final case class ExtendedTable(inner: MinTable, width: Int, canonical: Boolean, withSuffix: Boolean) extends MinimizerPriorities with Product with Serializable
Hybrid lookup/compute MinimizerPriorities, where minimizers consist of a prefix taken from the table and a computed suffix/prefix. This can give low minimizer density for long minimizers while avoiding the need for a huge table.
- inner
The inner minimizer ordering (containing the lookup table)
- width
Expanded width > inner.width
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- val canonical: Boolean
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lazy val
decoder: ThreadLocal[NTBitDecoder]
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def
humanReadable(priority: NTBitArray): NTSeq
Human-readable string corresponding to a given minimizer.
Human-readable string corresponding to a given minimizer. Not optimized for frequent use.
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def
humanReadable(priority: Long): NTSeq
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- val inner: MinTable
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def
isRefinementPriority(narrow: Long, wide: Long): Boolean
Test whether the wider (more specific) minimizer rank is a refinement of the narrow (more general) rank
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def
motifFor(priority: NTBitArray): NTBitArray
Get a representative minimizer for a given priority.
Get a representative minimizer for a given priority.
- Definition Classes
- ExtendedTable → MinimizerPriorities
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ne(arg0: AnyRef): Boolean
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def
numLargeBuckets: Long
Number of buckets (minimizers) expected to be very large (frequent), if any
Number of buckets (minimizers) expected to be very large (frequent), if any
- Definition Classes
- MinimizerPriorities
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def
numMinimizers: Option[Long]
Total number of distinct minimizers in this ordering
Total number of distinct minimizers in this ordering
- Definition Classes
- ExtendedTable → MinimizerPriorities
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def
priorityOf(motifArray: NTBitArray): NTBitArray
Get the priority of the given minimizer.
Get the priority of the given minimizer. If not every m-mer is a minimizer, then util.NTBitArray.empty indicates an invalid minimizer.
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- ExtendedTable → MinimizerPriorities
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val
width: Int
Minimizer width (m)
Minimizer width (m)
- Definition Classes
- ExtendedTable → MinimizerPriorities
- val withSuffix: Boolean
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def
writePriorityOf(motif: NTBitArray, buffer: NTBitArray): NTBitArray
Write the priority of the given minimizer to the provided buffer.
Write the priority of the given minimizer to the provided buffer. If not every m-mer is a minimizer, then util.NTBitArray.empty indicates an invalid minimizer.
- motif
The motif to get the priority of
- buffer
The buffer to write the priority to
- returns
The buffer for chaining
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