# Human Genome Visualization - Git Ignore Rules

# === LARGE FILES (>40MB) - NEVER COMMIT ===
# All zip files larger than 40MB (40,000 KB) - EXCLUDE ALL
*.zip
# Re-include small zip files if needed (but generally avoid)
!*.zip
# Exclude all large archives
*.tar.gz
*.tgz
*.7z
*.rar
*.bz2

# === GENOME DATA FILES (large, not our property) ===
# Genome sequence files
data/
*.fasta
*.fasta.gz
*.fa
*.fa.gz
*.fastq
*.fastq.gz
*.gb
*.gbk
*.genbank
*.gff
*.gff3
*.gtf
*.vcf
*.vcf.gz
*.bcf
*.sam
*.bam
*.bam.bai
*.cram
*.bigwig
*.bigbed
*.2bit
*.maf
*.hal

# NCBI dataset downloads and directories
ncbi_dataset/
*_genome.zip
*_genome/
day2-ecoli.zip
ncbi_dataset_wuhan*.zip
advanced-spiral-8*.zip

# === COMPILED BINARIES AND BUILD ARTIFACTS ===
*.dll
*.so
*.dylib
*.pyd
*.exe
dna_engine.dll
dna_engine_v2.dll
dna_engine_v3.dll
fasta_dna_unified_v1.exe
build/
dist/
*.egg-info/
*.whl

# === LARGE DATA FILES (>100MB should never be committed) ===
# Any file larger than 100MB
*.bam
*.sam
*.vcf
*.bcf
*.cram
*.bigwig
*.bigbed
*.fastq
*.fasta
# Temporary data files
*.tmp
*.temp
*.cache
*.log

# === PYTHON AND DEVELOPMENT ===
# Python bytecode
__pycache__/
*.py[cod]
*$py.class
*.pyc
.Python
pip-log.txt
pip-delete-this-directory.txt

# IDE and editor files
.vscode/
.idea/
*.swp
*.swo
*~
.project
.pydevproject
.settings/

# OS generated files
.DS_Store
.DS_Store?
._*
.Spotlight-V100
.Trashes
ehthumbs.db
Thumbs.db
desktop.ini

# === TESTING AND OUTPUT ===
# Test outputs and screenshots
test_output/
screenshots/
*.png
*.jpg
*.jpeg
*.gif
*.svg
frames/
mapping_results/
spiral_output.csv
spiral_output_bench.csv
test_results.json

# === BACKUP AND TEMPORARY ===
*.bak
*.backup
*.orig
*.rej
*~

# === SPECIFIC LARGE FILES IN THIS PROJECT ===
# Exclude any existing large zip files
*.zip
# Exclude data directories
bigG/
fudge10/
hdgl_analog_v30_c_so/
hdgl_harmonics_spiral10000_analog_v30/
micro-bot-digest/
tcc/

# === ENVIRONMENT AND SENSITIVE DATA ===
.env
.venv/
env/
ENV/
venv/
.conda/
conda-env/