read_service
************** /readgroupsets *****************/
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SearchReads(request)
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Gets a list of ReadAlignment s for one or more ReadGroup s.
searchReads operates over a genomic coordinate space of reference sequence
and position defined by the Reference s to which the requested ReadGroup s 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 IDs yields all reads in those read groups, 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 must be consistent
for a given repository, 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.
POST /reads/search must accept a JSON version of SearchReadsRequest as
the post body and will return a JSON version of SearchReadsResponse.
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SearchReadGroupSets(request)
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Gets a list of ReadGroupSet matching the search criteria.
POST /readgroupsets/search must accept a JSON version of
SearchReadGroupSetsRequest as the post body and will return a JSON
version of SearchReadGroupSetsResponse . Only readgroups that
match an optionally supplied biosampleId will be included in the
response.
Gets a ReadGroupSet by ID.
GET /readgroupsets/{read_group_set_id} will return a JSON version of
ReadGroupSet.
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message
SearchReadGroupSetsRequest
| Fields: |
- dataset_id (string) – The dataset to search.
- name (string) – Only return read group sets with this name (case-sensitive, exact match).
- biosample_id (string) – Specifying the id of a Biosample record will return only readgroups
with the given biosampleId.
- page_size (integer) – Specifies the maximum number of results to return in a single page.
If unspecified, a system default will be used.
- page_token (string) – The continuation token, which is used to page through large result sets.
To get the next page of results, set this parameter to the value of
next_page_token from the previous response.
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|---|
This request maps to the body of POST /readgroupsets/search as JSON.
TODO: Factor this out to a common API patterns section.
- If searching by a resource ID, and that resource is not found, the method
will return a 404 HTTP status code (NOT_FOUND).
- If searching by other attributes, e.g. name, and no matches are found, the
method will return a 200 HTTP status code (OK) with an empty result list.
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message
SearchReadGroupSetsResponse
| Fields: |
- read_group_sets (list of
ReadGroupSet) – The list of matching read group sets.
- next_page_token (string) – The continuation token, which is used to page through large result sets.
Provide this value in a subsequent request to return the next page of
results. This field will be empty if there aren’t any additional results.
|
|---|
This is the response from POST /readgroupsets/search expressed as JSON.
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message
GetReadGroupSetRequest
| Fields: |
- read_group_set_id (string) – The ID of the ReadGroupSet to be retrieved.
|
|---|
This request maps to the URL GET /readgroupsets/{read_group_set_id}.
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message
SearchReadsRequest
| Fields: |
- read_group_ids (string) – The ReadGroups to search. At least one id must be specified.
- reference_id (string) – The reference to query. Leaving blank returns results from all
references, including unmapped reads - this could be very large.
- start (long) – The start position (0-based) of this query.
If a reference is specified, this defaults to 0.
Genomic positions are non-negative integers less than reference length.
Requests spanning the join of circular genomes are represented as
two requests one on each side of the join (position 0).
- end (long) – The end position (0-based, exclusive) of this query.
If a reference is specified, this defaults to the
reference’s length.
- page_size (integer) – Specifies the maximum number of results to return in a single page.
If unspecified, a system default will be used.
- page_token (string) – The continuation token, which is used to page through large result sets.
To get the next page of results, set this parameter to the value of
next_page_token from the previous response.
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************** /reads *****************
This request maps to the body of POST /reads/search as JSON.
If a reference is specified, all queried ReadGroup`s must be aligned
to `ReferenceSet`s containing that same `Reference. If no reference is
specified, all ReadGroup`s must be aligned to the same `ReferenceSet.
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message
SearchReadsResponse
| Fields: |
- alignments (list of
ReadAlignment) – The list of matching alignment messages, sorted by position.
Unmapped reads, which have no position, are returned last.
- next_page_token (string) – The continuation token, which is used to page through large result sets.
Provide this value in a subsequent request to return the next page of
results. This field will be empty if there aren’t any additional results.
|
|---|
This is the response from POST /reads/search expressed as JSON.