Class: Google::Apis::GenomicsV1beta2::Variant
- Inherits:
-
Object
- Object
- Google::Apis::GenomicsV1beta2::Variant
- 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
-
#alternate_bases ⇒ Array<String>
The bases that appear instead of the reference bases.
-
#calls ⇒ Array<Google::Apis::GenomicsV1beta2::Call>
The variant calls for this particular variant.
-
#created ⇒ String
The date this variant was created, in milliseconds from the epoch.
-
#end ⇒ String
The end position (0-based) of this variant.
-
#filter ⇒ Array<String>
A list of filters (normally quality filters) this variant has failed.
-
#id ⇒ String
The Google generated ID of the variant, immutable.
-
#info ⇒ Hash<String,Array<String>>
A string which maps to an array of values.
-
#names ⇒ Array<String>
Names for the variant, for example a RefSNP ID.
-
#quality ⇒ Float
A measure of how likely this variant is to be real.
-
#reference_bases ⇒ String
The reference bases for this variant.
-
#reference_name ⇒ String
The reference on which this variant occurs.
-
#start ⇒ String
The position at which this variant occurs (0-based).
-
#variant_set_id ⇒ String
The ID of the variant set this variant belongs to.
Instance Method Summary collapse
-
#initialize(**args) ⇒ Variant
constructor
A new instance of Variant.
-
#update!(**args) ⇒ Object
Update properties of this object.
Methods included from Core::Hashable
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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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 |