Class: Bio::FinishM::ReadToNode

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

Instance Method Summary collapse

Methods included from Logging

#log

Constructor Details

#initialize(filename) ⇒ ReadToNode

Returns a new instance of ReadToNode.



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# File 'lib/assembly/read_to_node.rb', line 4

def initialize(filename)
  @bindings = Bio::FinishM::VelvetCBinding.new
  log.debug "Reading ReadToNode file #{filename}.."
  raise "Unable to find readToNode binary file" unless File.exist?(filename)
  @read_to_node = @bindings.read_read_id_to_node_id_lookup_table(filename)
  log.debug "Finished reading ReadToNode file"
  @cache = {}
end

Instance Method Details

#[](read_id) ⇒ Object

Return an array of node IDs that include the given read id



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# File 'lib/assembly/read_to_node.rb', line 14

def [](read_id)
  # cache
  cache = @cache[read_id]
  return cache unless cache.nil?

  res = @bindings.get_read_id_to_node_id_indexation(@read_to_node, read_id)

  #   # typedef struct {
  #   #   IDnum num_nodes;
  #   #   ReadIdNodeId* read_ids_node_ids;
  #   # } ReadIdToNodeIdIndexation;
  #   class ReadIdToNodeIdIndexationStruct < FFI::Struct
  #     layout :num_nodes, :int32,
  #     :read_ids_node_ids, :pointer
  #   end
  to_return = []
  structs = FFI::Pointer.new(Bio::FinishM::VelvetCBinding::ReadIdNodeIdStruct, res[:read_ids_node_ids].pointer)
  0.upto(res[:num_nodes]-1) do |i|
    to_return << Bio::FinishM::VelvetCBinding::ReadIdNodeIdStruct.new(structs[i])[:node_id].abs
  end
  @cache[read_id] = to_return
  return to_return
end