Class: Bio::Bam::SQLine
- Inherits:
-
Object
- Object
- Bio::Bam::SQLine
- Defined in:
- lib/bio-sambamba/samheader.rb
Overview
Represents a @SQ line from SAM header
Instance Attribute Summary collapse
-
#assembly ⇒ Object
readonly
Genome assembly identifier.
-
#md5 ⇒ Object
readonly
MD5 checksum of the sequence in uppercase, with gaps and spaces removed.
-
#sequence_length ⇒ Object
readonly
Reference sequence length.
-
#sequence_name ⇒ Object
readonly
Reference sequence name.
-
#species ⇒ Object
readonly
Species.
-
#uri ⇒ Object
readonly
URI of the sequence.
Instance Method Summary collapse
-
#initialize(json) ⇒ SQLine
constructor
Wrap JSON object from sambamba output.
Constructor Details
#initialize(json) ⇒ SQLine
Wrap JSON object from sambamba output
69 70 71 |
# 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 |