├── .github └── workflows │ └── cmake.yml ├── .gitignore ├── CMakeLists.txt ├── Doxyfile ├── LICENSE ├── README.md ├── boost-cmake ├── .gitignore ├── CMakeLists.txt ├── LICENSE.md ├── README.md ├── azure-pipelines.yml ├── build.sh ├── cmake │ ├── Modules │ │ ├── AddBoostLib.cmake │ │ ├── AddBoostTest.cmake │ │ ├── CheckBoostVersion.cmake │ │ ├── CheckPreprocessor.cmake │ │ ├── FindIconv.cmake │ │ ├── PlatformDetect.cmake │ │ ├── StandaloneBuild.cmake │ │ └── ccache.cmake │ └── Toolchains │ │ └── ios.cmake ├── libs │ ├── atomic.cmake │ ├── chrono.cmake │ ├── container.cmake │ ├── context.cmake │ ├── context │ │ ├── jump_combined.S │ │ ├── make_combined.S │ │ └── ontop_combined.S │ ├── coroutine.cmake │ ├── date_time.cmake │ ├── exception.cmake │ ├── fiber.cmake │ ├── filesystem.cmake │ ├── graph.cmake │ ├── graph_parallel.cmake │ ├── header.cmake │ ├── iostreams.cmake │ ├── locale.cmake │ ├── log.cmake │ ├── math.cmake │ ├── mpi.cmake │ ├── program_options.cmake │ ├── random.cmake │ ├── regex.cmake │ ├── serialization.cmake │ ├── system.cmake │ ├── test.cmake │ ├── thread.cmake │ ├── timer.cmake │ ├── type_erasure.cmake │ └── wave.cmake ├── patch │ └── 1.63.0 │ │ ├── context_0001_arm64_cpu.patch │ │ └── context_0002_macOS_execution_context.patch └── repack.sh ├── fast-lzma2 ├── .gitattributes ├── .gitignore ├── COPYING ├── LICENSE ├── Makefile ├── README.md ├── atomic.h ├── bench │ ├── Makefile │ ├── bench.c │ └── bench.vcxproj ├── build │ └── VS │ │ └── fast-lzma2.sln ├── compiler.h ├── count.h ├── data_block.h ├── dict_buffer.c ├── dict_buffer.h ├── dll │ ├── fast-lzma2.vcxproj │ └── fast-lzma2.vcxproj.filters ├── doc │ └── images │ │ └── bench_mt2.png ├── fast-lzma2.h ├── fastpos_table.h ├── fl2_common.c ├── fl2_compress.c ├── fl2_compress_internal.h ├── fl2_decompress.c ├── fl2_errors.h ├── fl2_internal.h ├── fl2_pool.c ├── fl2_pool.h ├── fl2_threading.c ├── fl2_threading.h ├── fuzzer │ ├── Makefile │ ├── datagen.c │ ├── datagen.h │ ├── fuzzer.c │ └── fuzzer.vcxproj ├── lzma2_dec.c ├── lzma2_dec.h ├── lzma2_enc.c ├── lzma2_enc.h ├── lzma_dec_x86_64.S ├── lzma_dec_x86_64.asm ├── mem.h ├── platform.h ├── radix_bitpack.c ├── radix_engine.h ├── radix_get.h ├── radix_internal.h ├── radix_mf.c ├── radix_mf.h ├── radix_struct.c ├── range_enc.c ├── range_enc.h ├── test │ ├── Makefile │ ├── file_test.c │ └── file_test.vcxproj ├── util.c ├── util.h ├── xxhash.c └── xxhash.h ├── include ├── AlignerTester.h ├── BBHashMap.h ├── BooPHF.h ├── Compressor.h ├── Consensus.h ├── ConsensusGraph.h ├── Contig.h ├── Decompressor.h ├── DirectoryUtils.h ├── Edits.h ├── OmpMutex.h ├── ReadAligner.h ├── ReadData.h ├── ReadFilter.h ├── StringAligner.h ├── Types.h ├── bsc_helper.h ├── dnaToBits.h ├── lzma2_helper.h └── testAligner.h ├── libbsc ├── adler32 │ ├── adler32.cpp │ └── adler32.h ├── bwt │ ├── bwt.cpp │ ├── bwt.h │ └── libsais │ │ ├── VERSION │ │ ├── libsais.c │ │ ├── libsais.h │ │ └── libsais_internal.h ├── coder │ ├── coder.cpp │ ├── coder.h │ ├── common │ │ ├── predictor.h │ │ ├── rangecoder.h │ │ └── tables.h │ └── qlfc │ │ ├── qlfc.cpp │ │ ├── qlfc.h │ │ ├── qlfc_model.cpp │ │ └── qlfc_model.h ├── filters.h ├── filters │ ├── detectors.cpp │ ├── preprocessing.cpp │ └── tables.h ├── libbsc.h ├── libbsc │ └── libbsc.cpp ├── lzp │ ├── lzp.cpp │ └── lzp.h ├── platform │ ├── platform.cpp │ └── platform.h └── st │ ├── st.cpp │ ├── st.cu │ ├── st.cuh │ └── st.h ├── logs ├── 2021 │ ├── 12x_coverage_experiment.log │ ├── banana.log │ ├── banana_converage_experiment.log │ ├── basecallers.log │ ├── chm13_75x.log │ ├── chm13_whole.log │ ├── ec_25x_filtered.log │ ├── hs1.log │ ├── hs2.log │ ├── hs2_edge_thr.log │ ├── hs2_minhash_k.log │ ├── hs2_minhash_nt.log │ ├── hs2_minimap2.log │ ├── hs2_renano.log │ ├── hs2_stage3_compressor.log │ ├── hs2_threads.log │ ├── hs3.log │ ├── hs3_minimap2.log │ ├── hs4.log │ ├── sa.log │ ├── sa_25x_filtereed.log │ ├── sa_renano.log │ ├── snail.log │ ├── zymo.log │ ├── zymo_minhash_k.log │ └── zymo_minhash_nt.log └── 2022 │ ├── banana.log │ ├── banana_coverage.log │ ├── chm13_coverage.log │ ├── gzip.log │ ├── hs1.log │ ├── hs2.log │ ├── hs2_compressor.log │ ├── hs2_edge_thr.log │ ├── hs2_minhash_k.log │ ├── hs2_minhash_nt.log │ ├── hs2_minimap.log │ ├── hs2_threads.log │ ├── hs3.log │ ├── hs3_minimap.log │ ├── hs4.log │ ├── new_zymo.log │ ├── sa.log │ ├── sa_basecall.log │ ├── snail.log │ ├── zymo.log │ ├── zymo_minhash_k.log │ └── zymo_minhash_nt.log ├── minimap2 ├── .gitignore ├── .gitmodules ├── .travis.yml ├── FAQ.md ├── LICENSE.txt ├── MANIFEST.in ├── Makefile ├── Makefile.simde ├── NEWS.md ├── README.md ├── align.c ├── bseq.c ├── bseq.h ├── chain.c ├── cookbook.md ├── esterr.c ├── example.c ├── format.c ├── hit.c ├── index.c ├── kalloc.c ├── kalloc.h ├── kdq.h ├── ketopt.h ├── khash.h ├── kseq.h ├── ksort.h ├── ksw2.h ├── ksw2_dispatch.c ├── ksw2_extd2_sse.c ├── ksw2_exts2_sse.c ├── ksw2_extz2_sse.c ├── ksw2_ll_sse.c ├── kthread.c ├── kthread.h ├── kvec.h ├── main.c ├── map.c ├── minimap.h ├── minimap2.1 ├── misc.c ├── misc │ ├── README.md │ └── paftools.js ├── mmpriv.h ├── options.c ├── pe.c ├── python │ ├── README.rst │ ├── cmappy.h │ ├── cmappy.pxd │ ├── mappy.pyx │ └── minimap2.py ├── sdust.c ├── sdust.h ├── setup.py ├── sketch.c ├── splitidx.c ├── sse2neon │ └── emmintrin.h ├── test │ ├── MT-human.fa │ ├── MT-orang.fa │ ├── q-inv.fa │ ├── q2.fa │ ├── t-inv.fa │ └── t2.fa └── tex │ ├── Makefile │ ├── bioinfo.cls │ ├── blasr-mc.eval │ ├── bowtie2-s3.sam.eval │ ├── bwa-s3.sam.eval │ ├── bwa.eval │ ├── eval2roc.pl │ ├── graphmap.eval │ ├── hs38-simu.sh │ ├── minialign.eval │ ├── minimap2.bib │ ├── minimap2.tex │ ├── mm2-s3.sam.eval │ ├── mm2.approx.eval │ ├── mm2.eval │ ├── natbib.bst │ ├── natbib.sty │ ├── ngmlr.eval │ ├── roc.gp │ └── snap-s3.sam.eval ├── src ├── AlignerTester.cpp ├── BBHashMap.cpp ├── Compressor.cpp ├── Consensus.cpp ├── ConsensusGraph.cpp ├── Contig.cpp ├── Decompressor.cpp ├── DirectoryUtils.cpp ├── Edits.cpp ├── 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