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

JBrowse - client-side genome browser

/**
 * Store class that encapsulates another store, and synthesizes
 * quantitative features that give the depth of coverage for the
 * features in it.
 */

define([
           'dojo/_base/declare',
           'JBrowse/Store/SeqFeature',
           'JBrowse/Util',
           'JBrowse/Model/CoverageFeature'
       ],
       function( declare, SeqFeatureStore, Util, CoverageFeature ) {

return declare( SeqFeatureStore, {

    constructor: function( args ) {
        this.store = args.store;
    },

    getGlobalStats: function( callback, errorCallback ) {
        callback( {} );
    },

    getFeatures: function( query, featureCallback, finishCallback, errorCallback ) {
        var leftBase  = query.start;
        var rightBase = query.end;
        var scale = query.scale || ( ('basesPerSpan' in query) ? 1/query.basesPerSpan : 10 ); // px/bp
        var widthBp = rightBase-leftBase;
        var widthPx = widthBp * scale;

        var binWidth = Math.ceil( 1/scale ); // in bp

        var coverageBins = new Array( Math.ceil( widthBp/binWidth ) );
        var binOverlap = function( bp, isRightEnd ) {
            var binCoord  = (bp-leftBase-1) / binWidth;
            var binNumber = Math.floor( binCoord );
            var overlap   = isRightEnd ? 1-(binCoord-binNumber) : binCoord - binNumber;
            return {
                bin: binNumber,
                overlap: overlap // between 0 and 1: proportion of this bin that the feature overlaps
            };
        };

        this.store.getFeatures(
            query,
            function( feature ) {
                            var startBO = binOverlap( feature.get('start'), false );
                            var endBO   = binOverlap( feature.get('end'),   true  );

                            // increment start and end partial-overlap bins by proportion of overlap
                            if( startBO.bin == endBO.bin ) {
                                coverageBins[startBO.bin] = (coverageBins[startBO.bin] || 0) + endBO.overlap + startBO.overlap - 1;
                            }
                            else {
                                coverageBins[startBO.bin] = (coverageBins[startBO.bin] || 0) + startBO.overlap;
                                coverageBins[endBO.bin]   = (coverageBins[endBO.bin]   || 0) + endBO.overlap;
                            }

                            // increment completely overlapped interior bins by 1
                            for( var i = startBO.bin+1; i <= endBO.bin-1; i++ ) {
                                coverageBins[i] = (coverageBins[i] || 0) + 1;
                            }
            },
            function () {
                // make fake features from the coverage
                for( var i = 0; i < coverageBins.length; i++ ) {
                    var score = (coverageBins[i] || 0);
                    var bpOffset = leftBase+binWidth*i;
                    featureCallback( new CoverageFeature({
                        start: bpOffset,
                        end:   bpOffset+binWidth,
                        score: score
                     }));
                }
                finishCallback();
            },
            errorCallback
        );
    }
});
});