king
/
v811_spc009
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
You can not select more than 25 topics Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
Branches Tags
${ item.name }
Create tag ${ searchTerm }
Create branch ${ searchTerm }
from 'main'
${ noResults }
v811_spc009/external/python/google-api-python-client/docs/dyn/genomics_v1.variants.html

1153 lines
54 KiB
Raw Permalink Blame History

<html><body>
<style>
body, h1, h2, h3, div, span, p, pre, a {
margin: 0;
padding: 0;
border: 0;
font-weight: inherit;
font-style: inherit;
font-size: 100%;
font-family: inherit;
vertical-align: baseline;
}
body {
font-size: 13px;
padding: 1em;
}
h1 {
font-size: 26px;
margin-bottom: 1em;
}
h2 {
font-size: 24px;
margin-bottom: 1em;
}
h3 {
font-size: 20px;
margin-bottom: 1em;
margin-top: 1em;
}
pre, code {
line-height: 1.5;
font-family: Monaco, 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', 'Lucida Console', monospace;
}
pre {
margin-top: 0.5em;
}
h1, h2, h3, p {
font-family: Arial, sans serif;
}
h1, h2, h3 {
border-bottom: solid #CCC 1px;
}
.toc_element {
margin-top: 0.5em;
}
.firstline {
margin-left: 2 em;
}
.method {
margin-top: 1em;
border: solid 1px #CCC;
padding: 1em;
background: #EEE;
}
.details {
font-weight: bold;
font-size: 14px;
}
</style>
<h1><a href="genomics_v1.html">Genomics API</a> . <a href="genomics_v1.variants.html">variants</a></h1>
<h2>Instance Methods</h2>
<p class="toc_element">
<code><a href="#create">create(body, x__xgafv=None)</a></code></p>
<p class="firstline">Creates a new variant.</p>
<p class="toc_element">
<code><a href="#delete">delete(variantId, x__xgafv=None)</a></code></p>
<p class="firstline">Deletes a variant.</p>
<p class="toc_element">
<code><a href="#get">get(variantId, x__xgafv=None)</a></code></p>
<p class="firstline">Gets a variant by ID.</p>
<p class="toc_element">
<code><a href="#import_">import_(body, x__xgafv=None)</a></code></p>
<p class="firstline">Creates variant data by asynchronously importing the provided information.</p>
<p class="toc_element">
<code><a href="#merge">merge(body, x__xgafv=None)</a></code></p>
<p class="firstline">Merges the given variants with existing variants.</p>
<p class="toc_element">
<code><a href="#patch">patch(variantId, body, x__xgafv=None, updateMask=None)</a></code></p>
<p class="firstline">Updates a variant.</p>
<p class="toc_element">
<code><a href="#search">search(body, x__xgafv=None)</a></code></p>
<p class="firstline">Gets a list of variants matching the criteria.</p>
<p class="toc_element">
<code><a href="#search_next">search_next(previous_request, previous_response)</a></code></p>
<p class="firstline">Retrieves the next page of results.</p>
<h3>Method Details</h3>
<div class="method">
<code class="details" id="create">create(body, x__xgafv=None)</code>
<pre>Creates a new variant.
For the definitions of variants and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Args:
body: object, The request body. (required)
The object takes the form of:
{ # 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.
#
# For more genomics resource definitions, see [Fundamentals of Google
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
#
# 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.
"info": { # A map of additional variant information. This must be of the form
# map<string, string[]> (string key mapping to a list of string values).
"a_key": [
"",
],
},
"variantSetId": "A String", # The ID of the variant set this variant belongs to.
"end": "A 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.
"calls": [ # The variant calls for this particular variant. Each one represents the
# determination of genotype with respect to this variant.
{ # 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.
"info": { # A map of additional variant call information. This must be of the form
# map<string, string[]> (string key mapping to a list of string values).
"a_key": [
"",
],
},
"genotype": [ # 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.
42,
],
"callSetId": "A String", # The ID of the call set this variant call belongs to.
"phaseset": "A 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 `*`.
"genotypeLikelihood": [ # 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`.
3.14,
],
"callSetName": "A String", # The name of the call set this variant call belongs to.
},
],
"created": "A String", # The date this variant was created, in milliseconds from the epoch.
"id": "A String", # The server-generated variant ID, unique across all variants.
"filter": [ # A list of filters (normally quality filters) this variant has failed.
# `PASS` indicates this variant has passed all filters.
"A String",
],
"start": "A String", # The position at which this variant occurs (0-based).
# This corresponds to the first base of the string of reference bases.
"names": [ # Names for the variant, for example a RefSNP ID.
"A String",
],
"alternateBases": [ # The bases that appear instead of the reference bases.
"A String",
],
"referenceName": "A String", # The reference on which this variant occurs.
# (such as `chr20` or `X`)
"quality": 3.14, # A measure of how likely this variant is to be real.
# A higher value is better.
"referenceBases": "A String", # The reference bases for this variant. They start at the given
# position.
}
x__xgafv: string, V1 error format.
Allowed values
1 - v1 error format
2 - v2 error format
Returns:
An object of the form:
{ # 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.
#
# For more genomics resource definitions, see [Fundamentals of Google
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
#
# 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.
"info": { # A map of additional variant information. This must be of the form
# map<string, string[]> (string key mapping to a list of string values).
"a_key": [
"",
],
},
"variantSetId": "A String", # The ID of the variant set this variant belongs to.
"end": "A 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.
"calls": [ # The variant calls for this particular variant. Each one represents the
# determination of genotype with respect to this variant.
{ # 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.
"info": { # A map of additional variant call information. This must be of the form
# map<string, string[]> (string key mapping to a list of string values).
"a_key": [
"",
],
},
"genotype": [ # 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.
42,
],
"callSetId": "A String", # The ID of the call set this variant call belongs to.
"phaseset": "A 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 `*`.
"genotypeLikelihood": [ # 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`.
3.14,
],
"callSetName": "A String", # The name of the call set this variant call belongs to.
},
],
"created": "A String", # The date this variant was created, in milliseconds from the epoch.
"id": "A String", # The server-generated variant ID, unique across all variants.
"filter": [ # A list of filters (normally quality filters) this variant has failed.
# `PASS` indicates this variant has passed all filters.
"A String",
],
"start": "A String", # The position at which this variant occurs (0-based).
# This corresponds to the first base of the string of reference bases.
"names": [ # Names for the variant, for example a RefSNP ID.
"A String",
],
"alternateBases": [ # The bases that appear instead of the reference bases.
"A String",
],
"referenceName": "A String", # The reference on which this variant occurs.
# (such as `chr20` or `X`)
"quality": 3.14, # A measure of how likely this variant is to be real.
# A higher value is better.
"referenceBases": "A String", # The reference bases for this variant. They start at the given
# position.
}</pre>
</div>
<div class="method">
<code class="details" id="delete">delete(variantId, x__xgafv=None)</code>
<pre>Deletes a variant.
For the definitions of variants and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Args:
variantId: string, The ID of the variant to be deleted. (required)
x__xgafv: string, V1 error format.
Allowed values
1 - v1 error format
2 - v2 error format
Returns:
An object of the form:
{ # A generic empty message that you can re-use to avoid defining duplicated
# empty messages in your APIs. A typical example is to use it as the request
# or the response type of an API method. For instance:
#
# service Foo {
# rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty);
# }
#
# The JSON representation for `Empty` is empty JSON object `{}`.
}</pre>
</div>
<div class="method">
<code class="details" id="get">get(variantId, x__xgafv=None)</code>
<pre>Gets a variant by ID.
For the definitions of variants and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Args:
variantId: string, The ID of the variant. (required)
x__xgafv: string, V1 error format.
Allowed values
1 - v1 error format
2 - v2 error format
Returns:
An object of the form:
{ # 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.
#
# For more genomics resource definitions, see [Fundamentals of Google
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
#
# 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.
"info": { # A map of additional variant information. This must be of the form
# map<string, string[]> (string key mapping to a list of string values).
"a_key": [
"",
],
},
"variantSetId": "A String", # The ID of the variant set this variant belongs to.
"end": "A 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.
"calls": [ # The variant calls for this particular variant. Each one represents the
# determination of genotype with respect to this variant.
{ # 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.
"info": { # A map of additional variant call information. This must be of the form
# map<string, string[]> (string key mapping to a list of string values).
"a_key": [
"",
],
},
"genotype": [ # 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.
42,
],
"callSetId": "A String", # The ID of the call set this variant call belongs to.
"phaseset": "A 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 `*`.
"genotypeLikelihood": [ # 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`.
3.14,
],
"callSetName": "A String", # The name of the call set this variant call belongs to.
},
],
"created": "A String", # The date this variant was created, in milliseconds from the epoch.
"id": "A String", # The server-generated variant ID, unique across all variants.
"filter": [ # A list of filters (normally quality filters) this variant has failed.
# `PASS` indicates this variant has passed all filters.
"A String",
],
"start": "A String", # The position at which this variant occurs (0-based).
# This corresponds to the first base of the string of reference bases.
"names": [ # Names for the variant, for example a RefSNP ID.
"A String",
],
"alternateBases": [ # The bases that appear instead of the reference bases.
"A String",
],
"referenceName": "A String", # The reference on which this variant occurs.
# (such as `chr20` or `X`)
"quality": 3.14, # A measure of how likely this variant is to be real.
# A higher value is better.
"referenceBases": "A String", # The reference bases for this variant. They start at the given
# position.
}</pre>
</div>
<div class="method">
<code class="details" id="import_">import_(body, x__xgafv=None)</code>
<pre>Creates variant data by asynchronously importing the provided information.
For the definitions of variant sets and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
The variants for import will be merged with any existing variant that
matches its reference sequence, start, end, reference bases, and
alternative bases. If no such variant exists, a new one will be created.
When variants are merged, the call information from the new variant
is added to the existing variant, and Variant info fields are merged
as specified in
infoMergeConfig.
As a special case, for single-sample VCF files, QUAL and FILTER fields will
be moved to the call level; these are sometimes interpreted in a
call-specific context.
Imported VCF headers are appended to the metadata already in a variant set.
Args:
body: object, The request body. (required)
The object takes the form of:
{ # The variant data import request.
"variantSetId": "A String", # Required. The variant set to which variant data should be imported.
"format": "A String", # The format of the variant data being imported. If unspecified, defaults to
# to `VCF`.
"sourceUris": [ # A list of URIs referencing variant files in Google Cloud Storage. URIs can
# include wildcards [as described
# here](https://cloud.google.com/storage/docs/gsutil/addlhelp/WildcardNames).
# Note that recursive wildcards ('**') are not supported.
"A String",
],
"infoMergeConfig": { # A mapping between info field keys and the InfoMergeOperations to
# be performed on them. This is plumbed down to the MergeVariantRequests
# generated by the resulting import job.
"a_key": "A String",
},
"normalizeReferenceNames": True or False, # Convert reference names to the canonical representation.
# hg19 haploytypes (those reference names containing "_hap")
# are not modified in any way.
# All other reference names are modified according to the following rules:
# The reference name is capitalized.
# The "chr" prefix is dropped for all autosomes and sex chromsomes.
# For example "chr17" becomes "17" and "chrX" becomes "X".
# All mitochondrial chromosomes ("chrM", "chrMT", etc) become "MT".
}
x__xgafv: string, V1 error format.
Allowed values
1 - v1 error format
2 - v2 error format
Returns:
An object of the form:
{ # This resource represents a long-running operation that is the result of a
# network API call.
"metadata": { # An OperationMetadata object. This will always be returned with the Operation.
"a_key": "", # Properties of the object. Contains field @type with type URL.
},
"error": { # The `Status` type defines a logical error model that is suitable for different # The error result of the operation in case of failure or cancellation.
# programming environments, including REST APIs and RPC APIs. It is used by
# [gRPC](https://github.com/grpc). The error model is designed to be:
#
# - Simple to use and understand for most users
# - Flexible enough to meet unexpected needs
#
# # Overview
#
# The `Status` message contains three pieces of data: error code, error message,
# and error details. The error code should be an enum value of
# google.rpc.Code, but it may accept additional error codes if needed. The
# error message should be a developer-facing English message that helps
# developers *understand* and *resolve* the error. If a localized user-facing
# error message is needed, put the localized message in the error details or
# localize it in the client. The optional error details may contain arbitrary
# information about the error. There is a predefined set of error detail types
# in the package `google.rpc` that can be used for common error conditions.
#
# # Language mapping
#
# The `Status` message is the logical representation of the error model, but it
# is not necessarily the actual wire format. When the `Status` message is
# exposed in different client libraries and different wire protocols, it can be
# mapped differently. For example, it will likely be mapped to some exceptions
# in Java, but more likely mapped to some error codes in C.
#
# # Other uses
#
# The error model and the `Status` message can be used in a variety of
# environments, either with or without APIs, to provide a
# consistent developer experience across different environments.
#
# Example uses of this error model include:
#
# - Partial errors. If a service needs to return partial errors to the client,
# it may embed the `Status` in the normal response to indicate the partial
# errors.
#
# - Workflow errors. A typical workflow has multiple steps. Each step may
# have a `Status` message for error reporting.
#
# - Batch operations. If a client uses batch request and batch response, the
# `Status` message should be used directly inside batch response, one for
# each error sub-response.
#
# - Asynchronous operations. If an API call embeds asynchronous operation
# results in its response, the status of those operations should be
# represented directly using the `Status` message.
#
# - Logging. If some API errors are stored in logs, the message `Status` could
# be used directly after any stripping needed for security/privacy reasons.
"message": "A String", # A developer-facing error message, which should be in English. Any
# user-facing error message should be localized and sent in the
# google.rpc.Status.details field, or localized by the client.
"code": 42, # The status code, which should be an enum value of google.rpc.Code.
"details": [ # A list of messages that carry the error details. There will be a
# common set of message types for APIs to use.
{
"a_key": "", # Properties of the object. Contains field @type with type URL.
},
],
},
"done": True or False, # If the value is `false`, it means the operation is still in progress.
# If true, the operation is completed, and either `error` or `response` is
# available.
"response": { # If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If importing Variants, an ImportVariantsResponse is returned. For pipelines and exports, an empty response is returned.
"a_key": "", # Properties of the object. Contains field @type with type URL.
},
"name": "A String", # The server-assigned name, which is only unique within the same service that originally returns it. For example&#58; `operations/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw`
}</pre>
</div>
<div class="method">
<code class="details" id="merge">merge(body, x__xgafv=None)</code>
<pre>Merges the given variants with existing variants.
For the definitions of variants and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Each variant will be
merged with an existing variant that matches its reference sequence,
start, end, reference bases, and alternative bases. If no such variant
exists, a new one will be created.
When variants are merged, the call information from the new variant
is added to the existing variant. Variant info fields are merged as
specified in the
infoMergeConfig
field of the MergeVariantsRequest.
Please exercise caution when using this method! It is easy to introduce
mistakes in existing variants and difficult to back out of them. For
example,
suppose you were trying to merge a new variant with an existing one and
both
variants contain calls that belong to callsets with the same callset ID.
// Existing variant - irrelevant fields trimmed for clarity
{
"variantSetId": "10473108253681171589",
"referenceName": "1",
"start": "10582",
"referenceBases": "G",
"alternateBases": [
"A"
],
"calls": [
{
"callSetId": "10473108253681171589-0",
"callSetName": "CALLSET0",
"genotype": [
0,
1
],
}
]
}
// New variant with conflicting call information
{
"variantSetId": "10473108253681171589",
"referenceName": "1",
"start": "10582",
"referenceBases": "G",
"alternateBases": [
"A"
],
"calls": [
{
"callSetId": "10473108253681171589-0",
"callSetName": "CALLSET0",
"genotype": [
1,
1
],
}
]
}
The resulting merged variant would overwrite the existing calls with those
from the new variant:
{
"variantSetId": "10473108253681171589",
"referenceName": "1",
"start": "10582",
"referenceBases": "G",
"alternateBases": [
"A"
],
"calls": [
{
"callSetId": "10473108253681171589-0",
"callSetName": "CALLSET0",
"genotype": [
1,
1
],
}
]
}
This may be the desired outcome, but it is up to the user to determine if
if that is indeed the case.
Args:
body: object, The request body. (required)
The object takes the form of:
{
"variantSetId": "A String", # The destination variant set.
"variants": [ # The variants to be merged with existing variants.
{ # 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.
#
# For more genomics resource definitions, see [Fundamentals of Google
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
#
# 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.
"info": { # A map of additional variant information. This must be of the form
# map<string, string[]> (string key mapping to a list of string values).
"a_key": [
"",
],
},
"variantSetId": "A String", # The ID of the variant set this variant belongs to.
"end": "A 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.
"calls": [ # The variant calls for this particular variant. Each one represents the
# determination of genotype with respect to this variant.
{ # 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.
"info": { # A map of additional variant call information. This must be of the form
# map<string, string[]> (string key mapping to a list of string values).
"a_key": [
"",
],
},
"genotype": [ # 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.
42,
],
"callSetId": "A String", # The ID of the call set this variant call belongs to.
"phaseset": "A 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 `*`.
"genotypeLikelihood": [ # 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`.
3.14,
],
"callSetName": "A String", # The name of the call set this variant call belongs to.
},
],
"created": "A String", # The date this variant was created, in milliseconds from the epoch.
"id": "A String", # The server-generated variant ID, unique across all variants.
"filter": [ # A list of filters (normally quality filters) this variant has failed.
# `PASS` indicates this variant has passed all filters.
"A String",
],
"start": "A String", # The position at which this variant occurs (0-based).
# This corresponds to the first base of the string of reference bases.
"names": [ # Names for the variant, for example a RefSNP ID.
"A String",
],
"alternateBases": [ # The bases that appear instead of the reference bases.
"A String",
],
"referenceName": "A String", # The reference on which this variant occurs.
# (such as `chr20` or `X`)
"quality": 3.14, # A measure of how likely this variant is to be real.
# A higher value is better.
"referenceBases": "A String", # The reference bases for this variant. They start at the given
# position.
},
],
"infoMergeConfig": { # A mapping between info field keys and the InfoMergeOperations to
# be performed on them.
"a_key": "A String",
},
}
x__xgafv: string, V1 error format.
Allowed values
1 - v1 error format
2 - v2 error format
Returns:
An object of the form:
{ # A generic empty message that you can re-use to avoid defining duplicated
# empty messages in your APIs. A typical example is to use it as the request
# or the response type of an API method. For instance:
#
# service Foo {
# rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty);
# }
#
# The JSON representation for `Empty` is empty JSON object `{}`.
}</pre>
</div>
<div class="method">
<code class="details" id="patch">patch(variantId, body, x__xgafv=None, updateMask=None)</code>
<pre>Updates a variant.
For the definitions of variants and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
This method supports patch semantics. Returns the modified variant without
its calls.
Args:
variantId: string, The ID of the variant to be updated. (required)
body: object, The request body. (required)
The object takes the form of:
{ # 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.
#
# For more genomics resource definitions, see [Fundamentals of Google
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
#
# 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.
"info": { # A map of additional variant information. This must be of the form
# map<string, string[]> (string key mapping to a list of string values).
"a_key": [
"",
],
},
"variantSetId": "A String", # The ID of the variant set this variant belongs to.
"end": "A 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.
"calls": [ # The variant calls for this particular variant. Each one represents the
# determination of genotype with respect to this variant.
{ # 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.
"info": { # A map of additional variant call information. This must be of the form
# map<string, string[]> (string key mapping to a list of string values).
"a_key": [
"",
],
},
"genotype": [ # 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.
42,
],
"callSetId": "A String", # The ID of the call set this variant call belongs to.
"phaseset": "A 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 `*`.
"genotypeLikelihood": [ # 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`.
3.14,
],
"callSetName": "A String", # The name of the call set this variant call belongs to.
},
],
"created": "A String", # The date this variant was created, in milliseconds from the epoch.
"id": "A String", # The server-generated variant ID, unique across all variants.
"filter": [ # A list of filters (normally quality filters) this variant has failed.
# `PASS` indicates this variant has passed all filters.
"A String",
],
"start": "A String", # The position at which this variant occurs (0-based).
# This corresponds to the first base of the string of reference bases.
"names": [ # Names for the variant, for example a RefSNP ID.
"A String",
],
"alternateBases": [ # The bases that appear instead of the reference bases.
"A String",
],
"referenceName": "A String", # The reference on which this variant occurs.
# (such as `chr20` or `X`)
"quality": 3.14, # A measure of how likely this variant is to be real.
# A higher value is better.
"referenceBases": "A String", # The reference bases for this variant. They start at the given
# position.
}
x__xgafv: string, V1 error format.
Allowed values
1 - v1 error format
2 - v2 error format
updateMask: string, An optional mask specifying which fields to update. At this time, mutable
fields are names and
info. Acceptable values are "names" and
"info". If unspecified, all mutable fields will be updated.
Returns:
An object of the form:
{ # 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.
#
# For more genomics resource definitions, see [Fundamentals of Google
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
#
# 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.
"info": { # A map of additional variant information. This must be of the form
# map<string, string[]> (string key mapping to a list of string values).
"a_key": [
"",
],
},
"variantSetId": "A String", # The ID of the variant set this variant belongs to.
"end": "A 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.
"calls": [ # The variant calls for this particular variant. Each one represents the
# determination of genotype with respect to this variant.
{ # 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.
"info": { # A map of additional variant call information. This must be of the form
# map<string, string[]> (string key mapping to a list of string values).
"a_key": [
"",
],
},
"genotype": [ # 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.
42,
],
"callSetId": "A String", # The ID of the call set this variant call belongs to.
"phaseset": "A 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 `*`.
"genotypeLikelihood": [ # 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`.
3.14,
],
"callSetName": "A String", # The name of the call set this variant call belongs to.
},
],
"created": "A String", # The date this variant was created, in milliseconds from the epoch.
"id": "A String", # The server-generated variant ID, unique across all variants.
"filter": [ # A list of filters (normally quality filters) this variant has failed.
# `PASS` indicates this variant has passed all filters.
"A String",
],
"start": "A String", # The position at which this variant occurs (0-based).
# This corresponds to the first base of the string of reference bases.
"names": [ # Names for the variant, for example a RefSNP ID.
"A String",
],
"alternateBases": [ # The bases that appear instead of the reference bases.
"A String",
],
"referenceName": "A String", # The reference on which this variant occurs.
# (such as `chr20` or `X`)
"quality": 3.14, # A measure of how likely this variant is to be real.
# A higher value is better.
"referenceBases": "A String", # The reference bases for this variant. They start at the given
# position.
}</pre>
</div>
<div class="method">
<code class="details" id="search">search(body, x__xgafv=None)</code>
<pre>Gets a list of variants matching the criteria.
For the definitions of variants and other genomics resources, see
[Fundamentals of Google
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Implements
[GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L126).
Args:
body: object, The request body. (required)
The object takes the form of:
{ # The variant search request.
"end": "A String", # The end of the window, 0-based exclusive. If unspecified or 0, defaults to
# the length of the reference.
"pageSize": 42, # The maximum number of variants to return in a single page. If unspecified,
# defaults to 5000. The maximum value is 10000.
"start": "A String", # The beginning of the window (0-based, inclusive) for which
# overlapping variants should be returned. If unspecified, defaults to 0.
"maxCalls": 42, # The maximum number of calls to return in a single page. Note that this
# limit may be exceeded in the event that a matching variant contains more
# calls than the requested maximum. If unspecified, defaults to 5000. The
# maximum value is 10000.
"pageToken": "A String", # The continuation token, which is used to page through large result sets.
# To get the next page of results, set this parameter to the value of
# `nextPageToken` from the previous response.
"variantSetIds": [ # At most one variant set ID must be provided. Only variants from this
# variant set will be returned. If omitted, a call set id must be included in
# the request.
"A String",
],
"variantName": "A String", # Only return variants which have exactly this name.
"referenceName": "A String", # Required. Only return variants in this reference sequence.
"callSetIds": [ # Only return variant calls which belong to call sets with these ids.
# Leaving this blank returns all variant calls. If a variant has no
# calls belonging to any of these call sets, it won't be returned at all.
"A String",
],
}
x__xgafv: string, V1 error format.
Allowed values
1 - v1 error format
2 - v2 error format
Returns:
An object of the form:
{ # The variant search response.
"nextPageToken": "A String", # The continuation token, which is used to page through large result sets.
# Provide this value in a subsequent request to return the next page of
# results. This field will be empty if there aren't any additional results.
"variants": [ # The list of matching Variants.
{ # 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.
#
# For more genomics resource definitions, see [Fundamentals of Google
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
#
# 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.
"info": { # A map of additional variant information. This must be of the form
# map<string, string[]> (string key mapping to a list of string values).
"a_key": [
"",
],
},
"variantSetId": "A String", # The ID of the variant set this variant belongs to.
"end": "A 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.
"calls": [ # The variant calls for this particular variant. Each one represents the
# determination of genotype with respect to this variant.
{ # 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.
"info": { # A map of additional variant call information. This must be of the form
# map<string, string[]> (string key mapping to a list of string values).
"a_key": [
"",
],
},
"genotype": [ # 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.
42,
],
"callSetId": "A String", # The ID of the call set this variant call belongs to.
"phaseset": "A 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 `*`.
"genotypeLikelihood": [ # 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`.
3.14,
],
"callSetName": "A String", # The name of the call set this variant call belongs to.
},
],
"created": "A String", # The date this variant was created, in milliseconds from the epoch.
"id": "A String", # The server-generated variant ID, unique across all variants.
"filter": [ # A list of filters (normally quality filters) this variant has failed.
# `PASS` indicates this variant has passed all filters.
"A String",
],
"start": "A String", # The position at which this variant occurs (0-based).
# This corresponds to the first base of the string of reference bases.
"names": [ # Names for the variant, for example a RefSNP ID.
"A String",
],
"alternateBases": [ # The bases that appear instead of the reference bases.
"A String",
],
"referenceName": "A String", # The reference on which this variant occurs.
# (such as `chr20` or `X`)
"quality": 3.14, # A measure of how likely this variant is to be real.
# A higher value is better.
"referenceBases": "A String", # The reference bases for this variant. They start at the given
# position.
},
],
}</pre>
</div>
<div class="method">
<code class="details" id="search_next">search_next(previous_request, previous_response)</code>
<pre>Retrieves the next page of results.
Args:
previous_request: The request for the previous page. (required)
previous_response: The response from the request for the previous page. (required)
Returns:
A request object that you can call 'execute()' on to request the next
page. Returns None if there are no more items in the collection.
</pre>
</div>
</body></html>
Reference in new issue View Git Blame Copy Permalink