net.maizegenetics.pangenome.db_loading

Interface PHGDataWriter

All Superinterfaces:

PHGData

All Known Implementing Classes:

PHGdbAccess

public interface PHGDataWriter
extends PHGData

Author:

lcj34

Method Summary

Modifier and Type	Method and Description
int	createRefRangeGroup(String method) Creates an entry in the ref_range_groups table using method_id associated with the name indicated via the method parameter.
boolean	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	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.
void	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.
boolean	putGameteGroupAndHaplotypes(List<String> gametes) Takes a list of gametes and stores to the gamete_groups and gamete_haplotypes table Skips if this grouping already exists
boolean	putGenoAndHaploTypeData(GenoHaploData ghData) Stores required data to the genotypes and haplotypes tables for each entry on the list.
void	putHaplotypeCountsData(String method, String methodDetails, String taxonName, String fastqFile, byte[] counts) This method adds data to the haplotype_counts table.
void	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	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.
int	putMethod(String name, DBLoadingUtils.MethodType type, String description) Adds a method, its type and its description to the anchor_methods table These are used to identify how sequences were created,how the were combined into consensus sequences, how haplotype counts were scores, how paths through the graph were create or how an edge was created.
void	putPathsData(String method, String methodDetails, com.google.common.collect.Multimap<Integer,HaplotypeNode> paths) This method stores paths data to the paths table.
boolean	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.
void	putRefRangeRefRangeGroups(int group_method_id, List<Integer> refRangeList) Takes a method id and a list of reference ranges.

Methods inherited from interface net.maizegenetics.pangenome.db_loading.PHGData

getChromNamesForHaplotype, getGameteGroupIDFromTaxaList, getGenoidFromLine, getHapCountsIDAndDataForVersionMethod, getHapCountsIDAndPathsForMethod, getHapidForGenoidHapNumber, getHapidHapNumberLineNamesForLines, getHapidMapFromLinenameHapNumber, getHapidsForGenoid, getHaplotypeIDFromFastaIDLine, getIntervalRangesWithIDForChrom, getLineNameHapNumberFromHapid, getMethodIdFromName, getRefRangeIDFromString

Method Detail

putAllAnchors

boolean 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

Parameters:

anchorData -

refGroupMethod - name of method used for creating this ref_range_group

Returns:

putGenoAndHaploTypeData

boolean putGenoAndHaploTypeData(GenoHaploData ghData)

Stores required data to the genotypes and haplotypes tables for each entry on the list.

Parameters:

ghData -

anchor_verion - Distinguishes pre-anchor cooridinates from trimmed anchor coordinates

Returns:

putRefAnchorData

boolean 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.

Parameters:

line_name -

hapnumber -

hapMethod - Name of method used to create anchors. Maps to method table for id.

adata - Anchor data, including chrom, start/end positions

refGroupMethod - Name of method used to create the ref_range_group

gvcf - String - name of gvcf file

variant_list - String - name of file containing list of variants

Returns:

putMethod

int putMethod(String name,
              DBLoadingUtils.MethodType type,
              String description)

Adds a method, its type and its description to the anchor_methods table These are used to identify how sequences were created,how the were combined into consensus sequences, how haplotype counts were scores, how paths through the graph were create or how an edge was created. The "type" field identifies the table to which the method belongs.

Parameters:

name -

type -

description -

Returns:

the methodId from the methods table

putAssemblyInterAnchorSequences

boolean 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. This method takes a multi-map as assembly. Inter-anchors that do not map to a reference inter-anchor are all given the anchorid 0.

Parameters:

line_name -

hapNumber -

method -

anchorSequences -

Returns:

putConsensusSequences

void 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. Adds the gamete_group and sequence data to the haplotpes table ; adds entries to gamete_groups and gamete_hapltoypes. *

Parameters:

consensusMap - Multimap>

methodId - method used for collapsing anchors

putGameteGroupAndHaplotypes

boolean putGameteGroupAndHaplotypes(List<String> gametes)

Takes a list of gametes and stores to the gamete_groups and gamete_haplotypes table Skips if this grouping already exists

Parameters:

gametes - list consisting of taxa/gamete number in the form taxaName_gameteNumber

Returns:

true if successful

putHaplotypesForGamete

void 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. It is used when loading genome_interval sequences or haplotype sequences for a single line.

Parameters:

gamete_grp_id -

method -

gvcf -

variant_list -

anchorSequences -

putHaplotypesForMultipleGroups

void 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. Entries on the map are for different gamete groups. The key is a Position item identifying the genome_interval id The value is a Tuple consisting of (x) AnchorDataPHG object with sequence, gvcf, etc; and (y) a List of taxa represented by the ANchorDataPHG sequence

Parameters:

mapWithGroupHash -

method_id - Id in the methods table for this group of sequences

putHaplotypeCountsData

void putHaplotypeCountsData(String method,
                            String methodDetails,
                            String taxonName,
                            String fastqFile,
                            byte[] counts)

This method adds data to the haplotype_counts table. The "data" is a Snappy compressed byte buffer of a 3xn array, found in parameter "counts" To see how this data is stored, examine DBLoadingUtils.encodeHapCountsArrayFromFile(), DBLoadingUtils.encodeHapCountsArrayFromMultiset() and DBLoadingUtils.decodeHapCountsArray()

Parameters:

method -

methodDetails -

taxonName -

fastqFile -

counts -

putPathsData

void putPathsData(String method,
                  String methodDetails,
                  com.google.common.collect.Multimap<Integer,HaplotypeNode> paths)

This method stores paths data to the paths table.

Parameters:

method - - Method Name for Path detemination process

methodDetails - Details of how these paths were created

paths - Compressed byte array of HaplotypeNode ids

createRefRangeGroup

int createRefRangeGroup(String method)

Creates an entry in the ref_range_groups table using method_id associated with the name indicated via the method parameter.

Parameters:

method -

Returns:

putRefRangeRefRangeGroups

void putRefRangeRefRangeGroups(int group_method_id,
                               List<Integer> refRangeList)

Takes a method id and a list of reference ranges. Populates the ref_range_ref_range_group table.

Parameters:

group_method_id -

refRangeList -