batch list of preference key value

[Guillaume Charbonnier]

Hello,

I would like to know where I can find the list of all available keys and values for the "preference" command in IGV batch script.

I am especially looking for the key setting the "Group autoscale".

Thanks

[Varun Gupta]

Hi,

Did you find a solution for this? If yes can you please share?

Regards,

Varun

[James Robinson]

The complete list of preferences are listed here. https://raw.githubusercontent.com/igvteam/igv/master/src/main/resources/org/broad/igv/prefs/preferences.tab

[Varun Gupta]

Hi Jim,

Is this the key value pair I should add in my batch script for getting group autoscale for each locus I am running? Here is my batch script:

snapshotDirectory /user/pebams

goto chr1:64,530,804-64,606,548

preference CHART.AUTOSCALE boolean TRUE

snapshot

goto chr1:64,027,448-64,124,328

preference CHART.AUTOSCALE boolean TRUE

snapshot

I am running the batch script but group autoscale doesn't seem to work?

[Varun Gupta]

even setDataRange auto doesn't work in the batch script.

I am using IGV 2.9.4

How can I fix this?

Thanks for all your help.

On Wednesday, August 4, 2021 at 6:44:18 PM UTC-4 James Robinson wrote:

[James Robinson]

The preferences are not relevant for this,  setDataRange is what you need to use.   If its not working give us an example script, using data we can access, preferably as a github issue. (github.com/igvteam/igv/issues).   Also see this issue which is relevant:  https://github.com/igvteam/igv/issues/997

The current version of igv is 2.10.3,  I do not know what issue may or may not have been present in earlier versions that might affect this.

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[Varun Gupta]

Hello Jim,

Thanks for the speedy reply. I came across the above post and installed version 2.10.3 and it seem to work with group autoscaling.

Thanks

Regards,

Varun