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  • 03:13
    cmdcolin opened #48
  • 03:12
    cmdcolin commented #36
  • 03:12

    cmdcolin on master

    Add failing test case and fix f… (compare)

  • 03:12
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  • Aug 22 07:48
    cmdcolin opened #36
  • Aug 22 07:47

    cmdcolin on fix_incorrect_chunk_merge

    Add failing test case and fix f… (compare)

  • Aug 22 07:44

    cmdcolin on fix_incorrect_chunk_merge

    Add failing test case and fix f… (compare)

  • Aug 21 21:58
    cmdcolin commented #1288
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    cmdcolin commented #1288
Colin Diesh
@cmdcolin
so if you truly need the specific bin sizes
then you will need to write custom code
Colin Diesh
@cmdcolin
here is a sketch of how you could try and start approaching this
instead of just specifying urlTemplates in the config, you can make an array in the config called customScales, and each element of the array is an object with urlTemplates, and then when you receive a getFeatures query, it gets an object called basesPerSpan which could correspond roughly to which zoom level you want to access
Arijit Panda
@arpanda
@cmdcolin Thanks for your reply. I will go through the documents and let you know if I can write the code for the configuration or not.
Colin Diesh
@cmdcolin
@arpanda sounds good. Please see https://jbrowse.org/docs/faq.html#how-do-i-modify-jbrowse-source-code for how you can get started with modifying jbrowse source code
which includes plugins
just run yarn watch in a command line window in the background while you modify the source code and then you can just refresh the browser and get your code changes like normal
JHibbard
@JHibbard
When programmatically controlling a JBrowser embedded in an iframe, can you change the "loc" without reloading the browser? I wrapped an iframe/embedded jbrowser in a React component and am passing down new urls as props, but changing the url causes the embedded browser to reload.
I'm trying to link JBrowser views / charts in a dashboard. The goal is to be able to modify either the JBrowser or a chart and trigger an update in the other.
Colin Diesh
@cmdcolin
@JHibbard if you get a ref e.g. with useRefto the iframe, then you can access some jbrowse internals I think
See
That link doesn't answer it directly
But it shows usage of the JBrowse global variable
Which you can call functions o
You could call JBrowse.navigateToLocation({ref,start,end}) I think
Colin Diesh
@cmdcolin
There are several different types of navigation functions depending on whether you want to search the enerate-names.pl index or not...can look at jbrowse's Browser.js if you want to dive deep(the JBrowse global variable in the iframe will be an instance of the Browser.js class)
JHibbard
@JHibbard
@cmdcolin Thanks! This is very helpful, I have it working now. Is there a good place in the documentation or wiki detailing these types of JS functions for development? There's a lot of pages between the wiki and docs (which is not a complaint!) just not sure where best to poke around.
Colin Diesh
@cmdcolin
Nice. Unfortunately, there is no real guide-to-the-source-code or API type docs
I made the FAQ some years ago to just try to brain dump lots of random ideas and answer hypotheticals
But it's not really any API documentation
And it's sort of true that the documentation was exploded into many different pages...I have been a little concerned about that, it used to be a single page wiki
(it actually is still available as the single page wiki just a little out of date)
Scott Cain
@scottcain
yah, I kind of like it on a single wiki page too :-/
JHibbard
@JHibbard
@cmdcolin Gotcha, it's so easy for that to happen for a long running project. I'll try to poke around the source/FAQ then, hopefully I won't need to bug the channel with too many questions on my quest to wrap JBrowse in a state management lib. :S
Colin Diesh
@cmdcolin
no worry :)
Colin Diesh
@cmdcolin
Scott Cain
@scottcain
@cmdcolin I’m writing Ahmet back
Colin Diesh
@cmdcolin
okey
unclear whether samples are tracks or different data folders
or what the requirements are lol
MeiyueWang
@MeiyueWang
Hi, I got error message " unable to load jbrowse.conf status:0" when I tried to open my Jbrowse. Is there something wrong with my web server?
image.png
Colin Diesh
@cmdcolin
She
Sorry posting on mobile. There status 0 write generally mean CORS errors. Can you check the javascript console/devtools for console messages
MeiyueWang
@MeiyueWang
Thank you a lot! We have solved this problem. Someone downloaded a lot of data from my JBrowse which makes jbrowse.conf blocked by the firewall. Can I make some settings not allow people to download track data from my Jbrowse?
JHibbard
@JHibbard

If you are programmatically controlling an iframe embedded JBrowse with JS, what's the best way to safely allow the outer page to control it? I'm getting:

"Blocked a frame with origin <fill-in-orgin-here> from accessing a cross-origin frame."

Colin Diesh
@cmdcolin
@JHibbard if the iframe is actually on another origin it might not be possible
@JHibbard if the iframe is on just a subdomain e.g. jbrowse.yoursite.org, which you view from a diff subdomainthen you can maybe set documentDomain=yoursite.org in the jbrowse.conf
JHibbard
@JHibbard
@cmdcolin Thanks! It would be very convenient to have jbrowse run on a different domain, but if that's not possible with the embedded JBrowse do you have a feel for "how buggy" embedding directly into a div is? I remember someone on chat saying it was difficult but not elaborating much.
Scott Cain
@scottcain
@JHibbard I did this as a quick mock up for a presentation I was giving last year: http://scottca.in/node/6 It has several JBrowse instances on a single page all in their own divs.
(Be sure to check out the worm div on the bottom of the page where you can flip the div so that the gene is in the same orientation as the other genes—obviously I just did that for fun :-)
If you wanted to change the view of any of these divs, you could just update the innerHTML of the named div that holds the instance, but that would require a complete redraw of the div (but hopefully not the whole page) so it would take a few seconds.
JHibbard
@JHibbard
@scottcain This is great, do you have a github link for the example? I'm excited to try this out :P
Scott Cain
@scottcain
Not really; I coded that page up by hand, but I can create a gist that shows a few divs worth of html and js.
Scott Cain
@scottcain
Here’s a gist for human and mouse from that page: https://gist.github.com/scottcain/aa99e669845a309b095eb00d2a9c771d
Scott Cain
@scottcain
It seems that I've run into some sort of security thing in safari that doesn't happen in chrome or firefox. I wanted to create a page that would load several views of JBrowse so that I could check that all of the data are present and rendering properly, so I have this: http://scottca.in/node/8. In chrome this loads just fine (if a little slow, but I am asking a lot of the browser). In safari, it loads much of what I expect, but then towards the bottom, it loads a jbrowse window but stops drawing tracks. The error message is "SecurityError: Attempt to use history.replaceState() more than 100 times per 30.000000 seconds". It's not a big deal--I can use other browsers. I just spent some time trying to figure out what I did wrong, rather than looking at at the console to see the error message. Anyway, I thought it was interesting.
Not surprisingly, Safari also gave me a warning message that this page was using a significant amount of memory and closing it might help my browser performance. No kidding.