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Ian Holmes

Ian Holmes

Member of 1 project: JBrowse

Ian Holmes's latest activity

Wednesday, August 12 2009
40 alignment tracks was created in JBrowse
  • Ian Holmes
    Ian Holmes created the ticket at 3:47 PM

    hopefully a straightforward[*] extension of sequence tracks

    [*] yes i realize this is a potentially fatal word. but really, as long as the tracks don't get fanc...
Monday, August 10 2009
39 Add grayscale option to wig2png.cc was created in JBrowse
  • Ian Holmes
    Ian Holmes created the ticket at 3:00 PM

    Pretty much self-explanatory.

    Subclassing MeanRenderer in wig2png.cc might work, but be careful not to conflict with other ways of breaking out this class hiera...
38 add optional vertical scaling field for image tracks in trackInfo.js was created in JBrowse
  • Ian Holmes
    Ian Holmes created the ticket at 2:57 PM

    Grayscale WIG tracks will only be one pixel high, therefore it'd be useful to allow them to be arbitrarily scaled in the Y axis.

    I'm assuming this is a modifica...
Friday, July 24 2009
37 "virtual tracks" as a mechanism for initiating analyses was created in JBrowse
  • Ian Holmes
    Ian Holmes created the ticket at 12:12 PM

    "virtual tracks" are tracks which display the results of running xrate on a window. As long as lazy loading (#4) is in place (along with tiled images), you can ...
Wednesday, July 15 2009
31 write an adaptor allowing Bio::Graphics to produce image tracks was created in JBrowse
  • Ian Holmes
    Ian Holmes created the ticket at 1:29 PM

    with the TiledImage and other infrastructure we have, it doesn't seem like this would be too hard.

    it would be a huge boon in terms of the diversity of visual r...
30 Screencast was created in JBrowse
  • Ian Holmes
    Ian Holmes created the ticket at 1:22 PM

    At some point we were discussing making a screencast for how to set the thing up...
29 auto-refresh of trackInfo.json was created in JBrowse
  • Ian Holmes
    Ian Holmes created the ticket at 12:23 AM

    the client should auto-refresh the track list

    this behavior could be toggled in trackInfo.json (and/or the refresh rate could be set)

    benefits: just seems cheap...
Wednesday, July 08 2009
28 Validate GFF/BED/WIG/FASTA input, give helpful feedback was created in JBrowse
  • Ian Holmes
    Ian Holmes created the ticket at 12:56 PM

    JBrowse server scripts currently give little or no (or cryptic) feedback about invalid input data. This problem gets much worse for the TWiki plugin (where inte...
Tuesday, July 07 2009
26 Documentation of wig2png C++ API was updated in JBrowse
  • Ian Holmes
    Ian Holmes commented at 11:32 AM

    Documentation of ImageTrack JSON format would be better -- see #27
27 Documentation of ImageTrack JSON format was created in JBrowse
  • Ian Holmes
    Ian Holmes created the ticket at 11:32 AM

    So people can write their own renderers.

    People love doing this. Love it. Hacking together your own glyphs for GBrowse is so popular that there was a massive ep...