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 Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(json) ⇒ RGLine

Wrap JSON object from sambamba output



105
106
107
 
# File 'lib/bio-sambamba/samheader.rb', line 105

def initialize(json)
  @json = json
end

Instance Attribute Details

#date ⇒ Object (readonly)

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



119
120
121
 
# File 'lib/bio-sambamba/samheader.rb', line 119

def date
  @date
end

#description ⇒ Object (readonly)

Description



116
117
118
 
# File 'lib/bio-sambamba/samheader.rb', line 116

def description
  @description
end

#flow_order ⇒ Object (readonly)

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.



125
126
127
 
# File 'lib/bio-sambamba/samheader.rb', line 125

def flow_order
  @flow_order
end

#identifier ⇒ Object (readonly)

Unique read group identifier



110
111
112
 
# File 'lib/bio-sambamba/samheader.rb', line 110

def identifier
  @identifier
end

#key_sequence ⇒ Object (readonly)

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



128
129
130
 
# File 'lib/bio-sambamba/samheader.rb', line 128

def key_sequence
  @key_sequence
end

#library ⇒ Object (readonly)

Library



131
132
133
 
# File 'lib/bio-sambamba/samheader.rb', line 131

def library
  @library
end

#platform ⇒ Object (readonly)

Platform/technology used to produce the reads



140
141
142
 
# File 'lib/bio-sambamba/samheader.rb', line 140

def platform
  @platform
end

#platform_unit ⇒ Object (readonly)

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



143
144
145
 
# File 'lib/bio-sambamba/samheader.rb', line 143

def platform_unit
  @platform_unit
end

#predicted_insert_size ⇒ Object (readonly)

Predicted median insert size



137
138
139
 
# File 'lib/bio-sambamba/samheader.rb', line 137

def predicted_insert_size
  @predicted_insert_size
end

#programs ⇒ Object (readonly)

Programs used for processing the read group



134
135
136
 
# File 'lib/bio-sambamba/samheader.rb', line 134

def programs
  @programs
end

#sample ⇒ Object (readonly)

Sample



146
147
148
 
# File 'lib/bio-sambamba/samheader.rb', line 146

def sample
  @sample
end

#sequencing_center ⇒ Object (readonly)

Name of sequencing center



113
114
115
 
# File 'lib/bio-sambamba/samheader.rb', line 113

def sequencing_center
  @sequencing_center
end