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Issues356 (356)

356 results

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356 results

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ga4gh/ga4gh-schemas

Add serialization helper functions to schemas

To make it easier to integrate the GA4GH data model, we should include the serialization helpers for the protobuf in our python module. This includes functions like .toJson, or .toDictionary.

enhancement

python

• david4096
·
• 2
·
• Opened 
  on Dec 7, 2016
·
• #750

ga4gh/ga4gh-schemas

Repo Manager GUI

By exposing the repo manager functionality over the web, we can develop user interfaces that make administering data sources much easier. The primary desire is to be able to add, remove, and alter hosted ...

• david4096
·
• 2
·
• Opened 
  on Dec 6, 2016
·
• #749

ga4gh/ga4gh-schemas

Architecture diagram in datarepo docs

- [ ] Add an Architecture diagram showing the registry DB, the server, the data container objects (like HtslibVariantSet, etc), etc, to the documentation for the data repository. - [ ] Explain ...

• david4096
·
• 1
·
• Opened 
  on Nov 30, 2016
·
• #748

ga4gh/ga4gh-schemas

Update serialization example to discuss stringified numbers

When serializing long protocol buffers wraps numbers in strings so they can be properly handled by JavaScript, which cannot always handle arbitrary precision arithmetic. This issue will close with some ...

Documentation

• david4096
·
• Opened 
  on Nov 30, 2016
·
• #747

ga4gh/ga4gh-schemas

Unify python install paths

There are currently two python install paths, one for generating documentation and the other for creating the protobuf bindings. The dependencies are in python/requirements.txt and ./requirements.txt respectively. ...

• david4096
·
• Opened 
  on Nov 28, 2016
·
• #745

ga4gh/ga4gh-schemas

Move setup.py to root directory

This will allow pip install to be done more naturally. The goal is to provide easy installation methods across a variety of languages. Eventually, the root directory should show how to install the schemas ...

• david4096
·
• 1
·
• Opened 
  on Nov 18, 2016
·
• #742

ga4gh/ga4gh-schemas

Use unsigned integer for positions

As suggested here https://github.com/ga4gh/schemas/pull/706#discussion-diff-85609058R178 Positions can be specified using unsigned, as opposed to signed integers since genomic coordinates are positive. ...

Discussion

• david4096
·
• 2
·
• Opened 
  on Oct 28, 2016
·
• #737

ga4gh/ga4gh-schemas

Sequence Annotations Feature Types

Currently the documentation is unclear about how to use ontology terms to specify a feature_type field in a SearchFeaturesRequest. There is a TODO in place that should be removed and replaced with the ...

enhancement

Sequence Annotation

• david4096
·
• Opened 
  on Oct 28, 2016
·
• #736

ga4gh/ga4gh-schemas

Call schema not suited for variant calls with no coverage

As recommended by @dcolligan, I am adding this issue here to describe a problem that I found on GA4GH schemas and was first described at ga4gh/server#1389. When the VCF file has variant calls with no ...

API Consistency

Beacon

bug

Major Enhancement

• wdesouza
·
• 3
·
• Opened 
  on Oct 25, 2016
·
• #727

ga4gh/ga4gh-schemas

Group of Individuals/Cohorts

The data model should provide a way to group individuals. It currently groups Samples and Individuals, but being able to make statements about groups should be included as a first class part of the data ...

MetadataTaskTeam

• david4096
·
• 7
·
• Opened 
  on Oct 17, 2016
·
• #724

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