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c

com.jnpersson.discount.bucket

KmerSubtractReducer

final case class KmerSubtractReducer(k: Int, forwardOnly: Boolean) extends CountReducer with Product with Serializable

Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule. k-mers are kept if they existed in bucket A, but not in bucket B.

Linear Supertypes
Serializable, Serializable, Product, Equals, CountReducer, Reducer, AnyRef, Any
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Inherited
  1. KmerSubtractReducer
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. CountReducer
  7. Reducer
  8. AnyRef
  9. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new KmerSubtractReducer(k: Int, forwardOnly: Boolean)

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()
  6. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  7. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  8. val forwardOnly: Boolean

    Whether to include only canonical (forward oriented) k-mers when reducing

    Whether to include only canonical (forward oriented) k-mers when reducing

    Definition Classes
    KmerSubtractReducer → Reducer
  9. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  10. def hasNonZeroTag(tags: Array[Tag]): Boolean
    Definition Classes
    Reducer
  11. def intersect: Boolean
    Definition Classes
    KmerSubtractReducer → CountReducer
  12. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  13. val k: Int
    Definition Classes
    KmerSubtractReducer → Reducer
  14. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  15. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  16. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  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
    KmerSubtractReducer → Reducer
  19. def reduceCounts(count1: Tag, count2: Tag): Tag
    Definition Classes
    KmerSubtractReducer → CountReducer
  20. 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
  21. def shouldKeep(table: KmerTable, kmer: Tag): 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
    KmerSubtractReducer → CountReducer → Reducer
  22. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  23. val tagOffset: Int
    Definition Classes
    CountReducer → Reducer
  24. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  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. 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

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from CountReducer

Inherited from Reducer

Inherited from AnyRef

Inherited from Any

Ungrouped