net.maizegenetics.dna.tag

Interface TagDataWriter

All Superinterfaces:

TagData

All Known Implementing Classes:

TagDataSQLite

public TagDataWriter
extends TagData

Defines writer to modify the GBS tag data store

Method Detail

putAllTag

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

Add a tag to list of known tags

Parameters:

tags -

Returns:

org.jetbrains.dokka.NodeRenderContent@1f0422ee: 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@648b4c73: 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.

putTagAlignments

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

Associates the specified Tag (key) with the specified cut site Position (value). Multiple associations are allowed, as Tags can map to multiple locations. Each tag should only have one best annotation.

Parameters:

tagAnnotatedPositionMap - Map of specific tag with Annotated Position of the tag cut site. Annotations should be cigarAlignment, isBest, alignmentApproach, forward, and supportValue

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

putAllTissue

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

Adds list of tissues to the tissue table

Parameters:

masterTissueList -

Returns:

org.jetbrains.dokka.NodeRenderContent@2b7a1169:

putTaxaTissueDistribution

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

Set distribution of taxa/tissue for each tag

Parameters:

taxon -

tags -

counts -

Returns:

org.jetbrains.dokka.NodeRenderContent@2d00302b: