net.maizegenetics.pangenome.hapCalling

Class KmerUtils

net.maizegenetics.pangenome.hapCalling.KmerUtils

public class KmerUtils

Method Detail

dnaToKmerLong

public static long dnaToKmerLong(@NotNull
                                 java.lang.String kmerAsDNA,
                                 int kmerSize)

Function to first check that the kmer lengths match, then encode the Long from the sequence

byteArrayToKmerLong

public static long byteArrayToKmerLong(@NotNull
                                       kotlin.Array[] kmerAsByte,
                                       int kmerSize)

Function to check the kmer lengths an then encode the Long from the ByteSeq

exportKmerToHapIdMapToTextFile

public static void exportKmerToHapIdMapToTextFile(@NotNull
                                                  java.lang.String fileName,
                                                  @NotNull
                                                  it.unimi.dsi.fastutil.longs.Long2ObjectMap<kotlin.Array[]> kmerMap)

Function to write out the Long2ObjectMap to a text file. It is in the format: kmerAsLong\tHapId1\tHapId2\tHapId3.....

importKmerToHapIdMapFromTextFile

@NotNull
public static it.unimi.dsi.fastutil.longs.Long2ObjectMap<kotlin.Array[]> importKmerToHapIdMapFromTextFile(@NotNull
                                                                                                                   java.lang.String fileName)

Import the KmerToHapIdMap from a text file. This will read from a file with the format: kmerAsLong\tHapId1\tHapId2\tHapId3.....

exportKmerToIntMap

public static void exportKmerToIntMap(@NotNull
                                      java.lang.String fileName,
                                      @NotNull
                                      it.unimi.dsi.fastutil.longs.Long2IntMap kmerMap)

Function to export the kmer to Id map

importKmerToIntMap

@NotNull
public static it.unimi.dsi.fastutil.longs.Long2IntMap importKmerToIntMap(@NotNull
                                                                                  java.lang.String fileName)

exportPurgeArray

public static void exportPurgeArray(@NotNull
                                    java.lang.String fileName,
                                    @NotNull
                                    KmerToRefRangeIdToPurgeArray purgeArray)

parseKmerLine

@NotNull
public static kotlin.Pair<java.lang.Long,kotlin.Array[]> parseKmerLine(@NotNull
                                                                                java.lang.String currentString)

Function to parse the Kmer line. This just splits the currentLine and then will convert the characters to integers and then add them to an array

exportKmerToHapIdMapToBinaryFile

public static void exportKmerToHapIdMapToBinaryFile(@NotNull
                                                    java.lang.String fileName,
                                                    @NotNull
                                                    it.unimi.dsi.fastutil.longs.Long2ObjectMap<kotlin.Array[]> kmerMap)

importKmerToHapIdMapFromBinaryFile

@NotNull
public static it.unimi.dsi.fastutil.longs.Long2ObjectMap<kotlin.Array[]> importKmerToHapIdMapFromBinaryFile(@NotNull
                                                                                                                     java.lang.String fileName)

markKmersForPurgeUsingHammingDistance

@NotNull
public static KmerToRefRangeIdToPurgeArray markKmersForPurgeUsingHammingDistance(@NotNull
                                                                                          KmerMap kmerToRefRange,
                                                                                          int kmerSize,
                                                                                          int minAllowedHammingDist,
                                                                                          boolean verboseLogging)

Method that will mark Kmers to purge using HammingDistance

Inputs are the KmerMap where it maps kmer -> RefRangeId

It will then export the Data Class KmerToRefRangeIdToPurgeArray which holds 3 primitive arrays We create a swapper then do the hamming calculation twice one for the first half of the kmer one time for the second half

hammingDistance

public static int hammingDistance(long kmer1,
                                  long kmer2)

Function to compute paired bit hamming distances for encoded kmers.

compareKmerLoop

public static void compareKmerLoop(@NotNull
                                   kotlin.Array[] kmerArray,
                                   @NotNull
                                   kotlin.Array[] refRangeIdArray,
                                   @NotNull
                                   kotlin.Array[] purgeArray,
                                   long mask,
                                   int minAllowedHammingDist,
                                   @NotNull
                                   it.unimi.dsi.fastutil.Swapper kmerRefRangePurgeSwapper)

Function critical to run the hamming distance comparison.

This will first create a Comparable and then sort the the arrays by the masked comparison Then loop through each kmer Loop through the kmers that match the masked version and compare the hamming distance If the ref Range ids are not the same and they have a hamming distance below what is input, mark the arrays to be purged