XML File Fails to Load Tracks on IGV v2.19.1

[tejaswi-alaparthi]

When attempting to load an XML file in IGV v2.19.1, none of the tracks are displayed. This issue occurs consistently with files that previously worked on earlier versions of IGV.

Expected Behavior:
Tracks referenced in the XML file should load and be visible in the IGV interface.

Observed Behavior:
The XML file is processed without any visible errors, but the tracks are not displayed.

Environment Details:
IGV Version: v2.19.1
Operating System: Windows 10
Java Version: Java 21.0.4

Session file:

igv_20250115.log

This issue started occurring after upgrading to v2.19.1. The same XML file works on earlier versions of IGV.

[jrobinso]

I can't reproduce the issue. Is it possible to zip and attach the XML file, or alternatively email it privately to igv-team@broadinstitute.org?

[mrvollger]

We have also seen this behavior where previously working XMLs no longer show data. After we played around some, we found that we used to only need to specify a "Resource," but now we need to define both a "Resource" and a "Track." I have attached a working and "broken" XML linked to public data if you want to see.

We aren't sure which version this stopped working on, though. And I am not sure if that working previously was just a quirk and the expected behavior is nothing to be shown without a track.

Archive.zip

[tejaswi-alaparthi]

We have also seen this behavior where previously working XMLs no longer show data. After we played around some, we found that we used to only need to specify a "Resource," but now we need to define both a "Resource" and a "Track." I have attached a working and "broken" XML linked to public data if you want to see.

We aren't sure which version this stopped working on, though. And I am not sure if that working previously was just a quirk and the expected behavior is nothing to be shown without a track.

Archive.zip

Thank you for your response and clarification! I agree with your suggestion about specifying the Tracks in the XML file. It seems to align well with the issue and should help in troubleshooting. To reproduce the issue, I loaded multiple BAM files and saved the session using the "Save Session" option under the "File" menu in the application. Then, I reloaded the saved XML file in a fresh IGV session, which worked perfectly. The only difference I noticed between the working XML and the failed XML is the Panel -> Tracks block in the XML file.

[sjneph]

As long as there is a single (even empty) panel block, it loads things correctly now. The panel block was not needed in the past. This more minimal example works now.

gm12878.working.zip

[jrobinso]

@sjneph Thanks, the empty panel block is the key. Its easy to reproduce now. That is not intended behavior, I will look into this and correct it. The panel block should not be needed. In fact it is strongly recommended that users not try to create "Panel" sections, the rules for matching tracks to associated panels for some track types are obscure and not documented.