├── .gitignore ├── .gitmodules ├── BloomfilterFiller.hpp ├── FastaSplitter.hpp ├── FastqSplitter.hpp ├── KmerBuilder.hpp ├── LICENSE ├── Makefile ├── README.md ├── ReadAnalyzer.hpp ├── ReadOutput.hpp ├── _config.yml ├── argument_parser.hpp ├── bloomfilter.h ├── common.hpp ├── example ├── ENSG00000277117.fa ├── ENSG00000277117.truth.ssv ├── sample_1.fq ├── sample_2.fq ├── sharked.sample_1.truth.fq └── sharked.sample_2.truth.fq ├── kmer_utils.hpp ├── kseq.h ├── main.cpp ├── small_vector.hpp └── xxhash.hpp /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlgoLab/shark/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AlgoLab/shark/HEAD/.gitmodules -------------------------------------------------------------------------------- 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