final case class CountersSubtractReducer(k: Int, forwardOnly: Boolean, intersect: Boolean) extends CountReducer with Product with Serializable
Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule. For each k-mer we calculate count_1 - count_2 and set the result to this value. Only positive counts are preserved in the output.
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Instance Constructors
- new CountersSubtractReducer(k: Int, forwardOnly: Boolean, intersect: Boolean)
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!=(arg0: Any): Boolean
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final
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##(): Int
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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
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- CountersSubtractReducer → Reducer
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final
def
getClass(): Class[_]
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- @native()
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def
hasNonZeroTag(tags: Array[Tag]): Boolean
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- Reducer
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val
intersect: Boolean
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- CountersSubtractReducer → CountReducer
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final
def
isInstanceOf[T0]: Boolean
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val
k: Int
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- CountersSubtractReducer → Reducer
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notify(): Unit
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notifyAll(): Unit
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def
preprocessFirst(bucket: ReducibleBucket): ReducibleBucket
Preprocess bucket A prior to op(A,B)
Preprocess bucket A prior to op(A,B)
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- Reducer
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def
preprocessSecond(bucket: ReducibleBucket): ReducibleBucket
Preprocess bucket B prior to op(A,B)
Preprocess bucket B prior to op(A,B)
- Definition Classes
- CountersSubtractReducer → Reducer
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def
reduceCounts(count1: Tag, count2: Tag): Tag
- Definition Classes
- CountersSubtractReducer → CountReducer
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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
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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
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- CountersSubtractReducer → CountReducer → Reducer
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final
def
synchronized[T0](arg0: ⇒ T0): T0
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val
tagOffset: Int
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- CountReducer → Reducer
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final
def
wait(): Unit
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def
wait(arg0: Long, arg1: Int): Unit
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def
wait(arg0: Long): Unit
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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