Class: Bio::Bam::SamHeader

Inherits:
Object
  • Object
show all
Includes:
SambambaStderrParser
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 10

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 48

def pg_lines
  @pg_lines ||= obj[4].map{|rec| PGLine.new(rec)}
end

#raw_contents ⇒ Object

Raw text of SAM header



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# File 'lib/bio-sambamba/samheader.rb', line 16

def raw_contents
  if @raw_contents.nil? then
    cmd = ['sambamba', 'view', '-H', @filename] + @opts
    Bio::Command.call_command_open3(cmd) do |pin, pout, perr|
      @raw_contents = pout.read
      raise_exception_if_stderr_is_not_empty(perr)
    end
  end
  @raw_contents
end

#rg_lines ⇒ Object

An array of RGLine objects



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# File 'lib/bio-sambamba/samheader.rb', line 43

def rg_lines
  @rg_lines ||= obj[3].map{|rec| RGLine.new(rec)}
end

#sorting_order ⇒ Object

Sorting order



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# File 'lib/bio-sambamba/samheader.rb', line 33

def sorting_order
  obj[1]
end

#sq_lines ⇒ Object

An array of SQLine objects



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

def sq_lines
  @sq_lines ||= obj[2].map{|rec| SQLine.new(rec)}
end

#version ⇒ Object

Format version



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# File 'lib/bio-sambamba/samheader.rb', line 28

def version
  obj[0]
end