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1.  final def !=(arg0: Any): Boolean

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2.  final def ##(): Int

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3.  final def ==(arg0: Any): Boolean

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4.  final def asInstanceOf[T0]: T0

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5.  def clone(): AnyRef

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6.  def countFeatures(reads: Dataset[NTSeq], table: MinTable, partitions: Int): SampledFrequencies
7.  def createSampledTable(input: Dataset[NTSeq], template: MinTable, sampledFraction: Double, persistLocation: Option[String] = None): MinTable

   Create a MinTable based on sampling reads for minimizer frequencies.

   Create a MinTable based on sampling reads for minimizer frequencies.

   input

   Input reads

   template

   Template table, containing minimizers to sort according to frequencies in the sample

   sampledFraction

   Fraction of input data to sample

   persistLocation

   Location to optionally write the new table to for later reuse

8.  final def eq(arg0: AnyRef): Boolean

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9.  def equals(arg0: Any): Boolean

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10.  def finalize(): Unit

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11.  final def getClass(): Class[_]

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12.  def hashCode(): Int

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13.  final def isInstanceOf[T0]: Boolean

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14.  def motifCounts(reads: Dataset[NTSeq], table: MinTable, partitions: Int): DataFrame

    Count motifs (m-length minimizers) in a set of reads.

    Count motifs (m-length minimizers) in a set of reads.

    table

    Template table with a motif set

15.  final def ne(arg0: AnyRef): Boolean

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16.  final def notify(): Unit

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17.  final def notifyAll(): Unit

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18.  def persistMinimizers(table: MinTable, location: String): Unit

    Write a MinTable's minimizer ordering to a file

    Write a MinTable's minimizer ordering to a file

    table

    The ordering to write

    location

    Prefix of the location to write to. A suffix will be appended to this name.

19.  def persistMinimizers(splitter: MinSplitter[_], location: String): Unit

    Write a splitter's minimizer ordering to a file

    Write a splitter's minimizer ordering to a file

    splitter

    Splitter containing the ordering to write

    location

    Prefix of the location to write to. A suffix will be appended to this name.

20.  def readMotifList(location: String): Array[String]
21.  def readMotifList(location: String, k: Int, m: Int): Array[String]

    Read a saved minimizer ordering/motif list

    Read a saved minimizer ordering/motif list

    location

    Location to read from. If the location is a directory, it will be scanned for files called minimizers_{k}_{m} for various values of m and k and the most optimal file will be used. If it is a file, the file will be read as is.

    k

    k-mer width

    m

    minimizer length

22.  final def synchronized[T0](arg0: ⇒ T0): T0

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23.  def toString(): String

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24.  final def wait(): Unit

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25.  final def wait(arg0: Long, arg1: Int): Unit

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26.  final def wait(arg0: Long): Unit

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27.  def writeFrequencies(f: SampledFrequencies, location: String): Unit