Annotations from .assembly file only display in the "scaffold_1" view, and not in the "all" view or the views for the individual scaffolds they belong to. [BUG]

[oneillkza]

Describe the bug Annotations from .assembly file only display in the "scaffold_1" view, and not in the "all" view or the views for the individual scaffolds they belong to. This prevents any of the assembly tools from working correctly.

To Reproduce Steps to reproduce the behavior:

1. Open .hic file
2. Open .assembly file
3. Annotations for scaffold boundaries do not display
4. Click scaffold_1 drop-down
5. Annotations for the whole genome are stuffed into scaffold_1
6. Click any other scaffold drop-down
7. No annotations are visible

Expected behavior Scaffold boundary annotations are expected to appear in the "all" scaffold view, and possible in the views for individual scaffolds? This also seems to be a necessary step for any of the assembly tools to work, and is the likely cause for #972

Screenshots

Desktop (please complete the following information):

• OS: Ubuntu 20.04
• Version Juicebox 2.13.07

Additional context Here's the assembly file, in case this helps:

scaffolds_FINAL_pg.assembly.gz

(I couldn't find an actual spec for this file format -- it seems to be some kind of juicer-only thing?)

It was generated from the SALSA final fasta using tools from PhaseGenomics

[dudcha]

Thanks for a detailed description of the issue you are experiencing. Closing since this is not a bug. Looks like you are trying to use JBAT on a sandboxes, non-assembly hic file. Please consult Genome Assembly Cookbook (dnazoo.org/methods) on 3D-DNA tool suite usage. Thanks, -Olga