self-expending | character during custom track configuration update

[Fabrice Darbellay]

Dear UCSC team,

I’m facing a new - started this wednesday - and highly mysterious issue with my sessions’ custom tracks.

Having not found any clear mention of this bug in any forums since a few days, I’m writing to you to hopefully get some inputs.

Situation is the following. 

Upon updating (Edit configuration) a couple of custom bedGraph tracks from a session - a session saved and on daily use since some years, working absolutely fine so far - I noticed the spontaneous appearance of a “|" character at the end of the updated configuration lane:

exemple:

track type=bedGraph name='isl2_invd13Z_norm (all smoothed windows - 11 fragments per window)' description='Isl2_norm (all smoothed windows - 11 fragments per window - region excluded=chr2:74073237-74078047)' visibility=full windowingFunction=maximum|

the original bedGraph header uploaded in USCS is the following:
track type=bedGraph name='Isl2_norm (all smoothed windows - 11 fragments per window)' description='Isl2_norm (all smoothed windows - 11 fragments per window - region excluded=chr2:74073237-74078047)' visibility=full windowingFunction=maximum

this seems to results in this error message upon visualization of the session o/ the genome (mm10 in my case)

• hui::wiggleWindowingStringToEnum() - Unknown option maximum|

now, the funny fact. I understand I have to get rid of this |, but I can't. 

I delete it from the Edit configuration lane, update the thing, and this guy is back again. 

Even more mysterious to me, I observe it incrementing everytime I update the configuration track without deleting it

exemple:

track type=bedGraph name=‘isl2_invd13Z_norm' visibility=full windowingFunction=maximum||

I never had this sort of bug in the past years, never used this | character in my bedGraph file configuration and moreover, this “|” character appeared systematically since a couple of days at the end of each of my tracks' configuration lane, in a couple of my sessions check so far. Interestingly these sessions are working great so far. I’m just wondering whether updating this configuration file is not messing up the whole thing…

I can share this session with you in case my explanations are not precise enough. I’m using your great tools and I never got such a mysterious event.

Best regards and many thanks for your valuable work,

Fabrice Darbellay

PhD student

Duboule Lab

EPFL - Switzerland

[Fabrice Darbellay]

Dear UCSC team,

Following my earlier email and after a couple of simple tests, I can now report a more educated description of this | (pipe) character self extension phenomen.

What I observe is the following.

Upon Submitting a configuration file from any custom tracks (Update Custome Track menu -  Edit configuration )an | character will be systematically added, 

If the configuration file already contains a I, an additional I character will be nevertheless added, resulting in an error message when trying to visualise the track in the browser.

• hui::wiggleWindowingStringToEnum() - Unknown option ...|

I hope this can be of some use for the community.

Best regards

Fabrice

In details, here is what I found:

a. starting situation when opening Edit configuration menu

track type=bedGraph name='isl2_invd13Z_norm (all smoothed windows - 11 fragments per window)' windowingFunction=maximum|

b. name edited to:

track type=bedGraph name='isl2' windowingFunction=maximum|

pushed Submit

c. error message when trying to visualise the track

• hui::wiggleWindowingStringToEnum() - Unknown option maximum|

d. reopen the Edit configuration menu, observed the following:

track type=bedGraph name='isl2' windowingFunction=maximum||

e. pushed Submit (no modification at all)

f. reopen the Edit configuration menu, observed the following:

track type=bedGraph name='isl2' windowingFunction=maximum||I

g. delete the III characters, pushed Submit 

h. can visualise again the track with the browser

i. reopen the Edit configuration menu, observed the following:

track type=bedGraph name='isl2' windowingFunction=maximum|

[Brian Lee]

Dear Fabrice,

Thank you for using the UCSC Genome Browser and alerting us to this issue.

Your input helped us determine the source of this concerning problem, which has now been fixed on our public site. Please let us know if you continue to see issues.

Thank you again for your inquiry and helping improve the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genomics Institute

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