sort readGroup in batch command is not working

[Timothee Cezard]

I sent an email to igv-...@broadinstitute.org before I saw this google
group.
Sorry for the duplication:
--
Hi IGV team,
I'm trying to run some batch script with IGV to get several screen shot
of interesting region but the "sort readGroup" command doesn't seem to
do anything.
I'm using IGV 2.0.34 on mac OS 10.6.8 and here is what I'm running:
snapshotDirectory ./
goto consensus_4100:64-65
sort readGroup
snapshot consensus_4100_64_65.png

The console output seems to say that everything is going fine:
INFO [2012-03-21 10:45:27,660] [BatchRunner.java:60]
[SwingWorker-pool-1-thread-2] Executing Command: snapshotDirectory ./
INFO [2012-03-21 10:45:29,683] [CommandExecutor.java:142]
[SwingWorker-pool-1-thread-2] OK
INFO [2012-03-21 10:45:29,684] [BatchRunner.java:60]
[SwingWorker-pool-1-thread-2] Executing Command: goto consensus_4100
INFO [2012-03-21 10:45:36,965] [CommandExecutor.java:142]
[SwingWorker-pool-1-thread-2] OK
INFO [2012-03-21 10:45:36,967] [BatchRunner.java:60]
[SwingWorker-pool-1-thread-2] Executing Command: sort readGroup
INFO [2012-03-21 10:45:39,015] [CommandExecutor.java:142]
[SwingWorker-pool-1-thread-2] OK
INFO [2012-03-21 10:45:39,017] [BatchRunner.java:60]
[SwingWorker-pool-1-thread-2] Executing Command: snapshot
consensus_4100_64_65.png
Snapshot:
/Users/tcezard/tools/mac-os/igv/IGV_2.0.34/./consensus_4100_64_65.png
INFO [2012-03-21 10:45:41,359] [CommandExecutor.java:142]
[SwingWorker-pool-1-thread-2] OK

But the read on the screenshot are not sorted by the readGroup
Is there something that I'm missing?

Thanks
Tim

--
Timothee Cezard
Bioinformatics Specialist
The GenePool
Room 3.54, Ashworth Laboratories
Kings building's campus
University of Edinburgh
EH9 3JT, Edinburgh, UK.

Phone: +44 131 650 7403

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

[Jacob Silterra]

This is a bug on our part, thanks for the report. It will be fixed in the next release (coming soon).

-Jacob

--
Jacob Silterra
Software Engineer
Broad Institute

[Timothee Cezard]

Thanks a lot Jacob for the quick reply.
Is there any way I can my hand on a dev version.
I have a couple hundred sites to go through and this would help me quite a lot.

BTW unrelated question:
Is there any plan to make read group as a sample annotation?

Thanks again
Tim

[Jacob Silterra]

Dev version at: http://www.broadinstitute.org/software/igv/download_dev
It should be fixed in that version.

Not sure about making read group a sample annotation.

-Jacob

[Timothee Cezard]

Awesome
Thanks Jacob !!
Tim