Initial commit

.gitignore

@@ -0,0 +1,46 @@
+# Python and environments
+__pycache__/
+*.py[cod]
+.venv/
+env/
+.env
+.git-mcp/
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+.coverage
+
+# Notebooks
+.ipynb_checkpoints/
+
+# Editor
+.DS_Store
+.idea/
+.vscode/
+
+# Genomics data (avoid accidental commits)
+*.bam
+*.bai
+*.sam
+*.cram
+*.crai
+*.vcf
+*.vcf.gz
+*.vcf.gz.tbi
+*.g.vcf
+*.g.vcf.gz
+*.g.vcf.gz.tbi
+*.bed
+*.bed.gz
+*.bed.gz.tbi
+*.fastq
+*.fastq.gz
+*.fq
+*.fq.gz
+
+# Reports / tmp
+*.log
+*.tmp
+tmp/
+reports/
+runtime/