├── INSTALL ├── LICENSE ├── README.md ├── bin ├── RepeatHMM_scripts │ ├── UnsymmetricPairAlignment │ │ ├── Makefile │ │ ├── UnsymmetricPairAlignment.c │ │ ├── UnsymmetricPairAlignment.i │ │ ├── __init__.py │ │ └── setup.py │ ├── __init__.py │ ├── getAlignment.py │ ├── getTransition_start_emission_prob_x.py │ ├── myBAMhandler.py │ ├── myCommonFun.py │ ├── myFASTQhandler.py │ ├── myGaussianMixtureModel.py │ ├── myHMM.py │ ├── myPredefinedPatternReader.py │ ├── myRepeatReAlignment.py │ ├── myScanWholeGenome.py │ ├── mySetting.py │ ├── myheader.py │ └── printHMMmatrix.py ├── __init__.py ├── reference_sts │ ├── hg19 │ │ └── hg19.predefined.pa │ └── hg38 │ │ └── hg38.predefined.pa └── repeatHMM.py ├── docs ├── Help on results interpretation.md ├── Install.md └── Usage.md ├── environment.yml └── setup.py /INSTALL: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/RepeatHMM/HEAD/INSTALL 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