class Bio::Bam::RGLine
Represents @RG line from SAM header, i.e. a read group
Public Class Methods
new(obj)
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Wrap MessagePack record from sambamba output
# File lib/bio-sambamba/samheader.rb, line 109 def initialize(obj) @obj = obj end
Public Instance Methods
date()
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Date the run was produced (ISO8601 date or date/time)
# File lib/bio-sambamba/samheader.rb, line 129 def date @obj['DT'] end
description()
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Description
# File lib/bio-sambamba/samheader.rb, line 124 def description @obj['DS'] end
flow_order()
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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()
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Unique read group identifier
# File lib/bio-sambamba/samheader.rb, line 114 def identifier @obj['ID'] end
key_sequence()
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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()
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Library
# File lib/bio-sambamba/samheader.rb, line 147 def library @obj['LB'] end
platform()
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Platform/technology used to produce the reads
# File lib/bio-sambamba/samheader.rb, line 162 def platform @obj['PL'] end
platform_unit()
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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()
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Predicted median insert size
# File lib/bio-sambamba/samheader.rb, line 157 def predicted_insert_size @obj['PI'] end
programs()
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Programs used for processing the read group
# File lib/bio-sambamba/samheader.rb, line 152 def programs @obj['PG'] end
sample()
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Sample
# File lib/bio-sambamba/samheader.rb, line 172 def sample @obj['SM'] end
sequencing_center()
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Name of sequencing center
# File lib/bio-sambamba/samheader.rb, line 119 def sequencing_center @obj['CN'] end