├── .gitignore ├── .travis.yml ├── LICENSE ├── Makefile.am ├── README.md ├── TODO ├── autogen.sh ├── configure.ac ├── scripts ├── find_blocks.py ├── plot_painting.py ├── summarise_contigs.py └── summarise_species.py ├── src ├── Makefile.am ├── counter │ ├── command_line_options.cpp │ ├── command_line_options.h │ ├── count.cpp │ ├── count.h │ ├── main.cpp │ ├── output.cpp │ └── output.h ├── lib │ ├── common.cpp │ ├── common.h │ ├── database.cpp │ ├── database.h │ ├── genome.cpp │ ├── genome.h │ ├── kmer.cpp │ ├── kmer.h │ └── kseq.h ├── merger │ ├── command_line_options.cpp │ ├── command_line_options.h │ ├── file.cpp │ ├── file.h │ ├── main.cpp │ ├── merge.cpp │ ├── merge.h │ ├── output.cpp │ ├── output.h │ ├── probability.cpp │ └── probability.h └── painter │ ├── command_line_options.cpp │ ├── command_line_options.h │ ├── main.cpp │ ├── output.cpp │ ├── output.h │ ├── paint.cpp │ └── paint.h └── tests ├── Makefile.am ├── catch.hpp ├── run_tests.cpp └── test_kmer_encoding.cpp 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