net.maizegenetics.dna.map

Class TagLocus

net.maizegenetics.dna.map.TagLocus

public class TagLocus

Aligns and calls SNPs for all tags at a given locus.

Constructor Detail

TagLocus

public TagLocus(int chromosome,
                byte strand,
                int startPosition,
                int tagLength,
                boolean includeRefGenome,
                boolean fuzzyStartPositions,
                double errorRate)

Method Detail

addTag

public void addTag(int tagTOPMIndex,
                   TagsOnPhysicalMap theTOPM,
                   TagsByTaxa theTBT,
                   boolean includeRefGenome,
                   boolean fuzzyStartPositions)

addRefTag

public void addRefTag(java.lang.String refTag,
                      int nLongsPerTag,
                      java.lang.String nullTag)

getSize

public int getSize()

getChromosome

public int getChromosome()

getStrand

public byte getStrand()

getMinStartPosition

public int getMinStartPosition()

getMaxStartPosition

public int getMaxStartPosition()

getMinTagLength

public int getMinTagLength()

getMaxTagLength

public int getMaxTagLength()

setMinStartPosition

public void setMinStartPosition(int newMinStartPosition)

getTOPMIndexOfTag

public int getTOPMIndexOfTag(int tagIndex)

getTBTIndexOfTag

public int getTBTIndexOfTag(int tagIndex)

getDivergenceOfTag

public int getDivergenceOfTag(int tagIndex)

getCallAtVariableSiteForTag

public byte getCallAtVariableSiteForTag(int site,
                                        int tagIndex)

getRefGeno

public byte getRefGeno(int site)

getNumberTaxaCovered

public int getNumberTaxaCovered()

getTotalNReads

public int getTotalNReads()

getCommonAlleles

public kotlin.Array[] getCommonAlleles()

getAlleleDepthsInTaxa

public kotlin.Array[] getAlleleDepthsInTaxa()

getSNPCallsVCF

public kotlin.Array[] getSNPCallsVCF(boolean callBiallelicSNPsWithGap,
                                     boolean includeReferenceTag)

getSNPCallsQuant

public kotlin.Array[] getSNPCallsQuant(boolean callBiallelicSNPsWithGap,
                                       boolean includeReferenceTag)

getSNPCallsQuant

public kotlin.Array[] getSNPCallsQuant(java.lang.String refSeq,
                                       boolean callBiallelicSNPsWithGap)

getPositionsOfVariableSites

public kotlin.Array[] getPositionsOfVariableSites()

getLocusReport

public java.lang.String getLocusReport(int minTaxaWithLocus,
                                       kotlin.Array[] varSiteKept)