Class: Google::Apis::GenomicsV1beta2::ReferenceSet

Inherits:
Object
  • Object
show all
Includes:
Core::Hashable
Defined in:
generated/google/apis/genomics_v1beta2/classes.rb,
generated/google/apis/genomics_v1beta2/representations.rb,
generated/google/apis/genomics_v1beta2/representations.rb

Overview

A reference set is a set of references which typically comprise a reference assembly for a species, such as GRCh38 which is representative of the human genome. A reference set defines a common coordinate space for comparing reference-aligned experimental data. A reference set contains 1 or more references.

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from Core::Hashable

process_value, #to_h

Constructor Details

#initialize(**args) ⇒ ReferenceSet

Returns a new instance of ReferenceSet



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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 2129

def initialize(**args)
   update!(**args)
end

Instance Attribute Details

#assembly_id ⇒ String

Public id of this reference set, such as GRCh37. Corresponds to the JSON property assemblyId

Returns:

  • (String) 


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 2082

def assembly_id
  @assembly_id
end

#description ⇒ String

Free text description of this reference set. Corresponds to the JSON property description

Returns:

  • (String) 


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 2087

def description
  @description
end

#id ⇒ String

The Google generated immutable ID of the reference set. Corresponds to the JSON property id

Returns:

  • (String) 


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 2092

def id
  @id
end

#md5checksum ⇒ String

Order-independent MD5 checksum which identifies this reference set. The checksum is computed by sorting all lower case hexidecimal string reference. md5checksum (for all reference in this set) in ascending lexicographic order, concatenating, and taking the MD5 of that value. The resulting value is represented in lower case hexadecimal format. Corresponds to the JSON property md5checksum

Returns:

  • (String) 


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 2101

def md5checksum
  @md5checksum
end

#ncbi_taxon_id ⇒ Fixnum

ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human) indicating the species which this assembly is intended to model. Note that contained references may specify a different ncbiTaxonId, as assemblies may contain reference sequences which do not belong to the modeled species, e.g. EBV in a human reference genome. Corresponds to the JSON property ncbiTaxonId

Returns:

  • (Fixnum) 


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 2110

def ncbi_taxon_id
  @ncbi_taxon_id
end

#reference_ids ⇒ Array<String>

The IDs of the reference objects that are part of this set. Reference. md5checksum must be unique within this set. Corresponds to the JSON property referenceIds

Returns:

  • (Array<String>) 


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 2116

def reference_ids
  @reference_ids
end

#source_accessions ⇒ Array<String>

All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, for example NC_000001.11. Corresponds to the JSON property sourceAccessions

Returns:

  • (Array<String>) 


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 2122

def source_accessions
  @source_accessions
end

#source_uri ⇒ String

The URI from which the references were obtained. Corresponds to the JSON property sourceURI

Returns:

  • (String) 


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 2127

def source_uri
  @source_uri
end

Instance Method Details

#update!(**args) ⇒ Object

Update properties of this object



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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 2134

def update!(**args)
  @assembly_id = args[:assembly_id] unless args[:assembly_id].nil?
  @description = args[:description] unless args[:description].nil?
  @id = args[:id] unless args[:id].nil?
  @md5checksum = args[:md5checksum] unless args[:md5checksum].nil?
  @ncbi_taxon_id = args[:ncbi_taxon_id] unless args[:ncbi_taxon_id].nil?
  @reference_ids = args[:reference_ids] unless args[:reference_ids].nil?
  @source_accessions = args[:source_accessions] unless args[:source_accessions].nil?
  @source_uri = args[:source_uri] unless args[:source_uri].nil?
end