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

[fedarko]

From @fedarko on May 22, 2017 17:52

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.

Copied from original issue: fedarko/MetagenomeScope#190

[fedarko]

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]

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

[fedarko]

For reading CIGAR strings, see this documentation.