├── .github └── workflows │ └── test_on_push.yml ├── .gitignore ├── CMakeLists.txt ├── LICENSE ├── README.md ├── data ├── LPA.subset.fa └── chm13#chr20_36805939-36807738.fa ├── scripts ├── denovo_repeat_annotation.py └── paf2dotplot └── src ├── align ├── align.cpp └── include │ ├── align_parameters.hpp │ ├── align_types.hpp │ ├── computeAlignments.hpp │ └── parseCmdArgs.hpp ├── common ├── args.hxx ├── argvparser.hpp ├── atomic_queue │ ├── atomic_queue.h │ ├── atomic_queue_mutex.h │ ├── barrier.h │ ├── cpu_base_frequency.h │ ├── defs.h │ ├── huge_pages.h │ ├── moodycamel.h │ └── spinlock.h ├── edlib.h ├── edlib.hxx ├── filesystem.hpp ├── gzstream.h ├── kseq.h ├── memcpyLink.h ├── murmur3.h ├── prettyprint.hpp ├── progress.hpp ├── seqiter.hpp ├── sparsehash │ ├── dense_hash_map │ ├── dense_hash_set │ ├── internal │ │ ├── densehashtable.h │ │ ├── hashtable-common.h │ │ ├── libc_allocator_with_realloc.h │ │ └── sparsehashtable.h │ ├── sparse_hash_map │ ├── sparse_hash_set │ ├── sparsetable │ └── traits └── wflign │ ├── .gitignore │ ├── CMakeLists.txt │ ├── LICENSE │ ├── README.md │ ├── deps │ ├── WFA │ │ ├── LICENSE │ │ ├── README.md │ │ ├── VERSION │ │ ├── benchmark │ │ │ ├── benchmark_edit.c │ │ │ ├── benchmark_edit.h │ │ │ ├── benchmark_gap_affine.c │ │ │ ├── benchmark_gap_affine.h │ │ │ ├── benchmark_gap_lineal.c │ │ │ ├── benchmark_gap_lineal.h │ │ │ ├── benchmark_utils.c │ │ │ └── benchmark_utils.h │ │ ├── edit │ │ │ ├── edit_cigar.c │ │ │ ├── edit_cigar.h │ │ │ ├── edit_dp.c │ │ │ ├── edit_dp.h │ │ │ ├── edit_table.c │ │ │ └── edit_table.h │ │ ├── gap_affine │ │ │ ├── affine_penalties.c │ │ │ ├── affine_penalties.h │ │ │ ├── affine_table.c │ │ │ ├── affine_table.h │ │ │ ├── affine_wavefront.c │ │ │ ├── affine_wavefront.h │ │ │ ├── affine_wavefront_align.c │ │ │ ├── affine_wavefront_align.h │ │ │ ├── affine_wavefront_backtrace.c │ │ │ ├── affine_wavefront_backtrace.h │ │ │ ├── affine_wavefront_display.c │ │ │ ├── affine_wavefront_display.h │ │ │ ├── affine_wavefront_extend.c │ │ │ ├── affine_wavefront_extend.h │ │ │ ├── affine_wavefront_penalties.c │ │ │ ├── affine_wavefront_penalties.h │ │ │ ├── affine_wavefront_reduction.c │ │ │ ├── affine_wavefront_reduction.h │ │ │ ├── affine_wavefront_utils.c │ │ │ ├── affine_wavefront_utils.h │ │ │ ├── swg.c │ │ │ ├── swg.h │ │ │ ├── wavefront_stats.c │ │ │ └── wavefront_stats.h │ │ ├── gap_lineal │ │ │ ├── lineal_penalties.h │ │ │ ├── nw.c │ │ │ └── nw.h │ │ ├── system │ │ │ ├── mm_allocator.c │ │ │ ├── mm_allocator.h │ │ │ ├── profiler_counter.c │ │ │ ├── profiler_counter.h │ │ │ ├── profiler_timer.c │ │ │ └── profiler_timer.h │ │ ├── tools │ │ │ ├── align_benchmark.c │ │ │ ├── examples │ │ │ │ ├── compile.examples.sh │ │ │ │ ├── wfa_adapt.c │ │ │ │ ├── wfa_basic.c │ │ │ │ └── wfa_repeated.c │ │ │ └── generate_dataset.c │ │ └── utils │ │ │ ├── commons.c │ │ │ ├── commons.h │ │ │ ├── dna_text.c │ │ │ ├── dna_text.h │ │ │ ├── string_padded.c │ │ │ ├── string_padded.h │ │ │ ├── vector.c │ │ │ └── vector.h │ ├── edlib │ │ ├── .github │ │ │ └── ISSUE_TEMPLATE │ │ │ │ └── bug_report.md │ │ ├── .gitignore │ │ ├── .travis.yml │ │ ├── CMakeLists.txt │ │ ├── Dockerfile │ │ ├── Doxyfile │ │ ├── LICENSE │ │ ├── README.md │ │ ├── apps │ │ │ ├── aligner │ │ │ │ ├── aligner.cpp │ │ │ │ └── test_data │ │ │ │ │ ├── query.fasta │ │ │ │ │ └── target.fasta │ │ │ └── hello-world │ │ │ │ └── helloWorld.c │ │ ├── appveyor.yml │ │ ├── bindings │ │ │ └── python │ │ │ │ ├── .gitignore │ │ │ │ ├── MANIFEST.in │ │ │ │ ├── README-tmpl.rst │ │ │ │ ├── README.md │ │ │ │ ├── cedlib.pxd │ │ │ │ ├── edlib.pyx │ │ │ │ ├── performance.py │ │ │ │ ├── setup.py │ │ │ │ └── test.py │ │ ├── edlib-config.cmake.in │ │ ├── edlib.pc.in │ │ ├── edlib │ │ │ ├── include │ │ │ │ └── edlib.h │ │ │ └── src │ │ │ │ └── edlib.cpp │ │ ├── images │ │ │ └── edlib-aligner-screenshot.png │ │ └── meson.build │ ├── patchmap │ │ ├── LICENSE │ │ ├── README.md │ │ ├── hashed_array_tree.hpp │ │ ├── patchmap.hpp │ │ ├── patchmap_interleaved.hpp │ │ ├── patchmap_v0.hpp │ │ └── sparse_patchmap.hpp │ └── wflambda │ │ ├── CMakeLists.txt │ │ ├── LICENSE │ │ ├── README.md │ │ ├── VERSION │ │ ├── benchmark │ │ ├── benchmark_edit.cpp │ │ ├── benchmark_edit.hpp │ │ ├── benchmark_gap_affine.cpp │ │ ├── benchmark_gap_affine.hpp │ │ ├── benchmark_gap_lineal.cpp │ │ ├── benchmark_gap_lineal.hpp │ │ ├── benchmark_utils.cpp │ │ └── benchmark_utils.hpp │ │ ├── edit │ │ ├── edit_cigar.cpp │ │ ├── edit_cigar.hpp │ │ ├── edit_dp.cpp │ │ ├── edit_dp.hpp │ │ ├── edit_table.cpp │ │ └── edit_table.hpp │ │ ├── gap_affine │ │ ├── affine_penalties.cpp │ │ ├── affine_penalties.hpp │ │ ├── affine_table.cpp │ │ ├── affine_table.hpp │ │ ├── affine_wavefront.cpp │ │ ├── affine_wavefront.hpp │ │ ├── affine_wavefront_align.cpp │ │ ├── affine_wavefront_align.hpp │ │ ├── affine_wavefront_backtrace.cpp │ │ ├── affine_wavefront_backtrace.hpp │ │ ├── affine_wavefront_display.cpp │ │ ├── affine_wavefront_display.hpp │ │ ├── affine_wavefront_extend.cpp │ │ ├── affine_wavefront_extend.hpp │ │ ├── affine_wavefront_penalties.cpp │ │ ├── affine_wavefront_penalties.hpp │ │ ├── affine_wavefront_reduction.cpp │ │ ├── affine_wavefront_reduction.hpp │ │ ├── affine_wavefront_utils.cpp │ │ ├── affine_wavefront_utils.hpp │ │ ├── swg.cpp │ │ ├── swg.hpp │ │ ├── wavefront_stats.cpp │ │ └── wavefront_stats.hpp │ │ ├── gap_lineal │ │ ├── lineal_penalties.hpp │ │ ├── nw.cpp │ │ └── nw.hpp │ │ ├── system │ │ ├── mm_allocator.cpp │ │ ├── mm_allocator.hpp │ │ ├── profiler_counter.cpp │ │ ├── profiler_counter.hpp │ │ ├── profiler_timer.cpp │ │ └── profiler_timer.hpp │ │ ├── tools │ │ ├── align_benchmark.cpp │ │ ├── examples │ │ │ ├── compile.examples.sh │ │ │ ├── wfa_adapt.cpp │ │ │ ├── wfa_basic.cpp │ │ │ └── wfa_repeated.cpp │ │ └── generate_dataset.cpp │ │ └── utils │ │ ├── commons.cpp │ │ ├── commons.hpp │ │ ├── dna_text.cpp │ │ ├── dna_text.hpp │ │ ├── string_padded.cpp │ │ ├── string_padded.hpp │ │ ├── vector.cpp │ │ └── 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