Regression: Missing/black chromosome name in batch mode using MATE_CHROMOSOME grouping since 2.12.0

[cbrueffer]

First of all, thanks for all your work on this software!

Working version: up to and including 2.11.9
Broken version: from 2.12.0 to latest (2.13.2 as of now)

I'm using IGV in batch mode and headless using xvfb-run with option SAM.GROUP_OPTION=MATE_CHROMOSOME. This should show the chromosome name in each "read group" in the top-left corner of each grouping. In batch mode this worked up to and including version 2.11.9. Since version 2.12.0, including the latest 2.13.2, only a black box is being printed.

Environment:

• IGV installed via Bioconda
• OpenJDK 11.0.15

The first (working) screenshot is from 2.11.9, the second (broken) from 2.12.0. Config, batch file etc are the same.

[jrobinso]

Could you provide a test script, it's o.k. if the bam file isn't reachable I'll substitute another.

[jrobinso]

@cbrueffer ignore test request, I can reproduce it.

Tangentially, I don't recall why we paint group labels (chromosome names in this case) with black background / white text, I think they should look as they do on screen.

[cbrueffer]

Glad to hear it, I was just putting the files together.

I was wondering the same, at first I thought it was an Xvfb artifact.

[jrobinso]

I tracked it down, its a java idiosyncrasy, found this in the java docs. I have switched from using "clearRect" to "fillRect" which seems to fix the problem. Fix will be in the next release, early August, and in the development snapshot within the next few minutes.

Beginning with Java 1.1, the background color of offscreen images may be system dependent. Applications should use setColor followed by fillRect to ensure that an offscreen image is cleared to a specific color

[cbrueffer]

Thanks a lot for the quick fix!