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Rename the augref module and feature throughout vg to "graph reference"
(gref) for clearer terminology:
- Rename src/augref.{hpp,cpp} -> src/gref.{hpp,cpp} (header guard
VG_AUGREF_HPP_INCLUDED -> VG_GREF_HPP_INCLUDED).
- Class AugRefCover -> GrefCover, all members and methods (e.g.
make_augref_name -> make_gref_name, is_augref_name -> is_gref_name,
set/get_augref_sample -> set/get_gref_sample, write_augref_segments
-> write_gref_segments, augref_intervals/augref_sample_name/
base_path_augref_counter -> gref_*).
- Update #includes in graph_caller.{hpp,cpp}, paths_main.cpp,
call_main.cpp, and deconstruct_main.cpp.
- vg paths CLI: --compute-augref/--min-augref-len/--augref-sample/
--augref-segs -> --compute-gref/--min-gref-len/--gref-sample/
--gref-segs; matching local variables and the OPT_AUGREF_SEGMENTS
enum value.
- Help text, log tags ("[augref]" -> "[gref]"), and comments updated to
say "graph reference" / "gref".
- Update test/t/11_vg_paths.t, 18_vg_call.t, 26_deconstruct.t to use
the new flag and file names.
The "_alt" path-name suffix is unchanged (it identifies graph reference
fragments in the graph data on disk and stays the same). The "augmented
graph" wording in call_main.cpp's file header refers to the unrelated
"vg augment" feature and is also unchanged.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Rename the augref module and feature throughout vg to "graph reference" (gref) to be a bit simpler (in the process of harmonizing with cactus and various writeups). Proper documentation in vg still pending, but interface hopefully close to final.
Changelog Entry
To be copied to the draft changelog by merger:
Description