Class: Bio::Bam::QueryBuilder

Inherits:
Object
  • Object
show all
Defined in:
lib/bio-sambamba/filtering.rb

Constant Summary collapse

@@default_value = 
{ :ref_id          =>  -1,
  :mate_ref_id     =>  -1,
  :position        =>   0,
  :mate_position   =>   0,
  :template_length =>   0,
  :mapping_quality => 255
}

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ QueryBuilder

Returns a new instance of QueryBuilder.



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# File 'lib/bio-sambamba/filtering.rb', line 56

def initialize
  @subexpressions = []
  class << @subexpressions
    def pjoin str
      self.map{|expr| '(' + expr + ')'}.join str
    end
  end
end

Instance Attribute Details

#subexpressions ⇒ Object

Returns the value of attribute subexpressions.



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# File 'lib/bio-sambamba/filtering.rb', line 54

def subexpressions
  @subexpressions
end

Instance Method Details

#expression ⇒ Object 



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# File 'lib/bio-sambamba/filtering.rb', line 129

def expression
  subexpressions.pjoin ' and '
end

#flag ⇒ Object 



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# File 'lib/bio-sambamba/filtering.rb', line 65

def flag
  FlagQueryBuilder.new(self)
end

#intersection(&block) ⇒ Object 



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# File 'lib/bio-sambamba/filtering.rb', line 123

def intersection &block
  qb = QueryBuilder.new
  qb.instance_eval &block
  @subexpressions << (qb.subexpressions.pjoin ' and ')
end

#negate(&block) ⇒ Object 



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# File 'lib/bio-sambamba/filtering.rb', line 110

def negate &block
  qb = QueryBuilder.new
  qb.instance_eval &block
  @subexpressions << ('not (' + qb.expression + ')')
end

#tag(tagname) ⇒ Object 



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# File 'lib/bio-sambamba/filtering.rb', line 69

def tag tagname
  TagQueryBuilder.new(self, tagname)
end

#union(&block) ⇒ Object 



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# File 'lib/bio-sambamba/filtering.rb', line 116

def union &block
  qb = QueryBuilder.new
  qb.instance_eval &block
  @subexpressions << (qb.subexpressions.pjoin ' or ')
  nil
end