BigWig.spec.js

require(['JBrowse/Store/BigWig','JBrowse/Model/XHRBlob'], function( BigWig, XHRBlob ) {
    describe( 'BigWig with tomato RNAseq coverage', function() {
        var b = new BigWig({
            blob: new XHRBlob('../data/SL2.40_all_rna_seq.v1.bigwig')
        });

        it('constructs', function(){ expect(b).toBeTruthy(); });

        it('returns empty array of features for a nonexistent chrom', function() {
            var v = b.getUnzoomedView();
            var wigData;
            v.readWigData( 'nonexistent', 1, 10000, function(features) {
                wigData = features;
            });
            waitsFor(function() { return wigData; });
            runs(function() {
                expect(wigData.length).toEqual(0);
            });
        });

        it('reads some good data unzoomed', function() {
            var v = b.getUnzoomedView();
            var wigData;
            v.readWigData( 'SL2.40ch01', 1, 100000, function(features) {
                wigData = features;
            });
            waitsFor(function() { return wigData; },1000);
            runs(function() {
                expect(wigData.length).toBeGreaterThan(10000);
                dojo.forEach( wigData.slice(0,20), function(feature) {
                    expect(feature.get('start')).toBeGreaterThan(0);
                    expect(feature.get('end')).toBeLessThan(100001);
                });
                     //console.log(wigData);
            });
        });

        it('reads some good data when zoomed', function() {
            var v = b.getView( 100000 );
            var wigData;
            v.readWigData( 'SL2.40ch01', 100000, 2000000, function(features) {
                wigData = features;
            });
            waitsFor(function() { return wigData; },1000);
            runs(function() {
                expect(wigData.length).toBeGreaterThan(19);
                expect(wigData.length).toBeLessThan(100);
                dojo.forEach( wigData, function(feature) {
                    expect(feature.get('start')).toBeGreaterThan(80000);
                    expect(feature.get('end')).toBeLessThan(2050000);
                });
                     //console.log(wigData);
            });
        });

        it('reads the file stats (the totalSummary section)', function() {
               var stats = b.getStats();
               expect(stats.basesCovered).toEqual(141149153);
               expect(stats.minVal).toEqual(1);
               expect(stats.maxVal).toEqual(62066);
               expect(stats.sumData).toEqual(16922295025);
               expect(stats.sumSquares).toEqual(45582937421360);
               expect(stats.stdDev).toEqual(555.4891087210976);
               expect(stats.mean).toEqual(119.88945498666932);
        });

        it('reads good data when zoomed very little', function() {
            var v = b.getView( 17.34 );
            var wigData;
            v.readWigData( 'SL2.40ch01', 19999, 24999, function(features) {
                wigData = features;
            });
            waitsFor(function() { return wigData; },1000);
            runs(function() {
                expect(wigData.length).toBeGreaterThan(19);
                expect(wigData.length).toBeLessThan(1000);
                dojo.forEach( wigData, function(feature) {
                    expect(feature.get('start')).toBeGreaterThan(10000);
                    expect(feature.get('end')).toBeLessThan(30000);
                });
                     //console.log(wigData);
            });
        });

    });
});