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 Method Summary collapse

Constructor Details

#initialize(obj) ⇒ SQLine

Wrap MessagePack record from sambamba output



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

def initialize(obj)
  @obj = obj
end

Instance Method Details

#assembly ⇒ Object

Genome assembly identifier



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# File 'lib/bio-sambamba/samheader.rb', line 84

def assembly
  @obj['AS']
end

#md5 ⇒ Object

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



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

def md5
  @obj['M5']
end

#sequence_length ⇒ Object

Reference sequence length



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# File 'lib/bio-sambamba/samheader.rb', line 79

def sequence_length
  @obj['LN']
end

#sequence_name ⇒ Object

Reference sequence name



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

def sequence_name
  @obj['SN']
end

#species ⇒ Object

Species



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# File 'lib/bio-sambamba/samheader.rb', line 94

def species
  @obj['SP']
end

#uri ⇒ Object

URI of the sequence



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# File 'lib/bio-sambamba/samheader.rb', line 99

def uri
  @obj['UR']
end