├── .gitignore ├── .gitmodules ├── .travis.yml ├── AUTHORS ├── CMakeLists.txt ├── LICENSE ├── MANIFEST.in ├── README.md ├── cobs ├── CMakeLists.txt ├── construction │ ├── classic_index.cpp │ ├── classic_index.hpp │ ├── compact_index.cpp │ └── compact_index.hpp ├── cortex_file.hpp ├── document_list.cpp ├── document_list.hpp ├── fasta_file.hpp ├── fasta_multifile.cpp ├── fasta_multifile.hpp ├── fastq_file.hpp ├── file │ ├── classic_index_header.cpp │ ├── classic_index_header.hpp │ ├── compact_index_header.cpp │ ├── compact_index_header.hpp │ ├── file_io_exception.hpp │ ├── header.hpp │ ├── kmer_buffer_header.cpp │ └── kmer_buffer_header.hpp ├── kmer.cpp ├── kmer.hpp ├── kmer_buffer.hpp ├── query │ ├── classic_index │ │ ├── mmap_search_file.cpp │ │ ├── mmap_search_file.hpp │ │ ├── search_file.cpp │ │ └── search_file.hpp │ ├── classic_search.cpp │ ├── classic_search.hpp │ ├── compact_index │ │ ├── aio_search_file.cpp │ │ ├── aio_search_file.hpp │ │ ├── mmap_search_file.cpp │ │ ├── mmap_search_file.hpp │ │ ├── search_file.cpp │ │ └── search_file.hpp │ ├── index_file.hpp │ └── search.hpp ├── settings.cpp ├── settings.hpp ├── text_file.hpp └── util │ ├── aio.cpp │ ├── aio.hpp │ ├── calc_signature_size.cpp │ ├── calc_signature_size.hpp │ ├── error_handling.cpp │ ├── error_handling.hpp │ ├── file.hpp │ ├── fs.hpp │ ├── misc.cpp │ ├── misc.hpp │ ├── parallel_for.cpp │ ├── parallel_for.hpp │ ├── process_file_batches.hpp │ ├── query.cpp │ ├── query.hpp │ ├── serialization.hpp │ ├── thread_object_array.hpp │ ├── timer.cpp │ ├── timer.hpp │ ├── zip_stream.cpp │ ├── zip_stream.hpp │ └── zip_stream_fwd.hpp ├── misc ├── format │ ├── analyze-source.pl │ └── uncrustify.cfg ├── mkdocs.sh └── python-wheels │ └── manylinux_x86_64.sh ├── python ├── CMakeLists.txt ├── cobs ├── docs │ ├── Makefile │ ├── _static │ │ └── cobs-index-architecture.png │ ├── cobs_index.rst │ ├── conf.py │ ├── index.rst │ ├── make.bat │ └── tutorial.rst ├── module.cpp ├── notes.md └── tests │ ├── __init__.py │ └── test_cobs_index.py ├── setup.py ├── src ├── CMakeLists.txt └── cobs.cpp └── tests ├── CMakeLists.txt ├── classic_index_construction.cpp ├── classic_index_query.cpp ├── compact_index_construction.cpp ├── compact_index_query.cpp ├── cortex_file.cpp ├── data ├── cortex │ ├── document.ctx │ ├── document_sorted.txt │ ├── sample1-k15.ctx │ ├── sample1-k15.txt │ ├── sample1-k19.ctx │ ├── sample1-k19.txt │ ├── sample1-k31.ctx │ └── sample1-k31.txt ├── fasta │ ├── sample1.fasta │ ├── sample2.fasta │ ├── sample3.fasta.gz │ ├── sample4.fasta │ ├── sample5.fasta │ ├── sample6.fasta │ └── sample7.fasta.gz ├── fasta_files.list ├── fasta_multi │ ├── sample1.mfasta │ └── sample2.mfasta ├── fastq │ ├── sample1.fastq │ ├── sample2.fastq.gz │ └── sample3.fastq └── text │ ├── sample1.txt │ └── sample2.txt ├── fasta_file.cpp ├── fasta_multifile.cpp ├── fastq_file.cpp ├── file.cpp ├── parameters.cpp ├── test_util.hpp ├── text_file.cpp └── util.cpp /.gitignore: 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