Won't load track details from previous session xml file

igvteam / igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

https://igv.org

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Won't load track details from previous session xml file #1601

Open ohmstead opened 1 month ago

ohmstead commented 1 month ago

I have an issue loading a previous session from a session xml file.

In a previous session, I changed the track height and set track colors to correspond to their conditions. However, when I reload the session from file, it loads in the tracks in the grey color and default height.

In the xml file, it specifies their custom height and color changes. I'm a little bit at a loss for why IGV doesn't incorporate these details.

I'm on macOS Sonoma 14.5. Plotting RNA-seq data. Below is my session session file in full text, since GitHub won't allow an XML file upload.

Thanks!

`<?xml version="1.0" encoding="UTF-8" standalone="no"?>

jrobinso commented 1 month ago

I can't really debug this visually, and could not load it even if you uploaded as it references local files. If you can diff the before and after hand-edit and post the changes here we might be able to pinpoint something.

BTW you can zip the XML file, or any other type, and upload the zipped file

ohmstead commented 1 month ago

Here's a link to an example bam.

Also attached a zipped xml. I didn't hand-edit it at all. igv_only_coverage.xml.zip

Appreciate your help!

jrobinso commented 1 month ago

I can't load your example BAM, it has non-standard sequence names (mm39_1, etc).

jrobinso commented 1 month ago

Attached is a session with a blue coverage track (see screenshot). I created this with IGV 2.18.4. You should be able to load it, after unzipping, it uses a public bam file. If you can recreate your issue starting with this session please zip and post it here, along with the exact steps you took to reproduce it.

igv_session.xml.zip