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GA4GH API v0.6.0a1

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@macieksmuga macieksmuga released this 15 Dec 23:59
v0.6.0a1
cf2bc1b

Changes to ga4gh/schemas master branch since version v0.5.1 (Oct 2, 2014)

Pervasive changes

Renamed all protocols and records to remove the "GA" prefix from
their names. (Hence GASearchVariantSetsRequest is now
SearchVariantSetsRequest, etc.)
The exception is GAException, which is unchanged.

There is no longer one unitary namespace. Objects now reside in
"org.ga4gh.models", methods in "org.ga4gh.methods".

Updated the version number to 0.6.0a1.

Changes visible to API clients

Additions

Dataset is now utilized throughout the API.

New methods, HTTP endpoints:

  • getDataset via GET datasets/<id>
  • searchDatasets via POST /datasets/search
  • getReadGroupSet via GET /readgroupsets/<id>
  • getReadGroup via GET /readgroups/<id>
  • getVariant via GET /variants/<id>
  • getVariantSet via GET /variantsets/<id>
  • getCallSet via GET /callsets/<id>

New and modified entities:

  • New record type ExternalIdentifier introduced.
  • New record type ReadStats now optionally part of a returned ReadGroup or ReadGroupSet object.
  • Position record type now specifies strand via new enum Strand (in place of boolean reverseStrand).

Field default values:

  • SearchReadsRequest.start as passed into /reads/search is optional and no longer defaults to 0.
  • Boolean fields in ReadAlignment as returned from /reads/search now default to null instead of false.

Field types:

  • SearchVariantSetsRequest as passed into /variantsets/search now takes a single dataset ID, not an array.

  • SearchCallSetsRequest as passed into /callsets/search now takes a single variant set ID, not an array.

  • SearchReferenceSetsRequest as passed into /referencesets/search changed two parameters from arrays to
    singletons:

    • md5checksum
    • accession

New fields:

  • SearchReferencesRequest passed into /references/search now accepts a referenceSetId parameter.
  • SearchVariantsRequest passed into /variants/search now takes a variantSetId parameter.
  • SearchReadsRequest passed into /reads/search now includes readGroupIds.
  • SearchReadGroupSetsRequest passed into /readgroupsets/search takes a datasetId.
  • ReferenceSet returned from /references/search now includes a name.
  • VariantSet returned from /variants/search adds name and reference set ID fields.
  • ReadGroup returned from /readgroups/<id> adds stats.

Changes internal to Schemas, documentation and organization

Removed

  • src/main/resources/avro/beacon.avdl
  • Files designated "Work In Progress" ("wip"):
    • src/main/resources/avro/wip/metadata.avdl
    • src/main/resources/avro/wip/metadatamethods.avdl
    • src/main/resources/avro/wip/variationReference.avdl

Changed

Moved GAException to methods.avdl.

Documentation

Using Doxygen to generate HTML documentation from schema (*.avdl) files.

Clarifications:

  • How the SearchReadGroupSetsRequest.name field is interpreted.
  • The meaning of SearchCallSetsRequest.name.
  • Reference, ReferenceSet docs.

Updated CONTRIBUTING.md to describe the latest contribution rules.

Moved GeneratingDocumentation.md to doc/.

README.md now includes information about the Metadata Task Team.

Tests

Added tests to ensure Maven processes the schemas into a jar file
successfully, and that we can compile the schemas into Python.

Assets 2
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