net.maizegenetics.pangenome.hapCalling

Class KmerMap

net.maizegenetics.pangenome.hapCalling.KmerMap

Direct Known Subclasses:

MutableKmerCounter, MutableKmerToIdMap

public class KmerMap

KmerMap provides high efficiency in both speed and memory efficiency for storing and counting kmers. It is backed with a primitive hashmap. All kmers are encoded into Longs, so only kmers upto to 32bp in length can be stored.

Constructor Detail

KmerMap

public KmerMap(@NotNull
               java.lang.String sequence,
               int kmerSize,
               int stepSize,
               @Nullable
               java.lang.Character kmerPrefix,
               int refRangeId,
               @NotNull
               KmerMapType mapType)

KmerMap provides high efficiency in both speed and memory efficiency for storing and counting kmers. It is backed with a primitive hashmap. All kmers are encoded into Longs, so only kmers upto to 32bp in length can be stored.

Method Detail

addDNASeqToMap

protected void addDNASeqToMap(@NotNull
                              java.lang.String dna)

kmersAsLongSet

@NotNull
public it.unimi.dsi.fastutil.longs.LongSet kmersAsLongSet()

kmersAsLongArray

@NotNull
public kotlin.Array[] kmersAsLongArray()

kmersAsLongList

@NotNull
public java.util.List<java.lang.Long> kmersAsLongList()

kmersAsDNA

@NotNull
public java.util.Set<java.lang.String> kmersAsDNA()

kmerLongSequence

@NotNull
public kotlin.sequences.Sequence<java.lang.Long> kmerLongSequence()

kmerDNASequence

@NotNull
public kotlin.sequences.Sequence<java.lang.String> kmerDNASequence()

size

public int size()

get

public int get(long kmer)

get

public int get(@NotNull
               java.lang.String kmerSeq)

asSequence

@NotNull
public kotlin.sequences.Sequence<kotlin.Pair> asSequence()

asDNASequence

@NotNull
public kotlin.sequences.Sequence<kotlin.Pair> asDNASequence()

toString

@NotNull
public NonExistentClass toString()

toStringLong

@NotNull
public NonExistentClass toStringLong()

getKmerSize

public int getKmerSize()

getStepSize

public int getStepSize()

getKmerPrefix

@Nullable
public java.lang.Character getKmerPrefix()

getRefRangeId

public int getRefRangeId()

getMapType

@NotNull
public KmerMapType getMapType()