Type Members

1.  final case class BucketStats(id: String, superKmers: Long, totalAbundance: Abundance, distinctKmers: Long, uniqueKmers: Long, maxAbundance: Abundance) extends Product with Serializable

   Statistics for a single bin/bucket.

   Statistics for a single bin/bucket.

   id

   Minimizer/bucket ID (human-readable)

   superKmers

   Total number of superkmers

   totalAbundance

   Total number of k-mers counted

   distinctKmers

   Total number of distinct k-mers

   uniqueKmers

   Total number of k-mers with abundance == 1

   maxAbundance

   Greatest abundance seen for a single k-mer

2.  trait CountReducer extends Reducer

   A reducer that handles k-mer count values stored in the longsForK(k) + 1 tag position.

3.  final case class CountersSubtractReducer(params: ReduceParams) extends CountReducer with Product with Serializable

   Implements the bucket.Rule.CountersSubtract reduction rule.

   Implements the bucket.Rule.CountersSubtract reduction rule. For each k-mer we calculate count_1 - count_2 and set the result to this value. Only positive counts are preserved in the output.

4.  abstract class KmerBucket extends AnyRef

   A bucket that maintains some number of super-mers and associated tags (e.g.

   A bucket that maintains some number of super-mers and associated tags (e.g. counts) of each k-mer.

5.  final case class KmerSubtractReducer(params: ReduceParams) extends CountReducer with Product with Serializable

   Implements the bucket.Rule.KmersSubtract reduction rule.

   Implements the bucket.Rule.KmersSubtract reduction rule. k-mers are kept if they existed in bucket A, but not in bucket B.

6.  final case class LeftReducer(params: ReduceParams) extends CountReducer with Product with Serializable

   Implements the bucket.Rule.Left reduction rule

7.  final case class MaxReducer(params: ReduceParams) extends CountReducer with Product with Serializable

   Implements the bucket.Rule.Max reduction rule

8.  final case class MinReducer(params: ReduceParams) extends CountReducer with Product with Serializable

   Implements the bucket.Rule.Min reduction rule

9.  final case class ReduceParams(k: Int, orientation: Orientation = Unchanged, intersect: Boolean = false) extends Product with Serializable

   K-mer reduction parameters

   K-mer reduction parameters

   k

   The length of k-mers

   orientation

   Orientation of k-mers to keep in the result

   intersect

   Whether the reduction is an intersection type (if not, it's a union)

10.  trait Reducer extends AnyRef

    A method for combining identical k-mers (which may have associated extra data)

11.  final case class ReducibleBucket(id: BucketId, supermers: Array[NTBitArray], tags: Array[Array[Int]]) extends KmerBucket with Product with Serializable

    A k-mer bucket that reduces (combines) identical k-mers using a supplied method, removing redundant super-mers in the process to keep the bucket compact.

    A k-mer bucket that reduces (combines) identical k-mers using a supplied method, removing redundant super-mers in the process to keep the bucket compact.

    id

    The minimizer/ID of this bucket

    supermers

    Super-mers containing the k-mers of this bucket. Some might not actually be present in the bucket (the super-mers may have gaps) and the tags define which are present. This arranges the k-mers in a 2D grid where rows identify the super-mer and columns identify the offset in the super-mer. (Super-mers may however have different lengths)

    tags

    Tags for each k-mer, for example k-mer counts in the case of k-mer counting. These follow the 2D coordinate scheme described above.

12.  final case class RightReducer(params: ReduceParams) extends CountReducer with Product with Serializable

    Implements the bucket.Rule.Right reduction rule

13.  sealed trait Rule extends Serializable

    k-mer combination (reduction) rules for combining indexes.

    k-mer combination (reduction) rules for combining indexes. Most of these support both intersection and union. An intersection is an operation that requires the k-mer to be present in every input index, or it will not be present in the output. A union may preserve the k-mer even if it is present in only one input index. Except for the case of the union Sum reduction, indexes must be compacted prior to reduction, that is, each k-mer must occur in each index with a nonzero value only once.

    These rules were inspired by the design of KMC3: https://github.com/refresh-bio/KMC

14.  final case class SumReducer(params: ReduceParams) extends CountReducer with Product with Serializable

    Implements the bucket.Rule.Sum reduction rule

15.  type Tag = Int