object CorrectUmis

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  1. case class UmiCorrectionMetrics (umi: String, total_matches: Long = 0, perfect_matches: Long = 0, one_mismatch_matches: Long = 0, two_mismatch_matches: Long = 0, other_matches: Long = 0, fraction_of_matches: Double = 0, representation: Double = 0) extends Metric with Product with Serializable

    Metrics for the correction of UMI sequences to a fixed set of known UMIs.

    Metrics for the correction of UMI sequences to a fixed set of known UMIs.

    umi

    the corrected UMI sequence (or all Ns for unmatched)

    total_matches

    the number of UMI sequences that matched/were corrected to this UMI

    perfect_matches

    the number of UMI sequences that were perfect matches to this UMI

    one_mismatch_matches

    the number of UMI sequences that matched with a single mismatch

    two_mismatch_matches

    the number of UMI sequences that matched with two mismatches

    other_matches

    the number of UMI sequences that matched with > 2 mismatches

    fraction_of_matches

    the fraction of all UMIs that matched or were corrected to this UMI

    representation

    the total_matches for this UMI divided by the mean total_matches for all UMIs

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  9. def findUmiPairsWithinDistance(umis: Seq[String], distance: Int): Seq[(String, String, Int)]

    Finds pairs of UMIs within the given set that are within some edit distance of each other.

    Finds pairs of UMIs within the given set that are within some edit distance of each other.

    umis

    the set of umis to check

    distance

    the maximum edit distance at which to report pairs of UMIs

    returns

    a Seq of three-tuples containing (umi1, umi2, edit_distance)

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