GA4GH API v0.6.0a1
Pre-releaseChanges 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 GETdatasets/<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 returnedReadGroup
orReadGroupSet
object. Position
record type now specifies strand via new enumStrand
(in place ofboolean 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 tonull
instead offalse
.
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 areferenceSetId
parameter.SearchVariantsRequest
passed into/variants/search
now takes avariantSetId
parameter.SearchReadsRequest
passed into/reads/search
now includesreadGroupIds
.SearchReadGroupSetsRequest
passed into/readgroupsets/search
takes adatasetId
.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>
addsstats
.
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.