final case class SpacedSeed(s: Int, inner: MinimizerPriorities) extends MinimizerPriorities with Product with Serializable
Apply spaced seed mask to some minimizer priorities s nts, 1 nt apart from each other, counting from the rightmost position, will be removed, yielding (width-s) nts. Masked positions will be set to A Example: TTCTGTGGG with s = 3 will be masked as TTC-G-G-G, yielding TTCAGAGAG
- s
the number of nts to mask out
- inner
inner priorities to mask
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new
SpacedSeed(s: Int, inner: MinimizerPriorities)
- s
the number of nts to mask out
- inner
inner priorities to mask
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def
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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.
- Definition Classes
- MinimizerPriorities
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def
humanReadable(priority: Long): NTSeq
- Definition Classes
- MinimizerPriorities
- val inner: MinimizerPriorities
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final
def
isInstanceOf[T0]: Boolean
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- def maskSpacesOnly(motif: NTBitArray): NTBitArray
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def
motifFor(priority: NTBitArray): NTBitArray
Not a true reverse function of priorityOf, since that loses information.
Not a true reverse function of priorityOf, since that loses information. We return a representative value.
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- SpacedSeed → MinimizerPriorities
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final
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notify(): Unit
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def
notifyAll(): Unit
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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, if available.
Total number of distinct minimizers in this ordering, if available. This may be an upper bound. The largest value returned by priorityOf will be smaller than this value.
- Definition Classes
- SpacedSeed → MinimizerPriorities
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def
priorityOf(motif: 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.
- Definition Classes
- SpacedSeed → MinimizerPriorities
- val s: Int
- final val spaceMask: NTBitArray
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final
def
synchronized[T0](arg0: ⇒ T0): T0
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def
wait(arg0: Long, arg1: Int): Unit
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wait(arg0: Long): Unit
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def
wait(): Unit
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val
width: Int
Minimizer width (m)
Minimizer width (m)
- Definition Classes
- SpacedSeed → MinimizerPriorities
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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
- Definition Classes
- SpacedSeed → MinimizerPriorities
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