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- All Implemented Interfaces:
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java.lang.AutoCloseable
,net.maizegenetics.pangenome.db_loading.PHGData
,net.maizegenetics.pangenome.db_loading.PHGDataWriter
public class PHGdbAccess implements PHGDataWriter, AutoCloseable
Access methods for postgres or SQL PHG dbs. WHen making changes, or adding new methods, test the SQL statements in both PostgreSQL and SQL to ensure compatibility.
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Constructor Summary
Constructors Constructor Description PHGdbAccess(Connection dbConnection)
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Method Summary
Modifier and Type Method Description void
updateReadMappingHash()
This prompts a call to private method loadReadMappingHash() to update this hash table int
getRefRangeIDFromString(String refData)
Returns reference range id int
getHaplotypeIDFromFastaIDLine(String idLine, String methodName)
Returns the haplotype_id from the haplotypes table based on the gamete_grp_id (calculated from the taxa list), the ref_range_id (calculated from the ref coordinates part of the idline) and the method. int
getMethodIdFromName(String method_name)
Returns method_id given a method name. Map<String, String>
getMethodDescriptionFromName(String method_name)
Method queries the db methods table for the description field given a methods name int
getGameteGroupIDFromTaxaList(List<String> gametes)
Takes a list of taxa and returns the corresponding gamete_group_id or 0 int
getGenoidFromLine(String line_name)
Return genoid List<Integer>
getGenoidsForTaxa(List<String> taxa)
int
getGenomeFileIdFromGenoid(int genoid)
Gets the id from the genome_file_data table based on the genoid . int
getGenomeFileIdFromGenoidAndFile(int genoid, String file)
Gets the id from the genome_file_data table based on the genoid and a filename Pair<Integer, String>
getGenomeFileHashFromGenoidandFile(int genoid, String file)
Given a genoid and a file name, return the hash value and id for that entry in the genome_file_data table. int
getHapidForGenoidHapNumber(int genoid, int hap_number)
Returns hapid for given line name and hap_number List<Integer>
getHapidsForGenoid(int genoid)
Returns list of hapids for a given line name Tuple<String, Integer>
getLineNameHapNumberFromHapid(int gameteid)
Method to retrieve both a line name and the hap number given a hapid. Map<Integer, String>
getHapidHapNumberLineNamesForLines(List<String> lineNames)
Retrieves line name and hapnumber, and returns them with the hapid. RangeMap<Position, Integer>
getIntervalRangesWithIDForChrom(String chrom)
Returns sorted treeRangeMap of Positions for specified chromosome List<String>
getChromNamesForHaplotype(String line_name, int hap_number, String version)
Method grabs a list of distinct chromosome names for a genome_interval version Map<String, Integer>
getHapidMapFromLinenameHapNumber()
Returns a map of created from the genotypes and haplotypes table. Map<Integer, Array<byte>>
getHapCountsIDAndPathsForMethod(String method)
THis method pulls the haplotype_counts_id and corresponding path for all entries in the paths table with the specified method. Map<Integer, Tuple<String, Array<byte>>>
getHapCountsIDAndDataForVersionMethod(String method)
This method pulls the haplotype_counts_id with corresponding genotypes line name and data for all DB entries based on the supplied method HashSet<String>
getTaxaForPathMethod(String method_name)
Method to get a list of all genoid line_names that have paths for method = method_name. Map<String, Array<byte>>
getTaxonPathsForMethod(String method_name)
Returns a map of taxon to paths for that taxon from the paths table for a specified method name. int
getReadMappingId(String line_name, String method_name, String file_group_name)
Method uses line_name, method_name and file_Group_name to fetch a read_mapping_id. List<Integer>
getHaplotypeList(int haplist_id)
Given a haplotype_list_id, query the haplotype_list table and return a list of haplotypes stored for that ID, or an empty list if there were none. Pair<Array<byte>, Integer>
getReadMappingsForId(int readMappingId)
Method to get the Read Mapping data from the DB using the read_mapping_id. List<Integer>
getReadMappingIdsForTaxaMethod(List<String> taxaList, String method)
This method takes a list of taxa and a method name. List<Integer>
getPathIdsForReadMappingIds(List<Integer> readMappingIds)
Returns path_ids from the read_mapping_paths table associated with the list of read_mapping_ids provided. List<ReadMappingDBRecord>
getReadMappingsForMethod(String methodName)
Method to get the mapping ids by method boolean
isFileGroupNew(String taxon, String fileGroupName, String methodName)
Method to check to see if a given taxon and fileGroup are already in the readMapping table of the DB. List<Integer>
getRefRangesForMethod(String methodName)
Method to return all reference ranges associated with a specified method name Map<String, List<List<Integer>>>
getPathsForTaxonMethod(List<String> taxon, String method_name)
Method takes a list of taxa and a method name and returns the paths (if populated in the paths table) stored for each taxon/method pair. List<String>
getDbTaxaNames()
Gets a list of the taxa currently in the database. int
getTaxaGroupIDFromName(String group_name)
Returns taxa_grp_id given a taxa group name. List<String>
getTaxaForTaxaGroup(String group_name)
Get the taxa that make up the specified taxa group List<String>
getAllTaxaGroupNames()
Returns a list of all taxa group names from the taxa_groups table int
putMethod(String name, DBLoadingUtils.MethodType type, Map<String, String> descriptionMap)
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. 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
putAllAnchors(List<AnchorDataPHG> adata, int refGroupMethodID)
Stores chrom, start pos, end pos to referenece_ranges table isFocus identifies focus intervals from the user's bed file void
putRefRangeRefRangeMethod(int method_id, List<Integer> refRangeIDList)
Takes a method id and a list of reference ranges. boolean
putGenoAndHaploTypeData(GenoHaploData ghData)
Stores required data to the genotypes and haplotypes tables for each entry on the list. boolean
putRefAnchorData(String line_name, int hapnumber, List<AnchorDataPHG> anchorData, int hapMethod, Set<String> refGrpMethods, String gvcf, String variant_list, int genomeFileId, int gvcfFileId)
Fills in the haplotypes table for the reference ranges. void
putHaplotypesForMultipleGroups(Multimap<Position, Tuple<AnchorDataPHG, String>> mapWithGroupHash, int method_id)
Add data to the haplotypes table. void
putHaplotypesForGamete(int gamete_grp_id, int method_id, Map<Integer, AnchorDataPHG> anchorSequences, int genomeFileId, int gvcfFileId)
Stores gamete sequence data to the haplotypes table This method associates all entries with the single gamete_grp_id which is passed in. void
putHaplotypesData(int gamete_grp_id, int method, Map<Integer, AnchorDataPHG> anchorSequences, String chromosome, int genomeFileId, int gvcfFileId)
Takes a gamete_grp_id, method_id, list of haplotype sequences, a chromosome and a genomeFileId. void
putHaplotypesData(int gamete_grp_id, int method, Map<Integer, AnchorDataPHG> anchorSequences, String chromosome, int genomeFileId, int gvcfFileId, int maxEntries)
Takes a gamete_grp_id, method_id, list of haplotype sequences, a chromosome, genomeFileId, and a number of MaxEntries. void
processHaplotypesData(int gamete_grp_id, int method, Map<Integer, AnchorDataPHG> anchorSequences, String chromosome, int genomeFileId, int gvcfFileId)
void
putConsensusSequences(Multimap<Position, Tuple<AnchorDataPHG, List<String>>> consensusMap, int method_id)
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
putHaplotypeCountsData(String method, Map<String, String> methodDetails, String taxonName, String fastqFile, Array<byte> counts)
This method adds data to the haplotype_counts table. int
putPathsData(String method, Map<String, String> methodDetails, String taxon, List<Integer> readMappingIds, Array<byte> pathBytes, boolean isTestMethod)
This method stores paths data to the paths table. int
putReadMappingData(String method, Map<String, String> methodDetails, String taxon, String file_group_name, Array<byte> mapping_data, boolean isTestMethod, int haplotypeListId)
Takes a method name, method details string, taxon name (should exist in the genotypes table), file_group_name, and a byte array of read mapping data. int
putHalotypeListData(List<Integer> hapids)
put data to the haplotype Lists table. int
putGenomeFileData(String genome_server_path, String genome_file, int genoid, int type)
Method takes information on a genome fasta file, stores to the PHG db, returns the genome_file_data entry id created for the table entry. int
putTaxaGroupName(String group_name)
Creates an entry in the taxa_groups table. void
putTaxaTaxaGroups(String group_name, List<String> taxaList)
Takes a taxa group name and a list of taxa. boolean
putAssemblyInterAnchorSequences(String line_name, int hapNumber, String method, Multimap<Integer, AnchorDataPHG> anchorSequences)
Adds inter-anchor sequences for the specified assembly to the anchor_sequences and anchor_haplotypes table. void
deletePaths(String method, List<String> taxa)
Deletes paths based on a method name and taxa. boolean
deleteReadMappingsCascade(List<Integer> readMappingIds)
Delete read_mappings from the read_mapping table based on provided ids. void
deleteReadMappingPathsById(List<Integer> readMappingIds)
Deletes from the read_mapping_paths table the ids in the ReadMappingIds List void
deleteReadMappingsById(List<Integer> readMappingIds)
Deletes from the read_mapping table based on the ids in the input List void
deletePathsById(List<Integer> pathsIds)
int
deleteMethodByName(String method)
Takes a method name and deletes the entry for it from the methods table. int
getHaplotypeListIDfromHash(String hash)
Given an MD5 hash value, returns the db id for that entry, or 0 if none exist void
close()
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Constructor Detail
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PHGdbAccess
PHGdbAccess(Connection dbConnection)
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Method Detail
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updateReadMappingHash
void updateReadMappingHash()
This prompts a call to private method loadReadMappingHash() to update this hash table
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getRefRangeIDFromString
int getRefRangeIDFromString(String refData)
Returns reference range id
- Parameters:
refData
- needs to be of form chr1:startpos:endPos
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getHaplotypeIDFromFastaIDLine
int getHaplotypeIDFromFastaIDLine(String idLine, String methodName)
Returns the haplotype_id from the haplotypes table based on the gamete_grp_id (calculated from the taxa list), the ref_range_id (calculated from the ref coordinates part of the idline) and the method.
- Parameters:
idLine
- expected form: refchr:refStartPos:refEndPos;taxa_hapnumber:taxa_hapnumber:etcmethodName
- This is the method used for creating the haplotypes
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getMethodIdFromName
int getMethodIdFromName(String method_name)
Returns method_id given a method name. or 0 if no id found for the given name
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getMethodDescriptionFromName
Map<String, String> getMethodDescriptionFromName(String method_name)
Method queries the db methods table for the description field given a methods name
- Parameters:
method_name
- : name of method
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getGameteGroupIDFromTaxaList
int getGameteGroupIDFromTaxaList(List<String> gametes)
Takes a list of taxa and returns the corresponding gamete_group_id or 0
- Parameters:
gametes
- Items on the list must be of the form taxon_hapNumber
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getGenoidFromLine
int getGenoidFromLine(String line_name)
Return genoid
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getGenoidsForTaxa
List<Integer> getGenoidsForTaxa(List<String> taxa)
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getGenomeFileIdFromGenoid
int getGenomeFileIdFromGenoid(int genoid)
Gets the id from the genome_file_data table based on the genoid .
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getGenomeFileIdFromGenoidAndFile
int getGenomeFileIdFromGenoidAndFile(int genoid, String file)
Gets the id from the genome_file_data table based on the genoid and a filename
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getGenomeFileHashFromGenoidandFile
Pair<Integer, String> getGenomeFileHashFromGenoidandFile(int genoid, String file)
Given a genoid and a file name, return the hash value and id for that entry in the genome_file_data table. If there is no entry, return null
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getHapidForGenoidHapNumber
int getHapidForGenoidHapNumber(int genoid, int hap_number)
Returns hapid for given line name and hap_number
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getHapidsForGenoid
List<Integer> getHapidsForGenoid(int genoid)
Returns list of hapids for a given line name
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getLineNameHapNumberFromHapid
Tuple<String, Integer> getLineNameHapNumberFromHapid(int gameteid)
Method to retrieve both a line name and the hap number given a hapid.
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getHapidHapNumberLineNamesForLines
Map<Integer, String> getHapidHapNumberLineNamesForLines(List<String> lineNames)
Retrieves line name and hapnumber, and returns them with the hapid. hapid is the key in the map. THe line name and hap number are concatenated with an underscore and returned as the string value for each hapid.
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getIntervalRangesWithIDForChrom
RangeMap<Position, Integer> getIntervalRangesWithIDForChrom(String chrom)
Returns sorted treeRangeMap of Positions for specified chromosome
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getChromNamesForHaplotype
List<String> getChromNamesForHaplotype(String line_name, int hap_number, String version)
Method grabs a list of distinct chromosome names for a genome_interval version
- Parameters:
version
- Version name for anchors
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getHapidMapFromLinenameHapNumber
Map<String, Integer> getHapidMapFromLinenameHapNumber()
Returns a map of created from the genotypes and haplotypes table.
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getHapCountsIDAndPathsForMethod
Map<Integer, Array<byte>> getHapCountsIDAndPathsForMethod(String method)
THis method pulls the haplotype_counts_id and corresponding path for all entries in the paths table with the specified method.
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getHapCountsIDAndDataForVersionMethod
Map<Integer, Tuple<String, Array<byte>>> getHapCountsIDAndDataForVersionMethod(String method)
This method pulls the haplotype_counts_id with corresponding genotypes line name and data for all DB entries based on the supplied method
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getTaxaForPathMethod
HashSet<String> getTaxaForPathMethod(String method_name)
Method to get a list of all genoid line_names that have paths for method = method_name.
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getTaxonPathsForMethod
Map<String, Array<byte>> getTaxonPathsForMethod(String method_name)
Returns a map of taxon to paths for that taxon from the paths table for a specified method name.
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getReadMappingId
int getReadMappingId(String line_name, String method_name, String file_group_name)
Method uses line_name, method_name and file_Group_name to fetch a read_mapping_id. -1 returned if the this combination is not present in the db.
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getHaplotypeList
List<Integer> getHaplotypeList(int haplist_id)
Given a haplotype_list_id, query the haplotype_list table and return a list of haplotypes stored for that ID, or an empty list if there were none.
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getReadMappingsForId
Pair<Array<byte>, Integer> getReadMappingsForId(int readMappingId)
Method to get the Read Mapping data from the DB using the read_mapping_id. Generally this is returned from PHGData.getReadMappingId(String line_name, String method_name, String file_group_name)
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getReadMappingIdsForTaxaMethod
List<Integer> getReadMappingIdsForTaxaMethod(List<String> taxaList, String method)
This method takes a list of taxa and a method name. It returns a list of read_mapping Ids based on these 2 parameters
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getPathIdsForReadMappingIds
List<Integer> getPathIdsForReadMappingIds(List<Integer> readMappingIds)
Returns path_ids from the read_mapping_paths table associated with the list of read_mapping_ids provided.
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getReadMappingsForMethod
List<ReadMappingDBRecord> getReadMappingsForMethod(String methodName)
Method to get the mapping ids by method
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isFileGroupNew
boolean isFileGroupNew(String taxon, String fileGroupName, String methodName)
Method to check to see if a given taxon and fileGroup are already in the readMapping table of the DB.
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getRefRangesForMethod
List<Integer> getRefRangesForMethod(String methodName)
Method to return all reference ranges associated with a specified method name
- Parameters:
methodName
- name of method group for which the user wants reference range ids
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getPathsForTaxonMethod
Map<String, List<List<Integer>>> getPathsForTaxonMethod(List<String> taxon, String method_name)
Method takes a list of taxa and a method name and returns the paths (if populated in the paths table) stored for each taxon/method pair. For each taxon, a List
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getDbTaxaNames
List<String> getDbTaxaNames()
Gets a list of the taxa currently in the database. Taxa are identified by the line_name field of the genotypes table
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getTaxaGroupIDFromName
int getTaxaGroupIDFromName(String group_name)
Returns taxa_grp_id given a taxa group name. or 0 if no id found for the given name
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getTaxaForTaxaGroup
List<String> getTaxaForTaxaGroup(String group_name)
Get the taxa that make up the specified taxa group
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getAllTaxaGroupNames
List<String> getAllTaxaGroupNames()
Returns a list of all taxa group names from the taxa_groups table
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putMethod
int putMethod(String name, DBLoadingUtils.MethodType type, Map<String, String> descriptionMap)
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.
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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
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putAllAnchors
boolean putAllAnchors(List<AnchorDataPHG> adata, int refGroupMethodID)
Stores chrom, start pos, end pos to referenece_ranges table isFocus identifies focus intervals from the user's bed file
- Parameters:
refGroupMethodID
- method_id used for creating this ref_range_group
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putRefRangeRefRangeMethod
void putRefRangeRefRangeMethod(int method_id, List<Integer> refRangeIDList)
Takes a method id and a list of reference ranges. Populates the ref_range_ref_range_method table.
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putGenoAndHaploTypeData
boolean putGenoAndHaploTypeData(GenoHaploData ghData)
Stores required data to the genotypes and haplotypes tables for each entry on the list.
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putRefAnchorData
boolean putRefAnchorData(String line_name, int hapnumber, List<AnchorDataPHG> anchorData, int hapMethod, Set<String> refGrpMethods, String gvcf, String variant_list, int genomeFileId, int gvcfFileId)
Fills in the haplotypes table for the reference ranges.
- Parameters:
hapMethod
- Name of method used to create anchors.gvcf
- String - name of gvcf filevariant_list
- String - name of file containing list of variantsgenomeFileId
- int - id for ref fasta entry in the genome_file_data tablegvcfFileId
- int - id for ref gvcf file enty in the genome_file_data table
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putHaplotypesForMultipleGroups
void putHaplotypesForMultipleGroups(Multimap<Position, 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:
method_id
- Id in the methods table for this group of sequences
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putHaplotypesForGamete
void putHaplotypesForGamete(int gamete_grp_id, int method_id, Map<Integer, AnchorDataPHG> anchorSequences, int genomeFileId, int gvcfFileId)
Stores gamete sequence data to the haplotypes table This method associates all entries with the single gamete_grp_id which is passed in. It is used when loading reference_ranges sequences or haplotype sequences for a single line. THe gidToVariantDataMap map is used to create the variant list blob for the db
- Parameters:
genomeFileId
- - genome_file_data table id for the fasta file this haplotype, -1 means none.gvcfFileId
- - genome_file_data table id for the gvcf file for this haplotype, -1 mean none
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putHaplotypesData
void putHaplotypesData(int gamete_grp_id, int method, Map<Integer, AnchorDataPHG> anchorSequences, String chromosome, int genomeFileId, int gvcfFileId)
Takes a gamete_grp_id, method_id, list of haplotype sequences, a chromosome and a genomeFileId. Starts the process of storing table data for the haplotypes to the db. This will set maxEntries to 10000 and will call the putHaplotypesData version below putHaplotypesData(int gamete_grp_id, int method, MapanchorSequences, String chromosome, int genomeFileId, gvcfFIleId)
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putHaplotypesData
void putHaplotypesData(int gamete_grp_id, int method, Map<Integer, AnchorDataPHG> anchorSequences, String chromosome, int genomeFileId, int gvcfFileId, int maxEntries)
Takes a gamete_grp_id, method_id, list of haplotype sequences, a chromosome, genomeFileId, and a number of MaxEntries. Starts the process of storing table data for the haplotypes to the db
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processHaplotypesData
void processHaplotypesData(int gamete_grp_id, int method, Map<Integer, AnchorDataPHG> anchorSequences, String chromosome, int genomeFileId, int gvcfFileId)
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putConsensusSequences
void putConsensusSequences(Multimap<Position, Tuple<AnchorDataPHG, List<String>>> consensusMap, int method_id)
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
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putHaplotypeCountsData
void putHaplotypeCountsData(String method, Map<String, String> methodDetails, String taxonName, String fastqFile, Array<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()
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putPathsData
int putPathsData(String method, Map<String, String> methodDetails, String taxon, List<Integer> readMappingIds, Array<byte> pathBytes, boolean isTestMethod)
This method stores paths data to the paths table.
- Parameters:
method
- - Method Name for Path detemination processmethodDetails
- Details of how these paths were createdtaxon
- Name of line for which data is being addedreadMappingIds
- List of read_mapping_idspathBytes
- Compressed byte array of paths dataisTestMethod
- Indicates if the method type should be PATHS ot TEST_PATHS
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putReadMappingData
int putReadMappingData(String method, Map<String, String> methodDetails, String taxon, String file_group_name, Array<byte> mapping_data, boolean isTestMethod, int haplotypeListId)
Takes a method name, method details string, taxon name (should exist in the genotypes table), file_group_name, and a byte array of read mapping data. This is stored to the PHG read_mapping table
- Parameters:
isTestMethod
- : indicates if method type should be set to a TEST methodhaplotypeListId
- : id from the haplotype_list table
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putHalotypeListData
int putHalotypeListData(List<Integer> hapids)
put data to the haplotype Lists table.
- Parameters:
hapids
- - list of integers representing haplotype ids
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putGenomeFileData
int putGenomeFileData(String genome_server_path, String genome_file, int genoid, int type)
Method takes information on a genome fasta file, stores to the PHG db, returns the genome_file_data entry id created for the table entry.
- Parameters:
genome_file
- local path to file name used for MD5 calculationgenoid
- genoid associated with this genome datatype
- the type of file, ie FASTA or GVCF from DBLoadingUtils.
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putTaxaGroupName
int putTaxaGroupName(String group_name)
Creates an entry in the taxa_groups table. If one already exists with the specified name, the id for it is returned.
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putTaxaTaxaGroups
void putTaxaTaxaGroups(String group_name, List<String> taxaList)
Takes a taxa group name and a list of taxa. Populates the taxa_groups and taxa_groups_genoid tables.
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putAssemblyInterAnchorSequences
boolean putAssemblyInterAnchorSequences(String line_name, int hapNumber, String method, 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.
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deletePaths
void deletePaths(String method, List<String> taxa)
Deletes paths based on a method name and taxa. It allows for either method or taxa to be null, but not both. Entries are deleted from both the read_mapping_paths and the paths
- Parameters:
method
- delete paths which have this methodtaxa
- list of taxa for which the paths should be deleted
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deleteReadMappingsCascade
boolean deleteReadMappingsCascade(List<Integer> readMappingIds)
Delete read_mappings from the read_mapping table based on provided ids. This will also delete entries from the read_mapping_paths and paths table that are associated with these read_mappings
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deleteReadMappingPathsById
void deleteReadMappingPathsById(List<Integer> readMappingIds)
Deletes from the read_mapping_paths table the ids in the ReadMappingIds List
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deleteReadMappingsById
void deleteReadMappingsById(List<Integer> readMappingIds)
Deletes from the read_mapping table based on the ids in the input List
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deletePathsById
void deletePathsById(List<Integer> pathsIds)
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deleteMethodByName
int deleteMethodByName(String method)
Takes a method name and deletes the entry for it from the methods table.
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getHaplotypeListIDfromHash
int getHaplotypeListIDfromHash(String hash)
Given an MD5 hash value, returns the db id for that entry, or 0 if none exist
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close
void close()
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