Class: Google::Apis::GenomicsV1::VariantCall
- Inherits:
-
Object
- Object
- Google::Apis::GenomicsV1::VariantCall
- 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
A call represents the determination of genotype with respect to a particular variant. It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named rs1234 in a call set with the name NA12345.
Instance Attribute Summary collapse
-
#call_set_id ⇒ String
The ID of the call set this variant call belongs to.
-
#call_set_name ⇒ String
The name of the call set this variant call belongs to.
-
#genotype ⇒ Array<Fixnum>
The genotype of this variant call.
-
#genotype_likelihood ⇒ Array<Float>
The genotype likelihoods for this variant call.
-
#info ⇒ Hash<String,Array<Object>>
A map of additional variant call information.
-
#phaseset ⇒ String
If this field is present, this variant call's genotype ordering implies the phase of the bases and is consistent with any other variant calls in the same reference sequence which have the same phaseset value.
Instance Method Summary collapse
-
#initialize(**args) ⇒ VariantCall
constructor
A new instance of VariantCall.
-
#update!(**args) ⇒ Object
Update properties of this object.
Methods included from Core::JsonObjectSupport
Methods included from Core::Hashable
Constructor Details
#initialize(**args) ⇒ VariantCall
Returns a new instance of VariantCall
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# File 'generated/google/apis/genomics_v1/classes.rb', line 3549 def initialize(**args) update!(**args) end |
Instance Attribute Details
#call_set_id ⇒ String
The ID of the call set this variant call belongs to.
Corresponds to the JSON property callSetId
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# File 'generated/google/apis/genomics_v1/classes.rb', line 3501 def call_set_id @call_set_id end |
#call_set_name ⇒ String
The name of the call set this variant call belongs to.
Corresponds to the JSON property callSetName
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# File 'generated/google/apis/genomics_v1/classes.rb', line 3506 def call_set_name @call_set_name end |
#genotype ⇒ Array<Fixnum>
The genotype of this variant call. Each value represents either the value
of the referenceBases
field or a 1-based index into
alternateBases
. If a variant had a referenceBases
value of T
and an alternateBases
value of ["A", "C"]
, and the genotype
was
[2, 1]
, that would mean the call
represented the heterozygous value CA
for this variant.
If the genotype
was instead [0, 1]
, the
represented value would be TA
. Ordering of the
genotype values is important if the phaseset
is present.
If a genotype is not called (that is, a .
is present in the
GT string) -1 is returned.
Corresponds to the JSON property genotype
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# File 'generated/google/apis/genomics_v1/classes.rb', line 3522 def genotype @genotype end |
#genotype_likelihood ⇒ Array<Float>
The genotype likelihoods for this variant call. Each array entry
represents how likely a specific genotype is for this call. The value
ordering is defined by the GL tag in the VCF spec.
If Phred-scaled genotype likelihood scores (PL) are available and
log10(P) genotype likelihood scores (GL) are not, PL scores are converted
to GL scores. If both are available, PL scores are stored in info
.
Corresponds to the JSON property genotypeLikelihood
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# File 'generated/google/apis/genomics_v1/classes.rb', line 3532 def genotype_likelihood @genotype_likelihood end |
#info ⇒ Hash<String,Array<Object>>
A map of additional variant call information. This must be of the form
mapinfo
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# File 'generated/google/apis/genomics_v1/classes.rb', line 3538 def info @info end |
#phaseset ⇒ String
If this field is present, this variant call's genotype ordering implies
the phase of the bases and is consistent with any other variant calls in
the same reference sequence which have the same phaseset value.
When importing data from VCF, if the genotype data was phased but no
phase set was specified this field will be set to *
.
Corresponds to the JSON property phaseset
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# File 'generated/google/apis/genomics_v1/classes.rb', line 3547 def phaseset @phaseset 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 3554 def update!(**args) @call_set_id = args[:call_set_id] if args.key?(:call_set_id) @call_set_name = args[:call_set_name] if args.key?(:call_set_name) @genotype = args[:genotype] if args.key?(:genotype) @genotype_likelihood = args[:genotype_likelihood] if args.key?(:genotype_likelihood) @info = args[:info] if args.key?(:info) @phaseset = args[:phaseset] if args.key?(:phaseset) end |