net.maizegenetics.dna.tag

Class TagDataSQLite

net.maizegenetics.dna.tag.TagDataSQLite

All Implemented Interfaces:

TagData, TagDataWriter

public class TagDataSQLite
implements TagDataWriter

Defines xxxx TAS-480

Field Detail

snpPosToIDMap

public com.google.common.collect.BiMap<net.maizegenetics.dna.map.Position,java.lang.Integer> snpPosToIDMap

Constructor Detail

TagDataSQLite

public TagDataSQLite(java.lang.String filename)

Method Detail

close

public void close()

getTaxaList

public TaxaList getTaxaList()

getTagsNameMap

public java.util.Map<net.maizegenetics.dna.tag.Tag,java.lang.String> getTagsNameMap()

putAllTag

public boolean putAllTag(java.util.Set<net.maizegenetics.dna.tag.Tag> tags)

putAllNamesTag

public boolean putAllNamesTag(java.util.Map<net.maizegenetics.dna.tag.Tag,java.lang.String> tagNameMap)

putTaxaList

public void putTaxaList(TaxaList taxaList)

putTaxaTissueDistribution

public boolean putTaxaTissueDistribution(java.lang.String taxon,
                                         java.lang.String tissue,
                                         java.util.List<net.maizegenetics.dna.tag.Tag> tags,
                                         kotlin.Array[] counts)

putTaxaDistribution

public void putTaxaDistribution(java.util.Map<net.maizegenetics.dna.tag.Tag,net.maizegenetics.dna.tag.TaxaDistribution> tagTaxaDistributionMap)

putTagAlignments

public void putTagAlignments(com.google.common.collect.Multimap<net.maizegenetics.dna.tag.Tag,net.maizegenetics.dna.map.Position> tagAnnotatedPositionMap)

putSNPQualityProfile

public void putSNPQualityProfile(java.util.Map<net.maizegenetics.dna.map.Position,java.util.Map> tagAnnotatedPositionMap,
                                 java.lang.String taxaSubset)

putSNPQualityProfile

public void putSNPQualityProfile(java.util.Map<net.maizegenetics.dna.map.Position,java.util.Map> tagAnnotatedPositionMap,
                                 java.lang.String taxaSubset,
                                 int counter)

setTagAlignmentBest

public void setTagAlignmentBest(Tag tag,
                                Position position,
                                boolean isBest)

putTagAlleles

public boolean putTagAlleles(com.google.common.collect.Multimap<net.maizegenetics.dna.tag.Tag,net.maizegenetics.dna.snp.Allele> tagAlleleMap)

putTagAlignmentApproach

public boolean putTagAlignmentApproach(java.lang.String tagAlignmentName,
                                       java.lang.String protocol)

getTaxaDistribution

public TaxaDistribution getTaxaDistribution(Tag tag)

getAlleles

public java.util.Set<net.maizegenetics.dna.snp.Allele> getAlleles(Tag tag)

getAlleleMap

public com.google.common.collect.Multimap<net.maizegenetics.dna.tag.Tag,net.maizegenetics.dna.snp.Allele> getAlleleMap()

getTagsForSNPPosition

public java.util.Set<net.maizegenetics.dna.tag.Tag> getTagsForSNPPosition(Position position)

getTagsForAllele

public java.util.Set<net.maizegenetics.dna.tag.Tag> getTagsForAllele(Position position,
                                                                     byte allele)

getTagsForAllele

public java.util.Set<net.maizegenetics.dna.tag.Tag> getTagsForAllele(Allele allele)

getAllelesTaxaDistForSNP

public com.google.common.collect.Multimap<net.maizegenetics.dna.snp.Allele,net.maizegenetics.dna.tag.TaxaDistribution> getAllelesTaxaDistForSNP(Position position)

getAllelesTagTaxaDistForSNP

public com.google.common.collect.Multimap<net.maizegenetics.dna.snp.Allele,java.util.Map> getAllelesTagTaxaDistForSNP(Position position)

getAllAllelesTaxaDistForSNP

public java.util.stream.Stream<com.google.common.collect.ImmutableMultimap> getAllAllelesTaxaDistForSNP()

getAllAllelesTaxaDistForSNPEntries

public java.util.stream.Stream<java.util.Map.Entry> getAllAllelesTaxaDistForSNPEntries()

getAllCountsForTagTissue

public Phenotype getAllCountsForTagTissue(Tag tag,
                                          java.lang.String tissue)

getAllCountsForTaxonTissue

public TableReport getAllCountsForTaxonTissue(Taxon taxon,
                                              java.lang.String tissue)

getAllCountsForTissue

public Phenotype getAllCountsForTissue(java.lang.String tissue)

getTags

public java.util.Set<net.maizegenetics.dna.tag.Tag> getTags()

getSNPPositions

public PositionList getSNPPositions()

getSNPPositions

public PositionList getSNPPositions(int minSupportValue)

getSNPPositions

public PositionList getSNPPositions(double minQualityScore)

getTagsForTaxon

public java.util.Set<net.maizegenetics.dna.tag.Tag> getTagsForTaxon(Taxon taxon)

getTagDepth

public java.util.Map<net.maizegenetics.dna.tag.Tag,java.lang.Integer> getTagDepth(Taxon taxon,
                                                                                  Position position)

getTagsWithDepth

public java.util.Map<net.maizegenetics.dna.tag.Tag,java.lang.Integer> getTagsWithDepth(int minimumDepth)

getTagCutPositions

public PositionList getTagCutPositions(boolean onlyBest)

getTagCutPositions

public PositionList getTagCutPositions(Chromosome chromosome,
                                       int firstPosition,
                                       int lastPosition,
                                       boolean onlyBest)

getTagCutPosition

public java.util.Map<net.maizegenetics.dna.tag.Tag,net.maizegenetics.dna.map.Position> getTagCutPosition(java.util.Set<net.maizegenetics.dna.tag.Tag> tagSet)

Get the cut position associated with each tag in a set. Return a map of Tag/Position from which the cut position/strand will be pulled. This is used in debugging with the SNPCutPosTagVerificationPlugin

Returns:

org.jetbrains.dokka.NodeRenderContent@3bdab443: map of Tag/Position

getTagAlignmentApproaches

public java.util.Map<java.lang.String,java.lang.String> getTagAlignmentApproaches()

getCutPositionTagTaxaMap

public java.util.Map<net.maizegenetics.dna.map.Position,java.util.Map> getCutPositionTagTaxaMap(Chromosome chromosome,
                                                                                                int firstPosition,
                                                                                                int lastPosition)

getCutPosForStrandTagTaxaMap

public java.util.Map<net.maizegenetics.dna.map.Position,java.util.Map> getCutPosForStrandTagTaxaMap(Chromosome chromosome,
                                                                                                    int firstPosition,
                                                                                                    int lastPosition,
                                                                                                    boolean direction)

getTagsTaxaMap

public java.util.Map<net.maizegenetics.dna.tag.Tag,net.maizegenetics.dna.tag.TaxaDistribution> getTagsTaxaMap(Position cutPosition)

getSNPPositionsForChromosomes

public PositionList getSNPPositionsForChromosomes(java.lang.Integer startChr,
                                                  java.lang.Integer endChr)

putSNPPositionQS

public void putSNPPositionQS(PositionList qsPL)

getSNPPositionQS

public com.google.common.collect.ListMultimap<java.lang.String,net.maizegenetics.util.Tuple> getSNPPositionQS(com.google.common.collect.HashMultimap<java.lang.String,java.lang.Integer> myMap)

getChromosomesFromCutPositions

public java.util.List<net.maizegenetics.dna.map.Chromosome> getChromosomesFromCutPositions()

clearTagTaxaDistributionData

public void clearTagTaxaDistributionData()

clearAlignmentData

public void clearAlignmentData()

clearDiscoveryData

public void clearDiscoveryData()

clearSNPQualityData

public void clearSNPQualityData()

getAllTagsTaxaMap

public java.util.Map<net.maizegenetics.dna.tag.Tag,net.maizegenetics.dna.tag.TaxaDistribution> getAllTagsTaxaMap()

putAllTissue

public boolean putAllTissue(java.util.ArrayList<java.lang.String> tissues)

getAllTissue

public java.util.Set<java.lang.String> getAllTissue()