# Build output
build/
build-*/
compile_commands.json

# Generated by cmake/embed_assets.cmake
**/generated/embedded_assets.cpp

# Benchmark and demo artefacts (regenerate with scripts/make_demo_data.py)
data/
results/
*.bam
*.bam.bai
*.cram
*.crai
*.bw
*.bigwig

# Locally built htslib (scripts/build_htslib_minimal.sh)
third_party/htslib-build/
third_party/htslib-install/

# LaTeX intermediates
docs/*.aux
docs/*.log
docs/*.out
docs/*.bbl
docs/*.blg
docs/*.synctex.gz
docs/*.fdb_latexmk
docs/*.fls

# Editor / OS
.vscode/
.idea/
.DS_Store
*.swp
