net.maizegenetics.dna.tag

Interface RepGenDataWriter

All Superinterfaces:

RepGenData

All Known Implementing Classes:

RepGenSQLite

public RepGenDataWriter
extends RepGenData

Method Detail

putAllTag

boolean putAllTag(java.util.Set<net.maizegenetics.dna.tag.Tag> tags,
                  java.util.Map<net.maizegenetics.dna.tag.Tag,net.maizegenetics.util.Tuple> tagInstanceAverageQS)

Add a tag to list of known tags

Parameters:

tags -

tagInstanceAverageQS - map showing number of tags, and average quality score for each tag

Returns:

org.jetbrains.dokka.NodeRenderContent@1c409a86: true if this set did not already contain the specified element

putAllNamesTag

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

Add a tag to list of known tags with their associated names (good for named contigs)

Parameters:

tagNameMap -

Returns:

org.jetbrains.dokka.NodeRenderContent@3cd10ca6: true if this set did not already contain the specified element

putAllRefTag

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

Add a reference tag to list of known reference tags

Returns:

org.jetbrains.dokka.NodeRenderContent@5e8071d2: true if this set did not already contain the specified element

putTaxaDistribution

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

Associates a map full of the specified Tag (key) with the specified TaxaDistribution (value). If there was a prior association is it replaced, as all pairs are unique.

putRefTagMapping

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

Associates the specified Reference Tag with the specified site Position (value).

Parameters:

tagAnnotatedPositionMap - Map of specific tag with chrom/positions specified.

putTagTagAlignments

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

Stores the Smith Waterman score from2 tag alignments. tag2 chrom/pos comes from the AlignmentInfo object. tag1 chrom/pos are separate parameters

Parameters:

tagAlignInfoMap - Map of specific tag to tag2 alignment data

putTagRefTagAlignments

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

Stores the Smith Waterman score from2 tag alignments. tag2 chrom/pos comes from the AlignmentInfo object. tag1 chrom/pos are separate parameters

Parameters:

tagAlignInfoMap - Map of specific tag to tag2 alignment data

putRefRefAlignments

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

Adds entries to the tagAlignments table for ref-ref alignments

Parameters:

tagAlignInfoMap - holds alignment info for each reftag-reftag pair

refGenome - name of the reference genome

Throws:

SQLException

setTagAlignmentBest

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

putTagAlleles

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

putTagAlignmentApproach

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

putTaxaList

void putTaxaList(TaxaList taxaList)

putSNPPositionQS

void putSNPPositionQS(PositionList qsPosL)

Stores a quality position in the snpposition table for each chromosome/position

clearTagTaxaDistributionData

void clearTagTaxaDistributionData()

Removes all data from the tagtaxadistribution table. This should be called from GBSSeqToTagDBPlugin when a user requests an "append" option (ie, db exists, and user opted NOT to clear it). AFter we grab the existing data it is cleared. It will be re-entered when GBSSeqToTagDBPlugin completes.

clearAlignmentData

void clearAlignmentData()

Removes all data from the DB that was added from SAMToGBSDBPlugin call. The tables cleared are CutPosition and TagCutPosition

clearDiscoveryData

void clearDiscoveryData()

Removes all data from the DB that was added from the DiscoverySNPCallerPluginV2 The tables cleared are Allele, TagAllele and SNPPosition

clearSNPQualityData

void clearSNPQualityData()

Removes all data from the snpQuality table

addMappingApproach

void addMappingApproach(java.lang.String name)

Adds a mapping approach strategy to the mappingApproach table

Parameters:

name -

addReferenceGenome

void addReferenceGenome(java.lang.String refGenome)

Adds a mapping approach strategy to the mappingApproach table

Throws:

SQLException

putAllelePairs

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

Adds entries to the allelepair table

Throws:

SQLExceptionƒ

putTagTagCorrelationMatrix

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

Adds entries to the tagCorrelations table for tag-tag correlation data

Parameters:

tagCorrelationMap - holds correltaions info for each tag/taxa-depth to tag/taxa-depth vector pair

Throws:

SQLException