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.
781 lines
38 KiB
781 lines
38 KiB
<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.readgroupsets.html">readgroupsets</a></h1>
|
|
<h2>Instance Methods</h2>
|
|
<p class="toc_element">
|
|
<code><a href="genomics_v1.readgroupsets.coveragebuckets.html">coveragebuckets()</a></code>
|
|
</p>
|
|
<p class="firstline">Returns the coveragebuckets Resource.</p>
|
|
|
|
<p class="toc_element">
|
|
<code><a href="#delete">delete(readGroupSetId, x__xgafv=None)</a></code></p>
|
|
<p class="firstline">Deletes a read group set.</p>
|
|
<p class="toc_element">
|
|
<code><a href="#export">export(readGroupSetId, body, x__xgafv=None)</a></code></p>
|
|
<p class="firstline">Exports a read group set to a BAM file in Google Cloud Storage.</p>
|
|
<p class="toc_element">
|
|
<code><a href="#get">get(readGroupSetId, x__xgafv=None)</a></code></p>
|
|
<p class="firstline">Gets a read group set by ID.</p>
|
|
<p class="toc_element">
|
|
<code><a href="#import_">import_(body, x__xgafv=None)</a></code></p>
|
|
<p class="firstline">Creates read group sets by asynchronously importing the provided</p>
|
|
<p class="toc_element">
|
|
<code><a href="#patch">patch(readGroupSetId, body, updateMask=None, x__xgafv=None)</a></code></p>
|
|
<p class="firstline">Updates a read group set.</p>
|
|
<p class="toc_element">
|
|
<code><a href="#search">search(body, x__xgafv=None)</a></code></p>
|
|
<p class="firstline">Searches for read group sets 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="delete">delete(readGroupSetId, x__xgafv=None)</code>
|
|
<pre>Deletes a read group set.
|
|
|
|
For the definitions of read group sets and other genomics resources, see
|
|
[Fundamentals of Google
|
|
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
|
|
Args:
|
|
readGroupSetId: string, The ID of the read group set to be deleted. The caller must have WRITE
|
|
permissions to the dataset associated with this read group set. (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="export">export(readGroupSetId, body, x__xgafv=None)</code>
|
|
<pre>Exports a read group set to a BAM file in Google Cloud Storage.
|
|
|
|
For the definitions of read group sets and other genomics resources, see
|
|
[Fundamentals of Google
|
|
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
|
|
Note that currently there may be some differences between exported BAM
|
|
files and the original BAM file at the time of import. See
|
|
ImportReadGroupSets
|
|
for caveats.
|
|
|
|
Args:
|
|
readGroupSetId: string, Required. The ID of the read group set to export. The caller must have
|
|
READ access to this read group set. (required)
|
|
body: object, The request body. (required)
|
|
The object takes the form of:
|
|
|
|
{ # The read group set export request.
|
|
"projectId": "A String", # Required. The Google Cloud project ID that owns this
|
|
# export. The caller must have WRITE access to this project.
|
|
"referenceNames": [ # The reference names to export. If this is not specified, all reference
|
|
# sequences, including unmapped reads, are exported.
|
|
# Use `*` to export only unmapped reads.
|
|
"A String",
|
|
],
|
|
"exportUri": "A String", # Required. A Google Cloud Storage URI for the exported BAM file.
|
|
# The currently authenticated user must have write access to the new file.
|
|
# An error will be returned if the URI already contains data.
|
|
}
|
|
|
|
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: `operations/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw`
|
|
}</pre>
|
|
</div>
|
|
|
|
<div class="method">
|
|
<code class="details" id="get">get(readGroupSetId, x__xgafv=None)</code>
|
|
<pre>Gets a read group set by ID.
|
|
|
|
For the definitions of read group sets and other genomics resources, see
|
|
[Fundamentals of Google
|
|
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
|
|
Args:
|
|
readGroupSetId: string, The ID of the read group set. (required)
|
|
x__xgafv: string, V1 error format.
|
|
Allowed values
|
|
1 - v1 error format
|
|
2 - v2 error format
|
|
|
|
Returns:
|
|
An object of the form:
|
|
|
|
{ # A read group set is a logical collection of read groups, which are
|
|
# collections of reads produced by a sequencer. A read group set typically
|
|
# models reads corresponding to one sample, sequenced one way, and aligned one
|
|
# way.
|
|
#
|
|
# * A read group set belongs to one dataset.
|
|
# * A read group belongs to one read group set.
|
|
# * A read belongs to one read group.
|
|
#
|
|
# For more genomics resource definitions, see [Fundamentals of Google
|
|
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
"info": { # A map of additional read group set information.
|
|
"a_key": [
|
|
"",
|
|
],
|
|
},
|
|
"name": "A String", # The read group set name. By default this will be initialized to the sample
|
|
# name of the sequenced data contained in this set.
|
|
"readGroups": [ # The read groups in this set. There are typically 1-10 read groups in a read
|
|
# group set.
|
|
{ # A read group is all the data that's processed the same way by the sequencer.
|
|
"info": { # A map of additional read group information. This must be of the form
|
|
# map<string, string[]> (string key mapping to a list of string values).
|
|
"a_key": [
|
|
"",
|
|
],
|
|
},
|
|
"predictedInsertSize": 42, # The predicted insert size of this read group. The insert size is the length
|
|
# the sequenced DNA fragment from end-to-end, not including the adapters.
|
|
"name": "A String", # The read group name. This corresponds to the @RG ID field in the SAM spec.
|
|
"programs": [ # The programs used to generate this read group. Programs are always
|
|
# identical for all read groups within a read group set. For this reason,
|
|
# only the first read group in a returned set will have this field
|
|
# populated.
|
|
{
|
|
"prevProgramId": "A String", # The ID of the program run before this one.
|
|
"commandLine": "A String", # The command line used to run this program.
|
|
"version": "A String", # The version of the program run.
|
|
"id": "A String", # The user specified locally unique ID of the program. Used along with
|
|
# `prevProgramId` to define an ordering between programs.
|
|
"name": "A String", # The display name of the program. This is typically the colloquial name of
|
|
# the tool used, for example 'bwa' or 'picard'.
|
|
},
|
|
],
|
|
"sampleId": "A String", # A client-supplied sample identifier for the reads in this read group.
|
|
"experiment": { # The experiment used to generate this read group.
|
|
"sequencingCenter": "A String", # The sequencing center used as part of this experiment.
|
|
"libraryId": "A String", # A client-supplied library identifier; a library is a collection of DNA
|
|
# fragments which have been prepared for sequencing from a sample. This
|
|
# field is important for quality control as error or bias can be introduced
|
|
# during sample preparation.
|
|
"instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to
|
|
# sequencing technology in the SAM spec.
|
|
"platformUnit": "A String", # The platform unit used as part of this experiment, for example
|
|
# flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
|
|
# @RG PU field in the SAM spec.
|
|
},
|
|
"referenceSetId": "A String", # The reference set the reads in this read group are aligned to.
|
|
"id": "A String", # The server-generated read group ID, unique for all read groups.
|
|
# Note: This is different than the @RG ID field in the SAM spec. For that
|
|
# value, see name.
|
|
"datasetId": "A String", # The dataset to which this read group belongs.
|
|
"description": "A String", # A free-form text description of this read group.
|
|
},
|
|
],
|
|
"filename": "A String", # The filename of the original source file for this read group set, if any.
|
|
"referenceSetId": "A String", # The reference set to which the reads in this read group set are aligned.
|
|
"id": "A String", # The server-generated read group set ID, unique for all read group sets.
|
|
"datasetId": "A String", # The dataset to which this read group set belongs.
|
|
}</pre>
|
|
</div>
|
|
|
|
<div class="method">
|
|
<code class="details" id="import_">import_(body, x__xgafv=None)</code>
|
|
<pre>Creates read group sets by asynchronously importing the provided
|
|
information.
|
|
|
|
For the definitions of read group sets and other genomics resources, see
|
|
[Fundamentals of Google
|
|
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
|
|
The caller must have WRITE permissions to the dataset.
|
|
|
|
## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import
|
|
|
|
- Tags will be converted to strings - tag types are not preserved
|
|
- Comments (`@CO`) in the input file header will not be preserved
|
|
- Original header order of references (`@SQ`) will not be preserved
|
|
- Any reverse stranded unmapped reads will be reverse complemented, and
|
|
their qualities (also the "BQ" and "OQ" tags, if any) will be reversed
|
|
- Unmapped reads will be stripped of positional information (reference name
|
|
and position)
|
|
|
|
Args:
|
|
body: object, The request body. (required)
|
|
The object takes the form of:
|
|
|
|
{ # The read group set import request.
|
|
"partitionStrategy": "A String", # The partition strategy describes how read groups are partitioned into read
|
|
# group sets.
|
|
"sourceUris": [ # A list of URIs pointing at [BAM
|
|
# files](https://samtools.github.io/hts-specs/SAMv1.pdf)
|
|
# in Google Cloud Storage.
|
|
# Those URIs can include wildcards (*), but do not add or remove
|
|
# matching files before import has completed.
|
|
#
|
|
# Note that Google Cloud Storage object listing is only eventually
|
|
# consistent: files added may be not be immediately visible to
|
|
# everyone. Thus, if using a wildcard it is preferable not to start
|
|
# the import immediately after the files are created.
|
|
"A String",
|
|
],
|
|
"referenceSetId": "A String", # The reference set to which the imported read group sets are aligned to, if
|
|
# any. The reference names of this reference set must be a superset of those
|
|
# found in the imported file headers. If no reference set id is provided, a
|
|
# best effort is made to associate with a matching reference set.
|
|
"datasetId": "A String", # Required. The ID of the dataset these read group sets will belong to. The
|
|
# caller must have WRITE permissions to this dataset.
|
|
}
|
|
|
|
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: `operations/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw`
|
|
}</pre>
|
|
</div>
|
|
|
|
<div class="method">
|
|
<code class="details" id="patch">patch(readGroupSetId, body, updateMask=None, x__xgafv=None)</code>
|
|
<pre>Updates a read group set.
|
|
|
|
For the definitions of read group sets and other genomics resources, see
|
|
[Fundamentals of Google
|
|
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
|
|
This method supports patch semantics.
|
|
|
|
Args:
|
|
readGroupSetId: string, The ID of the read group set to be updated. The caller must have WRITE
|
|
permissions to the dataset associated with this read group set. (required)
|
|
body: object, The request body. (required)
|
|
The object takes the form of:
|
|
|
|
{ # A read group set is a logical collection of read groups, which are
|
|
# collections of reads produced by a sequencer. A read group set typically
|
|
# models reads corresponding to one sample, sequenced one way, and aligned one
|
|
# way.
|
|
#
|
|
# * A read group set belongs to one dataset.
|
|
# * A read group belongs to one read group set.
|
|
# * A read belongs to one read group.
|
|
#
|
|
# For more genomics resource definitions, see [Fundamentals of Google
|
|
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
"info": { # A map of additional read group set information.
|
|
"a_key": [
|
|
"",
|
|
],
|
|
},
|
|
"name": "A String", # The read group set name. By default this will be initialized to the sample
|
|
# name of the sequenced data contained in this set.
|
|
"readGroups": [ # The read groups in this set. There are typically 1-10 read groups in a read
|
|
# group set.
|
|
{ # A read group is all the data that's processed the same way by the sequencer.
|
|
"info": { # A map of additional read group information. This must be of the form
|
|
# map<string, string[]> (string key mapping to a list of string values).
|
|
"a_key": [
|
|
"",
|
|
],
|
|
},
|
|
"predictedInsertSize": 42, # The predicted insert size of this read group. The insert size is the length
|
|
# the sequenced DNA fragment from end-to-end, not including the adapters.
|
|
"name": "A String", # The read group name. This corresponds to the @RG ID field in the SAM spec.
|
|
"programs": [ # The programs used to generate this read group. Programs are always
|
|
# identical for all read groups within a read group set. For this reason,
|
|
# only the first read group in a returned set will have this field
|
|
# populated.
|
|
{
|
|
"prevProgramId": "A String", # The ID of the program run before this one.
|
|
"commandLine": "A String", # The command line used to run this program.
|
|
"version": "A String", # The version of the program run.
|
|
"id": "A String", # The user specified locally unique ID of the program. Used along with
|
|
# `prevProgramId` to define an ordering between programs.
|
|
"name": "A String", # The display name of the program. This is typically the colloquial name of
|
|
# the tool used, for example 'bwa' or 'picard'.
|
|
},
|
|
],
|
|
"sampleId": "A String", # A client-supplied sample identifier for the reads in this read group.
|
|
"experiment": { # The experiment used to generate this read group.
|
|
"sequencingCenter": "A String", # The sequencing center used as part of this experiment.
|
|
"libraryId": "A String", # A client-supplied library identifier; a library is a collection of DNA
|
|
# fragments which have been prepared for sequencing from a sample. This
|
|
# field is important for quality control as error or bias can be introduced
|
|
# during sample preparation.
|
|
"instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to
|
|
# sequencing technology in the SAM spec.
|
|
"platformUnit": "A String", # The platform unit used as part of this experiment, for example
|
|
# flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
|
|
# @RG PU field in the SAM spec.
|
|
},
|
|
"referenceSetId": "A String", # The reference set the reads in this read group are aligned to.
|
|
"id": "A String", # The server-generated read group ID, unique for all read groups.
|
|
# Note: This is different than the @RG ID field in the SAM spec. For that
|
|
# value, see name.
|
|
"datasetId": "A String", # The dataset to which this read group belongs.
|
|
"description": "A String", # A free-form text description of this read group.
|
|
},
|
|
],
|
|
"filename": "A String", # The filename of the original source file for this read group set, if any.
|
|
"referenceSetId": "A String", # The reference set to which the reads in this read group set are aligned.
|
|
"id": "A String", # The server-generated read group set ID, unique for all read group sets.
|
|
"datasetId": "A String", # The dataset to which this read group set belongs.
|
|
}
|
|
|
|
updateMask: string, An optional mask specifying which fields to update. Supported fields:
|
|
|
|
* name.
|
|
* referenceSetId.
|
|
|
|
Leaving `updateMask` unset is equivalent to specifying all mutable
|
|
fields.
|
|
x__xgafv: string, V1 error format.
|
|
Allowed values
|
|
1 - v1 error format
|
|
2 - v2 error format
|
|
|
|
Returns:
|
|
An object of the form:
|
|
|
|
{ # A read group set is a logical collection of read groups, which are
|
|
# collections of reads produced by a sequencer. A read group set typically
|
|
# models reads corresponding to one sample, sequenced one way, and aligned one
|
|
# way.
|
|
#
|
|
# * A read group set belongs to one dataset.
|
|
# * A read group belongs to one read group set.
|
|
# * A read belongs to one read group.
|
|
#
|
|
# For more genomics resource definitions, see [Fundamentals of Google
|
|
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
"info": { # A map of additional read group set information.
|
|
"a_key": [
|
|
"",
|
|
],
|
|
},
|
|
"name": "A String", # The read group set name. By default this will be initialized to the sample
|
|
# name of the sequenced data contained in this set.
|
|
"readGroups": [ # The read groups in this set. There are typically 1-10 read groups in a read
|
|
# group set.
|
|
{ # A read group is all the data that's processed the same way by the sequencer.
|
|
"info": { # A map of additional read group information. This must be of the form
|
|
# map<string, string[]> (string key mapping to a list of string values).
|
|
"a_key": [
|
|
"",
|
|
],
|
|
},
|
|
"predictedInsertSize": 42, # The predicted insert size of this read group. The insert size is the length
|
|
# the sequenced DNA fragment from end-to-end, not including the adapters.
|
|
"name": "A String", # The read group name. This corresponds to the @RG ID field in the SAM spec.
|
|
"programs": [ # The programs used to generate this read group. Programs are always
|
|
# identical for all read groups within a read group set. For this reason,
|
|
# only the first read group in a returned set will have this field
|
|
# populated.
|
|
{
|
|
"prevProgramId": "A String", # The ID of the program run before this one.
|
|
"commandLine": "A String", # The command line used to run this program.
|
|
"version": "A String", # The version of the program run.
|
|
"id": "A String", # The user specified locally unique ID of the program. Used along with
|
|
# `prevProgramId` to define an ordering between programs.
|
|
"name": "A String", # The display name of the program. This is typically the colloquial name of
|
|
# the tool used, for example 'bwa' or 'picard'.
|
|
},
|
|
],
|
|
"sampleId": "A String", # A client-supplied sample identifier for the reads in this read group.
|
|
"experiment": { # The experiment used to generate this read group.
|
|
"sequencingCenter": "A String", # The sequencing center used as part of this experiment.
|
|
"libraryId": "A String", # A client-supplied library identifier; a library is a collection of DNA
|
|
# fragments which have been prepared for sequencing from a sample. This
|
|
# field is important for quality control as error or bias can be introduced
|
|
# during sample preparation.
|
|
"instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to
|
|
# sequencing technology in the SAM spec.
|
|
"platformUnit": "A String", # The platform unit used as part of this experiment, for example
|
|
# flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
|
|
# @RG PU field in the SAM spec.
|
|
},
|
|
"referenceSetId": "A String", # The reference set the reads in this read group are aligned to.
|
|
"id": "A String", # The server-generated read group ID, unique for all read groups.
|
|
# Note: This is different than the @RG ID field in the SAM spec. For that
|
|
# value, see name.
|
|
"datasetId": "A String", # The dataset to which this read group belongs.
|
|
"description": "A String", # A free-form text description of this read group.
|
|
},
|
|
],
|
|
"filename": "A String", # The filename of the original source file for this read group set, if any.
|
|
"referenceSetId": "A String", # The reference set to which the reads in this read group set are aligned.
|
|
"id": "A String", # The server-generated read group set ID, unique for all read group sets.
|
|
"datasetId": "A String", # The dataset to which this read group set belongs.
|
|
}</pre>
|
|
</div>
|
|
|
|
<div class="method">
|
|
<code class="details" id="search">search(body, x__xgafv=None)</code>
|
|
<pre>Searches for read group sets matching the criteria.
|
|
|
|
For the definitions of read group sets and other genomics resources, see
|
|
[Fundamentals of Google
|
|
Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
|
|
Implements
|
|
[GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135).
|
|
|
|
Args:
|
|
body: object, The request body. (required)
|
|
The object takes the form of:
|
|
|
|
{ # The read group set search request.
|
|
"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.
|
|
"datasetIds": [ # Restricts this query to read group sets within the given datasets. At least
|
|
# one ID must be provided.
|
|
"A String",
|
|
],
|
|
"name": "A String", # Only return read group sets for which a substring of the name matches this
|
|
# string.
|
|
"pageSize": 42, # The maximum number of results to return in a single page. If unspecified,
|
|
# defaults to 256. The maximum value is 1024.
|
|
}
|
|
|
|
x__xgafv: string, V1 error format.
|
|
Allowed values
|
|
1 - v1 error format
|
|
2 - v2 error format
|
|
|
|
Returns:
|
|
An object of the form:
|
|
|
|
{ # The read group set 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.
|
|
"readGroupSets": [ # The list of matching read group sets.
|
|
{ # A read group set is a logical collection of read groups, which are
|
|
# collections of reads produced by a sequencer. A read group set typically
|
|
# models reads corresponding to one sample, sequenced one way, and aligned one
|
|
# way.
|
|
#
|
|
# * A read group set belongs to one dataset.
|
|
# * A read group belongs to one read group set.
|
|
# * A read belongs to one read group.
|
|
#
|
|
# For more genomics resource definitions, see [Fundamentals of Google
|
|
# Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
|
"info": { # A map of additional read group set information.
|
|
"a_key": [
|
|
"",
|
|
],
|
|
},
|
|
"name": "A String", # The read group set name. By default this will be initialized to the sample
|
|
# name of the sequenced data contained in this set.
|
|
"readGroups": [ # The read groups in this set. There are typically 1-10 read groups in a read
|
|
# group set.
|
|
{ # A read group is all the data that's processed the same way by the sequencer.
|
|
"info": { # A map of additional read group information. This must be of the form
|
|
# map<string, string[]> (string key mapping to a list of string values).
|
|
"a_key": [
|
|
"",
|
|
],
|
|
},
|
|
"predictedInsertSize": 42, # The predicted insert size of this read group. The insert size is the length
|
|
# the sequenced DNA fragment from end-to-end, not including the adapters.
|
|
"name": "A String", # The read group name. This corresponds to the @RG ID field in the SAM spec.
|
|
"programs": [ # The programs used to generate this read group. Programs are always
|
|
# identical for all read groups within a read group set. For this reason,
|
|
# only the first read group in a returned set will have this field
|
|
# populated.
|
|
{
|
|
"prevProgramId": "A String", # The ID of the program run before this one.
|
|
"commandLine": "A String", # The command line used to run this program.
|
|
"version": "A String", # The version of the program run.
|
|
"id": "A String", # The user specified locally unique ID of the program. Used along with
|
|
# `prevProgramId` to define an ordering between programs.
|
|
"name": "A String", # The display name of the program. This is typically the colloquial name of
|
|
# the tool used, for example 'bwa' or 'picard'.
|
|
},
|
|
],
|
|
"sampleId": "A String", # A client-supplied sample identifier for the reads in this read group.
|
|
"experiment": { # The experiment used to generate this read group.
|
|
"sequencingCenter": "A String", # The sequencing center used as part of this experiment.
|
|
"libraryId": "A String", # A client-supplied library identifier; a library is a collection of DNA
|
|
# fragments which have been prepared for sequencing from a sample. This
|
|
# field is important for quality control as error or bias can be introduced
|
|
# during sample preparation.
|
|
"instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to
|
|
# sequencing technology in the SAM spec.
|
|
"platformUnit": "A String", # The platform unit used as part of this experiment, for example
|
|
# flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
|
|
# @RG PU field in the SAM spec.
|
|
},
|
|
"referenceSetId": "A String", # The reference set the reads in this read group are aligned to.
|
|
"id": "A String", # The server-generated read group ID, unique for all read groups.
|
|
# Note: This is different than the @RG ID field in the SAM spec. For that
|
|
# value, see name.
|
|
"datasetId": "A String", # The dataset to which this read group belongs.
|
|
"description": "A String", # A free-form text description of this read group.
|
|
},
|
|
],
|
|
"filename": "A String", # The filename of the original source file for this read group set, if any.
|
|
"referenceSetId": "A String", # The reference set to which the reads in this read group set are aligned.
|
|
"id": "A String", # The server-generated read group set ID, unique for all read group sets.
|
|
"datasetId": "A String", # The dataset to which this read group set belongs.
|
|
},
|
|
],
|
|
}</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> |