Class: Bio::Bam::RGLine

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

Overview

Represents @RG line from SAM header, i.e. a read group

Instance Method Summary collapse

Constructor Details

#initialize(obj) ⇒ RGLine

Wrap MessagePack record from sambamba output



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# File 'lib/bio-sambamba/samheader.rb', line 109

def initialize(obj)
  @obj = obj
end

Instance Method Details

#date ⇒ Object

Date the run was produced (ISO8601 date or date/time)



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

def date
  @obj['DT']
end

#description ⇒ Object

Description



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# File 'lib/bio-sambamba/samheader.rb', line 124

def description
  @obj['DS']
end

#flow_order ⇒ Object

Flow order. The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters.



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# File 'lib/bio-sambamba/samheader.rb', line 137

def flow_order
  @obj['FO']
end

#identifier ⇒ Object

Unique read group identifier



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# File 'lib/bio-sambamba/samheader.rb', line 114

def identifier
  @obj['ID']
end

#key_sequence ⇒ Object

The array of nucleotide bases that correspond to the key sequence of each read



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# File 'lib/bio-sambamba/samheader.rb', line 142

def key_sequence
  @obj['KS']
end

#library ⇒ Object

Library



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# File 'lib/bio-sambamba/samheader.rb', line 147

def library
  @obj['LB']
end

#platform ⇒ Object

Platform/technology used to produce the reads



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# File 'lib/bio-sambamba/samheader.rb', line 162

def platform
  @obj['PL']
end

#platform_unit ⇒ Object

Platform unit (e.g. flowcell-barcode lane for Illumina or slide for SOLiD). Unique identifier.



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# File 'lib/bio-sambamba/samheader.rb', line 167

def platform_unit
  @obj['PU']
end

#predicted_insert_size ⇒ Object

Predicted median insert size



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# File 'lib/bio-sambamba/samheader.rb', line 157

def predicted_insert_size
  @obj['PI']
end

#programs ⇒ Object

Programs used for processing the read group



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# File 'lib/bio-sambamba/samheader.rb', line 152

def programs
  @obj['PG']
end

#sample ⇒ Object

Sample



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# File 'lib/bio-sambamba/samheader.rb', line 172

def sample
  @obj['SM']
end

#sequencing_center ⇒ Object

Name of sequencing center



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# File 'lib/bio-sambamba/samheader.rb', line 119

def sequencing_center
  @obj['CN']
end