craft/.gitignore at main · FullLengthFanatic/craft · GitHub

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# Python
__pycache__/
*.py[cod]
*.egg-info/
*.egg
build/
dist/
.eggs/
.tox/
.pytest_cache/
.ruff_cache/
.coverage
.coverage.*
htmlcov/

# Virtual environments
.venv/
venv/
env/
ENV/

# Editors
.vscode/
.idea/
*.swp
*~

# OS
.DS_Store
Thumbs.db

# Bioinformatics data
*.bam
*.bai
*.sam
*.cram
*.crai
*.fa
*.fa.gz
*.fasta
*.fasta.gz
*.fai
*.gtf
*.gtf.gz
*.gff
*.gff3
*.bed
*.bed.gz
*.vcf
*.vcf.gz
*.tbi
*.h5
*.h5ad
*.mtx
*.mtx.gz

# Notebooks
.ipynb_checkpoints/

# Local run outputs
out/
output/
results/

# CRAFT outputs
per_isoform.tsv
per_isoform.json
report.html
annotated.h5ad
craft_out*/

# Benchmark caches (regenerable from run_bench*.py)
benchmarks/cache/

# External tool binaries (download from upstream)
.tools/

# Reference papers (local reading copies; not redistributable)
papers/