BioKotlin/biokotlin.kmer/KmerMultiSet

KmerMultiSet

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

A set of kmers with associated counts.

Constructors

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

Extracts the kmer count from a nucleotide sequence sequence. In general kmers from both strands should be extracted, unless strand specificity is really known. No kmers that include an ambiguous base pair will be included Using stepSize subsets of the kmers can be sampled

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

Properties

val bothStrands: Boolean

val keepMinOnly: Boolean

kmer2CountEntrySet

val kmer2CountEntrySet: Long2IntMap.FastEntrySet

All kmers (packed into longs) and there associated counts

val kmerSize: Int

val stepSize: Int

Functions

addKmersFromNewSeq

fun addKmersFromNewSeq(seq: NucSeq)

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

fun ambiguousKmers(): Long

Returns the number of ambiguous kmers in the set.

open override fun contains(kmer: Kmer): Boolean

Returns true if the set contains kmer.

open override fun getCountOf(kmer: Kmer): Int

Returns the number of times kmer appears in the set.

getEvenOddHashMap

fun getEvenOddHashMap(): Long2ObjectOpenHashMap<LongOpenHashSet>

Hashes the longs in the set based on their even nucleotides and their odd nucleotides, placing each long into two bins. Returns this map of bins.

open override fun isEmpty(): Boolean

Returns true if the set is empty

open override fun longSet(): LongSet

Returns the set of kmers, as their Long encodings.

minHammingDistance

fun minHammingDistance(kmer: Kmer, bothStrands: Boolean = true): Int

Returns the minimum hamming distance between the query kmer and all kmers in this map

fun sequenceLength(): Long

Returns the total length of sequence(s) used to generate this set.

open override fun set(): Set<Kmer>

Returns the set of kmers, without counts.

open override fun setSize(): Long

Returns the number of unique kmers in the set.

toSeqCountString

fun toSeqCountString(max: Int = Int.MAX_VALUE, separator: CharSequence = ""): String

Returns a string of all kmers in the set and their associated counts.

open override fun toString(): String

Summarizes set parameters and size in string format.