| Package | Description |
|---|---|
| net.maizegenetics.pangenome.db_loading | |
| net.maizegenetics.pangenome.processAssemblyGenomes |
| Modifier and Type | Method and Description |
|---|---|
int |
AnchorDataPHG.compareTo(AnchorDataPHG other) |
| Modifier and Type | Method and Description |
|---|---|
boolean |
PHGDataWriter.putAllAnchors(List<AnchorDataPHG> anchorData,
String refGroupMethod)
Stores chrom, start pos, end pos to referenece_ranges table
isFocus identifies focus intervals from the user's bed file
|
boolean |
PHGdbAccess.putAllAnchors(List<AnchorDataPHG> adata,
String refGroupMethod) |
boolean |
PHGDataWriter.putAssemblyInterAnchorSequences(String line_name,
int hapNumber,
String method,
com.google.common.collect.Multimap<Integer,AnchorDataPHG> anchorSequences)
Adds inter-anchor sequences for the specified assembly to the anchor_sequences
and anchor_haplotypes table.
|
boolean |
PHGdbAccess.putAssemblyInterAnchorSequences(String line_name,
int hapNumber,
String method,
com.google.common.collect.Multimap<Integer,AnchorDataPHG> anchorSequences) |
void |
PHGDataWriter.putConsensusSequences(com.google.common.collect.Multimap<net.maizegenetics.dna.map.Position,net.maizegenetics.util.Tuple<AnchorDataPHG,List<String>>> consensusMap,
int methodId)
This method takes a map of consensus data, finds the anchorIds based on Position,
finds the hapids of the taxa whose sequences at the specified anchorID map
to the consensus.
|
void |
PHGdbAccess.putConsensusSequences(com.google.common.collect.Multimap<net.maizegenetics.dna.map.Position,net.maizegenetics.util.Tuple<AnchorDataPHG,List<String>>> consensusMap,
int method_id) |
void |
PHGDataWriter.putHaplotypesForGamete(int gamete_grp_id,
String method,
Map<Integer,AnchorDataPHG> anchorSequences)
Stores gamete sequence data to the haplotypes table
This method associates all entries with the single gamete_grp_id which is passed.
|
void |
PHGdbAccess.putHaplotypesForGamete(int gamete_grp_id,
String method,
Map<Integer,AnchorDataPHG> anchorSequences) |
void |
PHGDataWriter.putHaplotypesForMultipleGroups(com.google.common.collect.Multimap<net.maizegenetics.dna.map.Position,net.maizegenetics.util.Tuple<AnchorDataPHG,String>> mapWithGroupHash,
int method_id)
Add data to the haplotypes table.
|
void |
PHGdbAccess.putHaplotypesForMultipleGroups(com.google.common.collect.Multimap<net.maizegenetics.dna.map.Position,net.maizegenetics.util.Tuple<AnchorDataPHG,String>> mapWithGroupHash,
int method_id) |
boolean |
PHGDataWriter.putRefAnchorData(String line_name,
int hapnumber,
List<AnchorDataPHG> adata,
String hapMethod,
String refGroupMethod,
String gvcf,
String variant_list)
Fills in the haplotypes table
for the reference ranges.
|
boolean |
PHGdbAccess.putRefAnchorData(String line_name,
int hapnumber,
List<AnchorDataPHG> anchorData,
String hapMethod,
String refGrpMethod,
String gvcf,
String variant_list) |
| 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
|
| Modifier and Type | Method and Description |
|---|---|
static void |
AssemblyHaplotypesPlugin.loadAssemblyDataToDB(int gamete_grp_id,
String method,
Connection dbConn,
Map<Integer,AnchorDataPHG> anchorSequences)
Load the assembly haplotype data to the database
|
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