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DUP,DEL and required positional parameters #94

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merged 7 commits into from Jun 22, 2017

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mbaudis commented May 3, 2017

This PR implements both the attributes for querying a subset of structural variants, such as currently possibly represented through the GA4GH variants schema, as well as the start[1..2], end[0..2] modifications to allow matching variants of imprecise alert, end and sequence composition.

The need for these changes as well as possible ways to implement them have been discussed previously:

Also, the moving ahead with structural variant definitions in both schemas and Beacon has been discussed with the VMC team (@reece, @sarahhunt), who at the present focus on the representation of precise variants.

Technical notes:

  • This changes the index numbers of the develop-proto branch; however, in this case it seems acceptable since proto had not been implemented as master.
  • There has been no change to beacon_server.proto
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mbaudis commented May 23, 2017

Re-opening after the 2017-05-23 Beacon workshop discussions in Hinxton.

Michael Baudis
implementing separate start end attributes
As per Beacon meeting Hinxton 2017-05-23
//
int64 start = 2; // required
int64 start_min = 3;

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mbaudis May 24, 2017

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Renumbering proto seems to be o.k, since proto version not in production yet.

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mbaudis commented May 28, 2017

The current variant_type attribute is defined as string, with suggested example values ("DUP", "DEL"). This reflects the status in the GA4GH schema.

As e.g. Dylan Spalding suggested, one may use sequence ontology for those types. While I support the general notion (and could see this in line with the GA4GH OntologyTerm usage), ATM this should be synced with general GA4GH variant definition efforts (and we have the confirmation that structural variants won't be addressed in the near future).

So I suggest to leave this at it is presented here.

@mbaudis mbaudis changed the title from Structural DUP,DEL and range match requirements to DUP,DEL and required positional parameters Jun 20, 2017

@juhtornr juhtornr merged commit b7dc88c into develop-proto Jun 22, 2017

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mbaudis commented Jun 22, 2017

@juhtornr Great - thanks!

@mbaudis mbaudis deleted the develop-proto-structural_and_ranges branch Mar 21, 2018

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