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graph-genome / graph_summarization

Browser for Graph Genomes built with VG based on Graph Summarization to provide semantic zoom. As a user zooms in on a graph genome, the topology becomes more complex. Provides visualization for variation within a species of plant or animal. Designed to scale up to thousands of specimens and provide useful visualizations.
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#13: Add Inversion support for DAGify method #17

Closed 6br closed 4 years ago

6br commented 5 years ago

This pull request is successor of #9, and I modified the original implementation to support inversion.

  1. Inverted nodes are aligned the same slice.
  2. Slice has "NodeTraversal" to store the strand of node.
6br commented 5 years ago

Inversion in DAGify have many breaking change on graph.py to support inversion (i.e. "-" strand on slices). If you don't prefer these changes, then please add comments.

josiahseaman commented 5 years ago

@6br Did you still want this merged with master or is the work not done yet? I noticed it currently has conflicts. I apologize if I'm the one that created those conflicts with master.

6br commented 5 years ago

I will fix the conflicts. I think I have done my implementation, but is it okay if Slice has "NodeTraversal" instead of "Node" to store the strand of nodes?

josiahseaman commented 5 years ago

Thank you @6br. Since the Django DB update has been merged now, it'll take some extra work to update this. I'm glad you're using NodeTraversal. That was the correct decision. I recommend you bring the current master into your branch as resolve the conflicts there.

josiahseaman commented 5 years ago

I'm looking through the changes in this branch and I think it'll definitely depend on the changes I'm working on in i23_halpo_db. The good news is I think we can get rid of Slices entirely. The GFA tests are already passing in my branch. Slices are still useful for test data, which I think we can replace with Django Fixtures These can be saved as files and slightly separated from code. They're also going to be more maintainable because it's just a saved database state.

How about I figure out how to handle the objects and you figure out what the core concept changed for directed DAGify LCS will be, then we'll followup the changes in i23_haplo_db?