final case class ReducibleBucket(id: BucketId, supermers: Array[ZeroNTBitArray], 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.
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new
ReducibleBucket(id: BucketId, supermers: Array[ZeroNTBitArray], 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.
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- def appendAndCompact(other: ReducibleBucket, reducer: Reducer): ReducibleBucket
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- val id: BucketId
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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
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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
- val supermers: Array[ZeroNTBitArray]
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- val tags: Array[Array[Int]]
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def
writeToSortedTable(k: Int, forwardOnly: Boolean): KmerTable
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def
writeToTable(k: Int, forwardOnly: Boolean, sort: Boolean): KmerTable
- Definition Classes
- KmerBucket