net.maizegenetics.analysis.gbs

Class SimpleGenotypeSBit

net.maizegenetics.analysis.gbs.SimpleGenotypeSBit

public class SimpleGenotypeSBit

Store sBit for tag genetic mapping and LD detection, optimized for really fast calculation

Field Detail

taxaNum

public int taxaNum

chrNum

public int chrNum

siteNum

public int siteNum

wordNum

public int wordNum

taxaNames

public java.lang.String[] taxaNames

chromosomeNumber

public kotlin.Array[] chromosomeNumber

chrStartIndex

public kotlin.Array[] chrStartIndex

First SNP index of gt chromosome in the whole SNP list

chrEndIndex

public kotlin.Array[] chrEndIndex

Last SNP index of gt chromosome in the whole SNP list, exclusive

position

public kotlin.Array[] position

maf

public kotlin.Array[] maf

obsMajor

public OpenBitSet[] obsMajor

obsMinor

public OpenBitSet[] obsMinor

Constructor Detail

SimpleGenotypeSBit

public SimpleGenotypeSBit(java.lang.String genotypeH5FileS,
                          java.lang.String sBitFileS)

Convert HDF5 Alignment/Genotype file to SimpleGenotypeSBit

Parameters:

genotypeH5FileS -

sBitFileS -

SimpleGenotypeSBit

public SimpleGenotypeSBit(java.lang.String inputfileS)

Read in HDF5 SimpleGenotypeSBit

Parameters:

inputfileS -

Method Detail

writeH5File

public void writeH5File(java.lang.String outputFileS)

readH5File

public void readH5File(java.lang.String inputFileS)

getSiteNum

public int getSiteNum()

getTaxaNum

public int getTaxaNum()

getTaxonIndex

public int getTaxonIndex(java.lang.String taxonName)

getSiteIndex

public int getSiteIndex(int chr,
                        int pos)

Return index of nearest site of given position

Parameters:

chr -

pos -

Returns:

org.jetbrains.dokka.NodeRenderContent@26e2974c:

getAdjacentSiteIndexRange

public kotlin.Array[] getAdjacentSiteIndexRange(int siteIndex,
                                                int siteNum)

getChrIndex

public int getChrIndex(int chr)

getChr

public int getChr(int index)

getChunkNum

public int getChunkNum()

Return the total number of chunks

Returns:

org.jetbrains.dokka.NodeRenderContent@71bb5a50:

getChunkSize

public int getChunkSize()

Return the chunk size (Number of tags in gt chunk)

Returns:

org.jetbrains.dokka.NodeRenderContent@cd6cd16:

getPosition

public int getPosition(int siteIndex)

getChromosomeNumber

public int getChromosomeNumber(int siteIndex)

writeBinaryFile

public void writeBinaryFile(java.lang.String outputFileS)

readBinaryFile

public void readBinaryFile(java.lang.String inputFileS)