Investigate whether the BAM files from ICGC work with the alignment track.

Note that first party ICGC data should include index files. For this data, you should be able to point the alignment track at the BAM and index file (with modification for adding the token).

The ICGC API returns the index file information (https://dcc.icgc.org/api/v1/repository/files/FI9893) so we can use this to create the track.

Investigate whether the TGZ files from ICGC are relevant to JBrowse. Can they be converted to tracks?

Note that these are controlled access files.

Add a login UI for storing user tokens to session storage. Can be based on the login flow for the GDC plugin.

Before doing this, ensure that there is a use for this in the browser. If all controlled data we want to display requires processing (ex. index file generation) then it doesn't make much sense to implement.

This would be similar in format to the GDC UI flow. The user would input a donor ID, and we would populate a table with all of the available file types. Clicking on one of the files shows metadata similar to the By File ID/Name view. If we can, we add the track. If we cannot, we tell them what commands they need to run locally.

Install the score client and select a region for BAM slicing. Generate a corresponding index file. Create an alignment track and point them to these files. Do the tracks work?

Next, try the same approach but using FUSE mounting (also requires the score client). Create an alignment track and point them to these files. Do the tracks work? The benefit of FUSE is that only blocks needed are pulled.

Could these use the BAM index files available?

See bottom of https://dcc.icgc.org/repositories/files/FI9994 for FUSE in action.

This would be similar in format to the GDC UI flow. The user would input a name or ID of a BAM file, and we would fetch some metadata on it. Since BAM slicing doesn't provide index files, we will need to generate the commands the user must run locally using the ICGC client to generate the BAM slice and index file.

To improve our community profile, we should add a code of conduct.

See https://docs.github.com/en/github/building-a-strong-community/adding-a-code-of-conduct-to-your-project

Investigate whether the BAM files from ICGC work with the variant track.

Note that first party ICGC data should include index files. For this data, you should be able to point the variant track at the BAM and index file (with modification for adding the token).

The ICGC API returns the index file information (https://dcc.icgc.org/api/v1/repository/files/FI819885) so we can use this to create the track.

This would be similar in format to the GDC UI flow. The user would input a name or ID of a file, and we would fetch some metadata on it. If we can, we add the track. If we cannot, we tell them what commands they need to run locally.