├── FM.cpp ├── FM.h ├── LICENCE ├── Makefile ├── README.md ├── benchmark ├── FM_count_200MB_Q50000.png ├── FM_locate_200MB_QL5.png ├── FM_locate_samplerate_50MB_QL6.png ├── bench_fmcount.cpp ├── bench_fmlocate.cpp ├── count.R ├── locate.R └── locate_samplerate.R ├── fmbuild.cpp ├── fmcount.cpp ├── fmextract.cpp ├── fmlocate.cpp ├── fmrecover.cpp ├── libcds ├── COPYRIGHT ├── Changelog ├── Doxyfile ├── Makefile ├── docs │ └── delete_me ├── includes │ └── delete_me ├── lib │ └── delete_me ├── src │ ├── Makefile │ ├── static │ │ ├── bitsequence │ │ │ ├── BitSequence.cpp │ │ │ ├── BitSequence.h │ │ │ ├── BitSequenceBuilder.h │ │ │ ├── BitSequenceBuilderDArray.cpp │ │ │ ├── BitSequenceBuilderDArray.h │ │ │ ├── BitSequenceBuilderRG.cpp │ │ │ ├── BitSequenceBuilderRG.h │ │ │ ├── BitSequenceBuilderRRR.cpp │ │ │ ├── BitSequenceBuilderRRR.h │ │ │ ├── BitSequenceBuilderSDArray.cpp │ │ │ ├── BitSequenceBuilderSDArray.h │ │ │ ├── BitSequenceDArray.cpp │ │ │ ├── BitSequenceDArray.h │ │ │ ├── BitSequenceRG.cpp │ │ │ ├── BitSequenceRG.h │ │ │ ├── BitSequenceRRR.cpp │ │ │ ├── BitSequenceRRR.h │ │ │ ├── BitSequenceSDArray.cpp │ │ │ ├── BitSequenceSDArray.h │ │ │ ├── Makefile │ │ │ ├── TableOffsetRRR.cpp │ │ │ ├── TableOffsetRRR.h │ │ │ ├── sdarraySadakane.cpp │ │ │ └── sdarraySadakane.h │ │ ├── coders │ │ │ ├── Coder.h │ │ │ ├── HuffmanCoder.cpp │ │ │ ├── HuffmanCoder.h │ │ │ ├── Makefile │ │ │ ├── huff.cpp │ │ │ └── huff.h │ │ ├── mapper │ │ │ ├── Makefile │ │ │ ├── Mapper.cpp │ │ │ ├── Mapper.h │ │ │ ├── MapperCont.cpp │ │ │ ├── MapperCont.h │ │ │ ├── MapperNone.cpp │ │ │ └── MapperNone.h │ │ ├── permutation │ │ │ ├── Makefile │ │ │ ├── Permutation.cpp │ │ │ ├── Permutation.h │ │ │ ├── PermutationBuilder.h │ │ │ ├── PermutationBuilderMRRR.cpp │ │ │ ├── PermutationBuilderMRRR.h │ │ │ ├── PermutationMRRR.cpp │ │ │ ├── PermutationMRRR.h │ │ │ ├── perm.cpp │ │ │ └── perm.h │ │ ├── sequence │ │ │ ├── BitmapsSequence.cpp │ │ │ ├── BitmapsSequence.h │ │ │ ├── Makefile │ │ │ ├── Sequence.cpp │ │ │ ├── Sequence.h │ │ │ ├── SequenceBuilder.h │ │ │ ├── SequenceBuilderGMR.cpp │ │ │ ├── SequenceBuilderGMR.h │ │ │ ├── SequenceBuilderGMRChunk.cpp │ │ │ ├── SequenceBuilderGMRChunk.h │ │ │ ├── SequenceBuilderWaveletTree.cpp │ │ │ ├── SequenceBuilderWaveletTree.h │ │ │ ├── SequenceBuilderWaveletTreeNoptrs.cpp │ │ │ ├── SequenceBuilderWaveletTreeNoptrs.h │ │ │ ├── SequenceGMR.cpp │ │ │ ├── SequenceGMR.h │ │ │ ├── SequenceGMRChunk.cpp │ │ │ ├── SequenceGMRChunk.h │ │ │ ├── WaveletTree.cpp │ │ │ ├── WaveletTree.h │ │ │ ├── WaveletTreeNoptrs.cpp │ │ │ ├── WaveletTreeNoptrs.h │ │ │ ├── wt_coder.cpp │ │ │ ├── wt_coder.h │ │ │ ├── wt_coder_binary.cpp │ │ │ ├── wt_coder_binary.h │ │ │ ├── wt_coder_huff.cpp │ │ │ ├── wt_coder_huff.h │ │ │ ├── wt_node.cpp │ │ │ ├── wt_node.h │ │ │ ├── wt_node_internal.cpp │ │ │ ├── wt_node_internal.h │ │ │ ├── wt_node_leaf.cpp │ │ │ └── wt_node_leaf.h │ │ ├── suffixtree │ │ │ ├── LCP.cpp │ │ │ ├── LCP.h │ │ │ ├── LCP_DAC.cpp │ │ │ ├── LCP_DAC.h │ │ │ ├── LCP_DAC_VAR.cpp │ │ │ ├── LCP_DAC_VAR.h │ │ │ ├── LCP_FMN.cpp │ │ │ ├── LCP_FMN.h │ │ │ ├── LCP_PT.cpp │ │ │ ├── LCP_PT.h │ │ │ ├── LCP_PhiSpare.cpp │ │ │ ├── LCP_PhiSpare.h │ │ │ ├── LCP_Sad.cpp │ │ │ ├── LCP_Sad.h │ │ │ ├── LCP_naive.cpp │ │ │ ├── LCP_naive.h │ │ │ ├── Makefile │ │ │ ├── NPR.cpp │ │ │ ├── NPR.h │ │ │ ├── NPR_CN.cpp │ │ │ ├── NPR_CN.h │ │ │ ├── NPR_FMN.cpp │ │ │ ├── NPR_FMN.h │ │ │ ├── NSV.cpp │ │ │ ├── NSV.h │ │ │ ├── PSV.cpp │ │ │ ├── PSV.h │ │ │ ├── RMQ_succinct.cpp │ │ │ ├── RMQ_succinct.h │ │ │ ├── RMQ_succinct_lcp.cpp │ │ │ ├── RMQ_succinct_lcp.h │ │ │ ├── SuffixTree.cpp │ │ │ ├── SuffixTree.h │ │ │ ├── SuffixTreeY.cpp │ │ │ ├── SuffixTreeY.h │ │ │ ├── factorization.cpp │ │ │ ├── factorization.h │ │ │ ├── factorization_var.cpp │ │ │ └── factorization_var.h │ │ └── textindex │ │ │ ├── Makefile │ │ │ ├── TextIndex.cpp │ │ │ ├── TextIndex.h │ │ │ ├── TextIndexCSA.cpp │ │ │ ├── TextIndexCSA.h │ │ │ ├── comparray4.cpp │ │ │ ├── comparray4.h │ │ │ ├── interface.h │ │ │ ├── mmap.cpp │ │ │ ├── mmap.h │ │ │ ├── qsufsort.cpp │ │ │ └── suftest3.test.cpp │ └── utils │ │ ├── Array.cpp │ │ ├── Array.h │ │ ├── BitString.cpp │ │ ├── BitString.h │ │ ├── Makefile │ │ ├── cppUtils.cpp │ │ ├── cppUtils.h │ │ ├── libcdsBasics.h │ │ ├── libcdsSDArray.h │ │ └── libcdsTrees.h └── tests │ ├── Makefile │ ├── runTests.py │ ├── testArray.cpp │ ├── testBitSequence.cpp │ ├── testHuffman.cpp │ ├── testLCP.cpp │ ├── testNPR.cpp │ ├── testSequence.cpp │ ├── testSuffixTree.cpp │ └── testTextIndex.cpp ├── libdivsufsort ├── AUTHORS ├── CMakeLists.txt ├── CMakeModules │ ├── AppendCompilerFlags.cmake │ ├── CheckFunctionKeywords.cmake │ ├── CheckLFS.cmake │ ├── ProjectCPack.cmake │ └── cmake_uninstall.cmake.in ├── COPYING ├── ChangeLog ├── ChangeLog.old ├── INSTALL ├── Makefile.am ├── Makefile.in ├── NEWS ├── README ├── VERSION ├── aclocal.m4 ├── config │ ├── config.guess │ ├── config.sub │ ├── depcomp │ ├── install-sh │ ├── ltmain.sh │ └── missing ├── configure ├── configure.ac ├── examples │ ├── CMakeLists.txt │ ├── Makefile.am │ ├── Makefile.in │ ├── bwt.c │ ├── mksary.c │ ├── sasearch.c │ ├── suftest.c │ └── unbwt.c ├── include │ ├── CMakeLists.txt │ ├── Makefile.am │ ├── Makefile.in │ ├── config.h.cmake │ ├── config.h.in │ ├── divsufsort.h.cmake │ ├── divsufsort64.h.in │ ├── divsufsort_private.h │ └── lfs.h.cmake ├── lib │ ├── CMakeLists.txt │ ├── Makefile.am │ ├── Makefile.in │ ├── divsufsort.c │ ├── libdivsufsort.sym │ ├── libdivsufsort64.sym │ ├── sssort.c │ ├── trsort.c │ └── utils.c ├── m4 │ ├── libtool.m4 │ ├── ltoptions.m4 │ ├── ltsugar.m4 │ ├── ltversion.m4 │ └── lt~obsolete.m4 └── pkgconfig │ ├── CMakeLists.txt │ └── libdivsufsort.pc.cmake ├── util.c └── util.h /FM.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mpetri/FM-Index/HEAD/FM.cpp -------------------------------------------------------------------------------- /FM.h: 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