├── .gitignore ├── .gitmodules ├── LICENSE.txt ├── Makefile ├── README.md ├── marginAlign ├── marginCaller ├── marginStats ├── requirements.txt ├── scripts ├── __init__.py ├── bioio.py ├── createAssemblyHub ├── createAssemblyHub.py ├── faToTwoBit ├── identityPlots.R ├── kmerAnalysis.py ├── modifyHmm ├── mutateReference.py ├── substitution_plot.R ├── substitutions ├── substitutions.py ├── uniquifyFastq └── uniquifyFastq.py ├── src ├── executionScript.sh └── margin │ ├── __init__.py │ ├── mappers │ ├── __init__.py │ ├── abstractMapper.py │ ├── bwa.py │ ├── last.py │ ├── last_hmm_0.txt │ ├── last_hmm_20.txt │ ├── last_hmm_40.txt │ └── minimap2.py │ ├── marginAlign.py │ ├── marginAlignLib.py │ ├── marginCaller.py │ ├── marginCallerLib.py │ ├── marginStats.py │ └── utils.py ├── submodules ├── Makefile └── README.txt └── tests ├── input.hmm ├── input.sam ├── inputBigMutations.sam ├── inputBigMutationsBwa.sam ├── inputBigMutationsLast.sam ├── lessReads.fq ├── mutations.txt ├── reads.fq ├── 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