wiki: add concise assembly-baked damage section
7fc6666
wiki: clean up Methods-and-Model
2d6c9b9
docs: fix min-length default to 1001
44953ad
docs: fix mismatch spectrum order
f4a3be6
wiki: fix SCG statement - typically single-copy, not definitionally
2458ae4
wiki: fix median contamination statistics
51eb961
wiki: update COMEBin benchmarks (all 9 HQ bins) + fix image format
7d8640b
architecture: fix CSS variables for rsvg-convert compatibility
5997138
architecture: vertical spine design with floating islands (AlphaFold-style)
71035b4
architecture: redesigned with OpenCode - cleaner ML-paper style
3dd3729
architecture: refined pipeline diagram with parallel runs + resolve flow
3b88c35
wiki: aDNA→InfoNCE weights + concat; CGR bypass only
c749554
wiki: show 3 parallel runs → resolve consensus flow
ab73a6c
wiki: fix diagram alignment, correct AMBER name, clarify InfoNCE and CGR
2f8f614
wiki: publication-quality architecture diagram with clean layout
4887a76
wiki: simplify architecture diagram (high-level overview)
55c2a6e
wiki: add PNG and PDF versions of architecture diagram
d7b9764
wiki: add AMBER architecture diagram
396db94
benchmarks: COMEBin best 3 runs (8.3 HQ mean, range 8-9)
2272e75
benchmarks: HQ-only tables, trim COMEBin to top 3, remove deconvolution and dataset sections
b7191ff
benchmarks: add SemiBin2, remove DAS Tool; add per-bin table for SemiBin2
7cd6ac8
env: add hmmer to environment.yml (required for hmmsearch)
f2a374f
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)
4c06be2
docs: expand README with full methods + refs; drop bacar_marker.hmm
- README: correct InfoNCE description (SCG hard negatives, not positive
pairs), remove SCG-SupCon, fix HMM default to checkm_markers_only.hmm,
add 16 references (COMEBin, InfoNCE, Leiden, HNSW, CheckM, CheckM2,
MapDamage, MIMAG, MetaBAT2, SemiBin2, CGR, EM, Briggs)
- Remove auxiliary/bacar_marker.hmm (40 markers, replaced by
checkm_markers_only.hmm with 206 CheckM universal markers)
- Update --hmm defaults in cmd_bin.cpp, cmd_seeds.cpp, seed_generator.h
- Clean up bacar_marker comments in seed_generator.cpp
56ad573
fix CI: igraph 0.10.x uses flat includes (igraph.h not igraph/igraph.h)
9a4fd2e
cmake: add diagnostic messages for igraph paths
da8b054
cmake: fix igraph include path for cmake 3.31 (FetchContent_Populate deprecation)
Use target_include_directories with igraph_SOURCE_DIR/BINARY_DIR from
FetchContent_MakeAvailable, which is reliable on all cmake versions.
The old include_directories block depended on libleidenalg_SOURCE_DIR
set by deprecated FetchContent_Populate, which cmake 3.31 may not
propagate to parent scope.
4788e11
track missing source files: marker_index, bin_confidence, partition_consensus, quality_hierarchical
These were referenced in CMakeLists.txt and included by tracked headers
but never committed, causing CI to fail with 'Cannot find source file'.
cf513f4
remove amber polish: deconvolve supersedes it (37x more corrections)
- Delete cmd_polish.cpp, polish_engine.h
- Move run_deconvolver() from polish.cpp → deconvolve.cpp (no Torch dep)
- Remove --polish flag and all polish fields from amber bin / binner.cpp
- CPU-only build (AMBER_USE_TORCH=OFF) now works: deconvolve/chimera/resolve/seeds/damage all build without CUDA
142acca
deconvolve: assembled sequence is wrong; no-modern-reads works; polish vs deconvolve comparison
1ca61f1