Constructor Detail

Method Detail

• connection

   static Connection connection(String propertiesFile)

  Creates a database connection given a properties file

  Parameters:

  propertiesFile - properties file

• connection

   static Connection connection(String host, String user, String password, String dbName)

  Creates a sqlite database connection.

  Parameters:

  host - hostname

  user - user id

  password - password

  dbName - database name

• referenceRangeMap

   static Map<Integer, ReferenceRange> referenceRangeMap(Connection database)

  Retrieves all ReferenceRange instances

  Parameters:

  database - database connection

• referenceRanges

   static SortedSet<ReferenceRange> referenceRanges(Connection database)

  Retrieves all ReferenceRange instances with specified genome interval version name.

  Parameters:

  database - database connection

• taxaListMap

   static Map<Integer, TaxaList> taxaListMap(Connection database)

  Retrieves all groups of taxa.

  Parameters:

  database - database connection

• createHaplotypeNodes

   static TreeMap<ReferenceRange, List<HaplotypeNode>> createHaplotypeNodes(Connection database, Map<Integer, ReferenceRange> referenceRangeMap, Map<Integer, TaxaList> taxaListMap, List<Tuple<String, String>> methods, boolean includeSequences, boolean includeVariantContext, SortedSet<Integer> includeHapids, List<String> chromosomes, TaxaList taxaToKeep)

• createHaplotypeNodesWithVariants

   static TreeMap<ReferenceRange, List<HaplotypeNode>> createHaplotypeNodesWithVariants(Connection database, Set<HaplotypeNode> includeHapNodes)

  Creates lists of HaplotypeNodes with variant contexts corresponding to the specified nodes organized by reference Range. LCJ June 16, 2022- this function is only called from MergeGVCFPlugin:extractNodesWithVariants() MergeGVCFPlugin has been deprecated, so I am not making changes here to pull gvcf files for the variants. If this function is called at some point from a non-deprecated method, we can re-look at what changes are needed.

  Parameters:

  database - database connection

  includeHapNodes - includes specified hapids

• createHaplotypeNodesWithVariants

   static HaplotypeGraph createHaplotypeNodesWithVariants(Connection database, HaplotypeGraph graph)

  Creates HaplotypeGraph with variant contexts corresponding to the given HaplotypeGraph.

  Parameters:

  database - database connection

  graph - graph without variant contexts

• addMissingSequenceNodes

   static HaplotypeGraph addMissingSequenceNodes(HaplotypeGraph graph)

• addMissingSequenceNodes

   static int addMissingSequenceNodes(TreeMap<ReferenceRange, List<HaplotypeNode>> result)

• taxaInNodes

   static TaxaList taxaInNodes(TreeMap<ReferenceRange, List<HaplotypeNode>> nodes)

• tree

   static TreeMap<ReferenceRange, List<HaplotypeNode>> tree(HaplotypeGraph graph)

• nodesSplitByIndividualTaxa

   static HaplotypeGraph nodesSplitByIndividualTaxa(HaplotypeGraph graph, double sameTaxonPercent)

• createHaplotypeNodes

   static TreeMap<ReferenceRange, List<HaplotypeNode>> createHaplotypeNodes(Connection database, List<Tuple<String, String>> methods, boolean includeSequences, boolean includeVariantContext, SortedSet<Integer> includeHapids, List<String> chromosomes, TaxaList taxaToKeep)

• createEdges

   static List<HaplotypeEdge> createEdges(Collection<HaplotypeNode> haplotypeNodes)

  Generates Edges based on HaplotypeNodes. Database information not used.

  Parameters:

  haplotypeNodes - HaplotypeNodes

• createEdges

   static List<HaplotypeEdge> createEdges(NavigableMap<ReferenceRange, List<HaplotypeNode>> rangeToNode)

• createEdges

   static List<HaplotypeEdge> createEdges(List<HaplotypeNode> leftNodes, List<HaplotypeNode> rightNodes)

• compareEdges

   static void compareEdges(List<HaplotypeEdge> edges1, List<HaplotypeEdge> edges2)

• getRefLineName

   static String getRefLineName(Connection database)

  Returns the line name of the reference genotype

• methodId

   static int methodId(Connection database, String method_name)

  Returns method id (methods.method_id) for given method name.

  Parameters:

  database - database connection

  method_name - method name

• subsetGraph

   static HaplotypeGraph subsetGraph(HaplotypeGraph graph, TaxaList taxa)

  Create graph that's a subset of the given graph which contains only nodes from the taxa list.

  Parameters:

  graph - original graph

  taxa - taxa list

• removeRefRanges

   static HaplotypeGraph removeRefRanges(HaplotypeGraph graph, double minPercentTaxa)

  Removes reference ranges from given graph that represent less than given minimum percent of total taxa.

  Parameters:

  graph - graph

  minPercentTaxa - minimum percent taxa

• removeRefRanges

   static HaplotypeGraph removeRefRanges(HaplotypeGraph graph, int minCountTaxa)

  Removes reference ranges from given graph that represent less than given minimum number of taxa.

  Parameters:

  graph - graph

  minCountTaxa - minimum number of taxa

• removeRefRanges

   static HaplotypeGraph removeRefRanges(HaplotypeGraph graph, List<ReferenceRange> ranges)

  Removes specified reference ranges from graph.

  Parameters:

  graph - graph

  ranges - reference ranges to remove

• keepRefRanges

   static HaplotypeGraph keepRefRanges(HaplotypeGraph graph, List<ReferenceRange> ranges)

  Creates graph that includes specified reference ranges.

  Parameters:

  graph - graph

  ranges - ranges to keep

• keepRefRangeIDs

   static HaplotypeGraph keepRefRangeIDs(HaplotypeGraph graph, List<Integer> rangeIDs)

• keepHapIDs

   static HaplotypeGraph keepHapIDs(HaplotypeGraph graph, SortedSet<Integer> hapids)

  Filters the given graph to keep only the specified haplotype ids.

  Parameters:

  graph - input graph

  hapids - list of haplotype ids to keep