net.maizegenetics.pangenome.hapCalling

Class MutableKmerToIdMap

KmerMap

net.maizegenetics.pangenome.hapCalling.MutableKmerToIdMap

public class MutableKmerToIdMap
extends KmerMap

Mutable version of the KmerMap which allows for unique kmer->id mappings. If a kmer is seen in multiple ids( or in the same id), its id in the map is set to -1 This datastructure can then be used to further purge out repetative kmers

Constructor Detail

MutableKmerToIdMap

public MutableKmerToIdMap(int kmerSize,
                          @Nullable
                          java.lang.Character kmerPrefix)

Mutable version of the KmerMap which allows for unique kmer->id mappings. If a kmer is seen in multiple ids( or in the same id), its id in the map is set to -1 This datastructure can then be used to further purge out repetative kmers

Method Detail

put

public int put(@NotNull
               java.lang.String kmer,
               int id)

Basic put function for String kmer and its associated id

put

public int put(@NotNull
               kotlin.Array[] kmerAsByte,
               int id)

Put function taking in a ByteArray representation of the kmer and its associated id

put

public int put(long kmer,
               int id)

Put function from a Long Representation of the kmer and its Id We apply the lambda here which will set the id to -1 if we have already seen this Id

putAll

@NotNull
public NonExistentClass putAll(@NotNull
                                        KmerMap newKmerMap)

Loop through the KmerMap and put each key-value pair into the existing map.

putAll

@NotNull
public NonExistentClass putAll(@NotNull
                                        it.unimi.dsi.fastutil.longs.LongSet kmerSet,
                                        int id)

Method to add in all the kmers stored in a primitive Long Set into the kmerToIdMap using the input id.