class Bio::Bam::RGLine

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

Public Class Methods

new(obj) click to toggle source

Wrap MessagePack record from sambamba output

# File lib/bio-sambamba/samheader.rb, line 109
def initialize(obj)
  @obj = obj
end

Public Instance Methods

date() click to toggle source

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

# File lib/bio-sambamba/samheader.rb, line 129
def date
  @obj['DT']
end
description() click to toggle source

Description

# File lib/bio-sambamba/samheader.rb, line 124
def description
  @obj['DS']
end
flow_order() click to toggle source

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.

# File lib/bio-sambamba/samheader.rb, line 137
def flow_order
  @obj['FO']
end
identifier() click to toggle source

Unique read group identifier

# File lib/bio-sambamba/samheader.rb, line 114
def identifier
  @obj['ID']
end
key_sequence() click to toggle source

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

# File lib/bio-sambamba/samheader.rb, line 142
def key_sequence
  @obj['KS']
end
library() click to toggle source

Library

# File lib/bio-sambamba/samheader.rb, line 147
def library
  @obj['LB']
end
platform() click to toggle source

Platform/technology used to produce the reads

# File lib/bio-sambamba/samheader.rb, line 162
def platform
  @obj['PL']
end
platform_unit() click to toggle source

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

# File lib/bio-sambamba/samheader.rb, line 167
def platform_unit
  @obj['PU']
end
predicted_insert_size() click to toggle source

Predicted median insert size

# File lib/bio-sambamba/samheader.rb, line 157
def predicted_insert_size
  @obj['PI']
end
programs() click to toggle source

Programs used for processing the read group

# File lib/bio-sambamba/samheader.rb, line 152
def programs
  @obj['PG']
end
sample() click to toggle source

Sample

# File lib/bio-sambamba/samheader.rb, line 172
def sample
  @obj['SM']
end
sequencing_center() click to toggle source

Name of sequencing center

# File lib/bio-sambamba/samheader.rb, line 119
def sequencing_center
  @obj['CN']
end