├── .idea ├── .gitignore ├── HiCAT.iml ├── inspectionProfiles │ └── profiles_settings.xml ├── misc.xml ├── modules.xml └── vcs.xml ├── HiCAT.py ├── HiCAT_HOR.py ├── HiCAT_manuscript_results ├── AT │ ├── 1 │ │ ├── out_all_layer.xls │ │ ├── out_hor.normal.fa │ │ ├── out_hor.raw.fa │ │ ├── out_monomer.fa │ │ ├── out_top_layer.xls │ │ ├── pattern_static.pdf │ │ ├── pattern_static.xls │ │ ├── plot_pattern.pdf │ │ └── sort_statistics.xls │ ├── 2 │ │ ├── out_all_layer.xls │ │ ├── out_hor.normal.fa │ │ ├── out_hor.raw.fa │ │ ├── out_monomer.fa │ │ ├── out_top_layer.xls │ │ ├── pattern_static.pdf │ │ ├── pattern_static.xls │ │ ├── plot_pattern.pdf │ │ └── sort_statistics.xls │ ├── 3 │ │ ├── out_all_layer.xls │ │ ├── out_hor.normal.fa │ │ ├── out_hor.raw.fa │ │ ├── out_monomer.fa │ │ ├── out_top_layer.xls │ │ ├── pattern_static.pdf │ │ ├── pattern_static.xls │ │ ├── plot_pattern.pdf │ │ └── sort_statistics.xls │ ├── 4 │ │ ├── out_all_layer.xls │ │ ├── out_hor.normal.fa │ │ ├── out_hor.raw.fa │ │ ├── out_monomer.fa │ │ ├── out_top_layer.xls │ │ ├── pattern_static.pdf │ │ ├── pattern_static.xls │ │ ├── plot_pattern.pdf │ │ └── sort_statistics.xls │ └── 5 │ │ ├── out_all_layer.xls │ │ ├── out_hor.normal.fa │ │ ├── out_hor.raw.fa │ │ ├── out_monomer.fa │ │ ├── out_top_layer.xls │ │ ├── pattern_static.pdf │ │ ├── pattern_static.xls │ │ ├── plot_pattern.pdf │ │ └── sort_statistics.xls └── human │ ├── 1 │ ├── out_all_layer.xls │ ├── out_hor.normal.fa │ ├── out_hor.raw.fa │ ├── out_monomer.fa │ ├── out_top_layer.xls │ ├── pattern_static.pdf │ ├── pattern_static.xls │ ├── plot_pattern.pdf │ └── sort_statistics.xls │ ├── 2 │ ├── out_all_layer.xls │ ├── out_hor.normal.fa │ ├── out_hor.raw.fa │ ├── out_monomer.fa │ ├── out_top_layer.xls │ ├── pattern_static.pdf │ ├── pattern_static.xls │ ├── plot_pattern.pdf │ └── sort_statistics.xls │ ├── 3 │ ├── out_all_layer.xls │ ├── out_hor.normal.fa │ ├── out_hor.raw.fa │ ├── out_monomer.fa │ ├── out_top_layer.xls │ ├── pattern_static.pdf │ ├── pattern_static.xls │ ├── plot_pattern.pdf │ └── sort_statistics.xls │ ├── 4 │ ├── out_all_layer.xls │ ├── out_hor.normal.fa │ ├── out_hor.raw.fa │ ├── out_monomer.fa │ ├── out_top_layer.xls │ ├── pattern_static.pdf │ ├── pattern_static.xls │ ├── plot_pattern.pdf │ └── sort_statistics.xls │ ├── 5 │ ├── out_all_layer.xls │ ├── out_hor.normal.fa │ ├── out_hor.raw.fa │ ├── out_monomer.fa │ ├── out_top_layer.xls │ ├── pattern_static.pdf │ ├── pattern_static.xls │ ├── plot_pattern.pdf │ └── sort_statistics.xls │ ├── 6 │ ├── out_all_layer.xls │ ├── out_hor.normal.fa │ ├── out_hor.raw.fa │ ├── out_monomer.fa │ ├── out_top_layer.xls │ ├── pattern_static.pdf │ ├── pattern_static.xls │ ├── plot_pattern.pdf │ └── sort_statistics.xls │ ├── 7 │ ├── out_all_layer.xls │ ├── out_hor.normal.fa │ ├── out_hor.raw.fa │ ├── out_monomer.fa │ ├── out_top_layer.xls │ ├── pattern_static.pdf │ ├── pattern_static.xls │ ├── plot_pattern.pdf │ └── sort_statistics.xls │ ├── 8 │ ├── out_all_layer.xls │ ├── out_hor.normal.fa │ ├── out_hor.raw.fa │ ├── out_monomer.fa │ ├── out_top_layer.xls │ ├── pattern_static.pdf │ ├── pattern_static.xls │ ├── plot_pattern.pdf │ └── sort_statistics.xls │ ├── 9 │ ├── out_all_layer.xls │ ├── out_hor.normal.fa │ ├── out_hor.raw.fa │ ├── out_monomer.fa │ ├── out_top_layer.xls │ ├── pattern_static.pdf │ ├── pattern_static.xls │ ├── plot_pattern.pdf │ └── sort_statistics.xls │ ├── 10 │ ├── out_all_layer.xls │ ├── out_hor.normal.fa │ ├── out_hor.raw.fa │ ├── out_monomer.fa │ ├── out_top_layer.xls │ ├── pattern_static.pdf │ ├── pattern_static.xls │ ├── plot_pattern.pdf │ └── sort_statistics.xls │ ├── 11 │ ├── out_all_layer.xls │ ├── out_hor.normal.fa │ ├── out_hor.raw.fa │ ├── out_monomer.fa │ ├── out_top_layer.xls │ ├── pattern_static.pdf │ ├── pattern_static.xls │ ├── plot_pattern.pdf │ └── sort_statistics.xls │ ├── 12 │ ├── out_all_layer.xls │ ├── out_hor.normal.fa │ ├── out_hor.raw.fa │ ├── out_monomer.fa │ ├── out_top_layer.xls │ ├── pattern_static.pdf │ ├── pattern_static.xls │ ├── plot_pattern.pdf │ └── sort_statistics.xls │ ├── 13 │ ├── out_all_layer.xls │ ├── out_hor.normal.fa │ ├── out_hor.raw.fa │ ├── out_monomer.fa │ ├── out_top_layer.xls │ ├── pattern_static.pdf │ ├── pattern_static.xls │ ├── plot_pattern.pdf │ └── sort_statistics.xls │ ├── 14 │ ├── out_all_layer.xls │ ├── out_hor.normal.fa │ ├── out_hor.raw.fa │ ├── out_monomer.fa │ ├── out_top_layer.xls │ ├── pattern_static.pdf │ ├── pattern_static.xls │ ├── plot_pattern.pdf │ └── sort_statistics.xls │ ├── 15 │ ├── out_all_layer.xls │ ├── out_hor.normal.fa │ ├── out_hor.raw.fa │ ├── out_monomer.fa │ ├── out_top_layer.xls │ ├── pattern_static.pdf │ ├── pattern_static.xls │ ├── plot_pattern.pdf │ └── sort_statistics.xls │ ├── 16 │ ├── out_all_layer.xls │ ├── out_hor.normal.fa │ ├── out_hor.raw.fa │ ├── out_monomer.fa │ ├── out_top_layer.xls │ ├── pattern_static.pdf │ ├── pattern_static.xls │ ├── plot_pattern.pdf │ └── sort_statistics.xls │ ├── 17 │ ├── out_all_layer.xls │ ├── out_hor.normal.fa │ ├── out_hor.raw.fa │ ├── out_monomer.fa │ ├── out_top_layer.xls │ ├── pattern_static.pdf │ ├── pattern_static.xls │ ├── plot_pattern.pdf │ └── sort_statistics.xls │ ├── 18 │ ├── out_all_layer.xls │ ├── out_hor.normal.fa │ ├── out_hor.raw.fa │ ├── out_monomer.fa │ ├── out_top_layer.xls │ ├── pattern_static.pdf │ ├── pattern_static.xls │ ├── plot_pattern.pdf │ └── sort_statistics.xls │ ├── 19 │ ├── out_all_layer.xls │ ├── out_hor.normal.fa │ ├── out_hor.raw.fa │ ├── out_monomer.fa │ ├── out_top_layer.xls │ ├── pattern_static.pdf │ ├── pattern_static.xls │ ├── plot_pattern.pdf │ └── sort_statistics.xls │ ├── 20 │ ├── out_all_layer.xls │ ├── out_hor.normal.fa │ ├── out_hor.raw.fa │ ├── out_monomer.fa │ ├── out_top_layer.xls │ ├── pattern_static.pdf │ ├── pattern_static.xls │ ├── plot_pattern.pdf │ └── sort_statistics.xls │ ├── 21 │ ├── out_all_layer.xls │ ├── out_hor.normal.fa │ ├── out_hor.raw.fa │ ├── out_monomer.fa │ ├── out_top_layer.xls │ ├── pattern_static.pdf │ ├── pattern_static.xls │ ├── plot_pattern.pdf │ └── sort_statistics.xls │ ├── 22 │ ├── out_all_layer.xls │ ├── out_hor.normal.fa │ ├── out_hor.raw.fa │ ├── out_monomer.fa │ ├── out_top_layer.xls │ ├── pattern_static.pdf │ ├── pattern_static.xls │ ├── plot_pattern.pdf │ └── sort_statistics.xls │ └── X │ ├── out_all_layer.xls │ ├── out_hor.normal.fa │ ├── out_hor.raw.fa │ ├── out_monomer.fa │ ├── out_top_layer.xls │ ├── pattern_static.pdf │ ├── pattern_static.xls │ ├── plot_pattern.pdf │ └── sort_statistics.xls ├── LICENSE ├── README.md ├── VERSION ├── environment.yaml ├── gb.png ├── getSingleSimilarityResult.py ├── install.sh ├── region_color.png ├── requirements.txt ├── simulation └── simulateHOR.py ├── stringdecomposer ├── Makefile ├── bin │ └── stringdecomposer └── stringdecomposer │ ├── __init__.py │ ├── __version__.py │ ├── main.py │ ├── models │ └── ont_logreg_model.txt │ ├── py │ ├── git.py │ └── standard_logger.py │ ├── src │ ├── edlib.cpp │ ├── edlib.h │ └── main.cpp │ └── test_data │ ├── DXZ1_star_monomers.fa │ ├── final_decomposition_fc89af8.tsv │ └── read.fa ├── testRunHiCAT.sh ├── testdata ├── AlphaSat.fa ├── cen21.fa ├── cen21.png └── cen21_moddotplot.bed └── visualization.py /.idea/.gitignore: -------------------------------------------------------------------------------- 1 | # Default ignored files 2 | /workspace.xml -------------------------------------------------------------------------------- /.idea/HiCAT.iml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xjtu-omics/HiCAT/HEAD/.idea/HiCAT.iml -------------------------------------------------------------------------------- /.idea/inspectionProfiles/profiles_settings.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xjtu-omics/HiCAT/HEAD/.idea/inspectionProfiles/profiles_settings.xml 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