Module: RGFATools::Artifacts

Included in:
RGFATools
Defined in:
lib/rgfatools/artifacts.rb

Overview

Methods which edit the graph components without traversal

Instance Method Summary collapse

Instance Method Details

#remove_dead_ends(minlen) ⇒ RGFA

Remove end segments, whose sequence length is under a specified value.

Parameters:

  • minlen (Integer) —

    the minimum length

Returns:



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# File 'lib/rgfatools/artifacts.rb', line 19

def remove_dead_ends(minlen)
  segments.each do |s|
    c = connectivity(s)
    rm(s) if s.length < minlen and
      (c[0] == 0 or c[1] == 0) and
        !cut_segment?(s)
  end
  self
end

#remove_small_components(minlen) ⇒ RGFA

Remove connected components whose sum of lengths of the segments is under a specified value.

Parameters:

  • minlen (Integer) —

    the minimum length

Returns:



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# File 'lib/rgfatools/artifacts.rb', line 10

def remove_small_components(minlen)
  rm(connected_components.select {|cc|
    cc.map{|sn|segment(sn).length}.reduce(:+) < minlen })
  self
end