net.maizegenetics.dna.tag

Class RepGenSQLite

net.maizegenetics.dna.tag.RepGenSQLite

All Implemented Interfaces:

RepGenData, RepGenDataWriter

public class RepGenSQLite
implements RepGenDataWriter

Field Detail

snpPosToIDMap

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

Constructor Detail

RepGenSQLite

public RepGenSQLite(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,
                         java.util.Map<net.maizegenetics.dna.tag.Tag,net.maizegenetics.util.Tuple> tagInstanceAverageQS)

putAllRefTag

public boolean putAllRefTag(com.google.common.collect.Multimap<net.maizegenetics.dna.tag.Tag,net.maizegenetics.dna.map.Position> refTagPositionMap,
                            java.lang.String refGenome)

putAllNamesTag

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

putTaxaList

public void putTaxaList(TaxaList taxaList)

putTaxaDistribution

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

putTagTagAlignments

public void putTagTagAlignments(com.google.common.collect.Multimap<net.maizegenetics.dna.tag.Tag,net.maizegenetics.analysis.gbs.repgen.AlignmentInfo> tagAlignInfoMap)

putTagRefTagAlignments

public void putTagRefTagAlignments(com.google.common.collect.Multimap<net.maizegenetics.dna.tag.Tag,net.maizegenetics.analysis.gbs.repgen.AlignmentInfo> tagAlignInfoMap,
                                   java.lang.String refGenome)

putRefRefAlignments

public void putRefRefAlignments(com.google.common.collect.Multimap<net.maizegenetics.analysis.gbs.repgen.RefTagData,net.maizegenetics.analysis.gbs.repgen.AlignmentInfo> tagAlignInfoMap,
                                java.lang.String refGenome)

putRefTagMapping

public void putRefTagMapping(com.google.common.collect.Multimap<net.maizegenetics.dna.tag.Tag,net.maizegenetics.dna.map.Position> refTagPositionMap,
                             java.lang.String refGenome)

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)

addReferenceGenome

public void addReferenceGenome(java.lang.String name)

addMappingApproach

public void addMappingApproach(java.lang.String name)

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()

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)

getAllAllelesTaxaDistForSNP

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

getAllAllelesTaxaDistForSNPEntries

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

getTags

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

getRefTags

public java.util.Set<net.maizegenetics.analysis.gbs.repgen.RefTagData> getRefTags()

getPhysicalMapPositions

public PositionList getPhysicalMapPositions()

getPhysicalMapPositions

public PositionList getPhysicalMapPositions(Chromosome chromosome,
                                            int firstPosition,
                                            int lastPosition)

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(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@58a0b125: 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)

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()

getTagCutPositions

public PositionList getTagCutPositions(boolean onlyBest)

putAllelePairs

public void putAllelePairs(com.google.common.collect.Multimap<net.maizegenetics.dna.tag.Tag,net.maizegenetics.util.Tuple> tagTagAlignMap)

getAllelesTagTaxaDistForSNP

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

getTagAlignmentsForTags

public com.google.common.collect.Multimap<net.maizegenetics.dna.tag.Tag,net.maizegenetics.analysis.gbs.repgen.AlignmentInfo> getTagAlignmentsForTags(java.util.List<net.maizegenetics.dna.tag.Tag> tags,
                                                                                                                                                     int minscore)

getAllNonRefTagAlignments

public com.google.common.collect.Multimap<net.maizegenetics.dna.tag.Tag,net.maizegenetics.analysis.gbs.repgen.AlignmentInfo> getAllNonRefTagAlignments(int minscore)

getRefAlignmentsForRefTags

public com.google.common.collect.Multimap<net.maizegenetics.analysis.gbs.repgen.RefTagData,net.maizegenetics.analysis.gbs.repgen.AlignmentInfo> getRefAlignmentsForRefTags(java.util.List<net.maizegenetics.analysis.gbs.repgen.RefTagData> refTags,
                                                                                                                                                                           int minscore)

getAllRefTagAlignments

public com.google.common.collect.Multimap<net.maizegenetics.analysis.gbs.repgen.RefTagData,net.maizegenetics.analysis.gbs.repgen.AlignmentInfo> getAllRefTagAlignments(int minscore)

getRefAlignmentsForTags

public com.google.common.collect.Multimap<net.maizegenetics.dna.tag.Tag,net.maizegenetics.analysis.gbs.repgen.AlignmentInfo> getRefAlignmentsForTags(java.util.List<net.maizegenetics.dna.tag.Tag> tags,
                                                                                                                                                     int minscore)

getTagAlignmentsForRefTag

public com.google.common.collect.Multimap<net.maizegenetics.dna.tag.Tag,net.maizegenetics.analysis.gbs.repgen.AlignmentInfo> getTagAlignmentsForRefTag(RefTagData refTag,
                                                                                                                                                       int minscore)

putTagTagCorrelationMatrix

public void putTagTagCorrelationMatrix(com.google.common.collect.Multimap<net.maizegenetics.dna.tag.Tag,net.maizegenetics.analysis.gbs.repgen.TagCorrelationInfo> tagCorrelationMap)

getCorrelationsForTags

public com.google.common.collect.Multimap<net.maizegenetics.dna.tag.Tag,net.maizegenetics.analysis.gbs.repgen.TagCorrelationInfo> getCorrelationsForTags(java.util.List<net.maizegenetics.dna.tag.Tag> tags)