BioKotlin/biokotlin.kmer/KmerBigSet

KmerBigSet

class KmerBigSet(val kmerSize: Int = 21, val bothStrands: Boolean = true, val stepSize: Int = 1, val keepMinOnly: Boolean = false) : AbstractKmerSet

A set of kmers capable of storing up to 134217728 * (2^31 − 1) unique kmers. Includes a count value for each kmer, up to 128. Recommended use is for dense tables where most possible kmers of length kmerSize are present or where the number of unique kmers exceeds MAX_VALUE of Int.

Constructors

KmerBigSet

constructor(kmerSize: Int = 21, bothStrands: Boolean = true, stepSize: Int = 1, keepMinOnly: Boolean = false)

Properties

bothStrands

val bothStrands: Boolean

keepMinOnly

val keepMinOnly: Boolean

kmerSize

val kmerSize: Int

stepSize

val stepSize: Int

Functions

addKmersFromNewSeq

fun addKmersFromNewSeq(seq: NucSeq)

Generates kmers from a nucleotide sequence and adds those kmers to this set.

addSet

fun addSet(kmers: AbstractSparseKmerSet, useCounts: Boolean = true)

Adds all kmers from kmers to this set. If kmers is a KmerMultiSet and useCounts is true, the count of each kmer in kmers will be added. If kmers is a KmerSet or useCounts is false, one count of each kmer in kmers will be added. kmers must have the same initialization parameters as this set: kmerSize, bothStrands, and keepMinOnly