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object SampledFrequencies extends Serializable

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  4. def apply(table: MinTable, counts: Iterator[(Int, Long)]): SampledFrequencies

    Sampled motif frequencies that may be used to construct a new minimizer ordering.

    Sampled motif frequencies that may be used to construct a new minimizer ordering.

    table

    Template table, whose ordering of motifs will be refined based on counted frequencies.

    counts

    Pairs of (minimizer rank, frequency). The minimizers should be a subset of those from the given template MinTable.

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  9. def fromReads(scanner: ShiftScanner, inputs: Iterator[NTSeq]): SampledFrequencies

    Constructs a SampledFrequencies object by in-memory counting all motifs in the input sequences, using the supplied ShiftScanner.

    Constructs a SampledFrequencies object by in-memory counting all motifs in the input sequences, using the supplied ShiftScanner. Intended for use only when Spark is not available.

    scanner

    Scanner to use for parsing valid minimizers

    inputs

    Input data to scan

    returns

    Frequencies of all valid motifs

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