├── .dockerignore ├── .gitignore ├── .gitmodules ├── API_ALIGN.md ├── CHANGES.md ├── CONFIG.md ├── Dockerfile ├── EXAMPLE.md ├── HAP_MERGING.md ├── NATIVE_INSTALL.md ├── README.md ├── Snakefile ├── files ├── docker │ ├── build_deps.sh │ ├── build_home.sh │ └── run ├── example │ ├── assemblies.tsv │ └── config.json ├── run_scripts │ └── runlocal.sh └── tracks │ ├── alignment_track_fields.tsv │ └── variant_track_fields.tsv ├── img └── logo │ ├── PAVLogo_Full.png │ ├── PAVLogo_Full.svg │ ├── PAVLogo_Icon.png │ └── PAVLogo_Icon.svg ├── pavlib ├── __init__.py ├── align │ ├── __init__.py │ ├── align.py │ ├── lift.py │ └── trim.py ├── asmstat.py ├── call.py ├── cigarcall.py ├── constants.py ├── density.py ├── inv.py ├── lgsv.py ├── pipeline.py ├── plot.py ├── seq.py ├── util.py └── vcf.py ├── profiles └── default │ └── config.yaml ├── rules ├── align.snakefile ├── call.snakefile ├── call_inv.snakefile ├── call_lg.snakefile ├── data.snakefile ├── definitions.snakefile ├── figures.snakefile ├── 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