"View mate region in split screen" not working with IGV windows versions 2.4 to 2.8.12

[Andrea Mafficini]

Hi,

I am posting this issue on behalf of a colleague who uses IGV on windows 10 (I work on linux and never encountered this issue). She reported that, when analyzing a gene fusion, she could not use the option "View mate region in split screen" for split paired-ends because nothing would happen and the program would get stuck to the last genomic coordinates after that.

I could reproduce the very same behavior on a couple of windows 10 machines using IGV 2.4.19 to 2.8.12. I tried both bundled JRE and system java installation, in the second case I used Oracle Java 11.0.9 JDK.

The issue seems to affect Windows 10, although another colleague reports similar behavior on an iMac too (bundled jdk11, 2.8.9). As I said before, I never had a problem with this on linux.

The fusion split screen is a killer feature for us as we mainly work with fusions. Any help is warmly appreciated.

Kindest regards

-- Andrea Mafficini PhD ARC-NET: Centre for Applied Research on Cancer Department of Diagnostics and Public Health University of Verona - Policlinico G.B. Rossi

[James Robinson]

Hi,

This is the first report of this we have had.   I cannot reproduce it,  could you provide a reproducible test case?    The 1000 Genomes files under "Load from Server..." for hg19 are all paired end if you can reproduce it with those.   Also, there might be information in the "igv.log" file present in an "igv" folder under the users home directory, please attach that or zip and email it to  igv-team (at) broadinstitute.org.

Jim

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[Andrea Mafficini]

Hi Jim,

I loaded one of the BAM files from the 1000 genomes as you kindly asked and the behavior was the same. The bam files I used before were aligned on hg38 with bwa so the reference does not seem to be involved.

Another bit of information I forgot in the previous email, user interface of windows 10 is localized (italian language and keyboard) while my linux system is set on english/US.

I previously started igv from the command prompt but no warning was issued when I tried "view mate region in split screen", it simply got stuck. The only thing that resurrected the user interface was changing reference genome build.

Please find attached the log file as per your request. I performed a clean install of v2.8.12 and loaded one of our bam first, then switched to hg19 and loaded one 1000G alignment.

Thank you so much for your support

Andrea

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-- 
Andrea Mafficini PhD
ARC-NET: Centre for Applied Research on Cancer
Department of Diagnostics and Public Health
University of Verona - Policlinico G.B. Rossi
Building: piastra odontoiatrica, 2nd floor
P.le L.A. Scuro, 10
37134 Verona
ITALY
Phone +39 045 812 4846
Fax   +39 045 802 7136

[James Robinson]

OK thanks,  when I have access to a Windows machine later I will see if I can reproduce this.   Could you tell me from what genomic region you selected the alignment for viewing in split screen?   Actually if you can "copy read details to clipboard" and past them here that would be best, then I can find and select the same alignment.

[Andrea Mafficini]

Hi Jim,

It looks like it's a localization issue. I changed the user interface of the window machine from which I produced the log file I sent you to English/US. Guess what? Now the "View mate region in split screen" command works perfectly...

I am attaching a screenshot of the region I used when the 1000G sample was loaded (chr12:25,404,399-25,405,863). I was using the same region before, when the command was not working. The only thing I changed was language/localization.

I hope this can be solved, it would be difficult to change the user language for everybody here :)

Thank you for your support

Andrea

[James Robinson]

Good information!   I'm pretty sure it's due to this code, the NumberFormat class is sensitive to localization.     I should be able to fix this.    If possible could you open a github issue at  https://github.com/igvteam/igv/issues?  You don't have to repeat everything just reference this thread.  

String startStr = NumberFormat.getInstance().format(s2);
String endStr = NumberFormat.getInstance().format(e2);
String mateLocus = mateChr + ":" + startStr + "-" + endStr;