Add custom error templates for error messages

Probably requires off-screen rendering of these tracks as well.

Searching for only a chromosome breaks the loading of annotation tracks and allele frequency patterns

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

http://10.0.224.68:81/5125-21?hg_type=37

• Refactor interactive canvas to use the track class
• Find other method of plotting scatters
• Make interactiveCanvas.redraw() not managing instances of annotation track classes

Add a homepage for Gens when no sample is chosen in the URL.
Maybe show the available samples?

Kallade varianter ifrån Scout ska visas i Gens

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.

1. Goto region http://10.0.224.64:5003/643594?region=8:138593260-145138636
2. Pan view so the annotated region is on the left edge of the screen
3. Zoom in on the new region

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.

To protect user information

Expand documentation with

• accessing files when running in docker
• add description of GUI
• add description of shortcuts

Increase the width for the div that contains the hover data to make it easier to hover on features such as exons.

Update the navigation shortcuts to something that is more intuitive.

Desired shortcuts

• shift + mouse down -- zoom in region
• arrow keys -- go left/ right in interactive window

If a sample is not found on the server the user only sees a 404 json request which is not user friendly.

• Add sample not found page
• Add 404 page
• Add 500 page

General slowness has been reported for samples

• 25-21 (chrome)

It currently way to slow and hard to navigate

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

See this for example:

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?

Arrows are being drawn "randomly" over the transcript since they are being drawn between exomes.

The current default region is not very helpful (1:100000-200000) and it should be 1:1-None

To reproduce

1. Display the entire chromosome
2. Click and drag the copy number profile track left
3. When exceeding the bounds of the chromosome the annotation tracks disappear

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

Add a chromosome band figure above the interactive canvas.

• The figure should pan with the interactive canvas when the interactive canvas is moved.

Currently a user is prevented to view the entire current chromosome by clicking in the overview track.