Batch command bug (regarding goto for multi-loci view)

[soymintc]

Previously in version 2.14.1, batch command with
goto 19:16780041-16782041 19:17553189-17555189
used to show two panels for the two regions, like

However in version 2.19.2, batch command with the same goto line would just show the whole chromosome view which is kind of weird.

[helgathorv]

It works for me. If you share a batch script that displays the error we can take a look.

[soymintc]

@helgathorv Interesting. Thank you for the quick response! Here's the batch script I was trying out.
The first snapshot is being created fine (single locus), but the second snapshot with 2 loci creates the erroneous (semantically) output.
I wonder if I screwed up something in the batch script.
What's even more weird is that the same script used to work with 2.14.1; I realized that there was a semantic error only after I upgraded my IGV version to 2.19.2.

new
snapshotDirectory ./
genome hg19
load test/test_tumor.bam
load test/test_normal.bam
goto 8:32534767-32536767
squish
maxPanelHeight 200
snapshot 8-32534767-32536767.png
goto 19:16780041-16782041 19:17553189-17555189
squish
maxPanelHeight 200
snapshot 19-16780041-16782041.19-17553189-17555189.png
exit

[helgathorv]

@soymintc Thanks for the test script. It does seem that there is a problem in the latest releases and we will look into it, but I don't have a timeline. In the meantime, 2.17.4 is the last release that does not have the problem, so if you want to update to a more recent version than 2.14.1 you can install 2.17.4 from here.

[helgathorv]

For debugging: This script shows how the view is not updated when the goto command has multiple loci - except after the last command of the script.

setSleepInterval 1000
snapshotDirectory /Users/helga/Downloads/BatchTest2
goto 1:16780041-16782041 1:17553189-17555189
goto 2:16780041-16782041 2:17553189-17555189
goto 3:16780041-16782041 3:17553189-17555189
goto 8:16780041-16782041 
goto 7:16780041-16782041
goto 1:16780041-16782041 1:17553189-17555189
goto 2:16780041-16782041 2:17553189-17555189

[soymintc]

@helgathorv Sounds great, thank you for looking into this matter quickly and providing me a workaround! Please feel free to close the ticket if you want.