SDK for PHP 3.x

Client: Aws\Omics\OmicsClient
Service ID: omics
Version: 2022-11-28

This page describes the parameters and results for the operations of the Amazon Omics (2022-11-28), and shows how to use the Aws\Omics\OmicsClient object to call the described operations. This documentation is specific to the 2022-11-28 API version of the service.

Operation Summary

Each of the following operations can be created from a client using $client->getCommand('CommandName'), where "CommandName" is the name of one of the following operations. Note: a command is a value that encapsulates an operation and the parameters used to create an HTTP request.

You can also create and send a command immediately using the magic methods available on a client object: $client->commandName(/* parameters */). You can send the command asynchronously (returning a promise) by appending the word "Async" to the operation name: $client->commandNameAsync(/* parameters */).

AbortMultipartReadSetUpload ( array $params = [] )
Stops a multipart upload.
AcceptShare ( array $params = [] )
Accept a resource share request.
BatchDeleteReadSet ( array $params = [] )
Deletes one or more read sets.
CancelAnnotationImportJob ( array $params = [] )
Cancels an annotation import job.
CancelRun ( array $params = [] )
Cancels a run.
CancelVariantImportJob ( array $params = [] )
Cancels a variant import job.
CompleteMultipartReadSetUpload ( array $params = [] )
Concludes a multipart upload once you have uploaded all the components.
CreateAnnotationStore ( array $params = [] )
Creates an annotation store.
CreateAnnotationStoreVersion ( array $params = [] )
Creates a new version of an annotation store.
CreateMultipartReadSetUpload ( array $params = [] )
Begins a multipart read set upload.
CreateReferenceStore ( array $params = [] )
Creates a reference store.
CreateRunGroup ( array $params = [] )
You can optionally create a run group to limit the compute resources for the runs that you add to the group.
CreateSequenceStore ( array $params = [] )
Creates a sequence store.
CreateShare ( array $params = [] )
Creates a cross-account shared resource.
CreateVariantStore ( array $params = [] )
Creates a variant store.
CreateWorkflow ( array $params = [] )
Creates a workflow.
DeleteAnnotationStore ( array $params = [] )
Deletes an annotation store.
DeleteAnnotationStoreVersions ( array $params = [] )
Deletes one or multiple versions of an annotation store.
DeleteReference ( array $params = [] )
Deletes a genome reference.
DeleteReferenceStore ( array $params = [] )
Deletes a genome reference store.
DeleteRun ( array $params = [] )
Deletes a workflow run.
DeleteRunGroup ( array $params = [] )
Deletes a workflow run group.
DeleteSequenceStore ( array $params = [] )
Deletes a sequence store.
DeleteShare ( array $params = [] )
Deletes a resource share.
DeleteVariantStore ( array $params = [] )
Deletes a variant store.
DeleteWorkflow ( array $params = [] )
Deletes a workflow.
GetAnnotationImportJob ( array $params = [] )
Gets information about an annotation import job.
GetAnnotationStore ( array $params = [] )
Gets information about an annotation store.
GetAnnotationStoreVersion ( array $params = [] )
Retrieves the metadata for an annotation store version.
GetReadSet ( array $params = [] )
Gets a file from a read set.
GetReadSetActivationJob ( array $params = [] )
Gets information about a read set activation job.
GetReadSetExportJob ( array $params = [] )
Gets information about a read set export job.
GetReadSetImportJob ( array $params = [] )
Gets information about a read set import job.
GetReadSetMetadata ( array $params = [] )
Gets details about a read set.
GetReference ( array $params = [] )
Gets a reference file.
GetReferenceImportJob ( array $params = [] )
Gets information about a reference import job.
GetReferenceMetadata ( array $params = [] )
Gets information about a genome reference's metadata.
GetReferenceStore ( array $params = [] )
Gets information about a reference store.
GetRun ( array $params = [] )
Gets information about a workflow run.
GetRunGroup ( array $params = [] )
Gets information about a workflow run group.
GetRunTask ( array $params = [] )
Gets information about a workflow run task.
GetSequenceStore ( array $params = [] )
Gets information about a sequence store.
GetShare ( array $params = [] )
Retrieves the metadata for the specified resource share.
GetVariantImportJob ( array $params = [] )
Gets information about a variant import job.
GetVariantStore ( array $params = [] )
Gets information about a variant store.
GetWorkflow ( array $params = [] )
Gets information about a workflow.
ListAnnotationImportJobs ( array $params = [] )
Retrieves a list of annotation import jobs.
ListAnnotationStoreVersions ( array $params = [] )
Lists the versions of an annotation store.
ListAnnotationStores ( array $params = [] )
Retrieves a list of annotation stores.
ListMultipartReadSetUploads ( array $params = [] )
Lists multipart read set uploads and for in progress uploads.
ListReadSetActivationJobs ( array $params = [] )
Retrieves a list of read set activation jobs.
ListReadSetExportJobs ( array $params = [] )
Retrieves a list of read set export jobs.
ListReadSetImportJobs ( array $params = [] )
Retrieves a list of read set import jobs.
ListReadSetUploadParts ( array $params = [] )
This operation will list all parts in a requested multipart upload for a sequence store.
ListReadSets ( array $params = [] )
Retrieves a list of read sets.
ListReferenceImportJobs ( array $params = [] )
Retrieves a list of reference import jobs.
ListReferenceStores ( array $params = [] )
Retrieves a list of reference stores.
ListReferences ( array $params = [] )
Retrieves a list of references.
ListRunGroups ( array $params = [] )
Retrieves a list of run groups.
ListRunTasks ( array $params = [] )
Retrieves a list of tasks for a run.
ListRuns ( array $params = [] )
Retrieves a list of runs.
ListSequenceStores ( array $params = [] )
Retrieves a list of sequence stores.
ListShares ( array $params = [] )
Retrieves the resource shares associated with an account.
ListTagsForResource ( array $params = [] )
Retrieves a list of tags for a resource.
ListVariantImportJobs ( array $params = [] )
Retrieves a list of variant import jobs.
ListVariantStores ( array $params = [] )
Retrieves a list of variant stores.
ListWorkflows ( array $params = [] )
Retrieves a list of workflows.
StartAnnotationImportJob ( array $params = [] )
Starts an annotation import job.
StartReadSetActivationJob ( array $params = [] )
Activates an archived read set.
StartReadSetExportJob ( array $params = [] )
Exports a read set to Amazon S3.
StartReadSetImportJob ( array $params = [] )
Starts a read set import job.
StartReferenceImportJob ( array $params = [] )
Starts a reference import job.
StartRun ( array $params = [] )
Starts a workflow run.
StartVariantImportJob ( array $params = [] )
Starts a variant import job.
TagResource ( array $params = [] )
Tags a resource.
UntagResource ( array $params = [] )
Removes tags from a resource.
UpdateAnnotationStore ( array $params = [] )
Updates an annotation store.
UpdateAnnotationStoreVersion ( array $params = [] )
Updates the description of an annotation store version.
UpdateRunGroup ( array $params = [] )
Updates a run group.
UpdateVariantStore ( array $params = [] )
Updates a variant store.
UpdateWorkflow ( array $params = [] )
Updates a workflow.
UploadReadSetPart ( array $params = [] )
This operation uploads a specific part of a read set.

Paginators

Paginators handle automatically iterating over paginated API results. Paginators are associated with specific API operations, and they accept the parameters that the corresponding API operation accepts. You can get a paginator from a client class using getPaginator($paginatorName, $operationParameters). This client supports the following paginators:

ListAnnotationImportJobs
ListAnnotationStoreVersions
ListAnnotationStores
ListMultipartReadSetUploads
ListReadSetActivationJobs
ListReadSetExportJobs
ListReadSetImportJobs
ListReadSetUploadParts
ListReadSets
ListReferenceImportJobs
ListReferenceStores
ListReferences
ListRunGroups
ListRunTasks
ListRuns
ListSequenceStores
ListShares
ListVariantImportJobs
ListVariantStores
ListWorkflows

Waiters

Waiters allow you to poll a resource until it enters into a desired state. A waiter has a name used to describe what it does, and is associated with an API operation. When creating a waiter, you can provide the API operation parameters associated with the corresponding operation. Waiters can be accessed using the getWaiter($waiterName, $operationParameters) method of a client object. This client supports the following waiters:

Waiter name API Operation Delay Max Attempts
AnnotationImportJobCreated GetAnnotationImportJob 30 20
AnnotationStoreCreated GetAnnotationStore 30 20
AnnotationStoreDeleted GetAnnotationStore 30 20
AnnotationStoreVersionCreated GetAnnotationStoreVersion 30 20
AnnotationStoreVersionDeleted GetAnnotationStoreVersion 30 20
ReadSetActivationJobCompleted GetReadSetActivationJob 30 20
ReadSetExportJobCompleted GetReadSetExportJob 30 20
ReadSetImportJobCompleted GetReadSetImportJob 30 20
ReferenceImportJobCompleted GetReferenceImportJob 30 20
RunCompleted GetRun 30 20
RunRunning GetRun 30 20
TaskCompleted GetRunTask 30 20
TaskRunning GetRunTask 30 20
VariantImportJobCreated GetVariantImportJob 30 20
VariantStoreCreated GetVariantStore 30 20
VariantStoreDeleted GetVariantStore 30 20
WorkflowActive GetWorkflow 3 10

Operations

AbortMultipartReadSetUpload

$result = $client->abortMultipartReadSetUpload([/* ... */]);
$promise = $client->abortMultipartReadSetUploadAsync([/* ... */]);

Stops a multipart upload.

Parameter Syntax

$result = $client->abortMultipartReadSetUpload([
    'sequenceStoreId' => '<string>', // REQUIRED
    'uploadId' => '<string>', // REQUIRED
]);

Parameter Details

Members
sequenceStoreId
Required: Yes
Type: string

The sequence store ID for the store involved in the multipart upload.

uploadId
Required: Yes
Type: string

The ID for the multipart upload.

Result Syntax

[]

Result Details

The results for this operation are always empty.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

NotSupportedOperationException:

The operation is not supported by Amazon Omics, or the API does not exist.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

AcceptShare

$result = $client->acceptShare([/* ... */]);
$promise = $client->acceptShareAsync([/* ... */]);

Accept a resource share request.

Parameter Syntax

$result = $client->acceptShare([
    'shareId' => '<string>', // REQUIRED
]);

Parameter Details

Members
shareId
Required: Yes
Type: string

The ID of the resource share.

Result Syntax

[
    'status' => 'PENDING|ACTIVATING|ACTIVE|DELETING|DELETED|FAILED',
]

Result Details

Members
status
Type: string

The status of the resource share.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

BatchDeleteReadSet

$result = $client->batchDeleteReadSet([/* ... */]);
$promise = $client->batchDeleteReadSetAsync([/* ... */]);

Deletes one or more read sets.

Parameter Syntax

$result = $client->batchDeleteReadSet([
    'ids' => ['<string>', ...], // REQUIRED
    'sequenceStoreId' => '<string>', // REQUIRED
]);

Parameter Details

Members
ids
Required: Yes
Type: Array of strings

The read sets' IDs.

sequenceStoreId
Required: Yes
Type: string

The read sets' sequence store ID.

Result Syntax

[
    'errors' => [
        [
            'code' => '<string>',
            'id' => '<string>',
            'message' => '<string>',
        ],
        // ...
    ],
]

Result Details

Members
errors
Type: Array of ReadSetBatchError structures

Errors returned by individual delete operations.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

CancelAnnotationImportJob

$result = $client->cancelAnnotationImportJob([/* ... */]);
$promise = $client->cancelAnnotationImportJobAsync([/* ... */]);

Cancels an annotation import job.

Parameter Syntax

$result = $client->cancelAnnotationImportJob([
    'jobId' => '<string>', // REQUIRED
]);

Parameter Details

Members
jobId
Required: Yes
Type: string

The job's ID.

Result Syntax

[]

Result Details

The results for this operation are always empty.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

CancelRun

$result = $client->cancelRun([/* ... */]);
$promise = $client->cancelRunAsync([/* ... */]);

Cancels a run.

Parameter Syntax

$result = $client->cancelRun([
    'id' => '<string>', // REQUIRED
]);

Parameter Details

Members
id
Required: Yes
Type: string

The run's ID.

Result Syntax

[]

Result Details

The results for this operation are always empty.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

CancelVariantImportJob

$result = $client->cancelVariantImportJob([/* ... */]);
$promise = $client->cancelVariantImportJobAsync([/* ... */]);

Cancels a variant import job.

Parameter Syntax

$result = $client->cancelVariantImportJob([
    'jobId' => '<string>', // REQUIRED
]);

Parameter Details

Members
jobId
Required: Yes
Type: string

The job's ID.

Result Syntax

[]

Result Details

The results for this operation are always empty.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

CompleteMultipartReadSetUpload

$result = $client->completeMultipartReadSetUpload([/* ... */]);
$promise = $client->completeMultipartReadSetUploadAsync([/* ... */]);

Concludes a multipart upload once you have uploaded all the components.

Parameter Syntax

$result = $client->completeMultipartReadSetUpload([
    'parts' => [ // REQUIRED
        [
            'checksum' => '<string>', // REQUIRED
            'partNumber' => <integer>, // REQUIRED
            'partSource' => 'SOURCE1|SOURCE2', // REQUIRED
        ],
        // ...
    ],
    'sequenceStoreId' => '<string>', // REQUIRED
    'uploadId' => '<string>', // REQUIRED
]);

Parameter Details

Members
parts
Required: Yes
Type: Array of CompleteReadSetUploadPartListItem structures

The individual uploads or parts of a multipart upload.

sequenceStoreId
Required: Yes
Type: string

The sequence store ID for the store involved in the multipart upload.

uploadId
Required: Yes
Type: string

The ID for the multipart upload.

Result Syntax

[
    'readSetId' => '<string>',
]

Result Details

Members
readSetId
Required: Yes
Type: string

The read set ID created for an uploaded read set.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

NotSupportedOperationException:

The operation is not supported by Amazon Omics, or the API does not exist.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

CreateAnnotationStore

$result = $client->createAnnotationStore([/* ... */]);
$promise = $client->createAnnotationStoreAsync([/* ... */]);

Creates an annotation store.

Parameter Syntax

$result = $client->createAnnotationStore([
    'description' => '<string>',
    'name' => '<string>',
    'reference' => [
        'referenceArn' => '<string>',
    ],
    'sseConfig' => [
        'keyArn' => '<string>',
        'type' => 'KMS', // REQUIRED
    ],
    'storeFormat' => 'GFF|TSV|VCF', // REQUIRED
    'storeOptions' => [
        'tsvStoreOptions' => [
            'annotationType' => 'GENERIC|CHR_POS|CHR_POS_REF_ALT|CHR_START_END_ONE_BASE|CHR_START_END_REF_ALT_ONE_BASE|CHR_START_END_ZERO_BASE|CHR_START_END_REF_ALT_ZERO_BASE',
            'formatToHeader' => ['<string>', ...],
            'schema' => [
                ['<string>', ...],
                // ...
            ],
        ],
    ],
    'tags' => ['<string>', ...],
    'versionName' => '<string>',
]);

Parameter Details

Members
description
Type: string

A description for the store.

name
Type: string

A name for the store.

reference
Type: ReferenceItem structure

The genome reference for the store's annotations.

sseConfig
Type: SseConfig structure

Server-side encryption (SSE) settings for the store.

storeFormat
Required: Yes
Type: string

The annotation file format of the store.

storeOptions
Type: StoreOptions structure

File parsing options for the annotation store.

tags
Type: Associative array of custom strings keys (TagKey) to strings

Tags for the store.

versionName
Type: string

The name given to an annotation store version to distinguish it from other versions.

Result Syntax

[
    'creationTime' => <DateTime>,
    'id' => '<string>',
    'name' => '<string>',
    'reference' => [
        'referenceArn' => '<string>',
    ],
    'status' => 'CREATING|UPDATING|DELETING|ACTIVE|FAILED',
    'storeFormat' => 'GFF|TSV|VCF',
    'storeOptions' => [
        'tsvStoreOptions' => [
            'annotationType' => 'GENERIC|CHR_POS|CHR_POS_REF_ALT|CHR_START_END_ONE_BASE|CHR_START_END_REF_ALT_ONE_BASE|CHR_START_END_ZERO_BASE|CHR_START_END_REF_ALT_ZERO_BASE',
            'formatToHeader' => ['<string>', ...],
            'schema' => [
                ['<string>', ...],
                // ...
            ],
        ],
    ],
    'versionName' => '<string>',
]

Result Details

Members
creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the store was created.

id
Required: Yes
Type: string

The store's ID.

name
Required: Yes
Type: string

The store's name.

reference
Type: ReferenceItem structure

The store's genome reference. Required for all stores except TSV format with generic annotations.

status
Required: Yes
Type: string

The store's status.

storeFormat
Type: string

The annotation file format of the store.

storeOptions
Type: StoreOptions structure

The store's file parsing options.

versionName
Required: Yes
Type: string

The name given to an annotation store version to distinguish it from other versions.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

CreateAnnotationStoreVersion

$result = $client->createAnnotationStoreVersion([/* ... */]);
$promise = $client->createAnnotationStoreVersionAsync([/* ... */]);

Creates a new version of an annotation store.

Parameter Syntax

$result = $client->createAnnotationStoreVersion([
    'description' => '<string>',
    'name' => '<string>', // REQUIRED
    'tags' => ['<string>', ...],
    'versionName' => '<string>', // REQUIRED
    'versionOptions' => [
        'tsvVersionOptions' => [
            'annotationType' => 'GENERIC|CHR_POS|CHR_POS_REF_ALT|CHR_START_END_ONE_BASE|CHR_START_END_REF_ALT_ONE_BASE|CHR_START_END_ZERO_BASE|CHR_START_END_REF_ALT_ZERO_BASE',
            'formatToHeader' => ['<string>', ...],
            'schema' => [
                ['<string>', ...],
                // ...
            ],
        ],
    ],
]);

Parameter Details

Members
description
Type: string

The description of an annotation store version.

name
Required: Yes
Type: string

The name of an annotation store version from which versions are being created.

tags
Type: Associative array of custom strings keys (TagKey) to strings

Any tags added to annotation store version.

versionName
Required: Yes
Type: string

The name given to an annotation store version to distinguish it from other versions.

versionOptions
Type: VersionOptions structure

The options for an annotation store version.

Result Syntax

[
    'creationTime' => <DateTime>,
    'id' => '<string>',
    'name' => '<string>',
    'status' => 'CREATING|UPDATING|DELETING|ACTIVE|FAILED',
    'storeId' => '<string>',
    'versionName' => '<string>',
    'versionOptions' => [
        'tsvVersionOptions' => [
            'annotationType' => 'GENERIC|CHR_POS|CHR_POS_REF_ALT|CHR_START_END_ONE_BASE|CHR_START_END_REF_ALT_ONE_BASE|CHR_START_END_ZERO_BASE|CHR_START_END_REF_ALT_ZERO_BASE',
            'formatToHeader' => ['<string>', ...],
            'schema' => [
                ['<string>', ...],
                // ...
            ],
        ],
    ],
]

Result Details

Members
creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

The time stamp for the creation of an annotation store version.

id
Required: Yes
Type: string

A generated ID for the annotation store

name
Required: Yes
Type: string

The name given to an annotation store version to distinguish it from other versions.

status
Required: Yes
Type: string

The status of a annotation store version.

storeId
Required: Yes
Type: string

The ID for the annotation store from which new versions are being created.

versionName
Required: Yes
Type: string

The name given to an annotation store version to distinguish it from other versions.

versionOptions
Type: VersionOptions structure

The options for an annotation store version.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

CreateMultipartReadSetUpload

$result = $client->createMultipartReadSetUpload([/* ... */]);
$promise = $client->createMultipartReadSetUploadAsync([/* ... */]);

Begins a multipart read set upload.

Parameter Syntax

$result = $client->createMultipartReadSetUpload([
    'clientToken' => '<string>',
    'description' => '<string>',
    'generatedFrom' => '<string>',
    'name' => '<string>', // REQUIRED
    'referenceArn' => '<string>',
    'sampleId' => '<string>', // REQUIRED
    'sequenceStoreId' => '<string>', // REQUIRED
    'sourceFileType' => 'FASTQ|BAM|CRAM|UBAM', // REQUIRED
    'subjectId' => '<string>', // REQUIRED
    'tags' => ['<string>', ...],
]);

Parameter Details

Members
clientToken
Type: string

An idempotency token that can be used to avoid triggering multiple multipart uploads.

description
Type: string

The description of the read set.

generatedFrom
Type: string

Where the source originated.

name
Required: Yes
Type: string

The name of the read set.

referenceArn
Type: string

The ARN of the reference.

sampleId
Required: Yes
Type: string

The source's sample ID.

sequenceStoreId
Required: Yes
Type: string

The sequence store ID for the store that is the destination of the multipart uploads.

sourceFileType
Required: Yes
Type: string

The type of file being uploaded.

subjectId
Required: Yes
Type: string

The source's subject ID.

tags
Type: Associative array of custom strings keys (TagKey) to strings

Any tags to add to the read set.

Result Syntax

[
    'creationTime' => <DateTime>,
    'description' => '<string>',
    'generatedFrom' => '<string>',
    'name' => '<string>',
    'referenceArn' => '<string>',
    'sampleId' => '<string>',
    'sequenceStoreId' => '<string>',
    'sourceFileType' => 'FASTQ|BAM|CRAM|UBAM',
    'subjectId' => '<string>',
    'tags' => ['<string>', ...],
    'uploadId' => '<string>',
]

Result Details

Members
creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

The creation time of the multipart upload.

description
Type: string

The description of the read set.

generatedFrom
Type: string

The source of the read set.

name
Type: string

The name of the read set.

referenceArn
Required: Yes
Type: string

The read set source's reference ARN.

sampleId
Required: Yes
Type: string

The source's sample ID.

sequenceStoreId
Required: Yes
Type: string

The sequence store ID for the store that the read set will be created in.

sourceFileType
Required: Yes
Type: string

The file type of the read set source.

subjectId
Required: Yes
Type: string

The source's subject ID.

tags
Type: Associative array of custom strings keys (TagKey) to strings

The tags to add to the read set.

uploadId
Required: Yes
Type: string

The ID for the initiated multipart upload.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

NotSupportedOperationException:

The operation is not supported by Amazon Omics, or the API does not exist.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

CreateReferenceStore

$result = $client->createReferenceStore([/* ... */]);
$promise = $client->createReferenceStoreAsync([/* ... */]);

Creates a reference store.

Parameter Syntax

$result = $client->createReferenceStore([
    'clientToken' => '<string>',
    'description' => '<string>',
    'name' => '<string>', // REQUIRED
    'sseConfig' => [
        'keyArn' => '<string>',
        'type' => 'KMS', // REQUIRED
    ],
    'tags' => ['<string>', ...],
]);

Parameter Details

Members
clientToken
Type: string

To ensure that requests don't run multiple times, specify a unique token for each request.

description
Type: string

A description for the store.

name
Required: Yes
Type: string

A name for the store.

sseConfig
Type: SseConfig structure

Server-side encryption (SSE) settings for the store.

tags
Type: Associative array of custom strings keys (TagKey) to strings

Tags for the store.

Result Syntax

[
    'arn' => '<string>',
    'creationTime' => <DateTime>,
    'description' => '<string>',
    'id' => '<string>',
    'name' => '<string>',
    'sseConfig' => [
        'keyArn' => '<string>',
        'type' => 'KMS',
    ],
]

Result Details

Members
arn
Required: Yes
Type: string

The store's ARN.

creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the store was created.

description
Type: string

The store's description.

id
Required: Yes
Type: string

The store's ID.

name
Type: string

The store's name.

sseConfig
Type: SseConfig structure

The store's SSE settings.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

CreateRunGroup

$result = $client->createRunGroup([/* ... */]);
$promise = $client->createRunGroupAsync([/* ... */]);

You can optionally create a run group to limit the compute resources for the runs that you add to the group.

Parameter Syntax

$result = $client->createRunGroup([
    'maxCpus' => <integer>,
    'maxDuration' => <integer>,
    'maxGpus' => <integer>,
    'maxRuns' => <integer>,
    'name' => '<string>',
    'requestId' => '<string>', // REQUIRED
    'tags' => ['<string>', ...],
]);

Parameter Details

Members
maxCpus
Type: int

The maximum number of CPUs that can run concurrently across all active runs in the run group.

maxDuration
Type: int

The maximum time for each run (in minutes). If a run exceeds the maximum run time, the run fails automatically.

maxGpus
Type: int

The maximum number of GPUs that can run concurrently across all active runs in the run group.

maxRuns
Type: int

The maximum number of runs that can be running at the same time.

name
Type: string

A name for the group.

requestId
Required: Yes
Type: string

To ensure that requests don't run multiple times, specify a unique ID for each request.

tags
Type: Associative array of custom strings keys (TagKey) to strings

Tags for the group.

Result Syntax

[
    'arn' => '<string>',
    'id' => '<string>',
    'tags' => ['<string>', ...],
]

Result Details

Members
arn
Type: string

The group's ARN.

id
Type: string

The group's ID.

tags
Type: Associative array of custom strings keys (TagKey) to strings

Tags for the run group.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

CreateSequenceStore

$result = $client->createSequenceStore([/* ... */]);
$promise = $client->createSequenceStoreAsync([/* ... */]);

Creates a sequence store.

Parameter Syntax

$result = $client->createSequenceStore([
    'clientToken' => '<string>',
    'description' => '<string>',
    'eTagAlgorithmFamily' => 'MD5up|SHA256up|SHA512up',
    'fallbackLocation' => '<string>',
    'name' => '<string>', // REQUIRED
    'sseConfig' => [
        'keyArn' => '<string>',
        'type' => 'KMS', // REQUIRED
    ],
    'tags' => ['<string>', ...],
]);

Parameter Details

Members
clientToken
Type: string

To ensure that requests don't run multiple times, specify a unique token for each request.

description
Type: string

A description for the store.

eTagAlgorithmFamily
Type: string

The ETag algorithm family to use for ingested read sets.

fallbackLocation
Type: string

An S3 location that is used to store files that have failed a direct upload.

name
Required: Yes
Type: string

A name for the store.

sseConfig
Type: SseConfig structure

Server-side encryption (SSE) settings for the store.

tags
Type: Associative array of custom strings keys (TagKey) to strings

Tags for the store.

Result Syntax

[
    'arn' => '<string>',
    'creationTime' => <DateTime>,
    'description' => '<string>',
    'eTagAlgorithmFamily' => 'MD5up|SHA256up|SHA512up',
    'fallbackLocation' => '<string>',
    'id' => '<string>',
    'name' => '<string>',
    'sseConfig' => [
        'keyArn' => '<string>',
        'type' => 'KMS',
    ],
]

Result Details

Members
arn
Required: Yes
Type: string

The store's ARN.

creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the store was created.

description
Type: string

The store's description.

eTagAlgorithmFamily
Type: string

The algorithm family of the ETag.

fallbackLocation
Type: string

An S3 location that is used to store files that have failed a direct upload.

id
Required: Yes
Type: string

The store's ID.

name
Type: string

The store's name.

sseConfig
Type: SseConfig structure

The store's SSE settings.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

CreateShare

$result = $client->createShare([/* ... */]);
$promise = $client->createShareAsync([/* ... */]);

Creates a cross-account shared resource. The resource owner makes an offer to share the resource with the principal subscriber (an AWS user with a different account than the resource owner).

The following resources support cross-account sharing:

  • HealthOmics variant stores

  • HealthOmics annotation stores

  • Private workflows

Parameter Syntax

$result = $client->createShare([
    'principalSubscriber' => '<string>', // REQUIRED
    'resourceArn' => '<string>', // REQUIRED
    'shareName' => '<string>',
]);

Parameter Details

Members
principalSubscriber
Required: Yes
Type: string

The principal subscriber is the account being offered shared access to the resource.

resourceArn
Required: Yes
Type: string

The ARN of the resource to be shared.

shareName
Type: string

A name that the owner defines for the share.

Result Syntax

[
    'shareId' => '<string>',
    'shareName' => '<string>',
    'status' => 'PENDING|ACTIVATING|ACTIVE|DELETING|DELETED|FAILED',
]

Result Details

Members
shareId
Type: string

The ID that HealthOmics generates for the share.

shareName
Type: string

The name of the share.

status
Type: string

The status of the share.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

CreateVariantStore

$result = $client->createVariantStore([/* ... */]);
$promise = $client->createVariantStoreAsync([/* ... */]);

Creates a variant store.

Parameter Syntax

$result = $client->createVariantStore([
    'description' => '<string>',
    'name' => '<string>',
    'reference' => [ // REQUIRED
        'referenceArn' => '<string>',
    ],
    'sseConfig' => [
        'keyArn' => '<string>',
        'type' => 'KMS', // REQUIRED
    ],
    'tags' => ['<string>', ...],
]);

Parameter Details

Members
description
Type: string

A description for the store.

name
Type: string

A name for the store.

reference
Required: Yes
Type: ReferenceItem structure

The genome reference for the store's variants.

sseConfig
Type: SseConfig structure

Server-side encryption (SSE) settings for the store.

tags
Type: Associative array of custom strings keys (TagKey) to strings

Tags for the store.

Result Syntax

[
    'creationTime' => <DateTime>,
    'id' => '<string>',
    'name' => '<string>',
    'reference' => [
        'referenceArn' => '<string>',
    ],
    'status' => 'CREATING|UPDATING|DELETING|ACTIVE|FAILED',
]

Result Details

Members
creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the store was created.

id
Required: Yes
Type: string

The store's ID.

name
Required: Yes
Type: string

The store's name.

reference
Type: ReferenceItem structure

The store's genome reference.

status
Required: Yes
Type: string

The store's status.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

CreateWorkflow

$result = $client->createWorkflow([/* ... */]);
$promise = $client->createWorkflowAsync([/* ... */]);

Creates a workflow.

Parameter Syntax

$result = $client->createWorkflow([
    'accelerators' => 'GPU',
    'definitionUri' => '<string>',
    'definitionZip' => <string || resource || Psr\Http\Message\StreamInterface>,
    'description' => '<string>',
    'engine' => 'WDL|NEXTFLOW|CWL',
    'main' => '<string>',
    'name' => '<string>',
    'parameterTemplate' => [
        '<WorkflowParameterName>' => [
            'description' => '<string>',
            'optional' => true || false,
        ],
        // ...
    ],
    'requestId' => '<string>', // REQUIRED
    'storageCapacity' => <integer>,
    'tags' => ['<string>', ...],
]);

Parameter Details

Members
accelerators
Type: string

The computational accelerator specified to run the workflow.

definitionUri
Type: string

The URI of a definition for the workflow.

definitionZip
Type: blob (string|resource|Psr\Http\Message\StreamInterface)

A ZIP archive for the workflow.

description
Type: string

A description for the workflow.

engine
Type: string

An engine for the workflow.

main
Type: string

The path of the main definition file for the workflow.

name
Type: string

A name for the workflow.

parameterTemplate
Type: Associative array of custom strings keys (WorkflowParameterName) to WorkflowParameter structures

A parameter template for the workflow.

requestId
Required: Yes
Type: string

To ensure that requests don't run multiple times, specify a unique ID for each request.

storageCapacity
Type: int

The default storage capacity for the workflow runs, in gibibytes.

tags
Type: Associative array of custom strings keys (TagKey) to strings

Tags for the workflow.

Result Syntax

[
    'arn' => '<string>',
    'id' => '<string>',
    'status' => 'CREATING|ACTIVE|UPDATING|DELETED|FAILED|INACTIVE',
    'tags' => ['<string>', ...],
]

Result Details

Members
arn
Type: string

The workflow's ARN.

id
Type: string

The workflow's ID.

status
Type: string

The workflow's status.

tags
Type: Associative array of custom strings keys (TagKey) to strings

The workflow's tags.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

DeleteAnnotationStore

$result = $client->deleteAnnotationStore([/* ... */]);
$promise = $client->deleteAnnotationStoreAsync([/* ... */]);

Deletes an annotation store.

Parameter Syntax

$result = $client->deleteAnnotationStore([
    'force' => true || false,
    'name' => '<string>', // REQUIRED
]);

Parameter Details

Members
force
Type: boolean

Whether to force deletion.

name
Required: Yes
Type: string

The store's name.

Result Syntax

[
    'status' => 'CREATING|UPDATING|DELETING|ACTIVE|FAILED',
]

Result Details

Members
status
Required: Yes
Type: string

The store's status.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

DeleteAnnotationStoreVersions

$result = $client->deleteAnnotationStoreVersions([/* ... */]);
$promise = $client->deleteAnnotationStoreVersionsAsync([/* ... */]);

Deletes one or multiple versions of an annotation store.

Parameter Syntax

$result = $client->deleteAnnotationStoreVersions([
    'force' => true || false,
    'name' => '<string>', // REQUIRED
    'versions' => ['<string>', ...], // REQUIRED
]);

Parameter Details

Members
force
Type: boolean

Forces the deletion of an annotation store version when imports are in-progress..

name
Required: Yes
Type: string

The name of the annotation store from which versions are being deleted.

versions
Required: Yes
Type: Array of strings

The versions of an annotation store to be deleted.

Result Syntax

[
    'errors' => [
        [
            'message' => '<string>',
            'versionName' => '<string>',
        ],
        // ...
    ],
]

Result Details

Members
errors
Type: Array of VersionDeleteError structures

Any errors that occur when attempting to delete an annotation store version.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

DeleteReference

$result = $client->deleteReference([/* ... */]);
$promise = $client->deleteReferenceAsync([/* ... */]);

Deletes a genome reference.

Parameter Syntax

$result = $client->deleteReference([
    'id' => '<string>', // REQUIRED
    'referenceStoreId' => '<string>', // REQUIRED
]);

Parameter Details

Members
id
Required: Yes
Type: string

The reference's ID.

referenceStoreId
Required: Yes
Type: string

The reference's store ID.

Result Syntax

[]

Result Details

The results for this operation are always empty.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

DeleteReferenceStore

$result = $client->deleteReferenceStore([/* ... */]);
$promise = $client->deleteReferenceStoreAsync([/* ... */]);

Deletes a genome reference store.

Parameter Syntax

$result = $client->deleteReferenceStore([
    'id' => '<string>', // REQUIRED
]);

Parameter Details

Members
id
Required: Yes
Type: string

The store's ID.

Result Syntax

[]

Result Details

The results for this operation are always empty.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

DeleteRun

$result = $client->deleteRun([/* ... */]);
$promise = $client->deleteRunAsync([/* ... */]);

Deletes a workflow run.

Parameter Syntax

$result = $client->deleteRun([
    'id' => '<string>', // REQUIRED
]);

Parameter Details

Members
id
Required: Yes
Type: string

The run's ID.

Result Syntax

[]

Result Details

The results for this operation are always empty.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

DeleteRunGroup

$result = $client->deleteRunGroup([/* ... */]);
$promise = $client->deleteRunGroupAsync([/* ... */]);

Deletes a workflow run group.

Parameter Syntax

$result = $client->deleteRunGroup([
    'id' => '<string>', // REQUIRED
]);

Parameter Details

Members
id
Required: Yes
Type: string

The run group's ID.

Result Syntax

[]

Result Details

The results for this operation are always empty.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

DeleteSequenceStore

$result = $client->deleteSequenceStore([/* ... */]);
$promise = $client->deleteSequenceStoreAsync([/* ... */]);

Deletes a sequence store.

Parameter Syntax

$result = $client->deleteSequenceStore([
    'id' => '<string>', // REQUIRED
]);

Parameter Details

Members
id
Required: Yes
Type: string

The sequence store's ID.

Result Syntax

[]

Result Details

The results for this operation are always empty.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

DeleteShare

$result = $client->deleteShare([/* ... */]);
$promise = $client->deleteShareAsync([/* ... */]);

Deletes a resource share. If you are the resource owner, the subscriber will no longer have access to the shared resource. If you are the subscriber, this operation deletes your access to the share.

Parameter Syntax

$result = $client->deleteShare([
    'shareId' => '<string>', // REQUIRED
]);

Parameter Details

Members
shareId
Required: Yes
Type: string

The ID for the resource share to be deleted.

Result Syntax

[
    'status' => 'PENDING|ACTIVATING|ACTIVE|DELETING|DELETED|FAILED',
]

Result Details

Members
status
Type: string

The status of the share being deleted.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

DeleteVariantStore

$result = $client->deleteVariantStore([/* ... */]);
$promise = $client->deleteVariantStoreAsync([/* ... */]);

Deletes a variant store.

Parameter Syntax

$result = $client->deleteVariantStore([
    'force' => true || false,
    'name' => '<string>', // REQUIRED
]);

Parameter Details

Members
force
Type: boolean

Whether to force deletion.

name
Required: Yes
Type: string

The store's name.

Result Syntax

[
    'status' => 'CREATING|UPDATING|DELETING|ACTIVE|FAILED',
]

Result Details

Members
status
Required: Yes
Type: string

The store's status.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

DeleteWorkflow

$result = $client->deleteWorkflow([/* ... */]);
$promise = $client->deleteWorkflowAsync([/* ... */]);

Deletes a workflow.

Parameter Syntax

$result = $client->deleteWorkflow([
    'id' => '<string>', // REQUIRED
]);

Parameter Details

Members
id
Required: Yes
Type: string

The workflow's ID.

Result Syntax

[]

Result Details

The results for this operation are always empty.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

GetAnnotationImportJob

$result = $client->getAnnotationImportJob([/* ... */]);
$promise = $client->getAnnotationImportJobAsync([/* ... */]);

Gets information about an annotation import job.

Parameter Syntax

$result = $client->getAnnotationImportJob([
    'jobId' => '<string>', // REQUIRED
]);

Parameter Details

Members
jobId
Required: Yes
Type: string

The job's ID.

Result Syntax

[
    'annotationFields' => ['<string>', ...],
    'completionTime' => <DateTime>,
    'creationTime' => <DateTime>,
    'destinationName' => '<string>',
    'formatOptions' => [
        'tsvOptions' => [
            'readOptions' => [
                'comment' => '<string>',
                'encoding' => '<string>',
                'escape' => '<string>',
                'escapeQuotes' => true || false,
                'header' => true || false,
                'lineSep' => '<string>',
                'quote' => '<string>',
                'quoteAll' => true || false,
                'sep' => '<string>',
            ],
        ],
        'vcfOptions' => [
            'ignoreFilterField' => true || false,
            'ignoreQualField' => true || false,
        ],
    ],
    'id' => '<string>',
    'items' => [
        [
            'jobStatus' => 'SUBMITTED|IN_PROGRESS|CANCELLED|COMPLETED|FAILED|COMPLETED_WITH_FAILURES',
            'source' => '<string>',
        ],
        // ...
    ],
    'roleArn' => '<string>',
    'runLeftNormalization' => true || false,
    'status' => 'SUBMITTED|IN_PROGRESS|CANCELLED|COMPLETED|FAILED|COMPLETED_WITH_FAILURES',
    'statusMessage' => '<string>',
    'updateTime' => <DateTime>,
    'versionName' => '<string>',
]

Result Details

Members
annotationFields
Type: Associative array of custom strings keys (AnnotationFieldMapKeyString) to strings

The annotation schema generated by the parsed annotation data.

completionTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job completed.

creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job was created.

destinationName
Required: Yes
Type: string

The job's destination annotation store.

formatOptions
Required: Yes
Type: FormatOptions structure

Formatting options for a file.

id
Required: Yes
Type: string

The job's ID.

items
Required: Yes
Type: Array of AnnotationImportItemDetail structures

The job's imported items.

roleArn
Required: Yes
Type: string

The job's service role ARN.

runLeftNormalization
Required: Yes
Type: boolean

The job's left normalization setting.

status
Required: Yes
Type: string

The job's status.

statusMessage
Required: Yes
Type: string

The job's status message.

updateTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job was updated.

versionName
Required: Yes
Type: string

The name of the annotation store version.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

GetAnnotationStore

$result = $client->getAnnotationStore([/* ... */]);
$promise = $client->getAnnotationStoreAsync([/* ... */]);

Gets information about an annotation store.

Parameter Syntax

$result = $client->getAnnotationStore([
    'name' => '<string>', // REQUIRED
]);

Parameter Details

Members
name
Required: Yes
Type: string

The store's name.

Result Syntax

[
    'creationTime' => <DateTime>,
    'description' => '<string>',
    'id' => '<string>',
    'name' => '<string>',
    'numVersions' => <integer>,
    'reference' => [
        'referenceArn' => '<string>',
    ],
    'sseConfig' => [
        'keyArn' => '<string>',
        'type' => 'KMS',
    ],
    'status' => 'CREATING|UPDATING|DELETING|ACTIVE|FAILED',
    'statusMessage' => '<string>',
    'storeArn' => '<string>',
    'storeFormat' => 'GFF|TSV|VCF',
    'storeOptions' => [
        'tsvStoreOptions' => [
            'annotationType' => 'GENERIC|CHR_POS|CHR_POS_REF_ALT|CHR_START_END_ONE_BASE|CHR_START_END_REF_ALT_ONE_BASE|CHR_START_END_ZERO_BASE|CHR_START_END_REF_ALT_ZERO_BASE',
            'formatToHeader' => ['<string>', ...],
            'schema' => [
                ['<string>', ...],
                // ...
            ],
        ],
    ],
    'storeSizeBytes' => <integer>,
    'tags' => ['<string>', ...],
    'updateTime' => <DateTime>,
]

Result Details

Members
creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the store was created.

description
Required: Yes
Type: string

The store's description.

id
Required: Yes
Type: string

The store's ID.

name
Required: Yes
Type: string

The store's name.

numVersions
Required: Yes
Type: int

An integer indicating how many versions of an annotation store exist.

reference
Required: Yes
Type: ReferenceItem structure

The store's genome reference.

sseConfig
Required: Yes
Type: SseConfig structure

The store's server-side encryption (SSE) settings.

status
Required: Yes
Type: string

The store's status.

statusMessage
Required: Yes
Type: string

A status message.

storeArn
Required: Yes
Type: string

The store's ARN.

storeFormat
Type: string

The store's annotation file format.

storeOptions
Type: StoreOptions structure

The store's parsing options.

storeSizeBytes
Required: Yes
Type: long (int|float)

The store's size in bytes.

tags
Required: Yes
Type: Associative array of custom strings keys (TagKey) to strings

The store's tags.

updateTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the store was updated.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

GetAnnotationStoreVersion

$result = $client->getAnnotationStoreVersion([/* ... */]);
$promise = $client->getAnnotationStoreVersionAsync([/* ... */]);

Retrieves the metadata for an annotation store version.

Parameter Syntax

$result = $client->getAnnotationStoreVersion([
    'name' => '<string>', // REQUIRED
    'versionName' => '<string>', // REQUIRED
]);

Parameter Details

Members
name
Required: Yes
Type: string

The name given to an annotation store version to distinguish it from others.

versionName
Required: Yes
Type: string

The name given to an annotation store version to distinguish it from others.

Result Syntax

[
    'creationTime' => <DateTime>,
    'description' => '<string>',
    'id' => '<string>',
    'name' => '<string>',
    'status' => 'CREATING|UPDATING|DELETING|ACTIVE|FAILED',
    'statusMessage' => '<string>',
    'storeId' => '<string>',
    'tags' => ['<string>', ...],
    'updateTime' => <DateTime>,
    'versionArn' => '<string>',
    'versionName' => '<string>',
    'versionOptions' => [
        'tsvVersionOptions' => [
            'annotationType' => 'GENERIC|CHR_POS|CHR_POS_REF_ALT|CHR_START_END_ONE_BASE|CHR_START_END_REF_ALT_ONE_BASE|CHR_START_END_ZERO_BASE|CHR_START_END_REF_ALT_ZERO_BASE',
            'formatToHeader' => ['<string>', ...],
            'schema' => [
                ['<string>', ...],
                // ...
            ],
        ],
    ],
    'versionSizeBytes' => <integer>,
]

Result Details

Members
creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

The time stamp for when an annotation store version was created.

description
Required: Yes
Type: string

The description for an annotation store version.

id
Required: Yes
Type: string

The annotation store version ID.

name
Required: Yes
Type: string

The name of the annotation store.

status
Required: Yes
Type: string

The status of an annotation store version.

statusMessage
Required: Yes
Type: string

The status of an annotation store version.

storeId
Required: Yes
Type: string

The store ID for annotation store version.

tags
Required: Yes
Type: Associative array of custom strings keys (TagKey) to strings

Any tags associated with an annotation store version.

updateTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

The time stamp for when an annotation store version was updated.

versionArn
Required: Yes
Type: string

The Arn for the annotation store.

versionName
Required: Yes
Type: string

The name given to an annotation store version to distinguish it from others.

versionOptions
Type: VersionOptions structure

The options for an annotation store version.

versionSizeBytes
Required: Yes
Type: long (int|float)

The size of the annotation store version in Bytes.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

GetReadSet

$result = $client->getReadSet([/* ... */]);
$promise = $client->getReadSetAsync([/* ... */]);

Gets a file from a read set.

Parameter Syntax

$result = $client->getReadSet([
    'file' => 'SOURCE1|SOURCE2|INDEX',
    'id' => '<string>', // REQUIRED
    'partNumber' => <integer>, // REQUIRED
    'sequenceStoreId' => '<string>', // REQUIRED
]);

Parameter Details

Members
file
Type: string

The file to retrieve.

id
Required: Yes
Type: string

The read set's ID.

partNumber
Required: Yes
Type: int

The part number to retrieve.

sequenceStoreId
Required: Yes
Type: string

The read set's sequence store ID.

Result Syntax

[
    'payload' => <string || resource || Psr\Http\Message\StreamInterface>,
]

Result Details

Members
payload
Type: blob (string|resource|Psr\Http\Message\StreamInterface)

The read set file payload.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

RangeNotSatisfiableException:

The ranges specified in the request are not valid.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

GetReadSetActivationJob

$result = $client->getReadSetActivationJob([/* ... */]);
$promise = $client->getReadSetActivationJobAsync([/* ... */]);

Gets information about a read set activation job.

Parameter Syntax

$result = $client->getReadSetActivationJob([
    'id' => '<string>', // REQUIRED
    'sequenceStoreId' => '<string>', // REQUIRED
]);

Parameter Details

Members
id
Required: Yes
Type: string

The job's ID.

sequenceStoreId
Required: Yes
Type: string

The job's sequence store ID.

Result Syntax

[
    'completionTime' => <DateTime>,
    'creationTime' => <DateTime>,
    'id' => '<string>',
    'sequenceStoreId' => '<string>',
    'sources' => [
        [
            'readSetId' => '<string>',
            'status' => 'NOT_STARTED|IN_PROGRESS|FINISHED|FAILED',
            'statusMessage' => '<string>',
        ],
        // ...
    ],
    'status' => 'SUBMITTED|IN_PROGRESS|CANCELLING|CANCELLED|FAILED|COMPLETED|COMPLETED_WITH_FAILURES',
    'statusMessage' => '<string>',
]

Result Details

Members
completionTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job completed.

creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job was created.

id
Required: Yes
Type: string

The job's ID.

sequenceStoreId
Required: Yes
Type: string

The job's sequence store ID.

sources
Type: Array of ActivateReadSetSourceItem structures

The job's source files.

status
Required: Yes
Type: string

The job's status.

statusMessage
Type: string

The job's status message.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

GetReadSetExportJob

$result = $client->getReadSetExportJob([/* ... */]);
$promise = $client->getReadSetExportJobAsync([/* ... */]);

Gets information about a read set export job.

Parameter Syntax

$result = $client->getReadSetExportJob([
    'id' => '<string>', // REQUIRED
    'sequenceStoreId' => '<string>', // REQUIRED
]);

Parameter Details

Members
id
Required: Yes
Type: string

The job's ID.

sequenceStoreId
Required: Yes
Type: string

The job's sequence store ID.

Result Syntax

[
    'completionTime' => <DateTime>,
    'creationTime' => <DateTime>,
    'destination' => '<string>',
    'id' => '<string>',
    'readSets' => [
        [
            'id' => '<string>',
            'status' => 'NOT_STARTED|IN_PROGRESS|FINISHED|FAILED',
            'statusMessage' => '<string>',
        ],
        // ...
    ],
    'sequenceStoreId' => '<string>',
    'status' => 'SUBMITTED|IN_PROGRESS|CANCELLING|CANCELLED|FAILED|COMPLETED|COMPLETED_WITH_FAILURES',
    'statusMessage' => '<string>',
]

Result Details

Members
completionTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job completed.

creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job was created.

destination
Required: Yes
Type: string

The job's destination in Amazon S3.

id
Required: Yes
Type: string

The job's ID.

readSets
Type: Array of ExportReadSetDetail structures

The job's read sets.

sequenceStoreId
Required: Yes
Type: string

The job's sequence store ID.

status
Required: Yes
Type: string

The job's status.

statusMessage
Type: string

The job's status message.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

GetReadSetImportJob

$result = $client->getReadSetImportJob([/* ... */]);
$promise = $client->getReadSetImportJobAsync([/* ... */]);

Gets information about a read set import job.

Parameter Syntax

$result = $client->getReadSetImportJob([
    'id' => '<string>', // REQUIRED
    'sequenceStoreId' => '<string>', // REQUIRED
]);

Parameter Details

Members
id
Required: Yes
Type: string

The job's ID.

sequenceStoreId
Required: Yes
Type: string

The job's sequence store ID.

Result Syntax

[
    'completionTime' => <DateTime>,
    'creationTime' => <DateTime>,
    'id' => '<string>',
    'roleArn' => '<string>',
    'sequenceStoreId' => '<string>',
    'sources' => [
        [
            'description' => '<string>',
            'generatedFrom' => '<string>',
            'name' => '<string>',
            'readSetId' => '<string>',
            'referenceArn' => '<string>',
            'sampleId' => '<string>',
            'sourceFileType' => 'FASTQ|BAM|CRAM|UBAM',
            'sourceFiles' => [
                'source1' => '<string>',
                'source2' => '<string>',
            ],
            'status' => 'NOT_STARTED|IN_PROGRESS|FINISHED|FAILED',
            'statusMessage' => '<string>',
            'subjectId' => '<string>',
            'tags' => ['<string>', ...],
        ],
        // ...
    ],
    'status' => 'SUBMITTED|IN_PROGRESS|CANCELLING|CANCELLED|FAILED|COMPLETED|COMPLETED_WITH_FAILURES',
    'statusMessage' => '<string>',
]

Result Details

Members
completionTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job completed.

creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job was created.

id
Required: Yes
Type: string

The job's ID.

roleArn
Required: Yes
Type: string

The job's service role ARN.

sequenceStoreId
Required: Yes
Type: string

The job's sequence store ID.

sources
Required: Yes
Type: Array of ImportReadSetSourceItem structures

The job's source files.

status
Required: Yes
Type: string

The job's status.

statusMessage
Type: string

The job's status message.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

GetReadSetMetadata

$result = $client->getReadSetMetadata([/* ... */]);
$promise = $client->getReadSetMetadataAsync([/* ... */]);

Gets details about a read set.

Parameter Syntax

$result = $client->getReadSetMetadata([
    'id' => '<string>', // REQUIRED
    'sequenceStoreId' => '<string>', // REQUIRED
]);

Parameter Details

Members
id
Required: Yes
Type: string

The read set's ID.

sequenceStoreId
Required: Yes
Type: string

The read set's sequence store ID.

Result Syntax

[
    'arn' => '<string>',
    'creationJobId' => '<string>',
    'creationTime' => <DateTime>,
    'creationType' => 'IMPORT|UPLOAD',
    'description' => '<string>',
    'etag' => [
        'algorithm' => 'FASTQ_MD5up|BAM_MD5up|CRAM_MD5up|FASTQ_SHA256up|BAM_SHA256up|CRAM_SHA256up|FASTQ_SHA512up|BAM_SHA512up|CRAM_SHA512up',
        'source1' => '<string>',
        'source2' => '<string>',
    ],
    'fileType' => 'FASTQ|BAM|CRAM|UBAM',
    'files' => [
        'index' => [
            'contentLength' => <integer>,
            'partSize' => <integer>,
            's3Access' => [
                's3Uri' => '<string>',
            ],
            'totalParts' => <integer>,
        ],
        'source1' => [
            'contentLength' => <integer>,
            'partSize' => <integer>,
            's3Access' => [
                's3Uri' => '<string>',
            ],
            'totalParts' => <integer>,
        ],
        'source2' => [
            'contentLength' => <integer>,
            'partSize' => <integer>,
            's3Access' => [
                's3Uri' => '<string>',
            ],
            'totalParts' => <integer>,
        ],
    ],
    'id' => '<string>',
    'name' => '<string>',
    'referenceArn' => '<string>',
    'sampleId' => '<string>',
    'sequenceInformation' => [
        'alignment' => '<string>',
        'generatedFrom' => '<string>',
        'totalBaseCount' => <integer>,
        'totalReadCount' => <integer>,
    ],
    'sequenceStoreId' => '<string>',
    'status' => 'ARCHIVED|ACTIVATING|ACTIVE|DELETING|DELETED|PROCESSING_UPLOAD|UPLOAD_FAILED',
    'statusMessage' => '<string>',
    'subjectId' => '<string>',
]

Result Details

Members
arn
Required: Yes
Type: string

The read set's ARN.

creationJobId
Type: string

The read set's creation job ID.

creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the read set was created.

creationType
Type: string

The creation type of the read set.

description
Type: string

The read set's description.

etag
Type: ETag structure

The entity tag (ETag) is a hash of the object meant to represent its semantic content.

fileType
Required: Yes
Type: string

The read set's file type.

files
Type: ReadSetFiles structure

The read set's files.

id
Required: Yes
Type: string

The read set's ID.

name
Type: string

The read set's name.

referenceArn
Type: string

The read set's genome reference ARN.

sampleId
Type: string

The read set's sample ID.

sequenceInformation
Type: SequenceInformation structure

The read set's sequence information.

sequenceStoreId
Required: Yes
Type: string

The read set's sequence store ID.

status
Required: Yes
Type: string

The read set's status.

statusMessage
Type: string

The status message for a read set. It provides more detail as to why the read set has a status.

subjectId
Type: string

The read set's subject ID.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

GetReference

$result = $client->getReference([/* ... */]);
$promise = $client->getReferenceAsync([/* ... */]);

Gets a reference file.

Parameter Syntax

$result = $client->getReference([
    'file' => 'SOURCE|INDEX',
    'id' => '<string>', // REQUIRED
    'partNumber' => <integer>, // REQUIRED
    'range' => '<string>',
    'referenceStoreId' => '<string>', // REQUIRED
]);

Parameter Details

Members
file
Type: string

The file to retrieve.

id
Required: Yes
Type: string

The reference's ID.

partNumber
Required: Yes
Type: int

The part number to retrieve.

range
Type: string

The range to retrieve.

referenceStoreId
Required: Yes
Type: string

The reference's store ID.

Result Syntax

[
    'payload' => <string || resource || Psr\Http\Message\StreamInterface>,
]

Result Details

Members
payload
Type: blob (string|resource|Psr\Http\Message\StreamInterface)

The reference file payload.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

RangeNotSatisfiableException:

The ranges specified in the request are not valid.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

GetReferenceImportJob

$result = $client->getReferenceImportJob([/* ... */]);
$promise = $client->getReferenceImportJobAsync([/* ... */]);

Gets information about a reference import job.

Parameter Syntax

$result = $client->getReferenceImportJob([
    'id' => '<string>', // REQUIRED
    'referenceStoreId' => '<string>', // REQUIRED
]);

Parameter Details

Members
id
Required: Yes
Type: string

The job's ID.

referenceStoreId
Required: Yes
Type: string

The job's reference store ID.

Result Syntax

[
    'completionTime' => <DateTime>,
    'creationTime' => <DateTime>,
    'id' => '<string>',
    'referenceStoreId' => '<string>',
    'roleArn' => '<string>',
    'sources' => [
        [
            'description' => '<string>',
            'name' => '<string>',
            'referenceId' => '<string>',
            'sourceFile' => '<string>',
            'status' => 'NOT_STARTED|IN_PROGRESS|FINISHED|FAILED',
            'statusMessage' => '<string>',
            'tags' => ['<string>', ...],
        ],
        // ...
    ],
    'status' => 'SUBMITTED|IN_PROGRESS|CANCELLING|CANCELLED|FAILED|COMPLETED|COMPLETED_WITH_FAILURES',
    'statusMessage' => '<string>',
]

Result Details

Members
completionTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job completed.

creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job was created.

id
Required: Yes
Type: string

The job's ID.

referenceStoreId
Required: Yes
Type: string

The job's reference store ID.

roleArn
Required: Yes
Type: string

The job's service role ARN.

sources
Required: Yes
Type: Array of ImportReferenceSourceItem structures

The job's source files.

status
Required: Yes
Type: string

The job's status.

statusMessage
Type: string

The job's status message.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

GetReferenceMetadata

$result = $client->getReferenceMetadata([/* ... */]);
$promise = $client->getReferenceMetadataAsync([/* ... */]);

Gets information about a genome reference's metadata.

Parameter Syntax

$result = $client->getReferenceMetadata([
    'id' => '<string>', // REQUIRED
    'referenceStoreId' => '<string>', // REQUIRED
]);

Parameter Details

Members
id
Required: Yes
Type: string

The reference's ID.

referenceStoreId
Required: Yes
Type: string

The reference's reference store ID.

Result Syntax

[
    'arn' => '<string>',
    'creationJobId' => '<string>',
    'creationTime' => <DateTime>,
    'creationType' => 'IMPORT',
    'description' => '<string>',
    'files' => [
        'index' => [
            'contentLength' => <integer>,
            'partSize' => <integer>,
            's3Access' => [
                's3Uri' => '<string>',
            ],
            'totalParts' => <integer>,
        ],
        'source' => [
            'contentLength' => <integer>,
            'partSize' => <integer>,
            's3Access' => [
                's3Uri' => '<string>',
            ],
            'totalParts' => <integer>,
        ],
    ],
    'id' => '<string>',
    'md5' => '<string>',
    'name' => '<string>',
    'referenceStoreId' => '<string>',
    'status' => 'ACTIVE|DELETING|DELETED',
    'updateTime' => <DateTime>,
]

Result Details

Members
arn
Required: Yes
Type: string

The reference's ARN.

creationJobId
Type: string

The reference's creation job ID.

creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the reference was created.

creationType
Type: string

The reference's creation type.

description
Type: string

The reference's description.

files
Type: ReferenceFiles structure

The reference's files.

id
Required: Yes
Type: string

The reference's ID.

md5
Required: Yes
Type: string

The reference's MD5 checksum.

name
Type: string

The reference's name.

referenceStoreId
Required: Yes
Type: string

The reference's reference store ID.

status
Type: string

The reference's status.

updateTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the reference was updated.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

GetReferenceStore

$result = $client->getReferenceStore([/* ... */]);
$promise = $client->getReferenceStoreAsync([/* ... */]);

Gets information about a reference store.

Parameter Syntax

$result = $client->getReferenceStore([
    'id' => '<string>', // REQUIRED
]);

Parameter Details

Members
id
Required: Yes
Type: string

The store's ID.

Result Syntax

[
    'arn' => '<string>',
    'creationTime' => <DateTime>,
    'description' => '<string>',
    'id' => '<string>',
    'name' => '<string>',
    'sseConfig' => [
        'keyArn' => '<string>',
        'type' => 'KMS',
    ],
]

Result Details

Members
arn
Required: Yes
Type: string

The store's ARN.

creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the store was created.

description
Type: string

The store's description.

id
Required: Yes
Type: string

The store's ID.

name
Type: string

The store's name.

sseConfig
Type: SseConfig structure

The store's server-side encryption (SSE) settings.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

GetRun

$result = $client->getRun([/* ... */]);
$promise = $client->getRunAsync([/* ... */]);

Gets information about a workflow run.

If a workflow is shared with you, you cannot export information about the run.

Parameter Syntax

$result = $client->getRun([
    'export' => ['<string>', ...],
    'id' => '<string>', // REQUIRED
]);

Parameter Details

Members
export
Type: Array of strings

The run's export format.

id
Required: Yes
Type: string

The run's ID.

Result Syntax

[
    'accelerators' => 'GPU',
    'arn' => '<string>',
    'creationTime' => <DateTime>,
    'definition' => '<string>',
    'digest' => '<string>',
    'failureReason' => '<string>',
    'id' => '<string>',
    'logLevel' => 'OFF|FATAL|ERROR|ALL',
    'logLocation' => [
        'engineLogStream' => '<string>',
        'runLogStream' => '<string>',
    ],
    'name' => '<string>',
    'outputUri' => '<string>',
    'parameters' => [
    ],
    'priority' => <integer>,
    'resourceDigests' => ['<string>', ...],
    'retentionMode' => 'RETAIN|REMOVE',
    'roleArn' => '<string>',
    'runGroupId' => '<string>',
    'runId' => '<string>',
    'runOutputUri' => '<string>',
    'startTime' => <DateTime>,
    'startedBy' => '<string>',
    'status' => 'PENDING|STARTING|RUNNING|STOPPING|COMPLETED|DELETED|CANCELLED|FAILED',
    'statusMessage' => '<string>',
    'stopTime' => <DateTime>,
    'storageCapacity' => <integer>,
    'storageType' => 'STATIC|DYNAMIC',
    'tags' => ['<string>', ...],
    'uuid' => '<string>',
    'workflowId' => '<string>',
    'workflowOwnerId' => '<string>',
    'workflowType' => 'PRIVATE|READY2RUN',
]

Result Details

Members
accelerators
Type: string

The computational accelerator used to run the workflow.

arn
Type: string

The run's ARN.

creationTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the run was created.

definition
Type: string

The run's definition.

digest
Type: string

The run's digest.

failureReason
Type: string

The reason a run has failed.

id
Type: string

The run's ID.

logLevel
Type: string

The run's log level.

logLocation
Type: RunLogLocation structure

The location of the run log.

name
Type: string

The run's name.

outputUri
Type: string

The run's output URI.

parameters
Type: document (null|bool|string|numeric) or an (array|associative array) whose members are all valid documents

The run's parameters.

priority
Type: int

The run's priority.

resourceDigests
Type: Associative array of custom strings keys (RunResourceDigestKey) to strings

The run's resource digests.

retentionMode
Type: string

The run's retention mode.

roleArn
Type: string

The run's service role ARN.

runGroupId
Type: string

The run's group ID.

runId
Type: string

The run's ID.

runOutputUri
Type: string

The destination for workflow outputs.

startTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the run started.

startedBy
Type: string

Who started the run.

status
Type: string

The run's status.

statusMessage
Type: string

The run's status message.

stopTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

The run's stop time.

storageCapacity
Type: int

The run's storage capacity in gibibytes. For dynamic storage, after the run has completed, this value is the maximum amount of storage used during the run.

storageType
Type: string

The run's storage type.

tags
Type: Associative array of custom strings keys (TagKey) to strings

The run's tags.

uuid
Type: string

The universally unique identifier for a run.

workflowId
Type: string

The run's workflow ID.

workflowOwnerId
Type: string

The ID of the workflow owner.

workflowType
Type: string

The run's workflow type.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

GetRunGroup

$result = $client->getRunGroup([/* ... */]);
$promise = $client->getRunGroupAsync([/* ... */]);

Gets information about a workflow run group.

Parameter Syntax

$result = $client->getRunGroup([
    'id' => '<string>', // REQUIRED
]);

Parameter Details

Members
id
Required: Yes
Type: string

The group's ID.

Result Syntax

[
    'arn' => '<string>',
    'creationTime' => <DateTime>,
    'id' => '<string>',
    'maxCpus' => <integer>,
    'maxDuration' => <integer>,
    'maxGpus' => <integer>,
    'maxRuns' => <integer>,
    'name' => '<string>',
    'tags' => ['<string>', ...],
]

Result Details

Members
arn
Type: string

The group's ARN.

creationTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the group was created.

id
Type: string

The group's ID.

maxCpus
Type: int

The group's maximum number of CPUs to use.

maxDuration
Type: int

The group's maximum run time in minutes.

maxGpus
Type: int

The maximum GPUs that can be used by a run group.

maxRuns
Type: int

The maximum number of concurrent runs for the group.

name
Type: string

The group's name.

tags
Type: Associative array of custom strings keys (TagKey) to strings

The group's tags.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

GetRunTask

$result = $client->getRunTask([/* ... */]);
$promise = $client->getRunTaskAsync([/* ... */]);

Gets information about a workflow run task.

Parameter Syntax

$result = $client->getRunTask([
    'id' => '<string>', // REQUIRED
    'taskId' => '<string>', // REQUIRED
]);

Parameter Details

Members
id
Required: Yes
Type: string

The workflow run ID.

taskId
Required: Yes
Type: string

The task's ID.

Result Syntax

[
    'cpus' => <integer>,
    'creationTime' => <DateTime>,
    'failureReason' => '<string>',
    'gpus' => <integer>,
    'instanceType' => '<string>',
    'logStream' => '<string>',
    'memory' => <integer>,
    'name' => '<string>',
    'startTime' => <DateTime>,
    'status' => 'PENDING|STARTING|RUNNING|STOPPING|COMPLETED|CANCELLED|FAILED',
    'statusMessage' => '<string>',
    'stopTime' => <DateTime>,
    'taskId' => '<string>',
]

Result Details

Members
cpus
Type: int

The task's CPU usage.

creationTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the task was created.

failureReason
Type: string

The reason a task has failed.

gpus
Type: int

The number of Graphics Processing Units (GPU) specified in the task.

instanceType
Type: string

The instance type for a task.

logStream
Type: string

The task's log stream.

memory
Type: int

The task's memory use in gigabytes.

name
Type: string

The task's name.

startTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

The task's start time.

status
Type: string

The task's status.

statusMessage
Type: string

The task's status message.

stopTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

The task's stop time.

taskId
Type: string

The task's ID.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

GetSequenceStore

$result = $client->getSequenceStore([/* ... */]);
$promise = $client->getSequenceStoreAsync([/* ... */]);

Gets information about a sequence store.

Parameter Syntax

$result = $client->getSequenceStore([
    'id' => '<string>', // REQUIRED
]);

Parameter Details

Members
id
Required: Yes
Type: string

The store's ID.

Result Syntax

[
    'arn' => '<string>',
    'creationTime' => <DateTime>,
    'description' => '<string>',
    'eTagAlgorithmFamily' => 'MD5up|SHA256up|SHA512up',
    'fallbackLocation' => '<string>',
    'id' => '<string>',
    'name' => '<string>',
    's3Access' => [
        's3AccessPointArn' => '<string>',
        's3Uri' => '<string>',
    ],
    'sseConfig' => [
        'keyArn' => '<string>',
        'type' => 'KMS',
    ],
]

Result Details

Members
arn
Required: Yes
Type: string

The store's ARN.

creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the store was created.

description
Type: string

The store's description.

eTagAlgorithmFamily
Type: string

The algorithm family of the ETag.

fallbackLocation
Type: string

An S3 location that is used to store files that have failed a direct upload.

id
Required: Yes
Type: string

The store's ID.

name
Type: string

The store's name.

s3Access
Type: SequenceStoreS3Access structure

The S3 metadata of a sequence store, including the ARN and S3 URI of the S3 bucket.

sseConfig
Type: SseConfig structure

The store's server-side encryption (SSE) settings.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

GetShare

$result = $client->getShare([/* ... */]);
$promise = $client->getShareAsync([/* ... */]);

Retrieves the metadata for the specified resource share.

Parameter Syntax

$result = $client->getShare([
    'shareId' => '<string>', // REQUIRED
]);

Parameter Details

Members
shareId
Required: Yes
Type: string

The ID of the share.

Result Syntax

[
    'share' => [
        'creationTime' => <DateTime>,
        'ownerId' => '<string>',
        'principalSubscriber' => '<string>',
        'resourceArn' => '<string>',
        'resourceId' => '<string>',
        'shareId' => '<string>',
        'shareName' => '<string>',
        'status' => 'PENDING|ACTIVATING|ACTIVE|DELETING|DELETED|FAILED',
        'statusMessage' => '<string>',
        'updateTime' => <DateTime>,
    ],
]

Result Details

Members
share
Type: ShareDetails structure

A resource share details object. The object includes the status, the resourceArn, and ownerId.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

GetVariantImportJob

$result = $client->getVariantImportJob([/* ... */]);
$promise = $client->getVariantImportJobAsync([/* ... */]);

Gets information about a variant import job.

Parameter Syntax

$result = $client->getVariantImportJob([
    'jobId' => '<string>', // REQUIRED
]);

Parameter Details

Members
jobId
Required: Yes
Type: string

The job's ID.

Result Syntax

[
    'annotationFields' => ['<string>', ...],
    'completionTime' => <DateTime>,
    'creationTime' => <DateTime>,
    'destinationName' => '<string>',
    'id' => '<string>',
    'items' => [
        [
            'jobStatus' => 'SUBMITTED|IN_PROGRESS|CANCELLED|COMPLETED|FAILED|COMPLETED_WITH_FAILURES',
            'source' => '<string>',
            'statusMessage' => '<string>',
        ],
        // ...
    ],
    'roleArn' => '<string>',
    'runLeftNormalization' => true || false,
    'status' => 'SUBMITTED|IN_PROGRESS|CANCELLED|COMPLETED|FAILED|COMPLETED_WITH_FAILURES',
    'statusMessage' => '<string>',
    'updateTime' => <DateTime>,
]

Result Details

Members
annotationFields
Type: Associative array of custom strings keys (AnnotationFieldMapKeyString) to strings

The annotation schema generated by the parsed annotation data.

completionTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job completed.

creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job was created.

destinationName
Required: Yes
Type: string

The job's destination variant store.

id
Required: Yes
Type: string

The job's ID.

items
Required: Yes
Type: Array of VariantImportItemDetail structures

The job's items.

roleArn
Required: Yes
Type: string

The job's service role ARN.

runLeftNormalization
Required: Yes
Type: boolean

The job's left normalization setting.

status
Required: Yes
Type: string

The job's status.

statusMessage
Required: Yes
Type: string

The job's status message.

updateTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job was updated.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

GetVariantStore

$result = $client->getVariantStore([/* ... */]);
$promise = $client->getVariantStoreAsync([/* ... */]);

Gets information about a variant store.

Parameter Syntax

$result = $client->getVariantStore([
    'name' => '<string>', // REQUIRED
]);

Parameter Details

Members
name
Required: Yes
Type: string

The store's name.

Result Syntax

[
    'creationTime' => <DateTime>,
    'description' => '<string>',
    'id' => '<string>',
    'name' => '<string>',
    'reference' => [
        'referenceArn' => '<string>',
    ],
    'sseConfig' => [
        'keyArn' => '<string>',
        'type' => 'KMS',
    ],
    'status' => 'CREATING|UPDATING|DELETING|ACTIVE|FAILED',
    'statusMessage' => '<string>',
    'storeArn' => '<string>',
    'storeSizeBytes' => <integer>,
    'tags' => ['<string>', ...],
    'updateTime' => <DateTime>,
]

Result Details

Members
creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the store was created.

description
Required: Yes
Type: string

The store's description.

id
Required: Yes
Type: string

The store's ID.

name
Required: Yes
Type: string

The store's name.

reference
Required: Yes
Type: ReferenceItem structure

The store's genome reference.

sseConfig
Required: Yes
Type: SseConfig structure

The store's server-side encryption (SSE) settings.

status
Required: Yes
Type: string

The store's status.

statusMessage
Required: Yes
Type: string

The store's status message.

storeArn
Required: Yes
Type: string

The store's ARN.

storeSizeBytes
Required: Yes
Type: long (int|float)

The store's size in bytes.

tags
Required: Yes
Type: Associative array of custom strings keys (TagKey) to strings

The store's tags.

updateTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the store was updated.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

GetWorkflow

$result = $client->getWorkflow([/* ... */]);
$promise = $client->getWorkflowAsync([/* ... */]);

Gets information about a workflow.

If a workflow is shared with you, you cannot export the workflow.

Parameter Syntax

$result = $client->getWorkflow([
    'export' => ['<string>', ...],
    'id' => '<string>', // REQUIRED
    'type' => 'PRIVATE|READY2RUN',
    'workflowOwnerId' => '<string>',
]);

Parameter Details

Members
export
Type: Array of strings

The export format for the workflow.

id
Required: Yes
Type: string

The workflow's ID.

type
Type: string

The workflow's type.

workflowOwnerId
Type: string

The ID of the workflow owner.

Result Syntax

[
    'accelerators' => 'GPU',
    'arn' => '<string>',
    'creationTime' => <DateTime>,
    'definition' => '<string>',
    'description' => '<string>',
    'digest' => '<string>',
    'engine' => 'WDL|NEXTFLOW|CWL',
    'id' => '<string>',
    'main' => '<string>',
    'metadata' => ['<string>', ...],
    'name' => '<string>',
    'parameterTemplate' => [
        '<WorkflowParameterName>' => [
            'description' => '<string>',
            'optional' => true || false,
        ],
        // ...
    ],
    'status' => 'CREATING|ACTIVE|UPDATING|DELETED|FAILED|INACTIVE',
    'statusMessage' => '<string>',
    'storageCapacity' => <integer>,
    'tags' => ['<string>', ...],
    'type' => 'PRIVATE|READY2RUN',
]

Result Details

Members
accelerators
Type: string

The computational accelerator specified to run the workflow.

arn
Type: string

The workflow's ARN.

creationTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the workflow was created.

definition
Type: string

The workflow's definition.

description
Type: string

The workflow's description.

digest
Type: string

The workflow's digest.

engine
Type: string

The workflow's engine.

id
Type: string

The workflow's ID.

main
Type: string

The path of the main definition file for the workflow.

metadata
Type: Associative array of custom strings keys (WorkflowMetadataKey) to strings

Gets metadata for workflow.

name
Type: string

The workflow's name.

parameterTemplate
Type: Associative array of custom strings keys (WorkflowParameterName) to WorkflowParameter structures

The workflow's parameter template.

status
Type: string

The workflow's status.

statusMessage
Type: string

The workflow's status message.

storageCapacity
Type: int

The workflow's default run storage capacity in gibibytes.

tags
Type: Associative array of custom strings keys (TagKey) to strings

The workflow's tags.

type
Type: string

The workflow's type.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

ListAnnotationImportJobs

$result = $client->listAnnotationImportJobs([/* ... */]);
$promise = $client->listAnnotationImportJobsAsync([/* ... */]);

Retrieves a list of annotation import jobs.

Parameter Syntax

$result = $client->listAnnotationImportJobs([
    'filter' => [
        'status' => 'SUBMITTED|IN_PROGRESS|CANCELLED|COMPLETED|FAILED|COMPLETED_WITH_FAILURES',
        'storeName' => '<string>',
    ],
    'ids' => ['<string>', ...],
    'maxResults' => <integer>,
    'nextToken' => '<string>',
]);

Parameter Details

Members
filter

A filter to apply to the list.

ids
Type: Array of strings

IDs of annotation import jobs to retrieve.

maxResults
Type: int

The maximum number of jobs to return in one page of results.

nextToken
Type: string

Specifies the pagination token from a previous request to retrieve the next page of results.

Result Syntax

[
    'annotationImportJobs' => [
        [
            'annotationFields' => ['<string>', ...],
            'completionTime' => <DateTime>,
            'creationTime' => <DateTime>,
            'destinationName' => '<string>',
            'id' => '<string>',
            'roleArn' => '<string>',
            'runLeftNormalization' => true || false,
            'status' => 'SUBMITTED|IN_PROGRESS|CANCELLED|COMPLETED|FAILED|COMPLETED_WITH_FAILURES',
            'updateTime' => <DateTime>,
            'versionName' => '<string>',
        ],
        // ...
    ],
    'nextToken' => '<string>',
]

Result Details

Members
annotationImportJobs
Type: Array of AnnotationImportJobItem structures

A list of jobs.

nextToken
Type: string

Specifies the pagination token from a previous request to retrieve the next page of results.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

ListAnnotationStoreVersions

$result = $client->listAnnotationStoreVersions([/* ... */]);
$promise = $client->listAnnotationStoreVersionsAsync([/* ... */]);

Lists the versions of an annotation store.

Parameter Syntax

$result = $client->listAnnotationStoreVersions([
    'filter' => [
        'status' => 'CREATING|UPDATING|DELETING|ACTIVE|FAILED',
    ],
    'maxResults' => <integer>,
    'name' => '<string>', // REQUIRED
    'nextToken' => '<string>',
]);

Parameter Details

Members
filter

A filter to apply to the list of annotation store versions.

maxResults
Type: int

The maximum number of annotation store versions to return in one page of results.

name
Required: Yes
Type: string

The name of an annotation store.

nextToken
Type: string

Specifies the pagination token from a previous request to retrieve the next page of results.

Result Syntax

[
    'annotationStoreVersions' => [
        [
            'creationTime' => <DateTime>,
            'description' => '<string>',
            'id' => '<string>',
            'name' => '<string>',
            'status' => 'CREATING|UPDATING|DELETING|ACTIVE|FAILED',
            'statusMessage' => '<string>',
            'storeId' => '<string>',
            'updateTime' => <DateTime>,
            'versionArn' => '<string>',
            'versionName' => '<string>',
            'versionSizeBytes' => <integer>,
        ],
        // ...
    ],
    'nextToken' => '<string>',
]

Result Details

Members
annotationStoreVersions
Type: Array of AnnotationStoreVersionItem structures

Lists all versions of an annotation store.

nextToken
Type: string

Specifies the pagination token from a previous request to retrieve the next page of results.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

ListAnnotationStores

$result = $client->listAnnotationStores([/* ... */]);
$promise = $client->listAnnotationStoresAsync([/* ... */]);

Retrieves a list of annotation stores.

Parameter Syntax

$result = $client->listAnnotationStores([
    'filter' => [
        'status' => 'CREATING|UPDATING|DELETING|ACTIVE|FAILED',
    ],
    'ids' => ['<string>', ...],
    'maxResults' => <integer>,
    'nextToken' => '<string>',
]);

Parameter Details

Members
filter
Type: ListAnnotationStoresFilter structure

A filter to apply to the list.

ids
Type: Array of strings

IDs of stores to list.

maxResults
Type: int

The maximum number of stores to return in one page of results.

nextToken
Type: string

Specify the pagination token from a previous request to retrieve the next page of results.

Result Syntax

[
    'annotationStores' => [
        [
            'creationTime' => <DateTime>,
            'description' => '<string>',
            'id' => '<string>',
            'name' => '<string>',
            'reference' => [
                'referenceArn' => '<string>',
            ],
            'sseConfig' => [
                'keyArn' => '<string>',
                'type' => 'KMS',
            ],
            'status' => 'CREATING|UPDATING|DELETING|ACTIVE|FAILED',
            'statusMessage' => '<string>',
            'storeArn' => '<string>',
            'storeFormat' => 'GFF|TSV|VCF',
            'storeSizeBytes' => <integer>,
            'updateTime' => <DateTime>,
        ],
        // ...
    ],
    'nextToken' => '<string>',
]

Result Details

Members
annotationStores
Type: Array of AnnotationStoreItem structures

A list of stores.

nextToken
Type: string

A pagination token that's included if more results are available.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

ListMultipartReadSetUploads

$result = $client->listMultipartReadSetUploads([/* ... */]);
$promise = $client->listMultipartReadSetUploadsAsync([/* ... */]);

Lists multipart read set uploads and for in progress uploads. Once the upload is completed, a read set is created and the upload will no longer be returned in the response.

Parameter Syntax

$result = $client->listMultipartReadSetUploads([
    'maxResults' => <integer>,
    'nextToken' => '<string>',
    'sequenceStoreId' => '<string>', // REQUIRED
]);

Parameter Details

Members
maxResults
Type: int

The maximum number of multipart uploads returned in a page.

nextToken
Type: string

Next token returned in the response of a previous ListMultipartReadSetUploads call. Used to get the next page of results.

sequenceStoreId
Required: Yes
Type: string

The Sequence Store ID used for the multipart uploads.

Result Syntax

[
    'nextToken' => '<string>',
    'uploads' => [
        [
            'creationTime' => <DateTime>,
            'description' => '<string>',
            'generatedFrom' => '<string>',
            'name' => '<string>',
            'referenceArn' => '<string>',
            'sampleId' => '<string>',
            'sequenceStoreId' => '<string>',
            'sourceFileType' => 'FASTQ|BAM|CRAM|UBAM',
            'subjectId' => '<string>',
            'tags' => ['<string>', ...],
            'uploadId' => '<string>',
        ],
        // ...
    ],
]

Result Details

Members
nextToken
Type: string

Next token returned in the response of a previous ListMultipartReadSetUploads call. Used to get the next page of results.

uploads
Type: Array of MultipartReadSetUploadListItem structures

An array of multipart uploads.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

NotSupportedOperationException:

The operation is not supported by Amazon Omics, or the API does not exist.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

ListReadSetActivationJobs

$result = $client->listReadSetActivationJobs([/* ... */]);
$promise = $client->listReadSetActivationJobsAsync([/* ... */]);

Retrieves a list of read set activation jobs.

Parameter Syntax

$result = $client->listReadSetActivationJobs([
    'filter' => [
        'createdAfter' => <integer || string || DateTime>,
        'createdBefore' => <integer || string || DateTime>,
        'status' => 'SUBMITTED|IN_PROGRESS|CANCELLING|CANCELLED|FAILED|COMPLETED|COMPLETED_WITH_FAILURES',
    ],
    'maxResults' => <integer>,
    'nextToken' => '<string>',
    'sequenceStoreId' => '<string>', // REQUIRED
]);

Parameter Details

Members
filter
Type: ActivateReadSetFilter structure

A filter to apply to the list.

maxResults
Type: int

The maximum number of read set activation jobs to return in one page of results.

nextToken
Type: string

Specify the pagination token from a previous request to retrieve the next page of results.

sequenceStoreId
Required: Yes
Type: string

The read set's sequence store ID.

Result Syntax

[
    'activationJobs' => [
        [
            'completionTime' => <DateTime>,
            'creationTime' => <DateTime>,
            'id' => '<string>',
            'sequenceStoreId' => '<string>',
            'status' => 'SUBMITTED|IN_PROGRESS|CANCELLING|CANCELLED|FAILED|COMPLETED|COMPLETED_WITH_FAILURES',
        ],
        // ...
    ],
    'nextToken' => '<string>',
]

Result Details

Members
activationJobs
Type: Array of ActivateReadSetJobItem structures

A list of jobs.

nextToken
Type: string

A pagination token that's included if more results are available.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

ListReadSetExportJobs

$result = $client->listReadSetExportJobs([/* ... */]);
$promise = $client->listReadSetExportJobsAsync([/* ... */]);

Retrieves a list of read set export jobs.

Parameter Syntax

$result = $client->listReadSetExportJobs([
    'filter' => [
        'createdAfter' => <integer || string || DateTime>,
        'createdBefore' => <integer || string || DateTime>,
        'status' => 'SUBMITTED|IN_PROGRESS|CANCELLING|CANCELLED|FAILED|COMPLETED|COMPLETED_WITH_FAILURES',
    ],
    'maxResults' => <integer>,
    'nextToken' => '<string>',
    'sequenceStoreId' => '<string>', // REQUIRED
]);

Parameter Details

Members
filter
Type: ExportReadSetFilter structure

A filter to apply to the list.

maxResults
Type: int

The maximum number of jobs to return in one page of results.

nextToken
Type: string

Specify the pagination token from a previous request to retrieve the next page of results.

sequenceStoreId
Required: Yes
Type: string

The jobs' sequence store ID.

Result Syntax

[
    'exportJobs' => [
        [
            'completionTime' => <DateTime>,
            'creationTime' => <DateTime>,
            'destination' => '<string>',
            'id' => '<string>',
            'sequenceStoreId' => '<string>',
            'status' => 'SUBMITTED|IN_PROGRESS|CANCELLING|CANCELLED|FAILED|COMPLETED|COMPLETED_WITH_FAILURES',
        ],
        // ...
    ],
    'nextToken' => '<string>',
]

Result Details

Members
exportJobs
Type: Array of ExportReadSetJobDetail structures

A list of jobs.

nextToken
Type: string

A pagination token that's included if more results are available.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

ListReadSetImportJobs

$result = $client->listReadSetImportJobs([/* ... */]);
$promise = $client->listReadSetImportJobsAsync([/* ... */]);

Retrieves a list of read set import jobs.

Parameter Syntax

$result = $client->listReadSetImportJobs([
    'filter' => [
        'createdAfter' => <integer || string || DateTime>,
        'createdBefore' => <integer || string || DateTime>,
        'status' => 'SUBMITTED|IN_PROGRESS|CANCELLING|CANCELLED|FAILED|COMPLETED|COMPLETED_WITH_FAILURES',
    ],
    'maxResults' => <integer>,
    'nextToken' => '<string>',
    'sequenceStoreId' => '<string>', // REQUIRED
]);

Parameter Details

Members
filter
Type: ImportReadSetFilter structure

A filter to apply to the list.

maxResults
Type: int

The maximum number of jobs to return in one page of results.

nextToken
Type: string

Specify the pagination token from a previous request to retrieve the next page of results.

sequenceStoreId
Required: Yes
Type: string

The jobs' sequence store ID.

Result Syntax

[
    'importJobs' => [
        [
            'completionTime' => <DateTime>,
            'creationTime' => <DateTime>,
            'id' => '<string>',
            'roleArn' => '<string>',
            'sequenceStoreId' => '<string>',
            'status' => 'SUBMITTED|IN_PROGRESS|CANCELLING|CANCELLED|FAILED|COMPLETED|COMPLETED_WITH_FAILURES',
        ],
        // ...
    ],
    'nextToken' => '<string>',
]

Result Details

Members
importJobs
Type: Array of ImportReadSetJobItem structures

A list of jobs.

nextToken
Type: string

A pagination token that's included if more results are available.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

ListReadSetUploadParts

$result = $client->listReadSetUploadParts([/* ... */]);
$promise = $client->listReadSetUploadPartsAsync([/* ... */]);

This operation will list all parts in a requested multipart upload for a sequence store.

Parameter Syntax

$result = $client->listReadSetUploadParts([
    'filter' => [
        'createdAfter' => <integer || string || DateTime>,
        'createdBefore' => <integer || string || DateTime>,
    ],
    'maxResults' => <integer>,
    'nextToken' => '<string>',
    'partSource' => 'SOURCE1|SOURCE2', // REQUIRED
    'sequenceStoreId' => '<string>', // REQUIRED
    'uploadId' => '<string>', // REQUIRED
]);

Parameter Details

Members
filter
Type: ReadSetUploadPartListFilter structure

Attributes used to filter for a specific subset of read set part uploads.

maxResults
Type: int

The maximum number of read set upload parts returned in a page.

nextToken
Type: string

Next token returned in the response of a previous ListReadSetUploadPartsRequest call. Used to get the next page of results.

partSource
Required: Yes
Type: string

The source file for the upload part.

sequenceStoreId
Required: Yes
Type: string

The Sequence Store ID used for the multipart uploads.

uploadId
Required: Yes
Type: string

The ID for the initiated multipart upload.

Result Syntax

[
    'nextToken' => '<string>',
    'parts' => [
        [
            'checksum' => '<string>',
            'creationTime' => <DateTime>,
            'lastUpdatedTime' => <DateTime>,
            'partNumber' => <integer>,
            'partSize' => <integer>,
            'partSource' => 'SOURCE1|SOURCE2',
        ],
        // ...
    ],
]

Result Details

Members
nextToken
Type: string

Next token returned in the response of a previous ListReadSetUploadParts call. Used to get the next page of results.

parts
Type: Array of ReadSetUploadPartListItem structures

An array of upload parts.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

NotSupportedOperationException:

The operation is not supported by Amazon Omics, or the API does not exist.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

ListReadSets

$result = $client->listReadSets([/* ... */]);
$promise = $client->listReadSetsAsync([/* ... */]);

Retrieves a list of read sets.

Parameter Syntax

$result = $client->listReadSets([
    'filter' => [
        'createdAfter' => <integer || string || DateTime>,
        'createdBefore' => <integer || string || DateTime>,
        'creationType' => 'IMPORT|UPLOAD',
        'generatedFrom' => '<string>',
        'name' => '<string>',
        'referenceArn' => '<string>',
        'sampleId' => '<string>',
        'status' => 'ARCHIVED|ACTIVATING|ACTIVE|DELETING|DELETED|PROCESSING_UPLOAD|UPLOAD_FAILED',
        'subjectId' => '<string>',
    ],
    'maxResults' => <integer>,
    'nextToken' => '<string>',
    'sequenceStoreId' => '<string>', // REQUIRED
]);

Parameter Details

Members
filter
Type: ReadSetFilter structure

A filter to apply to the list.

maxResults
Type: int

The maximum number of read sets to return in one page of results.

nextToken
Type: string

Specify the pagination token from a previous request to retrieve the next page of results.

sequenceStoreId
Required: Yes
Type: string

The jobs' sequence store ID.

Result Syntax

[
    'nextToken' => '<string>',
    'readSets' => [
        [
            'arn' => '<string>',
            'creationTime' => <DateTime>,
            'creationType' => 'IMPORT|UPLOAD',
            'description' => '<string>',
            'etag' => [
                'algorithm' => 'FASTQ_MD5up|BAM_MD5up|CRAM_MD5up|FASTQ_SHA256up|BAM_SHA256up|CRAM_SHA256up|FASTQ_SHA512up|BAM_SHA512up|CRAM_SHA512up',
                'source1' => '<string>',
                'source2' => '<string>',
            ],
            'fileType' => 'FASTQ|BAM|CRAM|UBAM',
            'id' => '<string>',
            'name' => '<string>',
            'referenceArn' => '<string>',
            'sampleId' => '<string>',
            'sequenceInformation' => [
                'alignment' => '<string>',
                'generatedFrom' => '<string>',
                'totalBaseCount' => <integer>,
                'totalReadCount' => <integer>,
            ],
            'sequenceStoreId' => '<string>',
            'status' => 'ARCHIVED|ACTIVATING|ACTIVE|DELETING|DELETED|PROCESSING_UPLOAD|UPLOAD_FAILED',
            'statusMessage' => '<string>',
            'subjectId' => '<string>',
        ],
        // ...
    ],
]

Result Details

Members
nextToken
Type: string

A pagination token that's included if more results are available.

readSets
Required: Yes
Type: Array of ReadSetListItem structures

A list of read sets.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

ListReferenceImportJobs

$result = $client->listReferenceImportJobs([/* ... */]);
$promise = $client->listReferenceImportJobsAsync([/* ... */]);

Retrieves a list of reference import jobs.

Parameter Syntax

$result = $client->listReferenceImportJobs([
    'filter' => [
        'createdAfter' => <integer || string || DateTime>,
        'createdBefore' => <integer || string || DateTime>,
        'status' => 'SUBMITTED|IN_PROGRESS|CANCELLING|CANCELLED|FAILED|COMPLETED|COMPLETED_WITH_FAILURES',
    ],
    'maxResults' => <integer>,
    'nextToken' => '<string>',
    'referenceStoreId' => '<string>', // REQUIRED
]);

Parameter Details

Members
filter
Type: ImportReferenceFilter structure

A filter to apply to the list.

maxResults
Type: int

The maximum number of jobs to return in one page of results.

nextToken
Type: string

Specify the pagination token from a previous request to retrieve the next page of results.

referenceStoreId
Required: Yes
Type: string

The job's reference store ID.

Result Syntax

[
    'importJobs' => [
        [
            'completionTime' => <DateTime>,
            'creationTime' => <DateTime>,
            'id' => '<string>',
            'referenceStoreId' => '<string>',
            'roleArn' => '<string>',
            'status' => 'SUBMITTED|IN_PROGRESS|CANCELLING|CANCELLED|FAILED|COMPLETED|COMPLETED_WITH_FAILURES',
        ],
        // ...
    ],
    'nextToken' => '<string>',
]

Result Details

Members
importJobs
Type: Array of ImportReferenceJobItem structures

A lis of jobs.

nextToken
Type: string

A pagination token that's included if more results are available.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

ListReferenceStores

$result = $client->listReferenceStores([/* ... */]);
$promise = $client->listReferenceStoresAsync([/* ... */]);

Retrieves a list of reference stores.

Parameter Syntax

$result = $client->listReferenceStores([
    'filter' => [
        'createdAfter' => <integer || string || DateTime>,
        'createdBefore' => <integer || string || DateTime>,
        'name' => '<string>',
    ],
    'maxResults' => <integer>,
    'nextToken' => '<string>',
]);

Parameter Details

Members
filter
Type: ReferenceStoreFilter structure

A filter to apply to the list.

maxResults
Type: int

The maximum number of stores to return in one page of results.

nextToken
Type: string

Specify the pagination token from a previous request to retrieve the next page of results.

Result Syntax

[
    'nextToken' => '<string>',
    'referenceStores' => [
        [
            'arn' => '<string>',
            'creationTime' => <DateTime>,
            'description' => '<string>',
            'id' => '<string>',
            'name' => '<string>',
            'sseConfig' => [
                'keyArn' => '<string>',
                'type' => 'KMS',
            ],
        ],
        // ...
    ],
]

Result Details

Members
nextToken
Type: string

A pagination token that's included if more results are available.

referenceStores
Required: Yes
Type: Array of ReferenceStoreDetail structures

A list of reference stores.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

ListReferences

$result = $client->listReferences([/* ... */]);
$promise = $client->listReferencesAsync([/* ... */]);

Retrieves a list of references.

Parameter Syntax

$result = $client->listReferences([
    'filter' => [
        'createdAfter' => <integer || string || DateTime>,
        'createdBefore' => <integer || string || DateTime>,
        'md5' => '<string>',
        'name' => '<string>',
    ],
    'maxResults' => <integer>,
    'nextToken' => '<string>',
    'referenceStoreId' => '<string>', // REQUIRED
]);

Parameter Details

Members
filter
Type: ReferenceFilter structure

A filter to apply to the list.

maxResults
Type: int

The maximum number of references to return in one page of results.

nextToken
Type: string

Specify the pagination token from a previous request to retrieve the next page of results.

referenceStoreId
Required: Yes
Type: string

The references' reference store ID.

Result Syntax

[
    'nextToken' => '<string>',
    'references' => [
        [
            'arn' => '<string>',
            'creationTime' => <DateTime>,
            'description' => '<string>',
            'id' => '<string>',
            'md5' => '<string>',
            'name' => '<string>',
            'referenceStoreId' => '<string>',
            'status' => 'ACTIVE|DELETING|DELETED',
            'updateTime' => <DateTime>,
        ],
        // ...
    ],
]

Result Details

Members
nextToken
Type: string

A pagination token that's included if more results are available.

references
Required: Yes
Type: Array of ReferenceListItem structures

A list of references.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

ListRunGroups

$result = $client->listRunGroups([/* ... */]);
$promise = $client->listRunGroupsAsync([/* ... */]);

Retrieves a list of run groups.

Parameter Syntax

$result = $client->listRunGroups([
    'maxResults' => <integer>,
    'name' => '<string>',
    'startingToken' => '<string>',
]);

Parameter Details

Members
maxResults
Type: int

The maximum number of run groups to return in one page of results.

name
Type: string

The run groups' name.

startingToken
Type: string

Specify the pagination token from a previous request to retrieve the next page of results.

Result Syntax

[
    'items' => [
        [
            'arn' => '<string>',
            'creationTime' => <DateTime>,
            'id' => '<string>',
            'maxCpus' => <integer>,
            'maxDuration' => <integer>,
            'maxGpus' => <integer>,
            'maxRuns' => <integer>,
            'name' => '<string>',
        ],
        // ...
    ],
    'nextToken' => '<string>',
]

Result Details

Members
items
Type: Array of RunGroupListItem structures

A list of groups.

nextToken
Type: string

A pagination token that's included if more results are available.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

ListRunTasks

$result = $client->listRunTasks([/* ... */]);
$promise = $client->listRunTasksAsync([/* ... */]);

Retrieves a list of tasks for a run.

Parameter Syntax

$result = $client->listRunTasks([
    'id' => '<string>', // REQUIRED
    'maxResults' => <integer>,
    'startingToken' => '<string>',
    'status' => 'PENDING|STARTING|RUNNING|STOPPING|COMPLETED|CANCELLED|FAILED',
]);

Parameter Details

Members
id
Required: Yes
Type: string

The run's ID.

maxResults
Type: int

The maximum number of run tasks to return in one page of results.

startingToken
Type: string

Specify the pagination token from a previous request to retrieve the next page of results.

status
Type: string

Filter the list by status.

Result Syntax

[
    'items' => [
        [
            'cpus' => <integer>,
            'creationTime' => <DateTime>,
            'gpus' => <integer>,
            'instanceType' => '<string>',
            'memory' => <integer>,
            'name' => '<string>',
            'startTime' => <DateTime>,
            'status' => 'PENDING|STARTING|RUNNING|STOPPING|COMPLETED|CANCELLED|FAILED',
            'stopTime' => <DateTime>,
            'taskId' => '<string>',
        ],
        // ...
    ],
    'nextToken' => '<string>',
]

Result Details

Members
items
Type: Array of TaskListItem structures

A list of tasks.

nextToken
Type: string

A pagination token that's included if more results are available.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

ListRuns

$result = $client->listRuns([/* ... */]);
$promise = $client->listRunsAsync([/* ... */]);

Retrieves a list of runs.

Parameter Syntax

$result = $client->listRuns([
    'maxResults' => <integer>,
    'name' => '<string>',
    'runGroupId' => '<string>',
    'startingToken' => '<string>',
    'status' => 'PENDING|STARTING|RUNNING|STOPPING|COMPLETED|DELETED|CANCELLED|FAILED',
]);

Parameter Details

Members
maxResults
Type: int

The maximum number of runs to return in one page of results.

name
Type: string

Filter the list by run name.

runGroupId
Type: string

Filter the list by run group ID.

startingToken
Type: string

Specify the pagination token from a previous request to retrieve the next page of results.

status
Type: string

The status of a run.

Result Syntax

[
    'items' => [
        [
            'arn' => '<string>',
            'creationTime' => <DateTime>,
            'id' => '<string>',
            'name' => '<string>',
            'priority' => <integer>,
            'startTime' => <DateTime>,
            'status' => 'PENDING|STARTING|RUNNING|STOPPING|COMPLETED|DELETED|CANCELLED|FAILED',
            'stopTime' => <DateTime>,
            'storageCapacity' => <integer>,
            'storageType' => 'STATIC|DYNAMIC',
            'workflowId' => '<string>',
        ],
        // ...
    ],
    'nextToken' => '<string>',
]

Result Details

Members
items
Type: Array of RunListItem structures

A list of runs.

nextToken
Type: string

A pagination token that's included if more results are available.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

ListSequenceStores

$result = $client->listSequenceStores([/* ... */]);
$promise = $client->listSequenceStoresAsync([/* ... */]);

Retrieves a list of sequence stores.

Parameter Syntax

$result = $client->listSequenceStores([
    'filter' => [
        'createdAfter' => <integer || string || DateTime>,
        'createdBefore' => <integer || string || DateTime>,
        'name' => '<string>',
    ],
    'maxResults' => <integer>,
    'nextToken' => '<string>',
]);

Parameter Details

Members
filter
Type: SequenceStoreFilter structure

A filter to apply to the list.

maxResults
Type: int

The maximum number of stores to return in one page of results.

nextToken
Type: string

Specify the pagination token from a previous request to retrieve the next page of results.

Result Syntax

[
    'nextToken' => '<string>',
    'sequenceStores' => [
        [
            'arn' => '<string>',
            'creationTime' => <DateTime>,
            'description' => '<string>',
            'eTagAlgorithmFamily' => 'MD5up|SHA256up|SHA512up',
            'fallbackLocation' => '<string>',
            'id' => '<string>',
            'name' => '<string>',
            'sseConfig' => [
                'keyArn' => '<string>',
                'type' => 'KMS',
            ],
        ],
        // ...
    ],
]

Result Details

Members
nextToken
Type: string

A pagination token that's included if more results are available.

sequenceStores
Required: Yes
Type: Array of SequenceStoreDetail structures

A list of sequence stores.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

ListShares

$result = $client->listShares([/* ... */]);
$promise = $client->listSharesAsync([/* ... */]);

Retrieves the resource shares associated with an account. Use the filter parameter to retrieve a specific subset of the shares.

Parameter Syntax

$result = $client->listShares([
    'filter' => [
        'resourceArns' => ['<string>', ...],
        'status' => ['<string>', ...],
        'type' => ['<string>', ...],
    ],
    'maxResults' => <integer>,
    'nextToken' => '<string>',
    'resourceOwner' => 'SELF|OTHER', // REQUIRED
]);

Parameter Details

Members
filter
Type: Filter structure

Attributes that you use to filter for a specific subset of resource shares.

maxResults
Type: int

The maximum number of shares to return in one page of results.

nextToken
Type: string

Next token returned in the response of a previous ListReadSetUploadPartsRequest call. Used to get the next page of results.

resourceOwner
Required: Yes
Type: string

The account that owns the resource shares.

Result Syntax

[
    'nextToken' => '<string>',
    'shares' => [
        [
            'creationTime' => <DateTime>,
            'ownerId' => '<string>',
            'principalSubscriber' => '<string>',
            'resourceArn' => '<string>',
            'resourceId' => '<string>',
            'shareId' => '<string>',
            'shareName' => '<string>',
            'status' => 'PENDING|ACTIVATING|ACTIVE|DELETING|DELETED|FAILED',
            'statusMessage' => '<string>',
            'updateTime' => <DateTime>,
        ],
        // ...
    ],
]

Result Details

Members
nextToken
Type: string

Next token returned in the response of a previous ListSharesResponse call. Used to get the next page of results.

shares
Required: Yes
Type: Array of ShareDetails structures

The shares available and their metadata details.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

ListTagsForResource

$result = $client->listTagsForResource([/* ... */]);
$promise = $client->listTagsForResourceAsync([/* ... */]);

Retrieves a list of tags for a resource.

Parameter Syntax

$result = $client->listTagsForResource([
    'resourceArn' => '<string>', // REQUIRED
]);

Parameter Details

Members
resourceArn
Required: Yes
Type: string

The resource's ARN.

Result Syntax

[
    'tags' => ['<string>', ...],
]

Result Details

Members
tags
Required: Yes
Type: Associative array of custom strings keys (TagKey) to strings

A list of tags.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

ListVariantImportJobs

$result = $client->listVariantImportJobs([/* ... */]);
$promise = $client->listVariantImportJobsAsync([/* ... */]);

Retrieves a list of variant import jobs.

Parameter Syntax

$result = $client->listVariantImportJobs([
    'filter' => [
        'status' => 'SUBMITTED|IN_PROGRESS|CANCELLED|COMPLETED|FAILED|COMPLETED_WITH_FAILURES',
        'storeName' => '<string>',
    ],
    'ids' => ['<string>', ...],
    'maxResults' => <integer>,
    'nextToken' => '<string>',
]);

Parameter Details

Members
filter
Type: ListVariantImportJobsFilter structure

A filter to apply to the list.

ids
Type: Array of strings

A list of job IDs.

maxResults
Type: int

The maximum number of import jobs to return in one page of results.

nextToken
Type: string

Specify the pagination token from a previous request to retrieve the next page of results.

Result Syntax

[
    'nextToken' => '<string>',
    'variantImportJobs' => [
        [
            'annotationFields' => ['<string>', ...],
            'completionTime' => <DateTime>,
            'creationTime' => <DateTime>,
            'destinationName' => '<string>',
            'id' => '<string>',
            'roleArn' => '<string>',
            'runLeftNormalization' => true || false,
            'status' => 'SUBMITTED|IN_PROGRESS|CANCELLED|COMPLETED|FAILED|COMPLETED_WITH_FAILURES',
            'updateTime' => <DateTime>,
        ],
        // ...
    ],
]

Result Details

Members
nextToken
Type: string

A pagination token that's included if more results are available.

variantImportJobs
Type: Array of VariantImportJobItem structures

A list of jobs.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

ListVariantStores

$result = $client->listVariantStores([/* ... */]);
$promise = $client->listVariantStoresAsync([/* ... */]);

Retrieves a list of variant stores.

Parameter Syntax

$result = $client->listVariantStores([
    'filter' => [
        'status' => 'CREATING|UPDATING|DELETING|ACTIVE|FAILED',
    ],
    'ids' => ['<string>', ...],
    'maxResults' => <integer>,
    'nextToken' => '<string>',
]);

Parameter Details

Members
filter
Type: ListVariantStoresFilter structure

A filter to apply to the list.

ids
Type: Array of strings

A list of store IDs.

maxResults
Type: int

The maximum number of stores to return in one page of results.

nextToken
Type: string

Specify the pagination token from a previous request to retrieve the next page of results.

Result Syntax

[
    'nextToken' => '<string>',
    'variantStores' => [
        [
            'creationTime' => <DateTime>,
            'description' => '<string>',
            'id' => '<string>',
            'name' => '<string>',
            'reference' => [
                'referenceArn' => '<string>',
            ],
            'sseConfig' => [
                'keyArn' => '<string>',
                'type' => 'KMS',
            ],
            'status' => 'CREATING|UPDATING|DELETING|ACTIVE|FAILED',
            'statusMessage' => '<string>',
            'storeArn' => '<string>',
            'storeSizeBytes' => <integer>,
            'updateTime' => <DateTime>,
        ],
        // ...
    ],
]

Result Details

Members
nextToken
Type: string

A pagination token that's included if more results are available.

variantStores
Type: Array of VariantStoreItem structures

A list of variant stores.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

ListWorkflows

$result = $client->listWorkflows([/* ... */]);
$promise = $client->listWorkflowsAsync([/* ... */]);

Retrieves a list of workflows.

Parameter Syntax

$result = $client->listWorkflows([
    'maxResults' => <integer>,
    'name' => '<string>',
    'startingToken' => '<string>',
    'type' => 'PRIVATE|READY2RUN',
]);

Parameter Details

Members
maxResults
Type: int

The maximum number of workflows to return in one page of results.

name
Type: string

Filter the list by workflow name.

startingToken
Type: string

Specify the pagination token from a previous request to retrieve the next page of results.

type
Type: string

Filter the list by workflow type.

Result Syntax

[
    'items' => [
        [
            'arn' => '<string>',
            'creationTime' => <DateTime>,
            'digest' => '<string>',
            'id' => '<string>',
            'metadata' => ['<string>', ...],
            'name' => '<string>',
            'status' => 'CREATING|ACTIVE|UPDATING|DELETED|FAILED|INACTIVE',
            'type' => 'PRIVATE|READY2RUN',
        ],
        // ...
    ],
    'nextToken' => '<string>',
]

Result Details

Members
items
Type: Array of WorkflowListItem structures

A list of workflow items.

nextToken
Type: string

A pagination token that's included if more results are available.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

StartAnnotationImportJob

$result = $client->startAnnotationImportJob([/* ... */]);
$promise = $client->startAnnotationImportJobAsync([/* ... */]);

Starts an annotation import job.

Parameter Syntax

$result = $client->startAnnotationImportJob([
    'annotationFields' => ['<string>', ...],
    'destinationName' => '<string>', // REQUIRED
    'formatOptions' => [
        'tsvOptions' => [
            'readOptions' => [
                'comment' => '<string>',
                'encoding' => '<string>',
                'escape' => '<string>',
                'escapeQuotes' => true || false,
                'header' => true || false,
                'lineSep' => '<string>',
                'quote' => '<string>',
                'quoteAll' => true || false,
                'sep' => '<string>',
            ],
        ],
        'vcfOptions' => [
            'ignoreFilterField' => true || false,
            'ignoreQualField' => true || false,
        ],
    ],
    'items' => [ // REQUIRED
        [
            'source' => '<string>', // REQUIRED
        ],
        // ...
    ],
    'roleArn' => '<string>', // REQUIRED
    'runLeftNormalization' => true || false,
    'versionName' => '<string>',
]);

Parameter Details

Members
annotationFields
Type: Associative array of custom strings keys (AnnotationFieldMapKeyString) to strings

The annotation schema generated by the parsed annotation data.

destinationName
Required: Yes
Type: string

A destination annotation store for the job.

formatOptions
Type: FormatOptions structure

Formatting options for the annotation file.

items
Required: Yes
Type: Array of AnnotationImportItemSource structures

Items to import.

roleArn
Required: Yes
Type: string

A service role for the job.

runLeftNormalization
Type: boolean

The job's left normalization setting.

versionName
Type: string

The name of the annotation store version.

Result Syntax

[
    'jobId' => '<string>',
]

Result Details

Members
jobId
Required: Yes
Type: string

The job's ID.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

StartReadSetActivationJob

$result = $client->startReadSetActivationJob([/* ... */]);
$promise = $client->startReadSetActivationJobAsync([/* ... */]);

Activates an archived read set. To reduce storage charges, Amazon Omics archives unused read sets after 30 days.

Parameter Syntax

$result = $client->startReadSetActivationJob([
    'clientToken' => '<string>',
    'sequenceStoreId' => '<string>', // REQUIRED
    'sources' => [ // REQUIRED
        [
            'readSetId' => '<string>', // REQUIRED
        ],
        // ...
    ],
]);

Parameter Details

Members
clientToken
Type: string

To ensure that jobs don't run multiple times, specify a unique token for each job.

sequenceStoreId
Required: Yes
Type: string

The read set's sequence store ID.

sources
Required: Yes
Type: Array of StartReadSetActivationJobSourceItem structures

The job's source files.

Result Syntax

[
    'creationTime' => <DateTime>,
    'id' => '<string>',
    'sequenceStoreId' => '<string>',
    'status' => 'SUBMITTED|IN_PROGRESS|CANCELLING|CANCELLED|FAILED|COMPLETED|COMPLETED_WITH_FAILURES',
]

Result Details

Members
creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job was created.

id
Required: Yes
Type: string

The job's ID.

sequenceStoreId
Required: Yes
Type: string

The read set's sequence store ID.

status
Required: Yes
Type: string

The job's status.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

StartReadSetExportJob

$result = $client->startReadSetExportJob([/* ... */]);
$promise = $client->startReadSetExportJobAsync([/* ... */]);

Exports a read set to Amazon S3.

Parameter Syntax

$result = $client->startReadSetExportJob([
    'clientToken' => '<string>',
    'destination' => '<string>', // REQUIRED
    'roleArn' => '<string>', // REQUIRED
    'sequenceStoreId' => '<string>', // REQUIRED
    'sources' => [ // REQUIRED
        [
            'readSetId' => '<string>', // REQUIRED
        ],
        // ...
    ],
]);

Parameter Details

Members
clientToken
Type: string

To ensure that jobs don't run multiple times, specify a unique token for each job.

destination
Required: Yes
Type: string

A location for exported files in Amazon S3.

roleArn
Required: Yes
Type: string

A service role for the job.

sequenceStoreId
Required: Yes
Type: string

The read set's sequence store ID.

sources
Required: Yes
Type: Array of ExportReadSet structures

The job's source files.

Result Syntax

[
    'creationTime' => <DateTime>,
    'destination' => '<string>',
    'id' => '<string>',
    'sequenceStoreId' => '<string>',
    'status' => 'SUBMITTED|IN_PROGRESS|CANCELLING|CANCELLED|FAILED|COMPLETED|COMPLETED_WITH_FAILURES',
]

Result Details

Members
creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job was created.

destination
Required: Yes
Type: string

The job's output location.

id
Required: Yes
Type: string

The job's ID.

sequenceStoreId
Required: Yes
Type: string

The read set's sequence store ID.

status
Required: Yes
Type: string

The job's status.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

StartReadSetImportJob

$result = $client->startReadSetImportJob([/* ... */]);
$promise = $client->startReadSetImportJobAsync([/* ... */]);

Starts a read set import job.

Parameter Syntax

$result = $client->startReadSetImportJob([
    'clientToken' => '<string>',
    'roleArn' => '<string>', // REQUIRED
    'sequenceStoreId' => '<string>', // REQUIRED
    'sources' => [ // REQUIRED
        [
            'description' => '<string>',
            'generatedFrom' => '<string>',
            'name' => '<string>',
            'referenceArn' => '<string>',
            'sampleId' => '<string>', // REQUIRED
            'sourceFileType' => 'FASTQ|BAM|CRAM|UBAM', // REQUIRED
            'sourceFiles' => [ // REQUIRED
                'source1' => '<string>', // REQUIRED
                'source2' => '<string>',
            ],
            'subjectId' => '<string>', // REQUIRED
            'tags' => ['<string>', ...],
        ],
        // ...
    ],
]);

Parameter Details

Members
clientToken
Type: string

To ensure that jobs don't run multiple times, specify a unique token for each job.

roleArn
Required: Yes
Type: string

A service role for the job.

sequenceStoreId
Required: Yes
Type: string

The read set's sequence store ID.

sources
Required: Yes
Type: Array of StartReadSetImportJobSourceItem structures

The job's source files.

Result Syntax

[
    'creationTime' => <DateTime>,
    'id' => '<string>',
    'roleArn' => '<string>',
    'sequenceStoreId' => '<string>',
    'status' => 'SUBMITTED|IN_PROGRESS|CANCELLING|CANCELLED|FAILED|COMPLETED|COMPLETED_WITH_FAILURES',
]

Result Details

Members
creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job was created.

id
Required: Yes
Type: string

The job's ID.

roleArn
Required: Yes
Type: string

The job's service role ARN.

sequenceStoreId
Required: Yes
Type: string

The read set's sequence store ID.

status
Required: Yes
Type: string

The job's status.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

StartReferenceImportJob

$result = $client->startReferenceImportJob([/* ... */]);
$promise = $client->startReferenceImportJobAsync([/* ... */]);

Starts a reference import job.

Parameter Syntax

$result = $client->startReferenceImportJob([
    'clientToken' => '<string>',
    'referenceStoreId' => '<string>', // REQUIRED
    'roleArn' => '<string>', // REQUIRED
    'sources' => [ // REQUIRED
        [
            'description' => '<string>',
            'name' => '<string>', // REQUIRED
            'sourceFile' => '<string>', // REQUIRED
            'tags' => ['<string>', ...],
        ],
        // ...
    ],
]);

Parameter Details

Members
clientToken
Type: string

To ensure that jobs don't run multiple times, specify a unique token for each job.

referenceStoreId
Required: Yes
Type: string

The job's reference store ID.

roleArn
Required: Yes
Type: string

A service role for the job.

sources
Required: Yes
Type: Array of StartReferenceImportJobSourceItem structures

The job's source files.

Result Syntax

[
    'creationTime' => <DateTime>,
    'id' => '<string>',
    'referenceStoreId' => '<string>',
    'roleArn' => '<string>',
    'status' => 'SUBMITTED|IN_PROGRESS|CANCELLING|CANCELLED|FAILED|COMPLETED|COMPLETED_WITH_FAILURES',
]

Result Details

Members
creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job was created.

id
Required: Yes
Type: string

The job's ID.

referenceStoreId
Required: Yes
Type: string

The job's reference store ID.

roleArn
Required: Yes
Type: string

The job's service role ARN.

status
Required: Yes
Type: string

The job's status.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

StartRun

$result = $client->startRun([/* ... */]);
$promise = $client->startRunAsync([/* ... */]);

Starts a workflow run. To duplicate a run, specify the run's ID and a role ARN. The remaining parameters are copied from the previous run.

StartRun will not support re-run for a workflow that is shared with you.

The total number of runs in your account is subject to a quota per Region. To avoid needing to delete runs manually, you can set the retention mode to REMOVE. Runs with this setting are deleted automatically when the run quoata is exceeded.

By default, the run uses STATIC storage. For STATIC storage, set the storageCapacity field. You can set the storage type to DYNAMIC. You do not set storageCapacity, because HealthOmics dynamically scales the storage up or down as required. For more information about static and dynamic storage, see Running workflows in the AWS HealthOmics User Guide.

Parameter Syntax

$result = $client->startRun([
    'logLevel' => 'OFF|FATAL|ERROR|ALL',
    'name' => '<string>',
    'outputUri' => '<string>',
    'parameters' => [
    ],
    'priority' => <integer>,
    'requestId' => '<string>', // REQUIRED
    'retentionMode' => 'RETAIN|REMOVE',
    'roleArn' => '<string>', // REQUIRED
    'runGroupId' => '<string>',
    'runId' => '<string>',
    'storageCapacity' => <integer>,
    'storageType' => 'STATIC|DYNAMIC',
    'tags' => ['<string>', ...],
    'workflowId' => '<string>',
    'workflowOwnerId' => '<string>',
    'workflowType' => 'PRIVATE|READY2RUN',
]);

Parameter Details

Members
logLevel
Type: string

A log level for the run.

name
Type: string

A name for the run.

outputUri
Type: string

An output URI for the run.

parameters
Type: document (null|bool|string|numeric) or an (array|associative array) whose members are all valid documents

Parameters for the run.

priority
Type: int

A priority for the run.

requestId
Required: Yes
Type: string

To ensure that requests don't run multiple times, specify a unique ID for each request.

retentionMode
Type: string

The retention mode for the run.

roleArn
Required: Yes
Type: string

A service role for the run.

runGroupId
Type: string

The run's group ID.

runId
Type: string

The ID of a run to duplicate.

storageCapacity
Type: int

A storage capacity for the run in gibibytes. This field is not required if the storage type is dynamic (the system ignores any value that you enter).

storageType
Type: string

The run's storage type. By default, the run uses STATIC storage type, which allocates a fixed amount of storage. If you set the storage type to DYNAMIC, HealthOmics dynamically scales the storage up or down, based on file system utilization.

tags
Type: Associative array of custom strings keys (TagKey) to strings

Tags for the run.

workflowId
Type: string

The run's workflow ID.

workflowOwnerId
Type: string

The ID of the workflow owner.

workflowType
Type: string

The run's workflow type.

Result Syntax

[
    'arn' => '<string>',
    'id' => '<string>',
    'runOutputUri' => '<string>',
    'status' => 'PENDING|STARTING|RUNNING|STOPPING|COMPLETED|DELETED|CANCELLED|FAILED',
    'tags' => ['<string>', ...],
    'uuid' => '<string>',
]

Result Details

Members
arn
Type: string

The run's ARN.

id
Type: string

The run's ID.

runOutputUri
Type: string

The destination for workflow outputs.

status
Type: string

The run's status.

tags
Type: Associative array of custom strings keys (TagKey) to strings

The run's tags.

uuid
Type: string

The universally unique identifier for a run.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

StartVariantImportJob

$result = $client->startVariantImportJob([/* ... */]);
$promise = $client->startVariantImportJobAsync([/* ... */]);

Starts a variant import job.

Parameter Syntax

$result = $client->startVariantImportJob([
    'annotationFields' => ['<string>', ...],
    'destinationName' => '<string>', // REQUIRED
    'items' => [ // REQUIRED
        [
            'source' => '<string>', // REQUIRED
        ],
        // ...
    ],
    'roleArn' => '<string>', // REQUIRED
    'runLeftNormalization' => true || false,
]);

Parameter Details

Members
annotationFields
Type: Associative array of custom strings keys (AnnotationFieldMapKeyString) to strings

The annotation schema generated by the parsed annotation data.

destinationName
Required: Yes
Type: string

The destination variant store for the job.

items
Required: Yes
Type: Array of VariantImportItemSource structures

Items to import.

roleArn
Required: Yes
Type: string

A service role for the job.

runLeftNormalization
Type: boolean

The job's left normalization setting.

Result Syntax

[
    'jobId' => '<string>',
]

Result Details

Members
jobId
Required: Yes
Type: string

The job's ID.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

TagResource

$result = $client->tagResource([/* ... */]);
$promise = $client->tagResourceAsync([/* ... */]);

Tags a resource.

Parameter Syntax

$result = $client->tagResource([
    'resourceArn' => '<string>', // REQUIRED
    'tags' => ['<string>', ...], // REQUIRED
]);

Parameter Details

Members
resourceArn
Required: Yes
Type: string

The resource's ARN.

tags
Required: Yes
Type: Associative array of custom strings keys (TagKey) to strings

Tags for the resource.

Result Syntax

[]

Result Details

The results for this operation are always empty.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

UntagResource

$result = $client->untagResource([/* ... */]);
$promise = $client->untagResourceAsync([/* ... */]);

Removes tags from a resource.

Parameter Syntax

$result = $client->untagResource([
    'resourceArn' => '<string>', // REQUIRED
    'tagKeys' => ['<string>', ...], // REQUIRED
]);

Parameter Details

Members
resourceArn
Required: Yes
Type: string

The resource's ARN.

tagKeys
Required: Yes
Type: Array of strings

Keys of tags to remove.

Result Syntax

[]

Result Details

The results for this operation are always empty.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

UpdateAnnotationStore

$result = $client->updateAnnotationStore([/* ... */]);
$promise = $client->updateAnnotationStoreAsync([/* ... */]);

Updates an annotation store.

Parameter Syntax

$result = $client->updateAnnotationStore([
    'description' => '<string>',
    'name' => '<string>', // REQUIRED
]);

Parameter Details

Members
description
Type: string

A description for the store.

name
Required: Yes
Type: string

A name for the store.

Result Syntax

[
    'creationTime' => <DateTime>,
    'description' => '<string>',
    'id' => '<string>',
    'name' => '<string>',
    'reference' => [
        'referenceArn' => '<string>',
    ],
    'status' => 'CREATING|UPDATING|DELETING|ACTIVE|FAILED',
    'storeFormat' => 'GFF|TSV|VCF',
    'storeOptions' => [
        'tsvStoreOptions' => [
            'annotationType' => 'GENERIC|CHR_POS|CHR_POS_REF_ALT|CHR_START_END_ONE_BASE|CHR_START_END_REF_ALT_ONE_BASE|CHR_START_END_ZERO_BASE|CHR_START_END_REF_ALT_ZERO_BASE',
            'formatToHeader' => ['<string>', ...],
            'schema' => [
                ['<string>', ...],
                // ...
            ],
        ],
    ],
    'updateTime' => <DateTime>,
]

Result Details

Members
creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the store was created.

description
Required: Yes
Type: string

The store's description.

id
Required: Yes
Type: string

The store's ID.

name
Required: Yes
Type: string

The store's name.

reference
Required: Yes
Type: ReferenceItem structure

The store's genome reference.

status
Required: Yes
Type: string

The store's status.

storeFormat
Type: string

The annotation file format of the store.

storeOptions
Type: StoreOptions structure

Parsing options for the store.

updateTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the store was updated.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

UpdateAnnotationStoreVersion

$result = $client->updateAnnotationStoreVersion([/* ... */]);
$promise = $client->updateAnnotationStoreVersionAsync([/* ... */]);

Updates the description of an annotation store version.

Parameter Syntax

$result = $client->updateAnnotationStoreVersion([
    'description' => '<string>',
    'name' => '<string>', // REQUIRED
    'versionName' => '<string>', // REQUIRED
]);

Parameter Details

Members
description
Type: string

The description of an annotation store.

name
Required: Yes
Type: string

The name of an annotation store.

versionName
Required: Yes
Type: string

The name of an annotation store version.

Result Syntax

[
    'creationTime' => <DateTime>,
    'description' => '<string>',
    'id' => '<string>',
    'name' => '<string>',
    'status' => 'CREATING|UPDATING|DELETING|ACTIVE|FAILED',
    'storeId' => '<string>',
    'updateTime' => <DateTime>,
    'versionName' => '<string>',
]

Result Details

Members
creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

The time stamp for when an annotation store version was created.

description
Required: Yes
Type: string

The description of an annotation store version.

id
Required: Yes
Type: string

The annotation store version ID.

name
Required: Yes
Type: string

The name of an annotation store.

status
Required: Yes
Type: string

The status of an annotation store version.

storeId
Required: Yes
Type: string

The annotation store ID.

updateTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

The time stamp for when an annotation store version was updated.

versionName
Required: Yes
Type: string

The name of an annotation store version.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

UpdateRunGroup

$result = $client->updateRunGroup([/* ... */]);
$promise = $client->updateRunGroupAsync([/* ... */]);

Updates a run group.

Parameter Syntax

$result = $client->updateRunGroup([
    'id' => '<string>', // REQUIRED
    'maxCpus' => <integer>,
    'maxDuration' => <integer>,
    'maxGpus' => <integer>,
    'maxRuns' => <integer>,
    'name' => '<string>',
]);

Parameter Details

Members
id
Required: Yes
Type: string

The group's ID.

maxCpus
Type: int

The maximum number of CPUs to use.

maxDuration
Type: int

A maximum run time for the group in minutes.

maxGpus
Type: int

The maximum GPUs that can be used by a run group.

maxRuns
Type: int

The maximum number of concurrent runs for the group.

name
Type: string

A name for the group.

Result Syntax

[]

Result Details

The results for this operation are always empty.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

UpdateVariantStore

$result = $client->updateVariantStore([/* ... */]);
$promise = $client->updateVariantStoreAsync([/* ... */]);

Updates a variant store.

Parameter Syntax

$result = $client->updateVariantStore([
    'description' => '<string>',
    'name' => '<string>', // REQUIRED
]);

Parameter Details

Members
description
Type: string

A description for the store.

name
Required: Yes
Type: string

A name for the store.

Result Syntax

[
    'creationTime' => <DateTime>,
    'description' => '<string>',
    'id' => '<string>',
    'name' => '<string>',
    'reference' => [
        'referenceArn' => '<string>',
    ],
    'status' => 'CREATING|UPDATING|DELETING|ACTIVE|FAILED',
    'updateTime' => <DateTime>,
]

Result Details

Members
creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the store was created.

description
Required: Yes
Type: string

The store's description.

id
Required: Yes
Type: string

The store's ID.

name
Required: Yes
Type: string

The store's name.

reference
Required: Yes
Type: ReferenceItem structure

The store's genome reference.

status
Required: Yes
Type: string

The store's status.

updateTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the store was updated.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

UpdateWorkflow

$result = $client->updateWorkflow([/* ... */]);
$promise = $client->updateWorkflowAsync([/* ... */]);

Updates a workflow.

Parameter Syntax

$result = $client->updateWorkflow([
    'description' => '<string>',
    'id' => '<string>', // REQUIRED
    'name' => '<string>',
]);

Parameter Details

Members
description
Type: string

A description for the workflow.

id
Required: Yes
Type: string

The workflow's ID.

name
Type: string

A name for the workflow.

Result Syntax

[]

Result Details

The results for this operation are always empty.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

UploadReadSetPart

$result = $client->uploadReadSetPart([/* ... */]);
$promise = $client->uploadReadSetPartAsync([/* ... */]);

This operation uploads a specific part of a read set. If you upload a new part using a previously used part number, the previously uploaded part will be overwritten.

Parameter Syntax

$result = $client->uploadReadSetPart([
    'partNumber' => <integer>, // REQUIRED
    'partSource' => 'SOURCE1|SOURCE2', // REQUIRED
    'payload' => <string || resource || Psr\Http\Message\StreamInterface>, // REQUIRED
    'sequenceStoreId' => '<string>', // REQUIRED
    'uploadId' => '<string>', // REQUIRED
]);

Parameter Details

Members
partNumber
Required: Yes
Type: int

The number of the part being uploaded.

partSource
Required: Yes
Type: string

The source file for an upload part.

payload
Required: Yes
Type: blob (string|resource|Psr\Http\Message\StreamInterface)

The read set data to upload for a part.

sequenceStoreId
Required: Yes
Type: string

The Sequence Store ID used for the multipart upload.

uploadId
Required: Yes
Type: string

The ID for the initiated multipart upload.

Result Syntax

[
    'checksum' => '<string>',
]

Result Details

Members
checksum
Required: Yes
Type: string

An identifier used to confirm that parts are being added to the intended upload.

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

NotSupportedOperationException:

The operation is not supported by Amazon Omics, or the API does not exist.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

Shapes

AccessDeniedException

Description

You do not have sufficient access to perform this action.

Members
message
Required: Yes
Type: string

ActivateReadSetFilter

Description

A read set activation job filter.

Members
createdAfter
Type: timestamp (string|DateTime or anything parsable by strtotime)

The filter's start date.

createdBefore
Type: timestamp (string|DateTime or anything parsable by strtotime)

The filter's end date.

status
Type: string

The filter's status.

ActivateReadSetJobItem

Description

A read set activation job.

Members
completionTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job completed.

creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job was created.

id
Required: Yes
Type: string

The job's ID.

sequenceStoreId
Required: Yes
Type: string

The job's sequence store ID.

status
Required: Yes
Type: string

The job's status.

ActivateReadSetSourceItem

Description

A source for a read set activation job.

Members
readSetId
Required: Yes
Type: string

The source's read set ID.

status
Required: Yes
Type: string

The source's status.

statusMessage
Type: string

The source's status message.

AnnotationImportItemDetail

Description

Details about an imported annotation item.

Members
jobStatus
Required: Yes
Type: string

The item's job status.

source
Required: Yes
Type: string

The source file's location in Amazon S3.

AnnotationImportItemSource

Description

A source for an annotation import job.

Members
source
Required: Yes
Type: string

The source file's location in Amazon S3.

AnnotationImportJobItem

Description

An annotation import job.

Members
annotationFields
Type: Associative array of custom strings keys (AnnotationFieldMapKeyString) to strings

The annotation schema generated by the parsed annotation data.

completionTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job completed.

creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job was created.

destinationName
Required: Yes
Type: string

The job's destination annotation store.

id
Required: Yes
Type: string

The job's ID.

roleArn
Required: Yes
Type: string

The job's service role ARN.

runLeftNormalization
Type: boolean

The job's left normalization setting.

status
Required: Yes
Type: string

The job's status.

updateTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job was updated.

versionName
Required: Yes
Type: string

The name of the annotation store version.

AnnotationStoreItem

Description

An annotation store.

Members
creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

The store's creation time.

description
Required: Yes
Type: string

The store's description.

id
Required: Yes
Type: string

The store's ID.

name
Required: Yes
Type: string

The store's name.

reference
Required: Yes
Type: ReferenceItem structure

The store's genome reference.

sseConfig
Required: Yes
Type: SseConfig structure

The store's server-side encryption (SSE) settings.

status
Required: Yes
Type: string

The store's status.

statusMessage
Required: Yes
Type: string

The store's status message.

storeArn
Required: Yes
Type: string

The store's ARN.

storeFormat
Required: Yes
Type: string

The store's file format.

storeSizeBytes
Required: Yes
Type: long (int|float)

The store's size in bytes.

updateTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the store was updated.

AnnotationStoreVersionItem

Description

Annotation store versions.

Members
creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

The time stamp for when an annotation store version was created.

description
Required: Yes
Type: string

The description of an annotation store version.

id
Required: Yes
Type: string

The annotation store version ID.

name
Required: Yes
Type: string

A name given to an annotation store version to distinguish it from others.

status
Required: Yes
Type: string

The status of an annotation store version.

statusMessage
Required: Yes
Type: string

The status of an annotation store version.

storeId
Required: Yes
Type: string

The store ID for an annotation store version.

updateTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

The time stamp for when an annotation store version was updated.

versionArn
Required: Yes
Type: string

The Arn for an annotation store version.

versionName
Required: Yes
Type: string

The name of an annotation store version.

versionSizeBytes
Required: Yes
Type: long (int|float)

The size of an annotation store version in Bytes.

CompleteReadSetUploadPartListItem

Description

Part of the response to the CompleteReadSetUpload API, including metadata.

Members
checksum
Required: Yes
Type: string

A unique identifier used to confirm that parts are being added to the correct upload.

partNumber
Required: Yes
Type: int

A number identifying the part in a read set upload.

partSource
Required: Yes
Type: string

The source file of the part being uploaded.

ConflictException

Description

The request cannot be applied to the target resource in its current state.

Members
message
Required: Yes
Type: string

ETag

Description

The entity tag (ETag) is a hash of the object representing its semantic content.

Members
algorithm
Type: string

The algorithm used to calculate the read set’s ETag(s).

source1
Type: string

The ETag hash calculated on Source1 of the read set.

source2
Type: string

The ETag hash calculated on Source2 of the read set.

ExportReadSet

Description

A read set.

Members
readSetId
Required: Yes
Type: string

The set's ID.

ExportReadSetDetail

Description

Details about a read set.

Members
id
Required: Yes
Type: string

The set's ID.

status
Required: Yes
Type: string

The set's status.

statusMessage
Type: string

The set's status message.

ExportReadSetFilter

Description

An read set export job filter.

Members
createdAfter
Type: timestamp (string|DateTime or anything parsable by strtotime)

The filter's start date.

createdBefore
Type: timestamp (string|DateTime or anything parsable by strtotime)

The filter's end date.

status
Type: string

A status to filter on.

ExportReadSetJobDetail

Description

Details about a read set export job.

Members
completionTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job completed.

creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job was created.

destination
Required: Yes
Type: string

The job's destination in Amazon S3.

id
Required: Yes
Type: string

The job's ID.

sequenceStoreId
Required: Yes
Type: string

The job's sequence store ID.

status
Required: Yes
Type: string

The job's status.

FileInformation

Description

Details about a file.

Members
contentLength
Type: long (int|float)

The file's content length.

partSize
Type: long (int|float)

The file's part size.

s3Access
Type: ReadSetS3Access structure

The S3 URI metadata of a sequence store.

totalParts
Type: int

The file's total parts.

Filter

Description

Use filters to return a subset of resources. You can define filters for specific parameters, such as the resource status.

Members
resourceArns
Type: Array of strings

Filter based on the Amazon Resource Number (ARN) of the resource. You can specify up to 10 values.

status
Type: Array of strings

Filter based on the resource status. You can specify up to 10 values.

type
Type: Array of strings

The type of resources to be filtered. You can specify one or more of the resource types.

FormatOptions

Description

Formatting options for a file.

Members
tsvOptions
Type: TsvOptions structure

Options for a TSV file.

vcfOptions
Type: VcfOptions structure

Options for a VCF file.

ImportReadSetFilter

Description

A filter for import read set jobs.

Members
createdAfter
Type: timestamp (string|DateTime or anything parsable by strtotime)

The filter's start date.

createdBefore
Type: timestamp (string|DateTime or anything parsable by strtotime)

The filter's end date.

status
Type: string

A status to filter on.

ImportReadSetJobItem

Description

An import read set job.

Members
completionTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job completed.

creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job was created.

id
Required: Yes
Type: string

The job's ID.

roleArn
Required: Yes
Type: string

The job's service role ARN.

sequenceStoreId
Required: Yes
Type: string

The job's sequence store ID.

status
Required: Yes
Type: string

The job's status.

ImportReadSetSourceItem

Description

A source for an import read set job.

Members
description
Type: string

The source's description.

generatedFrom
Type: string

Where the source originated.

name
Type: string

The source's name.

readSetId
Type: string

The source's read set ID.

referenceArn
Type: string

The source's genome reference ARN.

sampleId
Required: Yes
Type: string

The source's sample ID.

sourceFileType
Required: Yes
Type: string

The source's file type.

sourceFiles
Required: Yes
Type: SourceFiles structure

The source files' location in Amazon S3.

status
Required: Yes
Type: string

The source's status.

statusMessage
Type: string

The source's status message.

subjectId
Required: Yes
Type: string

The source's subject ID.

tags
Type: Associative array of custom strings keys (TagKey) to strings

The source's tags.

ImportReferenceFilter

Description

A filter for import references.

Members
createdAfter
Type: timestamp (string|DateTime or anything parsable by strtotime)

The filter's start date.

createdBefore
Type: timestamp (string|DateTime or anything parsable by strtotime)

The filter's end date.

status
Type: string

A status to filter on.

ImportReferenceJobItem

Description

An import reference job.

Members
completionTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job completed.

creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job was created.

id
Required: Yes
Type: string

The job's ID.

referenceStoreId
Required: Yes
Type: string

The job's reference store ID.

roleArn
Required: Yes
Type: string

The job's service role ARN.

status
Required: Yes
Type: string

The job's status.

ImportReferenceSourceItem

Description

An genome reference source.

Members
description
Type: string

The source's description.

name
Type: string

The source's name.

referenceId
Type: string

The source's reference ID.

sourceFile
Type: string

The source file's location in Amazon S3.

status
Required: Yes
Type: string

The source's status.

statusMessage
Type: string

The source's status message.

tags
Type: Associative array of custom strings keys (TagKey) to strings

The source's tags.

InternalServerException

Description

An unexpected error occurred. Try the request again.

Members
message
Required: Yes
Type: string

ListAnnotationImportJobsFilter

Description

A filter for annotation import jobs.

Members
status
Type: string

A status to filter on.

storeName
Type: string

A store name to filter on.

ListAnnotationStoreVersionsFilter

Description

Use filters to focus the returned annotation store versions on a specific parameter, such as the status of the annotation store.

Members
status
Type: string

The status of an annotation store version.

ListAnnotationStoresFilter

Description

A filter for annotation stores.

Members
status
Type: string

A status to filter on.

ListVariantImportJobsFilter

Description

A filter for variant import jobs.

Members
status
Type: string

A status to filter on.

storeName
Type: string

A store name to filter on.

ListVariantStoresFilter

Description

A filter for variant stores.

Members
status
Type: string

A status to filter on.

MultipartReadSetUploadListItem

Description

Part of the response to ListMultipartReadSetUploads, excluding completed and aborted multipart uploads.

Members
creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

The time stamp for when a direct upload was created.

description
Type: string

The description of a read set.

generatedFrom
Required: Yes
Type: string

The source of an uploaded part.

name
Type: string

The name of a read set.

referenceArn
Required: Yes
Type: string

The source's reference ARN.

sampleId
Required: Yes
Type: string

The read set source's sample ID.

sequenceStoreId
Required: Yes
Type: string

The sequence store ID used for the multipart upload.

sourceFileType
Required: Yes
Type: string

The type of file the read set originated from.

subjectId
Required: Yes
Type: string

The read set source's subject ID.

tags
Type: Associative array of custom strings keys (TagKey) to strings

Any tags you wish to add to a read set.

uploadId
Required: Yes
Type: string

The ID for the initiated multipart upload.

NotSupportedOperationException

Description

The operation is not supported by Amazon Omics, or the API does not exist.

Members
message
Required: Yes
Type: string

RangeNotSatisfiableException

Description

The ranges specified in the request are not valid.

Members
message
Required: Yes
Type: string

ReadOptions

Description

Read options for an annotation import job.

Members
comment
Type: string

The file's comment character.

encoding
Type: string

The file's encoding.

escape
Type: string

A character for escaping quotes in the file.

escapeQuotes
Type: boolean

Whether quotes need to be escaped in the file.

header
Type: boolean

Whether the file has a header row.

lineSep
Type: string

A line separator for the file.

quote
Type: string

The file's quote character.

quoteAll
Type: boolean

Whether all values need to be quoted, or just those that contain quotes.

sep
Type: string

The file's field separator.

ReadSetBatchError

Description

An error from a batch read set operation.

Members
code
Required: Yes
Type: string

The error's code.

id
Required: Yes
Type: string

The error's ID.

message
Required: Yes
Type: string

The error's message.

ReadSetFiles

Description

Files in a read set.

Members
index
Type: FileInformation structure

The files' index.

source1
Type: FileInformation structure

The location of the first file in Amazon S3.

source2
Type: FileInformation structure

The location of the second file in Amazon S3.

ReadSetFilter

Description

A filter for read sets.

Members
createdAfter
Type: timestamp (string|DateTime or anything parsable by strtotime)

The filter's start date.

createdBefore
Type: timestamp (string|DateTime or anything parsable by strtotime)

The filter's end date.

creationType
Type: string

The creation type of the read set.

generatedFrom
Type: string

Where the source originated.

name
Type: string

A name to filter on.

referenceArn
Type: string

A genome reference ARN to filter on.

sampleId
Type: string

The read set source's sample ID.

status
Type: string

A status to filter on.

subjectId
Type: string

The read set source's subject ID.

ReadSetListItem

Description

A read set.

Members
arn
Required: Yes
Type: string

The read set's ARN.

creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the read set was created.

creationType
Type: string

The creation type of the read set.

description
Type: string

The read set's description.

etag
Type: ETag structure

The entity tag (ETag) is a hash of the object representing its semantic content.

fileType
Required: Yes
Type: string

The read set's file type.

id
Required: Yes
Type: string

The read set's ID.

name
Type: string

The read set's name.

referenceArn
Type: string

The read set's genome reference ARN.

sampleId
Type: string

The read set's sample ID.

sequenceInformation
Type: SequenceInformation structure

Details about a sequence.

sequenceStoreId
Required: Yes
Type: string

The read set's sequence store ID.

status
Required: Yes
Type: string

The read set's status.

statusMessage
Type: string

The status for a read set. It provides more detail as to why the read set has a status.

subjectId
Type: string

The read set's subject ID.

ReadSetS3Access

Description

The S3 URI for each read set file.

Members
s3Uri
Type: string

The S3 URI for each read set file.

ReadSetUploadPartListFilter

Description

Filter settings that select for read set upload parts of interest.

Members
createdAfter
Type: timestamp (string|DateTime or anything parsable by strtotime)

Filters for read set uploads after a specified time.

createdBefore
Type: timestamp (string|DateTime or anything parsable by strtotime)

Filters for read set part uploads before a specified time.

ReadSetUploadPartListItem

Description

The metadata of a single part of a file that was added to a multipart upload. A list of these parts is returned in the response to the ListReadSetUploadParts API.

Members
checksum
Required: Yes
Type: string

A unique identifier used to confirm that parts are being added to the correct upload.

creationTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

The time stamp for when a direct upload was created.

lastUpdatedTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

The time stamp for the most recent update to an uploaded part.

partNumber
Required: Yes
Type: int

The number identifying the part in an upload.

partSize
Required: Yes
Type: long (int|float)

The size of the the part in an upload.

partSource
Required: Yes
Type: string

The origin of the part being direct uploaded.

ReferenceFiles

Description

A set of genome reference files.

Members
index
Type: FileInformation structure

The files' index.

source
Type: FileInformation structure

The source file's location in Amazon S3.

ReferenceFilter

Description

A filter for references.

Members
createdAfter
Type: timestamp (string|DateTime or anything parsable by strtotime)

The filter's start date.

createdBefore
Type: timestamp (string|DateTime or anything parsable by strtotime)

The filter's end date.

md5
Type: string

An MD5 checksum to filter on.

name
Type: string

A name to filter on.

ReferenceItem

Description

A genome reference.

Members
referenceArn
Type: string

The reference's ARN.

ReferenceListItem

Description

A genome reference.

Members
arn
Required: Yes
Type: string

The reference's ARN.

creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the reference was created.

description
Type: string

The reference's description.

id
Required: Yes
Type: string

The reference's ID.

md5
Required: Yes
Type: string

The reference's MD5 checksum.

name
Type: string

The reference's name.

referenceStoreId
Required: Yes
Type: string

The reference's store ID.

status
Type: string

The reference's status.

updateTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the reference was updated.

ReferenceStoreDetail

Description

Details about a reference store.

Members
arn
Required: Yes
Type: string

The store's ARN.

creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the store was created.

description
Type: string

The store's description.

id
Required: Yes
Type: string

The store's ID.

name
Type: string

The store's name.

sseConfig
Type: SseConfig structure

The store's server-side encryption (SSE) settings.

ReferenceStoreFilter

Description

A filter for reference stores.

Members
createdAfter
Type: timestamp (string|DateTime or anything parsable by strtotime)

The filter's start date.

createdBefore
Type: timestamp (string|DateTime or anything parsable by strtotime)

The filter's end date.

name
Type: string

The name to filter on.

RequestTimeoutException

Description

The request timed out.

Members
message
Required: Yes
Type: string

ResourceNotFoundException

Description

The target resource was not found in the current Region.

Members
message
Required: Yes
Type: string

RunGroupListItem

Description

A run group.

Members
arn
Type: string

The group's ARN.

creationTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the group was created.

id
Type: string

The group's ID.

maxCpus
Type: int

The group's maximum CPU count setting.

maxDuration
Type: int

The group's maximum duration setting in minutes.

maxGpus
Type: int

The maximum GPUs that can be used by a run group.

maxRuns
Type: int

The group's maximum concurrent run setting.

name
Type: string

The group's name.

RunListItem

Description

A workflow run.

Members
arn
Type: string

The run's ARN.

creationTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the run was created.

id
Type: string

The run's ID.

name
Type: string

The run's name.

priority
Type: int

The run's priority.

startTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the run started.

status
Type: string

The run's status.

stopTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the run stopped.

storageCapacity
Type: int

The run's storage capacity in gibibytes. For dynamic storage, after the run has completed, this value is the maximum amount of storage used during the run.

storageType
Type: string

The run's storage type.

workflowId
Type: string

The run's workflow ID.

RunLogLocation

Description

The URI for the run log.

Members
engineLogStream
Type: string

The log stream ARN for the engine log.

runLogStream
Type: string

The log stream ARN for the run log.

RunParameters

Members

SequenceInformation

Description

Details about a sequence.

Members
alignment
Type: string

The sequence's alignment setting.

generatedFrom
Type: string

Where the sequence originated.

totalBaseCount
Type: long (int|float)

The sequence's total base count.

totalReadCount
Type: long (int|float)

The sequence's total read count.

SequenceStoreDetail

Description

Details about a sequence store.

Members
arn
Required: Yes
Type: string

The store's ARN.

creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the store was created.

description
Type: string

The store's description.

eTagAlgorithmFamily
Type: string

The algorithm family of the ETag.

fallbackLocation
Type: string

An S3 location that is used to store files that have failed a direct upload.

id
Required: Yes
Type: string

The store's ID.

name
Type: string

The store's name.

sseConfig
Type: SseConfig structure

The store's server-side encryption (SSE) settings.

SequenceStoreFilter

Description

A filter for a sequence store.

Members
createdAfter
Type: timestamp (string|DateTime or anything parsable by strtotime)

The filter's start date.

createdBefore
Type: timestamp (string|DateTime or anything parsable by strtotime)

The filter's end date.

name
Type: string

A name to filter on.

SequenceStoreS3Access

Description

The S3 access metadata of the sequence store.

Members
s3AccessPointArn
Type: string

This is ARN of the access point associated with the S3 bucket storing read sets.

s3Uri
Type: string

The S3 URI of the sequence store.

ServiceQuotaExceededException

Description

The request exceeds a service quota.

Members
message
Required: Yes
Type: string

ShareDetails

Description

The details of a resource share.

Members
creationTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

The timestamp of when the resource share was created.

ownerId
Type: string

The account ID for the data owner. The owner creates the resource share.

principalSubscriber
Type: string

The principal subscriber is the account that is sharing the resource.

resourceArn
Type: string

The Arn of the shared resource.

resourceId
Type: string

The ID of the shared resource.

shareId
Type: string

The ID of the resource share.

shareName
Type: string

The name of the resource share.

status
Type: string

The status of the share.

statusMessage
Type: string

The status message for a resource share. It provides additional details about the share status.

updateTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

The timestamp of the resource share update.

SourceFiles

Description

Source files for a sequence.

Members
source1
Required: Yes
Type: string

The location of the first file in Amazon S3.

source2
Type: string

The location of the second file in Amazon S3.

SseConfig

Description

Server-side encryption (SSE) settings for a store.

Members
keyArn
Type: string

An encryption key ARN.

type
Required: Yes
Type: string

The encryption type.

StartReadSetActivationJobSourceItem

Description

A source for a read set activation job.

Members
readSetId
Required: Yes
Type: string

The source's read set ID.

StartReadSetImportJobSourceItem

Description

A source for a read set import job.

Members
description
Type: string

The source's description.

generatedFrom
Type: string

Where the source originated.

name
Type: string

The source's name.

referenceArn
Type: string

The source's reference ARN.

sampleId
Required: Yes
Type: string

The source's sample ID.

sourceFileType
Required: Yes
Type: string

The source's file type.

sourceFiles
Required: Yes
Type: SourceFiles structure

The source files' location in Amazon S3.

subjectId
Required: Yes
Type: string

The source's subject ID.

tags
Type: Associative array of custom strings keys (TagKey) to strings

The source's tags.

StartReferenceImportJobSourceItem

Description

A source for a reference import job.

Members
description
Type: string

The source's description.

name
Required: Yes
Type: string

The source's name.

sourceFile
Required: Yes
Type: string

The source file's location in Amazon S3.

tags
Type: Associative array of custom strings keys (TagKey) to strings

The source's tags.

StoreOptions

Description

Settings for a store.

Members
tsvStoreOptions
Type: TsvStoreOptions structure

File settings for a TSV store.

TaskListItem

Description

A workflow run task.

Members
cpus
Type: int

The task's CPU count.

creationTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the task was created.

gpus
Type: int

The number of Graphics Processing Units (GPU) specified for the task.

instanceType
Type: string

The instance type for a task.

memory
Type: int

The task's memory use in gigabyes.

name
Type: string

The task's name.

startTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the task started.

status
Type: string

The task's status.

stopTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the task stopped.

taskId
Type: string

The task's ID.

ThrottlingException

Description

The request was denied due to request throttling.

Members
message
Required: Yes
Type: string

TsvOptions

Description

Formatting options for a TSV file.

Members
readOptions
Type: ReadOptions structure

The file's read options.

TsvStoreOptions

Description

File settings for a TSV store.

Members
annotationType
Type: string

The store's annotation type.

formatToHeader
Type: Associative array of custom strings keys (FormatToHeaderKey) to strings

The store's header key to column name mapping.

schema
Type: Array of stringss

The store's schema.

TsvVersionOptions

Description

The options for a TSV file.

Members
annotationType
Type: string

The store version's annotation type.

formatToHeader
Type: Associative array of custom strings keys (FormatToHeaderKey) to strings

The annotation store version's header key to column name mapping.

schema
Type: Array of stringss

The TSV schema for an annotation store version.

ValidationException

Description

The input fails to satisfy the constraints specified by an AWS service.

Members
message
Required: Yes
Type: string

VariantImportItemDetail

Description

Details about an imported variant item.

Members
jobStatus
Required: Yes
Type: string

The item's job status.

source
Required: Yes
Type: string

The source file's location in Amazon S3.

statusMessage
Type: string

A message that provides additional context about a job

VariantImportItemSource

Description

A imported variant item's source.

Members
source
Required: Yes
Type: string

The source file's location in Amazon S3.

VariantImportJobItem

Description

A variant import job.

Members
annotationFields
Type: Associative array of custom strings keys (AnnotationFieldMapKeyString) to strings

The annotation schema generated by the parsed annotation data.

completionTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job completed.

creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job was created.

destinationName
Required: Yes
Type: string

The job's destination variant store.

id
Required: Yes
Type: string

The job's ID.

roleArn
Required: Yes
Type: string

The job's service role ARN.

runLeftNormalization
Type: boolean

The job's left normalization setting.

status
Required: Yes
Type: string

The job's status.

updateTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the job was updated.

VariantStoreItem

Description

A variant store.

Members
creationTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the store was created.

description
Required: Yes
Type: string

The store's description.

id
Required: Yes
Type: string

The store's ID.

name
Required: Yes
Type: string

The store's name.

reference
Required: Yes
Type: ReferenceItem structure

The store's genome reference.

sseConfig
Required: Yes
Type: SseConfig structure

The store's server-side encryption (SSE) settings.

status
Required: Yes
Type: string

The store's status.

statusMessage
Required: Yes
Type: string

The store's status message.

storeArn
Required: Yes
Type: string

The store's ARN.

storeSizeBytes
Required: Yes
Type: long (int|float)

The store's size in bytes.

updateTime
Required: Yes
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the store was updated.

VcfOptions

Description

Formatting options for a VCF file.

Members
ignoreFilterField
Type: boolean

The file's ignore filter field setting.

ignoreQualField
Type: boolean

The file's ignore qual field setting.

VersionDeleteError

Description

The error preventing deletion of the annotation store version.

Members
message
Required: Yes
Type: string

The message explaining the error in annotation store deletion.

versionName
Required: Yes
Type: string

The name given to an annotation store version.

VersionOptions

Description

The options for an annotation store version.

Members
tsvVersionOptions
Type: TsvVersionOptions structure

File settings for a version of a TSV store.

WorkflowListItem

Description

A workflow.

Members
arn
Type: string

The workflow's ARN.

creationTime
Type: timestamp (string|DateTime or anything parsable by strtotime)

When the workflow was created.

digest
Type: string

The workflow's digest.

id
Type: string

The workflow's ID.

metadata
Type: Associative array of custom strings keys (WorkflowMetadataKey) to strings

Any metadata available for workflow. The information listed may vary depending on the workflow, and there may also be no metadata to return.

name
Type: string

The workflow's name.

status
Type: string

The workflow's status.

type
Type: string

The workflow's type.

WorkflowParameter

Description

A workflow parameter.

Members
description
Type: string

The parameter's description.

optional
Type: boolean

Whether the parameter is optional.