DUP,DEL and required positional parameters

[mbaudis]

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:

• Document about range match implementation using start, end intervals
• Previous Github issues Add support to ask for more types of variants (more complex InDels and duplications) #20, added alternateBasesInfo #65, Feature evaluation Beacon for structural and metadata queries and quantitative results (ELIXIR D1.1)  #80

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

[mbaudis]

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

[mbaudis]

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

[mbaudis]

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]

@juhtornr Great - thanks!