google_api_genomics v0.0.1 API Reference

Modules

API calls for all endpoints tagged Annotations

API calls for all endpoints tagged Annotationsets

API calls for all endpoints tagged Callsets

API calls for all endpoints tagged Datasets

API calls for all endpoints tagged Operations

API calls for all endpoints tagged Readgroupsets

API calls for all endpoints tagged Reads

API calls for all endpoints tagged References

API calls for all endpoints tagged Referencesets

API calls for all endpoints tagged Variants

API calls for all endpoints tagged Variantsets

Handle Tesla connections for GoogleApi.Genomics.V1

Helper functions for deserializing responses into models

An annotation describes a region of reference genome. The value of an annotation may be one of several canonical types, supplemented by arbitrary info tags. An annotation is not inherently associated with a specific sample or individual (though a client could choose to use annotations in this way). Example canonical annotation types are `GENE` and `VARIANT`

An annotation set is a logical grouping of annotations that share consistent type information and provenance. Examples of annotation sets include 'all genes from refseq', and 'all variant annotations from ClinVar'

Associates `members` with a `role`

A call set is a collection of variant calls, typically for one sample. It belongs to a variant set. For more genomics resource definitions, see Fundamentals of Google Genomics

The request message for Operations.CancelOperation

A single CIGAR operation

Describes a Compute Engine resource that is being managed by a running pipeline

A bucket over which read coverage has been precomputed. A bucket corresponds to a specific range of the reference sequence

A Dataset is a collection of genomic data. For more genomics resource definitions, see Fundamentals of Google Genomics

A generic empty message that you can re-use to avoid defining duplicated empty messages in your APIs. A typical example is to use it as the request or the response type of an API method. For instance: service Foo { rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty); } The JSON representation for `Empty` is empty JSON object `{}`

The read group set export request

The variant data export request

Request message for `GetIamPolicy` method

The read group set import request

The read group set import response

The variant data import request

The variant data import response

A linear alignment can be represented by one CIGAR string. Describes the mapped position and local alignment of the read to the reference

The response message for Operations.ListOperations

This resource represents a long-running operation that is the result of a network API call

An event that occurred during an Operation

Metadata describing an Operation

Defines an Identity and Access Management (IAM) policy. It is used to specify access control policies for Cloud Platform resources. A `Policy` consists of a list of `bindings`. A `Binding` binds a list of `members` to a `role`, where the members can be user accounts, Google groups, Google domains, and service accounts. A `role` is a named list of permissions defined by IAM. Example { "bindings": [ { "role": "roles/owner", "members": [ "user:mike@example.com", "group:admins@example.com", "domain:google.com", "serviceAccount:my-other-app@appspot.gserviceaccount.com", ] }, { "role": "roles/viewer", "members": ["user:sean@example.com"] } ] } For a description of IAM and its features, see the IAM developer's guide

An abstraction for referring to a genomic position, in relation to some already known reference. For now, represents a genomic position as a reference name, a base number on that reference (0-based), and a determination of forward or reverse strand

A 0-based half-open genomic coordinate range for search requests

A read alignment describes a linear alignment of a string of DNA to a reference sequence, in addition to metadata about the fragment (the molecule of DNA sequenced) and the read (the bases which were read by the sequencer). A read is equivalent to a line in a SAM file. A read belongs to exactly one read group and exactly one read group set. For more genomics resource definitions, see Fundamentals of Google Genomics ### Reverse-stranded reads Mapped reads (reads having a non-null `alignment`) can be aligned to either the forward or the reverse strand of their associated reference. Strandedness of a mapped read is encoded by `alignment.position.reverseStrand`. If we consider the reference to be a forward-stranded coordinate space of `[0, reference.length)` with `0` as the left-most position and `reference.length` as the right-most position, reads are always aligned left to right. That is, `alignment.position.position` always refers to the left-most reference coordinate and `alignment.cigar` describes the alignment of this read to the reference from left to right. All per-base fields such as `alignedSequence` and `alignedQuality` share this same left-to-right orientation; this is true of reads which are aligned to either strand. For reverse-stranded reads, this means that `alignedSequence` is the reverse complement of the bases that were originally reported by the sequencing machine. ### Generating a reference-aligned sequence string When interacting with mapped reads, it's often useful to produce a string representing the local alignment of the read to reference. The following pseudocode demonstrates one way of doing this: out = "" offset = 0 for c in read.alignment.cigar { switch c.operation { case "ALIGNMENT_MATCH", "SEQUENCE_MATCH", "SEQUENCE_MISMATCH": out += read.alignedSequence[offset:offset+c.operationLength] offset += c.operationLength break case "CLIP_SOFT", "INSERT": offset += c.operationLength break case "PAD": out += repeat("*", c.operationLength) break case "DELETE": out += repeat("-", c.operationLength) break case "SKIP": out += repeat(" ", c.operationLength) break case "CLIP_HARD": break } } return out ### Converting to SAM's CIGAR string The following pseudocode generates a SAM CIGAR string from the `cigar` field. Note that this is a lossy conversion (`cigar.referenceSequence` is lost). cigarMap = { "ALIGNMENT_MATCH": "M", "INSERT": "I", "DELETE": "D", "SKIP": "N", "CLIP_SOFT": "S", "CLIP_HARD": "H", "PAD": "P", "SEQUENCE_MATCH": "=", "SEQUENCE_MISMATCH": "X", } cigarStr = "" for c in read.alignment.cigar { cigarStr += c.operationLength + cigarMap[c.operation] } return cigarStr

A read group is all the data that's processed the same way by the sequencer

A read group set is a logical collection of read groups, which are collections of reads produced by a sequencer. A read group set typically models reads corresponding to one sample, sequenced one way, and aligned one way. A read group set belongs to one dataset. A read group belongs to one read group set. * A read belongs to one read group. For more genomics resource definitions, see Fundamentals of Google Genomics

A reference is a canonical assembled DNA sequence, intended to act as a reference coordinate space for other genomic annotations. A single reference might represent the human chromosome 1 or mitochandrial DNA, for instance. A reference belongs to one or more reference sets. For more genomics resource definitions, see Fundamentals of Google Genomics

ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference

A reference set is a set of references which typically comprise a reference assembly for a species, such as `GRCh38` which is representative of the human genome. A reference set defines a common coordinate space for comparing reference-aligned experimental data. A reference set contains 1 or more references. For more genomics resource definitions, see Fundamentals of Google Genomics

Runtime metadata that will be populated in the runtimeMetadata field of the Operation associated with a RunPipeline execution

The read group set search request

The read group set search response

Request message for `SetIamPolicy` method

The `Status` type defines a logical error model that is suitable for different programming environments, including REST APIs and RPC APIs. It is used by gRPC. The error model is designed to be: - Simple to use and understand for most users - Flexible enough to meet unexpected needs # Overview The `Status` message contains three pieces of data: error code, error message, and error details. The error code should be an enum value of google.rpc.Code, but it may accept additional error codes if needed. The error message should be a developer-facing English message that helps developers understand and resolve the error. If a localized user-facing error message is needed, put the localized message in the error details or localize it in the client. The optional error details may contain arbitrary information about the error. There is a predefined set of error detail types in the package `google.rpc` that can be used for common error conditions. # Language mapping The `Status` message is the logical representation of the error model, but it is not necessarily the actual wire format. When the `Status` message is exposed in different client libraries and different wire protocols, it can be mapped differently. For example, it will likely be mapped to some exceptions in Java, but more likely mapped to some error codes in C. # Other uses The error model and the `Status` message can be used in a variety of environments, either with or without APIs, to provide a consistent developer experience across different environments. Example uses of this error model include: - Partial errors. If a service needs to return partial errors to the client, it may embed the `Status` in the normal response to indicate the partial errors. - Workflow errors. A typical workflow has multiple steps. Each step may have a `Status` message for error reporting. - Batch operations. If a client uses batch request and batch response, the `Status` message should be used directly inside batch response, one for each error sub-response. - Asynchronous operations. If an API call embeds asynchronous operation results in its response, the status of those operations should be represented directly using the `Status` message. - Logging. If some API errors are stored in logs, the message `Status` could be used directly after any stripping needed for security/privacy reasons

Request message for `TestIamPermissions` method

Response message for `TestIamPermissions` method

A transcript represents the assertion that a particular region of the reference genome may be transcribed as RNA

A variant represents a change in DNA sequence relative to a reference sequence. For example, a variant could represent a SNP or an insertion. Variants belong to a variant set. For more genomics resource definitions, see Fundamentals of Google Genomics Each of the calls on a variant represent a determination of genotype with respect to that variant. For example, a call might assign probability of 0.32 to the occurrence of a SNP named rs1234 in a sample named NA12345. A call belongs to a call set, which contains related calls typically from one sample

A call represents the determination of genotype with respect to a particular variant. It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named rs1234 in a call set with the name NA12345

A variant set is a collection of call sets and variants. It contains summary statistics of those contents. A variant set belongs to a dataset. For more genomics resource definitions, see Fundamentals of Google Genomics

Metadata describes a single piece of variant call metadata. These data include a top level key and either a single value string (value) or a list of key-value pairs (info.) Value and info are mutually exclusive

Helper functions for building Tesla requests