| Modifier and Type | Method and Description |
|---|---|
ReferenceRange |
HaplotypeGraph.firstReferenceRange()
Returns the first reference range in this graph.
|
ReferenceRange |
HaplotypeGraph.firstReferenceRange(net.maizegenetics.dna.map.Chromosome chr)
Returns the first reference range for the given chromosome.
|
ReferenceRange |
HaplotypeGraph.lastReferenceRange()
Returns the last reference range in this graph.
|
ReferenceRange |
HaplotypeGraph.lastReferenceRange(net.maizegenetics.dna.map.Chromosome chr)
Returns the last reference range for the given chromosome.
|
ReferenceRange |
HaplotypeNode.referenceRange()
Object containing the range of genomic coordinate values associated with a given HaplotypeNode and other details
associated with that range of values.
|
ReferenceRange |
HaplotypeSequence.referenceRange()
Reference Range in (alternative)reference genome
|
| Modifier and Type | Method and Description |
|---|---|
static TreeMap<ReferenceRange,List<HaplotypeNode>> |
CreateGraphUtils.createHaplotypeNodes(Connection database,
Map<Integer,ReferenceRange> referenceRangeMap,
Map<Integer,net.maizegenetics.taxa.TaxaList> taxaListMap,
String method,
boolean onlyAnchors,
boolean includeVariantContext,
SortedSet<Integer> includeHapids)
Creates lists of HaplotypeNodes organized by reference Range
based on the given method.
|
static TreeMap<ReferenceRange,List<HaplotypeNode>> |
CreateGraphUtils.createHaplotypeNodes(Connection database,
String method,
boolean onlyAnchors,
boolean includeVariantContext,
SortedSet<Integer> includeHapids)
Creates HaplotypeNode Lists with keys as ReferenceRanges.
|
static TreeMap<ReferenceRange,List<HaplotypeNode>> |
CreateGraphUtils.createHaplotypeNodesWithVariants(Connection database,
Set<HaplotypeNode> includeHapNodes)
Creates lists of HaplotypeNodes with variant contexts corresponding to the specified nodes
organized by reference Range.
|
List<ReferenceRange> |
HaplotypeGraph.referenceRangeList()
Returns list of reference ranges for whole graph.
|
static Map<Integer,ReferenceRange> |
CreateGraphUtils.referenceRangeMap(Connection database)
Retrieves all ReferenceRange instances
|
Set<ReferenceRange> |
HaplotypeGraph.referenceRanges()
Returns sorted set of reference ranges for whole graph.
|
static SortedSet<ReferenceRange> |
CreateGraphUtils.referenceRanges(Connection database)
Retrieves all ReferenceRange instances with specified genome interval version name.
|
Stream<ReferenceRange> |
HaplotypeGraph.referenceRangeStream()
Returns stream of reference ranges for entire graph.
|
Stream<ReferenceRange> |
HaplotypeGraph.referenceRangeStream(net.maizegenetics.dna.map.Chromosome chr)
Returns stream of reference ranges for given chromosome.
|
List<ReferenceRange> |
FilterGraphPlugin.refRanges()
Reference range list to remove from graph
|
TreeMap<ReferenceRange,List<HaplotypeNode>> |
HaplotypeGraph.tree(net.maizegenetics.dna.map.Chromosome chr)
Creates a sorted (on keys ReferenceRanges) map to list of HaplotypeNodes for given chromosome.
|
static TreeMap<ReferenceRange,List<HaplotypeNode>> |
CreateGraphUtils.tree(HaplotypeGraph graph) |
| Modifier and Type | Method and Description |
|---|---|
int |
ReferenceRange.compareTo(ReferenceRange o) |
static HaplotypeSequence |
HaplotypeSequence.getInstance(String sequence,
ReferenceRange referenceRange,
double qualityScore,
String seqHash)
Factory method to create HaplotypeSequence This allows a copy of the HaplotypeSequence to be returned instead of
the original mutable object
|
List<HaplotypeNode> |
HaplotypeGraph.nodes(ReferenceRange range)
Returns list of HaplotypeNodes for given ReferenceRange
|
int |
HaplotypeGraph.numberTaxa(ReferenceRange range)
Returns number of taxa represented by given reference range.
|
net.maizegenetics.taxa.TaxaList |
HaplotypeGraph.taxaInRange(ReferenceRange range)
Returns taxa represented by given reference range.
|
| Modifier and Type | Method and Description |
|---|---|
static int |
CreateGraphUtils.addInnerAnchorNodes(TreeMap<ReferenceRange,List<HaplotypeNode>> result,
Connection database,
Map<Integer,ReferenceRange> referenceRangeMap,
Map<Integer,net.maizegenetics.taxa.TaxaList> taxaListMap,
boolean includeVariantContext,
int hapMethodId) |
static int |
CreateGraphUtils.addInnerAnchorNodes(TreeMap<ReferenceRange,List<HaplotypeNode>> result,
Connection database,
Map<Integer,ReferenceRange> referenceRangeMap,
Map<Integer,net.maizegenetics.taxa.TaxaList> taxaListMap,
boolean includeVariantContext,
int hapMethodId) |
static int |
CreateGraphUtils.addMissingSequenceNodes(TreeMap<ReferenceRange,List<HaplotypeNode>> result) |
static void |
CreateGraphUtils.addUnconsolidatedNodes(Connection database,
Map<ReferenceRange,List<HaplotypeNode>> consensusNodes,
Map<Integer,ReferenceRange> referenceRangeMap,
Map<Integer,net.maizegenetics.taxa.TaxaList> taxaListMap,
boolean onlyAnchors)
Adds HaplotypeNodes to the given map for sequences that wasn't consolidated into a consensus sequence.
|
static void |
CreateGraphUtils.addUnconsolidatedNodes(Connection database,
Map<ReferenceRange,List<HaplotypeNode>> consensusNodes,
Map<Integer,ReferenceRange> referenceRangeMap,
Map<Integer,net.maizegenetics.taxa.TaxaList> taxaListMap,
boolean onlyAnchors)
Adds HaplotypeNodes to the given map for sequences that wasn't consolidated into a consensus sequence.
|
static List<HaplotypeEdge> |
CreateGraphUtils.createEdges(TreeMap<ReferenceRange,List<HaplotypeNode>> rangeToNode)
Generates Edges based on HaplotypeNodes.
|
static TreeMap<ReferenceRange,List<HaplotypeNode>> |
CreateGraphUtils.createHaplotypeNodes(Connection database,
Map<Integer,ReferenceRange> referenceRangeMap,
Map<Integer,net.maizegenetics.taxa.TaxaList> taxaListMap,
String method,
boolean onlyAnchors,
boolean includeVariantContext,
SortedSet<Integer> includeHapids)
Creates lists of HaplotypeNodes organized by reference Range
based on the given method.
|
static ReferenceRangeEmissionProbability |
ReferenceRangeEmissionProbability.getInstanceFromHapidCountMap(TreeMap<ReferenceRange,List<HaplotypeNode>> nodes,
Map<Integer,Integer> hapidCountMap,
double probCorrect) |
static ReferenceRangeEmissionProbability |
ReferenceRangeEmissionProbability.getInstanceFromHapidCounts(TreeMap<ReferenceRange,List<HaplotypeNode>> nodes,
com.google.common.collect.Multiset<Integer> hapidCounts,
double probCorrect) |
static ReferenceRangeEmissionProbability |
ReferenceRangeEmissionProbability.getInstanceFromNodeCounts(TreeMap<ReferenceRange,List<HaplotypeNode>> nodes,
com.google.common.collect.Multiset<HaplotypeNode> nodeCounts,
double probCorrect) |
static HaplotypeGraph |
CreateGraphUtils.keepRefRanges(HaplotypeGraph graph,
List<ReferenceRange> ranges)
Creates graph that includes specified reference ranges.
|
ReferenceRangeEmissionProbability.Builder |
ReferenceRangeEmissionProbability.Builder.nodeMap(TreeMap<ReferenceRange,List<HaplotypeNode>> nodeMap) |
FilterGraphPlugin |
FilterGraphPlugin.refRanges(List<ReferenceRange> value)
Set Reference Ranges.
|
static HaplotypeGraph |
CreateGraphUtils.removeRefRanges(HaplotypeGraph graph,
List<ReferenceRange> ranges)
Removes specified reference ranges from graph.
|
static net.maizegenetics.taxa.TaxaList |
CreateGraphUtils.taxaInNodes(TreeMap<ReferenceRange,List<HaplotypeNode>> nodes) |
| Modifier and Type | Method and Description |
|---|---|
static String |
ExtractFastaUtils.extractFastaSequence(List<htsjdk.variant.variantcontext.VariantContext> variants,
ReferenceRange referenceRange)
Method to extract out a fasta sequence given a list of variantContexts
This will fill in Ns whenever we do not have a variant context record for a given position
|
| Modifier and Type | Method and Description |
|---|---|
double[] |
ConvertGBSToSNPs.probabilityOfBeingCorrect(Map<Integer,Integer> hapidCountMap,
TreeMap<ReferenceRange,List<HaplotypeNode>> rangeToNodesMap) |
double[] |
ConvertGBSToSNPs.probabilityOfBeingCorrect(com.google.common.collect.Multiset<Integer> hapidCounts,
TreeMap<ReferenceRange,List<HaplotypeNode>> rangeToNodesMap) |
| Modifier and Type | Method and Description |
|---|---|
static List<List<htsjdk.variant.variantcontext.VariantContext>> |
FillIndelsIntoConsensus.addInIndels(ReferenceRange range,
net.maizegenetics.dna.map.GenomeSequence refSequence,
List<List<htsjdk.variant.variantcontext.VariantContext>> consensusSequences,
List<List<htsjdk.variant.variantcontext.VariantContext>> rawConsensusWithIndels,
int minComparableIndels,
FillIndelsIntoConsensus.INDEL_MERGE_RULE mergeRule)
Method to add in the indels which were removed for the merging process.
|
static net.maizegenetics.dna.snp.GenotypeTable |
MergeGVCFUtils.createGenotypeTableFromGVCFs(ReferenceRange refRange,
com.google.common.collect.Multimap<net.maizegenetics.taxa.Taxon,htsjdk.variant.variantcontext.VariantContext> taxonToVariantListMap,
net.maizegenetics.dna.map.GenomeSequence referenceSequence)
This method takes all the VariantContexts for all of the Taxon we need in our new GenotypeTable and will create a correctly encoded GenotypeTable
|
static net.maizegenetics.dna.snp.GenotypeTable |
MergeGVCFUtils.createGenotypeTableFromHaplotypeNodes(ReferenceRange refRange,
List<HaplotypeNode> nodesWithVariantContexts,
net.maizegenetics.dna.map.GenomeSequence referenceSequence)
Method to make a genotypeTable from a list of Haplotype Nodes.
|
| Modifier and Type | Method and Description |
|---|---|
Map<Integer,ReferenceRange> |
Mummer4DoonerBZStats.getAnchorFromIntervalsFile(String intervalsFile,
String chrom) |
static Map<Integer,ReferenceRange> |
AssemblyHaplotypesPlugin.referenceRangeForChromMap(Connection database,
String chrom)
Find all reference ranges for a particular chromosome
|
static Map<Integer,ReferenceRange> |
Mummer4DoonerBZStats.refRangesForChrom(Connection dbConn,
String chrom) |
Map<Integer,ReferenceRange> |
MummerAnalysisMetricsPlugin.refRangesForChrom(Connection dbConn,
String chrom) |
| Modifier and Type | Method and Description |
|---|---|
static Map<Integer,AnchorDataPHG> |
AssemblyHaplotypesPlugin.createAndLoadAssemblyData(Map<Integer,ReferenceRange> idByRangeMap,
List<htsjdk.variant.variantcontext.VariantContext> fullVC,
net.maizegenetics.dna.map.GenomeSequence refSequence,
Connection dbConn,
String assemblyName,
String outputDir,
String chrom,
int clusterSize)
Create the assembly genotype/haplotype data and load to the PHG database
|
static com.google.common.collect.RangeSet<net.maizegenetics.dna.map.Position> |
AssemblyHaplotypesPlugin.getAnchorRangeSet(Map<Integer,ReferenceRange> anchorEntries)
Create a RangeSet from a map of ranges
|
static Map<Integer,com.google.common.collect.Range<Integer>> |
Mummer4DoonerBZStats.getRangesForChrom(Map<Integer,ReferenceRange> refRangeMap,
net.maizegenetics.dna.map.Chromosome chrom,
DBLoadingUtils.AnchorType anchorType) |
static com.google.common.collect.RangeSet<Integer> |
MummerAnalysisMetricsPlugin.getRangesForChrom(Map<Integer,ReferenceRange> refRangeMap,
net.maizegenetics.dna.map.Chromosome chrom,
DBLoadingUtils.AnchorType anchorType) |
static List<htsjdk.variant.variantcontext.VariantContext> |
AssemblyProcessingUtils.splitRefRange(List<htsjdk.variant.variantcontext.VariantContext> variantContexts,
Map<Integer,ReferenceRange> anchorMapping,
net.maizegenetics.dna.map.GenomeSequence refSequence)
Method to split up the reference range by anchor mappings.
|
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