wiki: add concise assembly-baked damage section
wiki: clean up Methods-and-Model
docs: fix mismatch spectrum order
wiki: fix SCG statement - typically single-copy, not definitionally
wiki: fix broken links, drop bacar/SupCon, fix InfoNCE description
- Replace [[#anchor]] and {#anchor} with standard markdown anchors
- Fix cross-page anchor links (Methods-and-Model#assembly-damage-artifact)
- Fix [[README|Home#installation]] — Home has no installation section
- Correct InfoNCE: SCG markers are hard negatives, not positive pairs
- Remove SCG-SupCon loss section
- Replace bacar_marker.hmm with checkm_markers_only.hmm (206 markers)
- Update marker count 107→206 in formula and prose
- Remove --hmm flag from examples (auto-detected)
deconvolve: assembled sequence is wrong; no-modern-reads works; polish vs deconvolve comparison
methods: assembly damage artifact — suppression scaling table, encoder feature explanation, deconvolve fix
assembly damage artifact: explain baked-in damage + document amber polish
docs: remove sslib/dslib claim from mismatch spectrum description
docs: fix three feature dimension errors caught by code audit (mismatch spectrum, CGR layout, damage coverage)
docs: humanize Methods prose, fix em dash overuse and inline bold headers
docs: credit COMEBin baseline, frame AMBER as extension not replacement
docs: add loss formula, fix encoder row, expand resolve math
- README: show full SCG-SupCon loss with damage weights inline; fix
encoder feature table row; add p_cobin formula for resolve section
- Methods wiki: add LaTeX p_cobin formula + explain per-pair denominator
rationale; add resolve reproducibility note (3 runs → 10 HQ core,
≥5 runs → borderline bins accumulate evidence)
docs: add SCG-SupCon and internal C++ quality estimation
- README: rename section to SCG-supervised damage-aware contrastive
learning; explain P(i) = aug_views ∪ SCG co-members; 6 augmented views
- Methods wiki: full SCG-SupCon loss derivation with positive set
definition, exclusion mask, 6-view augmentation, damage weighting
- Methods wiki: new internal quality estimation section — 107-marker
C++ SCG engine, completeness/contamination formulae, dup_excess
definition; clarify CheckM2 is post-hoc only, not called during binning
production-ready repo: README, wiki, cmake refactor, CPU build path
- CMakeLists.txt: rename target amber_gpu→amber, AMBER_USE_TORCH default OFF,
split CORE vs TORCH sources, git version detection, install target, CTest
- cmake/version.h.in: git-based version header
- include/amber/config.hpp: VERSION from generated version.h
- src/bin2/encoder/damage_aware_infonce.h: move DamageProfile/DamageAccumulator
outside #ifdef USE_LIBTORCH (pure C++ structs, no LibTorch dependency)
- src/cli/cmd_bin_stub.cpp: amber bin error with CPU/GPU build instructions
- src/algorithms/damage_extraction_stub.cpp: amber damage stub when TORCH=OFF
- README.md: comprehensive with math overview, install paths, benchmarks, citation
- wiki/: Home, Methods-and-Model, aDNA-Features, Command-Reference,
Output-Formats, Quick-Start-Tutorial, Benchmarks, _Sidebar
- .github/workflows/ci.yml + release.yml: CI and tag-triggered releases
- conda_recipe/meta.yaml: Bioconda recipe skeleton
- environment.yml: dev environment
- .gitignore: fix 'amber' → '/amber' (was excluding include/amber/ directory)
- polish.cpp, strain_deconvolution.h: --write-modern-bam + deconv stats
- Snakefile: assemble_s17_modern rule, deconvolve modern_bam output