Does Dalliance supprt uncompressed BED files ?

[max-l]

I have bigbed files that work, but when I try to produce uncompressed bed files, I get :

 Uncaught RangeError: byte length of Int16Array should be a multiple of 2
at new Int16Array (native)

The bed file contains this single line :

  1 3845    13620   ENSDART00000152276  500 +   3845    13620   0,153,0 8   85,164,25,114,147,92,121,548    0,800,1332,1687,2401,5204,5394,9227

Do I need to give it a mime type ?

[dasmoth]

Textual BED files should be an option, but they need a somewhat different config from bigBeds. E.g.:

     {name: "MyFeatures",
      uri: "http://server/myfile.bed",
      tier_type: 'memstore',
      payload: 'bed'}

See http://www.biodalliance.org/config-source.html for more details.

[max-l]

Thanks @dasmoth I get this error with my single line BED file :

 Exception TypeError: Cannot read property 'timeout' of undefined

I load it like this :

   [
        {name: 'Genome',
         twoBitURI: assembly.assemblyUrl + '/complete-genome.2bit',
         stylesheet_uri: 'https://www.biodalliance.org/stylesheets/gencode.xml',
         tier_type: 'sequence'
        },
        {name: "MyFeatures",
         uri: '/api/1/lab/altorf/singleBed/psm/213803.bed',
         tier_type: 'memstore',
         stylesheet_uri: 'https://www.biodalliance.org/stylesheets/gencode.xml',
          payload: 'bed',
          collapseSuperGroups: true
        }
      ]

[dasmoth]

Bother, seems to be an unfixed issue in 0.13.7. Building your own from git should be fine, or try http://www.biodalliance.org/dev/dalliance-compiled.js

[dasmoth]

Have also pushed out 0.13.8 which includes the fix for this.

[max-l]

@dasmoth where can I get the 0.13.8 version ? I notice that this project does not use GIT tags. I notice that my code is broken in the 0.14 release (https://www.biodalliance.org/release-0.14/dalliance-compiled.js). I will have to hunt down what is the latest commitID under which my code works, (I suppose that will be in the 0.13.x branch) but I think that GIT tags would really be helpful for building and debugging specific versions.

[max-l]

ok, I found it : https://github.com/dasmoth/dalliance/commits/0.13.x so, for anyone who has the same question : to find a particular release, you go in the branch and look for commits that have "version bump" in their description, then in the DIFF, you look at the actual version change.

[dasmoth]

No, there haven't been git tags for individual releases (although there have been branches for major releases). I'll try adding tags for releases in the future.

There isn't yet a v0.14.0 final released. However, there probably ought to be, and I'm generally recommending using git master at this point. You can compile itself (checkout, npm install, run gulp). Or there's a reasonably up-to-date version at https://www.biodalliance.org/dev/dalliance-compiled.js.

If you're still having problems with the master branch, do let me know what's amiss and I'll see if I can help track it down.