trait CountReducer extends Reducer
A reducer that handles k-mer count values stored in the longsForK(k) + 1 tag position.
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abstract
def
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
- Reducer
- abstract def intersect: Boolean
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abstract
def
k: Int
- Definition Classes
- Reducer
- abstract def reduceCounts(count1: Tag, count2: Tag): Tag
Concrete Value Members
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final
def
!=(arg0: Any): Boolean
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final
def
##(): Int
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final
def
==(arg0: Any): Boolean
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final
def
asInstanceOf[T0]: T0
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final
def
eq(arg0: AnyRef): Boolean
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def
equals(arg0: Any): Boolean
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def
finalize(): Unit
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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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def
hashCode(): Int
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final
def
isInstanceOf[T0]: Boolean
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def
ne(arg0: AnyRef): Boolean
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def
notify(): Unit
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def
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)
- Definition Classes
- 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
- Reducer
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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: 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
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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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def
toString(): String
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final
def
wait(): Unit
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final
def
wait(arg0: Long, arg1: Int): Unit
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final
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