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Change to PanSN "scaffolds" with colon and dash coordinate ranges #97

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This changes the notation for subpaths, and adds some queries related to "scaffolds" that paths are on.

It also eliminates phase blocks. We are going to use possibly-fake coordinate ranges instead.

Problems:

  • Without phase blocks in the name you can't tell if a name is a haplotype name or a reference name by looking at it. We might need to add the list-of-reference-samples mechanic to PackedGraph and friends, or some other way to store the bit.
  • I have non-path-metadata-related code for parsing and dealing with a region type. But the region is just another way of parsing out the subpath from the rest of the name. Maybe some of that can/should belong to PathMetadata?
  • I'm not sure on the region accessors. I have one to get the region for a path in PathMetadata, but that means PathHandleGraph needs a path length query. Maybe the calls for working with regions need to be part of PathPositionHandleGraph, and I should have only scaffold-based calls on PathMetadata?
  • I don't actually have the get-path-step-at-these-scaffold-coordinates logic that we might need, or the see-if-step-is-in-region-set logic we would need for surject or rGFA.

@adamnovak adamnovak marked this pull request as draft April 12, 2024 22:14
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