├── .gitignore ├── .gitmodules ├── CondaEnvironment_linux.yml ├── CondaEnvironment_osx.yml ├── LICENSE.md ├── README.md ├── Snakemakes └── ErrorCorrect │ ├── README.md │ ├── Snakefile │ └── config.yaml ├── makefile ├── scripts └── gfa_string_to_int.py ├── src ├── Aligner.cpp ├── Aligner.h ├── AlignerMain.cpp ├── AlignmentGraph.cpp ├── AlignmentGraph.h ├── AlignmentSelection.cpp ├── AlignmentSelection.h ├── ArrayPriorityQueue.h ├── BigraphToDigraph.cpp ├── BigraphToDigraph.h ├── CommonUtils.cpp ├── CommonUtils.h ├── ComponentPriorityQueue.h ├── DNAString.cpp ├── DNAString.h ├── DiploidHeuristic.cpp ├── DiploidHeuristic.h ├── EValue.cpp ├── EValue.h ├── GfaGraph.cpp ├── GfaGraph.h ├── GraphAligner.h ├── GraphAlignerBitvectorBanded.h ├── GraphAlignerBitvectorCommon.h ├── GraphAlignerCommon.h ├── GraphAlignerGAFAlignment.h ├── GraphAlignerVGAlignment.h ├── GraphAlignerWrapper.cpp ├── GraphAlignerWrapper.h ├── MEMSeeder.cpp ├── MEMSeeder.h ├── MinimizerSeeder.cpp ├── MinimizerSeeder.h ├── 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