Kmer

value class Kmer(val encoding: Long) : Comparable<Kmer>

2-bit encoded representation of a short nucleotide sequence (32 bases or fewer) Encoding: A=0, C=1, T/U=2, G=3 For kmers smaller than 32 bp, leftmost digits are padded with 0 Ambiguous bases (eg. N) are not allowed

val kmer = Kmer(1432462)
val kmerFromString = Kmer("UGCACUGCCA")
val kmerFromSeq = Kmer(NucSeq("TCTCACCTACA")

val kmerFromString = Kmer("NTACCGANNTCG") // throw error - ambiguous bases
val kmerFromString = Kmer("TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT") // throw error - string too long

Constructors

Kmer

constructor(encoding: Long)

Properties

encoding

val encoding: Long

Functions

compareTo

open operator override fun compareTo(other: Kmer): Int

Follows comparisons of bits represented as unsigned long

hammingDistance

fun hammingDistance(other: Kmer): Int

Returns the Hamming Distance between this Kmer and other Kmer

reverseComplement

fun reverseComplement(kmerSize: Int): Kmer

Returns the reverse complement of a sequence already encoded in a 2-bit long. Note: polyA is used represent unknown, but reverse complement will change it to polyT which does not mean the same. kmerSize parameter is required to remove polyT padding

toSeq

fun toSeq(): NucSeq

Converts Kmer to NucSeq Includes any A padding at left

fun toSeq(kmerSize: Int): NucSeq

Converts Kmer to NucSeq, trimming A padding at left to kmerSize

toString

open override fun toString(): String

Converts 2-bit encoding to string By default, keeps any A padding at left

fun toString(kmerSize: Int): String

Converts 2-bit encoding to string, trimming leftmost bits so the resulting sequence length is kmerSize