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bihealth / sodar-server

SODAR: System for Omics Data Access and Retrieval
https://github.com/bihealth/sodar-server
MIT License
14 stars 3 forks source link

IGV session merging opens a new session #1932

Open mikkonie opened 6 months ago

mikkonie commented 6 months ago

Reported by @Nicolai-vKuegelgen. It's been noticed that IGV session merging opens a new session instead of actually merging. Merging BAM/VCF files into the current session still works as expected. Nicolai is using IGV version 2.17.3.

From the SODAR point of view, the only dfiference between opening a new session and merging a session file into the current one is the URL we link to for IGV. Namely, http://igv-host/load?merge=x&file=y, where x is true/false and y is the XML file SODAR generates.

I can confirm that the URL generating still works as it was originally implemented and nothing has been recently changed regading this.

Perhaps something has changed with the IGV API recently? I will try to look into it.

Comments and help are welcomed from any IGV experts, which I'm surely not :)

mikkonie commented 6 months ago

According to the IGV documentation, these links should still work like before. Unless they've e.g. changed the requirements for the XML file provided for merging.. But in that case, I guess they shouldn't be able to open as a new session either?

mikkonie commented 6 months ago

Nicolai also raised a good point: can someone verify that this has, in fact, provenly worked before as is expected here?

mikkonie commented 6 months ago

There has been some discussion indicating that this may have in fact never worked.

One possible solution would be to replace the link with a comma-separated list of BAM and VCF paths instead of a session XML file. According to the documentation, this should work.