├── .gitignore ├── LICENSE ├── README.md ├── logo ├── descriptive_diagram.svg ├── descriptive_diagram_correct.svg ├── descriptive_diagram_merge.svg ├── descriptive_diagram_patch.svg ├── descriptive_diagram_scaffold.svg ├── logo_banner.svg ├── ragtag_logo_small_1.0.svg ├── ragtag_logo_small_1.5.svg └── ragtag_logo_text.svg ├── ragtag.py ├── ragtag_agp2fa.py ├── ragtag_agpcheck.py ├── ragtag_asmstats.py ├── ragtag_break_query.py ├── ragtag_correct.py ├── ragtag_create_links.py ├── ragtag_delta2paf.py ├── ragtag_merge.py ├── ragtag_paf2delta.py ├── ragtag_patch.py ├── ragtag_rename.py ├── ragtag_scaffold.py ├── ragtag_splitasm.py ├── ragtag_stats.py ├── ragtag_update_gff.py ├── ragtag_utilities ├── AGPFile.py ├── Aligner.py ├── AlignmentReader.py ├── ContigAlignment.py ├── RestrictionFragmentMap.py ├── ScaffoldGraph.py ├── __init__.py └── utilities.py ├── setup.py └── tests ├── __init__.py └── integration_tests ├── .gitignore ├── run_run_tests.sh ├── run_tests.sh └── scripts ├── 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