Class: Google::Apis::GenomicsV1::Annotation

Inherits:
Object
  • Object
show all
Includes:
Core::Hashable, Core::JsonObjectSupport
Defined in:
generated/google/apis/genomics_v1/classes.rb,
generated/google/apis/genomics_v1/representations.rb,
generated/google/apis/genomics_v1/representations.rb

Overview

An annotation describes a region of reference genome. The value of an annotation may be one of several canonical types, supplemented by arbitrary info tags. An annotation is not inherently associated with a specific sample or individual (though a client could choose to use annotations in this way). Example canonical annotation types are GENE and VARIANT.

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from Core::JsonObjectSupport

#to_json

Methods included from Core::Hashable

process_value, #to_h

Constructor Details

#initialize(**args) ⇒ Annotation

Returns a new instance of Annotation



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# File 'generated/google/apis/genomics_v1/classes.rb', line 394

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

Instance Attribute Details

#annotation_set_id ⇒ String

The annotation set to which this annotation belongs. Corresponds to the JSON property annotationSetId

Returns:

  • (String) 


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# File 'generated/google/apis/genomics_v1/classes.rb', line 332

def annotation_set_id
  @annotation_set_id
end

#end ⇒ Fixnum

The end position of the range on the reference, 0-based exclusive. Corresponds to the JSON property end

Returns:

  • (Fixnum) 


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# File 'generated/google/apis/genomics_v1/classes.rb', line 386

def end
  @end
end

#id ⇒ String

The server-generated annotation ID, unique across all annotations. Corresponds to the JSON property id

Returns:

  • (String) 


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# File 'generated/google/apis/genomics_v1/classes.rb', line 350

def id
  @id
end

#info ⇒ Hash<String,Array<Object>>

A map of additional read alignment information. This must be of the form map (string key mapping to a list of string values). Corresponds to the JSON property info

Returns:

  • (Hash<String,Array<Object>>) 


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# File 'generated/google/apis/genomics_v1/classes.rb', line 381

def info
  @info
end

#name ⇒ String

The display name of this annotation. Corresponds to the JSON property name

Returns:

  • (String) 


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# File 'generated/google/apis/genomics_v1/classes.rb', line 337

def name
  @name
end

#reference_id ⇒ String

The ID of the Google Genomics reference associated with this range. Corresponds to the JSON property referenceId

Returns:

  • (String) 


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# File 'generated/google/apis/genomics_v1/classes.rb', line 355

def reference_id
  @reference_id
end

#reference_name ⇒ String

The display name corresponding to the reference specified by referenceId, for example chr1, 1, or chrX. Corresponds to the JSON property referenceName

Returns:

  • (String) 


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# File 'generated/google/apis/genomics_v1/classes.rb', line 369

def reference_name
  @reference_name
end

#reverse_strand ⇒ Boolean Also known as: reverse_strand?

Whether this range refers to the reverse strand, as opposed to the forward strand. Note that regardless of this field, the start/end position of the range always refer to the forward strand. Corresponds to the JSON property reverseStrand

Returns:

  • (Boolean) 


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# File 'generated/google/apis/genomics_v1/classes.rb', line 362

def reverse_strand
  @reverse_strand
end

#start ⇒ Fixnum

The start position of the range on the reference, 0-based inclusive. Corresponds to the JSON property start

Returns:

  • (Fixnum) 


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# File 'generated/google/apis/genomics_v1/classes.rb', line 327

def start
  @start
end

#transcript ⇒ Google::Apis::GenomicsV1::Transcript

A transcript represents the assertion that a particular region of the reference genome may be transcribed as RNA. Corresponds to the JSON property transcript

Returns:



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# File 'generated/google/apis/genomics_v1/classes.rb', line 392

def transcript
  @transcript
end

#type ⇒ String

The data type for this annotation. Must match the containing annotation set's type. Corresponds to the JSON property type

Returns:

  • (String) 


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# File 'generated/google/apis/genomics_v1/classes.rb', line 375

def type
  @type
end

#variant ⇒ Google::Apis::GenomicsV1::VariantAnnotation

A variant annotation, which describes the effect of a variant on the genome, the coding sequence, and/or higher level consequences at the organism level e.g. pathogenicity. This field is only set for annotations of type VARIANT. Corresponds to the JSON property variant

Returns:



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# File 'generated/google/apis/genomics_v1/classes.rb', line 345

def variant
  @variant
end

Instance Method Details

#update!(**args) ⇒ Object

Update properties of this object



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# File 'generated/google/apis/genomics_v1/classes.rb', line 399

def update!(**args)
  @start = args[:start] if args.key?(:start)
  @annotation_set_id = args[:annotation_set_id] if args.key?(:annotation_set_id)
  @name = args[:name] if args.key?(:name)
  @variant = args[:variant] if args.key?(:variant)
  @id = args[:id] if args.key?(:id)
  @reference_id = args[:reference_id] if args.key?(:reference_id)
  @reverse_strand = args[:reverse_strand] if args.key?(:reverse_strand)
  @reference_name = args[:reference_name] if args.key?(:reference_name)
  @type = args[:type] if args.key?(:type)
  @info = args[:info] if args.key?(:info)
  @end = args[:end] if args.key?(:end)
  @transcript = args[:transcript] if args.key?(:transcript)
end