alu/tra-analysis
1
0
Fork 0
mirror of https://github.com/titanscouting/tra-analysis.git synced 2025-09-09 00:07:20 +00:00
Code Issues Packages Projects Releases Wiki Activity

push all website files

Browse Source
This commit is contained in:
Jacob Levine
2019-01-06 13:14:45 -06:00
parent d7301e26c3
commit d2d5d4c04e
15662 changed files with 2166516 additions and 0 deletions
Download Patch File Download Diff File Expand all files Collapse all files

468
website/functions/node_modules/google-proto-files/google/genomics/v1/reads.proto generated vendored Normal file
View File

@@ -0,0 +1,468 @@
// Copyright 2016 Google Inc.
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
syntax = "proto3";
package google.genomics.v1;
import "google/api/annotations.proto";
import "google/genomics/v1/range.proto";
import "google/genomics/v1/readalignment.proto";
import "google/genomics/v1/readgroupset.proto";
import "google/longrunning/operations.proto";
import "google/protobuf/empty.proto";
import "google/protobuf/field_mask.proto";
option cc_enable_arenas = true;
option go_package = "google.golang.org/genproto/googleapis/genomics/v1;genomics";
option java_multiple_files = true;
option java_outer_classname = "ReadsProto";
option java_package = "com.google.genomics.v1";
service StreamingReadService {
// Returns a stream of all the reads matching the search request, ordered
// by reference name, position, and ID.
rpc StreamReads(StreamReadsRequest) returns (stream StreamReadsResponse) {
option (google.api.http) = { post: "/v1/reads:stream" body: "*" };
}
}
// The Readstore. A data store for DNA sequencing Reads.
service ReadServiceV1 {
// Creates read group sets by asynchronously importing the provided
// information.
//
// For the definitions of read group sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// The caller must have WRITE permissions to the dataset.
//
// ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import
//
// - Tags will be converted to strings - tag types are not preserved
// - Comments (`@CO`) in the input file header will not be preserved
// - Original header order of references (`@SQ`) will not be preserved
// - Any reverse stranded unmapped reads will be reverse complemented, and
// their qualities (also the "BQ" and "OQ" tags, if any) will be reversed
// - Unmapped reads will be stripped of positional information (reference name
// and position)
rpc ImportReadGroupSets(ImportReadGroupSetsRequest) returns (google.longrunning.Operation) {
option (google.api.http) = { post: "/v1/readgroupsets:import" body: "*" };
}
// Exports a read group set to a BAM file in Google Cloud Storage.
//
// For the definitions of read group sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Note that currently there may be some differences between exported BAM
// files and the original BAM file at the time of import. See
// [ImportReadGroupSets][google.genomics.v1.ReadServiceV1.ImportReadGroupSets]
// for caveats.
rpc ExportReadGroupSet(ExportReadGroupSetRequest) returns (google.longrunning.Operation) {
option (google.api.http) = { post: "/v1/readgroupsets/{read_group_set_id}:export" body: "*" };
}
// Searches for read group sets matching the criteria.
//
// For the definitions of read group sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Implements
// [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135).
rpc SearchReadGroupSets(SearchReadGroupSetsRequest) returns (SearchReadGroupSetsResponse) {
option (google.api.http) = { post: "/v1/readgroupsets/search" body: "*" };
}
// Updates a read group set.
//
// For the definitions of read group sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// This method supports patch semantics.
rpc UpdateReadGroupSet(UpdateReadGroupSetRequest) returns (ReadGroupSet) {
option (google.api.http) = { patch: "/v1/readgroupsets/{read_group_set_id}" body: "read_group_set" };
}
// Deletes a read group set.
//
// For the definitions of read group sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
rpc DeleteReadGroupSet(DeleteReadGroupSetRequest) returns (google.protobuf.Empty) {
option (google.api.http) = { delete: "/v1/readgroupsets/{read_group_set_id}" };
}
// Gets a read group set by ID.
//
// For the definitions of read group sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
rpc GetReadGroupSet(GetReadGroupSetRequest) returns (ReadGroupSet) {
option (google.api.http) = { get: "/v1/readgroupsets/{read_group_set_id}" };
}
// Lists fixed width coverage buckets for a read group set, each of which
// correspond to a range of a reference sequence. Each bucket summarizes
// coverage information across its corresponding genomic range.
//
// For the definitions of read group sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Coverage is defined as the number of reads which are aligned to a given
// base in the reference sequence. Coverage buckets are available at several
// precomputed bucket widths, enabling retrieval of various coverage 'zoom
// levels'. The caller must have READ permissions for the target read group
// set.
rpc ListCoverageBuckets(ListCoverageBucketsRequest) returns (ListCoverageBucketsResponse) {
option (google.api.http) = { get: "/v1/readgroupsets/{read_group_set_id}/coveragebuckets" };
}
// Gets a list of reads for one or more read group sets.
//
// For the definitions of read group sets and other genomics resources, see
// [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// Reads search operates over a genomic coordinate space of reference sequence
// & position defined over the reference sequences to which the requested
// read group sets are aligned.
//
// If a target positional range is specified, search returns all reads whose
// alignment to the reference genome overlap the range. A query which
// specifies only read group set IDs yields all reads in those read group
// sets, including unmapped reads.
//
// All reads returned (including reads on subsequent pages) are ordered by
// genomic coordinate (by reference sequence, then position). Reads with
// equivalent genomic coordinates are returned in an unspecified order. This
// order is consistent, such that two queries for the same content (regardless
// of page size) yield reads in the same order across their respective streams
// of paginated responses.
//
// Implements
// [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L85).
rpc SearchReads(SearchReadsRequest) returns (SearchReadsResponse) {
option (google.api.http) = { post: "/v1/reads/search" body: "*" };
}
}
// The read group set search request.
message SearchReadGroupSetsRequest {
// Restricts this query to read group sets within the given datasets. At least
// one ID must be provided.
repeated string dataset_ids = 1;
// Only return read group sets for which a substring of the name matches this
// string.
string name = 3;
// The continuation token, which is used to page through large result sets.
// To get the next page of results, set this parameter to the value of
// `nextPageToken` from the previous response.
string page_token = 2;
// The maximum number of results to return in a single page. If unspecified,
// defaults to 256. The maximum value is 1024.
int32 page_size = 4;
}
// The read group set search response.
message SearchReadGroupSetsResponse {
// The list of matching read group sets.
repeated ReadGroupSet read_group_sets = 1;
// The continuation token, which is used to page through large result sets.
// Provide this value in a subsequent request to return the next page of
// results. This field will be empty if there aren't any additional results.
string next_page_token = 2;
}
// The read group set import request.
message ImportReadGroupSetsRequest {
enum PartitionStrategy {
PARTITION_STRATEGY_UNSPECIFIED = 0;
// In most cases, this strategy yields one read group set per file. This is
// the default behavior.
//
// Allocate one read group set per file per sample. For BAM files, read
// groups are considered to share a sample if they have identical sample
// names. Furthermore, all reads for each file which do not belong to a read
// group, if any, will be grouped into a single read group set per-file.
PER_FILE_PER_SAMPLE = 1;
// Includes all read groups in all imported files into a single read group
// set. Requires that the headers for all imported files are equivalent. All
// reads which do not belong to a read group, if any, will be grouped into a
// separate read group set.
MERGE_ALL = 2;
}
// Required. The ID of the dataset these read group sets will belong to. The
// caller must have WRITE permissions to this dataset.
string dataset_id = 1;
// The reference set to which the imported read group sets are aligned to, if
// any. The reference names of this reference set must be a superset of those
// found in the imported file headers. If no reference set id is provided, a
// best effort is made to associate with a matching reference set.
string reference_set_id = 4;
// A list of URIs pointing at [BAM
// files](https://samtools.github.io/hts-specs/SAMv1.pdf)
// in Google Cloud Storage.
// Those URIs can include wildcards (*), but do not add or remove
// matching files before import has completed.
//
// Note that Google Cloud Storage object listing is only eventually
// consistent: files added may be not be immediately visible to
// everyone. Thus, if using a wildcard it is preferable not to start
// the import immediately after the files are created.
repeated string source_uris = 2;
// The partition strategy describes how read groups are partitioned into read
// group sets.
PartitionStrategy partition_strategy = 5;
}
// The read group set import response.
message ImportReadGroupSetsResponse {
// IDs of the read group sets that were created.
repeated string read_group_set_ids = 1;
}
// The read group set export request.
message ExportReadGroupSetRequest {
// Required. The Google Cloud project ID that owns this
// export. The caller must have WRITE access to this project.
string project_id = 1;
// Required. A Google Cloud Storage URI for the exported BAM file.
// The currently authenticated user must have write access to the new file.
// An error will be returned if the URI already contains data.
string export_uri = 2;
// Required. The ID of the read group set to export. The caller must have
// READ access to this read group set.
string read_group_set_id = 3;
// The reference names to export. If this is not specified, all reference
// sequences, including unmapped reads, are exported.
// Use `*` to export only unmapped reads.
repeated string reference_names = 4;
}
message UpdateReadGroupSetRequest {
// The ID of the read group set to be updated. The caller must have WRITE
// permissions to the dataset associated with this read group set.
string read_group_set_id = 1;
// The new read group set data. See `updateMask` for details on mutability of
// fields.
ReadGroupSet read_group_set = 2;
// An optional mask specifying which fields to update. Supported fields:
//
// * [name][google.genomics.v1.ReadGroupSet.name].
// * [referenceSetId][google.genomics.v1.ReadGroupSet.reference_set_id].
//
// Leaving `updateMask` unset is equivalent to specifying all mutable
// fields.
google.protobuf.FieldMask update_mask = 3;
}
message DeleteReadGroupSetRequest {
// The ID of the read group set to be deleted. The caller must have WRITE
// permissions to the dataset associated with this read group set.
string read_group_set_id = 1;
}
message GetReadGroupSetRequest {
// The ID of the read group set.
string read_group_set_id = 1;
}
message ListCoverageBucketsRequest {
// Required. The ID of the read group set over which coverage is requested.
string read_group_set_id = 1;
// The name of the reference to query, within the reference set associated
// with this query. Optional.
string reference_name = 3;
// The start position of the range on the reference, 0-based inclusive. If
// specified, `referenceName` must also be specified. Defaults to 0.
int64 start = 4;
// The end position of the range on the reference, 0-based exclusive. If
// specified, `referenceName` must also be specified. If unset or 0, defaults
// to the length of the reference.
int64 end = 5;
// The desired width of each reported coverage bucket in base pairs. This
// will be rounded down to the nearest precomputed bucket width; the value
// of which is returned as `bucketWidth` in the response. Defaults
// to infinity (each bucket spans an entire reference sequence) or the length
// of the target range, if specified. The smallest precomputed
// `bucketWidth` is currently 2048 base pairs; this is subject to
// change.
int64 target_bucket_width = 6;
// The continuation token, which is used to page through large result sets.
// To get the next page of results, set this parameter to the value of
// `nextPageToken` from the previous response.
string page_token = 7;
// The maximum number of results to return in a single page. If unspecified,
// defaults to 1024. The maximum value is 2048.
int32 page_size = 8;
}
// A bucket over which read coverage has been precomputed. A bucket corresponds
// to a specific range of the reference sequence.
message CoverageBucket {
// The genomic coordinate range spanned by this bucket.
Range range = 1;
// The average number of reads which are aligned to each individual
// reference base in this bucket.
float mean_coverage = 2;
}
message ListCoverageBucketsResponse {
// The length of each coverage bucket in base pairs. Note that buckets at the
// end of a reference sequence may be shorter. This value is omitted if the
// bucket width is infinity (the default behaviour, with no range or
// `targetBucketWidth`).
int64 bucket_width = 1;
// The coverage buckets. The list of buckets is sparse; a bucket with 0
// overlapping reads is not returned. A bucket never crosses more than one
// reference sequence. Each bucket has width `bucketWidth`, unless
// its end is the end of the reference sequence.
repeated CoverageBucket coverage_buckets = 2;
// The continuation token, which is used to page through large result sets.
// Provide this value in a subsequent request to return the next page of
// results. This field will be empty if there aren't any additional results.
string next_page_token = 3;
}
// The read search request.
message SearchReadsRequest {
// The IDs of the read groups sets within which to search for reads. All
// specified read group sets must be aligned against a common set of reference
// sequences; this defines the genomic coordinates for the query. Must specify
// one of `readGroupSetIds` or `readGroupIds`.
repeated string read_group_set_ids = 1;
// The IDs of the read groups within which to search for reads. All specified
// read groups must belong to the same read group sets. Must specify one of
// `readGroupSetIds` or `readGroupIds`.
repeated string read_group_ids = 5;
// The reference sequence name, for example `chr1`, `1`, or `chrX`. If set to
// `*`, only unmapped reads are returned. If unspecified, all reads (mapped
// and unmapped) are returned.
string reference_name = 7;
// The start position of the range on the reference, 0-based inclusive. If
// specified, `referenceName` must also be specified.
int64 start = 8;
// The end position of the range on the reference, 0-based exclusive. If
// specified, `referenceName` must also be specified.
int64 end = 9;
// The continuation token, which is used to page through large result sets.
// To get the next page of results, set this parameter to the value of
// `nextPageToken` from the previous response.
string page_token = 3;
// The maximum number of results to return in a single page. If unspecified,
// defaults to 256. The maximum value is 2048.
int32 page_size = 4;
}
// The read search response.
message SearchReadsResponse {
// The list of matching alignments sorted by mapped genomic coordinate,
// if any, ascending in position within the same reference. Unmapped reads,
// which have no position, are returned contiguously and are sorted in
// ascending lexicographic order by fragment name.
repeated Read alignments = 1;
// The continuation token, which is used to page through large result sets.
// Provide this value in a subsequent request to return the next page of
// results. This field will be empty if there aren't any additional results.
string next_page_token = 2;
}
// The stream reads request.
message StreamReadsRequest {
// The Google Cloud project ID which will be billed
// for this access. The caller must have WRITE access to this project.
// Required.
string project_id = 1;
// The ID of the read group set from which to stream reads.
string read_group_set_id = 2;
// The reference sequence name, for example `chr1`,
// `1`, or `chrX`. If set to *, only unmapped reads are
// returned.
string reference_name = 3;
// The start position of the range on the reference, 0-based inclusive. If
// specified, `referenceName` must also be specified.
int64 start = 4;
// The end position of the range on the reference, 0-based exclusive. If
// specified, `referenceName` must also be specified.
int64 end = 5;
// Restricts results to a shard containing approximately `1/totalShards`
// of the normal response payload for this query. Results from a sharded
// request are disjoint from those returned by all queries which differ only
// in their shard parameter. A shard may yield 0 results; this is especially
// likely for large values of `totalShards`.
//
// Valid values are `[0, totalShards)`.
int32 shard = 6;
// Specifying `totalShards` causes a disjoint subset of the normal response
// payload to be returned for each query with a unique `shard` parameter
// specified. A best effort is made to yield equally sized shards. Sharding
// can be used to distribute processing amongst workers, where each worker is
// assigned a unique `shard` number and all workers specify the same
// `totalShards` number. The union of reads returned for all sharded queries
// `[0, totalShards)` is equal to those returned by a single unsharded query.
//
// Queries for different values of `totalShards` with common divisors will
// share shard boundaries. For example, streaming `shard` 2 of 5
// `totalShards` yields the same results as streaming `shard`s 4 and 5 of 10
// `totalShards`. This property can be leveraged for adaptive retries.
int32 total_shards = 7;
}
message StreamReadsResponse {
repeated Read alignments = 1;
}