[WIP] Alt path cover #4804
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[WIP] Alt path cover #4804
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- Add src/altpaths.hpp and src/altpaths.cpp with AltPathsCover class
- Naming scheme: {reference_path}_alt{N} (e.g., GRCh38#chrY_alt1)
- CLI: vg paths -Q <prefix> --compute-altpaths [--min-altpath-len N]
- Add integration tests to test/t/11_vg_paths.t
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This is a revival of the now ancient #4113, but instead of using weird gymnastics to keep subpath intervals (a ala rgfa), it simply adds the new contigs to the existing linear reference they're derived from, leaves them REFERENCE sense, and adds a little suffix.
The cover is still computed in
vg paths.vg callandvg deconstructare now changed to work with these (optinonally).There's still some work before merging, most importantly: