@gmod/jbrowse/src/JBrowse/Store/SeqFeature/BAMCombination.js

JBrowse - client-side genome browser

define([
        'dojo/_base/declare',
        'dojo/_base/array',
        'JBrowse/Store/SeqFeature/CombinationBase',
        ],

        function(
            declare,
            array,
            CombinationBaseStore
        ) {

    return declare([CombinationBaseStore], {

        // An implementation of the CombinationBaseStore which works with BAM features.  Currently, the only supported option is
        // a straight concatenation of the features of two stores.

        // This combination store doesn't need to convert between spans and features, so these two functions are essentially irrelevant.
        createFeatures: function(spans) {
            return spans;
        },

        toSpan: function(features, query) {
            return features.map(function(feat) {
                return Object.assign(Object.create(feat), feat)
            });
        },

        // Only one supported operation - array concatenation
        opSpan: function(op, span1, span2, query) {

            if(op == "U") {
                this._appendStringToID( span1, "L" );
                this._appendStringToID( span2, "R" );
                return span1.concat( span2 );
            }
            console.error( "invalid operation" );
            return undefined;
        },

        _appendStringToID: function ( objArray, string ) {
            array.forEach( objArray, function( object ) {
                var oldID = object.id;
                if( typeof oldID == 'function' ) {
                    object.id = function() {
                        return oldID.call( object ) + string;
                    }
                } else {
                    object.id = oldID + string;
                }
            });
            return objArray;
        }

    });


});