final case class MinSplitter[+P <: MinimizerPriorities](priorities: P, k: Int) extends Product with Serializable
Split reads into superkmers by ranked motifs (minimizers). Such superkmers can be bucketed by the corresponding minimizer.
- priorities
Minimizer ordering to use for splitting
- k
k-mer length
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new
MinSplitter(priorities: P, k: Int)
- priorities
Minimizer ordering to use for splitting
- k
k-mer length
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def
humanReadable(id: BucketId): NTSeq
Generate a human-readable form (nucleotide sequence) of the bucket ID.
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- val k: Int
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- val priorities: P
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lazy val
scanner: ShiftScanner
A ShiftScanner associated with this splitter's MinTable
A ShiftScanner associated with this splitter's MinTable
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def
splitEncode(read: NTSeq): Iterator[Supermer]
Split a read into superkmers.
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def
splitEncodeLocation(read: InputFragment, sequenceIDs: Map[SeqTitle, SeqID]): Iterator[LocationSegment]
Split a read into super-mers, efficiently encoding them in binary form in the process, also preserving sequence ID and location.
Split a read into super-mers, efficiently encoding them in binary form in the process, also preserving sequence ID and location.
- read
The read to split
- sequenceIDs
IDs for each sequence title, to be preserved in the result
- returns
an iterator of superkmers with sequence ID and location populated
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def
splitRead(encoded: NTBitArray, matches: MinimizerPositions): Iterator[Supermer]
Split a read into super-mers, and return them together with the corresponding minimizer.
Split a read into super-mers, and return them together with the corresponding minimizer.
- encoded
the read to split
- matches
discovered motif ranks in the superkmer
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def
splitRead(encoded: NTBitArray, reverseComplement: Boolean = false): Iterator[Supermer]
Split an encoded read into superkmers.
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def
superkmerPositions(encoded: NTBitArray, matches: MinimizerPositions): Iterator[Minimizer]
Split an encoded read into superkmers, returning their length and position with the corresponding minimizer.
Split an encoded read into superkmers, returning their length and position with the corresponding minimizer.
- encoded
the read to split
- matches
discovered motif ranks in the superkmer
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def
superkmerPositions(encoded: NTBitArray): Iterator[Minimizer]
Split an encoded read into super-mers, returning only the position, minimizer, and length of each.
Split an encoded read into super-mers, returning only the position, minimizer, and length of each. The nucleotides of each super-mer will not be retained.
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def
superkmerPositions(read: NTSeq): Iterator[Minimizer]
Split a read into super-mers, returning only the position, minimizer, and length of each.
Split a read into super-mers, returning only the position, minimizer, and length of each. The nucleotides of each super-mer will not be retained.
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