ga4gh-server

Reference implementation of the APIs defined in ga4gh-schemas. RETIRED 2018-01-24

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0.3.6

0.3.6

This an alpha pre-release that contains some major updates. The most important changes are highlighted in bold below. We have also made some updates to the documentation.

Features:

  • Rename package from “ga4gh” to “ga4gh-server” #1582, #1583
  • Added support for BigWig files in a new Continuous Data object #1573 New endpoints and message types include:
  • POST /continuoussets/search
  • GET /continuoussets/{id}
  • POST /continuous/search
  • Continuous (new)
  • ContinuousSet (new)
  • Add ability to list and join peer server networks #1507 New endpoints and message types include:
  • POST /peers/list
  • POST /peers/announce
  • GET /info
  • ListPeersResponse (new)
  • Peer (new)
  • AnnouncePeerResponse (new)
  • GetInfoResponse (new)
  • Remove feature_id from ExpressionLevel and add ability to search by the Name field #1580 Impacts
  • POST /expressionlevels/search
  • GET /expressionlevels/{id}
  • Replaced info fields with rich type Attributes fields #1521 Impacts the following message types:
  • TranscriptEffect
  • VariantAnnotation
  • Individual
  • Biosample
  • Experiment (new)
  • Analysis (new)
  • Dataset
  • ReadGroup
  • ReadGroupSet
  • ReadAlignment
  • Reference
  • ReferenceSet
  • RnaQuantificationSet
  • RnaQuantification
  • ExpressionLevel
  • Feature
  • VariantSetMetadata
  • CallSet
  • Call
  • Variant
  • Replace NCBI taxon ID integer with ontology term #1551 Impacts the following message types:
  • Reference
  • ReferenceSet
  • Changed ontology term “id” to “term_id” #1513 Impacts the following message types:
  • OntologyTerm

Documentation:

  • Document auto-releases, constraint instructions #1578
  • Improved development document for virtualenv command #1550

Infrastructure:

  • Automatically deploy tagged releases to Pypi from Travis #1576

  • Refactor transcript annotation #1334

  • Speedups to rna quantification ingest #1564