Bigwig parsing and rendering support added #42
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…or variableStep wiggle and made the loop more efficient )
js/Track/Model/File/BIGWIG.js
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| bw.getValues(chr, start, end, function(features){ | ||
| model.receiveData(features, chr, start, end); | ||
| deferred.resolveWith(model); | ||
| }); |
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js/Track/Model/File/BIGWIG.js
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| var deferred = $.Deferred(); | ||
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| if(!this.url) this.data = new dallianceLib.BlobFetchable(this.track.dataFile); | ||
| else this.data = new dallianceLib.URLFetchable(this.url); |
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Replace the above two lines with
this.bigwigFile = this.bigwigFile || (this.url ? new dallianceLib.URLFetchable(this.url) : new dallianceLib.BlobFetchable(this.track.dataFile));
so that we don't make a new dallianceLib object every time getData is called
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ohh right I will do that
js/Track/Model/File/BIGWIG.js
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| if(!this.url) this.data = new dallianceLib.BlobFetchable(this.track.dataFile); | ||
| else this.data = new dallianceLib.URLFetchable(this.url); | ||
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| new BWReader(this.data, this.name, function(bw){ |
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- Replace this.data with this.bigwigFile
- We need to cache the BWReader (like the VCFReader is cached) to avoid making requests for the header of the file every time getData is called
js/lib/BWReader.js
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| @@ -0,0 +1,569 @@ | |||
| (function(){ | |||
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js/lib/BWReader.js
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| @@ -0,0 +1,569 @@ | |||
| (function(){ | |||
| var BWReader = function(data, name, callback){ | |||
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the "name" argument is never used, so can be removed
js/lib/BWReader.js
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| var vals = []; | ||
| var chromid = bbi.chroms.indexOf(chrom); | ||
| if(chromid == -1) chromid = bbi.chroms.indexOf("chr" + chrom); | ||
| if(chromid == -1) cb(null, "chrom not found"); |
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This needs to be cb([], "chrom not found") - currently it causes an error to be thrown in parseData if you go to a chromosome not present in the file
js/Track/Model/File/BIGWIG.js
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| return deferred; | ||
| } | ||
| }) |
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Please add ; to the end of the file
js/Track/library/File/BIGWIG.js
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| model : Genoverse.Track.Model.File.BIGWIG, | ||
| name : 'bigwig', | ||
| height : 100 | ||
| }) |
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- Please add ; to the end of the file
- Also add the line
Genoverse.Track.File.BW = Genoverse.Track.File.BIGWIG;to allow drag/drop to work (the file ending is .bw rather than .bigwig)
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I have seen files with both so adding this line will then allow suppor for both extensions
js/Track/Model/File/BIGWIG.js
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| else this.data = new dallianceLib.URLFetchable(this.url); | ||
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| new BWReader(this.data, this.name, function(bw){ | ||
| bw.getValues(chr, start, end, function(features){ |
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It is possible for bw to be null - need to check for this and immediately resolve the deferred if it is the case
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In addition to the changes requested above, there is a bug where features are missing when zooming out. Start at r=21:32684639-32684726, then press the zoom out button three times (you should end up at r=21:32684334-32685030). The third time causes more data to be loaded, but the features are drawn with a gap where the data from the original load should be present. This happens at all zoom levels. |
… requested region Returning all the data in the fetched blocks allows for a reduction in future read requests
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Hey simon I have fixed BEDParser and enabled support for BigBed , can you please merge this PR now ? |
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I have manually merged this PR with 0be9386 (along with some changes I made on top) |
Output preview :
http://i.imgur.com/354nOdu.png