Class: Bio::AssemblyGraphAlgorithms::CoverageBasedGraphFilter

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

Instance Method Summary collapse

Methods included from FinishM::Logging

#log

Instance Method Details

#remove_low_coverage_nodes(graph, threshold, options = {}) ⇒ Object

Remove all nodes from the graph that do not have sufficient coverage (i.e. possibly are sequencing error artefacts)

Options: :whitelisted_sequences: provide an enumerable of sequence IDs, don’t remove any nodes that have reads tracked to any of these IDs

Returns nodes_removed, arcs_removed (as objects, in particular order)



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

def remove_low_coverage_nodes(graph, threshold, options = {})
  graph.delete_nodes_if do |node|
    deleting = false
    if node.coverage and (node.coverage < threshold)
      deleting = true
    end

    if deleting and options[:whitelisted_sequences] and !node.short_reads.nil?
      options[:whitelisted_sequences].each do |seq_id|
        if node.short_reads.collect{|r| r.read_id}.include?(seq_id)
          deleting = false
          log.debug "Preserving low coverage but whitelisted node: #{node.node_id}" if log.debug?
        end
      end
    end
    deleting
  end
end