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/hash (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(k: Int, forwardOnly: Boolean, intersect: Boolean) extends CountReducer with Product with Serializable

   Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule.

   Implements the com.jnpersson.discount.spark.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(k: Int, forwardOnly: Boolean) extends CountReducer with Product with Serializable

   Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule.

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

6.  final case class LeftReducer(k: Int, forwardOnly: Boolean, intersect: Boolean) extends CountReducer with Product with Serializable

   Implements the com.jnpersson.discount.spark.Rule.Left reduction rule

7.  final case class MaxReducer(k: Int, forwardOnly: Boolean, intersect: Boolean) extends CountReducer with Product with Serializable

   Implements the com.jnpersson.discount.spark.Rule.Max reduction rule

8.  final case class MinReducer(k: Int, forwardOnly: Boolean, intersect: Boolean) extends CountReducer with Product with Serializable

   Implements the com.jnpersson.discount.spark.Rule.Min reduction rule

9.  trait Reducer extends AnyRef

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

10.  final case class ReducibleBucket(id: BucketId, supermers: Array[ZeroNTBitArray], 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.

11.  final case class RightReducer(k: Int, forwardOnly: Boolean, intersect: Boolean) extends CountReducer with Product with Serializable

    Implements the com.jnpersson.discount.spark.Rule.Right reduction rule

12.  final case class SumReducer(k: Int, forwardOnly: Boolean, intersect: Boolean) extends CountReducer with Product with Serializable

    Implements the com.jnpersson.discount.spark.Rule.Sum reduction rule

13.  type Tag = Int