Gene Annotations

[josiahseaman]

Showing Gene Annotations in an ODGI Matrix is a critical use case, but what that would even mean requires some thought. A single gene entry is not guaranteed to be entirely contiguous because different individuals can disagree on ordering of nodes.

Use Cases:

1. Choose one gene, generate a subgraph matrix for that one gene
2. Choose a region according to REF path.
3. Union of all available annotations into one track for pangenome

In both cases:

• Pull in neighboring loci nodes
• Sort optimally for this local area
• Fragments of an annotation sorted into a distant x value will still have a clickable link back to the main body. This is good, though it's better if it never comes up.
• Variation nodes inside of a gene annotation will be unannotated, but it should be clear from context the annotation is relevant.

Rendering Annotations

• Tubemap does not have any intrinsic support for annotations
• Each feature could be treated like a read, able to start and stop within nodes. Unfortunately, we're already making reads work double time.
• Single canonical annotation is easiest to think about though only 90% honest
• Best if we could piggyback synchronization on another browser that already renders annotation tracks
  • Requires expanding coordinate frame dynamically depending on pan-genome coordinate sizes
  • Could generate a new annotation track mapped to pan-genome coordinates to display in JBrowse