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License: Mozilla Public License 2.0
If a sample is not found on the server the user only sees a 404 json request which is not user friendly.
The current default region is not very helpful (1:100000-200000) and it should be 1:1-None
General slowness has been reported for samples
Currently a user is prevented to view the entire current chromosome by clicking in the overview track.
To protect user information
Update the navigation shortcuts to something that is more intuitive.
Desired shortcuts
Increase the width for the div that contains the hover data to make it easier to hover on features such as exons.
Searching for only a chromosome breaks the loading of annotation tracks and allele frequency patterns
The view controllers could be moved to some other part of the page to get more workspace.
Would it be possible to have gens under a LICENSE?
Moving into a production environment it would be good to know that gens is free to use for any application (or not if that is the case).
Thanks!
Add a homepage for Gens when no sample is chosen in the URL.
Maybe show the available samples?
A user would like to display multiple annotation tracks simultaneously to get a better overview.
Add legends to keep track on which view is the Transcripts or Annotations
Click a button to copy a "permalink" of the current location to the clipboard!
Example: http://10.0.224.64/gens/4224-12?region=X:45056201-45085400
Gens has three different utility scripts that loads data into the database. There is currently no method of migrating the database if we need to change the structure and no method of externally reindexing the database.
By merging the scripts into a small cli tool would allow us to introduce the expanded functionality without the clutter of maintaining several different scripts.
Probably requires off-screen rendering of these tracks as well.
Arrows are being drawn "randomly" over the transcript since they are being drawn between exomes.
Kallade varianter ifrån Scout ska visas i Gens
It currently way to slow and hard to navigate
A user would like to pin interesting variants in scout that they observe in Gens.
Blocked by, Clinical-Genomics/scout#4157
The remove method of collections has been removed in v. >=4 of pymongo requested from setup.py.
This breaks register_data_update in gens/db/annotation.py.
Mvh Anders
Expand documentation with
Sometimes we see mosaic deletions/duplication (or in somatic cases, perhaps low frequency ones). This are quite difficult to see at the current -4 to 4 Y-scale
It would be nice to have to possibility to zoom on the Y-level. I think that would improve things.
Perhaps it is possible to do this entirely on the client side?
Add a chromosome band figure above the interactive canvas.
Highlight the viewed range in the interactive view in the overview.
For example by drawing a transparent color over the viewed region in the overview.
The wrong chromosome band name is displayed in the Gens title.
Add custom error templates for error messages
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