class Bio::Bam::SQLine

Represents a @SQ line from SAM header

Public Class Methods

new(obj) click to toggle source

Wrap MessagePack record from sambamba output

# File lib/bio-sambamba/samheader.rb, line 69
def initialize(obj)
  @obj = obj
end

Public Instance Methods

assembly() click to toggle source

Genome assembly identifier

# File lib/bio-sambamba/samheader.rb, line 84
def assembly
  @obj['AS']
end
md5() click to toggle source

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

# File lib/bio-sambamba/samheader.rb, line 89
def md5
  @obj['M5']
end
sequence_length() click to toggle source

Reference sequence length

# File lib/bio-sambamba/samheader.rb, line 79
def sequence_length
  @obj['LN']
end
sequence_name() click to toggle source

Reference sequence name

# File lib/bio-sambamba/samheader.rb, line 74
def sequence_name
  @obj['SN']
end
species() click to toggle source

Species

# File lib/bio-sambamba/samheader.rb, line 94
def species
  @obj['SP']
end
uri() click to toggle source

URI of the sequence

# File lib/bio-sambamba/samheader.rb, line 99
def uri
  @obj['UR']
end