net.maizegenetics.dna.map

Class TagLocus

java.lang.Object

net.maizegenetics.dna.map.TagLocus

public class TagLocus
extends Object

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

Author:

jcg233

Constructor Summary

Constructors

Constructor and Description
TagLocus(int chromosome, byte strand, int startPosition, int tagLength, boolean includeRefGenome, boolean fuzzyStartPositions, double errorRate)

Method Summary

Modifier and Type	Method and Description
void	addRefTag(String refTag, int nLongsPerTag, String nullTag)
void	addTag(int tagTOPMIndex, TagsOnPhysicalMap theTOPM, TagsByTaxa theTBT, boolean includeRefGenome, boolean fuzzyStartPositions)
byte[][][]	getAlleleDepthsInTaxa()
byte	getCallAtVariableSiteForTag(int site, int tagIndex)
int	getChromosome()
byte[][]	getCommonAlleles()
int	getDivergenceOfTag(int tagIndex)
String	getLocusReport(int minTaxaWithLocus, boolean[] varSiteKept)
int	getMaxStartPosition()
int	getMaxTagLength()
int	getMinStartPosition()
int	getMinTagLength()
int	getNumberTaxaCovered()
int[]	getPositionsOfVariableSites()
byte	getRefGeno(int site)
int	getSize()
byte[][]	getSNPCallsQuant(boolean callBiallelicSNPsWithGap, boolean includeReferenceTag)
byte[][]	getSNPCallsQuant(String refSeq, boolean callBiallelicSNPsWithGap)
byte[][]	getSNPCallsVCF(boolean callBiallelicSNPsWithGap, boolean includeReferenceTag)
byte	getStrand()
int	getTBTIndexOfTag(int tagIndex)
int	getTOPMIndexOfTag(int tagIndex)
int	getTotalNReads()
void	setMinStartPosition(int newMinStartPosition)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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(String refTag,
                      int nLongsPerTag,
                      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 byte[][] getCommonAlleles()

getAlleleDepthsInTaxa

public byte[][][] getAlleleDepthsInTaxa()

getSNPCallsVCF

public byte[][] getSNPCallsVCF(boolean callBiallelicSNPsWithGap,
                               boolean includeReferenceTag)

getSNPCallsQuant

public byte[][] getSNPCallsQuant(boolean callBiallelicSNPsWithGap,
                                 boolean includeReferenceTag)

getSNPCallsQuant

public byte[][] getSNPCallsQuant(String refSeq,
                                 boolean callBiallelicSNPsWithGap)

getPositionsOfVariableSites

public int[] getPositionsOfVariableSites()

getLocusReport

public String getLocusReport(int minTaxaWithLocus,
                             boolean[] varSiteKept)