LICENSE
README.md
pyproject.toml
setup.py
src/gwas_pipeline/__init__.py
src/gwas_pipeline/__main__.py
src/gwas_pipeline/cli.py
src/gwas_pipeline/doctor.py
src/gwas_pipeline.egg-info/PKG-INFO
src/gwas_pipeline.egg-info/SOURCES.txt
src/gwas_pipeline.egg-info/dependency_links.txt
src/gwas_pipeline.egg-info/entry_points.txt
src/gwas_pipeline.egg-info/requires.txt
src/gwas_pipeline.egg-info/top_level.txt
src/gwas_pipeline/steps/__init__.py
src/gwas_pipeline/steps/step1_fastq_to_vcf.py
src/gwas_pipeline/steps/step2_gwas_analysis.py
src/gwas_pipeline/steps/step3_candidate_gene_extraction.py
src/gwas_pipeline/steps/step4_local_manhattan_ld.py
src/gwas_pipeline/steps/step5_amino_acid_mutation.py
src/gwas_pipeline/steps/step6_haplotype_analysis.py
src/gwas_pipeline/steps/step7_haplotype_network.py
src/gwas_pipeline/steps/step8_pi_tajima.py
src/gwas_pipeline/steps/step9_geo_visualization.py
tests/test_cli_smoke.py
tests/test_package_smoke.py