, LeftReducer, MaxReducer, MinReducer, RightReducer, SumReducer
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Inherited
  1. CountReducer
  2. Reducer
  3. AnyRef
  4. Any
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Visibility
  1. Public
  2. All

Abstract Value Members

  1. abstract def params: ReduceParams
    Definition Classes
    Reducer
  2. abstract def reduceCounts(count1: Tag, count2: Tag): Tag

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. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  5. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native() @IntrinsicCandidate()
  6. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  7. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  8. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @IntrinsicCandidate()
  9. def hasNonZeroTag(tags: Array[Tag]): Boolean
    Definition Classes
    Reducer
  10. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @IntrinsicCandidate()
  11. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  12. def k: Int
    Definition Classes
    Reducer
  13. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  14. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @IntrinsicCandidate()
  15. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @IntrinsicCandidate()
  16. def orientation: Orientation

    Orientation filter for k-mers

    Orientation filter for k-mers

    Definition Classes
    Reducer
  17. def preprocessFirst(bucket: ReducibleBucket): ReducibleBucket

    Preprocess bucket A prior to op(A,B)

    Preprocess bucket A prior to op(A,B)

    Definition Classes
    Reducer
  18. def preprocessSecond(bucket: ReducibleBucket): ReducibleBucket

    Preprocess bucket B prior to op(A,B)

    Preprocess bucket B prior to op(A,B)

    Definition Classes
    Reducer
  19. def reduceEqualKmers(table: KmerTable, into: Int, from: Int): Unit

    Apply a binary operation op(into, from) on the tags of the k-mers at these positions, writing the result in the tags of "into", writing the zero value into the tags of "from".

    Apply a binary operation op(into, from) on the tags of the k-mers at these positions, writing the result in the tags of "into", writing the zero value into the tags of "from". This method will only be called on equal k-mers.

    table

    The table containing k-mers

    into

    Target k-mer index in the table (k-mer A in op(A,B))

    from

    Source k-mer index in the table (k-mer B in op(A,B))

    Definition Classes
    CountReducer → Reducer
  20. def reduceKmers(table: KmerTable): KmerTable

    Reduce tags of a single KmerTable by combining equal k-mers.

    Reduce tags of a single KmerTable by combining equal k-mers. Requires that the table was sorted at construction time. Mutates the table.

    table

    the KmerTable

    Definition Classes
    Reducer
  21. def shouldKeep(table: KmerTable, kmer: Int): Boolean

    Whether to keep the k-mer (together with tag data) after reduction.

    Whether to keep the k-mer (together with tag data) after reduction.

    table

    The table containing k-mers

    kmer

    Index of k-mer to be tested

    Definition Classes
    CountReducer → Reducer
  22. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  23. val tagOffset: Int
    Definition Classes
    CountReducer → Reducer
  24. def toString(): String
    Definition Classes
    AnyRef → Any
  25. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  26. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  27. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  28. val zeroValue: Tag

    A special value that is used to indicate non-existent/redundant k-mers.

    A special value that is used to indicate non-existent/redundant k-mers. Should also have the property that op(A, zero) == op(zero, A) for all A

    Definition Classes
    Reducer

Deprecated Value Members

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

Inherited from Reducer

Inherited from AnyRef

Inherited from Any

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