Class: Google::Apis::GenomicsV1beta2::Variant

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 variant represents a change in DNA sequence relative to a reference sequence. For example, a variant could represent a SNP or an insertion. Variants belong to a variant set. Each of the calls on a variant represent a determination of genotype with respect to that variant. For example, a call might assign probability of 0.32 to the occurrence of a SNP named rs1234 in a sample named NA12345. A call belongs to a call set, which contains related calls typically from one sample.

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from Core::Hashable

process_value, #to_h

Constructor Details

#initialize(**args) ⇒ Variant

Returns a new instance of Variant.



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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 3126

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

Instance Attribute Details

#alternate_bases ⇒ Array<String>

The bases that appear instead of the reference bases. Corresponds to the JSON property alternateBases

Returns:

  • (Array<String>) 


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 3058

def alternate_bases
  @alternate_bases
end

#calls ⇒ Array<Google::Apis::GenomicsV1beta2::Call>

The variant calls for this particular variant. Each one represents the determination of genotype with respect to this variant. Corresponds to the JSON property calls

Returns:



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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 3064

def calls
  @calls
end

#created ⇒ String

The date this variant was created, in milliseconds from the epoch. Corresponds to the JSON property created

Returns:

  • (String) 


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 3069

def created
  @created
end

#end ⇒ String

The end position (0-based) of this variant. This corresponds to the first base after the last base in the reference allele. So, the length of the reference allele is (end - start). This is useful for variants that don't explicitly give alternate bases, for example large deletions. Corresponds to the JSON property end

Returns:

  • (String) 


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 3077

def end
  @end
end

#filter ⇒ Array<String>

A list of filters (normally quality filters) this variant has failed. PASS indicates this variant has passed all filters. Corresponds to the JSON property filter

Returns:

  • (Array<String>) 


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 3083

def filter
  @filter
end

#id ⇒ String

The Google generated ID of the variant, immutable. Corresponds to the JSON property id

Returns:

  • (String) 


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 3088

def id
  @id
end

#info ⇒ Hash<String,Array<String>>

A string which maps to an array of values. Corresponds to the JSON property info

Returns:

  • (Hash<String,Array<String>>) 


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 3093

def info
  @info
end

#names ⇒ Array<String>

Names for the variant, for example a RefSNP ID. Corresponds to the JSON property names

Returns:

  • (Array<String>) 


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 3098

def names
  @names
end

#quality ⇒ Float

A measure of how likely this variant is to be real. A higher value is better. Corresponds to the JSON property quality

Returns:

  • (Float) 


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 3103

def quality
  @quality
end

#reference_bases ⇒ String

The reference bases for this variant. They start at the given position. Corresponds to the JSON property referenceBases

Returns:

  • (String) 


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 3108

def reference_bases
  @reference_bases
end

#reference_name ⇒ String

The reference on which this variant occurs. (such as chr20 or X) Corresponds to the JSON property referenceName

Returns:

  • (String) 


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 3113

def reference_name
  @reference_name
end

#start ⇒ String

The position at which this variant occurs (0-based). This corresponds to the first base of the string of reference bases. Corresponds to the JSON property start

Returns:

  • (String) 


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 3119

def start
  @start
end

#variant_set_id ⇒ String

The ID of the variant set this variant belongs to. Corresponds to the JSON property variantSetId

Returns:

  • (String) 


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# File 'generated/google/apis/genomics_v1beta2/classes.rb', line 3124

def variant_set_id
  @variant_set_id
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 3131

def update!(**args)
  @alternate_bases = args[:alternate_bases] unless args[:alternate_bases].nil?
  @calls = args[:calls] unless args[:calls].nil?
  @created = args[:created] unless args[:created].nil?
  @end = args[:end] unless args[:end].nil?
  @filter = args[:filter] unless args[:filter].nil?
  @id = args[:id] unless args[:id].nil?
  @info = args[:info] unless args[:info].nil?
  @names = args[:names] unless args[:names].nil?
  @quality = args[:quality] unless args[:quality].nil?
  @reference_bases = args[:reference_bases] unless args[:reference_bases].nil?
  @reference_name = args[:reference_name] unless args[:reference_name].nil?
  @start = args[:start] unless args[:start].nil?
  @variant_set_id = args[:variant_set_id] unless args[:variant_set_id].nil?
end