Add _gn_so field in Variants collection. Related with opencb/opencga#500

add_gn_so_field_500.js

// Use migration script https://gist.github.com/pfurio/f7cd90af08e0073699f0beeeef1958ba
migrateCollection("variants", {"annotation.ct":{$exists:1}, "annotation._gn_so":{$exists:false}}, {"annotation.ct":1}, function (bulk, doc) {
    var id = doc._id;

    var fields = ["gn", "ensg", "enst", "uni_a", "uni_n"];
    var gn_so_obj = {}; /* Use as set */
    for (var i in doc.annotation[0].ct) {
        var ct = doc.annotation[0].ct[i];
        for (var so_idx in ct.so) {
            fields.forEach(function(field) {
                if (ct.hasOwnProperty(field))
                    gn_so_obj[ct[field] + "_" + ct.so[so_idx]] = true;
            })
        }
    }

    var gn_so = [];
    for(var k in gn_so_obj) gn_so.push(k);
    if (gn_so.length > 0) {
        bulk.find({_id: id}).update({$set: {"annotation.0._gn_so":gn_so}});
    }
});

// Create sparse index
db.variants.ensureIndex({"annotation._gn_so":1}, {sparse:true, background: true})