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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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I4 slices and paths #16

Closed josiahseaman closed 5 years ago

josiahseaman commented 5 years ago

4 Graph definition has been updated to Path based instead of Slice based definitions. All tests except for GFA to sliced graph working. I have not added in a full Slice definition yet. This should automatically merge, if it's not it's likely because I rebased to Simon's travis commits and it's just counting double. When merging just accept mine.

Toshiyuki, we should get our code fully merged together. Please use this as the basis for your topological sorts or DAG development. It looks like you've done a lot of great development, but it'll be extra work for you the longer we leave these concepts unmerged. In general, I found with GFA.from_graph() the code actually got much simpler when using a Graph definition that more closely matched XG and GFA. No slices, no problem.

6br commented 5 years ago

Josiah, I agree to merge our codes. To avoid any conflict due to the dependency of branches, I prefer to rebase the developing branch after this PR is merged into master. Also, I appreciate for your fast development!

6br commented 5 years ago

I reviewed codes and added several comments. Other lines look great to me!