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#
# Methods for the RGFA class, which involve a traversal of the graph following
# links
#
module RGFATools::PBubbles
require "set"
# Removes all p-bubbles in the graph
# @return [RGFA] self
def remove_p_bubbles
visited = Set.new
segment_names.each do |sn|
next if visited.include?(sn)
if connectivity(sn) == [1,1]
s1 = neighbours([sn, :B])[0]
s2 = neighbours([sn, :E])[0]
n1 = neighbours(s1).sort
n2 = neighbours(s2).sort
n1.each {|se| visited << se[0].name}
if n1 == n2.map{|se| se.invert_end_type}
remove_proven_p_bubble(s1, s2, n1)
end
end
end
return self
end
# Removes a p-bubble between segment_end1 and segment_end2
# @param [RGFA::SegmentEnd] segment_end1 a segment end
# @param [RGFA::SegmentEnd] segment_end2 another segment end
# @!macro [new] count_tag
# @param count_tag [Symbol] <i>(defaults to: +:RC+ or the value set by
# {#set_default_count_tag})</i> the count tag to use for coverage
# computation
# @!macro [new] unit_length
# @param unit_length [Integer] <i>(defaults to: 1 or the value set by
# {#set_count_unit_length})</i> the unit length to use for coverage
# computation
# @return [RGFA] self
#
def remove_p_bubble(segment_end1, segment_end2,
count_tag: @default[:count_tag],
unit_length: @default[:unit_length])
n1 = neighbours(segment_end1).sort
n2 = neighbours(segment_end2).sort
raise if n1 != n2.map{|se| se.invert_end_type}
raise if n1.any? {|se| connectivity(se[0]) != [1,1]}
remove_proven_p_bubble(segment_end1, segment_end2, n1,
count_tag: count_tag,
unit_length: unit_length)
return self
end
private
def remove_proven_p_bubble(segment_end1, segment_end2, alternatives,
count_tag: @default[:count_tag],
unit_length: @default[:unit_length])
coverages = alternatives.map{|s|segment!(s[0]).coverage(
count_tag: count_tag, unit_length: unit_length)}
alternatives.delete_at(coverages.index(coverages.max))
alternatives.each {|s| delete_segment(s[0])}
end
end
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