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com.jnpersson.kmers

MinimizerConfig

class MinimizerConfig extends AnyRef

Configuration parameters for the construction of a minimizer ordering for k-mers.

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Instance Constructors

  1. new MinimizerConfig(k: Int, minimizers: MinimizerSource = Bundled, m: Int = 10, ordering: MinimizerOrdering = Frequency, sample: Double = 0.01)(implicit spark: SparkSession)

    k

    k-mer length

    minimizers

    source of minimizers. See kmers.minimizer.MinimizerSource

    m

    minimizer width

    ordering

    minimizer ordering. See kmers.minimizer.MinimizerOrdering

    sample

    sample fraction for frequency orderings

    spark

    the SparkSession

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  9. def getSplitter(inFiles: Option[Seq[String]], persistHash: Option[String] = None): MinSplitter[_ <: MinimizerPriorities]

    Construct a read splitter for the given input files based on the settings in this object.

    Construct a read splitter for the given input files based on the settings in this object.

    inFiles

    Input files (for frequency orderings, which require sampling)

    persistHash

    Location to persist the generated minimizer ordering (for frequency orderings), if any

    returns

    a MinSplitter configured with a minimizer ordering and corresponding MinTable

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