Class: Bio::Bam::SamHeader

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

Overview

Represents SAM header

Instance Method Summary collapse

Constructor Details

#initialize(filename, opts = []) ⇒ SamHeader

Creates a new SamHeader object for a specified file, specifying additional options to pass to sambamba tool



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# File 'lib/bio-sambamba/samheader.rb', line 9

def initialize(filename, opts=[])
  @filename = filename
  @opts = opts
end

Instance Method Details

#pg_lines ⇒ Object

An array of PGLine objects



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# File 'lib/bio-sambamba/samheader.rb', line 50

def pg_lines
  @json ||= get_json
  @sq_lines ||= @json['pg_lines'].map{|json| PGLine.new(json)}
end

#raw_contents ⇒ Object

Raw text of SAM header



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# File 'lib/bio-sambamba/samheader.rb', line 15

def raw_contents
  if @raw_contents.nil? then
    @raw_contents = Bio::Command.query_command(['sambamba', '-H', @filename] + @opts)
    if @raw_contents.start_with? "sambamba" then
      raise @raw_contents
    end
  end
  @raw_contents
end

#rg_lines ⇒ Object

An array of RGLine objects



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# File 'lib/bio-sambamba/samheader.rb', line 44

def rg_lines
  @json ||= get_json
  @sq_lines ||= @json['rg_lines'].map{|json| RGLine.new(json)}
end

#sorting_order ⇒ Object

Sorting order



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# File 'lib/bio-sambamba/samheader.rb', line 32

def sorting_order
  @json ||= get_json
  @json['sorting_order']
end

#sq_lines ⇒ Object

An array of SQLine objects



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# File 'lib/bio-sambamba/samheader.rb', line 38

def sq_lines
  @json ||= get_json
  @sq_lines ||= @json['sq_lines'].map{|json| SQLine.new(json)}
end

#version ⇒ Object

Format version



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# File 'lib/bio-sambamba/samheader.rb', line 26

def version
  @json ||= get_json
  @json['format_version']
end