Skip to content
This repository has been archived by the owner on Sep 12, 2018. It is now read-only.

Visualize overlap attributes of edges (resolve ambiguities in GFA/LastGraph files) #190

Closed
fedarko opened this issue May 22, 2017 · 4 comments
Closed

Visualize overlap attributes of edges (resolve ambiguities in GFA/LastGraph files) #190

fedarko opened this issue May 22, 2017 · 4 comments
Assignees
@fedarko
Labels
highpriorityfeature

Comments

@fedarko
Copy link
Owner

fedarko commented May 22, 2017 •
edited
Loading

It's important that this is taken into account in at least some fashion.

GML
A negative mean attribute of an edge indicates overlap.

GFA
We should be able to use CIGAR strings for links in order to determine overlap.

Perhaps we could (at least temporarily) indicate overlap edges as dotted or dashed edges. Ideally we'd actually overlay nodes visually, but I'm not sure how to reconcile that with GraphViz' layout parameters.
@fedarko fedarko self-assigned this May 22, 2017
fedarko added a commit that referenced this issue May 22, 2017
@fedarko
Highlight non-overlapping GML edges (#190)
15bab6c 
Since it seems like the vast majority of edges in at least the
GML assembly graphs I'm working with now are overlaps, I figure using
the fancy option for non-overlapping edges is a more efficient
approach (and sort of makes sense if you think of non-overlapping
edges as "fragmented", I guess?).

Work remains to be done here to make this make sense for GFA and
LastGraph files. See #190 for more info.
@fedarko fedarko changed the title Visualize overlap attributes of edges Visualize overlap attributes of edges (resolve ambiguities in GFA/LastGraph files) May 22, 2017
@fedarko
Copy link
Owner Author

fedarko commented May 22, 2017

TODOs:

  • GFA support (read CIGAR string in the preprocessing step, and store that info in the .db file)
  • Ensure that this doesn't produce ambiguities in LastGraph files (since overlap data doesn't seem to be given for those graphs, make sure that the user knows that solid edges in that case don't mean overlaps)

@fedarko
Copy link
Owner Author

fedarko commented May 22, 2017

Look into collapsing overlapping nodes. And if that wouldn't be possible then figure out something else

@fedarko
Copy link
Owner Author

fedarko commented May 30, 2017

For reading CIGAR strings, see this documentation.

@fedarko fedarko mentioned this issue Jun 8, 2017
Closed
@fedarko fedarko mentioned this issue Aug 9, 2017
Open
@fedarko
Copy link
Owner Author

fedarko commented Aug 9, 2017

This issue was moved to marbl/MetagenomeScope#47

@fedarko fedarko closed this as completed Aug 9, 2017
Sign up for free to subscribe to this conversation on GitHub. Already have an account? Sign in.
Assignees

@fedarko fedarko

Labels
highpriorityfeature
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@fedarko