Class: Bio::Bam::SQLine

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

Overview

Represents a @SQ line from SAM header

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(json) ⇒ SQLine

Wrap JSON object from sambamba output



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# File 'lib/bio-sambamba/samheader.rb', line 69

def initialize(json)
  @json = json
end

Instance Attribute Details

#assembly ⇒ Object (readonly)

Genome assembly identifier



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# File 'lib/bio-sambamba/samheader.rb', line 80

def assembly
  @assembly
end

#md5 ⇒ Object (readonly)

MD5 checksum of the sequence in uppercase, with gaps and spaces removed



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# File 'lib/bio-sambamba/samheader.rb', line 83

def md5
  @md5
end

#sequence_length ⇒ Object (readonly)

Reference sequence length



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# File 'lib/bio-sambamba/samheader.rb', line 77

def sequence_length
  @sequence_length
end

#sequence_name ⇒ Object (readonly)

Reference sequence name



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# File 'lib/bio-sambamba/samheader.rb', line 74

def sequence_name
  @sequence_name
end

#species ⇒ Object (readonly)

Species



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# File 'lib/bio-sambamba/samheader.rb', line 86

def species
  @species
end

#uri ⇒ Object (readonly)

URI of the sequence



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# File 'lib/bio-sambamba/samheader.rb', line 89

def uri
  @uri
end