Gfa paths

[asl]

This PR provides an experimental support to load paths from GFA. One could then draw the graph along these paths (e.g. in SPAdes cases these are the scaffolds).

[ekg]

Could this be merged?

It's very useful.

[ekg]

@rrwick would it be better if we forked Bandage for future development?

[rlorigro]

I would also benefit quite a lot from being able to visualize paths, and I know several others in my lab would too.

[asl]

I went ahead and made a fork: https://github.com/asl/Bandage
Also, qt6 branch contains port to qt6.

[rlorigro]

Cool, thanks. I am running into a couple issues when attempting to build on Ubuntu 20, using the qmake recipe from the Readme.

I have resolved the first issue, which was actually on the main branch, and this link summarizes the issue and the working solution:
https://stackoverflow.com/a/52841306/5095925

The second issue is that when I switch to your gfa-paths branch, I am getting QT namespace-related errors, and I don't know if I can fix this on my own:

ui/mygraphicsview.cpp: In member function ‘QPointF MyGraphicsView::findIntersectionWithViewportBoundary(QLineF)’:
ui/mygraphicsview.cpp:243:14: error: ‘class QLineF’ has no member named ‘intersects’; did you mean ‘intersect’?
  243 |     if (line.intersects(boundary1, &intersection) == QLineF::BoundedIntersection)
      |              ^~~~~~~~~~
      |              intersect

It seems to suggest that references are being made to functions that come from a different version of qt? Here is nearly the same issue on stackoverflow again:
therecipe/qt#750

[ekg]

@asl you should merge your gfa-paths changes into master on the fork. I'll be happy to contribute some powerups, for path position queries in particular. CC @AndreaGuarracino

[asl]

@rlorigro gfa-paths branch is still with "old" qt5. I will need to find some time to merge everything together :)

[rlorigro]

Hmm ok. I think it's actually not related to qt6, if that's what you mean

[asl]

It does. intersects is deprecated in Qt5 and was removed from Qt6. Everything else depends on the exact version of Qt + additional flags. See asl@03892ef

[rlorigro]

I guess I am confused because I am attempting to build with QT_SELECT=5, and the issue i referenced (therecipe/qt#750) seems to indicate that it is an error involving the qt5 library itself.

[rlorigro]

The issue may be that Ubuntu20.04 uses qt 5.12: https://packages.ubuntu.com/focal/qtbase5-dev so I guess I will try upgrading

[asl]

So, I went ahead and merged everything into 'dev' branch of https://github.com/asl/Bandage repo. Now with GFA paths and Qt6.

[ekg]

IMO you should merge this into your master and post a static binary release. I'll publicize the fork and the path features. These will be helpful to existing users of Bandage.

…

On Fri, Sep 10, 2021, 10:31 Anton Korobeynikov ***@***.***> wrote: So, I went ahead and merged everything into 'dev' branch of https://github.com/asl/Bandage repo. Now with GFA paths and Qt6. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#64 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABDQEMPZOS7TGLNWUVBOMLUBG65TANCNFSM4E6A7PWA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[asl]

The 'dev' branch is default in the fork to emphasize the status (note that it includes several commits and bugfixes from 'development' branch of rrwick/bandage that are absent from master). I do not have bandwidth to do any binary releases, etc. so feel free to contribute :)

[ekg]

Totally understand! Thanks for the patch. I'll look into what's needed for a static build. If it's push button would you be able to post it? Or you can add me as a collaborator on your repo.

…

On Fri, Sep 10, 2021, 11:37 Anton Korobeynikov ***@***.***> wrote: The 'dev' branch is default in the fork to emphasize the status (note that it includes several commits and bugfixes from 'development' branch of rrwick/bandage that are absent from master). I do not have bandwidth to do any binary releases, etc. so feel free to contribute :) — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#64 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABDQEJEC3OMA4PL62AXPL3UBHGULANCNFSM4E6A7PWA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[asl]

Closing as the project is not going to update anymore. Those who need paths might use https://github.com/asl/Bandage/ instead