Tags: vgteam/vg
Tags
Rename augmented reference (augref) to graph reference (gref)
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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