SnHiC Output Directory Structure

When you run SnHiCPipeline.run(), the following directory structure is created:


output_dir/
├── cells/
│   ├── cell_001/
│   │   ├── aligned/        (sorted BAM)
│   │   ├── pairs/          (filtered .pairs.gz)
│   │   └── matrices/       (per-cell .cool)
│   └── cell_002/
│       └── ...
├── pseudobulk/
│   ├── pseudobulk.cool
│   └── pseudobulk.mcool
├── clustering/
│   ├── cell_bin_matrix.csv
│   ├── embeddings.npy
│   └── predictions.csv
└── qc/
    ├── cell_qc_summary.txt
    └── passing_cells.txt