Class: Bio::FinishM::CProbeNodeFinder

Inherits:
Object
  • Object
show all
Includes:
Logging
Defined in:
lib/assembly/c_probe_node_finder.rb

Instance Method Summary collapse

Methods included from Logging

#log

Instance Method Details

#find_probe_nodes(velvet_underground_graph, probe_read_ids) ⇒ Object

Return a minimal Array of node IDs that contain all probe read IDs



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# File 'lib/assembly/c_probe_node_finder.rb', line 19

def find_probe_nodes(velvet_underground_graph, probe_read_ids)
  @bindings ||= Bio::FinishM::VelvetCBinding.new

  c_probe_read_ids = FFI::MemoryPointer.new(:int32, probe_read_ids.length)
  c_probe_read_ids.write_array_of_int32(probe_read_ids)

  probe_nodes = @bindings.extract_best_probe_reads(
    velvet_underground_graph.internal_graph_struct,
    c_probe_read_ids,
    probe_read_ids.length)
  probe_nodes2 = probe_nodes.read_array_of_int32(probe_read_ids.length).collect{|n| n.abs}.uniq

  #clean up
  c_probe_read_ids.free

  return probe_nodes2
end

#find_probes(velvet_underground_graph, probe_read_ids) ⇒ Object

Return an array of [best_node, best_noded_read] that represent the probes in the graph



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# File 'lib/assembly/c_probe_node_finder.rb', line 5

def find_probes(velvet_underground_graph, probe_read_ids)
  # First use the C method to extract the set of interesting nodes
  log.debug "Extracting target nodes using the C method.." if log.debug?
  target_node_ids = find_probe_nodes(velvet_underground_graph, probe_read_ids)

  # Then iterate over just those nodes we know are interesting
  log.debug "Extracting from only those #{target_node_ids.length} nodes that are interesting.." if log.debug?
  target_node_ids_set = Set.new target_node_ids
  return Bio::AssemblyGraphAlgorithms::NodeFinder.new.find_unique_nodes_with_sequence_ids(
    velvet_underground_graph, probe_read_ids, :target_node_ids => target_node_ids_set
    )
end