Anton Korobeynikov

In GFA format to augment existing graph from external sources

Provide better UI for paths

9

* Model around GAF format: list all paths, some paths queries (like in #4) * Maybe join with BLAST hits and their paths @ekg I started to draft better UI...

Currently assembly graphs holds bunch of data structures with custom colors, styles, etc. It should be generalized and centralized.

Refactor error handling

1

Currently error handling is mix-and-match of different things: exceptions are thrown, error strings are returned, etc. Make uniform error handling.

Currently every node stores both incoming and outgoing edges. This doubles the memory required for edge storage, but more importantly, makes inefficient node-edge queries (e.g. we need to filter stuff...

[RFC] Load graphs and paths in 'vg' format

2

@ekg Do you think it will be useful?

Revamp the documentation

2

Update the docs from original Bandage wiki. Adding descriptions of new things, etc.

Examples would include: * minimap2 * hmmer * some gene calling (prodigal, maybe something else)

Support path annotations

1

@ekg Will it be possible for you to draft requirement here? Something more specific than just "use coordinates along the path", if anything?

When graph is reloaded we might end with stale annotations