├── COPYING ├── HiNT ├── .runhint.py.swp ├── ArgsValidator.py ├── BPsummarization.py ├── DoRegressionAllchroms.py ├── HiCprocessingPip.py ├── __init__.py ├── __pycache__ │ ├── ArgsValidator.cpython-36.pyc │ ├── __init__.cpython-36.pyc │ ├── corelib.cpython-36.pyc │ └── runhint.cpython-36.pyc ├── coolToMatrix.py ├── corelib.py ├── diff.py ├── doBICseq.py ├── externalScripts │ ├── .Rapp.history │ ├── extract_nonHiC.pl │ ├── generate_site_positions.py │ ├── getBreakPoints2steps.R │ └── plot.l2r.ms_zoom.R ├── getBPfromChimericReads.py ├── getGenomeRowSumsFromCool.py ├── getGenomeRowSumsFromHiC.py ├── getRankProduct.py ├── getRoughBreakpoints.py ├── hicToMatrix.py ├── prepare_regression.py ├── read_hic_header.py ├── runhint.py ├── straw.py └── straw.pyc ├── LICENSE ├── MANIFEST.in ├── README.md ├── bin └── hint ├── images └── HiNT_workflow.png ├── requirements.txt └── setup.py /COPYING: -------------------------------------------------------------------------------- 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