VCFX/.gitignore at main · ieeta-pt/VCFX · GitHub

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# Build directories
build/
bin/
site/

# Data directory (except README)
data/*
!data/README.md

# IDE-specific files
.vscode/
.idea/

# Compiled object files
*.o
*.obj

# Compiled dynamic libraries
*.so
*.dylib
*.dll

# Compiled static libraries
*.a
*.lib

# Executables
*.exe
*.out

# CMake generated files
CMakeCache.txt
CMakeFiles/
cmake_install.cmake
build*/Makefile

# OS-specific files
.DS_Store
Thumbs.db

# Other
tools.md
prompt.md
names.md
VCFX_Optimization_Guide.md

# Temporary outputs from genotype_query tests
tests/tmp/genotype_query/
tests/data/genotype_query/missing_malformed.vcf
tests/data/genotype_query/multi_sample.vcf
tests/data/genotype_query/single_sample.vcf
tests/expected/genotype_query/missing_malformed_01.vcf
tests/expected/genotype_query/multi_11_flexible.vcf
tests/expected/genotype_query/multi_11_strict.vcf
tests/expected/genotype_query/multi_12_flexible.vcf
tests/expected/genotype_query/no_match.vcf
tests/expected/genotype_query/single_sample_flex_01.vcf
tests/expected/genotype_query/single_sample_strict_01.vcf

# General temporary test output directories
tests/tmp/
tests/out/
tmp/
# Python tooling caches
.mypy_cache/
.ruff_cache/
python/VERSION
__pycache__/

# Benchmark artifacts
benchmarks/data/
benchmarks/results/
benchmarks/tasks.mk
benchmarks/results.csv
benchmarks/*.png
benchmarks/*.pdf
benchmarks/*.csv
benchmarks/*.log
benchmarks/*.md
benchmarks/out.log
benchmarks/harness_small.mk
benchmarks/tasks_small.mk
benchmarks/tasks_small.yaml
benchmarks/scripts/*.py
!benchmarks/scripts/run_task.sh
!benchmarks/scripts/run_task_detailed.sh

# Benchmark plotting scripts (temporary)
benchmarks/create_*.py
benchmarks/generate_*.py

!benchmarks/Makefile
!benchmarks/harness.mk
!benchmarks/mk_tasks.py

# Python build artifacts
python/dist/
python/*.egg-info/
*.egg-info/
dist/

# Testing artifacts
Testing/
validation_report.txt
tasks.mk
benchmark_progress.log

# Compressed test files (generated)
tests/data/*.vcf.gz