net.maizegenetics.dna.tag

Interface RepGenData

All Known Subinterfaces:

RepGenDataWriter

All Known Implementing Classes:

RepGenSQLite

public RepGenData

Method Detail

getTaxaDistribution

TaxaDistribution getTaxaDistribution(Tag tag)

Returns the TaxaDistribution for a given taxa. If distribution data is not available, null is returned.

getAlleles

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

Provides all SNP allele calls associated with a given tag.

Parameters:

tag - used for query

Returns:

org.jetbrains.dokka.NodeRenderContent@d266ae7: Map of position with allele state. The positions are the positions of the actual SNP (not the start of the tag). The Byte value is defined by class NucleotideAlignmentConstants. If no allele are available for a tag, the map will be empty.

getAlleleMap

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

Provides an iterator that goes through all tags with non-empty alleleMaps.

Returns:

org.jetbrains.dokka.NodeRenderContent@5b2c1f: an iterator of alleleMaps (Map of position with allele state. The positions are the positions of the actual SNP (not the start of the tag). The Byte value is defined by class NucleotideAlignmentConstants.)

getTagsForAllele

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

Return all tags that call a particular SNP position allele. Empty list is returned if there are no tags.

getTagsForAllele

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

Return all tags that call a particular SNP position allele. Empty list is returned if there are no tags.

getTags

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

Set of all tags

getTagsNameMap

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

Map of all tags with associated names

getSNPPositions

PositionList getSNPPositions()

Create the unique list of SNPs (variants) based on all alleles.

Returns:

org.jetbrains.dokka.NodeRenderContent@77900a3e: PositionList of all SNPs

getSNPPositions

PositionList getSNPPositions(int minSupportValue)

Create the unique list of SNPs (variants) based on all alleles. Only alleles with support values greater than the minSupportValue are considered.

Returns:

org.jetbrains.dokka.NodeRenderContent@7041f70f: PositionList of all SNPs

getSNPPositions

PositionList getSNPPositions(double minQualityScore)

Create the unique list of SNPs (variants) based on all alleles. Only positions with minimum quality score equal to or greater than the u are considered.

Returns:

org.jetbrains.dokka.NodeRenderContent@4e8ecab2: PositionList of all SNPs

getSNPPositionsForChromosomes

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

Get SNPs for specified chromosomes

Returns:

org.jetbrains.dokka.NodeRenderContent@17ec2ca8: PostionList of SNP positions for the requested chromosomes

getTagsForTaxon

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

Returns the list of tags present of a taxon. Note this could be a very compute intensive request.

getTagDepth

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

getTagsWithDepth

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

getTagCutPositions

PositionList getTagCutPositions(boolean onlyBest)

Get all of the genomic cut positions associated with all tags. Positions in the position list are annotated with cigarAlignment, isBest, alignmentApproach, and supportValue.

Returns:

org.jetbrains.dokka.NodeRenderContent@60da1591: iterator of annotated positions

getTagCutPositions

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

Get the unique list of position that tags to for a specific chromosome within a range.

Parameters:

chromosome - chromosome

firstPosition - first physical position in genome (value <0 will return physical >=0)

lastPosition - inclusive last physical position (value <0 will assume Integer.MAX)

onlyBest - only return positions flagged as best

Returns:

org.jetbrains.dokka.NodeRenderContent@1fdc7f0a: List of positions

getTagCutPosition

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

Get the cut position associated with a list of tags. Return a map of Tag/CutPosition The Position object is returned to facilitate grabbing both physical position and strand information.

Returns:

org.jetbrains.dokka.NodeRenderContent@273ffd19: map of tag, Tuple

getTagAlignmentApproaches

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

getCutPositionTagTaxaMap

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

Map of positions and with associated map of Tags and their taxa distribution and their alignment direction. Warning: This can be a very large data structure for entire chromosomes. Only the best positions are returned.

Parameters:

chromosome - chromosome

firstPosition - first physical position in genome (value <0 will return physical >=0)

lastPosition - inclusive last physical position (value <0 will assume Integer.MAX)

Returns:

org.jetbrains.dokka.NodeRenderContent@51c01c3a: Map of maps for position (key) to Map of Tag(key) to the Tuple(Direction,TaxaDistribution)(Value)

getCutPosForStrandTagTaxaMap

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

For a given snp position, Returns a Map of Allele with its associated Tag/TaxaDistribution Differs from getCutPositionTagTaxaMap() in that it now specifies on which strand the returned tags must appear.

Returns:

org.jetbrains.dokka.NodeRenderContent@6186fd0e: Map or null if not available.

getTaxaList

TaxaList getTaxaList()

Returns the taxa list associated with taxa distribution

Returns:

org.jetbrains.dokka.NodeRenderContent@1d5efa1b: TaxaList or null if not available.

getSNPPositionQS

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)

For a given map of chromosome/posiiton, Returns a map of chromsome (string) and Tuple (position,qualityScore)

Returns:

org.jetbrains.dokka.NodeRenderContent@45510b9c: Map or null if not available.

getAllelesTagTaxaDistForSNP

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

For a given snp position, Returns a Map of Allele with its associated Tag/TaxaDistribution

Returns:

org.jetbrains.dokka.NodeRenderContent@1421eec0: Map or null if not available.

getChromosomesFromCutPositions

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

Return all chromosomes stored in database. Returns a list of distinct chromsome objects from the cutPosition table

Returns:

org.jetbrains.dokka.NodeRenderContent@42190fc7: List or null if none found

getAllTagsTaxaMap

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

Return all tag/taxadistribution stored in database. Returns a Hashmap of tag.taxadistributions

Returns:

org.jetbrains.dokka.NodeRenderContent@28fdabbd: Map - map is empty if db table is empty

getPhysicalMapPositions

PositionList getPhysicalMapPositions()

Get all of the physical map positions associated with the ref tags.

Returns:

org.jetbrains.dokka.NodeRenderContent@653d48d5: iterator of annotated positions

getPhysicalMapPositions

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

Get the unique list of positions for ref tags for a specific chromosome within a range.

Parameters:

chromosome - chromosome

firstPosition - first physical position in genome (value <0 will return physical >=0)

lastPosition - inclusive last physical position (value <0 will assume Integer.MAX)

Returns:

org.jetbrains.dokka.NodeRenderContent@7e71ed5c: List of positions

getRefTags

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

Set of all reference tags

getTagAlignmentsForTags

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)

Method returns a map of all tag (non-ref) alignments for specified non-ref tags. All tags on the list must be non-ref tags as the tagID is pulled from the tagTagIDMap.

Returns:

org.jetbrains.dokka.NodeRenderContent@749ca262:

getRefAlignmentsForTags

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)

Map of all reftag alignments for specified non-ref tags. All tags on the list must be non-ref tags as the tagID is pulled from the tagTagIDMap.

Parameters:

tags - list of tags for which we want the ref tag alignment

minscore - minimum score value for alignment to be included

Returns:

org.jetbrains.dokka.NodeRenderContent@31f94f0f:

getTagAlignmentsForRefTag

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

Map of all non-reftag alignments for specified ref tag.

Parameters:

refTag - A ref tag for which we want the non-ref tag alignment

minscore - minimum score value for alignment to be included

Returns:

org.jetbrains.dokka.NodeRenderContent@3e8dc205:

getAllNonRefTagAlignments

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

Map of all non-ref tags and their alignments This method calls getTagAlignmentsForTags(). All tag-tag alignments are return

Parameters:

minscore - the minimum score required to pull the alignment minscore=0 means get them all

Returns:

org.jetbrains.dokka.NodeRenderContent@4fe7c385:

getAllRefTagAlignments

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

Map of all alignments for reference tags This returns reftag to reftag alignments.

Parameters:

minscore - the minimum score required to pull the alignment

Returns:

org.jetbrains.dokka.NodeRenderContent@5ef9e7a9:

getRefAlignmentsForRefTags

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)

Map of all alignments for specified ref tags having minimum specified score. minscore = 0 means get all tags. This returns refTag to refTag alignments from the reftag_reftag_Alignments table. It does not include refTag to non-refTag alignments.

Parameters:

minscore - the minimum score required to pull the alignment

Returns:

org.jetbrains.dokka.NodeRenderContent@25035a4e:

getCorrelationsForTags

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)

Grab correlations for specified tags