Could not modify insertion flag threshold from alignment preferences tab.

[Rahim Rajwani]

Hi !

When I change threshold to flag insertion on the alignment tab from preferences window, nothing changes on preview. Moreover, when I close and reopen the preferences window again threshold is restored to default. However, the changes on the general tab (such as background color change) are applied instantly.

Any guess what is wrong here?

Insertions appears as purple colored I by default. I just want to hide them.

Highly appreciate your guidance. Thanks.

[Jim Robinson]

Hi Rahim,

What you tired should work, so this is an IGV bug.  I will open a git issue for it and investigate.

Jim

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/a2e1d37d-802e-417e-b69d-4c7b0eb13912%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Jim Robinson]

Hi,

At last I think we have a solution for you.  There are 2 new options in the "snapshot" build,  

(1) hide indels < a base pair threshold,

(2) hide indels < a screen pixel size

The second option allows you to hide indels when zoomed out,  but still see them if you zoom in.   To access this option download IGV from http://software.broadinstitute.org/software/igv/download_snapshot.   Select "View > Preferences > Alignments tab and look for

Note that the development snapshot build is made available to gather feedback and refine features before final release, as such it is subject to change.  We welcome your feedback.

[Jim Robinson]

Yes, thanks for the tweaks.   I thought we would keep both options there for a while and see what feedback we get.   If "pixel size" is too hard to understand we might re-word the option to avoid saying "pixel".

That preferences form is a monster,  some day I might replace it with something easier to maintain, even it it is ugly for the end user.

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/0c8f473d-754e-458d-8332-a0146c13748c%40googlegroups.com.