KmerIO

class KmerIO(filename: String, isCompressed: Boolean = true) : Iterator<Pair<Kmer, Int>>

This class reads kmers from a text file (which may be LZ4 compressed) and can be used to construct KmerSet, KmerBigSet, and KmerMultiSet objects. It can also iterate through a kmer text file without constructing a set.

Constructors

KmerIO

constructor(filename: String, isCompressed: Boolean = true)

Functions

closeReader

fun closeReader()

Closes the file reader.

forEachRemaining

open fun forEachRemaining(p0: Consumer<in Pair<Kmer, Int>>)

hasNext

open operator override fun hasNext(): Boolean

Returns true if there is another kmer in the file.

open operator override fun next(): Pair<Kmer, Int>

Returns the next kmer in the file and its associated count as a pair.

readAll

fun readAll(): AbstractKmerSet

Returns an AbstractKmerSet of all kmers in the file. The header must specify a valid set type, or an exception will be thrown.

readBigSet

fun readBigSet(): KmerBigSet

Returns a KmerBigSet of all kmers in the file.

readKmerMultiSet

fun readKmerMultiSet(): KmerMultiSet

Returns a KmerMultiSet of all kmers in the file.

readKmerSet

fun readKmerSet(): KmerSet

Returns a KmerSet of all kmers in the file.