├── .clang-format ├── .drone.yml ├── .drone.yml.sig ├── .drone ├── build.sh ├── copy_build.sh └── test_map.sh ├── .gitignore ├── .vscode └── c_cpp_properties.json ├── CMakeLists.txt ├── License.md ├── README.md ├── TestingScripts └── python │ └── ComputeSyntheticStats.py ├── cmake ├── Modules │ ├── FindCereal.cmake │ ├── FindJellyfish.cmake │ ├── FindJemalloc.cmake │ ├── FindSSE.cmake │ └── FindTcmalloc.cmake ├── TestQuasiMap.cmake └── TestQuasiMapPerfectHash.cmake ├── current_version.txt ├── external ├── libdivsufsort.tar.gz └── libdivsufsort.zip ├── include ├── BooMap.hpp ├── BooPHF.hpp ├── Const.hpp ├── EnumCoder.hpp ├── FastxParser.hpp ├── FastxParserThreadUtils.hpp ├── FrugalBooMap.hpp ├── HitManager.hpp ├── IndexHeader.hpp ├── JFRaw.hpp ├── Kmer.hpp ├── PairAlignmentFormatter.hpp ├── PairSequenceParser.hpp ├── RapMapConfig.hpp ├── RapMapFileSystem.hpp ├── RapMapIndex.hpp ├── RapMapSAIndex.hpp ├── RapMapUtils.hpp ├── SACollector.hpp ├── SASearcher.hpp ├── ScopedTimer.hpp ├── SelectiveAlignmentUtils.hpp ├── SingleAlignmentFormatter.hpp ├── SparseHashSerializer.hpp ├── SpinLock.hpp ├── Type.hpp ├── Util.hpp ├── bar.h ├── bit_array.h ├── bit_macros.h ├── btree │ ├── btree.h │ ├── btree_container.h │ └── btree_map.h ├── chobo │ └── small_vector.hpp ├── concurrentqueue.h ├── digestpp │ ├── algorithm │ │ ├── blake.hpp │ │ ├── blake2.hpp │ │ ├── detail │ │ │ ├── blake2_provider.hpp │ │ │ ├── blake_provider.hpp │ │ │ ├── constants │ │ │ │ ├── blake2_constants.hpp │ │ │ │ ├── blake_constants.hpp │ │ │ │ ├── groestl_constants.hpp │ │ │ │ ├── jh_constants.hpp │ │ │ │ ├── kupyna_constants.hpp │ │ │ │ ├── md5_constants.hpp │ │ │ │ ├── sha1_constants.hpp │ │ │ │ ├── sha2_constants.hpp │ │ │ │ ├── sha3_constants.hpp │ │ │ │ ├── skein_constants.hpp │ │ │ │ ├── streebog_constants.hpp │ │ │ │ └── whirlpool_constants.hpp │ │ │ ├── groestl_provider.hpp │ │ │ ├── jh_provider.hpp │ │ │ ├── k12m14_provider.hpp │ │ │ ├── kmac_provider.hpp │ │ │ ├── kupyna_provider.hpp │ │ │ ├── md5_provider.hpp │ │ │ ├── sha1_provider.hpp │ │ │ ├── sha2_provider.hpp │ │ │ ├── sha3_provider.hpp │ │ │ ├── shake_provider.hpp │ │ │ ├── skein_provider.hpp │ │ │ ├── sm3_provider.hpp │ │ │ ├── streebog_provider.hpp │ │ │ └── whirlpool_provider.hpp │ │ ├── groestl.hpp │ │ ├── jh.hpp │ │ ├── k12m14.hpp │ │ ├── kmac.hpp │ │ ├── kupyna.hpp │ │ ├── md5.hpp │ │ ├── mixin │ │ │ ├── blake2_mixin.hpp │ │ │ ├── blake_mixin.hpp │ │ │ ├── cshake_mixin.hpp │ │ │ ├── k12m14_mixin.hpp │ │ │ ├── kmac_mixin.hpp │ │ │ ├── null_mixin.hpp │ │ │ └── skein_mixin.hpp │ │ ├── sha1.hpp │ │ ├── sha2.hpp │ │ ├── sha3.hpp │ │ ├── shake.hpp │ │ ├── skein.hpp │ │ ├── sm3.hpp │ │ ├── streebog.hpp │ │ └── whirlpool.hpp │ ├── detail │ │ ├── absorb_data.hpp │ │ ├── functions.hpp │ │ ├── stream_width_fixer.hpp │ │ ├── traits.hpp │ │ └── validate_hash_size.hpp │ ├── digestpp.hpp │ └── hasher.hpp ├── edlib.h ├── kseq.h ├── ksw2pp │ ├── KSW2Aligner.hpp │ ├── kalloc.h │ └── ksw2.h ├── macros.h ├── metro │ ├── metrohash.h │ ├── metrohash128.h │ ├── metrohash128crc.h │ ├── metrohash64.h │ ├── platform.h │ └── testvector.h ├── nonstd │ ├── optional.hpp │ └── string_view.hpp ├── picosha2.h ├── rank9b.h ├── sparsepp │ ├── spp.h │ ├── spp_config.h │ ├── spp_dlalloc.h │ ├── spp_memory.h │ ├── spp_smartptr.h │ ├── spp_stdint.h │ ├── spp_timer.h │ ├── spp_traits.h │ └── spp_utils.h ├── spdlog │ ├── async_logger.h │ ├── common.h │ ├── details │ │ ├── async_log_helper.h │ │ ├── async_logger_impl.h │ │ ├── file_helper.h │ │ ├── log_msg.h │ │ ├── logger_impl.h │ │ ├── mpmc_bounded_q.h │ │ ├── null_mutex.h │ │ ├── os.h │ │ ├── pattern_formatter_impl.h │ │ ├── registry.h │ │ └── spdlog_impl.h │ ├── fmt │ │ ├── bundled │ │ │ ├── container.h │ │ │ ├── format.cc │ │ │ ├── format.h │ │ │ ├── ostream.cc │ │ │ ├── ostream.h │ │ │ ├── posix.cc │ │ │ ├── posix.h │ │ │ ├── printf.cc │ │ │ ├── printf.h │ │ │ ├── string.h │ │ │ └── time.h │ │ ├── fmt.h │ │ └── ostr.h │ ├── formatter.h │ ├── logger.h │ ├── sinks │ │ ├── android_sink.h │ │ ├── ansicolor_sink.h │ │ ├── base_sink.h │ │ ├── dist_sink.h │ │ ├── file_sinks.h │ │ ├── msvc_sink.h │ │ ├── null_sink.h │ │ ├── ostream_sink.h │ │ ├── sink.h │ │ ├── stdout_sinks.h │ │ ├── syslog_sink.h │ │ ├── wincolor_sink.h │ │ └── windebug_sink.h │ ├── spdlog.h │ └── tweakme.h ├── stringpiece.h ├── tclap │ ├── Arg.h │ ├── ArgException.h │ ├── ArgTraits.h │ ├── CmdLine.h │ ├── CmdLineInterface.h │ ├── CmdLineOutput.h │ ├── Constraint.h │ ├── DocBookOutput.h │ ├── HelpVisitor.h │ ├── IgnoreRestVisitor.h │ ├── Makefile.am │ ├── Makefile.in │ ├── MultiArg.h │ ├── MultiSwitchArg.h │ ├── OptionalUnlabeledTracker.h │ ├── StandardTraits.h │ ├── StdOutput.h │ ├── SwitchArg.h │ ├── UnlabeledMultiArg.h │ ├── UnlabeledValueArg.h │ ├── ValueArg.h │ ├── ValuesConstraint.h │ ├── VersionVisitor.h │ ├── Visitor.h │ ├── XorHandler.h │ └── ZshCompletionOutput.h ├── tsl │ ├── array_growth_policy.h │ ├── array_hash.h │ ├── array_map.h │ ├── array_set.h │ ├── bhopscotch_map.h │ ├── bhopscotch_set.h │ ├── hopscotch_growth_policy.h │ ├── hopscotch_hash.h │ ├── hopscotch_map.h │ ├── hopscotch_set.h │ ├── robin_growth_policy.h │ ├── robin_hash.h │ ├── robin_map.h │ └── robin_set.h ├── xxhash.h └── zstr │ ├── strict_fstream.hpp │ └── zstr.hpp ├── sample_data ├── reads_1.fastq ├── reads_2.fastq └── transcripts.fasta ├── scripts ├── Dockerfile ├── RunRapMap.sh ├── add-header.sh ├── bump_version.sh ├── compile.sh ├── make-release.sh └── merge_branches.sh └── src ├── CMakeLists.txt ├── EnumCoder.cpp ├── EnumCoderTest.cpp ├── FastxParser.cpp ├── HitManager.cpp ├── RapMap.cpp ├── RapMapFileSystem.cpp ├── RapMapIndex.cpp ├── RapMapIndexer.cpp ├── RapMapMapper.cpp ├── RapMapSAIndex.cpp ├── RapMapSAIndexer.cpp ├── RapMapSAMapper.cpp ├── RapMapUtils.cpp ├── UtilTest.cpp ├── bit_array.c ├── edlib.cpp ├── ksw2pp ├── KSW2Aligner.cpp ├── kalloc.c ├── ksw2_dispatch.c ├── ksw2_extd.c ├── ksw2_extd2_sse.c ├── ksw2_extf2_sse.c ├── ksw2_exts2_sse.c ├── ksw2_extz.c ├── ksw2_extz2_sse.c 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