├── .gitignore ├── .travis.yml ├── LICENSE.md ├── README.md ├── docs ├── GettingStarted │ ├── index.rst │ ├── preprocessing.rst │ └── requirements.rst ├── Makefile ├── Project │ └── index.rst ├── PureCLIPTutorial │ ├── basicMode.rst │ ├── customCLmotifs.rst │ ├── faqs.rst │ ├── incorporateCLmotifs.rst │ ├── incorporateInput.rst │ ├── index.rst │ ├── output.rst │ └── userOptions.rst ├── SimulationFramework.rst ├── _static │ └── custom.css ├── _templates │ └── page.html ├── conf.py └── index.rst ├── pkg └── README ├── pkg_util └── pkg_check.py ├── src ├── ._.DS_Store ├── CMakeLists.txt ├── call_sites.h ├── call_sites_replicates.h ├── cmake │ ├── Boost.cmake │ ├── CMakeParseArguments.cmake │ ├── FindGSL.cmake │ ├── FindPackageHandleStandardArgs.cmake │ ├── FindPackageMessage.cmake │ └── SeqAn.cmake ├── density_functions.h ├── density_functions_crosslink.h ├── density_functions_crosslink_reg.h ├── density_functions_reg.h ├── hmm_1.h ├── parse_alignments.h ├── prepro_mle.h ├── pureclip.cpp 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